# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 11:58:36 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (1S)-1-methyl-7-(4-methylphenyl)-5-oxo-1,5-dihydro-1,6-naphthyridin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[NH+]1C=CC=C2C(=O)N=C(C=C12)c3ccc(C)cc3
#
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
 E9L  E9L  (1S)-1-methyl-7-(4-methylphenyl)-5-oxo-1,5-dihydro-1,6-naphthyridin-1-ium  ligand  34  19  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E9L
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
 E9L  C01   C  CH3   0  -0.723   6.1531  -0.4382  -0.1600
 E9L  C02   C  CR6   0   0.102   4.6676  -0.2565  -0.1366
 E9L  C03   C  CR16  0  -0.274   4.1005   0.9369   0.3180
 E9L  C04   C  CR16  0  -0.238   2.7319   1.1035   0.3644
 E9L  C05   C  CR6   0   0.047   1.8717   0.0733  -0.0345
 E9L  C06   C  CR16  0  -0.296   2.4362  -1.1206  -0.4905
 E9L  C07   C  CR16  0  -0.278   3.8108  -1.2755  -0.5452
 E9L  C08   C  CR6   0   0.270   0.4213   0.2830   0.0162
 E9L  C09   C  CR16  0  -0.382  -0.4629  -0.8690  -0.1035
 E9L  C10   C  CR6   0   0.454  -1.7794  -0.6424  -0.0964
 E9L  C11   C  CR6   0  -0.120  -2.3179   0.6791  -0.0044
 E9L  C12   C  C1    0  -0.179  -3.6340   0.8988  -0.2083
 E9L  C13   C  C1    0  -0.252  -4.5079  -0.1967  -0.5501
 E9L  C14   C  C1    0  -0.028  -4.0741  -1.4507  -0.5400
 E9L  N15   N  NT1   1  -0.699  -2.7192  -1.7631  -0.0937
 E9L  C16   C  CH3   0  -0.554  -2.8025  -2.3607   1.2951
 E9L  C17   C  CR6   0   0.450  -1.3538   1.7807   0.2350
 E9L  O18   O  O     0  -0.406  -1.7372   2.9136   0.4452
 E9L  N19   N  N     0  -0.483  -0.0086   1.4932   0.1871
 E9L  H01   H  HCH3  0   0.260   6.5199  -0.7116   0.8316
 E9L  H01A  H  HCH3  0   0.251   6.4503  -1.2284  -0.8477
 E9L  H01B  H  HCH3  0   0.252   6.6627   0.4806  -0.4489
 E9L  H03   H  HCR6  0   0.260   4.7435   1.7475   0.6388
 E9L  H04   H  HCR6  0   0.266   2.3169   2.0363   0.7194
 E9L  H06   H  HCR6  0   0.264   1.8200  -1.9399  -0.8349
 E9L  H07   H  HCR6  0   0.263   4.2224  -2.2062  -0.9150
 E9L  H09   H  HCR6  0   0.321  -0.0658  -1.8716  -0.1680
 E9L  H12   H  H     0   0.317  -4.0378   1.9010  -0.1646
 E9L  H13   H  H     0   0.323  -5.5315  -0.0009  -0.8326
 E9L  H14   H  H     0   0.364  -4.6570  -2.3259  -0.7828
 E9L  H15   H  HNT1  0   0.501  -2.3517  -2.4957  -0.7090
 E9L  H16   H  HCH3  0   0.312  -3.1690  -1.5956   1.9717
 E9L  H16A  H  HCH3  0   0.317  -3.4838  -3.2048   1.2582
 E9L  H16B  H  HCH3  0   0.315  -1.8078  -2.6886   1.5798

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
 E9L  C01  C02   single    1.497  0.020  1.497
 E9L  C02  C03   aromatic  1.397  0.020  1.397
 E9L  C02  C07   aromatic  1.393  0.020  1.393
 E9L  C03  C04   aromatic  1.379  0.020  1.379
 E9L  C04  C05   aromatic  1.400  0.020  1.400
 E9L  C05  C06   aromatic  1.397  0.020  1.397
 E9L  C05  C08   single    1.466  0.020  1.466
 E9L  C06  C07   aromatic  1.384  0.020  1.384
 E9L  C08  C09   single    1.457  0.020  1.457
 E9L  C08  N19   double    1.296  0.020  1.296
 E9L  C09  C10   double    1.336  0.020  1.336
 E9L  C10  C11   single    1.430  0.020  1.430
 E9L  C10  N15   single    1.463  0.020  1.463
 E9L  C11  C12   double    1.350  0.020  1.350
 E9L  C11  C17   single    1.483  0.020  1.483
 E9L  C12  C13   single    1.442  0.020  1.442
 E9L  C13  C14   double    1.327  0.020  1.327
 E9L  C14  N15   single    1.460  0.020  1.460
 E9L  N15  C16   single    1.514  0.020  1.514
 E9L  C17  O18   double    1.214  0.020  1.214
 E9L  C17  N19   single    1.376  0.020  1.376
 E9L  C01  H01   single    0.970  0.020  1.090
 E9L  C01  H01A  single    0.970  0.020  1.090
 E9L  C01  H01B  single    0.970  0.020  1.090
 E9L  C03  H03   single    0.930  0.020  1.080
 E9L  C04  H04   single    0.930  0.020  1.080
 E9L  C06  H06   single    0.930  0.020  1.080
 E9L  C07  H07   single    0.930  0.020  1.080
 E9L  C09  H09   single    0.930  0.020  1.080
 E9L  C12  H12   single    0.930  0.020  1.080
 E9L  C13  H13   single    0.930  0.020  1.080
 E9L  C14  H14   single    0.930  0.020  1.080
 E9L  N15  H15   single    0.890  0.020  1.040
 E9L  C16  H16   single    0.970  0.020  1.090
 E9L  C16  H16A  single    0.970  0.020  1.090
 E9L  C16  H16B  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
 E9L  H01B  C01  H01A  108.47  3.000
 E9L  H01B  C01  H01   107.14  3.000
 E9L  H01A  C01  H01   107.46  3.000
 E9L  H01B  C01  C02   111.47  3.000
 E9L  H01A  C01  C02   111.64  3.000
 E9L  H01   C01  C02   110.46  3.000
 E9L  C07   C02  C03   118.08  3.000
 E9L  C07   C02  C01   121.14  3.000
 E9L  C03   C02  C01   120.77  3.000
 E9L  H03   C03  C04   119.25  3.000
 E9L  H03   C03  C02   119.64  3.000
 E9L  C04   C03  C02   121.12  3.000
 E9L  H04   C04  C05   119.51  3.000
 E9L  H04   C04  C03   119.75  3.000
 E9L  C05   C04  C03   120.74  3.000
 E9L  C08   C05  C06   122.22  3.000
 E9L  C08   C05  C04   119.51  3.000
 E9L  C06   C05  C04   118.26  3.000
 E9L  H06   C06  C07   117.93  3.000
 E9L  H06   C06  C05   121.40  3.000
 E9L  C07   C06  C05   120.64  3.000
 E9L  H07   C07  C06   119.15  3.000
 E9L  H07   C07  C02   119.69  3.000
 E9L  C06   C07  C02   121.16  3.000
 E9L  N19   C08  C09   123.22  3.000
 E9L  N19   C08  C05   117.80  3.000
 E9L  C09   C08  C05   118.97  3.000
 E9L  H09   C09  C10   121.33  3.000
 E9L  H09   C09  C08   121.04  3.000
 E9L  C10   C09  C08   117.61  3.000
 E9L  N15   C10  C11   117.78  3.000
 E9L  N15   C10  C09   120.21  3.000
 E9L  C11   C10  C09   121.88  3.000
 E9L  C17   C11  C12   122.50  3.000
 E9L  C17   C11  C10   116.87  3.000
 E9L  C12   C11  C10   120.52  3.000
 E9L  H12   C12  C13   119.16  3.000
 E9L  H12   C12  C11   120.58  3.000
 E9L  C13   C12  C11   120.19  3.000
 E9L  H13   C13  C14   118.90  3.000
 E9L  H13   C13  C12   119.91  3.000
 E9L  C14   C13  C12   121.19  3.000
 E9L  H14   C14  N15   113.36  3.000
 E9L  H14   C14  C13   126.02  3.000
 E9L  N15   C14  C13   120.52  3.000
 E9L  H15   N15  C16   106.76  3.000
 E9L  H15   N15  C14   107.58  3.000
 E9L  C16   N15  C14   108.28  3.000
 E9L  H15   N15  C10   108.44  3.000
 E9L  C16   N15  C10   109.84  3.000
 E9L  C14   N15  C10   115.57  3.000
 E9L  H16B  C16  H16A  110.44  3.000
 E9L  H16B  C16  H16   111.04  3.000
 E9L  H16A  C16  H16   110.94  3.000
 E9L  H16B  C16  N15   108.02  3.000
 E9L  H16A  C16  N15   108.08  3.000
 E9L  H16   C16  N15   108.19  3.000
 E9L  N19   C17  O18   120.63  3.000
 E9L  N19   C17  C11   118.33  3.000
 E9L  O18   C17  C11   121.04  3.000
 E9L  C17   N19  C08   121.60  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
 E9L  CONST_01  C05  C04  C03  C02     0.00   0.0  0
 E9L  CONST_02  C05  C06  C07  C02     0.00   0.0  0
 E9L  CONST_03  C06  C07  C02  C03     0.00   0.0  0
 E9L  CONST_04  C06  C05  C04  C03     0.00   0.0  0
 E9L  CONST_05  C07  C02  C03  C04     0.00   0.0  0
 E9L  CONST_06  C07  C06  C05  C04     0.00   0.0  0
 E9L  CONST_07  C08  C05  C04  C03   180.00   0.0  0
 E9L  CONST_08  C08  C05  C06  C07   180.00   0.0  0
 E9L  CONST_09  C04  C03  C02  C01   180.00   0.0  0
 E9L  CONST_10  C06  C07  C02  C01   180.00   0.0  0
 E9L  CONST_11  H04  C04  C03  C02   180.00   0.0  0
 E9L  CONST_12  H06  C06  C07  C02   180.00   0.0  0
 E9L  CONST_13  H07  C07  C02  C03   180.00   0.0  0
 E9L  CONST_14  H03  C03  C04  C05   180.00   0.0  0
 E9L  Var_01    C09  C08  C05  C04  -166.18  30.0  2
 E9L  Var_02    C13  C12  C11  C10    -1.33  30.0  1
 E9L  Var_03    C14  C13  C12  C11     6.84  30.0  1
 E9L  Var_04    N15  C14  C13  C12     4.15  30.0  1
 E9L  Var_05    H01  C01  C02  C03    81.13  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 E9L  chir_01  N15  C10  C14  C16  positiv

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
 E9L  plan-1  C01  0.020
 E9L  plan-1  C02  0.020
 E9L  plan-1  C03  0.020
 E9L  plan-1  C04  0.020
 E9L  plan-1  C05  0.020
 E9L  plan-1  C06  0.020
 E9L  plan-1  C07  0.020
 E9L  plan-1  C08  0.020
 E9L  plan-1  H03  0.020
 E9L  plan-1  H04  0.020
 E9L  plan-1  H06  0.020
 E9L  plan-1  H07  0.020
 E9L  plan-2  C05  0.020
 E9L  plan-2  C08  0.020
 E9L  plan-2  C09  0.020
 E9L  plan-2  C10  0.020
 E9L  plan-2  C11  0.020
 E9L  plan-2  C12  0.020
 E9L  plan-2  N15  0.020
 E9L  plan-2  C17  0.020
 E9L  plan-2  O18  0.020
 E9L  plan-2  N19  0.020
 E9L  plan-2  H09  0.020

