# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 15:42:38 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: 7-(3,4-dimethoxyphenyl)-5-methyl-2-(4-methylsulfonylpiperazin-1-yl)carbonyl-thieno[3,2-c]pyridin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1OC)C2=CN(C)C(=O)c3cc(sc23)C(=O)N4CCN(CC4)[S](C)(=O)=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
 N1D  N1D  7-(3,4-dimethoxyphenyl)-5-methyl-2-(4-methylsulfonylpiperazin-1-yl)carbonyl-thieno[3,2-c]pyridin-4-one  ligand  58  33  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N1D
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
 N1D  C01   C  CH3   0  -0.439  -4.3959   5.3974   0.2715
 N1D  O05   O  O2    0  -0.461  -5.0116   4.2483  -0.2750
 N1D  C06   C  CR6   0   0.306  -4.4228   3.0580  -0.0695
 N1D  C07   C  CR16  0  -0.371  -3.2305   2.8643   0.6072
 N1D  C09   C  CR16  0  -0.325  -2.7090   1.5837   0.7758
 N1D  C11   C  CR6   0   0.038  -3.3730   0.4808   0.2645
 N1D  C12   C  CR16  0  -0.443  -4.5727   0.6739  -0.4323
 N1D  C14   C  CR6   0   0.332  -5.1027   1.9409  -0.6006
 N1D  O15   O  O2    0  -0.463  -6.2433   2.2158  -1.2567
 N1D  C16   C  CH3   0  -0.439  -6.9479   1.1439  -1.8505
 N1D  C20   C  CR6   0  -0.035  -2.8509  -0.8821   0.4692
 N1D  C21   C  CR16  0  -0.003  -3.6324  -1.8792   0.9652
 N1D  N23   N  NR6   0  -0.527  -3.1971  -3.1504   1.1846
 N1D  C24   C  CH3   0  -0.520  -4.1197  -4.1466   1.7141
 N1D  C28   C  CR6   0   0.555  -1.8986  -3.5647   0.9398
 N1D  O29   O  O     0  -0.485  -1.5500  -4.7161   1.1653
 N1D  C30   C  CR56  0  -0.020  -1.0428  -2.5368   0.4001
 N1D  C31   C  CR15  0  -0.172   0.3033  -2.7092  -0.0090
 N1D  C33   C  CR5   0  -0.342   0.8451  -1.5702  -0.5162
 N1D  S34   S  S2    0   0.274  -0.3055  -0.2639  -0.5365
 N1D  C35   C  CR56  0  -0.150  -1.5150  -1.2548   0.1744
 N1D  C36   C  C     0   0.549   2.1884  -1.5071  -1.1434
 N1D  O37   O  O     0  -0.466   2.6002  -2.4938  -1.7346
 N1D  N38   N  NT    0  -0.473   2.8808  -0.3436  -1.0888
 N1D  C39   C  CH2   0  -0.329   2.7867   0.6500  -0.0328
 N1D  C42   C  CH2   0  -0.297   4.0000   0.5783   0.8852
 N1D  N45   N  N     0  -0.585   5.2237   0.6973   0.0951
 N1D  C46   C  CH2   0  -0.309   5.3282  -0.3246  -0.9460
 N1D  C49   C  CH2   0  -0.323   4.1120  -0.2130  -1.8476
 N1D  S52   S  S     0   1.351   6.6114   1.0955   0.9074
 N1D  C53   C  CH3   0  -0.806   6.9928  -0.2798   1.9694
 N1D  O57   O  OS    0  -0.665   7.6668   1.2054  -0.0880
 N1D  O58   O  OS    0  -0.664   6.3051   2.2467   1.7415
 N1D  H011  H  HCH3  0   0.261  -5.0267   6.2417   0.0049
 N1D  H012  H  HCH3  0   0.230  -4.3231   5.3407   1.3609
 N1D  H013  H  HCH3  0   0.229  -3.3962   5.5604  -0.1397
 N1D  H07   H  HCR6  0   0.286  -2.6923   3.7030   1.0276
 N1D  H09   H  HCR6  0   0.258  -1.7963   1.4638   1.3453
 N1D  H12   H  HCR6  0   0.282  -5.0745  -0.1890  -0.8504
 N1D  H161  H  HCH3  0   0.229  -7.2888   0.4172  -1.1082
 N1D  H162  H  HCH3  0   0.262  -7.8161   1.5786  -2.3395
 N1D  H163  H  HCH3  0   0.230  -6.3436   0.6257  -2.5998
 N1D  H21   H  HCR6  0   0.310  -4.6638  -1.6918   1.2287
 N1D  H241  H  HCH3  0   0.263  -4.2173  -4.9809   1.0229
 N1D  H242  H  HCH3  0   0.263  -3.7691  -4.5229   2.6728
 N1D  H243  H  HCH3  0   0.260  -5.0942  -3.6895   1.8517
 N1D  H31   H  HCR5  0   0.278   0.8429  -3.6421   0.0666
 N1D  H391  H  HCH2  0   0.268   2.7204   1.6434  -0.4816
 N1D  H392  H  HCH2  0   0.283   1.9034   0.5012   0.5815
 N1D  H491  H  HCH2  0   0.282   4.1590  -0.9734  -2.6215
 N1D  H492  H  HCH2  0   0.268   4.1099   0.7660  -2.3336
 N1D  H421  H  HCH2  0   0.287   3.9357   1.3982   1.5981
 N1D  H422  H  HCH2  0   0.246   3.9742  -0.3658   1.4449
 N1D  H461  H  HCH2  0   0.285   6.2224  -0.1604  -1.5427
 N1D  H462  H  HCH2  0   0.247   5.3806  -1.3329  -0.5165
 N1D  H531  H  HCH3  0   0.293   7.0760  -1.1875   1.3751
 N1D  H532  H  HCH3  0   0.313   7.9444  -0.0718   2.4560
 N1D  H533  H  HCH3  0   0.293   6.2150  -0.3916   2.7211

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
 N1D  C01  O05   single    1.414  0.020  1.414
 N1D  O05  C06   single    1.344  0.020  1.344
 N1D  C06  C07   aromatic  1.385  0.020  1.385
 N1D  C06  C14   aromatic  1.411  0.020  1.411
 N1D  C07  C09   aromatic  1.393  0.020  1.393
 N1D  C09  C11   aromatic  1.385  0.020  1.385
 N1D  C11  C12   aromatic  1.401  0.020  1.401
 N1D  C11  C20   single    1.474  0.020  1.474
 N1D  C12  C14   aromatic  1.384  0.020  1.384
 N1D  C14  O15   single    1.344  0.020  1.344
 N1D  O15  C16   single    1.414  0.020  1.414
 N1D  C20  C21   double    1.361  0.020  1.361
 N1D  C20  C35   single    1.418  0.020  1.418
 N1D  C21  N23   single    1.361  0.020  1.361
 N1D  N23  C24   single    1.457  0.020  1.457
 N1D  N23  C28   single    1.385  0.020  1.385
 N1D  C28  O29   double    1.224  0.020  1.224
 N1D  C28  C30   single    1.442  0.020  1.442
 N1D  C30  C31   aromatic  1.417  0.020  1.417
 N1D  C30  C35   aromatic  1.385  0.020  1.385
 N1D  C31  C33   aromatic  1.359  0.020  1.359
 N1D  C33  S34   aromatic  1.741  0.020  1.741
 N1D  C33  C36   single    1.484  0.020  1.484
 N1D  S34  C35   aromatic  1.718  0.020  1.718
 N1D  C36  O37   double    1.222  0.020  1.222
 N1D  C36  N38   single    1.355  0.020  1.355
 N1D  N38  C39   single    1.453  0.020  1.453
 N1D  N38  C49   single    1.452  0.020  1.452
 N1D  C39  C42   single    1.523  0.020  1.523
 N1D  C42  N45   single    1.461  0.020  1.461
 N1D  N45  C46   single    1.463  0.020  1.463
 N1D  N45  S52   single    1.657  0.020  1.657
 N1D  C46  C49   single    1.518  0.020  1.518
 N1D  S52  C53   single    1.779  0.020  1.779
 N1D  S52  O57   double    1.455  0.020  1.455
 N1D  S52  O58   double    1.454  0.020  1.454
 N1D  C01  H011  single    0.970  0.020  1.090
 N1D  C01  H012  single    0.970  0.020  1.090
 N1D  C01  H013  single    0.970  0.020  1.090
 N1D  C07  H07   single    0.930  0.020  1.080
 N1D  C09  H09   single    0.930  0.020  1.080
 N1D  C12  H12   single    0.930  0.020  1.080
 N1D  C16  H161  single    0.970  0.020  1.090
 N1D  C16  H162  single    0.970  0.020  1.090
 N1D  C16  H163  single    0.970  0.020  1.090
 N1D  C21  H21   single    0.930  0.020  1.080
 N1D  C24  H241  single    0.970  0.020  1.090
 N1D  C24  H242  single    0.970  0.020  1.090
 N1D  C24  H243  single    0.970  0.020  1.090
 N1D  C31  H31   single    0.930  0.020  1.080
 N1D  C39  H391  single    0.970  0.020  1.090
 N1D  C39  H392  single    0.970  0.020  1.090
 N1D  C49  H491  single    0.970  0.020  1.090
 N1D  C49  H492  single    0.970  0.020  1.090
 N1D  C42  H421  single    0.970  0.020  1.090
 N1D  C42  H422  single    0.970  0.020  1.090
 N1D  C46  H461  single    0.970  0.020  1.090
 N1D  C46  H462  single    0.970  0.020  1.090
 N1D  C53  H531  single    0.970  0.020  1.090
 N1D  C53  H532  single    0.970  0.020  1.090
 N1D  C53  H533  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
 N1D  H013  C01  H012  108.76  3.000
 N1D  H013  C01  H011  108.82  3.000
 N1D  H012  C01  H011  108.86  3.000
 N1D  H013  C01  O05   111.97  3.000
 N1D  H012  C01  O05   111.84  3.000
 N1D  H011  C01  O05   106.49  3.000
 N1D  C06   O05  C01   118.04  3.000
 N1D  C14   C06  C07   119.21  3.000
 N1D  C14   C06  O05   115.62  3.000
 N1D  C07   C06  O05   125.17  3.000
 N1D  H07   C07  C09   118.66  3.000
 N1D  H07   C07  C06   120.66  3.000
 N1D  C09   C07  C06   120.67  3.000
 N1D  H09   C09  C11   120.67  3.000
 N1D  H09   C09  C07   118.76  3.000
 N1D  C11   C09  C07   120.53  3.000
 N1D  C20   C11  C12   120.00  3.000
 N1D  C20   C11  C09   121.01  3.000
 N1D  C12   C11  C09   118.97  3.000
 N1D  H12   C12  C14   120.37  3.000
 N1D  H12   C12  C11   118.64  3.000
 N1D  C14   C12  C11   120.99  3.000
 N1D  O15   C14  C12   124.86  3.000
 N1D  O15   C14  C06   115.50  3.000
 N1D  C12   C14  C06   119.63  3.000
 N1D  C16   O15  C14   118.23  3.000
 N1D  H163  C16  H162  108.83  3.000
 N1D  H163  C16  H161  108.82  3.000
 N1D  H162  C16  H161  108.80  3.000
 N1D  H163  C16  O15   111.83  3.000
 N1D  H162  C16  O15   106.49  3.000
 N1D  H161  C16  O15   111.98  3.000
 N1D  C35   C20  C21   115.11  3.000
 N1D  C35   C20  C11   123.23  3.000
 N1D  C21   C20  C11   121.66  3.000
 N1D  H21   C21  N23   115.32  3.000
 N1D  H21   C21  C20   120.66  3.000
 N1D  N23   C21  C20   124.01  3.000
 N1D  C28   N23  C24   116.95  3.000
 N1D  C28   N23  C21   123.41  3.000
 N1D  C24   N23  C21   119.63  3.000
 N1D  H243  C24  H242  108.86  3.000
 N1D  H243  C24  H241  108.85  3.000
 N1D  H242  C24  H241  108.89  3.000
 N1D  H243  C24  N23   109.06  3.000
 N1D  H242  C24  N23   110.65  3.000
 N1D  H241  C24  N23   110.50  3.000
 N1D  C30   C28  O29   124.77  3.000
 N1D  C30   C28  N23   114.16  3.000
 N1D  O29   C28  N23   121.06  3.000
 N1D  C35   C30  C31   112.91  3.000
 N1D  C35   C30  C28   121.23  3.000
 N1D  C31   C30  C28   125.79  3.000
 N1D  H31   C31  C33   123.40  3.000
 N1D  H31   C31  C30   123.99  3.000
 N1D  C33   C31  C30   112.60  3.000
 N1D  C36   C33  S34   124.16  3.000
 N1D  C36   C33  C31   123.65  3.000
 N1D  S34   C33  C31   111.69  3.000
 N1D  C35   S34  C33    91.59  3.000
 N1D  S34   C35  C30   111.19  3.000
 N1D  S34   C35  C20   126.72  3.000
 N1D  C30   C35  C20   122.06  3.000
 N1D  N38   C36  O37   122.73  3.000
 N1D  N38   C36  C33   118.82  3.000
 N1D  O37   C36  C33   118.38  3.000
 N1D  C49   N38  C39   111.91  3.000
 N1D  C49   N38  C36   119.30  3.000
 N1D  C39   N38  C36   125.69  3.000
 N1D  H392  C39  H391  107.91  3.000
 N1D  H392  C39  C42   107.49  3.000
 N1D  H391  C39  C42   109.81  3.000
 N1D  H392  C39  N38   111.72  3.000
 N1D  H391  C39  N38   109.11  3.000
 N1D  C42   C39  N38   110.75  3.000
 N1D  H422  C42  H421  108.21  3.000
 N1D  H422  C42  N45   111.43  3.000
 N1D  H421  C42  N45   110.01  3.000
 N1D  H422  C42  C39   109.21  3.000
 N1D  H421  C42  C39   108.19  3.000
 N1D  N45   C42  C39   109.71  3.000
 N1D  S52   N45  C46   117.20  3.000
 N1D  S52   N45  C42   117.12  3.000
 N1D  C46   N45  C42   112.82  3.000
 N1D  H462  C46  H461  108.32  3.000
 N1D  H462  C46  C49   109.77  3.000
 N1D  H461  C46  C49   108.77  3.000
 N1D  H462  C46  N45   111.52  3.000
 N1D  H461  C46  N45   110.11  3.000
 N1D  C49   C46  N45   108.31  3.000
 N1D  H492  C49  H491  108.08  3.000
 N1D  H492  C49  C46   109.36  3.000
 N1D  H491  C49  C46   109.70  3.000
 N1D  H492  C49  N38   108.14  3.000
 N1D  H491  C49  N38   110.25  3.000
 N1D  C46   C49  N38   111.24  3.000
 N1D  O58   S52  O57   119.03  3.000
 N1D  O58   S52  C53   108.35  3.000
 N1D  O57   S52  C53   108.14  3.000
 N1D  O58   S52  N45   107.16  3.000
 N1D  O57   S52  N45   106.88  3.000
 N1D  C53   S52  N45   106.65  3.000
 N1D  H533  C53  H532  109.63  3.000
 N1D  H533  C53  H531  110.27  3.000
 N1D  H532  C53  H531  109.67  3.000
 N1D  H533  C53  S52   109.80  3.000
 N1D  H532  C53  S52   107.85  3.000
 N1D  H531  C53  S52   109.59  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
 N1D  CONST_01  C11   C09  C07  C06     0.00   0.0  0
 N1D  CONST_02  C11   C12  C14  C06     0.00   0.0  0
 N1D  CONST_03  C12   C14  C06  C07     0.00   0.0  0
 N1D  CONST_04  C12   C11  C09  C07     0.00   0.0  0
 N1D  CONST_05  C14   C06  C07  C09     0.00   0.0  0
 N1D  CONST_06  C14   C12  C11  C09     0.00   0.0  0
 N1D  CONST_07  S34   C33  C31  C30     0.00   0.0  0
 N1D  CONST_08  C33   S34  C35  C30     0.00   0.0  0
 N1D  CONST_09  S34   C35  C30  C31     0.00   0.0  0
 N1D  CONST_10  C35   S34  C33  C31     0.00   0.0  0
 N1D  CONST_11  C35   C30  C31  C33     0.00   0.0  0
 N1D  CONST_12  C20   C11  C09  C07   180.00   0.0  0
 N1D  CONST_13  C20   C11  C12  C14   180.00   0.0  0
 N1D  CONST_14  C30   C28  N23  C21     0.00   0.0  0
 N1D  CONST_15  C09   C07  C06  O05   180.00   0.0  0
 N1D  CONST_16  C12   C14  C06  O05   180.00   0.0  0
 N1D  CONST_17  O15   C14  C06  C07   180.00   0.0  0
 N1D  CONST_18  O15   C14  C12  C11   180.00   0.0  0
 N1D  CONST_19  C36   C33  C31  C30   180.00   0.0  0
 N1D  CONST_20  C36   C33  S34  C35   180.00   0.0  0
 N1D  CONST_22  C49   N38  C36  C33   180.00   0.0  0
 N1D  CONST_23  O29   C28  N23  C21   180.00   0.0  0
 N1D  CONST_24  C30   C28  N23  C24   180.00   0.0  0
 N1D  CONST_25  H09   C09  C07  C06   180.00   0.0  0
 N1D  CONST_26  H12   C12  C14  C06   180.00   0.0  0
 N1D  CONST_27  H07   C07  C09  C11   180.00   0.0  0
 N1D  CONST_28  H31   C31  C30  C28     0.00   0.0  0
 N1D  CONST_30  C49   N38  C36  O37     0.00   0.0  0
 N1D  CONST_31  O29   C28  N23  C24     0.00   0.0  0
 N1D  Var_01    C21   C20  C11  C09   128.48  30.0  2
 N1D  Var_02    N45   C42  C39  N38    54.53  30.0  1
 N1D  Var_03    N45   C46  C49  N38   -56.88  30.0  1
 N1D  Var_04    C46   C49  N38  C39    57.50  30.0  1
 N1D  Var_05    C46   N45  C42  C39   -57.21  30.0  1
 N1D  Var_06    C49   N38  C39  C42   -55.75  30.0  1
 N1D  Var_07    C49   C46  N45  C42    57.86  30.0  1
 N1D  Var_08    N38   C36  C33  C31  -151.49  30.0  2
 N1D  Var_09    C07   C06  O05  C01    -1.98  30.0  2
 N1D  Var_10    C53   S52  N45  C42    66.73  30.0  3
 N1D  Var_11    H241  C24  N23  C21   120.39  30.0  3
 N1D  Var_12    H011  C01  O05  C06  -179.38  30.0  3
 N1D  Var_13    H161  C16  O15  C14    62.30  30.0  3
 N1D  Var_14    H531  C53  S52  N45    56.34  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
 N1D  plan-1  O05  0.020
 N1D  plan-1  C06  0.020
 N1D  plan-1  C07  0.020
 N1D  plan-1  C09  0.020
 N1D  plan-1  C11  0.020
 N1D  plan-1  C12  0.020
 N1D  plan-1  C14  0.020
 N1D  plan-1  O15  0.020
 N1D  plan-1  C20  0.020
 N1D  plan-1  H07  0.020
 N1D  plan-1  H09  0.020
 N1D  plan-1  H12  0.020
 N1D  plan-2  C11  0.020
 N1D  plan-2  C20  0.020
 N1D  plan-2  C21  0.020
 N1D  plan-2  N23  0.020
 N1D  plan-2  C24  0.020
 N1D  plan-2  C28  0.020
 N1D  plan-2  O29  0.020
 N1D  plan-2  C30  0.020
 N1D  plan-2  C31  0.020
 N1D  plan-2  C33  0.020
 N1D  plan-2  S34  0.020
 N1D  plan-2  C35  0.020
 N1D  plan-2  C36  0.020
 N1D  plan-2  H21  0.020
 N1D  plan-2  H31  0.020
 N1D  plan-3  C33  0.020
 N1D  plan-3  C36  0.020
 N1D  plan-3  O37  0.020
 N1D  plan-3  N38  0.020
 N1D  plan-3  C39  0.020
 N1D  plan-3  C49  0.020

