# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 15:42:54 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  26  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  -0.061  -3.1317  -0.0366  -0.0193
 KVD  C13   C  CR16  0  -0.291  -4.0419   1.0247  -0.0504
 KVD  C14   C  CR16  0  -0.250  -5.4035   0.7717  -0.0479
 KVD  C15   C  CR16  0  -0.213  -5.8732  -0.5350  -0.0145
 KVD  C16   C  CR16  0  -0.286  -4.9742  -1.5935   0.0161
 KVD  C17   C  CR16  0  -0.228  -3.6111  -1.3498   0.0138
 KVD  C04   C  CR6   0  -0.253   3.1351  -0.0371  -0.0421
 KVD  C05   C  CR16  0   0.009   3.5032   1.3066  -0.0416
 KVD  C07   C  CR16  0  -0.066   1.3374   1.9922  -0.0311
 KVD  C08   C  CR6   0  -0.128   0.8506   0.6794  -0.0302
 KVD  C09   C  CR16  0  -0.077   1.7840  -0.3517  -0.0358
 KVD  C10   C  CSP   0  -0.066  -0.5438   0.4220  -0.0242
 KVD  C11   C  CSP   0   0.163  -1.7325   0.2147  -0.0212
 KVD  N06   N  N     0  -0.437   2.6218   2.2959  -0.0367
 KVD  O01   O  OH1   0  -0.597   5.3794  -0.7137  -0.0499
 KVD  O03   O  O     0  -0.468   3.8202  -2.3092  -0.0512
 KVD  H131  H  HCR6  0   0.262  -3.6769   2.0426  -0.0777
 KVD  H141  H  HCR6  0   0.261  -6.1014   1.5972  -0.0723
 KVD  H151  H  HCR6  0   0.244  -6.9376  -0.7266  -0.0119
 KVD  H161  H  HCR6  0   0.266  -5.3354  -2.6126   0.0434
 KVD  H171  H  HCR6  0   0.262  -2.9101  -2.1729   0.0380
 KVD  H051  H  HCR6  0   0.304   4.5460   1.5984  -0.0454
 KVD  H071  H  HCR6  0   0.296   0.6379   2.8205  -0.0273
 KVD  H091  H  HCR6  0   0.292   1.4594  -1.3837  -0.0354
 KVD  H1    H  HOH1  0   0.507   5.9711  -1.4777  -0.0481
 KVD  C02   C  C     0   0.554   4.1205  -1.1458  -0.0483

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  1.389  0.020  1.389
 KVD  C14  C13   aromatic  1.385  0.020  1.385
 KVD  C15  C16   aromatic  1.389  0.020  1.389
 KVD  C13  C12   aromatic  1.398  0.020  1.398
 KVD  C16  C17   aromatic  1.385  0.020  1.385
 KVD  C12  C17   aromatic  1.398  0.020  1.398
 KVD  C12  C11   single    1.422  0.020  1.422
 KVD  C11  C10   triple    1.207  0.020  1.207
 KVD  O03  C02   double    1.201  0.020  1.201
 KVD  C10  C08   single    1.418  0.020  1.418
 KVD  C09  C08   aromatic  1.391  0.020  1.391
 KVD  C09  C04   aromatic  1.387  0.020  1.387
 KVD  C02  C04   single    1.483  0.020  1.483
 KVD  C02  O01   single    1.331  0.020  1.331
 KVD  C08  C07   aromatic  1.400  0.020  1.400
 KVD  C04  C05   aromatic  1.393  0.020  1.393
 KVD  C07  N06   aromatic  1.320  0.020  1.320
 KVD  C05  N06   aromatic  1.325  0.020  1.325
 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
 KVD  O01  H1    single    0.850  0.020  0.980

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  120.23  3.000
 KVD  C11   C12  C13  120.43  3.000
 KVD  C17   C12  C13  119.34  3.000
 KVD  H131  C13  C14  120.25  3.000
 KVD  H131  C13  C12  119.67  3.000
 KVD  C14   C13  C12  120.08  3.000
 KVD  H141  C14  C15  120.03  3.000
 KVD  H141  C14  C13  119.68  3.000
 KVD  C15   C14  C13  120.29  3.000
 KVD  H151  C15  C16  120.13  3.000
 KVD  H151  C15  C14  119.97  3.000
 KVD  C16   C15  C14  119.90  3.000
 KVD  H161  C16  C17  119.64  3.000
 KVD  H161  C16  C15  120.16  3.000
 KVD  C17   C16  C15  120.20  3.000
 KVD  H171  C17  C16  120.27  3.000
 KVD  H171  C17  C12  119.54  3.000
 KVD  C16   C17  C12  120.18  3.000
 KVD  C09   C04  C05  118.43  3.000
 KVD  C05   C04  C02  123.05  3.000
 KVD  C09   C04  C02  118.52  3.000
 KVD  H051  C05  N06  116.07  3.000
 KVD  H051  C05  C04  120.95  3.000
 KVD  N06   C05  C04  122.98  3.000
 KVD  H071  C07  N06  116.88  3.000
 KVD  H071  C07  C08  119.47  3.000
 KVD  N06   C07  C08  123.65  3.000
 KVD  C10   C08  C09  121.69  3.000
 KVD  C09   C08  C07  117.50  3.000
 KVD  C10   C08  C07  120.80  3.000
 KVD  H091  C09  C08  120.39  3.000
 KVD  H091  C09  C04  120.57  3.000
 KVD  C08   C09  C04  119.05  3.000
 KVD  C11   C10  C08  180.00  3.000
 KVD  C10   C11  C12  180.00  3.000
 KVD  C07   N06  C05  118.40  3.000
 KVD  H1    O01  C02  108.81  3.000
 KVD  O03   C02  O01  123.42  3.000
 KVD  O01   C02  C04  112.68  3.000
 KVD  O03   C02  C04  123.90  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  CONST_27  H1    O01  C02  C04   180.00   0.0  0
 KVD  Var_01    O03   C02  C04  C05  -179.86  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  H1    0.020
 KVD  plan-3  C02   0.020

