# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 13:54:09 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 4-({4-amino-6-[3-(hydroxymethyl)-1H-pyrazol-1-yl]pyrimidin-2-yl}amino)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(nc(Nc2ccc(cc2)C#N)n1)n3ccc(CO)n3
#
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
 8MY  8MY  4-({4-amino-6-[3-(hydroxymethyl)-1H-pyrazol-1-yl]pyrimidin-2-yl}amino)benzonitrile  ligand  36  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8MY
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
 8MY  C10  C  CR6   0   0.556   0.3554   2.2248   0.0971
 8MY  C13  C  CR6   0   0.576   1.8206   0.3953  -0.0502
 8MY  C15  C  CR15  0   0.061   3.3669  -1.5229  -0.1645
 8MY  C17  C  CR5   0   0.297   5.1929  -0.2922  -0.1515
 8MY  C22  C  CR16  0  -0.348  -3.5431  -1.8619  -0.0622
 8MY  C03  C  CR6   0  -0.021  -5.5899  -0.6115   0.0426
 8MY  C04  C  CR16  0  -0.230  -4.8522   0.5710   0.0708
 8MY  C05  C  CR16  0  -0.304  -3.4713   0.5487   0.0338
 8MY  C06  C  CR6   0   0.390  -2.7919  -0.6752  -0.0323
 8MY  C08  C  CR6   0   0.621  -0.4049   0.0963  -0.0326
 8MY  C12  C  CR16  0  -0.498   1.6809   1.7615   0.0422
 8MY  C16  C  CR15  0  -0.533   4.7267  -1.6289  -0.1938
 8MY  C18  C  CH2   0  -0.225   6.6063   0.1790  -0.1963
 8MY  C23  C  CR16  0  -0.229  -4.9180  -1.8347  -0.0254
 8MY  N01  N  NS    0  -0.264  -8.1640  -0.5419   0.1155
 8MY  N07  N  NH1   0  -0.769  -1.4224  -0.8198  -0.0745
 8MY  N09  N  N     0  -0.528  -0.6841   1.3822   0.0583
 8MY  N11  N  NH2   0  -0.829   0.0775   3.5300   0.1760
 8MY  N14  N  NR5   0  -0.396   3.0850  -0.1944  -0.1074
 8MY  N20  N  N     0  -0.304   4.1928   0.5553  -0.0922
 8MY  N21  N  N     0  -0.538   0.8047  -0.4546  -0.0899
 8MY  O19  O  OH1   0  -0.667   7.3633  -0.6080   0.6932
 8MY  H1   H  HCR5  0   0.302   2.5900  -2.2670  -0.1792
 8MY  H2   H  HCR6  0   0.283  -3.0344  -2.8167  -0.1156
 8MY  H3   H  HCR6  0   0.279  -5.3620   1.5239   0.1227
 8MY  H4   H  HCR6  0   0.302  -2.9220   1.4747   0.0568
 8MY  H5   H  HCR6  0   0.288   2.5231   2.4346   0.0736
 8MY  H6   H  HCR5  0   0.270   5.3098  -2.5331  -0.2439
 8MY  H7   H  HCH2  0   0.223   6.9768   0.0864  -1.2251
 8MY  H8   H  HCH2  0   0.220   6.6364   1.2458   0.0552
 8MY  H9   H  HCR6  0   0.281  -5.4735  -2.7623  -0.0496
 8MY  H10  H  HNH1  0   0.415  -1.0885  -1.7703  -0.1401
 8MY  H11  H  HNH2  0   0.403  -0.8725   3.8320   0.3082
 8MY  H12  H  HNH2  0   0.410   0.8071   4.2070   0.3103
 8MY  H13  H  HOH1  0   0.460   8.2923  -0.4018   0.5543
 8MY  C02  C  CSP   0   0.047  -7.0113  -0.5730   0.0827

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
 8MY  N11  C10  single    1.337  0.020  1.337
 8MY  C10  N09  aromatic  1.339  0.020  1.339
 8MY  C10  C12  aromatic  1.405  0.020  1.405
 8MY  N09  C08  aromatic  1.319  0.020  1.319
 8MY  C12  C13  aromatic  1.376  0.020  1.376
 8MY  O19  C18  single    1.408  0.020  1.408
 8MY  C08  N07  single    1.370  0.020  1.370
 8MY  C08  N21  aromatic  1.330  0.020  1.330
 8MY  N07  C06  single    1.378  0.020  1.378
 8MY  C13  N21  aromatic  1.325  0.020  1.325
 8MY  C13  N14  single    1.396  0.020  1.396
 8MY  C22  C06  aromatic  1.405  0.020  1.405
 8MY  C22  C23  aromatic  1.376  0.020  1.376
 8MY  N20  N14  aromatic  1.338  0.020  1.338
 8MY  N20  C17  aromatic  1.312  0.020  1.312
 8MY  N14  C15  aromatic  1.359  0.020  1.359
 8MY  C06  C05  aromatic  1.401  0.020  1.401
 8MY  C23  C03  aromatic  1.397  0.020  1.397
 8MY  C17  C18  single    1.491  0.020  1.491
 8MY  C17  C16  aromatic  1.416  0.020  1.416
 8MY  C15  C16  aromatic  1.364  0.020  1.364
 8MY  C05  C04  aromatic  1.382  0.020  1.382
 8MY  C03  C04  aromatic  1.394  0.020  1.394
 8MY  C03  C02  single    1.422  0.020  1.422
 8MY  C02  N01  triple    1.154  0.020  1.154
 8MY  C15  H1   single    0.930  0.020  1.080
 8MY  C22  H2   single    0.930  0.020  1.080
 8MY  C04  H3   single    0.930  0.020  1.080
 8MY  C05  H4   single    0.930  0.020  1.080
 8MY  C12  H5   single    0.930  0.020  1.080
 8MY  C16  H6   single    0.930  0.020  1.080
 8MY  C18  H7   single    0.970  0.020  1.090
 8MY  C18  H8   single    0.970  0.020  1.090
 8MY  C23  H9   single    0.930  0.020  1.080
 8MY  N07  H10  single    0.860  0.020  1.020
 8MY  N11  H11  single    0.860  0.020  1.020
 8MY  N11  H12  single    0.860  0.020  1.020
 8MY  O19  H13  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
 8MY  N11  C10  N09  117.05  3.000
 8MY  N09  C10  C12  121.59  3.000
 8MY  N11  C10  C12  121.36  3.000
 8MY  N21  C13  N14  114.97  3.000
 8MY  N14  C13  C12  120.92  3.000
 8MY  N21  C13  C12  124.11  3.000
 8MY  H1   C15  N14  121.79  3.000
 8MY  H1   C15  C16  131.74  3.000
 8MY  N14  C15  C16  106.47  3.000
 8MY  N20  C17  C18  121.32  3.000
 8MY  C18  C17  C16  127.56  3.000
 8MY  N20  C17  C16  111.10  3.000
 8MY  H2   C22  C23  119.21  3.000
 8MY  H2   C22  C06  119.64  3.000
 8MY  C23  C22  C06  121.14  3.000
 8MY  C23  C03  C04  119.28  3.000
 8MY  C04  C03  C02  120.35  3.000
 8MY  C23  C03  C02  120.37  3.000
 8MY  H3   C04  C05  119.11  3.000
 8MY  H3   C04  C03  119.92  3.000
 8MY  C05  C04  C03  120.98  3.000
 8MY  H4   C05  C06  120.31  3.000
 8MY  H4   C05  C04  119.69  3.000
 8MY  C06  C05  C04  120.00  3.000
 8MY  N07  C06  C05  125.10  3.000
 8MY  C05  C06  C22  118.65  3.000
 8MY  N07  C06  C22  116.25  3.000
 8MY  N21  C08  N09  126.80  3.000
 8MY  N21  C08  N07  113.40  3.000
 8MY  N09  C08  N07  119.79  3.000
 8MY  H5   C12  C13  122.83  3.000
 8MY  H5   C12  C10  121.97  3.000
 8MY  C13  C12  C10  115.19  3.000
 8MY  H6   C16  C17  127.99  3.000
 8MY  H6   C16  C15  127.29  3.000
 8MY  C17  C16  C15  104.72  3.000
 8MY  H8   C18  H7   106.73  3.000
 8MY  H8   C18  O19  112.58  3.000
 8MY  H7   C18  O19  111.31  3.000
 8MY  H8   C18  C17  109.07  3.000
 8MY  H7   C18  C17  108.76  3.000
 8MY  O19  C18  C17  108.30  3.000
 8MY  H9   C23  C03  120.32  3.000
 8MY  H9   C23  C22  119.73  3.000
 8MY  C03  C23  C22  119.95  3.000
 8MY  H10  N07  C08  112.70  3.000
 8MY  H10  N07  C06  115.44  3.000
 8MY  C08  N07  C06  131.85  3.000
 8MY  C08  N09  C10  116.82  3.000
 8MY  H12  N11  H11  117.79  3.000
 8MY  H12  N11  C10  121.00  3.000
 8MY  H11  N11  C10  119.83  3.000
 8MY  N20  N14  C15  112.12  3.000
 8MY  C15  N14  C13  127.04  3.000
 8MY  N20  N14  C13  120.84  3.000
 8MY  N14  N20  C17  105.58  3.000
 8MY  C08  N21  C13  115.48  3.000
 8MY  H13  O19  C18  107.95  3.000
 8MY  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
 8MY  CONST_01  N21  C08  N09  C10     0.00   0.0  0
 8MY  CONST_02  N21  C13  C12  C10     0.00   0.0  0
 8MY  CONST_03  N14  C13  C12  C10   180.00   0.0  0
 8MY  CONST_04  N09  C10  C12  C13     0.00   0.0  0
 8MY  CONST_05  N09  C08  N21  C13     0.00   0.0  0
 8MY  CONST_06  C17  N20  N14  C13   180.00   0.0  0
 8MY  CONST_07  C16  C15  N14  C13   180.00   0.0  0
 8MY  CONST_08  C12  C13  N14  C15   180.00   0.0  0
 8MY  CONST_09  N21  C13  N14  C15     0.00   0.0  0
 8MY  CONST_10  C17  N20  N14  C15     0.00   0.0  0
 8MY  CONST_11  N20  C17  C16  C15     0.00   0.0  0
 8MY  CONST_12  N14  C15  C16  C17     0.00   0.0  0
 8MY  CONST_13  C04  C05  C06  C22     0.00   0.0  0
 8MY  CONST_14  C04  C03  C23  C22     0.00   0.0  0
 8MY  CONST_15  C06  C22  C23  C03     0.00   0.0  0
 8MY  CONST_16  C06  C05  C04  C03     0.00   0.0  0
 8MY  CONST_17  C23  C22  C06  C05     0.00   0.0  0
 8MY  CONST_18  C23  C03  C04  C05     0.00   0.0  0
 8MY  CONST_19  C12  C10  N09  C08     0.00   0.0  0
 8MY  CONST_20  C12  C13  N21  C08     0.00   0.0  0
 8MY  CONST_21  N14  C13  N21  C08   180.00   0.0  0
 8MY  CONST_22  N20  N14  C13  C12     0.00   0.0  0
 8MY  CONST_23  N14  N20  C17  C16     0.00   0.0  0
 8MY  CONST_24  N20  N14  C15  C16     0.00   0.0  0
 8MY  CONST_25  N21  C13  N14  N20   180.00   0.0  0
 8MY  CONST_26  N07  C08  N09  C10   180.00   0.0  0
 8MY  CONST_27  N11  C10  C12  C13   180.00   0.0  0
 8MY  CONST_28  N07  C08  N21  C13   180.00   0.0  0
 8MY  CONST_29  C18  C17  C16  C15   180.00   0.0  0
 8MY  CONST_30  C02  C03  C23  C22   180.00   0.0  0
 8MY  CONST_31  C05  C04  C03  C02   180.00   0.0  0
 8MY  CONST_32  N07  C06  C05  C04   180.00   0.0  0
 8MY  CONST_33  N11  C10  N09  C08   180.00   0.0  0
 8MY  CONST_34  N14  N20  C17  C18   180.00   0.0  0
 8MY  CONST_35  N07  C06  C22  C23   180.00   0.0  0
 8MY  CONST_36  H1   C15  N14  C13     0.00   0.0  0
 8MY  CONST_37  H4   C05  C06  C22   180.00   0.0  0
 8MY  CONST_38  H2   C22  C23  C03   180.00   0.0  0
 8MY  CONST_39  H9   C23  C03  C04   180.00   0.0  0
 8MY  CONST_40  H3   C04  C05  C06   180.00   0.0  0
 8MY  CONST_41  H5   C12  C10  N09   180.00   0.0  0
 8MY  CONST_42  H6   C16  C15  N14   180.00   0.0  0
 8MY  CONST_43  H11  N11  C10  C12   180.00   0.0  0
 8MY  CONST_44  H12  N11  C10  C12     0.00   0.0  0
 8MY  Var_01    C08  N07  C06  C22  -178.30  30.0  2
 8MY  Var_02    N09  C08  N07  C06    -0.38  30.0  2
 8MY  Var_03    O19  C18  C17  C16   -45.98  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
 8MY  plan-1  C13  0.020
 8MY  plan-1  C15  0.020
 8MY  plan-1  C17  0.020
 8MY  plan-1  C16  0.020
 8MY  plan-1  C18  0.020
 8MY  plan-1  N14  0.020
 8MY  plan-1  N20  0.020
 8MY  plan-1  H1   0.020
 8MY  plan-1  H6   0.020
 8MY  plan-2  C10  0.020
 8MY  plan-2  C13  0.020
 8MY  plan-2  C08  0.020
 8MY  plan-2  C12  0.020
 8MY  plan-2  N07  0.020
 8MY  plan-2  N09  0.020
 8MY  plan-2  N11  0.020
 8MY  plan-2  N14  0.020
 8MY  plan-2  N21  0.020
 8MY  plan-2  H5   0.020
 8MY  plan-3  C22  0.020
 8MY  plan-3  C03  0.020
 8MY  plan-3  C04  0.020
 8MY  plan-3  C05  0.020
 8MY  plan-3  C06  0.020
 8MY  plan-3  C23  0.020
 8MY  plan-3  N01  0.020
 8MY  plan-3  N07  0.020
 8MY  plan-3  H2   0.020
 8MY  plan-3  H3   0.020
 8MY  plan-3  H4   0.020
 8MY  plan-3  H9   0.020
 8MY  plan-3  C02  0.020
 8MY  plan-4  C10  0.020
 8MY  plan-4  N11  0.020
 8MY  plan-4  H11  0.020
 8MY  plan-4  H12  0.020

