# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 22:53:28 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 2-({2-[(3-hydroxyphenyl)amino]pyrimidin-4-yl}amino)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccccc1Nc2ccnc(Nc3cccc(O)c3)n2
#
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
 859  859  2-({2-[(3-hydroxyphenyl)amino]pyrimidin-4-yl}amino)benzamide  ligand  39  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_859
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
 859  C1    C  CR6   0   0.599   1.1375   0.5482   7.1394
 859  N2    N  N     0  -0.520   1.6417  -0.2876   6.2404
 859  C3    C  CR6   0   0.577   1.1024  -0.2741   5.0265
 859  C4    C  CR16  0  -0.459   0.0429   0.5911   4.7087
 859  C5    C  CR16  0  -0.022  -0.3911   1.4069   5.7262
 859  N6    N  N     0  -0.491   0.1341   1.4066   6.9467
 859  N7    N  NH1   0  -0.785   1.5942  -1.0944   4.0616
 859  C8    C  CR6   0   0.341   2.6260  -2.0246   4.1649
 859  C9    C  CR6   0  -0.114   3.5414  -2.1710   3.1051
 859  C10   C  CR16  0  -0.288   4.5405  -3.1393   3.1982
 859  C11   C  CR16  0  -0.259   4.6656  -3.9395   4.3200
 859  C12   C  CR16  0  -0.238   3.7668  -3.7832   5.3657
 859  C13   C  CR16  0  -0.296   2.7505  -2.8474   5.2846
 859  N14   N  NH1   0  -0.773   1.6560   0.5833   8.4004
 859  C15   C  CR6   0   0.379   2.6780  -0.1271   9.0158
 859  C16   C  CR16  0  -0.380   2.8965   0.1558  10.3724
 859  C17   C  CR16  0  -0.234   3.8918  -0.5076  11.0631
 859  C18   C  CR16  0  -0.410   4.6905  -1.4593  10.4430
 859  C19   C  CR6   0   0.373   4.4730  -1.7345   9.0974
 859  C20   C  CR16  0  -0.425   3.4771  -1.0739   8.3796
 859  O21   O  OH1   0  -0.628   5.2032  -2.6435   8.4197
 859  C22   C  C     0   0.509   3.4232  -1.3421   1.8677
 859  N23   N  NH2   0  -0.794   4.5742  -1.0232   1.2654
 859  O24   O  O     0  -0.497   2.3302  -0.9888   1.4287
 859  H4    H  HCR6  0   0.275  -0.4071   0.6165   3.7266
 859  H5    H  HCR6  0   0.271  -1.2079   2.0997   5.5557
 859  HN7   H  HNH1  0   0.417   1.3148  -0.8871   3.1113
 859  H10   H  HCR6  0   0.267   5.2250  -3.2867   2.3724
 859  H11   H  HCR6  0   0.262   5.4485  -4.6835   4.3714
 859  H12   H  HCR6  0   0.260   3.8409  -4.4064   6.2464
 859  H13   H  HCR6  0   0.281   2.0391  -2.7605   6.0917
 859  HN14  H  HNH1  0   0.406   1.1882   1.2539   8.9910
 859  H16   H  HCR6  0   0.262   2.2842   0.8926  10.8779
 859  H17   H  HCR6  0   0.260   4.0504  -0.2813  12.1095
 859  H18   H  HCR6  0   0.265   5.4656  -1.9734  10.9989
 859  H20   H  HCR6  0   0.311   3.3332  -1.3083   7.3376
 859  HO21  H  HOH1  0   0.472   5.8594  -3.0428   9.0014
 859  H231  H  HNH2  0   0.417   5.4691  -1.1981   1.6881
 859  H232  H  HNH2  0   0.410   4.5631  -0.4770   0.4189

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
 859  C1   N6    aromatic  1.335  0.020  1.335
 859  C1   N2    aromatic  1.327  0.020  1.327
 859  C1   N14   single    1.364  0.020  1.364
 859  N2   C3    aromatic  1.328  0.020  1.328
 859  C3   C4    aromatic  1.404  0.020  1.404
 859  C3   N7    single    1.359  0.020  1.359
 859  C4   C5    aromatic  1.375  0.020  1.375
 859  C4   H4    single    0.930  0.020  1.080
 859  C5   N6    aromatic  1.329  0.020  1.329
 859  C5   H5    single    0.930  0.020  1.080
 859  N7   C8    single    1.393  0.020  1.393
 859  N7   HN7   single    0.860  0.020  1.020
 859  C8   C9    aromatic  1.408  0.020  1.408
 859  C8   C13   aromatic  1.395  0.020  1.395
 859  C9   C22   single    1.494  0.020  1.494
 859  C9   C10   aromatic  1.394  0.020  1.394
 859  C10  C11   aromatic  1.384  0.020  1.384
 859  C10  H10   single    0.930  0.020  1.080
 859  C11  C12   aromatic  1.388  0.020  1.388
 859  C11  H11   single    0.930  0.020  1.080
 859  C12  C13   aromatic  1.384  0.020  1.384
 859  C12  H12   single    0.930  0.020  1.080
 859  C13  H13   single    0.930  0.020  1.080
 859  N14  C15   single    1.388  0.020  1.388
 859  N14  HN14  single    0.860  0.020  1.020
 859  C15  C20   aromatic  1.393  0.020  1.393
 859  C15  C16   aromatic  1.403  0.020  1.403
 859  C16  C17   aromatic  1.381  0.020  1.381
 859  C16  H16   single    0.930  0.020  1.080
 859  C17  C18   aromatic  1.389  0.020  1.389
 859  C17  H17   single    0.930  0.020  1.080
 859  C18  C19   aromatic  1.391  0.020  1.391
 859  C18  H18   single    0.930  0.020  1.080
 859  C19  C20   aromatic  1.394  0.020  1.394
 859  C19  O21   single    1.349  0.020  1.349
 859  C20  H20   single    0.930  0.020  1.080
 859  O21  HO21  single    0.850  0.020  0.980
 859  C22  N23   single    1.338  0.020  1.338
 859  C22  O24   double    1.230  0.020  1.230
 859  N23  H231  single    0.860  0.020  1.020
 859  N23  H232  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
 859  N14   C1   N6    113.75  3.000
 859  N14   C1   N2    119.88  3.000
 859  N6    C1   N2    126.37  3.000
 859  C3    N2   C1    117.29  3.000
 859  N7    C3   C4    118.97  3.000
 859  N7    C3   N2    119.73  3.000
 859  C4    C3   N2    121.29  3.000
 859  H4    C4   C5    121.83  3.000
 859  H4    C4   C3    122.30  3.000
 859  C5    C4   C3    115.87  3.000
 859  H5    C5   N6    116.25  3.000
 859  H5    C5   C4    120.03  3.000
 859  N6    C5   C4    123.71  3.000
 859  C5    N6   C1    115.47  3.000
 859  HN7   N7   C8    114.26  3.000
 859  HN7   N7   C3    116.32  3.000
 859  C8    N7   C3    128.21  3.000
 859  C13   C8   C9    119.00  3.000
 859  C13   C8   N7    121.30  3.000
 859  C9    C8   N7    119.68  3.000
 859  C22   C9   C10   119.81  3.000
 859  C10   C9   C8    119.19  3.000
 859  C22   C9   C8    120.95  3.000
 859  H10   C10  C11   118.84  3.000
 859  H10   C10  C9    119.78  3.000
 859  C11   C10  C9    121.37  3.000
 859  H11   C11  C12   120.71  3.000
 859  H11   C11  C10   120.13  3.000
 859  C12   C11  C10   119.16  3.000
 859  H12   C12  C13   119.19  3.000
 859  H12   C12  C11   120.29  3.000
 859  C13   C12  C11   120.51  3.000
 859  H13   C13  C12   119.65  3.000
 859  H13   C13  C8    119.59  3.000
 859  C12   C13  C8    120.76  3.000
 859  HN14  N14  C15   114.96  3.000
 859  HN14  N14  C1    112.47  3.000
 859  C15   N14  C1    132.56  3.000
 859  C20   C15  C16   119.30  3.000
 859  C16   C15  N14   116.11  3.000
 859  C20   C15  N14   124.59  3.000
 859  H16   C16  C17   120.04  3.000
 859  H16   C16  C15   120.03  3.000
 859  C17   C16  C15   119.93  3.000
 859  H17   C17  C18   119.39  3.000
 859  H17   C17  C16   119.25  3.000
 859  C18   C17  C16   121.36  3.000
 859  H18   C18  C19   120.96  3.000
 859  H18   C18  C17   120.50  3.000
 859  C19   C18  C17   118.54  3.000
 859  O21   C19  C20   116.58  3.000
 859  O21   C19  C18   122.34  3.000
 859  C20   C19  C18   121.08  3.000
 859  H20   C20  C19   119.36  3.000
 859  H20   C20  C15   120.85  3.000
 859  C19   C20  C15   119.79  3.000
 859  HO21  O21  C19   110.17  3.000
 859  O24   C22  N23   122.38  3.000
 859  O24   C22  C9    121.69  3.000
 859  N23   C22  C9    115.92  3.000
 859  H232  N23  H231  117.23  3.000
 859  H232  N23  C22   119.87  3.000
 859  H231  N23  C22   122.36  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
 859  CONST_01  C4    C5   N6   C1      0.00   0.0  0
 859  CONST_02  C4    C3   N2   C1      0.00   0.0  0
 859  CONST_03  C5    N6   C1   N2      0.00   0.0  0
 859  CONST_04  C5    C4   C3   N2      0.00   0.0  0
 859  CONST_05  N6    C1   N2   C3      0.00   0.0  0
 859  CONST_06  N6    C5   C4   C3      0.00   0.0  0
 859  CONST_07  C11   C10  C9   C8      0.00   0.0  0
 859  CONST_08  C11   C12  C13  C8      0.00   0.0  0
 859  CONST_09  C12   C13  C8   C9      0.00   0.0  0
 859  CONST_10  C12   C11  C10  C9      0.00   0.0  0
 859  CONST_11  C13   C8   C9   C10     0.00   0.0  0
 859  CONST_12  C13   C12  C11  C10     0.00   0.0  0
 859  CONST_13  C18   C19  C20  C15     0.00   0.0  0
 859  CONST_14  C18   C17  C16  C15     0.00   0.0  0
 859  CONST_15  C19   C20  C15  C16     0.00   0.0  0
 859  CONST_16  C19   C18  C17  C16     0.00   0.0  0
 859  CONST_17  C20   C15  C16  C17     0.00   0.0  0
 859  CONST_18  C20   C19  C18  C17     0.00   0.0  0
 859  CONST_19  N7    C3   N2   C1    180.00   0.0  0
 859  CONST_20  N14   C1   N2   C3    180.00   0.0  0
 859  CONST_21  N7    C3   C4   C5    180.00   0.0  0
 859  CONST_22  N14   C1   N6   C5    180.00   0.0  0
 859  CONST_23  C10   C9   C8   N7    180.00   0.0  0
 859  CONST_24  C12   C13  C8   N7    180.00   0.0  0
 859  CONST_25  C22   C9   C10  C11   180.00   0.0  0
 859  CONST_26  C22   C9   C8   C13   180.00   0.0  0
 859  CONST_27  C19   C20  C15  N14   180.00   0.0  0
 859  CONST_28  C17   C16  C15  N14   180.00   0.0  0
 859  CONST_29  O21   C19  C20  C15   180.00   0.0  0
 859  CONST_30  O21   C19  C18  C17   180.00   0.0  0
 859  CONST_31  H5    C5   N6   C1    180.00   0.0  0
 859  CONST_32  H4    C4   C3   N2    180.00   0.0  0
 859  CONST_33  H10   C10  C9   C8    180.00   0.0  0
 859  CONST_34  H12   C12  C13  C8    180.00   0.0  0
 859  CONST_35  H13   C13  C8   C9    180.00   0.0  0
 859  CONST_36  H11   C11  C10  C9    180.00   0.0  0
 859  CONST_37  H17   C17  C16  C15   180.00   0.0  0
 859  CONST_38  H20   C20  C15  C16   180.00   0.0  0
 859  CONST_39  H18   C18  C17  C16   180.00   0.0  0
 859  CONST_40  H16   C16  C17  C18   180.00   0.0  0
 859  CONST_41  H231  N23  C22  C9      0.00   0.0  0
 859  CONST_42  H232  N23  C22  C9    180.00   0.0  0
 859  Var_01    C20   C15  N14  C1      2.59  30.0  2
 859  Var_02    C15   N14  C1   N2     -0.56  30.0  2
 859  Var_03    C8    N7   C3   N2      1.45  30.0  2
 859  Var_04    C9    C8   N7   C3   -140.45  30.0  2
 859  Var_05    N23   C22  C9   C8    147.25  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
 859  plan-1  C1    0.020
 859  plan-1  N2    0.020
 859  plan-1  C3    0.020
 859  plan-1  C4    0.020
 859  plan-1  C5    0.020
 859  plan-1  N6    0.020
 859  plan-1  N7    0.020
 859  plan-1  N14   0.020
 859  plan-1  H4    0.020
 859  plan-1  H5    0.020
 859  plan-2  N7    0.020
 859  plan-2  C8    0.020
 859  plan-2  C9    0.020
 859  plan-2  C10   0.020
 859  plan-2  C11   0.020
 859  plan-2  C12   0.020
 859  plan-2  C13   0.020
 859  plan-2  C22   0.020
 859  plan-2  H10   0.020
 859  plan-2  H11   0.020
 859  plan-2  H12   0.020
 859  plan-2  H13   0.020
 859  plan-3  N14   0.020
 859  plan-3  C15   0.020
 859  plan-3  C16   0.020
 859  plan-3  C17   0.020
 859  plan-3  C18   0.020
 859  plan-3  C19   0.020
 859  plan-3  C20   0.020
 859  plan-3  O21   0.020
 859  plan-3  H16   0.020
 859  plan-3  H17   0.020
 859  plan-3  H18   0.020
 859  plan-3  H20   0.020
 859  plan-4  C9    0.020
 859  plan-4  C22   0.020
 859  plan-4  N23   0.020
 859  plan-4  O24   0.020
 859  plan-4  H231  0.020
 859  plan-4  H232  0.020

