# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 15:40:36 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: 4-methoxy-6-phenyl-pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(nc(N)n1)c2ccccc2
#
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
 TE5  TE5  "4-methoxy-6-phenyl-pyrimidin-2-amine"
  ligand  26  15  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TE5
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
 TE5  C10  C  CR6   0   0.052   0.6576  -5.5589  5.5876
 TE5  C13  C  CR16  0  -0.259  -1.8660  -6.5893  6.2365
 TE5  C15  C  CR16  0  -0.276  -0.3310  -5.6995  4.6116
 TE5  C01  C  CH3   0  -0.418   6.4542  -3.7158  6.0307
 TE5  C03  C  CR6   0   0.578   4.2172  -4.3714  5.6392
 TE5  C04  C  CR16  0  -0.490   3.0209  -4.9069  6.1295
 TE5  C05  C  CR6   0   0.314   1.9865  -5.0148  5.2174
 TE5  C07  C  CR6   0   0.544   3.3165  -4.1449  3.5881
 TE5  C11  C  CR16  0  -0.329   0.3557  -5.9416  6.8961
 TE5  C12  C  CR16  0  -0.233  -0.8929  -6.4510  7.2173
 TE5  C14  C  CR16  0  -0.235  -1.5794  -6.2097  4.9323
 TE5  N06  N  N     0  -0.513   2.1345  -4.6328  3.9461
 TE5  N08  N  N     0  -0.511   4.3782  -3.9936  4.3922
 TE5  N09  N  NH2   0  -0.820   3.4808  -3.7926  2.2987
 TE5  H1   H  HCR6  0   0.259  -2.8402  -6.9881  6.4878
 TE5  H2   H  HCR6  0   0.254  -0.1167  -5.4066  3.5936
 TE5  H3   H  HCH3  0   0.248   7.1178  -3.7127  6.8912
 TE5  H4   H  HCH3  0   0.233   6.8887  -4.3304  5.2419
 TE5  H5   H  HCH3  0   0.233   6.3378  -2.6972  5.6599
 TE5  H6   H  HCR6  0   0.268   2.9414  -5.2078  7.1624
 TE5  H7   H  HCR6  0   0.254   1.0884  -5.8454  7.6858
 TE5  H8   H  HCR6  0   0.259  -1.1046  -6.7403  8.2383
 TE5  H9   H  HCR6  0   0.257  -2.3308  -6.3108  4.1598
 TE5  H10  H  HNH2  0   0.395   2.6697  -3.7212  1.7093
 TE5  H11  H  HNH2  0   0.395   4.2881  -3.2529  2.0394
 TE5  O02  O  O2    0  -0.460   5.2211  -4.2511  6.4962

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
 TE5  N09  C07  single    1.347  0.020  1.347
 TE5  C07  N06  aromatic  1.328  0.020  1.328
 TE5  C07  N08  aromatic  1.340  0.020  1.340
 TE5  N06  C05  aromatic  1.336  0.020  1.336
 TE5  N08  C03  aromatic  1.313  0.020  1.313
 TE5  C15  C14  aromatic  1.386  0.020  1.386
 TE5  C15  C10  aromatic  1.396  0.020  1.396
 TE5  C14  C13  aromatic  1.388  0.020  1.388
 TE5  C05  C10  single    1.483  0.020  1.483
 TE5  C05  C04  aromatic  1.383  0.020  1.383
 TE5  C10  C11  aromatic  1.396  0.020  1.396
 TE5  C01  O02  single    1.423  0.020  1.423
 TE5  C03  C04  aromatic  1.399  0.020  1.399
 TE5  C03  O02  single    1.325  0.020  1.325
 TE5  C13  C12  aromatic  1.389  0.020  1.389
 TE5  C11  C12  aromatic  1.386  0.020  1.386
 TE5  C13  H1   single    0.930  0.020  1.080
 TE5  C15  H2   single    0.930  0.020  1.080
 TE5  C01  H3   single    0.970  0.020  1.090
 TE5  C01  H4   single    0.970  0.020  1.090
 TE5  C01  H5   single    0.970  0.020  1.090
 TE5  C04  H6   single    0.930  0.020  1.080
 TE5  C11  H7   single    0.930  0.020  1.080
 TE5  C12  H8   single    0.930  0.020  1.080
 TE5  C14  H9   single    0.930  0.020  1.080
 TE5  N09  H10  single    0.890  0.020  1.040
 TE5  N09  H11  single    0.890  0.020  1.040

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
 TE5  C11  C10  C05  121.89  3.000
 TE5  C11  C10  C15  118.32  3.000
 TE5  C05  C10  C15  119.80  3.000
 TE5  H1   C13  C14  120.31  3.000
 TE5  H1   C13  C12  120.23  3.000
 TE5  C14  C13  C12  119.45  3.000
 TE5  H2   C15  C14  119.75  3.000
 TE5  H2   C15  C10  119.39  3.000
 TE5  C14  C15  C10  120.86  3.000
 TE5  H5   C01  H4   108.86  3.000
 TE5  H5   C01  H3   109.38  3.000
 TE5  H4   C01  H3   109.34  3.000
 TE5  H5   C01  O02  111.73  3.000
 TE5  H4   C01  O02  111.72  3.000
 TE5  H3   C01  O02  105.74  3.000
 TE5  O02  C03  N08  119.68  3.000
 TE5  O02  C03  C04  117.11  3.000
 TE5  N08  C03  C04  123.21  3.000
 TE5  H6   C04  C05  123.68  3.000
 TE5  H6   C04  C03  120.34  3.000
 TE5  C05  C04  C03  115.98  3.000
 TE5  N06  C05  C04  121.50  3.000
 TE5  C04  C05  C10  122.28  3.000
 TE5  N06  C05  C10  116.22  3.000
 TE5  N09  C07  N08  116.63  3.000
 TE5  N08  C07  N06  125.79  3.000
 TE5  N09  C07  N06  117.56  3.000
 TE5  H7   C11  C12  118.28  3.000
 TE5  H7   C11  C10  120.89  3.000
 TE5  C12  C11  C10  120.83  3.000
 TE5  H8   C12  C11  119.54  3.000
 TE5  H8   C12  C13  120.18  3.000
 TE5  C11  C12  C13  120.28  3.000
 TE5  H9   C14  C15  119.63  3.000
 TE5  H9   C14  C13  120.11  3.000
 TE5  C15  C14  C13  120.26  3.000
 TE5  C07  N06  C05  117.41  3.000
 TE5  C07  N08  C03  116.11  3.000
 TE5  H11  N09  H10  117.31  3.000
 TE5  H11  N09  C07  119.04  3.000
 TE5  H10  N09  C07  118.79  3.000
 TE5  C03  O02  C01  118.63  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
 TE5  CONST_01  C13  C14  C15  C10     0.00   0.0  0
 TE5  CONST_02  C07  N06  C05  C10   180.00   0.0  0
 TE5  CONST_03  C03  C04  C05  C10   180.00   0.0  0
 TE5  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 TE5  CONST_05  C12  C13  C14  C15     0.00   0.0  0
 TE5  CONST_06  N06  C05  C10  C15     0.00   0.0  0
 TE5  CONST_07  C04  C05  C10  C15   180.00   0.0  0
 TE5  CONST_08  C12  C11  C10  C15     0.00   0.0  0
 TE5  CONST_09  N06  C07  N08  C03     0.00   0.0  0
 TE5  CONST_10  N06  C05  C04  C03     0.00   0.0  0
 TE5  CONST_11  C07  N06  C05  C04     0.00   0.0  0
 TE5  CONST_12  C11  C10  C05  C04     0.00   0.0  0
 TE5  CONST_13  C07  N08  C03  C04     0.00   0.0  0
 TE5  CONST_14  N08  C07  N06  C05     0.00   0.0  0
 TE5  CONST_15  C14  C15  C10  C05   180.00   0.0  0
 TE5  CONST_16  C12  C11  C10  C05   180.00   0.0  0
 TE5  CONST_17  N08  C03  C04  C05     0.00   0.0  0
 TE5  CONST_18  C14  C15  C10  C11     0.00   0.0  0
 TE5  CONST_19  N06  C05  C10  C11   180.00   0.0  0
 TE5  CONST_20  C14  C13  C12  C11     0.00   0.0  0
 TE5  CONST_21  N09  C07  N08  C03   180.00   0.0  0
 TE5  CONST_22  N09  C07  N06  C05   180.00   0.0  0
 TE5  CONST_23  O02  C03  C04  C05   180.00   0.0  0
 TE5  CONST_24  O02  C03  N08  C07   180.00   0.0  0
 TE5  CONST_25  H9   C14  C15  C10   180.00   0.0  0
 TE5  CONST_26  H6   C04  C05  C10     0.00   0.0  0
 TE5  CONST_27  H8   C12  C11  C10   180.00   0.0  0
 TE5  CONST_28  H2   C15  C14  C13   180.00   0.0  0
 TE5  CONST_29  H7   C11  C12  C13   180.00   0.0  0
 TE5  CONST_30  H1   C13  C14  C15   180.00   0.0  0
 TE5  CONST_31  H7   C11  C10  C15   180.00   0.0  0
 TE5  CONST_32  H2   C15  C10  C05     0.00   0.0  0
 TE5  CONST_33  H7   C11  C10  C05     0.00   0.0  0
 TE5  CONST_34  H2   C15  C10  C11   180.00   0.0  0
 TE5  CONST_35  H1   C13  C12  C11   180.00   0.0  0
 TE5  CONST_36  H9   C14  C13  C12   180.00   0.0  0
 TE5  CONST_37  H8   C12  C13  C14   180.00   0.0  0
 TE5  CONST_38  H6   C04  C05  N06   180.00   0.0  0
 TE5  CONST_39  H6   C04  C03  N08   180.00   0.0  0
 TE5  CONST_40  H10  N09  C07  N06     0.00   0.0  0
 TE5  CONST_41  H11  N09  C07  N06   180.00   0.0  0
 TE5  CONST_42  H10  N09  C07  N08   180.00   0.0  0
 TE5  CONST_43  H11  N09  C07  N08     0.00   0.0  0
 TE5  Var_01    N08  C03  O02  C01    -0.24  30.0  2
 TE5  Var_02    C04  C03  O02  C01   179.73  30.0  2
 TE5  Var_03    H3   C01  O02  C03  -179.93  30.0  3
 TE5  Var_04    H4   C01  O02  C03   -61.07  30.0  3
 TE5  Var_05    H5   C01  O02  C03    61.16  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
 TE5  plan-1  C10  0.020
 TE5  plan-1  C13  0.020
 TE5  plan-1  C15  0.020
 TE5  plan-1  C05  0.020
 TE5  plan-1  C11  0.020
 TE5  plan-1  C12  0.020
 TE5  plan-1  C14  0.020
 TE5  plan-1  H1   0.020
 TE5  plan-1  H2   0.020
 TE5  plan-1  H7   0.020
 TE5  plan-1  H8   0.020
 TE5  plan-1  H9   0.020
 TE5  plan-2  C10  0.020
 TE5  plan-2  C03  0.020
 TE5  plan-2  C04  0.020
 TE5  plan-2  C05  0.020
 TE5  plan-2  C07  0.020
 TE5  plan-2  N06  0.020
 TE5  plan-2  N08  0.020
 TE5  plan-2  N09  0.020
 TE5  plan-2  H6   0.020
 TE5  plan-2  O02  0.020
 TE5  plan-3  C07  0.020
 TE5  plan-3  N09  0.020
 TE5  plan-3  H10  0.020
 TE5  plan-3  H11  0.020

