# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 05:28:43 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 4-[4-[(dimethylamino)methyl]-3,5-dimethoxy-phenyl]-2-methyl-2,7-naphthyridin-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(OC)c1CN(C)C)C2=CN(C)C(=O)c3cnccc23
#
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
 5SW  5SW  4-[4-[(dimethylamino)methyl]-3,5-dimethoxy-phenyl]-2-methyl-2,7-naphthyridin-1-one  ligand  49  26  .  2021-08-04  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5SW
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
 5SW  N3   N  N     0  -0.412  -3.9642   2.8503  -1.1801
 5SW  C4   C  CR16  0  -0.054  -4.4820   1.7232  -0.7417
 5SW  C5   C  CR66  0   0.355  -2.3203   0.7627  -0.2562
 5SW  C6   C  CR66  0  -0.272  -3.7198   0.6472  -0.2740
 5SW  C7   C  CR6   0   0.566  -4.3989  -0.5685   0.1641
 5SW  C10  C  CR6   0  -0.095  -1.5413  -0.3441   0.2238
 5SW  C13  C  CR6   0   0.403   2.0611  -1.3000  -0.2599
 5SW  C17  C  CR16  0  -0.473   0.6696  -1.3052  -0.3511
 5SW  C20  C  CR6   0   0.399   1.9756   0.6762   1.0976
 5SW  C21  C  CR6   0  -0.130   2.7382  -0.3094   0.4602
 5SW  C24  C  CH3   0  -0.438   1.9639   2.6806   2.3806
 5SW  C26  C  CH3   0  -0.438   2.2181  -3.3190  -1.5046
 5SW  C18  C  CR6   0   0.078  -0.0653  -0.3178   0.2937
 5SW  C1   C  CR16  0  -0.422  -1.7795   1.9633  -0.7420
 5SW  N8   N  NR6   0  -0.530  -3.5675  -1.5787   0.5930
 5SW  C2   C  CR16  0  -0.056  -2.6278   2.9515  -1.1808
 5SW  C16  C  CH3   0  -0.514   4.5792   1.5286  -0.9877
 5SW  C25  C  CH3   0  -0.520   6.2730  -0.1271  -0.7160
 5SW  C9   C  CR16  0   0.008  -2.2103  -1.4538   0.6158
 5SW  C12  C  CH3   0  -0.520  -4.1880  -2.8178   1.0418
 5SW  C19  C  CR16  0  -0.472   0.5832   0.6722   1.0229
 5SW  O23  O  O2    0  -0.467   2.6625   1.6089   1.7821
 5SW  O22  O  O2    0  -0.462   2.8335  -2.2313  -0.8451
 5SW  N15  N  NT    0  -0.394   4.8509   0.1328  -0.7238
 5SW  O11  O  O     0  -0.475  -5.6118  -0.7162   0.1599
 5SW  H1   H  HCR6  0   0.274  -5.5631   1.6438  -0.7522
 5SW  H2   H  HCR6  0   0.272   0.1469  -2.0549  -0.9288
 5SW  H3   H  HCH3  0   0.227   1.3904   3.2553   1.6487
 5SW  H4   H  HCH3  0   0.228   1.2890   2.3438   3.1719
 5SW  H5   H  HCH3  0   0.261   2.7172   3.3293   2.8206
 5SW  H6   H  HCH3  0   0.261   3.0225  -3.9707  -1.8367
 5SW  H7   H  HCH3  0   0.228   1.5593  -3.8831  -0.8391
 5SW  H8   H  HCH3  0   0.228   1.6456  -2.9997  -2.3794
 5SW  H9   H  HCR6  0   0.276  -0.7109   2.1199  -0.7806
 5SW  H10  H  HCR6  0   0.274  -2.2191   3.8821  -1.5570
 5SW  H11  H  HCH3  0   0.229   5.0441   1.8195  -1.9307
 5SW  H12  H  HCH3  0   0.234   3.5068   1.6998  -1.0839
 5SW  H13  H  HCH3  0   0.186   4.9589   2.2029  -0.2037
 5SW  H14  H  HCH3  0   0.229   6.4582  -1.1932  -0.5747
 5SW  H15  H  HCH3  0   0.231   6.7122   0.1633  -1.6719
 5SW  H16  H  HCH3  0   0.187   6.8143   0.4141   0.0772
 5SW  H17  H  HCR6  0   0.310  -1.6781  -2.3165   0.9919
 5SW  H18  H  HCH3  0   0.263  -4.7254  -3.2962   0.2255
 5SW  H19  H  HCH3  0   0.260  -3.4125  -3.4910   1.3929
 5SW  H20  H  HCH3  0   0.263  -4.8826  -2.6257   1.8565
 5SW  H21  H  HCR6  0   0.278  -0.0058   1.4171   1.5394
 5SW  H22  H  HCH2  0   0.216   4.5977   0.2609   1.3773
 5SW  H23  H  HCH2  0   0.240   4.5770  -1.3494   0.6902
 5SW  C14  C  CH2   0  -0.318   4.2422  -0.3242   0.5167

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
 5SW  C26  O22  single    1.413  0.020  1.413
 5SW  O22  C13  single    1.344  0.020  1.344
 5SW  C13  C17  aromatic  1.394  0.020  1.394
 5SW  C13  C21  aromatic  1.399  0.020  1.399
 5SW  C14  C21  single    1.505  0.020  1.505
 5SW  C14  N15  single    1.455  0.020  1.455
 5SW  C25  N15  single    1.446  0.020  1.446
 5SW  C17  C18  aromatic  1.390  0.020  1.390
 5SW  C21  C20  aromatic  1.400  0.020  1.400
 5SW  N15  C16  single    1.446  0.020  1.446
 5SW  C18  C10  single    1.478  0.020  1.478
 5SW  C18  C19  aromatic  1.390  0.020  1.390
 5SW  C20  C19  aromatic  1.394  0.020  1.394
 5SW  C20  O23  single    1.346  0.020  1.346
 5SW  C1   C2   aromatic  1.374  0.020  1.374
 5SW  C1   C5   aromatic  1.404  0.020  1.404
 5SW  C10  C5   single    1.436  0.020  1.436
 5SW  C10  C9   double    1.354  0.020  1.354
 5SW  C2   N3   aromatic  1.340  0.020  1.340
 5SW  C5   C6   aromatic  1.404  0.020  1.404
 5SW  C9   N8   single    1.363  0.020  1.363
 5SW  O23  C24  single    1.412  0.020  1.412
 5SW  N3   C4   aromatic  1.316  0.020  1.316
 5SW  C6   C4   aromatic  1.399  0.020  1.399
 5SW  C6   C7   single    1.460  0.020  1.460
 5SW  N8   C7   single    1.377  0.020  1.377
 5SW  N8   C12  single    1.457  0.020  1.457
 5SW  C7   O11  double    1.222  0.020  1.222
 5SW  C4   H1   single    0.930  0.020  1.080
 5SW  C17  H2   single    0.930  0.020  1.080
 5SW  C24  H3   single    0.970  0.020  1.090
 5SW  C24  H4   single    0.970  0.020  1.090
 5SW  C24  H5   single    0.970  0.020  1.090
 5SW  C26  H6   single    0.970  0.020  1.090
 5SW  C26  H7   single    0.970  0.020  1.090
 5SW  C26  H8   single    0.970  0.020  1.090
 5SW  C1   H9   single    0.930  0.020  1.080
 5SW  C2   H10  single    0.930  0.020  1.080
 5SW  C16  H11  single    0.970  0.020  1.090
 5SW  C16  H12  single    0.970  0.020  1.090
 5SW  C16  H13  single    0.970  0.020  1.090
 5SW  C25  H14  single    0.970  0.020  1.090
 5SW  C25  H15  single    0.970  0.020  1.090
 5SW  C25  H16  single    0.970  0.020  1.090
 5SW  C9   H17  single    0.930  0.020  1.080
 5SW  C12  H18  single    0.970  0.020  1.090
 5SW  C12  H19  single    0.970  0.020  1.090
 5SW  C12  H20  single    0.970  0.020  1.090
 5SW  C19  H21  single    0.930  0.020  1.080
 5SW  C14  H22  single    0.970  0.020  1.090
 5SW  C14  H23  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
 5SW  C2   N3   C4   117.21  3.000
 5SW  H1   C4   C6   119.35  3.000
 5SW  H1   C4   N3   116.88  3.000
 5SW  C6   C4   N3   123.77  3.000
 5SW  C1   C5   C10  124.47  3.000
 5SW  C10  C5   C6   118.78  3.000
 5SW  C1   C5   C6   116.74  3.000
 5SW  C7   C6   C5   121.89  3.000
 5SW  C7   C6   C4   119.16  3.000
 5SW  C5   C6   C4   118.94  3.000
 5SW  O11  C7   N8   120.78  3.000
 5SW  O11  C7   C6   124.16  3.000
 5SW  N8   C7   C6   115.06  3.000
 5SW  C9   C10  C18  119.63  3.000
 5SW  C9   C10  C5   117.42  3.000
 5SW  C18  C10  C5   122.95  3.000
 5SW  O22  C13  C21  115.88  3.000
 5SW  C21  C13  C17  121.27  3.000
 5SW  O22  C13  C17  122.85  3.000
 5SW  H2   C17  C18  119.01  3.000
 5SW  H2   C17  C13  121.33  3.000
 5SW  C18  C17  C13  119.66  3.000
 5SW  O23  C20  C19  122.62  3.000
 5SW  O23  C20  C21  116.20  3.000
 5SW  C19  C20  C21  121.18  3.000
 5SW  C14  C21  C20  122.30  3.000
 5SW  C20  C21  C13  117.98  3.000
 5SW  C14  C21  C13  119.72  3.000
 5SW  H5   C24  H4   108.59  3.000
 5SW  H5   C24  H3   108.71  3.000
 5SW  H4   C24  H3   108.83  3.000
 5SW  H5   C24  O23  106.35  3.000
 5SW  H4   C24  O23  112.23  3.000
 5SW  H3   C24  O23  112.01  3.000
 5SW  H8   C26  H7   108.81  3.000
 5SW  H8   C26  H6   108.54  3.000
 5SW  H7   C26  H6   108.82  3.000
 5SW  H8   C26  O22  112.13  3.000
 5SW  H7   C26  O22  112.06  3.000
 5SW  H6   C26  O22  106.36  3.000
 5SW  C19  C18  C17  120.18  3.000
 5SW  C19  C18  C10  120.23  3.000
 5SW  C17  C18  C10  119.58  3.000
 5SW  H9   C1   C2   119.65  3.000
 5SW  H9   C1   C5   121.15  3.000
 5SW  C2   C1   C5   119.19  3.000
 5SW  C12  N8   C9   119.80  3.000
 5SW  C12  N8   C7   117.57  3.000
 5SW  C9   N8   C7   122.63  3.000
 5SW  H10  C2   C1   119.70  3.000
 5SW  H10  C2   N3   116.17  3.000
 5SW  C1   C2   N3   124.13  3.000
 5SW  H13  C16  H12  107.80  3.000
 5SW  H13  C16  H11  107.77  3.000
 5SW  H12  C16  H11  107.52  3.000
 5SW  H13  C16  N15  113.34  3.000
 5SW  H12  C16  N15  110.64  3.000
 5SW  H11  C16  N15  109.57  3.000
 5SW  H16  C25  H15  107.58  3.000
 5SW  H16  C25  H14  107.64  3.000
 5SW  H15  C25  H14  107.76  3.000
 5SW  H16  C25  N15  113.50  3.000
 5SW  H15  C25  N15  110.08  3.000
 5SW  H14  C25  N15  110.08  3.000
 5SW  H17  C9   N8   115.01  3.000
 5SW  H17  C9   C10  120.77  3.000
 5SW  N8   C9   C10  124.21  3.000
 5SW  H20  C12  H19  108.87  3.000
 5SW  H20  C12  H18  108.92  3.000
 5SW  H19  C12  H18  108.84  3.000
 5SW  H20  C12  N8   110.64  3.000
 5SW  H19  C12  N8   108.84  3.000
 5SW  H18  C12  N8   110.68  3.000
 5SW  H21  C19  C18  119.15  3.000
 5SW  H21  C19  C20  121.10  3.000
 5SW  C18  C19  C20  119.74  3.000
 5SW  C24  O23  C20  119.28  3.000
 5SW  C26  O22  C13  119.09  3.000
 5SW  C14  N15  C25  110.51  3.000
 5SW  C25  N15  C16  111.06  3.000
 5SW  C14  N15  C16  112.33  3.000
 5SW  H23  C14  H22  106.01  3.000
 5SW  H23  C14  N15  107.58  3.000
 5SW  H22  C14  N15  111.39  3.000
 5SW  H23  C14  C21  108.75  3.000
 5SW  H22  C14  C21  110.31  3.000
 5SW  N15  C14  C21  112.51  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
 5SW  CONST_01  C5   C1   C2   N3      0.00   0.0  0
 5SW  CONST_02  C5   C6   C4   N3      0.00   0.0  0
 5SW  CONST_03  C1   C2   N3   C4      0.00   0.0  0
 5SW  CONST_04  C1   C5   C6   C4      0.00   0.0  0
 5SW  CONST_05  C2   C1   C5   C6      0.00   0.0  0
 5SW  CONST_06  C2   N3   C4   C6      0.00   0.0  0
 5SW  CONST_07  C19  C18  C17  C13     0.00   0.0  0
 5SW  CONST_08  C19  C20  C21  C13     0.00   0.0  0
 5SW  CONST_09  C20  C21  C13  C17     0.00   0.0  0
 5SW  CONST_10  C20  C19  C18  C17     0.00   0.0  0
 5SW  CONST_11  C18  C17  C13  C21     0.00   0.0  0
 5SW  CONST_12  C18  C19  C20  C21     0.00   0.0  0
 5SW  CONST_13  C13  C17  C18  C10   180.00   0.0  0
 5SW  CONST_14  C20  C19  C18  C10   180.00   0.0  0
 5SW  CONST_15  C9   N8   C7   C6      0.00   0.0  0
 5SW  CONST_16  O23  C20  C21  C13   180.00   0.0  0
 5SW  CONST_17  C14  C21  C13  C17   180.00   0.0  0
 5SW  CONST_18  O22  C13  C21  C20   180.00   0.0  0
 5SW  CONST_19  O22  C13  C17  C18   180.00   0.0  0
 5SW  CONST_20  O23  C20  C19  C18   180.00   0.0  0
 5SW  CONST_21  C14  C21  C20  C19   180.00   0.0  0
 5SW  CONST_22  C12  N8   C7   C6    180.00   0.0  0
 5SW  CONST_23  O11  C7   N8   C9    180.00   0.0  0
 5SW  CONST_24  H9   C1   C2   N3    180.00   0.0  0
 5SW  CONST_25  H10  C2   N3   C4    180.00   0.0  0
 5SW  CONST_26  H1   C4   C6   C5    180.00   0.0  0
 5SW  CONST_27  H2   C17  C18  C10     0.00   0.0  0
 5SW  CONST_28  H21  C19  C18  C10     0.00   0.0  0
 5SW  CONST_29  O11  C7   N8   C12     0.00   0.0  0
 5SW  Var_01    C17  C18  C10  C5   -124.27  30.0  2
 5SW  Var_02    N15  C14  C21  C13    75.29  30.0  1
 5SW  Var_03    C19  C20  O23  C24    -4.24  30.0  1
 5SW  Var_04    H18  C12  N8   C7     63.28  30.0  3
 5SW  Var_05    C25  N15  C14  C21  -169.51  30.0  3
 5SW  Var_06    H6   C26  O22  C13  -176.19  30.0  3
 5SW  Var_07    H3   C24  O23  C20   -58.11  30.0  3
 5SW  Var_08    H14  C25  N15  C16  -176.66  30.0  3
 5SW  Var_09    H11  C16  N15  C25    56.37  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
 5SW  plan-1  C10  0.020
 5SW  plan-1  C13  0.020
 5SW  plan-1  C17  0.020
 5SW  plan-1  C20  0.020
 5SW  plan-1  C21  0.020
 5SW  plan-1  C18  0.020
 5SW  plan-1  C19  0.020
 5SW  plan-1  O23  0.020
 5SW  plan-1  O22  0.020
 5SW  plan-1  H2   0.020
 5SW  plan-1  H21  0.020
 5SW  plan-1  C14  0.020
 5SW  plan-2  N3   0.020
 5SW  plan-2  C4   0.020
 5SW  plan-2  C5   0.020
 5SW  plan-2  C6   0.020
 5SW  plan-2  C7   0.020
 5SW  plan-2  C10  0.020
 5SW  plan-2  C18  0.020
 5SW  plan-2  C1   0.020
 5SW  plan-2  N8   0.020
 5SW  plan-2  C2   0.020
 5SW  plan-2  C9   0.020
 5SW  plan-2  C12  0.020
 5SW  plan-2  O11  0.020
 5SW  plan-2  H1   0.020
 5SW  plan-2  H9   0.020
 5SW  plan-2  H10  0.020
 5SW  plan-2  H17  0.020

