# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 16:26:26 2021
#   Inital geometry file: a 133 line input string
#   Ligand name: [(2R)-5-chloro-7-{2-[(2S)-1-chloro-2,3-dihydroxypropan-2-yl]thieno[3,2-b]pyridin-7-yl}-2,3-dihydro-1-benzofuran-2-yl](piperazin-1-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@](O)(CCl)c1sc2c(c1)nccc2c3cc(Cl)cc4C[C@@H](Oc34)C(=O)N5CCNCC5
#
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
 R4J  R4J  '[(2R)-5-chloro-7-{2-[(2S)-1-chloro-2,3-dihydroxypropan-2-yl]thieno[3,2-b]pyridin-7-yl}-2,3-dihydro-1-benzofuran-2-yl](piperazin-1-yl)methanone'  ligand  56  33  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R4J
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
 R4J  C2    C   CR6   0  -0.043  26.3630  -2.0807  27.1068
 R4J  C3    C   CR16  0  -0.255  26.0127  -1.3996  28.2614
 R4J  C4    C   CR6   0  -0.108  25.6792  -0.0450  28.2038
 R4J  C5    C   CR6   0   0.215  25.3669   0.7550  29.4035
 R4J  C6    C   CR16  0  -0.377  24.1129   1.2892  29.6447
 R4J  C7    C   CR16  0  -0.086  23.9119   2.1165  30.7532
 R4J  C11   C   CR5   0  -0.141  28.3464   1.6248  31.6848
 R4J  C16   C   CH2   0  -0.152  30.4643   2.9024  31.4735
 R4J  C18   C   CH2   0  -0.465  29.7631   1.8401  33.6818
 R4J  C24   C   CH2   0  -0.480  26.0470   0.8731  24.6786
 R4J  C27   C   C     0   0.567  27.4092   2.7838  25.6806
 R4J  O28   O   O     0  -0.485  28.3845   2.2433  25.1773
 R4J  C30   C   CH2   0  -0.312  28.8046   4.3561  26.9024
 R4J  C31   C   CH2   0  -0.299  28.8980   4.2159  28.4127
 R4J  C33   C   CH2   0  -0.296  26.5199   4.4845  28.6056
 R4J  C34   C   CH2   0  -0.312  26.4161   4.6065  27.0930
 R4J  CL1   CL  CL    0  -0.131  26.7628  -3.7661  27.2136
 R4J  N8    N   N     0  -0.432  24.8593   2.4566  31.6070
 R4J  C9    C   CR56  0   0.287  26.0767   1.9568  31.3864
 R4J  C10   C   CR15  0  -0.228  27.2462   2.2499  32.1599
 R4J  S12   S   S2    0   0.238  28.0286   0.6421  30.2821
 R4J  C13   C   CR56  0  -0.261  26.3630   1.0949  30.3132
 R4J  C14   C   CT    0   0.124  29.7707   1.7141  32.1566
 R4J  O15   O   OH1   0  -0.656  30.3860   0.5201  31.7484
 R4J  O17   O   OH1   0  -0.654  29.7905   4.0867  31.8059
 R4J  CL19  CL  CL    0  -0.155  31.4376   1.8411  34.3326
 R4J  C20   C   CR56  0   0.416  25.7253   0.5622  26.9618
 R4J  O21   O   O     0  -0.474  25.4556   1.8650  26.7422
 R4J  C22   C   CR15  0  -0.189  26.0043   2.1980  25.4518
 R4J  C25   C   CR56  0  -0.006  26.0952  -0.1128  25.8086
 R4J  C26   C   CR16  0  -0.294  26.4126  -1.4525  25.8634
 R4J  N29   N   NT    0  -0.454  27.5039   3.8782  26.4563
 R4J  N32   N   NH1   0  -0.603  27.8217   4.9554  29.0457
 R4J  H1    H   HCR6  0   0.284  25.9967  -1.9147  29.2129
 R4J  H2    H   HCR6  0   0.268  23.2874   1.0766  28.9788
 R4J  H3    H   HCR6  0   0.267  22.9249   2.5254  30.9371
 R4J  H4    H   HCH2  0   0.228  31.5136   2.9294  31.7931
 R4J  H5    H   HCH2  0   0.220  30.4619   2.7150  30.3932
 R4J  H6    H   HCH2  0   0.298  29.2950   2.7632  34.0119
 R4J  H7    H   HCH2  0   0.309  29.2489   0.9936  34.1319
 R4J  H8    H   HCH2  0   0.285  25.1373   0.7439  24.0875
 R4J  H9    H   HCH2  0   0.285  26.8974   0.8094  24.0043
 R4J  H11   H   HCH2  0   0.244  28.9107   5.4069  26.6169
 R4J  H12   H   HCH2  0   0.202  28.8829   3.1422  28.6617
 R4J  H13   H   HCH2  0   0.236  29.8557   4.6174  28.7497
 R4J  H14   H   HCH2  0   0.236  25.7409   5.0962  29.0651
 R4J  H15   H   HCH2  0   0.220  26.3246   3.4402  28.8834
 R4J  H16   H   HCH2  0   0.249  26.5088   5.6581  26.8051
 R4J  H17   H   HCH2  0   0.272  25.4430   4.2703  26.7510
 R4J  H18   H   HCR5  0   0.271  27.2310   2.9091  33.0157
 R4J  H19   H   HOH1  0   0.459  31.3339   0.5741  31.9191
 R4J  H20   H   HOH1  0   0.467  30.3568   4.8307  31.5819
 R4J  H21   H   HCR5  0   0.302  25.3458   2.9311  24.9835
 R4J  H22   H   HCR6  0   0.283  26.6998  -1.9999  24.9755
 R4J  H23   H   HNH1  0   0.353  27.9009   4.8527  30.0497
 R4J  H10   H   HCH2  0   0.266  29.5962   3.7946  26.4154

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
 R4J  O28  C27   double    1.223  0.020  1.223
 R4J  C24  C22   single    1.535  0.020  1.535
 R4J  C24  C25   single    1.500  0.020  1.500
 R4J  C27  C22   single    1.539  0.020  1.539
 R4J  C27  N29   single    1.345  0.020  1.345
 R4J  C22  O21   single    1.441  0.020  1.441
 R4J  C30  N29   single    1.456  0.020  1.456
 R4J  C30  C31   single    1.520  0.020  1.520
 R4J  N29  C34   single    1.456  0.020  1.456
 R4J  C25  C26   aromatic  1.378  0.020  1.378
 R4J  C25  C20   aromatic  1.386  0.020  1.386
 R4J  C26  C2    aromatic  1.394  0.020  1.394
 R4J  C34  C33   single    1.521  0.020  1.521
 R4J  O21  C20   single    1.348  0.020  1.348
 R4J  C31  N32   single    1.451  0.020  1.451
 R4J  C20  C4    aromatic  1.383  0.020  1.383
 R4J  C2   CL1   single    1.735  0.020  1.735
 R4J  C2   C3    aromatic  1.385  0.020  1.385
 R4J  C33  N32   single    1.453  0.020  1.453
 R4J  C4   C3    aromatic  1.396  0.020  1.396
 R4J  C4   C5    single    1.475  0.020  1.475
 R4J  C5   C6    aromatic  1.384  0.020  1.384
 R4J  C5   C13   aromatic  1.391  0.020  1.391
 R4J  C6   C7    aromatic  1.398  0.020  1.398
 R4J  C13  S12   aromatic  1.726  0.020  1.726
 R4J  C13  C9    aromatic  1.406  0.020  1.406
 R4J  S12  C11   aromatic  1.742  0.020  1.742
 R4J  C7   N8    aromatic  1.320  0.020  1.320
 R4J  C9   N8    aromatic  1.334  0.020  1.334
 R4J  C9   C10   aromatic  1.432  0.020  1.432
 R4J  C11  C10   aromatic  1.352  0.020  1.352
 R4J  C11  C14   single    1.503  0.020  1.503
 R4J  O15  C14   single    1.404  0.020  1.404
 R4J  C16  C14   single    1.536  0.020  1.536
 R4J  C16  O17   single    1.403  0.020  1.403
 R4J  C14  C18   single    1.530  0.020  1.530
 R4J  C18  CL19  single    1.797  0.020  1.797
 R4J  C3   H1    single    0.930  0.020  1.080
 R4J  C6   H2    single    0.930  0.020  1.080
 R4J  C7   H3    single    0.930  0.020  1.080
 R4J  C16  H4    single    0.970  0.020  1.090
 R4J  C16  H5    single    0.970  0.020  1.090
 R4J  C18  H6    single    0.970  0.020  1.090
 R4J  C18  H7    single    0.970  0.020  1.090
 R4J  C24  H8    single    0.970  0.020  1.090
 R4J  C24  H9    single    0.970  0.020  1.090
 R4J  C30  H10   single    0.970  0.020  1.090
 R4J  C30  H11   single    0.970  0.020  1.090
 R4J  C31  H12   single    0.970  0.020  1.090
 R4J  C31  H13   single    0.970  0.020  1.090
 R4J  C33  H14   single    0.970  0.020  1.090
 R4J  C33  H15   single    0.970  0.020  1.090
 R4J  C34  H16   single    0.970  0.020  1.090
 R4J  C34  H17   single    0.970  0.020  1.090
 R4J  C10  H18   single    0.930  0.020  1.080
 R4J  O15  H19   single    0.850  0.020  0.980
 R4J  O17  H20   single    0.850  0.020  0.980
 R4J  C22  H21   single    0.970  0.020  1.090
 R4J  C26  H22   single    0.930  0.020  1.080
 R4J  N32  H23   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
 R4J  C26   C2   CL1   118.97  3.000
 R4J  CL1   C2   C3    118.98  3.000
 R4J  C26   C2   C3    122.06  3.000
 R4J  H1    C3   C4    119.64  3.000
 R4J  H1    C3   C2    120.16  3.000
 R4J  C4    C3   C2    120.20  3.000
 R4J  C20   C4   C5    119.94  3.000
 R4J  C5    C4   C3    122.90  3.000
 R4J  C20   C4   C3    117.06  3.000
 R4J  C13   C5   C6    116.14  3.000
 R4J  C13   C5   C4    120.84  3.000
 R4J  C6    C5   C4    122.87  3.000
 R4J  H2    C6   C7    119.66  3.000
 R4J  H2    C6   C5    120.55  3.000
 R4J  C7    C6   C5    119.79  3.000
 R4J  H3    C7   N8    116.53  3.000
 R4J  H3    C7   C6    119.25  3.000
 R4J  N8    C7   C6    124.22  3.000
 R4J  C14   C11  S12   117.33  3.000
 R4J  C14   C11  C10   129.31  3.000
 R4J  S12   C11  C10   113.30  3.000
 R4J  H5    C16  H4    107.06  3.000
 R4J  H5    C16  O17   112.13  3.000
 R4J  H4    C16  O17   111.69  3.000
 R4J  H5    C16  C14   107.76  3.000
 R4J  H4    C16  C14   108.74  3.000
 R4J  O17   C16  C14   109.33  3.000
 R4J  H7    C18  H6    109.38  3.000
 R4J  H7    C18  CL19  106.92  3.000
 R4J  H6    C18  CL19  106.92  3.000
 R4J  H7    C18  C14   110.53  3.000
 R4J  H6    C18  C14   112.02  3.000
 R4J  CL19  C18  C14   110.88  3.000
 R4J  H9    C24  H8    107.98  3.000
 R4J  H9    C24  C25   113.80  3.000
 R4J  H8    C24  C25   110.89  3.000
 R4J  H9    C24  C22   112.64  3.000
 R4J  H8    C24  C22   110.58  3.000
 R4J  C25   C24  C22   100.88  3.000
 R4J  N29   C27  C22   117.37  3.000
 R4J  N29   C27  O28   122.73  3.000
 R4J  C22   C27  O28   119.89  3.000
 R4J  H11   C30  H10   108.00  3.000
 R4J  H11   C30  N29   108.79  3.000
 R4J  H10   C30  N29   110.13  3.000
 R4J  H11   C30  C31   109.99  3.000
 R4J  H10   C30  C31   110.68  3.000
 R4J  N29   C30  C31   109.22  3.000
 R4J  H13   C31  H12   107.48  3.000
 R4J  H13   C31  N32   109.18  3.000
 R4J  H12   C31  N32   112.81  3.000
 R4J  H13   C31  C30   109.07  3.000
 R4J  H12   C31  C30   108.27  3.000
 R4J  N32   C31  C30   109.94  3.000
 R4J  H15   C33  H14   107.42  3.000
 R4J  H15   C33  N32   113.02  3.000
 R4J  H14   C33  N32   109.29  3.000
 R4J  H15   C33  C34   108.40  3.000
 R4J  H14   C33  C34   108.96  3.000
 R4J  N32   C33  C34   109.66  3.000
 R4J  H17   C34  H16   106.91  3.000
 R4J  H17   C34  N29   112.18  3.000
 R4J  H16   C34  N29   107.61  3.000
 R4J  H17   C34  C33   110.48  3.000
 R4J  H16   C34  C33   109.44  3.000
 R4J  N29   C34  C33   110.11  3.000
 R4J  C9    N8   C7    116.83  3.000
 R4J  C13   C9   C10   111.80  3.000
 R4J  C10   C9   N8    125.38  3.000
 R4J  C13   C9   N8    122.80  3.000
 R4J  H18   C10  C9    122.76  3.000
 R4J  H18   C10  C11   124.90  3.000
 R4J  C9    C10  C11   112.34  3.000
 R4J  C13   S12  C11    90.77  3.000
 R4J  S12   C13  C9    111.78  3.000
 R4J  C9    C13  C5    120.20  3.000
 R4J  S12   C13  C5    127.95  3.000
 R4J  O15   C14  C18   111.22  3.000
 R4J  C18   C14  C16   112.44  3.000
 R4J  O15   C14  C16   109.31  3.000
 R4J  C18   C14  C11   108.24  3.000
 R4J  C16   C14  C11   109.52  3.000
 R4J  O15   C14  C11   105.88  3.000
 R4J  H19   O15  C14   109.37  3.000
 R4J  H20   O17  C16   108.38  3.000
 R4J  C25   C20  O21   112.85  3.000
 R4J  O21   C20  C4    124.31  3.000
 R4J  C25   C20  C4    122.82  3.000
 R4J  C22   O21  C20   107.03  3.000
 R4J  H21   C22  O21   108.05  3.000
 R4J  H21   C22  C27   111.04  3.000
 R4J  O21   C22  C27   107.60  3.000
 R4J  H21   C22  C24   112.38  3.000
 R4J  O21   C22  C24   105.20  3.000
 R4J  C27   C22  C24   112.21  3.000
 R4J  C26   C25  C20   120.11  3.000
 R4J  C20   C25  C24   107.34  3.000
 R4J  C26   C25  C24   132.55  3.000
 R4J  H22   C26  C25   121.36  3.000
 R4J  H22   C26  C2    120.90  3.000
 R4J  C25   C26  C2    117.74  3.000
 R4J  C34   N29  C30   111.68  3.000
 R4J  C34   N29  C27   127.36  3.000
 R4J  C30   N29  C27   120.46  3.000
 R4J  H23   N32  C33   109.74  3.000
 R4J  H23   N32  C31   108.84  3.000
 R4J  C33   N32  C31   111.55  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
 R4J  CONST_01  C20  C25  C26  C2     0.00   0.0  0
 R4J  CONST_02  C20  C4   C3   C2     0.00   0.0  0
 R4J  CONST_03  C5   C4   C3   C2   180.00   0.0  0
 R4J  CONST_04  C25  C26  C2   C3     0.00   0.0  0
 R4J  CONST_05  C25  C20  C4   C3     0.00   0.0  0
 R4J  CONST_08  C26  C25  C20  C4     0.00   0.0  0
 R4J  CONST_09  C26  C2   C3   C4     0.00   0.0  0
 R4J  CONST_10  C7   C6   C5   C4   180.00   0.0  0
 R4J  CONST_11  S12  C13  C5   C4     0.00   0.0  0
 R4J  CONST_12  C9   C13  C5   C4   180.00   0.0  0
 R4J  CONST_13  C25  C20  C4   C5   180.00   0.0  0
 R4J  CONST_14  N8   C7   C6   C5     0.00   0.0  0
 R4J  CONST_15  C11  S12  C13  C5   180.00   0.0  0
 R4J  CONST_16  N8   C9   C13  C5     0.00   0.0  0
 R4J  CONST_17  C10  C9   C13  C5   180.00   0.0  0
 R4J  CONST_19  S12  C13  C5   C6   180.00   0.0  0
 R4J  CONST_20  C9   C13  C5   C6     0.00   0.0  0
 R4J  CONST_21  C9   N8   C7   C6     0.00   0.0  0
 R4J  CONST_22  C13  C5   C6   C7     0.00   0.0  0
 R4J  CONST_23  C13  C9   N8   C7     0.00   0.0  0
 R4J  CONST_24  C10  C9   N8   C7   180.00   0.0  0
 R4J  CONST_25  C9   C13  S12  C11    0.00   0.0  0
 R4J  CONST_26  C13  C9   C10  C11    0.00   0.0  0
 R4J  CONST_27  N8   C9   C10  C11  180.00   0.0  0
 R4J  CONST_28  S12  C13  C9   N8   180.00   0.0  0
 R4J  CONST_29  S12  C11  C10  C9     0.00   0.0  0
 R4J  CONST_30  S12  C13  C9   C10    0.00   0.0  0
 R4J  CONST_31  C13  S12  C11  C10    0.00   0.0  0
 R4J  CONST_33  O21  C20  C4   C5     0.00   0.0  0
 R4J  CONST_34  CL1  C2   C3   C4   180.00   0.0  0
 R4J  CONST_35  C25  C26  C2   CL1  180.00   0.0  0
 R4J  CONST_36  C14  C11  C10  C9   180.00   0.0  0
 R4J  CONST_37  C14  C11  S12  C13  180.00   0.0  0
 R4J  CONST_38  C22  C27  N29  C30  180.00   0.0  0
 R4J  CONST_39  C22  C27  N29  C34    0.00   0.0  0
 R4J  CONST_40  H22  C26  C2   C3   180.00   0.0  0
 R4J  CONST_41  H2   C6   C5   C4     0.00   0.0  0
 R4J  CONST_42  H1   C3   C4   C5     0.00   0.0  0
 R4J  CONST_43  H3   C7   C6   C5   180.00   0.0  0
 R4J  CONST_44  H18  C10  C9   N8     0.00   0.0  0
 R4J  CONST_45  C30  N29  C27  O28    0.00   0.0  0
 R4J  CONST_46  C34  N29  C27  O28  180.00   0.0  0
 R4J  Var_01    C33  C34  N29  C30  -57.69  30.0  1
 R4J  Var_02    C33  N32  C31  C30   58.91  30.0  1
 R4J  Var_03    C34  N29  C30  C31   58.06  30.0  1
 R4J  Var_04    C34  C33  N32  C31  -57.86  30.0  1
 R4J  Var_05    C22  C24  C25  C20   15.56  30.0  1
 R4J  Var_06    C25  C20  O21  C22  -15.88  30.0  1
 R4J  Var_07    N32  C31  C30  N29  -57.73  30.0  1
 R4J  Var_08    N32  C33  C34  N29   56.30  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
 R4J  chir_01  C14  C11  C16  C18  negativ
 R4J  chir_02  C22  C24  C27  O21  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
 R4J  plan-1  C2   0.020
 R4J  plan-1  C3   0.020
 R4J  plan-1  C4   0.020
 R4J  plan-1  C5   0.020
 R4J  plan-1  C24  0.020
 R4J  plan-1  CL1  0.020
 R4J  plan-1  C20  0.020
 R4J  plan-1  O21  0.020
 R4J  plan-1  C25  0.020
 R4J  plan-1  C26  0.020
 R4J  plan-1  H1   0.020
 R4J  plan-1  H22  0.020
 R4J  plan-2  C4   0.020
 R4J  plan-2  C5   0.020
 R4J  plan-2  C6   0.020
 R4J  plan-2  C7   0.020
 R4J  plan-2  C11  0.020
 R4J  plan-2  N8   0.020
 R4J  plan-2  C9   0.020
 R4J  plan-2  C10  0.020
 R4J  plan-2  S12  0.020
 R4J  plan-2  C13  0.020
 R4J  plan-2  C14  0.020
 R4J  plan-2  H2   0.020
 R4J  plan-2  H3   0.020
 R4J  plan-2  H18  0.020
 R4J  plan-3  C27  0.020
 R4J  plan-3  O28  0.020
 R4J  plan-3  C30  0.020
 R4J  plan-3  C34  0.020
 R4J  plan-3  C22  0.020
 R4J  plan-3  N29  0.020

