# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 15:14:05 2022
#   Inital geometry file: a 106 line input string
#   Ligand name: 3-({4-amino-6-[(4-cyanophenyl)amino]-1,3,5-triazin-2-yl}oxy)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(Nc2ccc(cc2)C#N)nc(Oc3cccc(c3)C(O)=O)n1
#
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
 VPS  VPS  '3-({4-amino-6-[(4-cyanophenyl)amino]-1,3,5-triazin-2-yl}oxy)benzoic acid'  ligand  37  26  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VPS
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
 VPS  C10  C  CR6    0   0.575   -8.3510  16.8222  18.5889
 VPS  N12  N  N      0  -0.490   -7.8523  15.7247  19.1828
 VPS  C13  C  CR6    0   0.612   -8.7391  15.0518  19.8762
 VPS  C15  C  CR6    0   0.360   -9.1375  13.2126  21.2548
 VPS  C17  C  CR16   0  -0.245   -9.9091  12.5606  23.4130
 VPS  C26  C  C1     0  -0.237  -13.9327  14.3434  21.1140
 VPS  C03  C  C      0  -0.012  -15.1190  15.0742  21.1486
 VPS  C04  C  C1     0  -0.230  -15.1420  16.3674  20.6222
 VPS  C05  C  C1     0  -0.337  -13.9989  16.9098  20.0782
 VPS  C06  C  C      0   0.379  -12.7998  16.1832  20.0455
 VPS  C08  C  CR6    0   0.626  -10.4083  16.4324  19.3843
 VPS  C16  C  CR16   0  -0.313   -9.0330  13.3027  22.6307
 VPS  C18  C  CR16   0  -0.291  -10.8855  11.7744  22.8204
 VPS  C19  C  CR6    0  -0.102  -10.9764  11.6781  21.4329
 VPS  C23  C  CR16   0  -0.348  -10.0737  12.3914  20.6516
 VPS  C25  C  C1     0  -0.302  -12.7840  14.8863  20.5732
 VPS  N01  N  NS     0  -0.258  -17.2388  14.0350  22.1795
 VPS  N07  N  NH1    0  -0.763  -11.7123  16.8087  19.4571
 VPS  N09  N  N      0  -0.508   -9.6261  17.2158  18.6560
 VPS  N11  N  NH2    0  -0.809   -7.5088  17.5664  17.8773
 VPS  N24  N  N      0  -0.527  -10.0152  15.3430  20.0333
 VPS  O14  O  O2     0  -0.492   -8.2649  13.9613  20.4796
 VPS  H1   H  HCR6   0   0.255   -9.8389  12.6187  24.4916
 VPS  H2   H  H      0   0.272  -13.9017  13.3352  21.5086
 VPS  H3   H  H      0   0.280  -16.0543  16.9482  20.6393
 VPS  H4   H  H      0   0.284  -14.0306  17.9133  19.6709
 VPS  H5   H  HCR6   0   0.267   -8.2883  13.9450  23.0835
 VPS  H6   H  HCR6   0   0.246  -11.5851  11.2281  23.4383
 VPS  H7   H  HCR6   0   0.263  -10.1284  12.3268  19.5723
 VPS  H8   H  H      0   0.331  -11.8821  14.2989  20.5676
 VPS  H9   H  HNH1   0   0.418  -11.9058  17.6848  18.9929
 VPS  H10  H  HNH2   0   0.407   -7.8292  18.3954  17.4081
 VPS  H11  H  HNH2   0   0.408   -6.5418  17.3050  17.7957
 VPS  C20  C  C      0   0.403  -12.0750  10.8472  20.7716
 VPS  C02  C  CSP    0   0.046  -16.2923  14.5043  21.7172
 VPS  O21  O  O      0  -0.579  -11.9737  10.6699  19.5439
 VPS  O22  O  OC    -1  -0.587  -12.9781  10.4367  21.5252

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
 VPS  N11  C10  single    1.330  0.020  1.330
 VPS  C10  N09  aromatic  1.336  0.020  1.336
 VPS  C10  N12  aromatic  1.344  0.020  1.344
 VPS  N09  C08  aromatic  1.325  0.020  1.325
 VPS  N12  C13  aromatic  1.311  0.020  1.311
 VPS  C08  N07  single    1.359  0.020  1.359
 VPS  C08  N24  aromatic  1.328  0.020  1.328
 VPS  N07  C06  single    1.386  0.020  1.386
 VPS  C05  C06  aromatic  1.402  0.020  1.402
 VPS  C05  C04  aromatic  1.377  0.020  1.377
 VPS  C13  N24  aromatic  1.318  0.020  1.318
 VPS  C13  O14  single    1.334  0.020  1.334
 VPS  O21  C20  deloc     1.244  0.020  1.244
 VPS  C06  C25  aromatic  1.400  0.020  1.400
 VPS  C04  C03  aromatic  1.396  0.020  1.396
 VPS  O14  C15  single    1.387  0.020  1.387
 VPS  C23  C15  aromatic  1.384  0.020  1.384
 VPS  C23  C19  aromatic  1.391  0.020  1.391
 VPS  C25  C26  aromatic  1.381  0.020  1.381
 VPS  C03  C26  aromatic  1.394  0.020  1.394
 VPS  C03  C02  single    1.423  0.020  1.423
 VPS  C15  C16  aromatic  1.383  0.020  1.383
 VPS  C20  C19  single    1.528  0.020  1.528
 VPS  C20  O22  deloc     1.246  0.020  1.246
 VPS  C19  C18  aromatic  1.394  0.020  1.394
 VPS  C02  N01  triple    1.153  0.020  1.153
 VPS  C16  C17  aromatic  1.389  0.020  1.389
 VPS  C18  C17  aromatic  1.387  0.020  1.387
 VPS  C17  H1   single    0.930  0.020  1.080
 VPS  C26  H2   single    0.930  0.020  1.080
 VPS  C04  H3   single    0.930  0.020  1.080
 VPS  C05  H4   single    0.930  0.020  1.080
 VPS  C16  H5   single    0.930  0.020  1.080
 VPS  C18  H6   single    0.930  0.020  1.080
 VPS  C23  H7   single    0.930  0.020  1.080
 VPS  C25  H8   single    0.930  0.020  1.080
 VPS  N07  H9   single    0.860  0.020  1.020
 VPS  N11  H10  single    0.860  0.020  1.020
 VPS  N11  H11  single    0.860  0.020  1.020

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
 VPS  N11  C10  N09  117.79  3.000
 VPS  N09  C10  N12  124.93  3.000
 VPS  N11  C10  N12  117.28  3.000
 VPS  C13  N12  C10  113.69  3.000
 VPS  O14  C13  N24  118.09  3.000
 VPS  O14  C13  N12  114.73  3.000
 VPS  N24  C13  N12  127.17  3.000
 VPS  O14  C15  C23  120.17  3.000
 VPS  C23  C15  C16  121.57  3.000
 VPS  O14  C15  C16  118.26  3.000
 VPS  H1   C17  C18  120.13  3.000
 VPS  H1   C17  C16  119.44  3.000
 VPS  C18  C17  C16  120.41  3.000
 VPS  H2   C26  C25  119.00  3.000
 VPS  H2   C26  C03  120.23  3.000
 VPS  C25  C26  C03  120.77  3.000
 VPS  C04  C03  C02  120.53  3.000
 VPS  C02  C03  C26  120.11  3.000
 VPS  C04  C03  C26  119.36  3.000
 VPS  H3   C04  C05  119.66  3.000
 VPS  H3   C04  C03  120.34  3.000
 VPS  C05  C04  C03  120.00  3.000
 VPS  H4   C05  C06  119.75  3.000
 VPS  H4   C05  C04  119.27  3.000
 VPS  C06  C05  C04  120.98  3.000
 VPS  N07  C06  C25  124.70  3.000
 VPS  C25  C06  C05  118.73  3.000
 VPS  N07  C06  C05  116.55  3.000
 VPS  N24  C08  N09  125.38  3.000
 VPS  N24  C08  N07  119.02  3.000
 VPS  N09  C08  N07  115.60  3.000
 VPS  H5   C16  C17  121.01  3.000
 VPS  H5   C16  C15  120.45  3.000
 VPS  C17  C16  C15  118.54  3.000
 VPS  H6   C18  C19  119.45  3.000
 VPS  H6   C18  C17  119.85  3.000
 VPS  C19  C18  C17  120.70  3.000
 VPS  C23  C19  C18  118.78  3.000
 VPS  C18  C19  C20  121.02  3.000
 VPS  C23  C19  C20  120.16  3.000
 VPS  H7   C23  C19  119.78  3.000
 VPS  H7   C23  C15  120.28  3.000
 VPS  C19  C23  C15  119.91  3.000
 VPS  H8   C25  C06  120.86  3.000
 VPS  H8   C25  C26  118.98  3.000
 VPS  C06  C25  C26  120.16  3.000
 VPS  H9   N07  C08  113.53  3.000
 VPS  H9   N07  C06  115.87  3.000
 VPS  C08  N07  C06  130.60  3.000
 VPS  C08  N09  C10  114.63  3.000
 VPS  H11  N11  H10  118.90  3.000
 VPS  H11  N11  C10  120.47  3.000
 VPS  H10  N11  C10  120.62  3.000
 VPS  C08  N24  C13  114.18  3.000
 VPS  C15  O14  C13  118.08  3.000
 VPS  O22  C20  O21  127.50  3.000
 VPS  O22  C20  C19  116.01  3.000
 VPS  O21  C20  C19  116.48  3.000
 VPS  N01  C02  C03  180.00  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
 VPS  CONST_01  N24  C08  N09  C10     0.00   0.0  0
 VPS  CONST_02  N24  C13  N12  C10     0.00   0.0  0
 VPS  CONST_03  C08  N09  C10  N12     0.00   0.0  0
 VPS  CONST_04  C08  N24  C13  N12     0.00   0.0  0
 VPS  CONST_05  N09  C10  N12  C13     0.00   0.0  0
 VPS  CONST_06  N09  C08  N24  C13     0.00   0.0  0
 VPS  CONST_07  C18  C19  C23  C15     0.00   0.0  0
 VPS  CONST_08  C18  C17  C16  C15     0.00   0.0  0
 VPS  CONST_09  C23  C15  C16  C17     0.00   0.0  0
 VPS  CONST_10  C23  C19  C18  C17     0.00   0.0  0
 VPS  CONST_11  C05  C06  C25  C26     0.00   0.0  0
 VPS  CONST_12  C05  C04  C03  C26     0.00   0.0  0
 VPS  CONST_13  C06  C05  C04  C03     0.00   0.0  0
 VPS  CONST_14  C06  C25  C26  C03     0.00   0.0  0
 VPS  CONST_15  C25  C06  C05  C04     0.00   0.0  0
 VPS  CONST_16  C25  C26  C03  C04     0.00   0.0  0
 VPS  CONST_17  C19  C23  C15  C16     0.00   0.0  0
 VPS  CONST_18  C19  C18  C17  C16     0.00   0.0  0
 VPS  CONST_19  N07  C08  N09  C10   180.00   0.0  0
 VPS  CONST_20  O14  C13  N12  C10   180.00   0.0  0
 VPS  CONST_21  N11  C10  N12  C13   180.00   0.0  0
 VPS  CONST_22  N07  C08  N24  C13   180.00   0.0  0
 VPS  CONST_23  C20  C19  C23  C15   180.00   0.0  0
 VPS  CONST_24  O14  C15  C16  C17   180.00   0.0  0
 VPS  CONST_25  C20  C19  C18  C17   180.00   0.0  0
 VPS  CONST_26  N07  C06  C25  C26   180.00   0.0  0
 VPS  CONST_27  C05  C04  C03  C02   180.00   0.0  0
 VPS  CONST_28  C25  C26  C03  C02   180.00   0.0  0
 VPS  CONST_29  N07  C06  C05  C04   180.00   0.0  0
 VPS  CONST_30  N11  C10  N09  C08   180.00   0.0  0
 VPS  CONST_31  O14  C13  N24  C08   180.00   0.0  0
 VPS  CONST_32  O14  C15  C23  C19   180.00   0.0  0
 VPS  CONST_33  H1   C17  C16  C15   180.00   0.0  0
 VPS  CONST_34  H3   C04  C03  C26   180.00   0.0  0
 VPS  CONST_35  H4   C05  C04  C03   180.00   0.0  0
 VPS  CONST_36  H8   C25  C26  C03   180.00   0.0  0
 VPS  CONST_37  H2   C26  C03  C04   180.00   0.0  0
 VPS  CONST_38  H7   C23  C15  C16   180.00   0.0  0
 VPS  CONST_39  H6   C18  C17  C16   180.00   0.0  0
 VPS  CONST_40  H5   C16  C17  C18   180.00   0.0  0
 VPS  CONST_41  H10  N11  C10  N12   180.00   0.0  0
 VPS  CONST_42  H11  N11  C10  N12     0.00   0.0  0
 VPS  Var_01    C23  C15  O14  C13    75.65  30.0  2
 VPS  Var_02    N24  C13  O14  C15    -1.11  30.0  2
 VPS  Var_03    C08  N07  C06  C05   172.96  30.0  2
 VPS  Var_04    N09  C08  N07  C06   175.16  30.0  2
 VPS  Var_05    O21  C20  C19  C18  -170.58  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
 VPS  plan-1  C10  0.020
 VPS  plan-1  N12  0.020
 VPS  plan-1  C13  0.020
 VPS  plan-1  C08  0.020
 VPS  plan-1  N07  0.020
 VPS  plan-1  N09  0.020
 VPS  plan-1  N11  0.020
 VPS  plan-1  N24  0.020
 VPS  plan-1  O14  0.020
 VPS  plan-2  C26  0.020
 VPS  plan-2  C03  0.020
 VPS  plan-2  C04  0.020
 VPS  plan-2  C05  0.020
 VPS  plan-2  C06  0.020
 VPS  plan-2  C25  0.020
 VPS  plan-2  N01  0.020
 VPS  plan-2  N07  0.020
 VPS  plan-2  H2   0.020
 VPS  plan-2  H3   0.020
 VPS  plan-2  H4   0.020
 VPS  plan-2  H8   0.020
 VPS  plan-2  C02  0.020
 VPS  plan-3  C15  0.020
 VPS  plan-3  C17  0.020
 VPS  plan-3  C16  0.020
 VPS  plan-3  C18  0.020
 VPS  plan-3  C19  0.020
 VPS  plan-3  C23  0.020
 VPS  plan-3  O14  0.020
 VPS  plan-3  H1   0.020
 VPS  plan-3  H5   0.020
 VPS  plan-3  H6   0.020
 VPS  plan-3  H7   0.020
 VPS  plan-3  C20  0.020
 VPS  plan-4  C10  0.020
 VPS  plan-4  N11  0.020
 VPS  plan-4  H10  0.020
 VPS  plan-4  H11  0.020
 VPS  plan-5  C19  0.020
 VPS  plan-5  C20  0.020
 VPS  plan-5  O21  0.020
 VPS  plan-5  O22  0.020

