From c0d77b6c43adad38c896aca3d567f844e8adae4e Mon Sep 17 00:00:00 2001 From: Co Quach Date: Fri, 22 Oct 2021 17:12:52 -0500 Subject: [PATCH] update terminal_group molecule bank --- .../molecules/one_port/pdbs/2pyrrole.pdb | 22 +++++++++ .../molecules/one_port/pdbs/acetyl-ch3.pdb | 24 ---------- .../molecules/one_port/pdbs/acetyl-h.pdb | 18 -------- .../pdbs/{hydroxyl-ch3.pdb => acetyl.pdb} | 12 ++--- .../molecules/one_port/pdbs/amino-ch3.pdb | 18 -------- .../pdbs/{hydroxyl-h.pdb => amino.pdb} | 6 +-- .../molecules/one_port/pdbs/benzoicacid.pdb | 34 ++++++++++++++ .../molecules/one_port/pdbs/carboxyl-ch3.pdb | 20 -------- .../molecules/one_port/pdbs/carboxyl-h.pdb | 14 ------ .../molecules/one_port/pdbs/carboxyl.pdb | 12 +++++ .../one_port/pdbs/{amino-h.pdb => ch3.pdb} | 10 ++-- .../molecules/one_port/pdbs/cyano-ch3.pdb | 16 ------- .../molecules/one_port/pdbs/cyano.pdb | 8 ++++ .../one_port/pdbs/cyclopropyl-ch3.pdb | 28 ----------- .../molecules/one_port/pdbs/cyclopropyl-h.pdb | 22 --------- .../molecules/one_port/pdbs/cyclopropyl.pdb | 20 ++++++++ .../pdbs/{nitro-h.pdb => difluoromethyl.pdb} | 8 ++-- .../molecules/one_port/pdbs/ethylene-ch3.pdb | 22 --------- .../molecules/one_port/pdbs/ethylene-h.pdb | 16 ------- .../molecules/one_port/pdbs/ethylene.pdb | 14 ++++++ .../one_port/pdbs/fluorophenyl-ch3.pdb | 34 -------------- .../one_port/pdbs/fluorophenyl-h.pdb | 28 ----------- .../molecules/one_port/pdbs/fluorophenyl.pdb | 26 +++++++++++ .../one_port/pdbs/{cyano-h.pdb => formyl.pdb} | 6 +-- .../molecules/one_port/pdbs/hydroxyl.pdb | 8 ++++ .../molecules/one_port/pdbs/isopropyl-ch3.pdb | 32 ------------- .../molecules/one_port/pdbs/isopropyl-h.pdb | 26 ----------- .../molecules/one_port/pdbs/isopropyl.pdb | 24 ++++++++++ .../one_port/pdbs/isopropylbenzene.pdb | 46 +++++++++++++++++++ .../molecules/one_port/pdbs/methoxy-ch3.pdb | 22 --------- .../molecules/one_port/pdbs/methoxy-h.pdb | 16 ------- .../molecules/one_port/pdbs/methoxy.pdb | 14 ++++++ .../molecules/one_port/pdbs/methyl-ch3.pdb | 20 -------- .../molecules/one_port/pdbs/methyl-h.pdb | 14 ------ .../molecules/one_port/pdbs/nitro-ch3.pdb | 11 ----- .../molecules/one_port/pdbs/nitro.pdb | 10 ++++ .../one_port/pdbs/nitrophenyl-ch3.pdb | 38 --------------- .../molecules/one_port/pdbs/nitrophenyl-h.pdb | 32 ------------- .../molecules/one_port/pdbs/oh.pdb | 8 ++++ .../one_port/pdbs/pentafluorophenyl.pdb | 26 +++++++++++ .../one_port/pdbs/perfluoromethyl-ch3.pdb | 20 -------- .../one_port/pdbs/perfluoromethyl-h.pdb | 14 ------ .../one_port/pdbs/perfluoromethyl.pdb | 12 +++++ .../molecules/one_port/pdbs/phenol.pdb | 30 ++++++++++++ .../molecules/one_port/pdbs/phenyl-ch3.pdb | 34 -------------- .../molecules/one_port/pdbs/phenyl-h.pdb | 28 ----------- .../molecules/one_port/pdbs/phenyl.pdb | 26 +++++++++++ .../one_port/pdbs/phenyl_unfunctionalized.pdb | 16 +++++++ .../molecules/one_port/pdbs/pyrrole-ch3.pdb | 30 ------------ .../molecules/one_port/pdbs/pyrrole-h.pdb | 24 ---------- .../molecules/one_port/pdbs/toluene.pdb | 34 ++++++++++++++ .../molecules/one_port/pdbs/triazole.pdb | 18 ++++++++ 52 files changed, 429 insertions(+), 642 deletions(-) create mode 100644 surface_coatings/molecules/one_port/pdbs/2pyrrole.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/acetyl-ch3.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/acetyl-h.pdb rename surface_coatings/molecules/one_port/pdbs/{hydroxyl-ch3.pdb => acetyl.pdb} (61%) mode change 100755 => 100644 delete mode 100755 surface_coatings/molecules/one_port/pdbs/amino-ch3.pdb rename surface_coatings/molecules/one_port/pdbs/{hydroxyl-h.pdb => amino.pdb} (64%) mode change 100755 => 100644 create mode 100644 surface_coatings/molecules/one_port/pdbs/benzoicacid.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/carboxyl-ch3.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/carboxyl-h.pdb create mode 100644 surface_coatings/molecules/one_port/pdbs/carboxyl.pdb rename surface_coatings/molecules/one_port/pdbs/{amino-h.pdb => ch3.pdb} (57%) mode change 100755 => 100644 delete mode 100755 surface_coatings/molecules/one_port/pdbs/cyano-ch3.pdb create mode 100644 surface_coatings/molecules/one_port/pdbs/cyano.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/cyclopropyl-ch3.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/cyclopropyl-h.pdb create mode 100644 surface_coatings/molecules/one_port/pdbs/cyclopropyl.pdb rename surface_coatings/molecules/one_port/pdbs/{nitro-h.pdb => difluoromethyl.pdb} (58%) mode change 100755 => 100644 delete mode 100755 surface_coatings/molecules/one_port/pdbs/ethylene-ch3.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/ethylene-h.pdb create mode 100644 surface_coatings/molecules/one_port/pdbs/ethylene.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/fluorophenyl-ch3.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/fluorophenyl-h.pdb create mode 100644 surface_coatings/molecules/one_port/pdbs/fluorophenyl.pdb rename surface_coatings/molecules/one_port/pdbs/{cyano-h.pdb => formyl.pdb} (64%) mode change 100755 => 100644 create mode 100644 surface_coatings/molecules/one_port/pdbs/hydroxyl.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/isopropyl-ch3.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/isopropyl-h.pdb create mode 100644 surface_coatings/molecules/one_port/pdbs/isopropyl.pdb create mode 100644 surface_coatings/molecules/one_port/pdbs/isopropylbenzene.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/methoxy-ch3.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/methoxy-h.pdb create mode 100644 surface_coatings/molecules/one_port/pdbs/methoxy.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/methyl-ch3.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/methyl-h.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/nitro-ch3.pdb create mode 100644 surface_coatings/molecules/one_port/pdbs/nitro.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/nitrophenyl-ch3.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/nitrophenyl-h.pdb create mode 100644 surface_coatings/molecules/one_port/pdbs/oh.pdb create mode 100644 surface_coatings/molecules/one_port/pdbs/pentafluorophenyl.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/perfluoromethyl-ch3.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/perfluoromethyl-h.pdb create mode 100644 surface_coatings/molecules/one_port/pdbs/perfluoromethyl.pdb create mode 100644 surface_coatings/molecules/one_port/pdbs/phenol.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/phenyl-ch3.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/phenyl-h.pdb create mode 100644 surface_coatings/molecules/one_port/pdbs/phenyl.pdb create mode 100644 surface_coatings/molecules/one_port/pdbs/phenyl_unfunctionalized.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/pyrrole-ch3.pdb delete mode 100755 surface_coatings/molecules/one_port/pdbs/pyrrole-h.pdb create mode 100644 surface_coatings/molecules/one_port/pdbs/toluene.pdb create mode 100644 surface_coatings/molecules/one_port/pdbs/triazole.pdb diff --git a/surface_coatings/molecules/one_port/pdbs/2pyrrole.pdb b/surface_coatings/molecules/one_port/pdbs/2pyrrole.pdb new file mode 100644 index 0000000..f905d07 --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/2pyrrole.pdb @@ -0,0 +1,22 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 C UNL 1 -0.464 -0.403 -0.000 1.00 0.00 C +HETATM 2 C UNL 1 0.906 0.495 -0.000 1.00 0.00 C +HETATM 3 N UNL 1 -1.789 0.434 -0.000 1.00 0.00 N +HETATM 4 C UNL 1 -1.241 2.017 -0.000 1.00 0.00 C +HETATM 5 C UNL 1 0.510 2.047 -0.000 1.00 0.00 C +HETATM 6 H UNL 1 -2.900 0.129 -0.000 1.00 0.00 H +HETATM 7 H UNL 1 -2.002 2.976 -0.000 1.00 0.00 H +HETATM 8 H UNL 1 1.149 3.006 -0.000 1.00 0.00 H +HETATM 9 H UNL 1 1.971 -0.008 -0.000 1.00 0.00 H +CONECT 1 2 3 +CONECT 2 1 5 9 +CONECT 3 1 4 6 +CONECT 4 3 5 7 +CONECT 5 2 4 8 +CONECT 6 3 +CONECT 7 4 +CONECT 8 5 +CONECT 9 2 +MASTER 0 0 0 0 0 0 0 0 9 0 9 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/acetyl-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/acetyl-ch3.pdb deleted file mode 100755 index 4bbab56..0000000 --- a/surface_coatings/molecules/one_port/pdbs/acetyl-ch3.pdb +++ /dev/null @@ -1,24 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.198 -1.434 -0.181 1.00 0.00 C -HETATM 2 H UNL 1 1.652 -0.426 0.331 1.00 0.00 H -HETATM 3 C UNL 1 0.606 -0.189 0.045 1.00 0.00 C -HETATM 4 H UNL 1 0.144 0.409 0.859 1.00 0.00 H -HETATM 5 H UNL 1 0.622 0.417 -0.885 1.00 0.00 H -HETATM 6 O UNL 1 -1.372 -1.336 -0.502 1.00 0.00 O -HETATM 7 C UNL 1 0.405 -2.799 -0.022 1.00 0.00 C -HETATM 8 H UNL 1 1.474 -2.739 0.272 1.00 0.00 H -HETATM 9 H UNL 1 -0.146 -3.359 0.762 1.00 0.00 H -HETATM 10 H UNL 1 0.332 -3.351 -0.982 1.00 0.00 H -CONECT 1 3 6 7 -CONECT 2 3 -CONECT 3 2 1 4 5 -CONECT 4 3 -CONECT 5 3 -CONECT 6 1 -CONECT 7 1 8 9 10 -CONECT 8 7 -CONECT 9 7 -CONECT 10 7 -MASTER 0 0 0 0 0 0 0 0 10 0 10 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/acetyl-h.pdb b/surface_coatings/molecules/one_port/pdbs/acetyl-h.pdb deleted file mode 100755 index f2052d6..0000000 --- a/surface_coatings/molecules/one_port/pdbs/acetyl-h.pdb +++ /dev/null @@ -1,18 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.597 0.751 0.000 1.00 0.00 C -HETATM 2 C UNL 1 0.479 1.787 0.000 1.00 0.00 C -HETATM 3 O UNL 1 -1.773 1.078 0.000 1.00 0.00 O -HETATM 4 H UNL 1 -0.332 -0.301 0.000 1.00 0.00 H -HETATM 5 H UNL 1 0.043 2.809 0.000 1.00 0.00 H -HETATM 6 H UNL 1 1.110 1.664 0.905 1.00 0.00 H -HETATM 7 H UNL 1 1.110 1.664 -0.905 1.00 0.00 H -CONECT 1 2 3 4 -CONECT 2 1 5 6 7 -CONECT 3 1 -CONECT 4 1 -CONECT 5 2 -CONECT 6 2 -CONECT 7 2 -MASTER 0 0 0 0 0 0 0 0 7 0 7 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/hydroxyl-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/acetyl.pdb old mode 100755 new mode 100644 similarity index 61% rename from surface_coatings/molecules/one_port/pdbs/hydroxyl-ch3.pdb rename to surface_coatings/molecules/one_port/pdbs/acetyl.pdb index 1dcff66..2640d00 --- a/surface_coatings/molecules/one_port/pdbs/hydroxyl-ch3.pdb +++ b/surface_coatings/molecules/one_port/pdbs/acetyl.pdb @@ -1,11 +1,11 @@ COMPND UNNAMED AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 O UNL 1 -0.176 -0.103 1.047 1.00 0.00 O -HETATM 2 H UNL 1 -0.052 -0.030 0.065 1.00 0.00 H -HETATM 3 C UNL 1 -1.373 -0.802 1.233 1.00 0.00 C -HETATM 4 H UNL 1 -1.559 -0.911 2.321 1.00 0.00 H -HETATM 5 H UNL 1 -2.222 -0.238 0.790 1.00 0.00 H -HETATM 6 H UNL 1 -1.298 -1.819 0.790 1.00 0.00 H +HETATM 1 C UNL 1 0.008 -1.332 -0.000 1.00 0.00 C +HETATM 2 O UNL 1 -1.393 -1.317 -0.000 1.00 0.00 O +HETATM 3 C UNL 1 0.830 -0.023 -0.000 1.00 0.00 C +HETATM 4 H UNL 1 -0.419 -0.008 -0.000 1.00 0.00 H +HETATM 5 H UNL 1 0.814 1.164 -0.000 1.00 0.00 H +HETATM 6 H UNL 1 2.032 -0.008 -0.000 1.00 0.00 H CONECT 1 2 3 CONECT 2 1 CONECT 3 1 4 5 6 diff --git a/surface_coatings/molecules/one_port/pdbs/amino-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/amino-ch3.pdb deleted file mode 100755 index 99aa886..0000000 --- a/surface_coatings/molecules/one_port/pdbs/amino-ch3.pdb +++ /dev/null @@ -1,18 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 N UNL 1 -0.348 -0.036 0.000 1.00 0.00 N -HETATM 2 H UNL 1 0.569 0.465 0.000 1.00 0.00 H -HETATM 3 H UNL 1 -1.276 0.445 0.000 1.00 0.00 H -HETATM 4 C UNL 1 -0.339 -1.490 0.000 1.00 0.00 C -HETATM 5 H UNL 1 0.706 -1.864 0.000 1.00 0.00 H -HETATM 6 H UNL 1 -0.860 -1.865 0.905 1.00 0.00 H -HETATM 7 H UNL 1 -0.860 -1.865 -0.905 1.00 0.00 H -CONECT 1 2 3 4 -CONECT 2 1 -CONECT 3 1 -CONECT 4 1 5 6 7 -CONECT 5 4 -CONECT 6 4 -CONECT 7 4 -MASTER 0 0 0 0 0 0 0 0 7 0 7 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/hydroxyl-h.pdb b/surface_coatings/molecules/one_port/pdbs/amino.pdb old mode 100755 new mode 100644 similarity index 64% rename from surface_coatings/molecules/one_port/pdbs/hydroxyl-h.pdb rename to surface_coatings/molecules/one_port/pdbs/amino.pdb index f435039..efe888b --- a/surface_coatings/molecules/one_port/pdbs/hydroxyl-h.pdb +++ b/surface_coatings/molecules/one_port/pdbs/amino.pdb @@ -1,8 +1,8 @@ COMPND UNNAMED AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 O HOH 1 -1.521 0.548 -0.009 1.00 0.00 O -HETATM 2 H HOH 0 -1.786 1.497 -0.108 1.00 0.00 H -HETATM 3 H HOH 0 -2.270 0.038 -0.406 1.00 0.00 H +HETATM 1 N UNL 1 -0.342 0.038 -0.000 1.00 0.00 N +HETATM 2 H UNL 1 0.647 0.784 -0.000 1.00 0.00 H +HETATM 3 H UNL 1 -1.378 0.693 -0.000 1.00 0.00 H CONECT 1 2 3 CONECT 2 1 CONECT 3 1 diff --git a/surface_coatings/molecules/one_port/pdbs/benzoicacid.pdb b/surface_coatings/molecules/one_port/pdbs/benzoicacid.pdb new file mode 100644 index 0000000..40535ed --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/benzoicacid.pdb @@ -0,0 +1,34 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 O UNL 1 1.065 0.556 -0.054 1.00 0.00 O +HETATM 2 C UNL 1 2.245 0.091 -0.026 1.00 0.00 C +HETATM 3 O UNL 1 2.835 -0.542 -0.953 1.00 0.00 O +HETATM 4 C UNL 1 3.025 0.309 1.230 1.00 0.00 C +HETATM 5 C UNL 1 2.993 1.550 1.869 1.00 0.00 C +HETATM 6 C UNL 1 3.726 1.759 3.035 1.00 0.00 C +HETATM 7 C UNL 1 4.476 0.720 3.581 1.00 0.00 C +HETATM 8 C UNL 1 4.499 -0.524 2.956 1.00 0.00 C +HETATM 9 C UNL 1 3.782 -0.723 1.779 1.00 0.00 C +HETATM 10 H UNL 1 3.713 -0.844 -0.829 1.00 0.00 H +HETATM 11 H UNL 1 2.424 2.316 1.476 1.00 0.00 H +HETATM 12 H UNL 1 3.714 2.683 3.493 1.00 0.00 H +HETATM 13 H UNL 1 5.014 0.872 4.449 1.00 0.00 H +HETATM 14 H UNL 1 5.046 -1.298 3.364 1.00 0.00 H +HETATM 15 H UNL 1 3.812 -1.642 1.309 1.00 0.00 H +CONECT 1 2 +CONECT 2 1 3 4 +CONECT 3 2 10 +CONECT 4 2 5 9 +CONECT 5 4 6 11 +CONECT 6 5 7 12 +CONECT 7 6 8 13 +CONECT 8 7 9 14 +CONECT 9 8 4 15 +CONECT 10 3 +CONECT 11 5 +CONECT 12 6 +CONECT 13 7 +CONECT 14 8 +CONECT 15 9 +MASTER 0 0 0 0 0 0 0 0 15 0 15 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/carboxyl-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/carboxyl-ch3.pdb deleted file mode 100755 index f309164..0000000 --- a/surface_coatings/molecules/one_port/pdbs/carboxyl-ch3.pdb +++ /dev/null @@ -1,20 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.487 0.014 0.025 1.00 0.00 C -HETATM 2 O UNL 1 -1.631 0.440 -0.004 1.00 0.00 O -HETATM 3 O UNL 1 0.556 0.870 0.036 1.00 0.00 O -HETATM 4 H UNL 1 0.422 1.828 0.021 1.00 0.00 H -HETATM 5 C UNL 1 -0.234 -1.460 0.049 1.00 0.00 C -HETATM 6 H UNL 1 -1.191 -2.024 0.037 1.00 0.00 H -HETATM 7 H UNL 1 0.365 -1.748 -0.840 1.00 0.00 H -HETATM 8 H UNL 1 0.328 -1.724 0.969 1.00 0.00 H -CONECT 1 2 3 5 -CONECT 2 1 -CONECT 3 1 4 -CONECT 4 3 -CONECT 5 1 6 7 8 -CONECT 6 5 -CONECT 7 5 -CONECT 8 5 -MASTER 0 0 0 0 0 0 0 0 8 0 8 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/carboxyl-h.pdb b/surface_coatings/molecules/one_port/pdbs/carboxyl-h.pdb deleted file mode 100755 index 84a808b..0000000 --- a/surface_coatings/molecules/one_port/pdbs/carboxyl-h.pdb +++ /dev/null @@ -1,14 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.972 0.707 0.005 1.00 0.00 C -HETATM 2 O UNL 1 -2.111 1.148 -0.008 1.00 0.00 O -HETATM 3 O UNL 1 0.085 1.544 -0.036 1.00 0.00 O -HETATM 4 H UNL 1 -0.809 -0.364 0.049 1.00 0.00 H -HETATM 5 H UNL 1 -0.033 2.503 -0.075 1.00 0.00 H -CONECT 1 2 3 4 -CONECT 2 1 -CONECT 3 1 5 -CONECT 4 1 -CONECT 5 3 -MASTER 0 0 0 0 0 0 0 0 5 0 5 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/carboxyl.pdb b/surface_coatings/molecules/one_port/pdbs/carboxyl.pdb new file mode 100644 index 0000000..d53e675 --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/carboxyl.pdb @@ -0,0 +1,12 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 C UNL 1 -0.251 0.023 -0.000 1.00 0.00 C +HETATM 2 O UNL 1 -1.712 0.053 -0.000 1.00 0.00 O +HETATM 3 O UNL 1 0.632 1.362 -0.000 1.00 0.00 O +HETATM 4 H UNL 1 0.601 2.519 -0.000 1.00 0.00 H +CONECT 1 2 3 +CONECT 2 1 +CONECT 3 1 4 +CONECT 4 3 +MASTER 0 0 0 0 0 0 0 0 4 0 4 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/amino-h.pdb b/surface_coatings/molecules/one_port/pdbs/ch3.pdb old mode 100755 new mode 100644 similarity index 57% rename from surface_coatings/molecules/one_port/pdbs/amino-h.pdb rename to surface_coatings/molecules/one_port/pdbs/ch3.pdb index cc9d770..33ddb26 --- a/surface_coatings/molecules/one_port/pdbs/amino-h.pdb +++ b/surface_coatings/molecules/one_port/pdbs/ch3.pdb @@ -1,9 +1,9 @@ COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 N UNL 1 -0.806 0.349 -0.012 1.00 0.00 N -HETATM 2 H UNL 1 -0.773 0.952 -0.865 1.00 0.00 H -HETATM 3 H UNL 1 -1.767 0.380 0.396 1.00 0.00 H -HETATM 4 H UNL 1 -0.575 -0.635 -0.277 1.00 0.00 H +AUTHOR GENERATED BY OPEN BABEL +ATOM 1 C LIG A 1 -1.750 1.662 0.000 1.00 0.00 C +ATOM 2 H LIG A 1 -0.680 1.662 0.000 1.00 0.00 H +ATOM 3 H LIG A 1 -2.107 2.431 0.653 1.00 0.00 H +ATOM 4 H LIG A 1 -2.107 1.843 -0.993 1.00 0.00 H CONECT 1 2 3 4 CONECT 2 1 CONECT 3 1 diff --git a/surface_coatings/molecules/one_port/pdbs/cyano-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/cyano-ch3.pdb deleted file mode 100755 index 9bad8f5..0000000 --- a/surface_coatings/molecules/one_port/pdbs/cyano-ch3.pdb +++ /dev/null @@ -1,16 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.341 -1.051 0.000 1.00 0.00 C -HETATM 2 N UNL 1 -0.366 0.106 0.000 1.00 0.00 N -HETATM 3 C UNL 1 -0.310 -2.514 0.000 1.00 0.00 C -HETATM 4 H UNL 1 -1.348 -2.906 0.000 1.00 0.00 H -HETATM 5 H UNL 1 0.221 -2.873 -0.906 1.00 0.00 H -HETATM 6 H UNL 1 0.221 -2.873 0.906 1.00 0.00 H -CONECT 1 2 3 -CONECT 2 1 -CONECT 3 1 4 5 6 -CONECT 4 3 -CONECT 5 3 -CONECT 6 3 -MASTER 0 0 0 0 0 0 0 0 6 0 6 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/cyano.pdb b/surface_coatings/molecules/one_port/pdbs/cyano.pdb new file mode 100644 index 0000000..5de8b14 --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/cyano.pdb @@ -0,0 +1,8 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 C UNL 1 -0.358 -0.906 -0.000 1.00 0.00 C +HETATM 2 N UNL 1 -0.358 0.388 -0.000 1.00 0.00 N +CONECT 1 2 +CONECT 2 1 +MASTER 0 0 0 0 0 0 0 0 2 0 2 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/cyclopropyl-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/cyclopropyl-ch3.pdb deleted file mode 100755 index e87eae0..0000000 --- a/surface_coatings/molecules/one_port/pdbs/cyclopropyl-ch3.pdb +++ /dev/null @@ -1,28 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.131 -0.479 -0.545 1.00 0.00 C -HETATM 2 C UNL 1 0.401 0.649 0.315 1.00 0.00 C -HETATM 3 C UNL 1 -1.044 0.681 -0.197 1.00 0.00 C -HETATM 4 H UNL 1 -1.863 0.277 0.438 1.00 0.00 H -HETATM 5 H UNL 1 -1.273 1.164 -1.171 1.00 0.00 H -HETATM 6 H UNL 1 0.885 1.521 -0.173 1.00 0.00 H -HETATM 7 H UNL 1 0.294 0.627 1.421 1.00 0.00 H -HETATM 8 H UNL 1 0.418 -0.477 -1.511 1.00 0.00 H -HETATM 9 C UNL 1 -0.265 -1.781 0.248 1.00 0.00 C -HETATM 10 H UNL 1 -0.756 -1.632 1.234 1.00 0.00 H -HETATM 11 H UNL 1 -0.868 -2.502 -0.341 1.00 0.00 H -HETATM 12 H UNL 1 0.743 -2.216 0.416 1.00 0.00 H -CONECT 1 2 3 8 9 -CONECT 2 1 3 6 7 -CONECT 3 1 2 4 5 -CONECT 4 3 -CONECT 5 3 -CONECT 6 2 -CONECT 7 2 -CONECT 8 1 -CONECT 9 1 10 11 12 -CONECT 10 9 -CONECT 11 9 -CONECT 12 9 -MASTER 0 0 0 0 0 0 0 0 12 0 12 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/cyclopropyl-h.pdb b/surface_coatings/molecules/one_port/pdbs/cyclopropyl-h.pdb deleted file mode 100755 index 3a88029..0000000 --- a/surface_coatings/molecules/one_port/pdbs/cyclopropyl-h.pdb +++ /dev/null @@ -1,22 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -1.130 -0.610 -0.027 1.00 0.00 C -HETATM 2 C UNL 1 -0.614 0.816 0.049 1.00 0.00 C -HETATM 3 C UNL 1 -2.103 0.554 -0.076 1.00 0.00 C -HETATM 4 H UNL 1 -1.254 -1.105 -1.013 1.00 0.00 H -HETATM 5 H UNL 1 -1.406 -1.152 0.903 1.00 0.00 H -HETATM 6 H UNL 1 -0.141 0.877 1.053 1.00 0.00 H -HETATM 7 H UNL 1 0.011 0.923 -0.863 1.00 0.00 H -HETATM 8 H UNL 1 -2.375 1.011 -1.051 1.00 0.00 H -HETATM 9 H UNL 1 -2.528 0.965 0.865 1.00 0.00 H -CONECT 1 2 3 4 5 -CONECT 2 1 3 6 7 -CONECT 3 1 2 8 9 -CONECT 4 1 -CONECT 5 1 -CONECT 6 2 -CONECT 7 2 -CONECT 8 3 -CONECT 9 3 -MASTER 0 0 0 0 0 0 0 0 9 0 9 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/cyclopropyl.pdb b/surface_coatings/molecules/one_port/pdbs/cyclopropyl.pdb new file mode 100644 index 0000000..7a2fbb9 --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/cyclopropyl.pdb @@ -0,0 +1,20 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 C UNL 1 -0.358 -0.327 -0.000 1.00 0.00 C +HETATM 2 C UNL 1 0.616 0.906 -0.000 1.00 0.00 C +HETATM 3 C UNL 1 -1.423 0.860 -0.000 1.00 0.00 C +HETATM 4 H UNL 1 -1.682 1.986 -0.000 1.00 0.00 H +HETATM 5 H UNL 1 -2.474 0.373 -0.000 1.00 0.00 H +HETATM 6 H UNL 1 0.845 2.047 -0.000 1.00 0.00 H +HETATM 7 H UNL 1 1.728 0.373 -0.000 1.00 0.00 H +HETATM 8 H UNL 1 0.814 -0.358 -0.000 1.00 0.00 H +CONECT 1 2 3 8 +CONECT 2 1 3 6 7 +CONECT 3 1 2 4 5 +CONECT 4 3 +CONECT 5 3 +CONECT 6 2 +CONECT 7 2 +CONECT 8 1 +MASTER 0 0 0 0 0 0 0 0 8 0 8 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/nitro-h.pdb b/surface_coatings/molecules/one_port/pdbs/difluoromethyl.pdb old mode 100755 new mode 100644 similarity index 58% rename from surface_coatings/molecules/one_port/pdbs/nitro-h.pdb rename to surface_coatings/molecules/one_port/pdbs/difluoromethyl.pdb index 19e7d03..2b3222a --- a/surface_coatings/molecules/one_port/pdbs/nitro-h.pdb +++ b/surface_coatings/molecules/one_port/pdbs/difluoromethyl.pdb @@ -1,9 +1,9 @@ COMPND UNNAMED AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 N UNL 1 -0.436 0.474 0.078 1.00 0.00 N -HETATM 2 O UNL 1 0.592 1.312 -0.197 1.00 0.00 O -HETATM 3 O UNL 1 -1.583 1.132 -0.215 1.00 0.00 O -HETATM 4 H UNL 1 -0.401 -0.679 0.242 1.00 0.00 H +HETATM 1 C UNL 1 1.258 0.254 0.340 1.00 0.00 C +HETATM 2 F UNL 1 0.165 0.840 0.843 1.00 0.00 F +HETATM 3 F UNL 1 2.350 -0.332 -0.163 1.00 0.00 F +HETATM 4 H UNL 1 0.901 0.440 -0.652 1.00 0.00 H CONECT 1 2 3 4 CONECT 2 1 CONECT 3 1 diff --git a/surface_coatings/molecules/one_port/pdbs/ethylene-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/ethylene-ch3.pdb deleted file mode 100755 index e637771..0000000 --- a/surface_coatings/molecules/one_port/pdbs/ethylene-ch3.pdb +++ /dev/null @@ -1,22 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 H UNL 1 -1.503 1.066 0.000 1.00 0.00 H -HETATM 2 C UNL 1 -0.418 1.035 0.000 1.00 0.00 C -HETATM 3 H UNL 1 0.132 1.970 0.000 1.00 0.00 H -HETATM 4 C UNL 1 0.242 -0.127 0.000 1.00 0.00 C -HETATM 5 C UNL 1 -0.469 -1.446 0.000 1.00 0.00 C -HETATM 6 H UNL 1 1.328 -0.120 0.000 1.00 0.00 H -HETATM 7 H UNL 1 -1.573 -1.322 0.000 1.00 0.00 H -HETATM 8 H UNL 1 -0.176 -2.020 -0.904 1.00 0.00 H -HETATM 9 H UNL 1 -0.176 -2.020 0.904 1.00 0.00 H -CONECT 1 2 -CONECT 2 3 1 4 -CONECT 3 2 -CONECT 4 2 5 6 -CONECT 5 4 7 8 9 -CONECT 6 4 -CONECT 7 5 -CONECT 8 5 -CONECT 9 5 -MASTER 0 0 0 0 0 0 0 0 9 0 9 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/ethylene-h.pdb b/surface_coatings/molecules/one_port/pdbs/ethylene-h.pdb deleted file mode 100755 index 804824c..0000000 --- a/surface_coatings/molecules/one_port/pdbs/ethylene-h.pdb +++ /dev/null @@ -1,16 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.928 -0.251 0.000 1.00 0.00 C -HETATM 2 C UNL 1 -0.339 0.943 0.000 1.00 0.00 C -HETATM 3 H UNL 1 -0.420 -1.111 -0.423 1.00 0.00 H -HETATM 4 H UNL 1 -1.920 -0.371 0.423 1.00 0.00 H -HETATM 5 H UNL 1 0.653 1.063 -0.423 1.00 0.00 H -HETATM 6 H UNL 1 -0.847 1.803 0.423 1.00 0.00 H -CONECT 1 2 3 4 -CONECT 2 1 5 6 -CONECT 3 1 -CONECT 4 1 -CONECT 5 2 -CONECT 6 2 -MASTER 0 0 0 0 0 0 0 0 6 0 6 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/ethylene.pdb b/surface_coatings/molecules/one_port/pdbs/ethylene.pdb new file mode 100644 index 0000000..8ac3105 --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/ethylene.pdb @@ -0,0 +1,14 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 C UNL 1 -0.373 -0.205 -0.000 1.00 0.00 C +HETATM 2 C UNL 1 -0.388 1.393 -0.000 1.00 0.00 C +HETATM 3 H UNL 1 0.814 -0.190 -0.000 1.00 0.00 H +HETATM 4 H UNL 1 0.601 2.078 -0.000 1.00 0.00 H +HETATM 5 H UNL 1 -1.271 2.123 -0.000 1.00 0.00 H +CONECT 1 2 3 +CONECT 2 1 4 5 +CONECT 3 1 +CONECT 4 2 +CONECT 5 2 +MASTER 0 0 0 0 0 0 0 0 5 0 5 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/fluorophenyl-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/fluorophenyl-ch3.pdb deleted file mode 100755 index 7f63e52..0000000 --- a/surface_coatings/molecules/one_port/pdbs/fluorophenyl-ch3.pdb +++ /dev/null @@ -1,34 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.286 -0.615 0.000 1.00 0.00 C -HETATM 2 C UNL 1 0.897 0.143 0.000 1.00 0.00 C -HETATM 3 C UNL 1 -1.526 0.042 0.000 1.00 0.00 C -HETATM 4 C UNL 1 -1.582 1.440 0.000 1.00 0.00 C -HETATM 5 C UNL 1 0.837 1.540 0.000 1.00 0.00 C -HETATM 6 C UNL 1 -0.402 2.189 0.000 1.00 0.00 C -HETATM 7 F UNL 1 -0.458 3.543 0.000 1.00 0.00 F -HETATM 8 H UNL 1 1.752 2.119 0.000 1.00 0.00 H -HETATM 9 H UNL 1 -2.542 1.941 0.000 1.00 0.00 H -HETATM 10 H UNL 1 -2.447 -0.527 0.000 1.00 0.00 H -HETATM 11 H UNL 1 1.864 -0.345 0.000 1.00 0.00 H -HETATM 12 C UNL 1 -0.239 -2.115 0.000 1.00 0.00 C -HETATM 13 H UNL 1 0.806 -2.490 0.000 1.00 0.00 H -HETATM 14 H UNL 1 -0.752 -2.504 0.904 1.00 0.00 H -HETATM 15 H UNL 1 -0.752 -2.504 -0.904 1.00 0.00 H -CONECT 1 2 3 12 -CONECT 2 1 5 11 -CONECT 3 1 4 10 -CONECT 4 3 6 9 -CONECT 5 2 6 8 -CONECT 6 4 5 7 -CONECT 7 6 -CONECT 8 5 -CONECT 9 4 -CONECT 10 3 -CONECT 11 2 -CONECT 12 1 13 14 15 -CONECT 13 12 -CONECT 14 12 -CONECT 15 12 -MASTER 0 0 0 0 0 0 0 0 15 0 15 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/fluorophenyl-h.pdb b/surface_coatings/molecules/one_port/pdbs/fluorophenyl-h.pdb deleted file mode 100755 index 4fe7bd1..0000000 --- a/surface_coatings/molecules/one_port/pdbs/fluorophenyl-h.pdb +++ /dev/null @@ -1,28 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.474 -0.801 0.000 1.00 0.00 C -HETATM 2 C UNL 1 0.734 -0.095 0.000 1.00 0.00 C -HETATM 3 C UNL 1 -1.689 -0.108 0.000 1.00 0.00 C -HETATM 4 C UNL 1 -1.697 1.291 0.000 1.00 0.00 C -HETATM 5 C UNL 1 -0.489 1.997 0.000 1.00 0.00 C -HETATM 6 C UNL 1 0.727 1.304 0.000 1.00 0.00 C -HETATM 7 F UNL 1 -0.496 3.353 0.000 1.00 0.00 F -HETATM 8 H UNL 1 -0.468 -1.883 0.000 1.00 0.00 H -HETATM 9 H UNL 1 1.674 -0.631 0.000 1.00 0.00 H -HETATM 10 H UNL 1 -2.623 -0.655 0.000 1.00 0.00 H -HETATM 11 H UNL 1 -2.638 1.825 0.000 1.00 0.00 H -HETATM 12 H UNL 1 1.662 1.849 0.000 1.00 0.00 H -CONECT 1 2 3 8 -CONECT 2 1 6 9 -CONECT 3 1 4 10 -CONECT 4 3 5 11 -CONECT 5 4 6 7 -CONECT 6 5 2 12 -CONECT 7 5 -CONECT 8 1 -CONECT 9 2 -CONECT 10 3 -CONECT 11 4 -CONECT 12 6 -MASTER 0 0 0 0 0 0 0 0 12 0 12 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/fluorophenyl.pdb b/surface_coatings/molecules/one_port/pdbs/fluorophenyl.pdb new file mode 100644 index 0000000..e435c34 --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/fluorophenyl.pdb @@ -0,0 +1,26 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 C UNL 1 -0.297 -0.860 -0.000 1.00 0.00 C +HETATM 2 C UNL 1 1.119 0.084 -0.000 1.00 0.00 C +HETATM 3 C UNL 1 -1.758 0.053 -0.000 1.00 0.00 C +HETATM 4 C UNL 1 -1.789 1.636 -0.000 1.00 0.00 C +HETATM 5 C UNL 1 1.088 1.697 -0.000 1.00 0.00 C +HETATM 6 C UNL 1 -0.434 2.748 -0.000 1.00 0.00 C +HETATM 7 F UNL 1 -0.449 3.920 -0.000 1.00 0.00 F +HETATM 8 H UNL 1 1.971 2.474 -0.000 1.00 0.00 H +HETATM 9 H UNL 1 -2.793 2.200 -0.000 1.00 0.00 H +HETATM 10 H UNL 1 -2.732 -0.753 -0.000 1.00 0.00 H +HETATM 11 H UNL 1 2.184 -0.571 -0.000 1.00 0.00 H +CONECT 1 2 3 +CONECT 2 1 5 11 +CONECT 3 1 4 10 +CONECT 4 3 6 9 +CONECT 5 2 6 8 +CONECT 6 4 5 7 +CONECT 7 6 +CONECT 8 5 +CONECT 9 4 +CONECT 10 3 +CONECT 11 2 +MASTER 0 0 0 0 0 0 0 0 11 0 11 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/cyano-h.pdb b/surface_coatings/molecules/one_port/pdbs/formyl.pdb old mode 100755 new mode 100644 similarity index 64% rename from surface_coatings/molecules/one_port/pdbs/cyano-h.pdb rename to surface_coatings/molecules/one_port/pdbs/formyl.pdb index 89b55b5..9193c39 --- a/surface_coatings/molecules/one_port/pdbs/cyano-h.pdb +++ b/surface_coatings/molecules/one_port/pdbs/formyl.pdb @@ -1,8 +1,8 @@ COMPND UNNAMED AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.557 -0.450 0.000 1.00 0.00 C -HETATM 2 N UNL 1 -0.449 0.702 0.000 1.00 0.00 N -HETATM 3 H UNL 1 -0.655 -1.504 0.000 1.00 0.00 H +HETATM 1 C UNL 1 -0.388 -0.571 -0.000 1.00 0.00 C +HETATM 2 O UNL 1 -1.789 -0.556 -0.000 1.00 0.00 O +HETATM 3 H UNL 1 0.145 0.464 -0.000 1.00 0.00 H CONECT 1 2 3 CONECT 2 1 CONECT 3 1 diff --git a/surface_coatings/molecules/one_port/pdbs/hydroxyl.pdb b/surface_coatings/molecules/one_port/pdbs/hydroxyl.pdb new file mode 100644 index 0000000..dde0b73 --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/hydroxyl.pdb @@ -0,0 +1,8 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 O HOH 1 -0.297 -0.556 -0.000 1.00 0.00 O +HETATM 2 H HOH 0 -0.312 0.586 -0.000 1.00 0.00 H +CONECT 1 2 +CONECT 2 1 +MASTER 0 0 0 0 0 0 0 0 2 0 2 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/isopropyl-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/isopropyl-ch3.pdb deleted file mode 100755 index b0d755d..0000000 --- a/surface_coatings/molecules/one_port/pdbs/isopropyl-ch3.pdb +++ /dev/null @@ -1,32 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.458 -0.161 -0.420 1.00 0.00 C -HETATM 2 C UNL 1 0.766 0.423 0.294 1.00 0.00 C -HETATM 3 C UNL 1 -1.750 0.335 0.240 1.00 0.00 C -HETATM 4 H UNL 1 -0.448 0.184 -1.477 1.00 0.00 H -HETATM 5 H UNL 1 0.737 1.533 0.257 1.00 0.00 H -HETATM 6 H UNL 1 1.698 0.085 -0.205 1.00 0.00 H -HETATM 7 H UNL 1 0.792 0.101 1.358 1.00 0.00 H -HETATM 8 H UNL 1 -1.798 1.444 0.203 1.00 0.00 H -HETATM 9 H UNL 1 -2.634 -0.068 -0.298 1.00 0.00 H -HETATM 10 H UNL 1 -1.799 0.010 1.302 1.00 0.00 H -HETATM 11 C UNL 1 -0.405 -1.692 -0.407 1.00 0.00 C -HETATM 12 H UNL 1 0.519 -2.048 -0.912 1.00 0.00 H -HETATM 13 H UNL 1 -0.413 -2.078 0.635 1.00 0.00 H -HETATM 14 H UNL 1 -1.279 -2.111 -0.951 1.00 0.00 H -CONECT 1 2 3 4 11 -CONECT 2 1 5 6 7 -CONECT 3 1 8 9 10 -CONECT 4 1 -CONECT 5 2 -CONECT 6 2 -CONECT 7 2 -CONECT 8 3 -CONECT 9 3 -CONECT 10 3 -CONECT 11 1 12 13 14 -CONECT 12 11 -CONECT 13 11 -CONECT 14 11 -MASTER 0 0 0 0 0 0 0 0 14 0 14 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/isopropyl-h.pdb b/surface_coatings/molecules/one_port/pdbs/isopropyl-h.pdb deleted file mode 100755 index f8c9202..0000000 --- a/surface_coatings/molecules/one_port/pdbs/isopropyl-h.pdb +++ /dev/null @@ -1,26 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.356 -0.505 0.019 1.00 0.00 C -HETATM 2 C UNL 1 0.885 0.382 -0.001 1.00 0.00 C -HETATM 3 C UNL 1 -1.634 0.328 -0.001 1.00 0.00 C -HETATM 4 H UNL 1 -0.342 -1.174 -0.868 1.00 0.00 H -HETATM 5 H UNL 1 -0.342 -1.132 0.938 1.00 0.00 H -HETATM 6 H UNL 1 0.899 1.004 -0.921 1.00 0.00 H -HETATM 7 H UNL 1 0.899 1.047 0.889 1.00 0.00 H -HETATM 8 H UNL 1 1.796 -0.252 0.014 1.00 0.00 H -HETATM 9 H UNL 1 -1.676 0.948 -0.921 1.00 0.00 H -HETATM 10 H UNL 1 -2.517 -0.345 0.015 1.00 0.00 H -HETATM 11 H UNL 1 -1.676 0.991 0.890 1.00 0.00 H -CONECT 1 2 3 4 5 -CONECT 2 1 6 7 8 -CONECT 3 1 9 10 11 -CONECT 4 1 -CONECT 5 1 -CONECT 6 2 -CONECT 7 2 -CONECT 8 2 -CONECT 9 3 -CONECT 10 3 -CONECT 11 3 -MASTER 0 0 0 0 0 0 0 0 11 0 11 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/isopropyl.pdb b/surface_coatings/molecules/one_port/pdbs/isopropyl.pdb new file mode 100644 index 0000000..bfba48c --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/isopropyl.pdb @@ -0,0 +1,24 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 C UNL 1 -0.388 -0.419 -0.000 1.00 0.00 C +HETATM 2 C UNL 1 0.906 0.434 -0.000 1.00 0.00 C +HETATM 3 C UNL 1 -1.819 0.327 -0.000 1.00 0.00 C +HETATM 4 H UNL 1 -0.419 0.738 -0.000 1.00 0.00 H +HETATM 5 H UNL 1 0.875 1.621 -0.000 1.00 0.00 H +HETATM 6 H UNL 1 1.956 1.088 -0.000 1.00 0.00 H +HETATM 7 H UNL 1 1.910 -0.403 -0.000 1.00 0.00 H +HETATM 8 H UNL 1 -1.849 1.575 -0.000 1.00 0.00 H +HETATM 9 H UNL 1 -3.052 0.799 -0.000 1.00 0.00 H +HETATM 10 H UNL 1 -2.611 -0.586 -0.000 1.00 0.00 H +CONECT 1 2 3 4 +CONECT 2 1 5 6 7 +CONECT 3 1 8 9 10 +CONECT 4 1 +CONECT 5 2 +CONECT 6 2 +CONECT 7 2 +CONECT 8 3 +CONECT 9 3 +CONECT 10 3 +MASTER 0 0 0 0 0 0 0 0 10 0 10 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/isopropylbenzene.pdb b/surface_coatings/molecules/one_port/pdbs/isopropylbenzene.pdb new file mode 100644 index 0000000..4f3fd19 --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/isopropylbenzene.pdb @@ -0,0 +1,46 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 C UNL 1 1.264 0.621 0.469 1.00 0.00 C +HETATM 2 C UNL 1 2.279 -0.328 -0.137 1.00 0.00 C +HETATM 3 C UNL 1 2.689 -1.470 0.766 1.00 0.00 C +HETATM 4 C UNL 1 2.820 -0.151 -1.493 1.00 0.00 C +HETATM 5 C UNL 1 2.702 1.072 -2.160 1.00 0.00 C +HETATM 6 C UNL 1 3.219 1.245 -3.444 1.00 0.00 C +HETATM 7 C UNL 1 3.855 0.185 -4.083 1.00 0.00 C +HETATM 8 C UNL 1 3.978 -1.040 -3.437 1.00 0.00 C +HETATM 9 C UNL 1 3.467 -1.203 -2.150 1.00 0.00 C +HETATM 10 H UNL 1 1.017 0.295 1.458 1.00 0.00 H +HETATM 11 H UNL 1 0.380 0.631 -0.134 1.00 0.00 H +HETATM 12 H UNL 1 1.678 1.607 0.511 1.00 0.00 H +HETATM 13 H UNL 1 2.678 -0.214 -1.123 1.00 0.00 H +HETATM 14 H UNL 1 2.172 -1.390 1.700 1.00 0.00 H +HETATM 15 H UNL 1 3.744 -1.427 0.939 1.00 0.00 H +HETATM 16 H UNL 1 2.442 -2.401 0.300 1.00 0.00 H +HETATM 17 H UNL 1 2.225 1.860 -1.695 1.00 0.00 H +HETATM 18 H UNL 1 3.130 2.156 -3.919 1.00 0.00 H +HETATM 19 H UNL 1 4.235 0.308 -5.034 1.00 0.00 H +HETATM 20 H UNL 1 4.447 -1.829 -3.910 1.00 0.00 H +HETATM 21 H UNL 1 3.568 -2.113 -1.674 1.00 0.00 H +CONECT 1 2 10 11 12 +CONECT 2 1 3 4 13 +CONECT 3 2 14 15 16 +CONECT 4 2 5 9 +CONECT 5 4 6 17 +CONECT 6 5 7 18 +CONECT 7 6 8 19 +CONECT 8 7 9 20 +CONECT 9 8 4 21 +CONECT 10 1 +CONECT 11 1 +CONECT 12 1 +CONECT 13 2 +CONECT 14 3 +CONECT 15 3 +CONECT 16 3 +CONECT 17 5 +CONECT 18 6 +CONECT 19 7 +CONECT 20 8 +CONECT 21 9 +MASTER 0 0 0 0 0 0 0 0 21 0 21 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/methoxy-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/methoxy-ch3.pdb deleted file mode 100755 index 73bcf86..0000000 --- a/surface_coatings/molecules/one_port/pdbs/methoxy-ch3.pdb +++ /dev/null @@ -1,22 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 O UNL 1 -1.058 -0.278 0.539 1.00 0.00 O -HETATM 2 C UNL 1 -0.384 0.892 0.136 1.00 0.00 C -HETATM 3 H UNL 1 -0.441 1.033 -0.966 1.00 0.00 H -HETATM 4 H UNL 1 0.669 0.897 0.495 1.00 0.00 H -HETATM 5 H UNL 1 -0.889 1.763 0.601 1.00 0.00 H -HETATM 6 C UNL 1 -0.429 -1.396 -0.042 1.00 0.00 C -HETATM 7 H UNL 1 -0.970 -2.309 0.283 1.00 0.00 H -HETATM 8 H UNL 1 -0.488 -1.362 -1.153 1.00 0.00 H -HETATM 9 H UNL 1 0.622 -1.498 0.309 1.00 0.00 H -CONECT 1 2 6 -CONECT 2 1 3 4 5 -CONECT 3 2 -CONECT 4 2 -CONECT 5 2 -CONECT 6 1 7 8 9 -CONECT 7 6 -CONECT 8 6 -CONECT 9 6 -MASTER 0 0 0 0 0 0 0 0 9 0 9 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/methoxy-h.pdb b/surface_coatings/molecules/one_port/pdbs/methoxy-h.pdb deleted file mode 100755 index 97f2584..0000000 --- a/surface_coatings/molecules/one_port/pdbs/methoxy-h.pdb +++ /dev/null @@ -1,16 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 O UNL 1 -1.424 -0.697 0.001 1.00 0.00 O -HETATM 2 C UNL 1 -1.252 0.690 0.025 1.00 0.00 C -HETATM 3 H UNL 1 -1.810 -0.940 0.882 1.00 0.00 H -HETATM 4 H UNL 1 -0.820 1.016 -0.943 1.00 0.00 H -HETATM 5 H UNL 1 -2.233 1.198 0.155 1.00 0.00 H -HETATM 6 H UNL 1 -0.547 0.978 0.835 1.00 0.00 H -CONECT 1 2 3 -CONECT 2 1 4 5 6 -CONECT 3 1 -CONECT 4 2 -CONECT 5 2 -CONECT 6 2 -MASTER 0 0 0 0 0 0 0 0 6 0 6 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/methoxy.pdb b/surface_coatings/molecules/one_port/pdbs/methoxy.pdb new file mode 100644 index 0000000..9d0166a --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/methoxy.pdb @@ -0,0 +1,14 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 O UNL 1 -0.464 -0.205 -0.000 1.00 0.00 O +HETATM 2 C UNL 1 -0.495 1.317 -0.000 1.00 0.00 C +HETATM 3 H UNL 1 -1.682 1.332 -0.000 1.00 0.00 H +HETATM 4 H UNL 1 0.708 1.332 -0.000 1.00 0.00 H +HETATM 5 H UNL 1 -0.540 2.458 -0.000 1.00 0.00 H +CONECT 1 2 +CONECT 2 1 3 4 5 +CONECT 3 2 +CONECT 4 2 +CONECT 5 2 +MASTER 0 0 0 0 0 0 0 0 5 0 5 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/methyl-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/methyl-ch3.pdb deleted file mode 100755 index ed0c6a4..0000000 --- a/surface_coatings/molecules/one_port/pdbs/methyl-ch3.pdb +++ /dev/null @@ -1,20 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.096 0.187 -0.106 1.00 0.00 C -HETATM 2 H UNL 1 0.898 0.542 -0.449 1.00 0.00 H -HETATM 3 H UNL 1 -0.860 0.450 -0.868 1.00 0.00 H -HETATM 4 H UNL 1 -0.350 0.687 0.852 1.00 0.00 H -HETATM 5 C UNL 1 -0.064 -1.319 0.093 1.00 0.00 C -HETATM 6 H UNL 1 -1.058 -1.675 0.436 1.00 0.00 H -HETATM 7 H UNL 1 0.190 -1.820 -0.865 1.00 0.00 H -HETATM 8 H UNL 1 0.699 -1.583 0.855 1.00 0.00 H -CONECT 1 2 3 4 5 -CONECT 2 1 -CONECT 3 1 -CONECT 4 1 -CONECT 5 1 6 7 8 -CONECT 6 5 -CONECT 7 5 -CONECT 8 5 -MASTER 0 0 0 0 0 0 0 0 8 0 8 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/methyl-h.pdb b/surface_coatings/molecules/one_port/pdbs/methyl-h.pdb deleted file mode 100755 index 013dfbd..0000000 --- a/surface_coatings/molecules/one_port/pdbs/methyl-h.pdb +++ /dev/null @@ -1,14 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.760 0.524 0.000 1.00 0.00 C -HETATM 2 H UNL 1 0.342 0.603 -0.095 1.00 0.00 H -HETATM 3 H UNL 1 -1.017 -0.388 0.577 1.00 0.00 H -HETATM 4 H UNL 1 -1.151 1.418 0.527 1.00 0.00 H -HETATM 5 H UNL 1 -1.215 0.462 -1.010 1.00 0.00 H -CONECT 1 2 3 4 5 -CONECT 2 1 -CONECT 3 1 -CONECT 4 1 -CONECT 5 1 -MASTER 0 0 0 0 0 0 0 0 5 0 5 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/nitro-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/nitro-ch3.pdb deleted file mode 100755 index 413c6b9..0000000 --- a/surface_coatings/molecules/one_port/pdbs/nitro-ch3.pdb +++ /dev/null @@ -1,11 +0,0 @@ -COMPND NITROMETHANE -AUTHOR DAVE WOODCOCK 96 05 08 -ATOM 1 C 1 0.945 -0.279 -0.118 1.00 0.00 -ATOM 2 N 1 -0.433 0.057 0.180 1.00 0.00 -ATOM 3 O 1 -1.141 0.923 -0.662 1.00 0.00 -ATOM 4 O 1 -1.056 -0.485 1.311 1.00 0.00 -ATOM 5 H 1 0.998 -0.759 -1.095 1.00 0.00 -ATOM 6 H 1 1.326 -0.959 0.643 1.00 0.00 -ATOM 7 H 1 1.546 0.630 -0.127 1.00 0.00 -TER 8 1 -END diff --git a/surface_coatings/molecules/one_port/pdbs/nitro.pdb b/surface_coatings/molecules/one_port/pdbs/nitro.pdb new file mode 100644 index 0000000..0661a7f --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/nitro.pdb @@ -0,0 +1,10 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 N UNL 1 -0.251 -0.799 -0.000 1.00 0.00 N +HETATM 2 O UNL 1 -1.438 -0.129 -0.000 1.00 0.00 O +HETATM 3 O UNL 1 1.088 0.099 -0.000 1.00 0.00 O +CONECT 1 2 3 +CONECT 2 1 +CONECT 3 1 +MASTER 0 0 0 0 0 0 0 0 3 0 3 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/nitrophenyl-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/nitrophenyl-ch3.pdb deleted file mode 100755 index b160874..0000000 --- a/surface_coatings/molecules/one_port/pdbs/nitrophenyl-ch3.pdb +++ /dev/null @@ -1,38 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.313 -0.614 0.000 1.00 0.00 C -HETATM 2 C UNL 1 0.876 0.135 0.000 1.00 0.00 C -HETATM 3 C UNL 1 -1.548 0.053 0.000 1.00 0.00 C -HETATM 4 C UNL 1 -1.593 1.451 0.000 1.00 0.00 C -HETATM 5 C UNL 1 0.827 1.533 0.000 1.00 0.00 C -HETATM 6 C UNL 1 -0.407 2.190 0.000 1.00 0.00 C -HETATM 7 H UNL 1 -0.794 -2.499 -0.904 1.00 0.00 H -HETATM 8 H UNL 1 1.744 2.106 0.000 1.00 0.00 H -HETATM 9 H UNL 1 -2.548 1.962 0.000 1.00 0.00 H -HETATM 10 H UNL 1 -2.474 -0.509 0.000 1.00 0.00 H -HETATM 11 H UNL 1 1.839 -0.360 0.000 1.00 0.00 H -HETATM 12 C UNL 1 -0.278 -2.114 0.000 1.00 0.00 C -HETATM 13 H UNL 1 0.765 -2.498 0.000 1.00 0.00 H -HETATM 14 H UNL 1 -0.794 -2.499 0.904 1.00 0.00 H -HETATM 15 N UNL 1 -0.480 3.751 0.012 1.00 0.00 N -HETATM 16 O UNL 1 0.790 4.482 0.176 1.00 0.00 O -HETATM 17 O UNL 1 -1.820 4.417 -0.136 1.00 0.00 O -CONECT 1 2 3 12 -CONECT 2 1 5 11 -CONECT 3 1 4 10 -CONECT 4 3 6 9 -CONECT 5 2 6 8 -CONECT 6 4 5 15 -CONECT 7 12 -CONECT 8 5 -CONECT 9 4 -CONECT 10 3 -CONECT 11 2 -CONECT 12 1 7 13 14 -CONECT 13 12 -CONECT 14 12 -CONECT 15 6 16 17 -CONECT 16 15 -CONECT 17 15 -MASTER 0 0 0 0 0 0 0 0 17 0 17 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/nitrophenyl-h.pdb b/surface_coatings/molecules/one_port/pdbs/nitrophenyl-h.pdb deleted file mode 100755 index f572b65..0000000 --- a/surface_coatings/molecules/one_port/pdbs/nitrophenyl-h.pdb +++ /dev/null @@ -1,32 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 N UNL 1 -0.303 0.315 0.145 1.00 0.00 N -HETATM 2 O UNL 1 0.770 0.780 -0.107 1.00 0.00 O -HETATM 3 O UNL 1 -1.386 0.883 -0.284 1.00 0.00 O -HETATM 4 C UNL 1 -0.319 -1.081 0.477 1.00 0.00 C -HETATM 5 C UNL 1 -1.544 -1.776 0.585 1.00 0.00 C -HETATM 6 C UNL 1 -1.567 -3.135 0.912 1.00 0.00 C -HETATM 7 C UNL 1 -0.374 -3.822 1.140 1.00 0.00 C -HETATM 8 C UNL 1 0.847 -3.152 1.043 1.00 0.00 C -HETATM 9 C UNL 1 0.879 -1.793 0.716 1.00 0.00 C -HETATM 10 H UNL 1 1.841 -1.301 0.650 1.00 0.00 H -HETATM 11 H UNL 1 1.771 -3.686 1.222 1.00 0.00 H -HETATM 12 H UNL 1 -2.484 -1.266 0.416 1.00 0.00 H -HETATM 13 H UNL 1 -2.513 -3.656 0.991 1.00 0.00 H -HETATM 14 H UNL 1 -0.395 -4.874 1.394 1.00 0.00 H -CONECT 1 2 3 4 -CONECT 2 1 -CONECT 3 1 -CONECT 4 1 5 9 -CONECT 5 4 6 12 -CONECT 6 5 7 13 -CONECT 7 6 8 14 -CONECT 8 7 9 11 -CONECT 9 8 4 10 -CONECT 10 9 -CONECT 11 8 -CONECT 12 5 -CONECT 13 6 -CONECT 14 7 -MASTER 0 0 0 0 0 0 0 0 14 0 14 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/oh.pdb b/surface_coatings/molecules/one_port/pdbs/oh.pdb new file mode 100644 index 0000000..a631bbd --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/oh.pdb @@ -0,0 +1,8 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL +HETATM 1 O HOH 1 0.000 0.000 1.019 1.00 0.00 O +HETATM 2 H HOH 0 0.000 0.000 0.049 1.00 0.00 H +CONECT 1 2 +CONECT 2 1 +MASTER 0 0 0 0 0 0 0 0 2 0 2 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/pentafluorophenyl.pdb b/surface_coatings/molecules/one_port/pdbs/pentafluorophenyl.pdb new file mode 100644 index 0000000..0b6c14d --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/pentafluorophenyl.pdb @@ -0,0 +1,26 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 C UNL 1 -0.297 -0.860 -0.000 1.00 0.00 C +HETATM 2 C UNL 1 1.119 0.084 -0.000 1.00 0.00 C +HETATM 3 C UNL 1 -1.758 0.053 -0.000 1.00 0.00 C +HETATM 4 C UNL 1 -1.789 1.636 -0.000 1.00 0.00 C +HETATM 5 C UNL 1 1.088 1.697 -0.000 1.00 0.00 C +HETATM 6 C UNL 1 -0.434 2.748 -0.000 1.00 0.00 C +HETATM 7 F UNL 1 -0.449 3.920 -0.000 1.00 0.00 F +HETATM 8 F UNL 1 1.971 2.474 -0.000 1.00 0.00 F +HETATM 9 F UNL 1 -2.793 2.200 -0.000 1.00 0.00 F +HETATM 10 F UNL 1 -2.732 -0.753 -0.000 1.00 0.00 F +HETATM 11 F UNL 1 2.184 -0.571 -0.000 1.00 0.00 F +CONECT 1 2 3 +CONECT 2 1 5 11 +CONECT 3 1 4 10 +CONECT 4 3 6 9 +CONECT 5 2 6 8 +CONECT 6 4 5 7 +CONECT 7 6 +CONECT 8 5 +CONECT 9 4 +CONECT 10 3 +CONECT 11 2 +MASTER 0 0 0 0 0 0 0 0 11 0 11 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/perfluoromethyl-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/perfluoromethyl-ch3.pdb deleted file mode 100755 index 40519ba..0000000 --- a/surface_coatings/molecules/one_port/pdbs/perfluoromethyl-ch3.pdb +++ /dev/null @@ -1,20 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.060 0.193 0.238 1.00 0.00 C -HETATM 2 F UNL 1 0.981 0.442 1.114 1.00 0.00 F -HETATM 3 F UNL 1 -1.253 0.560 0.833 1.00 0.00 F -HETATM 4 F UNL 1 0.125 0.940 -0.912 1.00 0.00 F -HETATM 5 C UNL 1 -0.094 -1.286 -0.112 1.00 0.00 C -HETATM 6 H UNL 1 0.863 -1.585 -0.590 1.00 0.00 H -HETATM 7 H UNL 1 -0.242 -1.890 0.809 1.00 0.00 H -HETATM 8 H UNL 1 -0.929 -1.490 -0.815 1.00 0.00 H -CONECT 1 2 3 4 5 -CONECT 2 1 -CONECT 3 1 -CONECT 4 1 -CONECT 5 1 6 7 8 -CONECT 6 5 -CONECT 7 5 -CONECT 8 5 -MASTER 0 0 0 0 0 0 0 0 8 0 8 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/perfluoromethyl-h.pdb b/surface_coatings/molecules/one_port/pdbs/perfluoromethyl-h.pdb deleted file mode 100755 index 6d88a7b..0000000 --- a/surface_coatings/molecules/one_port/pdbs/perfluoromethyl-h.pdb +++ /dev/null @@ -1,14 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.201 0.698 0.282 1.00 0.00 C -HETATM 2 F UNL 1 -0.963 -0.389 -0.101 1.00 0.00 F -HETATM 3 F UNL 1 -0.856 1.864 -0.064 1.00 0.00 F -HETATM 4 F UNL 1 1.023 0.650 -0.357 1.00 0.00 F -HETATM 5 H UNL 1 -0.046 0.672 1.380 1.00 0.00 H -CONECT 1 2 3 4 5 -CONECT 2 1 -CONECT 3 1 -CONECT 4 1 -CONECT 5 1 -MASTER 0 0 0 0 0 0 0 0 5 0 5 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/perfluoromethyl.pdb b/surface_coatings/molecules/one_port/pdbs/perfluoromethyl.pdb new file mode 100644 index 0000000..dd4c7a8 --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/perfluoromethyl.pdb @@ -0,0 +1,12 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 C UNL 1 -0.129 0.282 -0.000 1.00 0.00 C +HETATM 2 F UNL 1 1.012 0.282 -0.000 1.00 0.00 F +HETATM 3 F UNL 1 -1.301 0.297 -0.000 1.00 0.00 F +HETATM 4 F UNL 1 -0.160 1.454 -0.000 1.00 0.00 F +CONECT 1 2 3 4 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +MASTER 0 0 0 0 0 0 0 0 4 0 4 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/phenol.pdb b/surface_coatings/molecules/one_port/pdbs/phenol.pdb new file mode 100644 index 0000000..5d61bf1 --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/phenol.pdb @@ -0,0 +1,30 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 C UNL 1 -1.402 -0.066 0.044 1.00 0.00 C +HETATM 2 C UNL 1 -0.766 1.165 0.004 1.00 0.00 C +HETATM 3 C UNL 1 0.630 1.221 -0.052 1.00 0.00 C +HETATM 4 C UNL 1 1.452 0.082 -0.070 1.00 0.00 C +HETATM 5 C UNL 1 0.753 -1.136 -0.027 1.00 0.00 C +HETATM 6 C UNL 1 -0.640 -1.225 0.029 1.00 0.00 C +HETATM 7 O UNL 1 2.723 0.148 -0.120 1.00 0.00 O +HETATM 8 H UNL 1 -2.432 -0.120 0.085 1.00 0.00 H +HETATM 9 H UNL 1 -1.320 2.036 0.014 1.00 0.00 H +HETATM 10 H UNL 1 1.080 2.149 -0.081 1.00 0.00 H +HETATM 11 H UNL 1 1.299 -2.012 -0.038 1.00 0.00 H +HETATM 12 H UNL 1 -1.100 -2.149 0.058 1.00 0.00 H +HETATM 13 H UNL 1 3.148 0.983 -0.147 1.00 0.00 H +CONECT 1 2 6 8 +CONECT 2 1 3 9 +CONECT 3 2 4 10 +CONECT 4 3 5 7 +CONECT 5 4 6 11 +CONECT 6 5 1 12 +CONECT 7 4 13 +CONECT 8 1 +CONECT 9 2 +CONECT 10 3 +CONECT 11 5 +CONECT 12 6 +CONECT 13 7 +MASTER 0 0 0 0 0 0 0 0 13 0 13 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/phenyl-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/phenyl-ch3.pdb deleted file mode 100755 index abca264..0000000 --- a/surface_coatings/molecules/one_port/pdbs/phenyl-ch3.pdb +++ /dev/null @@ -1,34 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.313 -0.614 0.000 1.00 0.00 C -HETATM 2 C UNL 1 0.876 0.135 0.000 1.00 0.00 C -HETATM 3 C UNL 1 -1.548 0.053 0.000 1.00 0.00 C -HETATM 4 C UNL 1 -1.593 1.451 0.000 1.00 0.00 C -HETATM 5 C UNL 1 0.827 1.533 0.000 1.00 0.00 C -HETATM 6 C UNL 1 -0.407 2.190 0.000 1.00 0.00 C -HETATM 7 H UNL 1 -0.443 3.272 0.000 1.00 0.00 H -HETATM 8 H UNL 1 1.744 2.106 0.000 1.00 0.00 H -HETATM 9 H UNL 1 -2.548 1.962 0.000 1.00 0.00 H -HETATM 10 H UNL 1 -2.474 -0.509 0.000 1.00 0.00 H -HETATM 11 H UNL 1 1.839 -0.360 0.000 1.00 0.00 H -HETATM 12 C UNL 1 -0.278 -2.114 0.000 1.00 0.00 C -HETATM 13 H UNL 1 0.765 -2.498 0.000 1.00 0.00 H -HETATM 14 H UNL 1 -0.794 -2.499 0.904 1.00 0.00 H -HETATM 15 H UNL 1 -0.794 -2.499 -0.904 1.00 0.00 H -CONECT 1 2 3 12 -CONECT 2 1 5 11 -CONECT 3 1 4 10 -CONECT 4 3 6 9 -CONECT 5 2 6 8 -CONECT 6 4 5 7 -CONECT 7 6 -CONECT 8 5 -CONECT 9 4 -CONECT 10 3 -CONECT 11 2 -CONECT 12 1 13 14 15 -CONECT 13 12 -CONECT 14 12 -CONECT 15 12 -MASTER 0 0 0 0 0 0 0 0 15 0 15 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/phenyl-h.pdb b/surface_coatings/molecules/one_port/pdbs/phenyl-h.pdb deleted file mode 100755 index e3d924b..0000000 --- a/surface_coatings/molecules/one_port/pdbs/phenyl-h.pdb +++ /dev/null @@ -1,28 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.475 -0.797 0.000 1.00 0.00 C -HETATM 2 C UNL 1 0.733 -0.092 0.000 1.00 0.00 C -HETATM 3 C UNL 1 -1.690 -0.103 0.000 1.00 0.00 C -HETATM 4 C UNL 1 -1.696 1.296 0.000 1.00 0.00 C -HETATM 5 C UNL 1 -0.488 2.001 0.000 1.00 0.00 C -HETATM 6 C UNL 1 0.727 1.307 0.000 1.00 0.00 C -HETATM 7 H UNL 1 1.661 1.853 0.000 1.00 0.00 H -HETATM 8 H UNL 1 -0.470 -1.879 0.000 1.00 0.00 H -HETATM 9 H UNL 1 1.673 -0.628 0.000 1.00 0.00 H -HETATM 10 H UNL 1 -2.624 -0.649 0.000 1.00 0.00 H -HETATM 11 H UNL 1 -2.636 1.833 0.000 1.00 0.00 H -HETATM 12 H UNL 1 -0.493 3.083 0.000 1.00 0.00 H -CONECT 1 2 3 8 -CONECT 2 1 6 9 -CONECT 3 1 4 10 -CONECT 4 3 5 11 -CONECT 5 4 6 12 -CONECT 6 2 5 7 -CONECT 7 6 -CONECT 8 1 -CONECT 9 2 -CONECT 10 3 -CONECT 11 4 -CONECT 12 5 -MASTER 0 0 0 0 0 0 0 0 12 0 12 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/phenyl.pdb b/surface_coatings/molecules/one_port/pdbs/phenyl.pdb new file mode 100644 index 0000000..7953526 --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/phenyl.pdb @@ -0,0 +1,26 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 C UNL 1 -0.297 -0.860 -0.000 1.00 0.00 C +HETATM 2 C UNL 1 1.119 0.084 -0.000 1.00 0.00 C +HETATM 3 C UNL 1 -1.758 0.053 -0.000 1.00 0.00 C +HETATM 4 C UNL 1 -1.789 1.636 -0.000 1.00 0.00 C +HETATM 5 C UNL 1 1.088 1.697 -0.000 1.00 0.00 C +HETATM 6 C UNL 1 -0.434 2.748 -0.000 1.00 0.00 C +HETATM 7 H UNL 1 -0.449 3.920 -0.000 1.00 0.00 H +HETATM 8 H UNL 1 1.971 2.474 -0.000 1.00 0.00 H +HETATM 9 H UNL 1 -2.793 2.200 -0.000 1.00 0.00 H +HETATM 10 H UNL 1 -2.732 -0.753 -0.000 1.00 0.00 H +HETATM 11 H UNL 1 2.184 -0.571 -0.000 1.00 0.00 H +CONECT 1 2 3 +CONECT 2 1 5 11 +CONECT 3 1 4 10 +CONECT 4 3 6 9 +CONECT 5 2 6 8 +CONECT 6 4 5 7 +CONECT 7 6 +CONECT 8 5 +CONECT 9 4 +CONECT 10 3 +CONECT 11 2 +MASTER 0 0 0 0 0 0 0 0 11 0 11 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/phenyl_unfunctionalized.pdb b/surface_coatings/molecules/one_port/pdbs/phenyl_unfunctionalized.pdb new file mode 100644 index 0000000..54789fa --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/phenyl_unfunctionalized.pdb @@ -0,0 +1,16 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 C UNL 1 -1.895 0.114 -0.000 1.00 0.00 C +HETATM 2 C UNL 1 -1.910 1.606 -0.000 1.00 0.00 C +HETATM 3 C UNL 1 -0.525 2.367 -0.000 1.00 0.00 C +HETATM 4 C UNL 1 0.708 1.606 -0.000 1.00 0.00 C +HETATM 5 C UNL 1 0.799 0.023 -0.000 1.00 0.00 C +HETATM 6 C UNL 1 -0.419 -0.875 -0.000 1.00 0.00 C +CONECT 1 2 6 +CONECT 2 1 3 +CONECT 3 2 4 +CONECT 4 3 5 +CONECT 5 4 6 +CONECT 6 5 1 +MASTER 0 0 0 0 0 0 0 0 6 0 6 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/pyrrole-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/pyrrole-ch3.pdb deleted file mode 100755 index 0abeb4f..0000000 --- a/surface_coatings/molecules/one_port/pdbs/pyrrole-ch3.pdb +++ /dev/null @@ -1,30 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.415 -0.399 0.000 1.00 0.00 C -HETATM 2 C UNL 1 0.718 0.390 0.000 1.00 0.00 C -HETATM 3 N UNL 1 -1.518 0.372 0.000 1.00 0.00 N -HETATM 4 C UNL 1 -1.103 1.653 0.000 1.00 0.00 C -HETATM 5 C UNL 1 0.278 1.698 0.000 1.00 0.00 C -HETATM 6 H UNL 1 -2.509 0.044 0.000 1.00 0.00 H -HETATM 7 H UNL 1 -1.766 2.508 0.000 1.00 0.00 H -HETATM 8 H UNL 1 0.894 2.587 0.000 1.00 0.00 H -HETATM 9 H UNL 1 1.746 0.054 0.000 1.00 0.00 H -HETATM 10 C UNL 1 -0.444 -1.893 0.000 1.00 0.00 C -HETATM 11 H UNL 1 0.588 -2.304 0.000 1.00 0.00 H -HETATM 12 H UNL 1 -0.975 -2.253 0.905 1.00 0.00 H -HETATM 13 H UNL 1 -0.975 -2.253 -0.905 1.00 0.00 H -CONECT 1 2 3 10 -CONECT 2 1 5 9 -CONECT 3 1 4 6 -CONECT 4 3 5 7 -CONECT 5 2 4 8 -CONECT 6 3 -CONECT 7 4 -CONECT 8 5 -CONECT 9 2 -CONECT 10 1 11 12 13 -CONECT 11 10 -CONECT 12 10 -CONECT 13 10 -MASTER 0 0 0 0 0 0 0 0 13 0 13 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/pyrrole-h.pdb b/surface_coatings/molecules/one_port/pdbs/pyrrole-h.pdb deleted file mode 100755 index b8983f9..0000000 --- a/surface_coatings/molecules/one_port/pdbs/pyrrole-h.pdb +++ /dev/null @@ -1,24 +0,0 @@ -COMPND UNNAMED -AUTHOR GENERATED BY OPEN BABEL 2.3.90 -HETATM 1 C UNL 1 -0.411 -0.407 0.000 1.00 0.00 C -HETATM 2 C UNL 1 0.718 0.386 0.000 1.00 0.00 C -HETATM 3 N UNL 1 -1.511 0.367 0.000 1.00 0.00 N -HETATM 4 C UNL 1 -1.100 1.648 0.000 1.00 0.00 C -HETATM 5 C UNL 1 0.279 1.695 0.000 1.00 0.00 C -HETATM 6 H UNL 1 -2.501 0.036 0.000 1.00 0.00 H -HETATM 7 H UNL 1 -1.764 2.502 0.000 1.00 0.00 H -HETATM 8 H UNL 1 0.896 2.583 0.000 1.00 0.00 H -HETATM 9 H UNL 1 1.745 0.048 0.000 1.00 0.00 H -HETATM 10 H UNL 1 -0.427 -1.489 0.000 1.00 0.00 H -CONECT 1 2 3 10 -CONECT 2 1 5 9 -CONECT 3 1 4 6 -CONECT 4 3 5 7 -CONECT 5 8 2 4 -CONECT 6 3 -CONECT 7 4 -CONECT 8 5 -CONECT 9 2 -CONECT 10 1 -MASTER 0 0 0 0 0 0 0 0 10 0 10 0 -END diff --git a/surface_coatings/molecules/one_port/pdbs/toluene.pdb b/surface_coatings/molecules/one_port/pdbs/toluene.pdb new file mode 100644 index 0000000..13548ae --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/toluene.pdb @@ -0,0 +1,34 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 C UNL 1 1.065 -0.072 0.093 1.00 0.00 C +HETATM 2 C UNL 1 2.564 -0.052 0.003 1.00 0.00 C +HETATM 3 C UNL 1 3.237 1.166 -0.035 1.00 0.00 C +HETATM 4 C UNL 1 4.628 1.183 -0.118 1.00 0.00 C +HETATM 5 C UNL 1 5.338 -0.015 -0.162 1.00 0.00 C +HETATM 6 C UNL 1 4.660 -1.231 -0.124 1.00 0.00 C +HETATM 7 C UNL 1 3.269 -1.251 -0.041 1.00 0.00 C +HETATM 8 H UNL 1 0.696 0.932 0.117 1.00 0.00 H +HETATM 9 H UNL 1 0.768 -0.583 0.985 1.00 0.00 H +HETATM 10 H UNL 1 0.664 -0.580 -0.759 1.00 0.00 H +HETATM 11 H UNL 1 2.709 2.052 -0.002 1.00 0.00 H +HETATM 12 H UNL 1 5.132 2.083 -0.146 1.00 0.00 H +HETATM 13 H UNL 1 6.368 -0.001 -0.224 1.00 0.00 H +HETATM 14 H UNL 1 5.187 -2.118 -0.157 1.00 0.00 H +HETATM 15 H UNL 1 2.764 -2.151 -0.013 1.00 0.00 H +CONECT 1 2 8 9 10 +CONECT 2 1 3 7 +CONECT 3 2 4 11 +CONECT 4 3 5 12 +CONECT 5 4 6 13 +CONECT 6 5 7 14 +CONECT 7 6 2 15 +CONECT 8 1 +CONECT 9 1 +CONECT 10 1 +CONECT 11 3 +CONECT 12 4 +CONECT 13 5 +CONECT 14 6 +CONECT 15 7 +MASTER 0 0 0 0 0 0 0 0 15 0 15 0 +END diff --git a/surface_coatings/molecules/one_port/pdbs/triazole.pdb b/surface_coatings/molecules/one_port/pdbs/triazole.pdb new file mode 100644 index 0000000..96d19e5 --- /dev/null +++ b/surface_coatings/molecules/one_port/pdbs/triazole.pdb @@ -0,0 +1,18 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.3.90 +HETATM 1 N UNL 1 -0.114 -1.073 -0.000 1.00 0.00 N +HETATM 2 N UNL 1 1.347 -0.419 -0.000 1.00 0.00 N +HETATM 3 C UNL 1 -1.606 -0.510 -0.000 1.00 0.00 C +HETATM 4 C UNL 1 0.708 1.088 -0.000 1.00 0.00 C +HETATM 5 N UNL 1 -1.104 1.104 -0.000 1.00 0.00 N +HETATM 6 H UNL 1 1.408 2.063 -0.000 1.00 0.00 H +HETATM 7 H UNL 1 -2.839 -0.814 -0.000 1.00 0.00 H +CONECT 1 2 3 +CONECT 2 1 4 +CONECT 3 1 5 7 +CONECT 4 2 5 6 +CONECT 5 3 4 +CONECT 6 4 +CONECT 7 3 +MASTER 0 0 0 0 0 0 0 0 7 0 7 0 +END