# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 20:15:56 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 2-{(carboxymethyl)[(2-oxo-1,2-dihydro-1,8-naphthyridin-3-yl)acetyl]amino}ethanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+]CCN(CC(O)=O)C(=O)CC1=Cc2cccnc2NC1=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
 OPN  OPN  2-{(carboxymethyl)[(2-oxo-1,2-dihydro-1,8-naphthyridin-3-yl)acetyl]amino}ethanaminium  ligand  39  22  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_OPN
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
 OPN  N1'   N  NT3   1  -0.777  -3.8116  -3.4552   0.8024
 OPN  C2'   C  CH2   0  -0.310  -3.1674  -2.3552   0.0455
 OPN  C3'   C  CH2   0  -0.370  -3.2758  -1.0368   0.7994
 OPN  N4'   N  NT    0  -0.457  -2.6737   0.0233   0.0236
 OPN  C5'   C  CH2   0  -0.452  -3.5011   0.7219  -0.9244
 OPN  C'    C  C     0   0.551  -3.9447   2.0702  -0.3970
 OPN  O1'   O  O     0  -0.432  -3.8158   2.4345   0.7412
 OPN  C7'   C  C     0   0.596  -1.3882   0.4329   0.1466
 OPN  O7'   O  O     0  -0.475  -0.9649   1.3684  -0.5104
 OPN  C8'   C  CH2   0  -0.678  -0.4890  -0.2757   1.1449
 OPN  C1    C  CR6   0  -0.055   0.9261  -0.2330   0.6758
 OPN  C6    C  CR16  0  -0.235   1.9082   0.4378   1.3075
 OPN  C2    C  CR6   0   0.557   1.2065  -0.9875  -0.5441
 OPN  O2    O  OC    0  -0.468   0.3489  -1.6156  -1.1510
 OPN  N3    N  NR16  0  -0.717   2.5041  -0.9496  -0.9764
 OPN  C4    C  CR66  0   0.485   3.5252  -0.2768  -0.3648
 OPN  C5    C  CR66  0  -0.039   3.2501   0.4403   0.8091
 OPN  C7    C  CR16  0  -0.190   4.3146   1.1175   1.4039
 OPN  C8    C  CR16  0  -0.337   5.5647   1.0525   0.8233
 OPN  C9    C  CR16  0  -0.054   5.7125   0.3046  -0.3430
 OPN  N10   N  N     0  -0.427   4.7228  -0.3477  -0.9303
 OPN  OXT   O  OH1   0  -0.590  -4.5234   2.7821  -1.3522
 OPN  H1'1  H  HNT3  0   0.474  -4.7947  -3.2665   0.9978
 OPN  H1'2  H  HNT3  0   0.474  -3.3535  -3.6328   1.6961
 OPN  H1'3  H  HNT3  0   0.485  -3.7798  -4.3289   0.2775
 OPN  H2'1  H  HCH2  0   0.302  -2.1295  -2.6365  -0.1203
 OPN  H2'2  H  HCH2  0   0.305  -3.6670  -2.2980  -0.9193
 OPN  H3'1  H  HCH2  0   0.303  -4.3227  -0.7868   0.9779
 OPN  H3'2  H  HCH2  0   0.298  -2.8132  -1.1081   1.7829
 OPN  H5'1  H  HCH2  0   0.306  -2.9911   0.8481  -1.8800
 OPN  H5'2  H  HCH2  0   0.313  -4.3953   0.1290  -1.1318
 OPN  H8'1  H  HCH2  0   0.314  -0.5839   0.2397   2.1047
 OPN  H8'2  H  HCH2  0   0.284  -0.7842  -1.3111   1.3166
 OPN  H6    H  HCR6  0   0.279   1.6931   0.9928   2.2135
 OPN  HN3   H  HNR6  0   0.416   2.7304  -1.4592  -1.8218
 OPN  H7    H  HCR6  0   0.281   4.1501   1.6860   2.3104
 OPN  H8    H  HCR6  0   0.277   6.4132   1.5659   1.2517
 OPN  H9    H  HCR6  0   0.276   6.6821   0.2329  -0.8219
 OPN  HXT   H  HOH1  0   0.486  -4.8392   3.6278  -0.9997

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
 OPN  N1'  C2'   single    1.483  0.020  1.483
 OPN  N1'  H1'1  single    0.890  0.020  1.040
 OPN  N1'  H1'2  single    0.890  0.020  1.040
 OPN  N1'  H1'3  single    0.890  0.020  1.040
 OPN  C2'  C3'   single    1.523  0.020  1.523
 OPN  C2'  H2'1  single    0.970  0.020  1.090
 OPN  C2'  H2'2  single    0.970  0.020  1.090
 OPN  C3'  N4'   single    1.445  0.020  1.445
 OPN  C3'  H3'1  single    0.970  0.020  1.090
 OPN  C3'  H3'2  single    0.970  0.020  1.090
 OPN  N4'  C5'   single    1.439  0.020  1.439
 OPN  N4'  C7'   single    1.355  0.020  1.355
 OPN  C5'  C'    single    1.514  0.020  1.514
 OPN  C5'  H5'1  single    0.970  0.020  1.090
 OPN  C5'  H5'2  single    0.970  0.020  1.090
 OPN  C'   O1'   double    1.202  0.020  1.202
 OPN  C'   OXT   single    1.324  0.020  1.324
 OPN  C7'  O7'   double    1.219  0.020  1.219
 OPN  C7'  C8'   single    1.519  0.020  1.519
 OPN  C8'  C1    single    1.491  0.020  1.491
 OPN  C8'  H8'1  single    0.970  0.020  1.090
 OPN  C8'  H8'2  single    0.970  0.020  1.090
 OPN  C1   C6    aromatic  1.347  0.020  1.347
 OPN  C1   C2    aromatic  1.461  0.020  1.461
 OPN  C6   C5    aromatic  1.431  0.020  1.431
 OPN  C6   H6    single    0.930  0.020  1.080
 OPN  C2   O2    double    1.224  0.020  1.224
 OPN  C2   N3    aromatic  1.368  0.020  1.368
 OPN  N3   C4    aromatic  1.367  0.020  1.367
 OPN  N3   HN3   single    0.860  0.020  1.020
 OPN  C4   C5    aromatic  1.403  0.020  1.403
 OPN  C4   N10   aromatic  1.326  0.020  1.326
 OPN  C5   C7    aromatic  1.395  0.020  1.395
 OPN  C7   C8    aromatic  1.380  0.020  1.380
 OPN  C7   H7    single    0.930  0.020  1.080
 OPN  C8   C9    aromatic  1.393  0.020  1.393
 OPN  C8   H8    single    0.930  0.020  1.080
 OPN  C9   N10   aromatic  1.323  0.020  1.323
 OPN  C9   H9    single    0.930  0.020  1.080
 OPN  OXT  HXT   single    0.850  0.020  0.980

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
 OPN  H1'3  N1'  H1'2  106.73  3.000
 OPN  H1'3  N1'  H1'1  106.69  3.000
 OPN  H1'2  N1'  H1'1  107.30  3.000
 OPN  H1'3  N1'  C2'   111.06  3.000
 OPN  H1'2  N1'  C2'   112.42  3.000
 OPN  H1'1  N1'  C2'   112.29  3.000
 OPN  H2'2  C2'  H2'1  108.45  3.000
 OPN  H2'2  C2'  C3'   111.15  3.000
 OPN  H2'1  C2'  C3'   111.54  3.000
 OPN  H2'2  C2'  N1'   107.00  3.000
 OPN  H2'1  C2'  N1'   107.49  3.000
 OPN  C3'   C2'  N1'   111.03  3.000
 OPN  H3'2  C3'  H3'1  105.95  3.000
 OPN  H3'2  C3'  N4'   110.84  3.000
 OPN  H3'1  C3'  N4'   108.63  3.000
 OPN  H3'2  C3'  C2'   111.11  3.000
 OPN  H3'1  C3'  C2'   110.35  3.000
 OPN  N4'   C3'  C2'   109.86  3.000
 OPN  C7'   N4'  C5'   117.29  3.000
 OPN  C7'   N4'  C3'   124.64  3.000
 OPN  C5'   N4'  C3'   118.05  3.000
 OPN  H5'2  C5'  H5'1  106.21  3.000
 OPN  H5'2  C5'  C'    108.03  3.000
 OPN  H5'1  C5'  C'    109.83  3.000
 OPN  H5'2  C5'  N4'   109.39  3.000
 OPN  H5'1  C5'  N4'   111.38  3.000
 OPN  C'    C5'  N4'   111.79  3.000
 OPN  OXT   C'   O1'   124.53  3.000
 OPN  OXT   C'   C5'   110.82  3.000
 OPN  O1'   C'   C5'   124.63  3.000
 OPN  C8'   C7'  O7'   120.45  3.000
 OPN  C8'   C7'  N4'   118.71  3.000
 OPN  O7'   C7'  N4'   120.83  3.000
 OPN  H8'2  C8'  H8'1  106.60  3.000
 OPN  H8'2  C8'  C1    109.49  3.000
 OPN  H8'1  C8'  C1    110.17  3.000
 OPN  H8'2  C8'  C7'   112.72  3.000
 OPN  H8'1  C8'  C7'   107.80  3.000
 OPN  C1    C8'  C7'   109.98  3.000
 OPN  C2    C1   C6    120.58  3.000
 OPN  C2    C1   C8'   115.45  3.000
 OPN  C6    C1   C8'   123.96  3.000
 OPN  H6    C6   C5    118.43  3.000
 OPN  H6    C6   C1    120.16  3.000
 OPN  C5    C6   C1    121.41  3.000
 OPN  N3    C2   O2    121.47  3.000
 OPN  N3    C2   C1    115.55  3.000
 OPN  O2    C2   C1    122.98  3.000
 OPN  HN3   N3   C4    117.01  3.000
 OPN  HN3   N3   C2    117.50  3.000
 OPN  C4    N3   C2    125.49  3.000
 OPN  N10   C4   C5    124.14  3.000
 OPN  N10   C4   N3    117.22  3.000
 OPN  C5    C4   N3    118.64  3.000
 OPN  C7    C5   C4    117.08  3.000
 OPN  C7    C5   C6    124.60  3.000
 OPN  C4    C5   C6    118.31  3.000
 OPN  H7    C7   C8    120.98  3.000
 OPN  H7    C7   C5    119.73  3.000
 OPN  C8    C7   C5    119.29  3.000
 OPN  H8    C8   C9    120.24  3.000
 OPN  H8    C8   C7    121.49  3.000
 OPN  C9    C8   C7    118.27  3.000
 OPN  H9    C9   N10   116.14  3.000
 OPN  H9    C9   C8    120.02  3.000
 OPN  N10   C9   C8    123.84  3.000
 OPN  C9    N10  C4    117.38  3.000
 OPN  HXT   OXT  C'    110.43  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
 OPN  CONST_01  C4    C5   C6   C1      0.00   0.0  0
 OPN  CONST_02  C7    C5   C6   C1    180.00   0.0  0
 OPN  CONST_03  C4    N3   C2   C1      0.00   0.0  0
 OPN  CONST_04  N3    C2   C1   C6      0.00   0.0  0
 OPN  CONST_05  N3    C4   C5   C6      0.00   0.0  0
 OPN  CONST_06  N10   C4   C5   C6    180.00   0.0  0
 OPN  CONST_07  C8    C7   C5   C6    180.00   0.0  0
 OPN  CONST_08  C5    C6   C1   C2      0.00   0.0  0
 OPN  CONST_09  C5    C4   N3   C2      0.00   0.0  0
 OPN  CONST_10  N10   C4   N3   C2    180.00   0.0  0
 OPN  CONST_11  C7    C5   C4   N3    180.00   0.0  0
 OPN  CONST_12  C9    N10  C4   N3    180.00   0.0  0
 OPN  CONST_13  C8    C7   C5   C4      0.00   0.0  0
 OPN  CONST_14  C8    C9   N10  C4      0.00   0.0  0
 OPN  CONST_15  C9    N10  C4   C5      0.00   0.0  0
 OPN  CONST_16  C9    C8   C7   C5      0.00   0.0  0
 OPN  CONST_17  N10   C4   C5   C7      0.00   0.0  0
 OPN  CONST_18  N10   C9   C8   C7      0.00   0.0  0
 OPN  CONST_19  C5    C6   C1   C8'   180.00   0.0  0
 OPN  CONST_20  N3    C2   C1   C8'   180.00   0.0  0
 OPN  CONST_21  O2    C2   C1   C6    180.00   0.0  0
 OPN  CONST_22  C4    N3   C2   O2    180.00   0.0  0
 OPN  CONST_23  HN3   N3   C2   C1    180.00   0.0  0
 OPN  CONST_24  H7    C7   C5   C6      0.00   0.0  0
 OPN  CONST_25  H6    C6   C1   C2    180.00   0.0  0
 OPN  CONST_26  H9    C9   N10  C4    180.00   0.0  0
 OPN  CONST_27  H8    C8   C7   C5    180.00   0.0  0
 OPN  CONST_28  O7'   C7'  N4'  C3'   180.00   0.0  0
 OPN  CONST_29  C8'   C7'  N4'  C3'     0.00   0.0  0
 OPN  CONST_30  O7'   C7'  N4'  C5'     0.00   0.0  0
 OPN  CONST_31  C8'   C7'  N4'  C5'   180.00   0.0  0
 OPN  CONST_32  HXT   OXT  C'   C5'   180.00   0.0  0
 OPN  Var_01    C6    C1   C8'  C7'   113.98  30.0  2
 OPN  Var_02    C1    C8'  C7'  N4'   150.34  30.0  3
 OPN  Var_03    N4'   C3'  C2'  N1'  -178.42  30.0  3
 OPN  Var_04    C5'   N4'  C3'  C2'    88.30  30.0  3
 OPN  Var_05    C'    C5'  N4'  C3'   101.95  30.0  3
 OPN  Var_06    O1'   C'   C5'  N4'   -11.31  30.0  3
 OPN  Var_07    H1'1  N1'  C2'  C3'    57.83  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
 OPN  plan-1  C8'  0.020
 OPN  plan-1  C1   0.020
 OPN  plan-1  C6   0.020
 OPN  plan-1  C2   0.020
 OPN  plan-1  O2   0.020
 OPN  plan-1  N3   0.020
 OPN  plan-1  C4   0.020
 OPN  plan-1  C5   0.020
 OPN  plan-1  C7   0.020
 OPN  plan-1  C8   0.020
 OPN  plan-1  C9   0.020
 OPN  plan-1  N10  0.020
 OPN  plan-1  H6   0.020
 OPN  plan-1  HN3  0.020
 OPN  plan-1  H7   0.020
 OPN  plan-1  H8   0.020
 OPN  plan-1  H9   0.020
 OPN  plan-2  C3'  0.020
 OPN  plan-2  N4'  0.020
 OPN  plan-2  C5'  0.020
 OPN  plan-2  C7'  0.020
 OPN  plan-2  O7'  0.020
 OPN  plan-2  C8'  0.020
 OPN  plan-3  C5'  0.020
 OPN  plan-3  C'   0.020
 OPN  plan-3  O1'  0.020
 OPN  plan-3  OXT  0.020
 OPN  plan-3  HXT  0.020

