# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 03:22:09 2021
#   Inital geometry file: a 65 line input string
#   Ligand name: N~4~-(3-chlorophenyl)pyrimidine-4,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(Nc2cccc(Cl)c2)ncn1
#
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
 PBY  PBY  N~4~-(3-chlorophenyl)pyrimidine-4,6-diamine  ligand  24  15  .  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_PBY
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
 PBY  C2    C   CR6   0   0.374   8.7194   4.6936   -8.3575
 PBY  C3    C   CR6   0   0.571   8.8313   7.0219   -9.2940
 PBY  C11   C   CR16  0   0.074   7.3152   8.0375  -10.6149
 PBY  C12   C   CR16  0  -0.247   7.7966   2.0943   -7.7878
 PBY  C10   C   CR6   0   0.506   9.1462   9.2446  -10.0753
 PBY  C4    C   CR16  0  -0.331   9.4624   3.8320   -7.5395
 PBY  C5    C   CR16  0  -0.311   7.5071   4.2390   -8.8863
 PBY  C6    C   CR16  0  -0.508   9.6212   8.1674   -9.3271
 PBY  C8    C   CR6   0  -0.021   8.9952   2.5607   -7.2711
 PBY  C9    C   CR16  0  -0.248   7.0691   2.9559   -8.5940
 PBY  N1    N   NH1   0  -0.785   9.2705   5.9479   -8.5739
 PBY  N14   N   N     0  -0.477   7.9697   9.1729  -10.7265
 PBY  N15   N   NH2   0  -0.831   9.8426  10.3864  -10.2023
 PBY  N7    N   N     0  -0.496   7.6652   6.9530   -9.9439
 PBY  CL13  CL  CL    0  -0.130   9.9448   1.5215   -6.2562
 PBY  H1    H   HCR6  0   0.251   6.3661   7.9811  -11.1394
 PBY  H2    H   HCR6  0   0.275   7.4442   1.0958   -7.5710
 PBY  H3    H   HCR6  0   0.287  10.4040   4.1618   -7.1182
 PBY  H4    H   HCR6  0   0.291   6.9176   4.8800   -9.5194
 PBY  H5    H   HCR6  0   0.277  10.5637   8.2229   -8.7977
 PBY  H6    H   HCR6  0   0.267   6.1291   2.6198   -9.0118
 PBY  H7    H   HNH1  0   0.416  10.1581   6.0947   -8.1180
 PBY  H8    H   HNH2  0   0.395   9.4047  11.1812  -10.6348
 PBY  H9    H   HNH2  0   0.403  10.6506  10.5595   -9.6310

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
 PBY  C11  N14   aromatic  1.315  0.020  1.315
 PBY  C11  N7    aromatic  1.322  0.020  1.322
 PBY  N14  C10   aromatic  1.347  0.020  1.347
 PBY  N7   C3    aromatic  1.337  0.020  1.337
 PBY  C10  N15   single    1.343  0.020  1.343
 PBY  C10  C6    aromatic  1.395  0.020  1.395
 PBY  C3   C6    aromatic  1.392  0.020  1.392
 PBY  C3   N1    single    1.366  0.020  1.366
 PBY  C5   C9    aromatic  1.387  0.020  1.387
 PBY  C5   C2    aromatic  1.399  0.020  1.399
 PBY  N1   C2    single    1.387  0.020  1.387
 PBY  C9   C12   aromatic  1.386  0.020  1.386
 PBY  C2   C4    aromatic  1.401  0.020  1.401
 PBY  C12  C8    aromatic  1.386  0.020  1.386
 PBY  C4   C8    aromatic  1.381  0.020  1.381
 PBY  C8   CL13  single    1.735  0.020  1.735
 PBY  C11  H1    single    0.930  0.020  1.080
 PBY  C12  H2    single    0.930  0.020  1.080
 PBY  C4   H3    single    0.930  0.020  1.080
 PBY  C5   H4    single    0.930  0.020  1.080
 PBY  C6   H5    single    0.930  0.020  1.080
 PBY  C9   H6    single    0.930  0.020  1.080
 PBY  N1   H7    single    0.860  0.020  1.020
 PBY  N15  H8    single    0.860  0.020  1.020
 PBY  N15  H9    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
 PBY  N1    C2   C5   125.41  3.000
 PBY  N1    C2   C4   115.87  3.000
 PBY  C5    C2   C4   118.72  3.000
 PBY  N7    C3   N1   119.76  3.000
 PBY  N1    C3   C6   118.51  3.000
 PBY  N7    C3   C6   121.73  3.000
 PBY  H1    C11  N7   115.71  3.000
 PBY  H1    C11  N14  116.03  3.000
 PBY  N7    C11  N14  128.26  3.000
 PBY  H2    C12  C9   121.31  3.000
 PBY  H2    C12  C8   121.20  3.000
 PBY  C9    C12  C8   117.49  3.000
 PBY  N15   C10  N14  116.90  3.000
 PBY  N15   C10  C6   122.04  3.000
 PBY  N14   C10  C6   121.04  3.000
 PBY  H3    C4   C8   119.93  3.000
 PBY  H3    C4   C2   120.06  3.000
 PBY  C8    C4   C2   120.02  3.000
 PBY  H4    C5   C9   120.12  3.000
 PBY  H4    C5   C2   120.23  3.000
 PBY  C9    C5   C2   119.65  3.000
 PBY  H5    C6   C10  121.28  3.000
 PBY  H5    C6   C3   121.65  3.000
 PBY  C10   C6   C3   117.07  3.000
 PBY  CL13  C8   C4   118.68  3.000
 PBY  CL13  C8   C12  119.32  3.000
 PBY  C4    C8   C12  122.00  3.000
 PBY  H6    C9   C5   118.70  3.000
 PBY  H6    C9   C12  119.17  3.000
 PBY  C5    C9   C12  122.13  3.000
 PBY  H7    N1   C3   114.01  3.000
 PBY  H7    N1   C2   114.26  3.000
 PBY  C3    N1   C2   131.73  3.000
 PBY  C10   N14  C11  116.09  3.000
 PBY  H9    N15  H8   117.31  3.000
 PBY  H9    N15  C10  120.64  3.000
 PBY  H8    N15  C10  119.13  3.000
 PBY  C11   N7   C3   115.80  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
 PBY  CONST_01  C12   C9   C5   C2     0.00   0.0  0
 PBY  CONST_02  C12   C8   C4   C2     0.00   0.0  0
 PBY  CONST_03  N14   C11  N7   C3     0.00   0.0  0
 PBY  CONST_04  N14   C10  C6   C3     0.00   0.0  0
 PBY  CONST_05  C6    C10  N14  C11    0.00   0.0  0
 PBY  CONST_06  C6    C3   N7   C11    0.00   0.0  0
 PBY  CONST_07  N7    C11  N14  C10    0.00   0.0  0
 PBY  CONST_08  N7    C3   C6   C10    0.00   0.0  0
 PBY  CONST_09  C9    C5   C2   C4     0.00   0.0  0
 PBY  CONST_10  C9    C12  C8   C4     0.00   0.0  0
 PBY  CONST_11  C8    C12  C9   C5     0.00   0.0  0
 PBY  CONST_12  C8    C4   C2   C5     0.00   0.0  0
 PBY  CONST_13  CL13  C8   C4   C2   180.00   0.0  0
 PBY  CONST_14  N15   C10  C6   C3   180.00   0.0  0
 PBY  CONST_15  N15   C10  N14  C11  180.00   0.0  0
 PBY  CONST_16  N1    C3   N7   C11  180.00   0.0  0
 PBY  CONST_17  N1    C3   C6   C10  180.00   0.0  0
 PBY  CONST_18  N1    C2   C4   C8   180.00   0.0  0
 PBY  CONST_19  N1    C2   C5   C9   180.00   0.0  0
 PBY  CONST_20  CL13  C8   C12  C9   180.00   0.0  0
 PBY  CONST_21  H6    C9   C5   C2   180.00   0.0  0
 PBY  CONST_22  H1    C11  N7   C3   180.00   0.0  0
 PBY  CONST_23  H4    C5   C9   C12  180.00   0.0  0
 PBY  CONST_24  H3    C4   C8   C12  180.00   0.0  0
 PBY  CONST_25  H2    C12  C8   C4   180.00   0.0  0
 PBY  CONST_26  H5    C6   C10  N14  180.00   0.0  0
 PBY  CONST_27  H8    N15  C10  C6   180.00   0.0  0
 PBY  CONST_28  H9    N15  C10  C6     0.00   0.0  0
 PBY  Var_01    N7    C3   N1   C2     0.20  30.0  1
 PBY  Var_02    C5    C2   N1   C3     0.52  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
 PBY  plan-1  C3    0.020
 PBY  plan-1  C11   0.020
 PBY  plan-1  C10   0.020
 PBY  plan-1  C6    0.020
 PBY  plan-1  N1    0.020
 PBY  plan-1  N14   0.020
 PBY  plan-1  N15   0.020
 PBY  plan-1  N7    0.020
 PBY  plan-1  H1    0.020
 PBY  plan-1  H5    0.020
 PBY  plan-2  C2    0.020
 PBY  plan-2  C12   0.020
 PBY  plan-2  C4    0.020
 PBY  plan-2  C5    0.020
 PBY  plan-2  C8    0.020
 PBY  plan-2  C9    0.020
 PBY  plan-2  N1    0.020
 PBY  plan-2  CL13  0.020
 PBY  plan-2  H2    0.020
 PBY  plan-2  H3    0.020
 PBY  plan-2  H4    0.020
 PBY  plan-2  H6    0.020
 PBY  plan-3  C10   0.020
 PBY  plan-3  N15   0.020
 PBY  plan-3  H8    0.020
 PBY  plan-3  H9    0.020

