# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 19:17:37 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 5-(thiophen-2-yl)pyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cncc(c1)c2sccc2
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 VM1  VM1  '5-(thiophen-2-yl)pyridine-3-carboxylic acid'  ligand  21  14  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VM1
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 VM1  O1A   O  O     0  -0.430   2.8264  -2.0867   0.3295
 VM1  C1B   C  C     0   0.541   3.0611  -0.9133   0.1766
 VM1  O1C   O  OH1   0  -0.591   4.2815  -0.4071   0.1221
 VM1  S1D   S  S2    0   0.226  -2.3036  -1.2262  -0.5604
 VM1  C1E   C  CR15  0  -0.464  -3.9339  -0.8188  -0.2402
 VM1  C1F   C  CR15  0  -0.171  -4.0503   0.4541   0.2293
 VM1  C1G   C  CR6   0  -0.158   2.0040   0.1180   0.0269
 VM1  C1H   C  CR16  0  -0.208   0.6739  -0.2791   0.0576
 VM1  C1I   C  CR6   0   0.073  -0.3300   0.6715  -0.0811
 VM1  C1J   C  CR5   0  -0.222  -1.7474   0.3288  -0.0552
 VM1  C1K   C  CR15  0  -0.238  -2.7989   1.1124   0.3355
 VM1  C1L   C  CR16  0  -0.052   2.2876   1.4717  -0.1295
 VM1  N1M   N  N     0  -0.390   1.3395   2.3890  -0.2635
 VM1  C1N   C  CR16  0  -0.088   0.0758   1.9991  -0.2486
 VM1  HO1C  H  HOH1  0   0.492   4.9407  -1.1100   0.2248
 VM1  H1F   H  HCR5  0   0.273  -4.9937   0.9089   0.4934
 VM1  H1H   H  HCR6  0   0.277   0.4311  -1.3246   0.2039
 VM1  H1K   H  HCR5  0   0.270  -2.6823   2.1205   0.7080
 VM1  H1L   H  HCR6  0   0.282   3.3081   1.8327  -0.1511
 VM1  H1N   H  HCR6  0   0.275  -0.6680   2.7762  -0.3868
 VM1  H1E   H  HCR5  0   0.302  -4.7184  -1.5380  -0.4171

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 VM1  C1B  O1A   double    1.206  0.020  1.206
 VM1  C1G  C1B   single    1.484  0.020  1.484
 VM1  C1B  O1C   single    1.322  0.020  1.322
 VM1  O1C  HO1C  single    0.850  0.020  0.980
 VM1  C1E  S1D   aromatic  1.711  0.020  1.711
 VM1  S1D  C1J   aromatic  1.727  0.020  1.727
 VM1  C1E  C1F   aromatic  1.362  0.020  1.362
 VM1  C1E  H1E   single    0.930  0.020  1.080
 VM1  C1F  C1K   aromatic  1.418  0.020  1.418
 VM1  C1F  H1F   single    0.930  0.020  1.080
 VM1  C1H  C1G   aromatic  1.388  0.020  1.388
 VM1  C1L  C1G   aromatic  1.392  0.020  1.392
 VM1  C1I  C1H   aromatic  1.389  0.020  1.389
 VM1  C1H  H1H   single    0.930  0.020  1.080
 VM1  C1J  C1I   single    1.459  0.020  1.459
 VM1  C1N  C1I   aromatic  1.398  0.020  1.398
 VM1  C1J  C1K   aromatic  1.368  0.020  1.368
 VM1  C1K  H1K   single    0.930  0.020  1.080
 VM1  N1M  C1L   aromatic  1.326  0.020  1.326
 VM1  C1L  H1L   single    0.930  0.020  1.080
 VM1  C1N  N1M   aromatic  1.323  0.020  1.323
 VM1  C1N  H1N   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 VM1  C1G   C1B  O1C  112.77  3.000
 VM1  O1C   C1B  O1A  123.86  3.000
 VM1  C1G   C1B  O1A  123.37  3.000
 VM1  HO1C  O1C  C1B  110.23  3.000
 VM1  C1J   S1D  C1E   92.16  3.000
 VM1  H1E   C1E  C1F  128.14  3.000
 VM1  H1E   C1E  S1D  120.23  3.000
 VM1  C1F   C1E  S1D  111.63  3.000
 VM1  H1F   C1F  C1K  123.86  3.000
 VM1  H1F   C1F  C1E  123.54  3.000
 VM1  C1K   C1F  C1E  112.60  3.000
 VM1  C1L   C1G  C1H  118.41  3.000
 VM1  C1L   C1G  C1B  122.82  3.000
 VM1  C1H   C1G  C1B  118.77  3.000
 VM1  H1H   C1H  C1I  120.79  3.000
 VM1  H1H   C1H  C1G  119.58  3.000
 VM1  C1I   C1H  C1G  119.62  3.000
 VM1  C1N   C1I  C1J  120.48  3.000
 VM1  C1N   C1I  C1H  116.86  3.000
 VM1  C1J   C1I  C1H  122.66  3.000
 VM1  C1K   C1J  C1I  128.12  3.000
 VM1  C1K   C1J  S1D  110.59  3.000
 VM1  C1I   C1J  S1D  121.29  3.000
 VM1  H1K   C1K  C1J  123.34  3.000
 VM1  H1K   C1K  C1F  123.63  3.000
 VM1  C1J   C1K  C1F  113.01  3.000
 VM1  H1L   C1L  N1M  116.18  3.000
 VM1  H1L   C1L  C1G  121.23  3.000
 VM1  N1M   C1L  C1G  122.58  3.000
 VM1  C1N   N1M  C1L  118.56  3.000
 VM1  H1N   C1N  N1M  116.27  3.000
 VM1  H1N   C1N  C1I  119.77  3.000
 VM1  N1M   C1N  C1I  123.96  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 VM1  CONST_01  C1K   C1F  C1E  S1D    0.00   0.0  0
 VM1  CONST_04  C1F   C1K  C1J  S1D    0.00   0.0  0
 VM1  CONST_05  C1I   C1J  S1D  C1E  180.00   0.0  0
 VM1  CONST_06  C1K   C1J  S1D  C1E    0.00   0.0  0
 VM1  CONST_07  C1J   C1K  C1F  C1E    0.00   0.0  0
 VM1  CONST_08  C1J   S1D  C1E  C1F    0.00   0.0  0
 VM1  CONST_09  C1I   C1J  C1K  C1F  180.00   0.0  0
 VM1  CONST_10  C1J   C1I  C1H  C1G  180.00   0.0  0
 VM1  CONST_11  C1N   C1I  C1H  C1G    0.00   0.0  0
 VM1  CONST_12  C1N   N1M  C1L  C1G    0.00   0.0  0
 VM1  CONST_13  N1M   C1L  C1G  C1H    0.00   0.0  0
 VM1  CONST_15  N1M   C1N  C1I  C1H    0.00   0.0  0
 VM1  CONST_16  C1L   C1G  C1H  C1I    0.00   0.0  0
 VM1  CONST_17  C1L   N1M  C1N  C1I    0.00   0.0  0
 VM1  CONST_18  N1M   C1N  C1I  C1J  180.00   0.0  0
 VM1  CONST_20  C1I   C1H  C1G  C1B  180.00   0.0  0
 VM1  CONST_21  N1M   C1L  C1G  C1B  180.00   0.0  0
 VM1  CONST_22  H1F   C1F  C1E  S1D  180.00   0.0  0
 VM1  CONST_23  H1K   C1K  C1J  S1D  180.00   0.0  0
 VM1  CONST_24  H1L   C1L  C1G  C1H  180.00   0.0  0
 VM1  CONST_25  H1N   C1N  C1I  C1H  180.00   0.0  0
 VM1  CONST_26  H1E   C1E  S1D  C1J  180.00   0.0  0
 VM1  CONST_27  H1H   C1H  C1I  C1J    0.00   0.0  0
 VM1  CONST_28  HO1C  O1C  C1B  C1G  180.00   0.0  0
 VM1  Var_01    C1H   C1G  C1B  O1A   -0.28  30.0  2

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 VM1  plan-1  S1D   0.020
 VM1  plan-1  C1E   0.020
 VM1  plan-1  C1F   0.020
 VM1  plan-1  C1I   0.020
 VM1  plan-1  C1J   0.020
 VM1  plan-1  C1K   0.020
 VM1  plan-1  H1F   0.020
 VM1  plan-1  H1K   0.020
 VM1  plan-1  H1E   0.020
 VM1  plan-2  C1B   0.020
 VM1  plan-2  C1G   0.020
 VM1  plan-2  C1H   0.020
 VM1  plan-2  C1I   0.020
 VM1  plan-2  C1J   0.020
 VM1  plan-2  C1L   0.020
 VM1  plan-2  N1M   0.020
 VM1  plan-2  C1N   0.020
 VM1  plan-2  H1H   0.020
 VM1  plan-2  H1L   0.020
 VM1  plan-2  H1N   0.020
 VM1  plan-3  O1A   0.020
 VM1  plan-3  C1B   0.020
 VM1  plan-3  O1C   0.020
 VM1  plan-3  C1G   0.020
 VM1  plan-3  HO1C  0.020

