# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 07:03:18 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 2-amino-N-(furan-2-ylmethyl)-4-oxo-3,4-dihydropteridine-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2nc(cnc2C(=O)N1)C(=O)NCc3occc3
#
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
 JP3  JP3  2-amino-N-(furan-2-ylmethyl)-4-oxo-3,4-dihydropteridine-7-carboxamide  ligand  31  21  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JP3
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
 JP3  C1    C  CR6   0   0.706  -3.5245   1.8711   0.5083
 JP3  N1    N  NH2   0  -0.819  -4.0067   2.9926   1.0321
 JP3  O1    O  O     0  -0.428  -4.8590  -0.6767  -1.5354
 JP3  C2    C  CR6   0   0.548  -4.0567  -0.0560  -0.8741
 JP3  N2    N  NR16  0  -0.715  -4.3879   1.1255  -0.2479
 JP3  O2    O  O     0  -0.468   1.7358  -2.5042  -0.4377
 JP3  C3    C  CR66  0  -0.029  -2.6632  -0.4465  -0.6403
 JP3  N3    N  N     0  -0.506  -2.2815   1.5287   0.7230
 JP3  O3    O  O     0  -0.405   4.3001  -0.1563  -0.8704
 JP3  C4    C  CR66  0   0.404  -1.8520   0.3826   0.1599
 JP3  N4    N  N     0  -0.427  -0.5816   0.0225   0.3818
 JP3  C5    C  CR6   0   0.092  -0.1497  -1.0917  -0.1646
 JP3  N5    N  N     0  -0.348  -2.2206  -1.5683  -1.1883
 JP3  C6    C  CR16  0  -0.104  -0.9680  -1.9025  -0.9617
 JP3  N6    N  NH1   0  -0.631   1.9459  -0.6853   0.9060
 JP3  C7    C  C     0   0.540   1.2791  -1.4986   0.0830
 JP3  C8    C  CH2   0  -0.407   3.3391  -0.8581   1.2503
 JP3  C9    C  CR5   0   0.364   4.2398   0.0283   0.4661
 JP3  C10   C  CR15  0  -0.377   5.0548   1.0487   0.8269
 JP3  C11   C  CR15  0  -0.334   5.6618   1.5229  -0.3771
 JP3  C12   C  CR15  0  -0.007   5.1616   0.7543  -1.3712
 JP3  HN1   H  HNH2  0   0.425  -4.9616   3.2842   0.9123
 JP3  HN1A  H  HNH2  0   0.422  -3.4105   3.5561   1.6138
 JP3  HN2   H  HNR6  0   0.435  -5.3409   1.4472  -0.3657
 JP3  H6    H  HCR6  0   0.283  -0.5976  -2.8165  -1.4047
 JP3  HN6   H  HNH1  0   0.413   1.4639   0.1344   1.2456
 JP3  H8    H  HCH2  0   0.290   3.4708  -0.6294   2.3075
 JP3  H8A   H  HCH2  0   0.276   3.6054  -1.9070   1.1138
 JP3  H10   H  HCR5  0   0.264   5.2028   1.4222   1.8275
 JP3  H11   H  HCR5  0   0.264   6.3696   2.3287  -0.4823
 JP3  H12   H  HCR5  0   0.278   5.3179   0.7373  -2.4376

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
 JP3  N3   C1    double    1.307  0.020  1.307
 JP3  C1   N2    single    1.369  0.020  1.369
 JP3  C1   N1    single    1.328  0.020  1.328
 JP3  N1   HN1   single    0.860  0.020  1.020
 JP3  N1   HN1A  single    0.860  0.020  1.020
 JP3  C2   O1    double    1.211  0.020  1.211
 JP3  C3   C2    single    1.466  0.020  1.466
 JP3  C2   N2    single    1.378  0.020  1.378
 JP3  N2   HN2   single    0.860  0.020  1.020
 JP3  O2   C7    double    1.221  0.020  1.221
 JP3  N5   C3    aromatic  1.325  0.020  1.325
 JP3  C4   C3    aromatic  1.409  0.020  1.409
 JP3  C4   N3    single    1.347  0.020  1.347
 JP3  C9   O3    aromatic  1.351  0.020  1.351
 JP3  C12  O3    aromatic  1.350  0.020  1.350
 JP3  N4   C4    aromatic  1.339  0.020  1.339
 JP3  C5   N4    aromatic  1.314  0.020  1.314
 JP3  C7   C5    single    1.506  0.020  1.506
 JP3  C5   C6    aromatic  1.401  0.020  1.401
 JP3  C6   N5    aromatic  1.316  0.020  1.316
 JP3  C6   H6    single    0.930  0.020  1.080
 JP3  C8   N6    single    1.445  0.020  1.445
 JP3  N6   C7    single    1.335  0.020  1.335
 JP3  N6   HN6   single    0.860  0.020  1.020
 JP3  C8   C9    single    1.487  0.020  1.487
 JP3  C8   H8    single    0.970  0.020  1.090
 JP3  C8   H8A   single    0.970  0.020  1.090
 JP3  C10  C9    aromatic  1.355  0.020  1.355
 JP3  C10  C11   aromatic  1.429  0.020  1.429
 JP3  C10  H10   single    0.930  0.020  1.080
 JP3  C11  C12   aromatic  1.352  0.020  1.352
 JP3  C11  H11   single    0.930  0.020  1.080
 JP3  C12  H12   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
 JP3  N3    C1   N2   123.22  3.000
 JP3  N2    C1   N1   116.67  3.000
 JP3  N3    C1   N1   120.11  3.000
 JP3  HN1A  N1   HN1  118.00  3.000
 JP3  HN1A  N1   C1   119.07  3.000
 JP3  HN1   N1   C1   122.86  3.000
 JP3  C3    C2   N2   112.61  3.000
 JP3  N2    C2   O1   121.91  3.000
 JP3  C3    C2   O1   125.48  3.000
 JP3  HN2   N2   C2   116.47  3.000
 JP3  HN2   N2   C1   119.00  3.000
 JP3  C2    N2   C1   124.52  3.000
 JP3  N5    C3   C4   122.74  3.000
 JP3  C4    C3   C2   118.76  3.000
 JP3  N5    C3   C2   118.50  3.000
 JP3  C4    N3   C1   117.22  3.000
 JP3  C12   O3   C9   107.66  3.000
 JP3  N4    C4   N3   117.52  3.000
 JP3  N4    C4   C3   118.82  3.000
 JP3  N3    C4   C3   123.66  3.000
 JP3  C5    N4   C4   118.10  3.000
 JP3  C7    C5   C6   119.42  3.000
 JP3  C6    C5   N4   122.37  3.000
 JP3  C7    C5   N4   118.21  3.000
 JP3  C6    N5   C3   117.50  3.000
 JP3  H6    C6   N5   118.04  3.000
 JP3  H6    C6   C5   121.49  3.000
 JP3  N5    C6   C5   120.46  3.000
 JP3  HN6   N6   C8   118.49  3.000
 JP3  HN6   N6   C7   117.60  3.000
 JP3  C8    N6   C7   123.73  3.000
 JP3  N6    C7   C5   114.23  3.000
 JP3  N6    C7   O2   125.28  3.000
 JP3  C5    C7   O2   120.48  3.000
 JP3  H8A   C8   H8   107.08  3.000
 JP3  H8A   C8   C9   111.06  3.000
 JP3  H8    C8   C9   108.26  3.000
 JP3  H8A   C8   N6   108.69  3.000
 JP3  H8    C8   N6   108.81  3.000
 JP3  C9    C8   N6   112.76  3.000
 JP3  C10   C9   C8   132.28  3.000
 JP3  C10   C9   O3   109.85  3.000
 JP3  C8    C9   O3   117.86  3.000
 JP3  H10   C10  C11  127.48  3.000
 JP3  H10   C10  C9   126.20  3.000
 JP3  C11   C10  C9   106.32  3.000
 JP3  H11   C11  C12  126.59  3.000
 JP3  H11   C11  C10  127.53  3.000
 JP3  C12   C11  C10  105.88  3.000
 JP3  H12   C12  C11  133.05  3.000
 JP3  H12   C12  O3   116.67  3.000
 JP3  C11   C12  O3   110.29  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
 JP3  CONST_01  C5    C6   N5   C3      0.00   0.0  0
 JP3  CONST_02  C5    N4   C4   C3      0.00   0.0  0
 JP3  CONST_03  C11   C10  C9   O3      0.00   0.0  0
 JP3  CONST_04  C10   C11  C12  O3      0.00   0.0  0
 JP3  CONST_05  C6    N5   C3   C4      0.00   0.0  0
 JP3  CONST_06  C6    C5   N4   C4      0.00   0.0  0
 JP3  CONST_07  N5    C3   C4   N4      0.00   0.0  0
 JP3  CONST_08  N5    C6   C5   N4      0.00   0.0  0
 JP3  CONST_09  C11   C12  O3   C9      0.00   0.0  0
 JP3  CONST_10  C12   C11  C10  C9      0.00   0.0  0
 JP3  CONST_11  C12   O3   C9   C10     0.00   0.0  0
 JP3  CONST_12  C3    C2   N2   C1      0.00   0.0  0
 JP3  CONST_13  N3    C1   N2   C2      0.00   0.0  0
 JP3  CONST_14  C4    N3   C1   N2      0.00   0.0  0
 JP3  CONST_15  C7    C5   N4   C4    180.00   0.0  0
 JP3  CONST_16  C7    C5   C6   N5    180.00   0.0  0
 JP3  CONST_17  C12   O3   C9   C8    180.00   0.0  0
 JP3  CONST_18  C11   C10  C9   C8    180.00   0.0  0
 JP3  CONST_19  O1    C2   N2   C1    180.00   0.0  0
 JP3  CONST_20  C4    N3   C1   N1    180.00   0.0  0
 JP3  CONST_21  C2    N2   C1   N1    180.00   0.0  0
 JP3  CONST_22  H6    C6   N5   C3    180.00   0.0  0
 JP3  CONST_23  H10   C10  C9   O3    180.00   0.0  0
 JP3  CONST_24  H11   C11  C12  O3    180.00   0.0  0
 JP3  CONST_25  H12   C12  O3   C9    180.00   0.0  0
 JP3  CONST_26  HN2   N2   C2   C3    180.00   0.0  0
 JP3  CONST_27  HN1   N1   C1   N2      0.00   0.0  0
 JP3  CONST_28  HN1A  N1   C1   N2    180.00   0.0  0
 JP3  CONST_29  C8    N6   C7   C5    180.00   0.0  0
 JP3  CONST_30  HN6   N6   C7   C5      0.00   0.0  0
 JP3  CONST_31  C8    N6   C7   O2      0.00   0.0  0
 JP3  Var_01    N4    C5   C7   O2   -177.74  30.0  2
 JP3  Var_02    N6    C8   C9   O3    -64.02  30.0  2
 JP3  Var_03    C9    C8   N6   C7     99.42  30.0  1

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
 JP3  plan-1  O3    0.020
 JP3  plan-1  C8    0.020
 JP3  plan-1  C9    0.020
 JP3  plan-1  C10   0.020
 JP3  plan-1  C11   0.020
 JP3  plan-1  C12   0.020
 JP3  plan-1  H10   0.020
 JP3  plan-1  H11   0.020
 JP3  plan-1  H12   0.020
 JP3  plan-2  C1    0.020
 JP3  plan-2  N1    0.020
 JP3  plan-2  O1    0.020
 JP3  plan-2  C2    0.020
 JP3  plan-2  N2    0.020
 JP3  plan-2  C3    0.020
 JP3  plan-2  N3    0.020
 JP3  plan-2  C4    0.020
 JP3  plan-2  N4    0.020
 JP3  plan-2  C5    0.020
 JP3  plan-2  N5    0.020
 JP3  plan-2  C6    0.020
 JP3  plan-2  C7    0.020
 JP3  plan-2  HN1   0.020
 JP3  plan-2  HN1A  0.020
 JP3  plan-2  HN2   0.020
 JP3  plan-2  H6    0.020
 JP3  plan-3  O2    0.020
 JP3  plan-3  C5    0.020
 JP3  plan-3  N6    0.020
 JP3  plan-3  C7    0.020
 JP3  plan-3  C8    0.020
 JP3  plan-3  HN6   0.020

