# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 23:33:55 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 4-[(3-chlorophenyl)methyl]-N-[[(3S)-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]-3-oxidanylidene-1,4-benzothiazine-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(CN2C(=O)CSc3ccc(cc23)C(=O)NC[C@H]4COc5ccccc5O4)c1
#
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
 R4N  R4N  4-[(3-chlorophenyl)methyl]-N-[[(3S)-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]-3-oxidanylidene-1,4-benzothiazine-6-carboxamide  ligand  54  33  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R4N
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
 R4N  C1    C   CR16  0  -0.267  -7.0187   0.8858   2.6131
 R4N  C2    C   CR16  0  -0.267  -6.3243  -0.3117   2.7328
 R4N  C3    C   CR16  0  -0.245   3.2373   1.1759   2.5161
 R4N  C4    C   CR16  0  -0.308  -0.0829  -2.2430  -0.4496
 R4N  C5    C   CR16  0  -0.268   3.7400   0.5033   1.4137
 R4N  C6    C   CR16  0  -0.363  -6.8183   1.6942   1.5044
 R4N  C7    C   CR16  0  -0.361  -5.4149  -0.6853   1.7551
 R4N  C8    C   CR16  0  -0.256   0.9433  -3.0507   0.0061
 R4N  C9    C   CR16  0  -0.230   2.5814   2.3911   2.3675
 R4N  C10   C   CR16  0  -0.313   1.5390  -0.7352  -1.3815
 R4N  C11   C   CR16  0  -0.263   2.9292   2.2498  -0.0205
 R4N  C12   C   CR6   0  -0.022   0.2127  -1.0883  -1.1682
 R4N  C13   C   CR6   0   0.100   3.5922   1.0400   0.1383
 R4N  C14   C   CR6   0   0.458   2.5794  -1.5218  -0.9036
 R4N  C15   C   CR6   0   0.313  -5.9155   1.3203   0.5173
 R4N  C16   C   CR6   0   0.311  -5.2023   0.1252   0.6471
 R4N  C17   C   CR6   0  -0.192   2.2679  -2.7039  -0.2216
 R4N  C18   C   CR6   0  -0.021   2.4367   2.9125   1.0931
 R4N  C19   C   C     0   0.553   4.9772  -1.9510  -1.1377
 R4N  C20   C   C     0   0.543  -0.8395  -0.1668  -1.6985
 R4N  C21   C   CH2   0  -0.711   4.6431  -3.4189  -1.0705
 R4N  C22   C   CH2   0  -0.194  -5.1033   1.5230  -1.6582
 R4N  C23   C   CH1   0  -0.027  -3.8909   0.7426  -1.1928
 R4N  C25   C   CH2   0  -0.322  -3.1841   0.0604  -2.3513
 R4N  N26   N   NT    0  -0.573   3.9136  -1.0925  -1.0418
 R4N  N27   N   NH1   0  -0.651  -2.0452  -0.7145  -1.9273
 R4N  O28   O   O     0  -0.450   6.1209  -1.5645  -1.2703
 R4N  O29   O   O     0  -0.477  -0.5963   1.0117  -1.9158
 R4N  O30   O   O2    0  -0.480  -5.7504   2.1324  -0.5551
 R4N  O31   O   O2    0  -0.484  -4.2988  -0.2695  -0.2817
 R4N  S32   S   S2    0   0.106   3.5676  -3.7323   0.3455
 R4N  CL33  CL  CL    0  -0.130   1.6070   4.4204   0.8783
 R4N  H1    H   HCR6  0   0.256  -7.7240   1.1882   3.3755
 R4N  H2    H   HCR6  0   0.256  -6.4796  -0.9527   3.5902
 R4N  H6    H   HCR6  0   0.266  -7.3616   2.6246   1.3937
 R4N  H7    H   HCR6  0   0.265  -4.8601  -1.6115   1.8405
 R4N  H5    H   HCR6  0   0.253   4.2418  -0.4467   1.5524
 R4N  H9    H   HCR6  0   0.280   2.1898   2.9159   3.2281
 R4N  H4    H   HCR6  0   0.263  -1.1022  -2.5276  -0.2246
 R4N  H8    H   HCR6  0   0.278   0.7149  -3.9617   0.5435
 R4N  H10   H   HCR6  0   0.276   1.7472   0.1709  -1.9316
 R4N  H11   H   HCR6  0   0.277   2.7939   2.6698  -1.0095
 R4N  H211  H   HCH2  0   0.325   4.1541  -3.7550  -1.9876
 R4N  H212  H   HCH2  0   0.327   5.5592  -3.9889  -0.9339
 R4N  H27   H   HNH1  0   0.414  -2.1810  -1.7016  -1.7905
 R4N  H221  H   HCH2  0   0.263  -4.8076   2.3242  -2.3343
 R4N  H222  H   HCH2  0   0.239  -5.7987   0.8614  -2.1885
 R4N  H23   H   HCH1  0   0.259  -3.1968   1.4256  -0.6864
 R4N  H251  H   HCH2  0   0.273  -3.8740  -0.6086  -2.8667
 R4N  H252  H   HCH2  0   0.265  -2.8719   0.8192  -3.0693
 R4N  C24   C   CH2   0  -0.401   4.1671   0.3433  -1.0670
 R4N  H3    H   HCR6  0   0.269   3.3554   0.7548   3.5055
 R4N  H241  H   HCH2  0   0.280   3.7851   0.7881  -1.9883
 R4N  H242  H   HCH2  0   0.309   5.2463   0.4784  -1.0922

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
 R4N  C1   C2    aromatic  1.389  0.020  1.389
 R4N  C1   C6    aromatic  1.387  0.020  1.387
 R4N  C2   C7    aromatic  1.387  0.020  1.387
 R4N  C3   C5    aromatic  1.386  0.020  1.386
 R4N  C3   C9    aromatic  1.389  0.020  1.389
 R4N  C4   C8    aromatic  1.383  0.020  1.383
 R4N  C4   C12   aromatic  1.392  0.020  1.392
 R4N  C5   C13   aromatic  1.392  0.020  1.392
 R4N  C6   C15   aromatic  1.389  0.020  1.389
 R4N  C7   C16   aromatic  1.389  0.020  1.389
 R4N  C8   C17   aromatic  1.388  0.020  1.388
 R4N  C9   C18   aromatic  1.385  0.020  1.385
 R4N  C10  C12   aromatic  1.389  0.020  1.389
 R4N  C10  C14   aromatic  1.389  0.020  1.389
 R4N  C11  C13   aromatic  1.389  0.020  1.389
 R4N  C11  C18   aromatic  1.386  0.020  1.386
 R4N  C12  C20   single    1.496  0.020  1.496
 R4N  C13  C24   single    1.506  0.020  1.506
 R4N  C14  C17   aromatic  1.400  0.020  1.400
 R4N  C14  N26   single    1.408  0.020  1.408
 R4N  C15  C16   aromatic  1.398  0.020  1.398
 R4N  C15  O30   single    1.355  0.020  1.355
 R4N  C16  O31   single    1.355  0.020  1.355
 R4N  C17  S32   single    1.752  0.020  1.752
 R4N  C18  CL33  single    1.734  0.020  1.734
 R4N  C19  C21   single    1.507  0.020  1.507
 R4N  C19  N26   single    1.370  0.020  1.370
 R4N  C19  O28   double    1.215  0.020  1.215
 R4N  C20  N27   single    1.344  0.020  1.344
 R4N  C20  O29   double    1.223  0.020  1.223
 R4N  C21  S32   single    1.806  0.020  1.806
 R4N  C22  C23   single    1.515  0.020  1.515
 R4N  C22  O30   single    1.417  0.020  1.417
 R4N  C23  C25   single    1.519  0.020  1.519
 R4N  C23  O31   single    1.422  0.020  1.422
 R4N  C24  N26   single    1.458  0.020  1.458
 R4N  C25  N27   single    1.441  0.020  1.441
 R4N  C1   H1    single    0.930  0.020  1.080
 R4N  C2   H2    single    0.930  0.020  1.080
 R4N  C6   H6    single    0.930  0.020  1.080
 R4N  C7   H7    single    0.930  0.020  1.080
 R4N  C3   H3    single    0.930  0.020  1.080
 R4N  C5   H5    single    0.930  0.020  1.080
 R4N  C9   H9    single    0.930  0.020  1.080
 R4N  C4   H4    single    0.930  0.020  1.080
 R4N  C8   H8    single    0.930  0.020  1.080
 R4N  C10  H10   single    0.930  0.020  1.080
 R4N  C11  H11   single    0.930  0.020  1.080
 R4N  C24  H241  single    0.970  0.020  1.090
 R4N  C24  H242  single    0.970  0.020  1.090
 R4N  C21  H211  single    0.970  0.020  1.090
 R4N  C21  H212  single    0.970  0.020  1.090
 R4N  N27  H27   single    0.860  0.020  1.020
 R4N  C22  H221  single    0.970  0.020  1.090
 R4N  C22  H222  single    0.970  0.020  1.090
 R4N  C23  H23   single    0.970  0.020  1.090
 R4N  C25  H251  single    0.970  0.020  1.090
 R4N  C25  H252  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
 R4N  H1    C1   C6    119.65  3.000
 R4N  H1    C1   C2    120.41  3.000
 R4N  C6    C1   C2    119.94  3.000
 R4N  H2    C2   C7    119.56  3.000
 R4N  H2    C2   C1    120.48  3.000
 R4N  C7    C2   C1    119.96  3.000
 R4N  H3    C3   C9    119.34  3.000
 R4N  H3    C3   C5    119.94  3.000
 R4N  C9    C3   C5    120.72  3.000
 R4N  H4    C4   C12   121.71  3.000
 R4N  H4    C4   C8    118.48  3.000
 R4N  C12   C4   C8    119.80  3.000
 R4N  H5    C5   C13   120.31  3.000
 R4N  H5    C5   C3    119.46  3.000
 R4N  C13   C5   C3    120.23  3.000
 R4N  H6    C6   C15   118.99  3.000
 R4N  H6    C6   C1    120.66  3.000
 R4N  C15   C6   C1    120.34  3.000
 R4N  H7    C7   C16   118.91  3.000
 R4N  H7    C7   C2    120.72  3.000
 R4N  C16   C7   C2    120.37  3.000
 R4N  H8    C8   C17   119.55  3.000
 R4N  H8    C8   C4    119.91  3.000
 R4N  C17   C8   C4    120.53  3.000
 R4N  H9    C9   C18   120.79  3.000
 R4N  H9    C9   C3    120.69  3.000
 R4N  C18   C9   C3    118.51  3.000
 R4N  H10   C10  C14   120.39  3.000
 R4N  H10   C10  C12   118.39  3.000
 R4N  C14   C10  C12   121.23  3.000
 R4N  H11   C11  C18   120.25  3.000
 R4N  H11   C11  C13   120.13  3.000
 R4N  C18   C11  C13   119.62  3.000
 R4N  C20   C12  C10   117.43  3.000
 R4N  C20   C12  C4    123.01  3.000
 R4N  C10   C12  C4    119.53  3.000
 R4N  C24   C13  C11   119.58  3.000
 R4N  C24   C13  C5    120.97  3.000
 R4N  C11   C13  C5    119.44  3.000
 R4N  N26   C14  C17   121.07  3.000
 R4N  N26   C14  C10   120.21  3.000
 R4N  C17   C14  C10   118.63  3.000
 R4N  O30   C15  C16   121.57  3.000
 R4N  O30   C15  C6    118.70  3.000
 R4N  C16   C15  C6    119.73  3.000
 R4N  O31   C16  C15   121.72  3.000
 R4N  O31   C16  C7    118.62  3.000
 R4N  C15   C16  C7    119.66  3.000
 R4N  S32   C17  C14   119.23  3.000
 R4N  S32   C17  C8    120.55  3.000
 R4N  C14   C17  C8    120.22  3.000
 R4N  CL33  C18  C11   119.08  3.000
 R4N  CL33  C18  C9    119.43  3.000
 R4N  C11   C18  C9    121.48  3.000
 R4N  O28   C19  N26   122.63  3.000
 R4N  O28   C19  C21   121.58  3.000
 R4N  N26   C19  C21   115.79  3.000
 R4N  O29   C20  N27   122.75  3.000
 R4N  O29   C20  C12   121.12  3.000
 R4N  N27   C20  C12   116.13  3.000
 R4N  H212  C21  H211  108.74  3.000
 R4N  H212  C21  S32   108.20  3.000
 R4N  H211  C21  S32   109.78  3.000
 R4N  H212  C21  C19   109.23  3.000
 R4N  H211  C21  C19   111.19  3.000
 R4N  S32   C21  C19   109.64  3.000
 R4N  H222  C22  H221  108.40  3.000
 R4N  H222  C22  O30   110.27  3.000
 R4N  H221  C22  O30   106.91  3.000
 R4N  H222  C22  C23   110.20  3.000
 R4N  H221  C22  C23   110.63  3.000
 R4N  O30   C22  C23   110.36  3.000
 R4N  H23   C23  O31   109.19  3.000
 R4N  H23   C23  C25   109.70  3.000
 R4N  O31   C23  C25   107.61  3.000
 R4N  H23   C23  C22   109.10  3.000
 R4N  O31   C23  C22   109.51  3.000
 R4N  C25   C23  C22   111.68  3.000
 R4N  H252  C25  H251  107.27  3.000
 R4N  H252  C25  N27   109.98  3.000
 R4N  H251  C25  N27   108.00  3.000
 R4N  H252  C25  C23   108.84  3.000
 R4N  H251  C25  C23   109.98  3.000
 R4N  N27   C25  C23   112.63  3.000
 R4N  C24   N26  C19   118.73  3.000
 R4N  C24   N26  C14   117.81  3.000
 R4N  C19   N26  C14   123.45  3.000
 R4N  H27   N27  C25   117.46  3.000
 R4N  H27   N27  C20   119.86  3.000
 R4N  C25   N27  C20   122.67  3.000
 R4N  C22   O30  C15   114.46  3.000
 R4N  C23   O31  C16   115.05  3.000
 R4N  C21   S32  C17    94.95  3.000
 R4N  H242  C24  H241  106.07  3.000
 R4N  H242  C24  N26   107.17  3.000
 R4N  H241  C24  N26   110.78  3.000
 R4N  H242  C24  C13   109.86  3.000
 R4N  H241  C24  C13   110.68  3.000
 R4N  N26   C24  C13   112.04  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
 R4N  CONST_01  C16   C7   C2   C1      0.00   0.0  0
 R4N  CONST_02  C16   C15  C6   C1      0.00   0.0  0
 R4N  CONST_03  C15   C6   C1   C2      0.00   0.0  0
 R4N  CONST_04  C15   C16  C7   C2      0.00   0.0  0
 R4N  CONST_05  C11   C13  C5   C3      0.00   0.0  0
 R4N  CONST_06  C11   C18  C9   C3      0.00   0.0  0
 R4N  CONST_07  C14   C17  C8   C4      0.00   0.0  0
 R4N  CONST_08  C14   C10  C12  C4      0.00   0.0  0
 R4N  CONST_09  C18   C9   C3   C5      0.00   0.0  0
 R4N  CONST_10  C18   C11  C13  C5      0.00   0.0  0
 R4N  CONST_11  C7    C2   C1   C6      0.00   0.0  0
 R4N  CONST_12  C7    C16  C15  C6      0.00   0.0  0
 R4N  CONST_13  C10   C12  C4   C8      0.00   0.0  0
 R4N  CONST_14  C10   C14  C17  C8      0.00   0.0  0
 R4N  CONST_15  C13   C5   C3   C9      0.00   0.0  0
 R4N  CONST_16  C13   C11  C18  C9      0.00   0.0  0
 R4N  CONST_17  C17   C8   C4   C12     0.00   0.0  0
 R4N  CONST_18  C17   C14  C10  C12     0.00   0.0  0
 R4N  CONST_19  C21   C19  N26  C14     0.00   0.0  0
 R4N  CONST_20  C24   C13  C5   C3    180.00   0.0  0
 R4N  CONST_21  CL33  C18  C9   C3    180.00   0.0  0
 R4N  CONST_22  C20   C12  C4   C8    180.00   0.0  0
 R4N  CONST_23  CL33  C18  C11  C13   180.00   0.0  0
 R4N  CONST_24  C20   C12  C10  C14   180.00   0.0  0
 R4N  CONST_25  C24   C13  C11  C18   180.00   0.0  0
 R4N  CONST_26  O28   C19  N26  C14   180.00   0.0  0
 R4N  CONST_27  C24   N26  C19  C21   180.00   0.0  0
 R4N  CONST_28  H7    C7   C2   C1    180.00   0.0  0
 R4N  CONST_29  H6    C6   C1   C2    180.00   0.0  0
 R4N  CONST_30  H10   C10  C12  C4    180.00   0.0  0
 R4N  CONST_31  H9    C9   C3   C5    180.00   0.0  0
 R4N  CONST_32  H11   C11  C13  C5    180.00   0.0  0
 R4N  CONST_33  H2    C2   C1   C6    180.00   0.0  0
 R4N  CONST_34  H1    C1   C2   C7    180.00   0.0  0
 R4N  CONST_35  H5    C5   C3   C9    180.00   0.0  0
 R4N  CONST_36  H4    C4   C12  C10   180.00   0.0  0
 R4N  CONST_37  H8    C8   C4   C12   180.00   0.0  0
 R4N  CONST_38  H3    C3   C5   C13   180.00   0.0  0
 R4N  CONST_39  O28   C19  N26  C24     0.00   0.0  0
 R4N  CONST_40  C25   N27  C20  C12   180.00   0.0  0
 R4N  CONST_41  H27   N27  C20  C12     0.00   0.0  0
 R4N  CONST_42  O29   C20  N27  C25     0.00   0.0  0
 R4N  Var_01    C19   N26  C14  C10  -151.68  30.0  1
 R4N  Var_02    C23   C22  O30  C15   -45.49  30.0  1
 R4N  Var_03    C19   C21  S32  C17    61.29  30.0  1
 R4N  Var_04    S32   C21  C19  N26   -49.14  30.0  1
 R4N  Var_05    N26   C24  C13  C5     44.16  30.0  2
 R4N  Var_06    C14   N26  C24  C13    54.67  30.0  3
 R4N  Var_07    N27   C20  C12  C4    -25.30  30.0  2
 R4N  Var_08    C23   C25  N27  C20   -82.37  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
 R4N  chir_01  C23  C22  C25  O31  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
 R4N  plan-1  C3    0.020
 R4N  plan-1  C5    0.020
 R4N  plan-1  C9    0.020
 R4N  plan-1  C11   0.020
 R4N  plan-1  C13   0.020
 R4N  plan-1  C18   0.020
 R4N  plan-1  CL33  0.020
 R4N  plan-1  H5    0.020
 R4N  plan-1  H9    0.020
 R4N  plan-1  H11   0.020
 R4N  plan-1  C24   0.020
 R4N  plan-1  H3    0.020
 R4N  plan-2  C1    0.020
 R4N  plan-2  C2    0.020
 R4N  plan-2  C6    0.020
 R4N  plan-2  C7    0.020
 R4N  plan-2  C15   0.020
 R4N  plan-2  C16   0.020
 R4N  plan-2  O30   0.020
 R4N  plan-2  O31   0.020
 R4N  plan-2  H1    0.020
 R4N  plan-2  H2    0.020
 R4N  plan-2  H6    0.020
 R4N  plan-2  H7    0.020
 R4N  plan-3  C4    0.020
 R4N  plan-3  C8    0.020
 R4N  plan-3  C10   0.020
 R4N  plan-3  C12   0.020
 R4N  plan-3  C14   0.020
 R4N  plan-3  C17   0.020
 R4N  plan-3  C20   0.020
 R4N  plan-3  N26   0.020
 R4N  plan-3  S32   0.020
 R4N  plan-3  H4    0.020
 R4N  plan-3  H8    0.020
 R4N  plan-3  H10   0.020
 R4N  plan-4  C12   0.020
 R4N  plan-4  C20   0.020
 R4N  plan-4  C25   0.020
 R4N  plan-4  N27   0.020
 R4N  plan-4  O29   0.020
 R4N  plan-4  H27   0.020
 R4N  plan-5  C14   0.020
 R4N  plan-5  C19   0.020
 R4N  plan-5  C21   0.020
 R4N  plan-5  N26   0.020
 R4N  plan-5  O28   0.020
 R4N  plan-5  C24   0.020

