# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 12:16:19 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 6-[5-chloranyl-4-[(1~{S})-1-oxidanylethyl]pyridin-3-yl]-3,4-dihydro-2~{H}-1,8-naphthyridine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)c1c(Cl)cncc1c2cnc3N(CCCc3c2)C(N)=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
 JRE  JRE  6-[5-chloranyl-4-[(1~{S})-1-oxidanylethyl]pyridin-3-yl]-3,4-dihydro-2~{H}-1,8-naphthyridine-1-carboxamide  ligand  40  23  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JRE
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
 JRE  C5   C   CR6   0   0.293   2.5598  -0.0232   0.0467
 JRE  C6   C   CR6   0  -0.182   3.8859   0.2483  -0.2771
 JRE  C8   C   CR16  0  -0.022   4.2093   1.0238  -1.3802
 JRE  C10  C   CR16  0  -0.063   2.0206   1.3196  -1.8769
 JRE  C13  C   CR16  0  -0.094  -0.6177  -0.4059  -1.4155
 JRE  C15  C   CR6   0   0.494  -2.5636   0.0686  -0.3157
 JRE  C17  C   CH2   0  -0.491  -2.6296   1.6040   1.7168
 JRE  C21  C   C     0   0.642  -4.7052  -0.4306  -1.3299
 JRE  C24  C   CR16  0  -0.214  -0.5361   1.0465   0.4481
 JRE  C1   C   CH3   0  -0.691   2.2989  -0.1989   2.5481
 JRE  C2   C   CH1   0  -0.065   2.1446  -0.9116   1.2105
 JRE  O4   O   OH1   0  -0.651   2.7757  -2.1681   1.1687
 JRE  CL7  CL  CL    0  -0.116   5.2101  -0.3506   0.6699
 JRE  N9   N   N     0  -0.399   3.2905   1.5464  -2.1738
 JRE  C11  C   CR6   0  -0.092   1.5988   0.5595  -0.7897
 JRE  C12  C   CR6   0  -0.092   0.1443   0.3941  -0.5733
 JRE  N14  N   N     0  -0.422  -1.9209  -0.5751  -1.2810
 JRE  C16  C   CR6   0  -0.020  -1.9047   0.9028   0.6021
 JRE  C18  C   CH2   0  -0.456  -4.1354   1.5534   1.5288
 JRE  C19  C   CH2   0  -0.325  -4.5547   0.1623   1.0869
 JRE  N20  N   NT    0  -0.582  -3.9328  -0.1602  -0.1969
 JRE  N22  N   NH2   0  -0.826  -5.8540  -1.0964  -1.0722
 JRE  O23  O   O     0  -0.491  -4.3927  -0.0611  -2.4468
 JRE  H1   H   HCR6  0   0.288   5.2482   1.2203  -1.6201
 JRE  H2   H   HCR6  0   0.272   1.2809   1.7671  -2.5319
 JRE  H3   H   HCR6  0   0.261  -0.1421  -0.9503  -2.2253
 JRE  H4   H   HCH2  0   0.257  -2.3600   1.1269   2.6636
 JRE  H5   H   HCH2  0   0.264  -2.2844   2.6373   1.7885
 JRE  H6   H   HCR6  0   0.263   0.0026   1.6966   1.1297
 JRE  H7   H   HCH3  0   0.240   1.7087   0.7166   2.5637
 JRE  H8   H   HCH3  0   0.253   1.9387  -0.8400   3.3531
 JRE  H9   H   HCH3  0   0.234   3.3338   0.0697   2.7600
 JRE  H10  H   HCH1  0   0.258   1.0836  -1.1281   1.0764
 JRE  H11  H   HOH1  0   0.446   3.6457  -2.1065   1.5752
 JRE  H12  H   HCH2  0   0.254  -4.6433   1.8114   2.4586
 JRE  H13  H   HCH2  0   0.244  -4.4542   2.2762   0.7741
 JRE  H14  H   HCH2  0   0.251  -4.2731  -0.5809   1.8386
 JRE  H15  H   HCH2  0   0.269  -5.6345   0.1207   0.9769
 JRE  H16  H   HNH2  0   0.409  -5.9623  -1.6622  -0.2476
 JRE  H17  H   HNH2  0   0.405  -6.4260  -1.3517  -1.8597

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
 JRE  O23  C21  double    1.217  0.020  1.217
 JRE  N22  C21  single    1.353  0.020  1.353
 JRE  C21  N20  single    1.398  0.020  1.398
 JRE  N20  C19  single    1.462  0.020  1.462
 JRE  N20  C15  single    1.393  0.020  1.393
 JRE  C19  C18  single    1.519  0.020  1.519
 JRE  N14  C15  aromatic  1.326  0.020  1.326
 JRE  N14  C13  aromatic  1.321  0.020  1.321
 JRE  C15  C16  aromatic  1.404  0.020  1.404
 JRE  C18  C17  single    1.518  0.020  1.518
 JRE  C13  C12  aromatic  1.389  0.020  1.389
 JRE  C16  C17  single    1.503  0.020  1.503
 JRE  C16  C24  aromatic  1.385  0.020  1.385
 JRE  C12  C24  aromatic  1.390  0.020  1.390
 JRE  C12  C11  single    1.480  0.020  1.480
 JRE  C10  C11  aromatic  1.392  0.020  1.392
 JRE  C10  N9   aromatic  1.324  0.020  1.324
 JRE  C11  C5   aromatic  1.401  0.020  1.401
 JRE  N9   C8   aromatic  1.322  0.020  1.322
 JRE  C5   C2   single    1.522  0.020  1.522
 JRE  C5   C6   aromatic  1.392  0.020  1.392
 JRE  C8   C6   aromatic  1.387  0.020  1.387
 JRE  C2   C1   single    1.523  0.020  1.523
 JRE  C2   O4   single    1.407  0.020  1.407
 JRE  C6   CL7  single    1.735  0.020  1.735
 JRE  C8   H1   single    0.930  0.020  1.080
 JRE  C10  H2   single    0.930  0.020  1.080
 JRE  C13  H3   single    0.930  0.020  1.080
 JRE  C17  H4   single    0.970  0.020  1.090
 JRE  C17  H5   single    0.970  0.020  1.090
 JRE  C24  H6   single    0.930  0.020  1.080
 JRE  C1   H7   single    0.970  0.020  1.090
 JRE  C1   H8   single    0.970  0.020  1.090
 JRE  C1   H9   single    0.970  0.020  1.090
 JRE  C2   H10  single    0.970  0.020  1.090
 JRE  O4   H11  single    0.850  0.020  0.980
 JRE  C18  H12  single    0.970  0.020  1.090
 JRE  C18  H13  single    0.970  0.020  1.090
 JRE  C19  H14  single    0.970  0.020  1.090
 JRE  C19  H15  single    0.970  0.020  1.090
 JRE  N22  H16  single    0.890  0.020  1.040
 JRE  N22  H17  single    0.890  0.020  1.040

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
 JRE  C11  C5   C2   120.81  3.000
 JRE  C2   C5   C6   123.49  3.000
 JRE  C11  C5   C6   115.69  3.000
 JRE  CL7  C6   C8   116.70  3.000
 JRE  CL7  C6   C5   122.21  3.000
 JRE  C8   C6   C5   121.09  3.000
 JRE  H1   C8   N9   117.49  3.000
 JRE  H1   C8   C6   120.06  3.000
 JRE  N9   C8   C6   122.45  3.000
 JRE  H2   C10  C11  119.36  3.000
 JRE  H2   C10  N9   116.63  3.000
 JRE  C11  C10  N9   124.02  3.000
 JRE  H3   C13  N14  116.35  3.000
 JRE  H3   C13  C12  120.05  3.000
 JRE  N14  C13  C12  123.59  3.000
 JRE  N20  C15  C16  120.19  3.000
 JRE  C16  C15  N14  122.45  3.000
 JRE  N20  C15  N14  117.30  3.000
 JRE  H5   C17  H4   106.14  3.000
 JRE  H5   C17  C18  110.69  3.000
 JRE  H4   C17  C18  109.70  3.000
 JRE  H5   C17  C16  109.74  3.000
 JRE  H4   C17  C16  108.63  3.000
 JRE  C18  C17  C16  111.77  3.000
 JRE  O23  C21  N22  122.84  3.000
 JRE  N22  C21  N20  114.22  3.000
 JRE  O23  C21  N20  122.90  3.000
 JRE  H6   C24  C16  118.88  3.000
 JRE  H6   C24  C12  119.98  3.000
 JRE  C16  C24  C12  121.12  3.000
 JRE  H9   C1   H8   108.36  3.000
 JRE  H9   C1   H7   107.73  3.000
 JRE  H8   C1   H7   107.73  3.000
 JRE  H9   C1   C2   112.46  3.000
 JRE  H8   C1   C2   109.86  3.000
 JRE  H7   C1   C2   110.55  3.000
 JRE  H10  C2   O4   104.80  3.000
 JRE  H10  C2   C1   107.41  3.000
 JRE  O4   C2   C1   113.49  3.000
 JRE  H10  C2   C5   106.69  3.000
 JRE  O4   C2   C5   112.11  3.000
 JRE  C1   C2   C5   111.75  3.000
 JRE  H11  O4   C2   109.63  3.000
 JRE  C10  N9   C8   117.68  3.000
 JRE  C12  C11  C10  118.23  3.000
 JRE  C10  C11  C5   119.05  3.000
 JRE  C12  C11  C5   122.71  3.000
 JRE  C11  C12  C24  122.43  3.000
 JRE  C11  C12  C13  120.99  3.000
 JRE  C24  C12  C13  116.57  3.000
 JRE  C15  N14  C13  119.34  3.000
 JRE  C24  C16  C17  120.71  3.000
 JRE  C24  C16  C15  116.92  3.000
 JRE  C17  C16  C15  122.37  3.000
 JRE  H13  C18  H12  107.25  3.000
 JRE  H13  C18  C19  108.93  3.000
 JRE  H12  C18  C19  109.65  3.000
 JRE  H13  C18  C17  110.66  3.000
 JRE  H12  C18  C17  110.39  3.000
 JRE  C19  C18  C17  109.90  3.000
 JRE  H15  C19  H14  107.42  3.000
 JRE  H15  C19  N20  108.99  3.000
 JRE  H14  C19  N20  110.12  3.000
 JRE  H15  C19  C18  109.81  3.000
 JRE  H14  C19  C18  110.57  3.000
 JRE  N20  C19  C18  109.88  3.000
 JRE  C19  N20  C21  121.29  3.000
 JRE  C19  N20  C15  117.16  3.000
 JRE  C21  N20  C15  120.38  3.000
 JRE  H17  N22  H16  115.96  3.000
 JRE  H17  N22  C21  117.29  3.000
 JRE  H16  N22  C21  121.63  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
 JRE  CONST_03  N9   C10  C11  C5     0.00   0.0  0
 JRE  CONST_04  N9   C8   C6   C5     0.00   0.0  0
 JRE  CONST_05  C12  C11  C5   C6   180.00   0.0  0
 JRE  CONST_06  C10  C11  C5   C6     0.00   0.0  0
 JRE  CONST_07  C10  N9   C8   C6     0.00   0.0  0
 JRE  CONST_08  C11  C10  N9   C8     0.00   0.0  0
 JRE  CONST_09  C11  C5   C6   C8     0.00   0.0  0
 JRE  CONST_12  C16  C15  N14  C13    0.00   0.0  0
 JRE  CONST_13  C16  C24  C12  C13    0.00   0.0  0
 JRE  CONST_14  C12  C13  N14  C15    0.00   0.0  0
 JRE  CONST_15  C12  C24  C16  C15    0.00   0.0  0
 JRE  CONST_16  N14  C15  C16  C24    0.00   0.0  0
 JRE  CONST_17  N14  C13  C12  C24    0.00   0.0  0
 JRE  CONST_18  C12  C11  C10  N9   180.00   0.0  0
 JRE  CONST_19  N14  C13  C12  C11  180.00   0.0  0
 JRE  CONST_20  C16  C24  C12  C11  180.00   0.0  0
 JRE  CONST_21  C2   C5   C6   C8   180.00   0.0  0
 JRE  CONST_22  C2   C5   C11  C10  180.00   0.0  0
 JRE  CONST_23  C12  C11  C5   C2     0.00   0.0  0
 JRE  CONST_24  C11  C5   C6   CL7  180.00   0.0  0
 JRE  CONST_25  N9   C8   C6   CL7  180.00   0.0  0
 JRE  CONST_26  H2   C10  C11  C5   180.00   0.0  0
 JRE  CONST_27  H1   C8   C6   C5   180.00   0.0  0
 JRE  CONST_28  H6   C24  C12  C13  180.00   0.0  0
 JRE  CONST_29  H3   C13  N14  C15  180.00   0.0  0
 JRE  CONST_35  H17  N22  C21  N20  180.00   0.0  0
 JRE  Var_01    C18  C19  N20  C15   48.71  30.0  1
 JRE  Var_02    C18  C17  C16  C15  -12.89  30.0  1
 JRE  Var_03    N20  C19  C18  C17  -61.54  30.0  1
 JRE  Var_04    C19  N20  C15  N14  159.91  30.0  1
 JRE  Var_05    C19  C18  C17  C16   43.24  30.0  1

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
 JRE  chir_01  C2  C5  C1  O4  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
 JRE  plan-1  C5   0.020
 JRE  plan-1  C6   0.020
 JRE  plan-1  C8   0.020
 JRE  plan-1  C10  0.020
 JRE  plan-1  C2   0.020
 JRE  plan-1  CL7  0.020
 JRE  plan-1  N9   0.020
 JRE  plan-1  C11  0.020
 JRE  plan-1  C12  0.020
 JRE  plan-1  H1   0.020
 JRE  plan-1  H2   0.020
 JRE  plan-2  C13  0.020
 JRE  plan-2  C15  0.020
 JRE  plan-2  C17  0.020
 JRE  plan-2  C24  0.020
 JRE  plan-2  C11  0.020
 JRE  plan-2  C12  0.020
 JRE  plan-2  N14  0.020
 JRE  plan-2  C16  0.020
 JRE  plan-2  N20  0.020
 JRE  plan-2  H3   0.020
 JRE  plan-2  H6   0.020
 JRE  plan-3  C15  0.020
 JRE  plan-3  C21  0.020
 JRE  plan-3  C19  0.020
 JRE  plan-3  N20  0.020
 JRE  plan-3  N22  0.020
 JRE  plan-3  O23  0.020
 JRE  plan-3  H16  0.020
 JRE  plan-3  H17  0.020

