# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 09:38:50 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  38  22  .  2022-07-22  2022-07-26
;
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  -4.0921  -3.3489   1.0100
 OPN  C2'   C  CH2    0  -0.308  -3.3846  -2.4038   0.1113
 OPN  C3'   C  CH2    0  -0.358  -3.2581  -1.0308   0.7546
 OPN  N4'   N  NT     0  -0.436  -2.6306  -0.1155  -0.1673
 OPN  C5'   C  CH2    0  -0.470  -3.5177   0.6536  -1.0127
 OPN  C'    C  C      0   0.416  -4.0357   1.9481  -0.3459
 OPN  O1'   O  O      0  -0.592  -3.7081   2.1541   0.8338
 OPN  C7'   C  C      0   0.586  -1.3349   0.2490  -0.0895
 OPN  O7'   O  O      0  -0.491  -0.8695   1.1369  -0.7874
 OPN  C8'   C  CH2    0  -0.691  -0.4459  -0.4851   0.9060
 OPN  C1    C  CR6    0  -0.053   0.9858  -0.3460   0.5152
 OPN  C6    C  CR16   0  -0.235   1.8881   0.3632   1.2201
 OPN  C2    C  CR6    0   0.546   1.3806  -1.0366  -0.7121
 OPN  O2    O  OC     0  -0.466   0.6080  -1.7070  -1.3819
 OPN  N3    N  NR16   0  -0.718   2.6942  -0.8918  -1.0734
 OPN  C4    C  CR66   0   0.483   3.6338  -0.1748  -0.3873
 OPN  C5    C  CR66   0  -0.036   3.2505   0.4765   0.7945
 OPN  C7    C  CR16   0  -0.192   4.2335   1.2011   1.4678
 OPN  C8    C  CR16   0  -0.337   5.5131   1.2435   0.9522
 OPN  C9    C  CR16   0  -0.055   5.7719   0.5520  -0.2291
 OPN  N10   N  N      0  -0.428   4.8608  -0.1433  -0.8902
 OPN  OXT   O  OC    -1  -0.620  -4.7557   2.6560  -1.0761
 OPN  H1'1  H  HNT3   0   0.473  -5.0265  -3.0200   1.2534
 OPN  H1'2  H  HNT3   0   0.473  -3.5886  -3.5035   1.8832
 OPN  H1'3  H  HNT3   0   0.483  -4.2051  -4.2614   0.5697
 OPN  H2'1  H  HCH2   0   0.297  -2.4111  -2.8364  -0.1097
 OPN  H2'2  H  HCH2   0   0.302  -3.9587  -2.3553  -0.8117
 OPN  H3'1  H  HCH2   0   0.291  -4.2448  -0.6422   1.0131
 OPN  H3'2  H  HCH2   0   0.287  -2.7075  -1.0949   1.6925
 OPN  H5'1  H  HCH2   0   0.261  -3.0170   0.8960  -1.9497
 OPN  H5'2  H  HCH2   0   0.254  -4.3727   0.0259  -1.2800
 OPN  H8'1  H  HCH2   0   0.305  -0.6057  -0.0537   1.8985
 OPN  H8'2  H  HCH2   0   0.284  -0.7058  -1.5429   0.9822
 OPN  H6    H  HCR6   0   0.277   1.5909   0.8683   2.1322
 OPN  HN3   H  HNR6   0   0.414   2.9983  -1.3536  -1.9217
 OPN  H7    H  HCR6   0   0.280   3.9847   1.7213   2.3843
 OPN  H8    H  HCR6   0   0.276   6.3008   1.7968   1.4425
 OPN  H9    H  HCR6   0   0.275   6.7675   0.5638  -0.6572

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    1.484  0.020  1.484
 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    1.522  0.020  1.522
 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    1.443  0.020  1.443
 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    1.447  0.020  1.447
 OPN  N4'  C7'   single    1.348  0.020  1.348
 OPN  C5'  C'    single    1.546  0.020  1.546
 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'   deloc     1.242  0.020  1.242
 OPN  C'   OXT   deloc     1.246  0.020  1.246
 OPN  C7'  O7'   double    1.221  0.020  1.221
 OPN  C7'  C8'   single    1.523  0.020  1.523
 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  1.463  0.020  1.463
 OPN  C6   C5    aromatic  1.432  0.020  1.432
 OPN  C6   H6    single    0.930  0.020  1.080
 OPN  C2   O2    double    1.223  0.020  1.223
 OPN  C2   N3    aromatic  1.370  0.020  1.370
 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

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  106.79  3.000
 OPN  H1'3  N1'  H1'1  106.87  3.000
 OPN  H1'2  N1'  H1'1  107.26  3.000
 OPN  H1'3  N1'  C2'   111.19  3.000
 OPN  H1'2  N1'  C2'   112.32  3.000
 OPN  H1'1  N1'  C2'   112.08  3.000
 OPN  H2'2  C2'  H2'1  108.52  3.000
 OPN  H2'2  C2'  C3'   111.24  3.000
 OPN  H2'1  C2'  C3'   111.73  3.000
 OPN  H2'2  C2'  N1'   106.90  3.000
 OPN  H2'1  C2'  N1'   107.25  3.000
 OPN  C3'   C2'  N1'   111.00  3.000
 OPN  H3'2  C3'  H3'1  105.89  3.000
 OPN  H3'2  C3'  N4'   111.57  3.000
 OPN  H3'1  C3'  N4'   108.58  3.000
 OPN  H3'2  C3'  C2'   110.66  3.000
 OPN  H3'1  C3'  C2'   110.26  3.000
 OPN  N4'   C3'  C2'   109.78  3.000
 OPN  C7'   N4'  C5'   118.64  3.000
 OPN  C7'   N4'  C3'   123.55  3.000
 OPN  C5'   N4'  C3'   116.35  3.000
 OPN  H5'2  C5'  H5'1  106.06  3.000
 OPN  H5'2  C5'  C'    108.91  3.000
 OPN  H5'1  C5'  C'    109.80  3.000
 OPN  H5'2  C5'  N4'   108.48  3.000
 OPN  H5'1  C5'  N4'   109.81  3.000
 OPN  C'    C5'  N4'   113.49  3.000
 OPN  OXT   C'   O1'   127.95  3.000
 OPN  OXT   C'   C5'   114.62  3.000
 OPN  O1'   C'   C5'   117.42  3.000
 OPN  C8'   C7'  O7'   120.09  3.000
 OPN  C8'   C7'  N4'   117.92  3.000
 OPN  O7'   C7'  N4'   121.99  3.000
 OPN  H8'2  C8'  H8'1  106.50  3.000
 OPN  H8'2  C8'  C1    109.71  3.000
 OPN  H8'1  C8'  C1    109.96  3.000
 OPN  H8'2  C8'  C7'   111.94  3.000
 OPN  H8'1  C8'  C7'   108.52  3.000
 OPN  C1    C8'  C7'   110.14  3.000
 OPN  C2    C1   C6    120.46  3.000
 OPN  C2    C1   C8'   115.80  3.000
 OPN  C6    C1   C8'   123.74  3.000
 OPN  H6    C6   C5    118.29  3.000
 OPN  H6    C6   C1    120.14  3.000
 OPN  C5    C6   C1    121.57  3.000
 OPN  N3    C2   O2    121.28  3.000
 OPN  N3    C2   C1    115.48  3.000
 OPN  O2    C2   C1    123.23  3.000
 OPN  HN3   N3   C4    116.97  3.000
 OPN  HN3   N3   C2    117.43  3.000
 OPN  C4    N3   C2    125.61  3.000
 OPN  N10   C4   C5    124.14  3.000
 OPN  N10   C4   N3    117.26  3.000
 OPN  C5    C4   N3    118.60  3.000
 OPN  C7    C5   C4    117.09  3.000
 OPN  C7    C5   C6    124.64  3.000
 OPN  C4    C5   C6    118.27  3.000
 OPN  H7    C7   C8    120.96  3.000
 OPN  H7    C7   C5    119.75  3.000
 OPN  C8    C7   C5    119.29  3.000
 OPN  H8    C8   C9    120.24  3.000
 OPN  H8    C8   C7    121.48  3.000
 OPN  C9    C8   C7    118.28  3.000
 OPN  H9    C9   N10   116.17  3.000
 OPN  H9    C9   C8    120.01  3.000
 OPN  N10   C9   C8    123.82  3.000
 OPN  C9    N10  C4    117.39  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  Var_01    C6    C1   C8'  C7'   111.65  30.0  2
 OPN  Var_02    C1    C8'  C7'  N4'   158.52  30.0  3
 OPN  Var_03    N4'   C3'  C2'  N1'  -177.00  30.0  3
 OPN  Var_04    C5'   N4'  C3'  C2'    92.14  30.0  3
 OPN  Var_05    C'    C5'  N4'  C3'    85.32  30.0  3
 OPN  Var_06    O1'   C'   C5'  N4'    -3.71  30.0  3
 OPN  Var_07    H1'1  N1'  C2'  C3'    58.62  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

