# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 12:42:11 2022
#   Inital geometry file: a 73 line input string
#   Ligand name: 6-(4-methoxyphenyl)pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)c2cc(N)nc(N)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
 QYH  QYH  6-(4-methoxyphenyl)pyrimidine-2,4-diamine  ligand  28  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QYH
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
 QYH  C1   C  CH3   0  -0.436  -3.5765  -10.2501  11.4433
 QYH  N1   N  NH2   0  -0.831   4.1012  -12.1039  17.3484
 QYH  O1   O  O2    0  -0.463  -3.2630  -10.8728  12.6734
 QYH  C2   C  CR6   0   0.378  -1.9742  -10.9750  13.0344
 QYH  N2   N  N     0  -0.509   4.6716  -11.6643  15.1792
 QYH  C3   C  CR16  0  -0.364  -0.9026  -10.4888  12.2878
 QYH  N3   N  NH2   0  -0.824   5.2414  -11.2780  12.9986
 QYH  C4   C  CR16  0  -0.268   0.3934  -10.6518  12.7545
 QYH  N4   N  N     0  -0.521   3.0135  -11.2740  13.5174
 QYH  C5   C  CR6   0   0.030   0.6635  -11.2834  13.9656
 QYH  C6   C  CR16  0  -0.301  -0.4237  -11.7694  14.6986
 QYH  C7   C  CR16  0  -0.324  -1.7188  -11.6229  14.2462
 QYH  C8   C  CR6   0   0.296   2.0555  -11.4292  14.4383
 QYH  C9   C  CR16  0  -0.479   2.3529  -11.6962  15.7603
 QYH  C10  C  CR6   0   0.508   3.7153  -11.8137  16.0923
 QYH  C11  C  CR6   0   0.524   4.2703  -11.3978  13.9362
 QYH  H1   H  HCH3  0   0.260  -4.6587  -10.2866  11.3464
 QYH  H2   H  HCH3  0   0.229  -3.2559   -9.2054  11.4204
 QYH  H3   H  HCH3  0   0.230  -3.1293  -10.7747  10.5951
 QYH  H4   H  HNH2  0   0.390   5.0736  -12.0202  17.5907
 QYH  H5   H  HNH2  0   0.400   3.4388  -12.0613  18.1030
 QYH  H6   H  HCR6  0   0.278  -1.0549   -9.9816  11.3450
 QYH  H7   H  HNH2  0   0.386   4.9940  -10.8483  12.1239
 QYH  H8   H  HNH2  0   0.386   6.1839  -11.1274  13.3153
 QYH  H9   H  HCR6  0   0.254   1.2131  -10.2711  12.1607
 QYH  H10  H  HCR6  0   0.251  -0.2666  -12.2932  15.6324
 QYH  H11  H  HCR6  0   0.263  -2.5454  -12.0156  14.8250
 QYH  H12  H  HCR6  0   0.259   1.5948  -11.7915  16.5240

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
 QYH  C1   O1   single    1.414  0.020  1.414
 QYH  C3   C4   aromatic  1.387  0.020  1.387
 QYH  C3   C2   aromatic  1.394  0.020  1.394
 QYH  C4   C5   aromatic  1.392  0.020  1.392
 QYH  O1   C2   single    1.342  0.020  1.342
 QYH  C2   C7   aromatic  1.398  0.020  1.398
 QYH  N3   C11  single    1.355  0.020  1.355
 QYH  N4   C11  aromatic  1.330  0.020  1.330
 QYH  N4   C8   aromatic  1.338  0.020  1.338
 QYH  C5   C8   single    1.477  0.020  1.477
 QYH  C5   C6   aromatic  1.398  0.020  1.398
 QYH  C11  N2   aromatic  1.333  0.020  1.333
 QYH  C7   C6   aromatic  1.380  0.020  1.380
 QYH  C8   C9   aromatic  1.381  0.020  1.381
 QYH  N2   C10  aromatic  1.331  0.020  1.331
 QYH  C9   C10  aromatic  1.407  0.020  1.407
 QYH  C10  N1   single    1.346  0.020  1.346
 QYH  C1   H1   single    0.970  0.020  1.090
 QYH  C1   H2   single    0.970  0.020  1.090
 QYH  C1   H3   single    0.970  0.020  1.090
 QYH  N1   H4   single    0.890  0.020  1.040
 QYH  N1   H5   single    0.890  0.020  1.040
 QYH  C3   H6   single    0.930  0.020  1.080
 QYH  N3   H7   single    0.890  0.020  1.040
 QYH  N3   H8   single    0.890  0.020  1.040
 QYH  C4   H9   single    0.930  0.020  1.080
 QYH  C6   H10  single    0.930  0.020  1.080
 QYH  C7   H11  single    0.930  0.020  1.080
 QYH  C9   H12  single    0.930  0.020  1.080

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
 QYH  H3   C1   H2   108.82  3.000
 QYH  H3   C1   H1   108.78  3.000
 QYH  H2   C1   H1   108.79  3.000
 QYH  H3   C1   O1   111.90  3.000
 QYH  H2   C1   O1   111.97  3.000
 QYH  H1   C1   O1   106.47  3.000
 QYH  H5   N1   H4   116.92  3.000
 QYH  H5   N1   C10  120.18  3.000
 QYH  H4   N1   C10  118.97  3.000
 QYH  C2   O1   C1   118.71  3.000
 QYH  C7   C2   C3   119.06  3.000
 QYH  C7   C2   O1   116.35  3.000
 QYH  C3   C2   O1   124.59  3.000
 QYH  C11  N2   C10  116.49  3.000
 QYH  H6   C3   C4   118.69  3.000
 QYH  H6   C3   C2   121.50  3.000
 QYH  C4   C3   C2   119.82  3.000
 QYH  H8   N3   H7   116.14  3.000
 QYH  H8   N3   C11  117.84  3.000
 QYH  H7   N3   C11  117.60  3.000
 QYH  H9   C4   C5   119.36  3.000
 QYH  H9   C4   C3   118.83  3.000
 QYH  C5   C4   C3   121.82  3.000
 QYH  C11  N4   C8   116.68  3.000
 QYH  C8   C5   C6   122.04  3.000
 QYH  C6   C5   C4   117.57  3.000
 QYH  C8   C5   C4   120.39  3.000
 QYH  H10  C6   C7   118.08  3.000
 QYH  H10  C6   C5   120.51  3.000
 QYH  C7   C6   C5   121.40  3.000
 QYH  H11  C7   C6   120.18  3.000
 QYH  H11  C7   C2   119.48  3.000
 QYH  C6   C7   C2   120.34  3.000
 QYH  C9   C8   C5   121.89  3.000
 QYH  C9   C8   N4   121.81  3.000
 QYH  C5   C8   N4   116.30  3.000
 QYH  H12  C9   C10  120.35  3.000
 QYH  H12  C9   C8   122.86  3.000
 QYH  C10  C9   C8   116.77  3.000
 QYH  C9   C10  N2   121.63  3.000
 QYH  C9   C10  N1   121.06  3.000
 QYH  N2   C10  N1   117.30  3.000
 QYH  N4   C11  N3   116.81  3.000
 QYH  N4   C11  N2   126.61  3.000
 QYH  N3   C11  N2   116.55  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
 QYH  CONST_01  C5   C4  C3   C2    0.00   0.0  0
 QYH  CONST_02  C5   C6  C7   C2    0.00   0.0  0
 QYH  CONST_03  C8   N4  C11  N2    0.00   0.0  0
 QYH  CONST_04  C8   C9  C10  N2    0.00   0.0  0
 QYH  CONST_05  C8   C5  C4   C3  180.00   0.0  0
 QYH  CONST_06  C6   C5  C4   C3    0.00   0.0  0
 QYH  CONST_07  C6   C7  C2   C3    0.00   0.0  0
 QYH  CONST_08  C7   C2  C3   C4    0.00   0.0  0
 QYH  CONST_11  C7   C6  C5   C4    0.00   0.0  0
 QYH  CONST_12  C10  N2  C11  N4    0.00   0.0  0
 QYH  CONST_14  C10  C9  C8   N4    0.00   0.0  0
 QYH  CONST_15  C11  N4  C8   C5  180.00   0.0  0
 QYH  CONST_16  C10  C9  C8   C5  180.00   0.0  0
 QYH  CONST_18  C8   C5  C6   C7  180.00   0.0  0
 QYH  CONST_19  C11  N4  C8   C9    0.00   0.0  0
 QYH  CONST_20  C11  N2  C10  C9    0.00   0.0  0
 QYH  CONST_21  C11  N2  C10  N1  180.00   0.0  0
 QYH  CONST_22  C8   C9  C10  N1  180.00   0.0  0
 QYH  CONST_23  C4   C3  C2   O1  180.00   0.0  0
 QYH  CONST_24  C6   C7  C2   O1  180.00   0.0  0
 QYH  CONST_25  C8   N4  C11  N3  180.00   0.0  0
 QYH  CONST_26  C10  N2  C11  N3  180.00   0.0  0
 QYH  CONST_27  H9   C4  C3   C2  180.00   0.0  0
 QYH  CONST_28  H10  C6  C7   C2  180.00   0.0  0
 QYH  CONST_29  H12  C9  C10  N2  180.00   0.0  0
 QYH  CONST_30  H11  C7  C2   C3  180.00   0.0  0
 QYH  CONST_31  H6   C3  C4   C5  180.00   0.0  0
 QYH  CONST_34  H4   N1  C10  N2    0.00   0.0  0
 QYH  CONST_35  H5   N1  C10  N2  180.00   0.0  0
 QYH  Var_01    C3   C2  O1   C1    1.03  30.0  2
 QYH  Var_02    H1   C1  O1   C2  179.30  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
 QYH  plan-1  O1   0.020
 QYH  plan-1  C2   0.020
 QYH  plan-1  C3   0.020
 QYH  plan-1  C4   0.020
 QYH  plan-1  C5   0.020
 QYH  plan-1  C6   0.020
 QYH  plan-1  C7   0.020
 QYH  plan-1  C8   0.020
 QYH  plan-1  H6   0.020
 QYH  plan-1  H9   0.020
 QYH  plan-1  H10  0.020
 QYH  plan-1  H11  0.020
 QYH  plan-2  N1   0.020
 QYH  plan-2  N2   0.020
 QYH  plan-2  N3   0.020
 QYH  plan-2  N4   0.020
 QYH  plan-2  C5   0.020
 QYH  plan-2  C8   0.020
 QYH  plan-2  C9   0.020
 QYH  plan-2  C10  0.020
 QYH  plan-2  C11  0.020
 QYH  plan-2  H12  0.020
 QYH  plan-3  N1   0.020
 QYH  plan-3  C10  0.020
 QYH  plan-3  H4   0.020
 QYH  plan-3  H5   0.020
 QYH  plan-4  N3   0.020
 QYH  plan-4  C11  0.020
 QYH  plan-4  H7   0.020
 QYH  plan-4  H8   0.020

