# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 10:49:42 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 7-amino-6-(aminomethyl)-5-(2-bromophenyl)-1,3-dimethylpyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2nc(N)c(CN)c(c3ccccc3Br)c2C1=O
#
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
 0WG  0WG  7-amino-6-(aminomethyl)-5-(2-bromophenyl)-1,3-dimethylpyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione  ligand  40  24  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0WG
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
 0WG  C1   C   CH3   0  -0.527   4.4056   1.3173   0.3390
 0WG  N2   N   NR6   0  -0.596   3.3070   0.4051   0.0429
 0WG  C3   C   CR66  0   0.558   2.0238   0.8835  -0.1221
 0WG  N4   N   N     0  -0.509   1.8568   2.1853   0.0088
 0WG  C5   C   CR6   0   0.462   0.6407   2.6979  -0.1393
 0WG  N6   N   NH2   0  -0.823   0.5078   4.0264  -0.0041
 0WG  C7   C   CR6   0  -0.087  -0.5120   1.8966  -0.3923
 0WG  C8   C   CH2   0  -0.387  -1.8688   2.5487  -0.3921
 0WG  N9   N   NH2   0  -0.800  -1.9429   3.6315  -1.3679
 0WG  C10  C   CR6   0   0.158  -0.3100   0.5468  -0.5582
 0WG  C11  C   CR6   0   0.105  -1.4743  -0.3183  -0.8771
 0WG  C12  C   CR16  0  -0.269  -1.9181  -0.4049  -2.1924
 0WG  C13  C   CR16  0  -0.242  -3.0300  -1.1635  -2.5223
 0WG  C14  C   CR16  0  -0.262  -3.7205  -1.8449  -1.5306
 0WG  C15  C   CR16  0  -0.229  -3.2999  -1.7657  -0.2105
 0WG  C16  C   CR6   0  -0.141  -2.1846  -1.0037   0.1009
 0WG  BR1  BR  BR    0  -0.047  -1.6211  -0.9012   1.9004
 0WG  C18  C   CR66  0  -0.235   0.9879   0.0005  -0.4295
 0WG  C19  C   CR6   0   0.545   1.2675  -1.4120  -0.5769
 0WG  O20  O   O     0  -0.449   0.4513  -2.2555  -0.8967
 0WG  N21  N   NR6   0  -0.594   2.5757  -1.7954  -0.3105
 0WG  C22  C   CH3   0  -0.529   2.8605  -3.2231  -0.3929
 0WG  C23  C   CR6   0   0.745   3.6062  -0.9343   0.0069
 0WG  O24  O   O     0  -0.488   4.7315  -1.3329   0.2364
 0WG  H1   H   HCH3  0   0.252   4.6029   1.3578   1.4098
 0WG  H2   H   HCH3  0   0.258   5.3033   0.9891  -0.1744
 0WG  H3   H   HCH3  0   0.269   4.1416   2.3088  -0.0058
 0WG  H4   H   HNH2  0   0.390   1.3479   4.5773   0.0589
 0WG  H5   H   HNH2  0   0.413  -0.3026   4.4451  -0.4508
 0WG  H6   H   HCH2  0   0.243  -2.6476   1.7934  -0.5226
 0WG  H7   H   HCH2  0   0.253  -2.0354   2.9863   0.5976
 0WG  H8   H   HNH2  0   0.354  -1.9065   3.2521  -2.3060
 0WG  H9   H   HNH2  0   0.366  -2.8347   4.1016  -1.2827
 0WG  H11  H   HCR6  0   0.259  -1.3793   0.1308  -2.9637
 0WG  H12  H   HCR6  0   0.264  -3.3580  -1.2192  -3.5516
 0WG  H13  H   HCR6  0   0.267  -4.5923  -2.4367  -1.7758
 0WG  H14  H   HCR6  0   0.279  -3.8422  -2.2942   0.5621
 0WG  H15  H   HCH3  0   0.267   3.8849  -3.4023  -0.0941
 0WG  H16  H   HCH3  0   0.254   2.1991  -3.7768   0.2693
 0WG  H17  H   HCH3  0   0.253   2.7202  -3.5820  -1.4107

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
 0WG  C22  N21  single    1.458  0.020  1.458
 0WG  O24  C23  double    1.216  0.020  1.216
 0WG  N21  C23  single    1.380  0.020  1.380
 0WG  N21  C19  single    1.389  0.020  1.389
 0WG  O20  C19  double    1.216  0.020  1.216
 0WG  C23  N2   single    1.373  0.020  1.373
 0WG  C19  C18  single    1.447  0.020  1.447
 0WG  C13  C12  aromatic  1.386  0.020  1.386
 0WG  C13  C14  aromatic  1.387  0.020  1.387
 0WG  N2   C1   single    1.458  0.020  1.458
 0WG  N2   C3   single    1.379  0.020  1.379
 0WG  C12  C11  aromatic  1.391  0.020  1.391
 0WG  C18  C3   aromatic  1.395  0.020  1.395
 0WG  C18  C10  aromatic  1.414  0.020  1.414
 0WG  C14  C15  aromatic  1.388  0.020  1.388
 0WG  C3   N4   aromatic  1.319  0.020  1.319
 0WG  C11  C10  single    1.485  0.020  1.485
 0WG  C11  C16  aromatic  1.389  0.020  1.389
 0WG  C10  C7   aromatic  1.375  0.020  1.375
 0WG  C15  C16  aromatic  1.386  0.020  1.386
 0WG  C16  BR1  single    1.888  0.020  1.888
 0WG  N4   C5   aromatic  1.328  0.020  1.328
 0WG  C7   C5   aromatic  1.427  0.020  1.427
 0WG  C7   C8   single    1.505  0.020  1.505
 0WG  C5   N6   single    1.342  0.020  1.342
 0WG  C8   N9   single    1.459  0.020  1.459
 0WG  C1   H1   single    0.970  0.020  1.090
 0WG  C1   H2   single    0.970  0.020  1.090
 0WG  C1   H3   single    0.970  0.020  1.090
 0WG  N6   H4   single    0.890  0.020  1.040
 0WG  N6   H5   single    0.890  0.020  1.040
 0WG  C8   H6   single    0.970  0.020  1.090
 0WG  C8   H7   single    0.970  0.020  1.090
 0WG  N9   H8   single    0.890  0.020  1.040
 0WG  N9   H9   single    0.890  0.020  1.040
 0WG  C12  H11  single    0.930  0.020  1.080
 0WG  C13  H12  single    0.930  0.020  1.080
 0WG  C14  H13  single    0.930  0.020  1.080
 0WG  C15  H14  single    0.930  0.020  1.080
 0WG  C22  H15  single    0.970  0.020  1.090
 0WG  C22  H16  single    0.970  0.020  1.090
 0WG  C22  H17  single    0.970  0.020  1.090

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
 0WG  H3   C1   H2   109.16  3.000
 0WG  H3   C1   H1   108.86  3.000
 0WG  H2   C1   H1   109.06  3.000
 0WG  H3   C1   N2   108.94  3.000
 0WG  H2   C1   N2   109.75  3.000
 0WG  H1   C1   N2   111.05  3.000
 0WG  C23  N2   C3   122.55  3.000
 0WG  C3   N2   C1   120.54  3.000
 0WG  C23  N2   C1   116.83  3.000
 0WG  C18  C3   N4   123.53  3.000
 0WG  N4   C3   N2   116.63  3.000
 0WG  C18  C3   N2   119.83  3.000
 0WG  C5   N4   C3   119.07  3.000
 0WG  C7   C5   N6   119.60  3.000
 0WG  N6   C5   N4   117.49  3.000
 0WG  C7   C5   N4   122.88  3.000
 0WG  H5   N6   H4   117.90  3.000
 0WG  H5   N6   C5   116.28  3.000
 0WG  H4   N6   C5   117.74  3.000
 0WG  C10  C7   C8   123.90  3.000
 0WG  C8   C7   C5   119.01  3.000
 0WG  C10  C7   C5   117.01  3.000
 0WG  H7   C8   H6   106.01  3.000
 0WG  H7   C8   N9   107.46  3.000
 0WG  H6   C8   N9   113.38  3.000
 0WG  H7   C8   C7   108.08  3.000
 0WG  H6   C8   C7   110.05  3.000
 0WG  N9   C8   C7   111.53  3.000
 0WG  H9   N9   H8   106.48  3.000
 0WG  H9   N9   C8   109.46  3.000
 0WG  H8   N9   C8   109.85  3.000
 0WG  C18  C10  C11  120.93  3.000
 0WG  C11  C10  C7   118.85  3.000
 0WG  C18  C10  C7   120.21  3.000
 0WG  C16  C11  C12  118.15  3.000
 0WG  C16  C11  C10  122.48  3.000
 0WG  C12  C11  C10  119.31  3.000
 0WG  H11  C12  C13  120.03  3.000
 0WG  H11  C12  C11  118.96  3.000
 0WG  C13  C12  C11  121.02  3.000
 0WG  H12  C13  C14  120.27  3.000
 0WG  H12  C13  C12  119.87  3.000
 0WG  C14  C13  C12  119.86  3.000
 0WG  H13  C14  C15  119.41  3.000
 0WG  H13  C14  C13  120.51  3.000
 0WG  C15  C14  C13  120.08  3.000
 0WG  H14  C15  C16  120.76  3.000
 0WG  H14  C15  C14  119.97  3.000
 0WG  C16  C15  C14  119.27  3.000
 0WG  BR1  C16  C15  118.94  3.000
 0WG  BR1  C16  C11  119.43  3.000
 0WG  C15  C16  C11  121.62  3.000
 0WG  C19  C18  C10  123.03  3.000
 0WG  C10  C18  C3   117.19  3.000
 0WG  C19  C18  C3   119.77  3.000
 0WG  N21  C19  O20  119.40  3.000
 0WG  O20  C19  C18  125.02  3.000
 0WG  N21  C19  C18  115.58  3.000
 0WG  C23  N21  C22  118.57  3.000
 0WG  C23  N21  C19  125.11  3.000
 0WG  C22  N21  C19  116.32  3.000
 0WG  H17  C22  H16  108.85  3.000
 0WG  H17  C22  H15  109.01  3.000
 0WG  H16  C22  H15  108.87  3.000
 0WG  H17  C22  N21  110.52  3.000
 0WG  H16  C22  N21  110.20  3.000
 0WG  H15  C22  N21  109.36  3.000
 0WG  O24  C23  N21  122.01  3.000
 0WG  N21  C23  N2   116.88  3.000
 0WG  O24  C23  N2   121.11  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
 0WG  CONST_01  C11  C10  C18  C3    180.00   0.0  0
 0WG  CONST_02  C7   C10  C18  C3      0.00   0.0  0
 0WG  CONST_03  C7   C5   N4   C3      0.00   0.0  0
 0WG  CONST_04  C10  C18  C3   N4      0.00   0.0  0
 0WG  CONST_05  C10  C7   C5   N4      0.00   0.0  0
 0WG  CONST_06  C18  C3   N4   C5      0.00   0.0  0
 0WG  CONST_07  C18  C10  C7   C5      0.00   0.0  0
 0WG  CONST_08  C11  C10  C7   C5    180.00   0.0  0
 0WG  CONST_11  C13  C12  C11  C10   180.00   0.0  0
 0WG  CONST_12  C15  C16  C11  C10   180.00   0.0  0
 0WG  CONST_13  C14  C13  C12  C11     0.00   0.0  0
 0WG  CONST_14  C14  C15  C16  C11     0.00   0.0  0
 0WG  CONST_15  C15  C14  C13  C12     0.00   0.0  0
 0WG  CONST_17  C15  C16  C11  C12     0.00   0.0  0
 0WG  CONST_18  C16  C11  C12  C13     0.00   0.0  0
 0WG  CONST_19  C16  C15  C14  C13     0.00   0.0  0
 0WG  CONST_21  C19  C18  C10  C11     0.00   0.0  0
 0WG  CONST_22  C19  N21  C23  N2      0.00   0.0  0
 0WG  CONST_23  N21  C23  N2   C3      0.00   0.0  0
 0WG  CONST_24  C23  N21  C19  C18     0.00   0.0  0
 0WG  CONST_25  N6   C5   N4   C3    180.00   0.0  0
 0WG  CONST_26  C8   C7   C5   N4    180.00   0.0  0
 0WG  CONST_27  C10  C7   C5   N6    180.00   0.0  0
 0WG  CONST_28  C18  C10  C7   C8    180.00   0.0  0
 0WG  CONST_29  C11  C10  C7   C8      0.00   0.0  0
 0WG  CONST_30  BR1  C16  C11  C10     0.00   0.0  0
 0WG  CONST_31  BR1  C16  C11  C12   180.00   0.0  0
 0WG  CONST_32  BR1  C16  C15  C14   180.00   0.0  0
 0WG  CONST_33  N21  C23  N2   C1    180.00   0.0  0
 0WG  CONST_34  C22  N21  C23  N2    180.00   0.0  0
 0WG  CONST_35  O24  C23  N2   C3    180.00   0.0  0
 0WG  CONST_36  C22  N21  C19  C18   180.00   0.0  0
 0WG  CONST_37  O24  C23  N21  C19   180.00   0.0  0
 0WG  CONST_38  C23  N21  C19  O20   180.00   0.0  0
 0WG  CONST_39  H11  C12  C11  C10     0.00   0.0  0
 0WG  CONST_40  H12  C13  C12  C11   180.00   0.0  0
 0WG  CONST_41  H14  C15  C16  C11   180.00   0.0  0
 0WG  CONST_42  H13  C14  C13  C12   180.00   0.0  0
 0WG  CONST_43  O24  C23  N2   C1      0.00   0.0  0
 0WG  CONST_44  C22  N21  C19  O20     0.00   0.0  0
 0WG  CONST_45  O24  C23  N21  C22     0.00   0.0  0
 0WG  CONST_46  H4   N6   C5   N4      0.00   0.0  0
 0WG  Var_01    N9   C8   C7   C5     57.66  30.0  2
 0WG  Var_02    H1   C1   N2   C3     96.47  30.0  3
 0WG  Var_03    H15  C22  N21  C19  -175.78  30.0  3
 0WG  Var_04    H8   N9   C8   C7     68.59  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
 0WG  plan-1  C10  0.020
 0WG  plan-1  C11  0.020
 0WG  plan-1  C12  0.020
 0WG  plan-1  C13  0.020
 0WG  plan-1  C14  0.020
 0WG  plan-1  C15  0.020
 0WG  plan-1  C16  0.020
 0WG  plan-1  BR1  0.020
 0WG  plan-1  H11  0.020
 0WG  plan-1  H12  0.020
 0WG  plan-1  H13  0.020
 0WG  plan-1  H14  0.020
 0WG  plan-2  C1   0.020
 0WG  plan-2  N2   0.020
 0WG  plan-2  C3   0.020
 0WG  plan-2  N4   0.020
 0WG  plan-2  C5   0.020
 0WG  plan-2  N6   0.020
 0WG  plan-2  C7   0.020
 0WG  plan-2  C8   0.020
 0WG  plan-2  C10  0.020
 0WG  plan-2  C11  0.020
 0WG  plan-2  C18  0.020
 0WG  plan-2  C19  0.020
 0WG  plan-2  O20  0.020
 0WG  plan-2  N21  0.020
 0WG  plan-2  C22  0.020
 0WG  plan-2  C23  0.020
 0WG  plan-2  O24  0.020
 0WG  plan-3  C5   0.020
 0WG  plan-3  N6   0.020
 0WG  plan-3  H4   0.020
 0WG  plan-3  H5   0.020

