# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 07:26:56 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 5-(phenylethynyl)pyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cncc(c1)C#Cc2ccccc2
#
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
 KVD  KVD  '5-(phenylethynyl)pyridine-3-carboxylic acid'  ligand  25  17  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KVD
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
 KVD  C12   C  CR6    0  -0.111  -3.1193  -0.0211  -0.0259
 KVD  C13   C  CR16   0  -0.294  -4.0394   1.0320  -0.0637
 KVD  C14   C  CR16   0  -0.247  -5.3991   0.7660  -0.0745
 KVD  C15   C  CR16   0  -0.253  -5.8572  -0.5456  -0.0472
 KVD  C16   C  CR16   0  -0.247  -4.9480  -1.5959  -0.0097
 KVD  C17   C  CR16   0  -0.295  -3.5866  -1.3395   0.0011
 KVD  C04   C  CR6    0  -0.182   3.1504  -0.0298  -0.0274
 KVD  C05   C  CR16   0  -0.084   3.5122   1.3140   0.0047
 KVD  C07   C  CR16   0  -0.100   1.3504   2.0245   0.0255
 KVD  C08   C  CR6    0  -0.181   0.8642   0.7140  -0.0066
 KVD  C09   C  CR16   0  -0.227   1.7962  -0.3241  -0.0328
 KVD  C10   C  CSP    0   0.139  -0.5335   0.4612  -0.0119
 KVD  C11   C  CSP    0   0.139  -1.7212   0.2426  -0.0160
 KVD  N06   N  N      0  -0.395   2.6400   2.3173   0.0309
 KVD  O01   O  OC    -1  -0.587   5.3873  -0.7678  -0.0524
 KVD  O03   O  O      0  -0.585   3.7667  -2.3020  -0.0750
 KVD  H131  H  HCR6   0   0.261  -3.6835   2.0538  -0.0852
 KVD  H141  H  HCR6   0   0.265  -6.1044   1.5858  -0.1042
 KVD  H151  H  HCR6   0   0.264  -6.9202  -0.7474  -0.0553
 KVD  H161  H  HCR6   0   0.264  -5.2996  -2.6191   0.0118
 KVD  H171  H  HCR6   0   0.263  -2.8781  -2.1567   0.0305
 KVD  H051  H  HCR6   0   0.262   4.5606   1.5878   0.0102
 KVD  H071  H  HCR6   0   0.264   0.6550   2.8565   0.0475
 KVD  H091  H  HCR6   0   0.261   1.4627  -1.3532  -0.0560
 KVD  C02   C  C      0   0.408   4.1990  -1.1356  -0.0542

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
 KVD  C14  C15   aromatic  1.390  0.020  1.390
 KVD  C14  C13   aromatic  1.386  0.020  1.386
 KVD  C15  C16   aromatic  1.390  0.020  1.390
 KVD  C13  C12   aromatic  1.399  0.020  1.399
 KVD  C16  C17   aromatic  1.385  0.020  1.385
 KVD  C12  C17   aromatic  1.399  0.020  1.399
 KVD  C12  C11   single    1.423  0.020  1.423
 KVD  C11  C10   triple    1.208  0.020  1.208
 KVD  O03  C02   deloc     1.244  0.020  1.244
 KVD  C10  C08   single    1.420  0.020  1.420
 KVD  C09  C08   aromatic  1.395  0.020  1.395
 KVD  C09  C04   aromatic  1.386  0.020  1.386
 KVD  C02  C04   single    1.524  0.020  1.524
 KVD  C02  O01   deloc     1.244  0.020  1.244
 KVD  C08  C07   aromatic  1.398  0.020  1.398
 KVD  C04  C05   aromatic  1.392  0.020  1.392
 KVD  C07  N06   aromatic  1.322  0.020  1.322
 KVD  C05  N06   aromatic  1.330  0.020  1.330
 KVD  C13  H131  single    0.930  0.020  1.080
 KVD  C14  H141  single    0.930  0.020  1.080
 KVD  C15  H151  single    0.930  0.020  1.080
 KVD  C16  H161  single    0.930  0.020  1.080
 KVD  C17  H171  single    0.930  0.020  1.080
 KVD  C05  H051  single    0.930  0.020  1.080
 KVD  C07  H071  single    0.930  0.020  1.080
 KVD  C09  H091  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
 KVD  C11   C12  C17  120.18  3.000
 KVD  C11   C12  C13  120.46  3.000
 KVD  C17   C12  C13  119.36  3.000
 KVD  H131  C13  C14  120.25  3.000
 KVD  H131  C13  C12  119.68  3.000
 KVD  C14   C13  C12  120.07  3.000
 KVD  H141  C14  C15  120.06  3.000
 KVD  H141  C14  C13  119.64  3.000
 KVD  C15   C14  C13  120.30  3.000
 KVD  H151  C15  C16  120.13  3.000
 KVD  H151  C15  C14  119.99  3.000
 KVD  C16   C15  C14  119.88  3.000
 KVD  H161  C16  C17  119.62  3.000
 KVD  H161  C16  C15  120.17  3.000
 KVD  C17   C16  C15  120.22  3.000
 KVD  H171  C17  C16  120.26  3.000
 KVD  H171  C17  C12  119.58  3.000
 KVD  C16   C17  C12  120.17  3.000
 KVD  C09   C04  C05  117.33  3.000
 KVD  C05   C04  C02  121.46  3.000
 KVD  C09   C04  C02  121.21  3.000
 KVD  H051  C05  N06  116.35  3.000
 KVD  H051  C05  C04  119.71  3.000
 KVD  N06   C05  C04  123.95  3.000
 KVD  H071  C07  N06  117.08  3.000
 KVD  H071  C07  C08  119.77  3.000
 KVD  N06   C07  C08  123.15  3.000
 KVD  C10   C08  C09  121.65  3.000
 KVD  C09   C08  C07  117.74  3.000
 KVD  C10   C08  C07  120.60  3.000
 KVD  H091  C09  C08  120.14  3.000
 KVD  H091  C09  C04  120.22  3.000
 KVD  C08   C09  C04  119.64  3.000
 KVD  C11   C10  C08  180.00  3.000
 KVD  C10   C11  C12  180.00  3.000
 KVD  C07   N06  C05  118.19  3.000
 KVD  O03   C02  O01  127.53  3.000
 KVD  O01   C02  C04  116.27  3.000
 KVD  O03   C02  C04  116.19  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
 KVD  CONST_01  C15   C14  C13  C12    0.00   0.0  0
 KVD  CONST_02  C15   C16  C17  C12    0.00   0.0  0
 KVD  CONST_03  C16   C15  C14  C13    0.00   0.0  0
 KVD  CONST_04  C16   C17  C12  C13    0.00   0.0  0
 KVD  CONST_05  C17   C16  C15  C14    0.00   0.0  0
 KVD  CONST_06  C17   C12  C13  C14    0.00   0.0  0
 KVD  CONST_07  C07   C08  C09  C04    0.00   0.0  0
 KVD  CONST_08  C07   N06  C05  C04    0.00   0.0  0
 KVD  CONST_09  C08   C09  C04  C05    0.00   0.0  0
 KVD  CONST_10  C08   C07  N06  C05    0.00   0.0  0
 KVD  CONST_11  N06   C07  C08  C09    0.00   0.0  0
 KVD  CONST_12  N06   C05  C04  C09    0.00   0.0  0
 KVD  CONST_13  C11   C12  C13  C14  180.00   0.0  0
 KVD  CONST_14  C11   C12  C17  C16  180.00   0.0  0
 KVD  CONST_15  C08   C09  C04  C02  180.00   0.0  0
 KVD  CONST_16  N06   C05  C04  C02  180.00   0.0  0
 KVD  CONST_17  C10   C08  C09  C04  180.00   0.0  0
 KVD  CONST_18  N06   C07  C08  C10  180.00   0.0  0
 KVD  CONST_19  H141  C14  C13  C12  180.00   0.0  0
 KVD  CONST_20  H161  C16  C17  C12  180.00   0.0  0
 KVD  CONST_21  H151  C15  C14  C13  180.00   0.0  0
 KVD  CONST_22  H171  C17  C12  C13  180.00   0.0  0
 KVD  CONST_23  H131  C13  C14  C15  180.00   0.0  0
 KVD  CONST_24  H091  C09  C04  C05  180.00   0.0  0
 KVD  CONST_25  H071  C07  N06  C05  180.00   0.0  0
 KVD  CONST_26  H051  C05  N06  C07  180.00   0.0  0
 KVD  Var_01    O03   C02  C04  C05  179.64  30.0  3

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
 KVD  plan-1  C12   0.020
 KVD  plan-1  C13   0.020
 KVD  plan-1  C14   0.020
 KVD  plan-1  C15   0.020
 KVD  plan-1  C16   0.020
 KVD  plan-1  C17   0.020
 KVD  plan-1  C10   0.020
 KVD  plan-1  C11   0.020
 KVD  plan-1  H131  0.020
 KVD  plan-1  H141  0.020
 KVD  plan-1  H151  0.020
 KVD  plan-1  H161  0.020
 KVD  plan-1  H171  0.020
 KVD  plan-2  C04   0.020
 KVD  plan-2  C05   0.020
 KVD  plan-2  C07   0.020
 KVD  plan-2  C08   0.020
 KVD  plan-2  C09   0.020
 KVD  plan-2  C10   0.020
 KVD  plan-2  C11   0.020
 KVD  plan-2  N06   0.020
 KVD  plan-2  H051  0.020
 KVD  plan-2  H071  0.020
 KVD  plan-2  H091  0.020
 KVD  plan-2  C02   0.020
 KVD  plan-3  C04   0.020
 KVD  plan-3  O01   0.020
 KVD  plan-3  O03   0.020
 KVD  plan-3  C02   0.020

