# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 10:11:08 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 4-aminopyrido[2,3-d]pyrimidin-5(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2NC=CC(=O)c12
#
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
 3WA  3WA  4-aminopyrido[2,3-d]pyrimidin-5(8H)-one  ligand  18  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3WA
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
 3WA  C1   C  CR66  0  -0.326   0.0078   0.2699   0.0291
 3WA  C2   C  CR66  0   0.532   0.0672  -1.1260   0.0211
 3WA  C3   C  CR6   0   0.470   1.2183   1.0808   0.0362
 3WA  N6   N  N     0  -0.464  -1.0045  -1.9223   0.0095
 3WA  C7   C  CR16  0  -0.466   2.4470   0.3229   0.0210
 3WA  C11  C  CR16  0   0.072   2.4337  -1.0274   0.0180
 3WA  C12  C  CR16  0   0.086  -2.1625  -1.2920  -0.0169
 3WA  C4   C  CR6   0   0.518  -1.3118   0.8088   0.0123
 3WA  N5   N  NR16  0  -0.665   1.2800  -1.7334   0.0180
 3WA  O8   O  O     0  -0.488   1.2018   2.3166   0.0533
 3WA  N9   N  N     0  -0.437  -2.3817   0.0085  -0.0264
 3WA  N10  N  NH2   0  -0.811  -1.5270   2.1199   0.0398
 3WA  H1   H  HCR6  0   0.260   3.3922   0.8461   0.0100
 3WA  H2   H  HCR6  0   0.294   3.3378  -1.6174   0.0154
 3WA  H3   H  HCR6  0   0.241  -3.0459  -1.9222  -0.0370
 3WA  H4   H  HNR6  0   0.399   1.3062  -2.7405   0.0380
 3WA  H5   H  HNH2  0   0.408  -0.7404   2.7504   0.0152
 3WA  H6   H  HNH2  0   0.375  -2.4688   2.4590  -0.0461

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
 3WA  N9   C12  aromatic  1.319  0.020  1.319
 3WA  N9   C4   aromatic  1.337  0.020  1.337
 3WA  C12  N6   aromatic  1.319  0.020  1.319
 3WA  N10  C4   single    1.329  0.020  1.329
 3WA  C4   C1   aromatic  1.425  0.020  1.425
 3WA  N6   C2   aromatic  1.335  0.020  1.335
 3WA  C1   C2   aromatic  1.397  0.020  1.397
 3WA  C1   C3   single    1.457  0.020  1.457
 3WA  C2   N5   single    1.356  0.020  1.356
 3WA  C3   O8   double    1.236  0.020  1.236
 3WA  C3   C7   single    1.444  0.020  1.444
 3WA  N5   C11  single    1.353  0.020  1.353
 3WA  C11  C7   double    1.350  0.020  1.350
 3WA  C7   H1   single    0.930  0.020  1.080
 3WA  C11  H2   single    0.930  0.020  1.080
 3WA  C12  H3   single    0.930  0.020  1.080
 3WA  N5   H4   single    0.860  0.020  1.020
 3WA  N10  H5   single    0.860  0.020  1.020
 3WA  N10  H6   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
 3WA  C4   C1   C3   123.97  3.000
 3WA  C3   C1   C2   121.38  3.000
 3WA  C4   C1   C2   114.64  3.000
 3WA  N5   C2   N6   116.78  3.000
 3WA  N5   C2   C1   119.04  3.000
 3WA  N6   C2   C1   124.18  3.000
 3WA  O8   C3   C7   122.44  3.000
 3WA  C7   C3   C1   114.51  3.000
 3WA  O8   C3   C1   123.05  3.000
 3WA  C12  N6   C2   114.83  3.000
 3WA  H1   C7   C11  119.53  3.000
 3WA  H1   C7   C3   119.37  3.000
 3WA  C11  C7   C3   121.10  3.000
 3WA  H2   C11  N5   115.41  3.000
 3WA  H2   C11  C7   122.56  3.000
 3WA  N5   C11  C7   122.03  3.000
 3WA  H3   C12  N9   115.92  3.000
 3WA  H3   C12  N6   115.96  3.000
 3WA  N9   C12  N6   128.13  3.000
 3WA  N10  C4   N9   117.49  3.000
 3WA  N10  C4   C1   121.51  3.000
 3WA  N9   C4   C1   121.00  3.000
 3WA  H4   N5   C11  119.97  3.000
 3WA  H4   N5   C2   118.08  3.000
 3WA  C11  N5   C2   121.94  3.000
 3WA  C4   N9   C12  117.20  3.000
 3WA  H6   N10  H5   121.21  3.000
 3WA  H6   N10  C4   118.88  3.000
 3WA  H5   N10  C4   119.34  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
 3WA  CONST_01  C12  N9   C4   C1     0.00  0.0  0
 3WA  CONST_02  C12  N6   C2   C1     0.00  0.0  0
 3WA  CONST_03  N9   C12  N6   C2     0.00  0.0  0
 3WA  CONST_04  N9   C4   C1   C2     0.00  0.0  0
 3WA  CONST_05  C4   N9   C12  N6     0.00  0.0  0
 3WA  CONST_06  C4   C1   C2   N6     0.00  0.0  0
 3WA  CONST_07  N10  C4   C1   C2   180.00  0.0  0
 3WA  CONST_08  N10  C4   C1   C3     0.00  0.0  0
 3WA  CONST_09  N10  C4   N9   C12  180.00  0.0  0
 3WA  CONST_10  H3   C12  N6   C2   180.00  0.0  0
 3WA  CONST_11  H5   N10  C4   C1     0.00  0.0  0
 3WA  CONST_12  H6   N10  C4   C1   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
 3WA  plan-1  C1   0.020
 3WA  plan-1  C2   0.020
 3WA  plan-1  C3   0.020
 3WA  plan-1  N6   0.020
 3WA  plan-1  C7   0.020
 3WA  plan-1  C11  0.020
 3WA  plan-1  C12  0.020
 3WA  plan-1  C4   0.020
 3WA  plan-1  N5   0.020
 3WA  plan-1  O8   0.020
 3WA  plan-1  N9   0.020
 3WA  plan-1  N10  0.020
 3WA  plan-1  H1   0.020
 3WA  plan-1  H2   0.020
 3WA  plan-1  H3   0.020
 3WA  plan-1  H4   0.020
 3WA  plan-2  C4   0.020
 3WA  plan-2  N10  0.020
 3WA  plan-2  H5   0.020
 3WA  plan-2  H6   0.020

