# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 05:35:31 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: 4-phenylpyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: c1ccc(cc1)c2ccncn2
#
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
 RW1  RW1  '4-phenylpyrimidine       '  ligand  20  12  .  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_RW1
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
 RW1  C2   C  CR16  0   0.031  -2.6895   1.0891   0.2471
 RW1  N3   N  N     0  -0.399  -3.4740   0.0398   0.0524
 RW1  C4   C  CR16  0  -0.009  -2.8493  -1.1109  -0.1743
 RW1  C5   C  CR16  0  -0.328  -1.4718  -1.2174  -0.2004
 RW1  N1   N  N     0  -0.377  -1.3687   1.0997   0.2478
 RW1  C6   C  CR6   0   0.238  -0.7382  -0.0554   0.0298
 RW1  C7   C  CR6   0  -0.049   0.7375  -0.0319   0.0308
 RW1  C8   C  CR16  0  -0.191   1.4150   1.1752  -0.1518
 RW1  C12  C  CR16  0  -0.269   1.4789  -1.1995   0.2154
 RW1  C11  C  CR16  0  -0.242   2.8651  -1.1620   0.2122
 RW1  C10  C  CR16  0  -0.233   3.5299   0.0416   0.0194
 RW1  C9   C  CR16  0  -0.244   2.8002   1.2098  -0.1630
 RW1  H2   H  HCR6  0   0.221  -3.1809   2.0393   0.4271
 RW1  H4   H  HCR6  0   0.296  -3.4704  -1.9822  -0.3485
 RW1  H5   H  HCR6  0   0.279  -1.0028  -2.1674  -0.4098
 RW1  H8   H  HCR6  0   0.267   0.8515   2.0871  -0.2954
 RW1  H12  H  HCR6  0   0.245   0.9828  -2.1463   0.3855
 RW1  H11  H  HCR6  0   0.271   3.4254  -2.0746   0.3664
 RW1  H10  H  HCR6  0   0.237   4.6116   0.0699   0.0135
 RW1  H9   H  HCR6  0   0.257   3.3119   2.1509  -0.3166

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
 RW1  C2   N3   aromatic  1.325  0.020  1.325
 RW1  C2   N1   aromatic  1.321  0.020  1.321
 RW1  N3   C4   aromatic  1.329  0.020  1.329
 RW1  C4   C5   aromatic  1.382  0.020  1.382
 RW1  C5   C6   aromatic  1.393  0.020  1.393
 RW1  N1   C6   aromatic  1.334  0.020  1.334
 RW1  C6   C7   single    1.476  0.020  1.476
 RW1  C7   C8   aromatic  1.396  0.020  1.396
 RW1  C7   C12  aromatic  1.395  0.020  1.395
 RW1  C8   C9   aromatic  1.386  0.020  1.386
 RW1  C12  C11  aromatic  1.387  0.020  1.387
 RW1  C11  C10  aromatic  1.388  0.020  1.388
 RW1  C10  C9   aromatic  1.389  0.020  1.389
 RW1  C2   H2   single    0.930  0.020  1.080
 RW1  C4   H4   single    0.930  0.020  1.080
 RW1  C5   H5   single    0.930  0.020  1.080
 RW1  C8   H8   single    0.930  0.020  1.080
 RW1  C12  H12  single    0.930  0.020  1.080
 RW1  C11  H11  single    0.930  0.020  1.080
 RW1  C10  H10  single    0.930  0.020  1.080
 RW1  C9   H9   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
 RW1  H2   C2   N1   116.48  3.000
 RW1  H2   C2   N3   116.74  3.000
 RW1  N1   C2   N3   126.78  3.000
 RW1  C4   N3   C2   115.63  3.000
 RW1  H4   C4   C5   120.41  3.000
 RW1  H4   C4   N3   117.00  3.000
 RW1  C5   C4   N3   122.59  3.000
 RW1  H5   C5   C6   122.49  3.000
 RW1  H5   C5   C4   120.28  3.000
 RW1  C6   C5   C4   117.22  3.000
 RW1  C6   N1   C2   117.75  3.000
 RW1  C7   C6   N1   117.30  3.000
 RW1  C7   C6   C5   122.67  3.000
 RW1  N1   C6   C5   120.02  3.000
 RW1  C12  C7   C8   118.88  3.000
 RW1  C12  C7   C6   121.20  3.000
 RW1  C8   C7   C6   119.92  3.000
 RW1  H8   C8   C9   119.91  3.000
 RW1  H8   C8   C7   119.57  3.000
 RW1  C9   C8   C7   120.51  3.000
 RW1  H12  C12  C11  118.83  3.000
 RW1  H12  C12  C7   120.61  3.000
 RW1  C11  C12  C7   120.55  3.000
 RW1  H11  C11  C10  120.20  3.000
 RW1  H11  C11  C12  119.64  3.000
 RW1  C10  C11  C12  120.16  3.000
 RW1  H10  C10  C9   120.15  3.000
 RW1  H10  C10  C11  120.14  3.000
 RW1  C9   C10  C11  119.71  3.000
 RW1  H9   C9   C10  120.10  3.000
 RW1  H9   C9   C8   119.71  3.000
 RW1  C10  C9   C8   120.20  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
 RW1  CONST_01  C5   C4   N3   C2     0.00  0.0  0
 RW1  CONST_02  C5   C6   N1   C2     0.00  0.0  0
 RW1  CONST_03  C7   C6   N1   C2   180.00  0.0  0
 RW1  CONST_04  C6   N1   C2   N3     0.00  0.0  0
 RW1  CONST_05  C6   C5   C4   N3     0.00  0.0  0
 RW1  CONST_06  N1   C2   N3   C4     0.00  0.0  0
 RW1  CONST_07  N1   C6   C5   C4     0.00  0.0  0
 RW1  CONST_08  C7   C6   C5   C4   180.00  0.0  0
 RW1  CONST_13  C9   C8   C7   C6   180.00  0.0  0
 RW1  CONST_14  C11  C12  C7   C6   180.00  0.0  0
 RW1  CONST_15  C10  C9   C8   C7     0.00  0.0  0
 RW1  CONST_16  C10  C11  C12  C7     0.00  0.0  0
 RW1  CONST_17  C11  C12  C7   C8     0.00  0.0  0
 RW1  CONST_18  C11  C10  C9   C8     0.00  0.0  0
 RW1  CONST_19  C9   C8   C7   C12    0.00  0.0  0
 RW1  CONST_20  C9   C10  C11  C12    0.00  0.0  0
 RW1  CONST_21  H4   C4   N3   C2   180.00  0.0  0
 RW1  CONST_22  H5   C5   C4   N3   180.00  0.0  0
 RW1  CONST_23  H2   C2   N3   C4   180.00  0.0  0
 RW1  CONST_24  H8   C8   C7   C6     0.00  0.0  0
 RW1  CONST_25  H12  C12  C7   C6     0.00  0.0  0
 RW1  CONST_26  H9   C9   C8   C7   180.00  0.0  0
 RW1  CONST_27  H11  C11  C12  C7   180.00  0.0  0
 RW1  CONST_28  H10  C10  C9   C8   180.00  0.0  0

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
 RW1  plan-1  C2   0.020
 RW1  plan-1  N3   0.020
 RW1  plan-1  C4   0.020
 RW1  plan-1  C5   0.020
 RW1  plan-1  N1   0.020
 RW1  plan-1  C6   0.020
 RW1  plan-1  C7   0.020
 RW1  plan-1  H2   0.020
 RW1  plan-1  H4   0.020
 RW1  plan-1  H5   0.020
 RW1  plan-2  C6   0.020
 RW1  plan-2  C7   0.020
 RW1  plan-2  C8   0.020
 RW1  plan-2  C12  0.020
 RW1  plan-2  C11  0.020
 RW1  plan-2  C10  0.020
 RW1  plan-2  C9   0.020
 RW1  plan-2  H8   0.020
 RW1  plan-2  H12  0.020
 RW1  plan-2  H11  0.020
 RW1  plan-2  H10  0.020
 RW1  plan-2  H9   0.020

