# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 03:18:29 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: N-[5-(2,3-dimethylphenyl)-1,2,3,4-tetrahydro-1,6-naphthyridin-7-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1cc2NCCCc2c(n1)c3cccc(C)c3C
#
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
 S3O  S3O  N-[5-(2,3-dimethylphenyl)-1,2,3,4-tetrahydro-1,6-naphthyridin-7-yl]acetamide  ligand  43  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_S3O
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
 S3O  C01  C  CH2   0  -0.474  -0.2865  -3.8691   0.9230
 S3O  C02  C  CH2   0  -0.269  -1.6609  -4.1531   0.3442
 S3O  N03  N  NH1   0  -0.703  -2.4159  -2.9243   0.2504
 S3O  C04  C  CR6   0   0.497  -1.8472  -1.7194   0.0361
 S3O  C05  C  CR6   0  -0.054  -0.4425  -1.5868  -0.0702
 S3O  C06  C  CH2   0  -0.489   0.4249  -2.8073   0.0923
 S3O  C07  C  CR16  0  -0.514  -2.6292  -0.5641  -0.0562
 S3O  C08  C  CR6   0   0.492  -1.9980   0.6529  -0.2681
 S3O  N09  N  N     0  -0.441  -0.6923   0.7879  -0.4029
 S3O  C10  C  CR6   0   0.105   0.0564  -0.3135  -0.2917
 S3O  C11  C  CR6   0   0.033   1.5191  -0.0853  -0.4406
 S3O  N12  N  NH1   0  -0.731  -2.8066   1.7902  -0.3723
 S3O  C13  C  CR6   0   0.024   2.2165   0.6867   0.4962
 S3O  C14  C  CR6   0   0.078   3.5815   0.9396   0.2909
 S3O  C15  C  CR16  0  -0.309   4.2161   0.4055  -0.8277
 S3O  C16  C  CR16  0  -0.251   3.5242  -0.3711  -1.7446
 S3O  C17  C  CR16  0  -0.294   2.1751  -0.6133  -1.5488
 S3O  C18  C  CH3   0  -0.744   4.3690   1.7811   1.2554
 S3O  C19  C  CH3   0  -0.742   1.5141   1.2449   1.7019
 S3O  C20  C  C     0   0.498  -2.4840   3.0945  -0.1351
 S3O  C21  C  CH3   0  -0.787  -3.6400   4.0474  -0.3324
 S3O  O22  O  O     0  -0.452  -1.3831   3.4861   0.1961
 S3O  H1   H  HCH2  0   0.235  -0.3904  -3.5282   1.9563
 S3O  H2   H  HCH2  0   0.224  -1.5578  -4.6294  -0.6382
 S3O  H3   H  HCH2  0   0.252   1.3730  -2.5376   0.5598
 S3O  H4   H  HCR6  0   0.268  -3.7063  -0.6239   0.0487
 S3O  H5   H  HNH1  0   0.413  -3.7831   1.6022  -0.5335
 S3O  H6   H  HCR6  0   0.243   5.2701   0.6048  -0.9822
 S3O  H7   H  HCR6  0   0.249   4.0327  -0.7790  -2.6086
 S3O  H8   H  HCR6  0   0.245   1.6200  -1.2050  -2.2668
 S3O  H9   H  HCH3  0   0.245   4.4219   1.3240   2.2459
 S3O  H10  H  HCH3  0   0.249   5.3904   1.9213   0.9045
 S3O  H11  H  HCH3  0   0.244   3.9261   2.7699   1.3880
 S3O  H12  H  HCH3  0   0.254   1.0815   2.2241   1.4881
 S3O  H13  H  HCH3  0   0.242   0.6931   0.6061   2.0239
 S3O  H14  H  HCH3  0   0.240   2.1907   1.3569   2.5474
 S3O  H15  H  HCH3  0   0.251  -4.6054   3.5566  -0.4424
 S3O  H16  H  HCH3  0   0.267  -3.6917   4.7337   0.5114
 S3O  H17  H  HCH3  0   0.272  -3.4615   4.6441  -1.2280
 S3O  H18  H  HCH2  0   0.248   0.2986  -4.7890   0.9427
 S3O  H19  H  HCH2  0   0.251  -2.2124  -4.8455   0.9802
 S3O  H20  H  HNH1  0   0.392  -3.4199  -2.9805   0.2673
 S3O  H21  H  HCH2  0   0.242   0.6784  -3.2303  -0.8852

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
 S3O  C01  C02  single    1.518  0.020  1.518
 S3O  C01  C06  single    1.524  0.020  1.524
 S3O  C02  N03  single    1.445  0.020  1.445
 S3O  C19  C13  single    1.503  0.020  1.503
 S3O  C18  C14  single    1.503  0.020  1.503
 S3O  C06  C05  single    1.506  0.020  1.506
 S3O  N03  C04  single    1.349  0.020  1.349
 S3O  C13  C14  aromatic  1.403  0.020  1.403
 S3O  C13  C11  aromatic  1.400  0.020  1.400
 S3O  C14  C15  aromatic  1.392  0.020  1.392
 S3O  C05  C04  aromatic  1.415  0.020  1.415
 S3O  C05  C10  aromatic  1.385  0.020  1.385
 S3O  C04  C07  aromatic  1.398  0.020  1.398
 S3O  C11  C10  single    1.488  0.020  1.488
 S3O  C11  C17  aromatic  1.392  0.020  1.392
 S3O  C10  N09  aromatic  1.336  0.020  1.336
 S3O  C15  C16  aromatic  1.387  0.020  1.387
 S3O  C07  C08  aromatic  1.387  0.020  1.387
 S3O  N09  C08  aromatic  1.320  0.020  1.320
 S3O  C17  C16  aromatic  1.385  0.020  1.385
 S3O  C08  N12  single    1.399  0.020  1.399
 S3O  N12  C20  single    1.364  0.020  1.364
 S3O  C20  O22  double    1.215  0.020  1.215
 S3O  C20  C21  single    1.511  0.020  1.511
 S3O  C01  H1   single    0.970  0.020  1.090
 S3O  C02  H2   single    0.970  0.020  1.090
 S3O  C06  H3   single    0.970  0.020  1.090
 S3O  C07  H4   single    0.930  0.020  1.080
 S3O  N12  H5   single    0.860  0.020  1.020
 S3O  C15  H6   single    0.930  0.020  1.080
 S3O  C16  H7   single    0.930  0.020  1.080
 S3O  C17  H8   single    0.930  0.020  1.080
 S3O  C18  H9   single    0.970  0.020  1.090
 S3O  C18  H10  single    0.970  0.020  1.090
 S3O  C18  H11  single    0.970  0.020  1.090
 S3O  C19  H12  single    0.970  0.020  1.090
 S3O  C19  H13  single    0.970  0.020  1.090
 S3O  C19  H14  single    0.970  0.020  1.090
 S3O  C21  H15  single    0.970  0.020  1.090
 S3O  C21  H16  single    0.970  0.020  1.090
 S3O  C21  H17  single    0.970  0.020  1.090
 S3O  C01  H18  single    0.970  0.020  1.090
 S3O  C02  H19  single    0.970  0.020  1.090
 S3O  N03  H20  single    0.860  0.020  1.020
 S3O  C06  H21  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
 S3O  H18  C01  H1   107.27  3.000
 S3O  H18  C01  C06  110.31  3.000
 S3O  H1   C01  C06  110.02  3.000
 S3O  H18  C01  C02  109.57  3.000
 S3O  H1   C01  C02  109.44  3.000
 S3O  C06  C01  C02  110.19  3.000
 S3O  H19  C02  H2   107.12  3.000
 S3O  H19  C02  N03  108.28  3.000
 S3O  H2   C02  N03  111.11  3.000
 S3O  H19  C02  C01  110.76  3.000
 S3O  H2   C02  C01  109.74  3.000
 S3O  N03  C02  C01  109.80  3.000
 S3O  H20  N03  C04  118.25  3.000
 S3O  H20  N03  C02  118.23  3.000
 S3O  C04  N03  C02  123.32  3.000
 S3O  C07  C04  C05  118.22  3.000
 S3O  C07  C04  N03  120.83  3.000
 S3O  C05  C04  N03  120.93  3.000
 S3O  C10  C05  C06  123.69  3.000
 S3O  C10  C05  C04  117.11  3.000
 S3O  C06  C05  C04  119.19  3.000
 S3O  H21  C06  H3   106.07  3.000
 S3O  H21  C06  C05  110.50  3.000
 S3O  H3   C06  C05  110.27  3.000
 S3O  H21  C06  C01  108.99  3.000
 S3O  H3   C06  C01  110.13  3.000
 S3O  C05  C06  C01  110.76  3.000
 S3O  H4   C07  C08  121.03  3.000
 S3O  H4   C07  C04  120.25  3.000
 S3O  C08  C07  C04  118.72  3.000
 S3O  N12  C08  N09  118.75  3.000
 S3O  N12  C08  C07  117.48  3.000
 S3O  N09  C08  C07  123.75  3.000
 S3O  C10  N09  C08  117.48  3.000
 S3O  C11  C10  N09  114.58  3.000
 S3O  N09  C10  C05  124.69  3.000
 S3O  C11  C10  C05  120.73  3.000
 S3O  C17  C11  C13  120.48  3.000
 S3O  C17  C11  C10  119.00  3.000
 S3O  C13  C11  C10  120.49  3.000
 S3O  H5   N12  C20  115.81  3.000
 S3O  H5   N12  C08  114.86  3.000
 S3O  C20  N12  C08  128.86  3.000
 S3O  C19  C13  C14  120.34  3.000
 S3O  C14  C13  C11  119.08  3.000
 S3O  C19  C13  C11  120.58  3.000
 S3O  C18  C14  C15  119.44  3.000
 S3O  C15  C14  C13  119.46  3.000
 S3O  C18  C14  C13  121.11  3.000
 S3O  H6   C15  C16  119.60  3.000
 S3O  H6   C15  C14  119.16  3.000
 S3O  C16  C15  C14  121.24  3.000
 S3O  H7   C16  C17  120.31  3.000
 S3O  H7   C16  C15  120.31  3.000
 S3O  C17  C16  C15  119.39  3.000
 S3O  H8   C17  C16  120.07  3.000
 S3O  H8   C17  C11  119.56  3.000
 S3O  C16  C17  C11  120.36  3.000
 S3O  H11  C18  H10  107.64  3.000
 S3O  H11  C18  H9   106.78  3.000
 S3O  H10  C18  H9   107.50  3.000
 S3O  H11  C18  C14  111.87  3.000
 S3O  H10  C18  C14  110.90  3.000
 S3O  H9   C18  C14  111.91  3.000
 S3O  H14  C19  H13  107.42  3.000
 S3O  H14  C19  H12  107.82  3.000
 S3O  H13  C19  H12  106.59  3.000
 S3O  H14  C19  C13  111.76  3.000
 S3O  H13  C19  C13  111.82  3.000
 S3O  H12  C19  C13  111.18  3.000
 S3O  O22  C20  C21  121.72  3.000
 S3O  C21  C20  N12  113.53  3.000
 S3O  O22  C20  N12  124.75  3.000
 S3O  H17  C21  H16  107.41  3.000
 S3O  H17  C21  H15  107.98  3.000
 S3O  H16  C21  H15  108.68  3.000
 S3O  H17  C21  C20  109.09  3.000
 S3O  H16  C21  C20  109.43  3.000
 S3O  H15  C21  C20  114.04  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
 S3O  CONST_01  C11  C10  C05  C04  180.00   0.0  0
 S3O  CONST_02  N09  C10  C05  C04    0.00   0.0  0
 S3O  CONST_03  N09  C08  C07  C04    0.00   0.0  0
 S3O  CONST_04  C08  C07  C04  C05    0.00   0.0  0
 S3O  CONST_07  C08  N09  C10  C05    0.00   0.0  0
 S3O  CONST_08  C10  C05  C04  C07    0.00   0.0  0
 S3O  CONST_09  C10  N09  C08  C07    0.00   0.0  0
 S3O  CONST_10  C11  C10  N09  C08  180.00   0.0  0
 S3O  CONST_13  C14  C13  C11  C10  180.00   0.0  0
 S3O  CONST_14  C16  C17  C11  C10  180.00   0.0  0
 S3O  CONST_15  C15  C14  C13  C11    0.00   0.0  0
 S3O  CONST_16  C15  C16  C17  C11    0.00   0.0  0
 S3O  CONST_17  C16  C15  C14  C13    0.00   0.0  0
 S3O  CONST_18  C16  C17  C11  C13    0.00   0.0  0
 S3O  CONST_19  C17  C11  C13  C14    0.00   0.0  0
 S3O  CONST_20  C17  C16  C15  C14    0.00   0.0  0
 S3O  CONST_21  C11  C10  C05  C06    0.00   0.0  0
 S3O  CONST_22  N12  C08  C07  C04  180.00   0.0  0
 S3O  CONST_23  C19  C13  C11  C10    0.00   0.0  0
 S3O  CONST_24  N12  C08  N09  C10  180.00   0.0  0
 S3O  CONST_25  C18  C14  C13  C11  180.00   0.0  0
 S3O  CONST_26  C19  C13  C14  C15  180.00   0.0  0
 S3O  CONST_27  C18  C14  C15  C16  180.00   0.0  0
 S3O  CONST_28  C19  C13  C11  C17  180.00   0.0  0
 S3O  CONST_29  H4   C07  C04  N03    0.00   0.0  0
 S3O  CONST_30  H8   C17  C11  C10    0.00   0.0  0
 S3O  CONST_31  H7   C16  C17  C11  180.00   0.0  0
 S3O  CONST_32  H6   C15  C14  C13  180.00   0.0  0
 S3O  CONST_36  O22  C20  N12  C08    0.00   0.0  0
 S3O  CONST_37  C21  C20  N12  C08  180.00   0.0  0
 S3O  Var_01    C04  N03  C02  C01   30.99  30.0  1
 S3O  Var_02    C04  C05  C06  C01  -24.57  30.0  1
 S3O  Var_03    C05  C06  C01  C02   52.58  30.0  1
 S3O  Var_04    C05  C04  N03  C02   -1.99  30.0  1
 S3O  Var_05    C06  C01  C02  N03  -55.46  30.0  1
 S3O  Var_06    H12  C19  C13  C11  -88.74  30.0  2
 S3O  Var_07    H9   C18  C14  C13   63.55  30.0  2
 S3O  Var_08    H15  C21  C20  N12   11.37  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
 S3O  plan-1  C10  0.020
 S3O  plan-1  C11  0.020
 S3O  plan-1  C13  0.020
 S3O  plan-1  C14  0.020
 S3O  plan-1  C15  0.020
 S3O  plan-1  C16  0.020
 S3O  plan-1  C17  0.020
 S3O  plan-1  C18  0.020
 S3O  plan-1  C19  0.020
 S3O  plan-1  H6   0.020
 S3O  plan-1  H7   0.020
 S3O  plan-1  H8   0.020
 S3O  plan-2  C08  0.020
 S3O  plan-2  N12  0.020
 S3O  plan-2  C20  0.020
 S3O  plan-2  C21  0.020
 S3O  plan-2  O22  0.020
 S3O  plan-2  H5   0.020
 S3O  plan-3  N03  0.020
 S3O  plan-3  C04  0.020
 S3O  plan-3  C05  0.020
 S3O  plan-3  C06  0.020
 S3O  plan-3  C07  0.020
 S3O  plan-3  C08  0.020
 S3O  plan-3  N09  0.020
 S3O  plan-3  C10  0.020
 S3O  plan-3  C11  0.020
 S3O  plan-3  N12  0.020
 S3O  plan-3  H4   0.020

