# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 10:21:05 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: N-{[4-(hydroxycarbamoyl)phenyl]methyl}-2-(trifluoromethyl)pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)c1ccc(CNC(=O)c2cccnc2C(F)(F)F)cc1
#
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
 P6Y  P6Y  N-{[4-(hydroxycarbamoyl)phenyl]methyl}-2-(trifluoromethyl)pyridine-3-carboxamide  ligand  36  24  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P6Y
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
 P6Y  C13  C  CR6   0  -0.077  -2.3889   0.7054   0.3214
 P6Y  C15  C  CR16  0  -0.304  -2.5897   3.0932   0.3249
 P6Y  C24  C  CR16  0  -0.264   4.0511  -0.8483  -1.0677
 P6Y  C05  C  CR6   0  -0.074   4.3462  -0.1082   0.0732
 P6Y  C06  C  CR16  0  -0.247   3.3495   0.0937   1.0273
 P6Y  C07  C  CR16  0  -0.281   2.0775  -0.4097   0.8273
 P6Y  C08  C  CR6   0   0.127   1.7751  -1.1427  -0.3192
 P6Y  C09  C  CH2   0  -0.381   0.3893  -1.6985  -0.5273
 P6Y  C11  C  C     0   0.479  -1.5260  -0.5136   0.4685
 P6Y  C14  C  CR16  0  -0.140  -1.7940   1.9617   0.3456
 P6Y  C16  C  CR16  0  -0.061  -3.9647   2.9282   0.2742
 P6Y  C18  C  CR6   0  -0.039  -3.7787   0.6603   0.2527
 P6Y  C19  C  CT    0   1.056  -4.5299  -0.6495   0.1885
 P6Y  C23  C  CR16  0  -0.296   2.7745  -1.3589  -1.2586
 P6Y  F20  F  F     0  -0.311  -4.7300  -1.1624   1.4070
 P6Y  F21  F  F     0  -0.296  -5.7245  -0.4996  -0.3770
 P6Y  F22  F  F     0  -0.310  -3.8653  -1.5635  -0.5280
 P6Y  N03  N  NH1   0  -0.383   6.4230   0.7224  -0.7675
 P6Y  N10  N  NH1   0  -0.608  -0.6189  -0.6622  -0.5059
 P6Y  N17  N  N     0  -0.412  -4.5426   1.7365   0.2287
 P6Y  O01  O  O     0  -0.459   6.1207   0.6268   1.4743
 P6Y  O04  O  OH1   0  -0.539   7.6099   1.3791  -0.6297
 P6Y  O12  O  O     0  -0.466  -1.6461  -1.2502   1.4326
 P6Y  H1   H  HCR6  0   0.290  -2.1555   4.0824   0.3504
 P6Y  H2   H  HCR6  0   0.267   4.8120  -1.0542  -1.8095
 P6Y  H3   H  HCR6  0   0.264   3.5702   0.6528   1.9269
 P6Y  H4   H  HCR6  0   0.258   1.3165  -0.2395   1.5794
 P6Y  H5   H  HCH2  0   0.279   0.3370  -2.2258  -1.4805
 P6Y  H6   H  HCH2  0   0.279   0.1525  -2.4215   0.2526
 P6Y  H7   H  HCR6  0   0.289  -0.7164   2.0544   0.3950
 P6Y  H8   H  HCR6  0   0.284  -4.6249   3.7865   0.2639
 P6Y  H9   H  HCR6  0   0.264   2.5604  -1.9375  -2.1490
 P6Y  H10  H  HNH1  0   0.418   5.9711   0.8824  -1.6572
 P6Y  H11  H  HNH1  0   0.417  -0.6241  -0.0120  -1.2766
 P6Y  H12  H  HOH1  0   0.480   8.2968   0.7105  -0.7459
 P6Y  C02  C  C     0   0.498   5.7020   0.4528   0.3447

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
 P6Y  O04  N03  single    1.363  0.020  1.363
 P6Y  N03  C02  single    1.353  0.020  1.353
 P6Y  O01  C02  double    1.217  0.020  1.217
 P6Y  C02  C05  single    1.492  0.020  1.492
 P6Y  F20  C19  single    1.337  0.020  1.337
 P6Y  F22  C19  single    1.338  0.020  1.338
 P6Y  C05  C06  aromatic  1.395  0.020  1.395
 P6Y  C05  C24  aromatic  1.392  0.020  1.392
 P6Y  C06  C07  aromatic  1.383  0.020  1.383
 P6Y  F21  C19  single    1.330  0.020  1.330
 P6Y  C19  C18  single    1.511  0.020  1.511
 P6Y  C24  C23  aromatic  1.388  0.020  1.388
 P6Y  C07  C08  aromatic  1.394  0.020  1.394
 P6Y  N17  C18  aromatic  1.320  0.020  1.320
 P6Y  N17  C16  aromatic  1.325  0.020  1.325
 P6Y  C23  C08  aromatic  1.389  0.020  1.389
 P6Y  C18  C13  aromatic  1.392  0.020  1.392
 P6Y  C08  C09  single    1.508  0.020  1.508
 P6Y  O12  C11  double    1.219  0.020  1.219
 P6Y  C16  C15  aromatic  1.386  0.020  1.386
 P6Y  C13  C11  single    1.501  0.020  1.501
 P6Y  C13  C14  aromatic  1.390  0.020  1.390
 P6Y  C11  N10  single    1.339  0.020  1.339
 P6Y  N10  C09  single    1.446  0.020  1.446
 P6Y  C15  C14  aromatic  1.383  0.020  1.383
 P6Y  C15  H1   single    0.930  0.020  1.080
 P6Y  C24  H2   single    0.930  0.020  1.080
 P6Y  C06  H3   single    0.930  0.020  1.080
 P6Y  C07  H4   single    0.930  0.020  1.080
 P6Y  C09  H5   single    0.970  0.020  1.090
 P6Y  C09  H6   single    0.970  0.020  1.090
 P6Y  C14  H7   single    0.930  0.020  1.080
 P6Y  C16  H8   single    0.930  0.020  1.080
 P6Y  C23  H9   single    0.930  0.020  1.080
 P6Y  N03  H10  single    0.890  0.020  1.040
 P6Y  N10  H11  single    0.860  0.020  1.020
 P6Y  O04  H12  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
 P6Y  C18  C13  C14  117.22  3.000
 P6Y  C14  C13  C11  119.09  3.000
 P6Y  C18  C13  C11  123.54  3.000
 P6Y  H1   C15  C16  120.57  3.000
 P6Y  H1   C15  C14  121.14  3.000
 P6Y  C16  C15  C14  118.29  3.000
 P6Y  H2   C24  C23  118.83  3.000
 P6Y  H2   C24  C05  120.93  3.000
 P6Y  C23  C24  C05  120.23  3.000
 P6Y  C06  C05  C02  118.06  3.000
 P6Y  C06  C05  C24  119.10  3.000
 P6Y  C02  C05  C24  122.81  3.000
 P6Y  H3   C06  C07  119.74  3.000
 P6Y  H3   C06  C05  119.86  3.000
 P6Y  C07  C06  C05  120.39  3.000
 P6Y  H4   C07  C08  120.07  3.000
 P6Y  H4   C07  C06  119.25  3.000
 P6Y  C08  C07  C06  120.67  3.000
 P6Y  C23  C08  C09  120.72  3.000
 P6Y  C09  C08  C07  120.45  3.000
 P6Y  C23  C08  C07  118.82  3.000
 P6Y  H6   C09  H5   107.12  3.000
 P6Y  H6   C09  N10  108.27  3.000
 P6Y  H5   C09  N10  109.03  3.000
 P6Y  H6   C09  C08  110.22  3.000
 P6Y  H5   C09  C08  110.06  3.000
 P6Y  N10  C09  C08  112.01  3.000
 P6Y  O12  C11  N10  125.09  3.000
 P6Y  N10  C11  C13  114.09  3.000
 P6Y  O12  C11  C13  120.77  3.000
 P6Y  H7   C14  C15  120.21  3.000
 P6Y  H7   C14  C13  120.27  3.000
 P6Y  C15  C14  C13  119.52  3.000
 P6Y  H8   C16  N17  116.52  3.000
 P6Y  H8   C16  C15  120.73  3.000
 P6Y  N17  C16  C15  122.75  3.000
 P6Y  N17  C18  C19  114.72  3.000
 P6Y  N17  C18  C13  123.52  3.000
 P6Y  C19  C18  C13  121.76  3.000
 P6Y  F22  C19  F21  107.18  3.000
 P6Y  F21  C19  F20  107.24  3.000
 P6Y  F22  C19  F20  107.47  3.000
 P6Y  F21  C19  C18  111.52  3.000
 P6Y  F22  C19  C18  111.58  3.000
 P6Y  F20  C19  C18  111.60  3.000
 P6Y  H9   C23  C08  119.80  3.000
 P6Y  H9   C23  C24  119.42  3.000
 P6Y  C08  C23  C24  120.77  3.000
 P6Y  H10  N03  O04  113.70  3.000
 P6Y  H10  N03  C02  121.15  3.000
 P6Y  O04  N03  C02  118.48  3.000
 P6Y  H11  N10  C11  118.75  3.000
 P6Y  H11  N10  C09  117.02  3.000
 P6Y  C11  N10  C09  124.22  3.000
 P6Y  C18  N17  C16  118.70  3.000
 P6Y  H12  O04  N03  105.88  3.000
 P6Y  O01  C02  N03  123.46  3.000
 P6Y  O01  C02  C05  122.36  3.000
 P6Y  N03  C02  C05  114.18  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
 P6Y  CONST_01  C16  N17  C18  C13     0.00   0.0  0
 P6Y  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 P6Y  CONST_03  C18  N17  C16  C15     0.00   0.0  0
 P6Y  CONST_04  C18  C13  C14  C15     0.00   0.0  0
 P6Y  CONST_05  C07  C06  C05  C24     0.00   0.0  0
 P6Y  CONST_06  C07  C08  C23  C24     0.00   0.0  0
 P6Y  CONST_07  C08  C07  C06  C05     0.00   0.0  0
 P6Y  CONST_08  C08  C23  C24  C05     0.00   0.0  0
 P6Y  CONST_09  C23  C24  C05  C06     0.00   0.0  0
 P6Y  CONST_10  C23  C08  C07  C06     0.00   0.0  0
 P6Y  CONST_11  N17  C18  C13  C14     0.00   0.0  0
 P6Y  CONST_12  N17  C16  C15  C14     0.00   0.0  0
 P6Y  CONST_13  C11  C13  C14  C15   180.00   0.0  0
 P6Y  CONST_14  C09  C08  C23  C24   180.00   0.0  0
 P6Y  CONST_15  C07  C06  C05  C02   180.00   0.0  0
 P6Y  CONST_16  C23  C24  C05  C02   180.00   0.0  0
 P6Y  CONST_17  C09  C08  C07  C06   180.00   0.0  0
 P6Y  CONST_18  N17  C18  C13  C11   180.00   0.0  0
 P6Y  CONST_19  C19  C18  C13  C14   180.00   0.0  0
 P6Y  CONST_20  C19  C18  N17  C16   180.00   0.0  0
 P6Y  CONST_21  H1   C15  C14  C13   180.00   0.0  0
 P6Y  CONST_22  H3   C06  C05  C24   180.00   0.0  0
 P6Y  CONST_23  H4   C07  C06  C05   180.00   0.0  0
 P6Y  CONST_24  H9   C23  C24  C05   180.00   0.0  0
 P6Y  CONST_25  H2   C24  C05  C06   180.00   0.0  0
 P6Y  CONST_26  H8   C16  C15  C14   180.00   0.0  0
 P6Y  CONST_27  H7   C14  C15  C16   180.00   0.0  0
 P6Y  CONST_28  C09  N10  C11  C13   180.00   0.0  0
 P6Y  CONST_29  O04  N03  C02  C05   180.00   0.0  0
 P6Y  CONST_30  H11  N10  C11  C13     0.00   0.0  0
 P6Y  CONST_32  O12  C11  N10  C09     0.00   0.0  0
 P6Y  CONST_33  O04  N03  C02  O01     0.00   0.0  0
 P6Y  Var_01    F20  C19  C18  C13    84.41  30.0  3
 P6Y  Var_02    N03  C02  C05  C24    27.99  30.0  2
 P6Y  Var_03    N10  C09  C08  C07    57.65  30.0  2
 P6Y  Var_04    O12  C11  C13  C14   115.69  30.0  2
 P6Y  Var_05    C11  N10  C09  C08  -110.66  30.0  1

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
 P6Y  plan-1  C24  0.020
 P6Y  plan-1  C05  0.020
 P6Y  plan-1  C06  0.020
 P6Y  plan-1  C07  0.020
 P6Y  plan-1  C08  0.020
 P6Y  plan-1  C09  0.020
 P6Y  plan-1  C23  0.020
 P6Y  plan-1  H2   0.020
 P6Y  plan-1  H3   0.020
 P6Y  plan-1  H4   0.020
 P6Y  plan-1  H9   0.020
 P6Y  plan-1  C02  0.020
 P6Y  plan-2  C13  0.020
 P6Y  plan-2  C15  0.020
 P6Y  plan-2  C11  0.020
 P6Y  plan-2  C14  0.020
 P6Y  plan-2  C16  0.020
 P6Y  plan-2  C18  0.020
 P6Y  plan-2  C19  0.020
 P6Y  plan-2  N17  0.020
 P6Y  plan-2  H1   0.020
 P6Y  plan-2  H7   0.020
 P6Y  plan-2  H8   0.020
 P6Y  plan-3  C13  0.020
 P6Y  plan-3  C09  0.020
 P6Y  plan-3  C11  0.020
 P6Y  plan-3  N10  0.020
 P6Y  plan-3  O12  0.020
 P6Y  plan-3  H11  0.020
 P6Y  plan-4  C05  0.020
 P6Y  plan-4  N03  0.020
 P6Y  plan-4  O01  0.020
 P6Y  plan-4  O04  0.020
 P6Y  plan-4  H10  0.020
 P6Y  plan-4  C02  0.020

