# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 23:33:54 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: (2Z,3S)-3-hydroxy-5'-[(4-hydroxypiperidin-1-yl)sulfonyl]-3-methyl-1,3-dihydro-2,3'-biindol-2'(1'H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(O)\C(Nc2ccccc12)=C3\C(=O)Nc4ccc(cc34)[S](=O)(=O)N5CCC(O)CC5
#
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
 RYU  RYU  (2Z,3S)-3-hydroxy-5'-[(4-hydroxypiperidin-1-yl)sulfonyl]-3-methyl-1,3-dihydro-2,3'-biindol-2'(1'H)-one  ligand  54  31  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RYU
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
 RYU  C1    C  CR16  0  -0.333   3.1001   0.7634  -4.1173
 RYU  C2    C  CR16  0  -0.262   3.5850   0.3469  -5.3581
 RYU  C3    C  CR16  0  -0.261   2.8252  -0.4909  -6.1654
 RYU  C4    C  CR16  0  -0.325   1.5687  -0.9413  -5.7649
 RYU  C5    C  CR56  0   0.396   1.1156  -0.5200  -4.5297
 RYU  C6    C  CR56  0   0.087   1.8610   0.3176  -3.7132
 RYU  C7    C  CR5   0   0.013   1.0608   0.6162  -2.4637
 RYU  C71   C  CH3   0  -0.691   0.6395   2.0868  -2.4571
 RYU  O71   O  OH1   0  -0.640   1.6998   0.2208  -1.2797
 RYU  C8    C  CR5   0   0.482  -0.1677  -0.2751  -2.6668
 RYU  N9    N  NR15  0  -0.756  -0.0796  -0.8262  -3.8875
 RYU  C10   C  CR5   0  -0.203  -1.2130  -0.4852  -1.8067
 RYU  C11   C  CR5   0   0.535  -2.3653  -1.2920  -2.2153
 RYU  O11   O  O     0  -0.488  -2.5516  -1.8903  -3.2697
 RYU  N12   N  NR15  0  -0.766  -3.2528  -1.2560  -1.1702
 RYU  C13   C  CR56  0   0.397  -2.7669  -0.5195  -0.1193
 RYU  C14   C  CR56  0   0.051  -1.4901  -0.0209  -0.4584
 RYU  C15   C  CR16  0  -0.408  -0.8034   0.7216   0.4873
 RYU  C16   C  CR6   0  -0.199  -1.4073   0.9656   1.7195
 RYU  C17   C  CR16  0  -0.259  -2.6763   0.4861   2.0319
 RYU  C18   C  CR16  0  -0.300  -3.3700  -0.2716   1.1006
 RYU  S19   S  S     0   1.370  -0.4731   1.7981   2.9628
 RYU  O19   O  OS    0  -0.656   0.5237   2.6337   2.3107
 RYU  O1    O  OS    0  -0.656  -1.3968   2.4053   3.9086
 RYU  N20   N  N     0  -0.560   0.3558   0.6185   3.7887
 RYU  C21   C  CH2   0  -0.324   1.3634  -0.1100   3.0107
 RYU  C22   C  CH2   0  -0.454   2.2909  -0.8680   3.9474
 RYU  C23   C  CH1   0   0.064   1.4999  -1.8121   4.8342
 RYU  O23   O  OH1   0  -0.671   2.4013  -2.4658   5.6989
 RYU  C24   C  CH2   0  -0.472   0.4387  -1.0236   5.5889
 RYU  C25   C  CH2   0  -0.319  -0.4615  -0.2644   4.6272
 RYU  H1    H  HCR6  0   0.261   3.6898   1.4247  -3.4939
 RYU  H2    H  HCR6  0   0.260   4.5575   0.6809  -5.6933
 RYU  H3    H  HCR6  0   0.264   3.2132  -0.8030  -7.1260
 RYU  H4    H  HCR6  0   0.272   0.9801  -1.5950  -6.3948
 RYU  H711  H  HCH3  0   0.257   1.5216   2.7223  -2.3532
 RYU  H712  H  HCH3  0   0.256   0.1507   2.3549  -3.3934
 RYU  H713  H  HCH3  0   0.258  -0.0472   2.3116  -1.6418
 RYU  H71   H  HOH1  0   0.465   2.4009   0.8518  -1.0806
 RYU  H9    H  HNR5  0   0.425  -0.7983  -1.4389  -4.2512
 RYU  H12   H  HNR5  0   0.414  -4.1405  -1.7351  -1.1773
 RYU  H15   H  HCR6  0   0.269   0.1899   1.0903   0.2876
 RYU  H17   H  HCR6  0   0.283  -3.1280   0.6971   2.9912
 RYU  H18   H  HCR6  0   0.278  -4.3544  -0.6582   1.3273
 RYU  H211  H  HCH2  0   0.237   0.8799  -0.8140   2.3196
 RYU  H212  H  HCH2  0   0.275   1.9433   0.5919   2.4156
 RYU  H221  H  HCH2  0   0.254   3.0144  -1.4198   3.3430
 RYU  H222  H  HCH2  0   0.236   2.8466  -0.1573   4.5660
 RYU  H23   H  HCH1  0   0.196   0.9869  -2.5404   4.1858
 RYU  HA    H  HOH1  0   0.450   1.9062  -3.0987   6.2286
 RYU  H241  H  HCH2  0   0.252  -0.1859  -1.6922   6.1868
 RYU  H242  H  HCH2  0   0.236   0.9218  -0.3201   6.2732
 RYU  H251  H  HCH2  0   0.277  -1.1771   0.3276   5.1924
 RYU  H252  H  HCH2  0   0.235  -1.0250  -0.9746   4.0065

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
 RYU  C1   C2    aromatic  1.396  0.020  1.396
 RYU  C1   C6    aromatic  1.377  0.020  1.377
 RYU  C1   H1    single    0.930  0.020  1.080
 RYU  C2   C3    aromatic  1.390  0.020  1.390
 RYU  C2   H2    single    0.930  0.020  1.080
 RYU  C3   C4    aromatic  1.394  0.020  1.394
 RYU  C3   H3    single    0.930  0.020  1.080
 RYU  C4   C5    aromatic  1.381  0.020  1.381
 RYU  C4   H4    single    0.930  0.020  1.080
 RYU  C5   C6    aromatic  1.387  0.020  1.387
 RYU  C5   N9    single    1.391  0.020  1.391
 RYU  C6   C7    single    1.513  0.020  1.513
 RYU  C7   C71   single    1.530  0.020  1.530
 RYU  C7   O71   single    1.402  0.020  1.402
 RYU  C7   C8    single    1.531  0.020  1.531
 RYU  C71  H711  single    0.970  0.020  1.090
 RYU  C71  H712  single    0.970  0.020  1.090
 RYU  C71  H713  single    0.970  0.020  1.090
 RYU  O71  H71   single    0.850  0.020  0.980
 RYU  C8   N9    single    1.342  0.020  1.342
 RYU  C8   C10   double    1.370  0.020  1.370
 RYU  N9   H9    single    0.860  0.020  1.020
 RYU  C10  C11   single    1.465  0.020  1.465
 RYU  C10  C14   single    1.453  0.020  1.453
 RYU  C11  O11   double    1.227  0.020  1.227
 RYU  C11  N12   single    1.372  0.020  1.372
 RYU  N12  C13   single    1.372  0.020  1.372
 RYU  N12  H12   single    0.860  0.020  1.020
 RYU  C13  C14   aromatic  1.412  0.020  1.412
 RYU  C13  C18   aromatic  1.383  0.020  1.383
 RYU  C14  C15   aromatic  1.385  0.020  1.385
 RYU  C15  C16   aromatic  1.394  0.020  1.394
 RYU  C15  H15   single    0.930  0.020  1.080
 RYU  C16  C17   aromatic  1.392  0.020  1.392
 RYU  C16  S19   single    1.764  0.020  1.764
 RYU  C17  C18   aromatic  1.387  0.020  1.387
 RYU  C17  H17   single    0.930  0.020  1.080
 RYU  C18  H18   single    0.930  0.020  1.080
 RYU  S19  O19   double    1.455  0.020  1.455
 RYU  S19  O1    double    1.455  0.020  1.455
 RYU  S19  N20   single    1.662  0.020  1.662
 RYU  N20  C21   single    1.467  0.020  1.467
 RYU  N20  C25   single    1.466  0.020  1.466
 RYU  C21  C22   single    1.521  0.020  1.521
 RYU  C21  H211  single    0.970  0.020  1.090
 RYU  C21  H212  single    0.970  0.020  1.090
 RYU  C22  C23   single    1.518  0.020  1.518
 RYU  C22  H221  single    0.970  0.020  1.090
 RYU  C22  H222  single    0.970  0.020  1.090
 RYU  C23  O23   single    1.410  0.020  1.410
 RYU  C23  C24   single    1.522  0.020  1.522
 RYU  C23  H23   single    0.970  0.020  1.090
 RYU  O23  HA    single    0.850  0.020  0.980
 RYU  C24  C25   single    1.520  0.020  1.520
 RYU  C24  H241  single    0.970  0.020  1.090
 RYU  C24  H242  single    0.970  0.020  1.090
 RYU  C25  H251  single    0.970  0.020  1.090
 RYU  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
 RYU  H1    C1   C6    121.22  3.000
 RYU  H1    C1   C2    120.30  3.000
 RYU  C6    C1   C2    118.47  3.000
 RYU  H2    C2   C3    119.85  3.000
 RYU  H2    C2   C1    119.72  3.000
 RYU  C3    C2   C1    120.43  3.000
 RYU  H3    C3   C4    119.02  3.000
 RYU  H3    C3   C2    119.59  3.000
 RYU  C4    C3   C2    121.39  3.000
 RYU  H4    C4   C5    121.77  3.000
 RYU  H4    C4   C3    121.23  3.000
 RYU  C5    C4   C3    117.00  3.000
 RYU  N9    C5   C6    108.84  3.000
 RYU  N9    C5   C4    128.86  3.000
 RYU  C6    C5   C4    122.30  3.000
 RYU  C7    C6   C5    108.72  3.000
 RYU  C7    C6   C1    130.84  3.000
 RYU  C5    C6   C1    120.40  3.000
 RYU  C8    C7   O71   108.27  3.000
 RYU  C8    C7   C71   109.83  3.000
 RYU  O71   C7   C71   113.13  3.000
 RYU  C8    C7   C6    101.53  3.000
 RYU  O71   C7   C6    113.61  3.000
 RYU  C71   C7   C6    109.81  3.000
 RYU  H713  C71  H712  108.03  3.000
 RYU  H713  C71  H711  108.53  3.000
 RYU  H712  C71  H711  107.51  3.000
 RYU  H713  C71  C7    112.04  3.000
 RYU  H712  C71  C7    110.87  3.000
 RYU  H711  C71  C7    109.72  3.000
 RYU  H71   O71  C7    108.73  3.000
 RYU  C10   C8   N9    123.92  3.000
 RYU  C10   C8   C7    128.18  3.000
 RYU  N9    C8   C7    107.88  3.000
 RYU  H9    N9   C8    121.93  3.000
 RYU  H9    N9   C5    125.28  3.000
 RYU  C8    N9   C5    112.70  3.000
 RYU  C14   C10  C11   106.56  3.000
 RYU  C14   C10  C8    132.78  3.000
 RYU  C11   C10  C8    120.64  3.000
 RYU  N12   C11  O11   124.72  3.000
 RYU  N12   C11  C10   106.38  3.000
 RYU  O11   C11  C10   128.90  3.000
 RYU  H12   N12  C13   124.88  3.000
 RYU  H12   N12  C11   123.48  3.000
 RYU  C13   N12  C11   111.62  3.000
 RYU  C18   C13  C14   122.87  3.000
 RYU  C18   C13  N12   128.11  3.000
 RYU  C14   C13  N12   109.02  3.000
 RYU  C15   C14  C13   118.28  3.000
 RYU  C15   C14  C10   135.30  3.000
 RYU  C13   C14  C10   106.41  3.000
 RYU  H15   C15  C16   120.20  3.000
 RYU  H15   C15  C14   120.92  3.000
 RYU  C16   C15  C14   118.87  3.000
 RYU  S19   C16  C17   119.16  3.000
 RYU  S19   C16  C15   118.44  3.000
 RYU  C17   C16  C15   122.21  3.000
 RYU  H17   C17  C18   119.58  3.000
 RYU  H17   C17  C16   120.84  3.000
 RYU  C18   C17  C16   119.58  3.000
 RYU  H18   C18  C17   120.66  3.000
 RYU  H18   C18  C13   121.17  3.000
 RYU  C17   C18  C13   118.17  3.000
 RYU  N20   S19  O1    106.85  3.000
 RYU  N20   S19  O19   106.78  3.000
 RYU  O1    S19  O19   119.12  3.000
 RYU  N20   S19  C16   106.23  3.000
 RYU  O1    S19  C16   108.60  3.000
 RYU  O19   S19  C16   108.54  3.000
 RYU  C25   N20  C21   112.77  3.000
 RYU  C25   N20  S19   115.70  3.000
 RYU  C21   N20  S19   115.57  3.000
 RYU  H212  C21  H211  107.70  3.000
 RYU  H212  C21  C22   109.48  3.000
 RYU  H211  C21  C22   109.66  3.000
 RYU  H212  C21  N20   109.63  3.000
 RYU  H211  C21  N20   110.46  3.000
 RYU  C22   C21  N20   109.87  3.000
 RYU  H222  C22  H221  107.74  3.000
 RYU  H222  C22  C23   109.79  3.000
 RYU  H221  C22  C23   110.75  3.000
 RYU  H222  C22  C21   109.53  3.000
 RYU  H221  C22  C21   108.36  3.000
 RYU  C23   C22  C21   110.62  3.000
 RYU  H23   C23  C24   108.03  3.000
 RYU  H23   C23  O23   110.62  3.000
 RYU  C24   C23  O23   112.44  3.000
 RYU  H23   C23  C22   108.06  3.000
 RYU  C24   C23  C22   109.31  3.000
 RYU  O23   C23  C22   108.28  3.000
 RYU  HA    O23  C23   108.28  3.000
 RYU  H242  C24  H241  107.67  3.000
 RYU  H242  C24  C25   109.64  3.000
 RYU  H241  C24  C25   108.25  3.000
 RYU  H242  C24  C23   109.60  3.000
 RYU  H241  C24  C23   110.65  3.000
 RYU  C25   C24  C23   110.97  3.000
 RYU  H252  C25  H251  107.94  3.000
 RYU  H252  C25  C24   109.77  3.000
 RYU  H251  C25  C24   109.44  3.000
 RYU  H252  C25  N20   110.61  3.000
 RYU  H251  C25  N20   109.65  3.000
 RYU  C24   C25  N20   109.41  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
 RYU  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 RYU  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 RYU  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 RYU  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 RYU  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 RYU  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 RYU  CONST_07  C16  C15  C14  C13    0.00   0.0  0
 RYU  CONST_08  C16  C17  C18  C13    0.00   0.0  0
 RYU  CONST_09  C17  C18  C13  C14    0.00   0.0  0
 RYU  CONST_10  C17  C16  C15  C14    0.00   0.0  0
 RYU  CONST_11  C18  C13  C14  C15    0.00   0.0  0
 RYU  CONST_12  C18  C17  C16  C15    0.00   0.0  0
 RYU  CONST_13  C13  N12  C11  C10    0.00   0.0  0
 RYU  CONST_14  S19  C16  C15  C14  180.00   0.0  0
 RYU  CONST_15  S19  C16  C17  C18  180.00   0.0  0
 RYU  CONST_16  C13  N12  C11  O11  180.00   0.0  0
 RYU  CONST_17  H3   C3   C2   C1   180.00   0.0  0
 RYU  CONST_18  H4   C4   C3   C2   180.00   0.0  0
 RYU  CONST_19  H1   C1   C2   C3   180.00   0.0  0
 RYU  CONST_20  H2   C2   C3   C4   180.00   0.0  0
 RYU  CONST_21  H15  C15  C14  C10    0.00   0.0  0
 RYU  CONST_22  H18  C18  C13  N12    0.00   0.0  0
 RYU  CONST_23  H17  C17  C18  C13  180.00   0.0  0
 RYU  CONST_24  H12  N12  C11  C10  180.00   0.0  0
 RYU  Var_01    C8   N9   C5   C4   177.72  30.0  1
 RYU  Var_02    C7   C8   N9   C5     4.95  30.0  1
 RYU  Var_03    C11  C10  C8   C7   174.92  30.0  2
 RYU  Var_04    C23  C22  C21  N20   57.06  30.0  1
 RYU  Var_05    C23  C24  C25  N20  -57.05  30.0  1
 RYU  Var_06    C24  C25  N20  C21   59.00  30.0  1
 RYU  Var_07    C25  N20  C21  C22  -59.20  30.0  1
 RYU  Var_08    N20  S19  C16  C15  -87.69  30.0  2
 RYU  Var_09    C21  N20  S19  C16   65.07  30.0  3

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
 RYU  chir_01  C7   C6   O71  C8   positiv
 RYU  chir_02  C23  C22  O23  C24  negativ

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
 RYU  plan-1  C5   0.020
 RYU  plan-1  C8   0.020
 RYU  plan-1  N9   0.020
 RYU  plan-1  H9   0.020
 RYU  plan-2  C1   0.020
 RYU  plan-2  C2   0.020
 RYU  plan-2  C3   0.020
 RYU  plan-2  C4   0.020
 RYU  plan-2  C5   0.020
 RYU  plan-2  C6   0.020
 RYU  plan-2  C7   0.020
 RYU  plan-2  N9   0.020
 RYU  plan-2  H1   0.020
 RYU  plan-2  H2   0.020
 RYU  plan-2  H3   0.020
 RYU  plan-2  H4   0.020
 RYU  plan-3  C8   0.020
 RYU  plan-3  C10  0.020
 RYU  plan-3  C11  0.020
 RYU  plan-3  O11  0.020
 RYU  plan-3  N12  0.020
 RYU  plan-3  C13  0.020
 RYU  plan-3  C14  0.020
 RYU  plan-3  C15  0.020
 RYU  plan-3  C16  0.020
 RYU  plan-3  C17  0.020
 RYU  plan-3  C18  0.020
 RYU  plan-3  S19  0.020
 RYU  plan-3  H12  0.020
 RYU  plan-3  H15  0.020
 RYU  plan-3  H17  0.020
 RYU  plan-3  H18  0.020

