# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 02:52:19 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-amino-7-(pyridin-3-ylmethyl)-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2c(Cc3cccnc3)c[nH]c2C(=O)N1
#
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
 BC3  BC3  2-amino-7-(pyridin-3-ylmethyl)-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one  ligand  29  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BC3
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
 BC3  N01   N  NH2   0  -0.841  -2.3295   2.9320  -0.3436
 BC3  C02   C  CR6   0   0.637  -2.0904   1.6067  -0.1998
 BC3  N03   N  N     0  -0.504  -0.9973   1.0804  -0.6619
 BC3  C04   C  CR56  0   0.168  -0.8966  -0.2690  -0.5133
 BC3  C05   C  CR5   0  -0.018   0.1527  -1.1315  -0.9196
 BC3  C06   C  CH2   0  -0.626   1.4293  -0.7293  -1.5882
 BC3  C07   C  CR6   0   0.055   2.4183  -0.1404  -0.6155
 BC3  C08   C  CR16  0  -0.199   3.3468  -0.9296   0.0523
 BC3  C09   C  CR16  0  -0.318   4.2157  -0.3413   0.9582
 BC3  C10   C  CR16  0  -0.078   4.1244   1.0262   1.1690
 BC3  N11   N  N     0  -0.403   3.2437   1.7972   0.5411
 BC3  C12   C  CR16  0  -0.098   2.4189   1.2213  -0.3249
 BC3  C13   C  CR15  0  -0.060  -0.2353  -2.4006  -0.5434
 BC3  N14   N  NR15  0  -0.655  -1.4442  -2.3561   0.0616
 BC3  C15   C  CR56  0   0.131  -1.8697  -1.0591   0.0889
 BC3  C16   C  CR6   0   0.512  -3.0677  -0.4993   0.6040
 BC3  O17   O  O     0  -0.488  -3.9984  -1.0726   1.1546
 BC3  N18   N  NR16  0  -0.718  -3.0820   0.8781   0.4060
 BC3  HN01  H  HNH2  0   0.401  -1.5301   3.4964  -0.5792
 BC3  HN0A  H  HNH2  0   0.403  -2.9949   3.3806   0.2638
 BC3  H06   H  HCH2  0   0.267   1.8754  -1.5966  -2.0792
 BC3  H06A  H  HCH2  0   0.264   1.2186  -0.0022  -2.3757
 BC3  H08   H  HCR6  0   0.263   3.3937  -1.9958  -0.1377
 BC3  H09   H  HCR6  0   0.268   4.9527  -0.9284   1.4890
 BC3  H10   H  HCR6  0   0.260   4.7890   1.5183   1.8704
 BC3  H12   H  HCR6  0   0.254   1.7024   1.8715  -0.8164
 BC3  H13   H  HCR5  0   0.287   0.2800  -3.3386  -0.6784
 BC3  HN14  H  HNR5  0   0.415  -1.9532  -3.1529   0.4062
 BC3  HN18  H  HNR6  0   0.422  -3.9067   1.3627   0.7358

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
 BC3  N01  C02   single    1.354  0.020  1.354
 BC3  C02  N03   double    1.298  0.020  1.298
 BC3  C02  N18   single    1.372  0.020  1.372
 BC3  N03  C04   single    1.361  0.020  1.361
 BC3  C04  C05   aromatic  1.418  0.020  1.418
 BC3  C04  C15   aromatic  1.391  0.020  1.391
 BC3  C05  C06   single    1.496  0.020  1.496
 BC3  C05  C13   aromatic  1.379  0.020  1.379
 BC3  C06  C07   single    1.507  0.020  1.507
 BC3  C07  C08   aromatic  1.390  0.020  1.390
 BC3  C07  C12   aromatic  1.392  0.020  1.392
 BC3  C08  C09   aromatic  1.386  0.020  1.386
 BC3  C09  C10   aromatic  1.387  0.020  1.387
 BC3  C10  N11   aromatic  1.328  0.020  1.328
 BC3  N11  C12   aromatic  1.327  0.020  1.327
 BC3  C13  N14   aromatic  1.353  0.020  1.353
 BC3  N14  C15   aromatic  1.365  0.020  1.365
 BC3  C15  C16   single    1.419  0.020  1.419
 BC3  C16  O17   double    1.224  0.020  1.224
 BC3  C16  N18   single    1.392  0.020  1.392
 BC3  N01  HN01  single    0.890  0.020  1.040
 BC3  N01  HN0A  single    0.890  0.020  1.040
 BC3  C06  H06   single    0.970  0.020  1.090
 BC3  C06  H06A  single    0.970  0.020  1.090
 BC3  C08  H08   single    0.930  0.020  1.080
 BC3  C09  H09   single    0.930  0.020  1.080
 BC3  C10  H10   single    0.930  0.020  1.080
 BC3  C12  H12   single    0.930  0.020  1.080
 BC3  C13  H13   single    0.930  0.020  1.080
 BC3  N14  HN14  single    0.860  0.020  1.020
 BC3  N18  HN18  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
 BC3  HN0A  N01  HN01  114.61  3.000
 BC3  HN0A  N01  C02   119.26  3.000
 BC3  HN01  N01  C02   115.68  3.000
 BC3  N18   C02  N03   123.41  3.000
 BC3  N18   C02  N01   116.05  3.000
 BC3  N03   C02  N01   120.51  3.000
 BC3  C04   N03  C02   115.17  3.000
 BC3  C15   C04  C05   107.24  3.000
 BC3  C15   C04  N03   123.97  3.000
 BC3  C05   C04  N03   128.79  3.000
 BC3  C13   C05  C06   127.53  3.000
 BC3  C13   C05  C04   105.87  3.000
 BC3  C06   C05  C04   126.59  3.000
 BC3  H06A  C06  H06   106.46  3.000
 BC3  H06A  C06  C07   109.38  3.000
 BC3  H06   C06  C07   109.42  3.000
 BC3  H06A  C06  C05   109.66  3.000
 BC3  H06   C06  C05   109.63  3.000
 BC3  C07   C06  C05   112.12  3.000
 BC3  C12   C07  C08   117.06  3.000
 BC3  C12   C07  C06   121.14  3.000
 BC3  C08   C07  C06   121.79  3.000
 BC3  H08   C08  C09   120.33  3.000
 BC3  H08   C08  C07   120.21  3.000
 BC3  C09   C08  C07   119.46  3.000
 BC3  H09   C09  C10   120.38  3.000
 BC3  H09   C09  C08   121.16  3.000
 BC3  C10   C09  C08   118.46  3.000
 BC3  H10   C10  N11   116.66  3.000
 BC3  H10   C10  C09   120.36  3.000
 BC3  N11   C10  C09   122.97  3.000
 BC3  C12   N11  C10   117.94  3.000
 BC3  H12   C12  N11   116.47  3.000
 BC3  H12   C12  C07   119.42  3.000
 BC3  N11   C12  C07   124.11  3.000
 BC3  H13   C13  N14   120.77  3.000
 BC3  H13   C13  C05   129.17  3.000
 BC3  N14   C13  C05   110.07  3.000
 BC3  HN14  N14  C15   125.99  3.000
 BC3  HN14  N14  C13   125.40  3.000
 BC3  C15   N14  C13   108.59  3.000
 BC3  C16   C15  N14   130.17  3.000
 BC3  C16   C15  C04   121.58  3.000
 BC3  N14   C15  C04   108.24  3.000
 BC3  N18   C16  O17   121.32  3.000
 BC3  N18   C16  C15   110.33  3.000
 BC3  O17   C16  C15   128.35  3.000
 BC3  HN18  N18  C16   115.85  3.000
 BC3  HN18  N18  C02   118.61  3.000
 BC3  C16   N18  C02   125.54  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
 BC3  CONST_01  N14   C13  C05  C04    0.00   0.0  0
 BC3  CONST_02  C13   N14  C15  C04    0.00   0.0  0
 BC3  CONST_03  N14   C15  C04  C05    0.00   0.0  0
 BC3  CONST_04  C15   N14  C13  C05    0.00   0.0  0
 BC3  CONST_05  C10   C09  C08  C07    0.00   0.0  0
 BC3  CONST_06  C10   N11  C12  C07    0.00   0.0  0
 BC3  CONST_07  N11   C12  C07  C08    0.00   0.0  0
 BC3  CONST_08  N11   C10  C09  C08    0.00   0.0  0
 BC3  CONST_09  C12   C07  C08  C09    0.00   0.0  0
 BC3  CONST_10  C12   N11  C10  C09    0.00   0.0  0
 BC3  CONST_11  C15   C04  C05  C13    0.00   0.0  0
 BC3  CONST_12  C15   C16  N18  C02    0.00   0.0  0
 BC3  CONST_13  C16   N18  C02  N03    0.00   0.0  0
 BC3  CONST_14  N18   C02  N03  C04    0.00   0.0  0
 BC3  CONST_15  C06   C05  C04  N03    0.00   0.0  0
 BC3  CONST_16  C15   C04  C05  C06  180.00   0.0  0
 BC3  CONST_17  N14   C13  C05  C06  180.00   0.0  0
 BC3  CONST_18  C09   C08  C07  C06  180.00   0.0  0
 BC3  CONST_19  N11   C12  C07  C06  180.00   0.0  0
 BC3  CONST_20  C04   N03  C02  N01  180.00   0.0  0
 BC3  CONST_21  C16   N18  C02  N01  180.00   0.0  0
 BC3  CONST_22  O17   C16  N18  C02  180.00   0.0  0
 BC3  CONST_23  H13   C13  C05  C04  180.00   0.0  0
 BC3  CONST_24  HN14  N14  C15  C04  180.00   0.0  0
 BC3  CONST_25  H09   C09  C08  C07  180.00   0.0  0
 BC3  CONST_26  H12   C12  C07  C08  180.00   0.0  0
 BC3  CONST_27  H10   C10  C09  C08  180.00   0.0  0
 BC3  CONST_28  H08   C08  C09  C10  180.00   0.0  0
 BC3  CONST_29  HN18  N18  C02  N03  180.00   0.0  0
 BC3  Var_01    C07   C06  C05  C04   77.47  30.0  2
 BC3  Var_02    C08   C07  C06  C05   90.31  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
 BC3  plan-1  C06   0.020
 BC3  plan-1  C07   0.020
 BC3  plan-1  C08   0.020
 BC3  plan-1  C09   0.020
 BC3  plan-1  C10   0.020
 BC3  plan-1  N11   0.020
 BC3  plan-1  C12   0.020
 BC3  plan-1  H08   0.020
 BC3  plan-1  H09   0.020
 BC3  plan-1  H10   0.020
 BC3  plan-1  H12   0.020
 BC3  plan-2  N01   0.020
 BC3  plan-2  C02   0.020
 BC3  plan-2  N03   0.020
 BC3  plan-2  C04   0.020
 BC3  plan-2  C05   0.020
 BC3  plan-2  C06   0.020
 BC3  plan-2  C13   0.020
 BC3  plan-2  N14   0.020
 BC3  plan-2  C15   0.020
 BC3  plan-2  C16   0.020
 BC3  plan-2  O17   0.020
 BC3  plan-2  N18   0.020
 BC3  plan-2  HN01  0.020
 BC3  plan-2  HN0A  0.020
 BC3  plan-2  H13   0.020
 BC3  plan-2  HN14  0.020
 BC3  plan-2  HN18  0.020

