# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 03:41:38 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 1-methyl-5-{[(2S)-2-(phenoxymethyl)pyrrolidin-1-yl]sulfonyl}-1H-indole-2,3-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)C(=O)c2cc(ccc12)[S](=O)(=O)N3CCC[C@H]3COc4ccccc4
#
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
 MSI  MSI  1-methyl-5-{[(2S)-2-(phenoxymethyl)pyrrolidin-1-yl]sulfonyl}-1H-indole-2,3-dione  ligand  48  28  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MSI
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
 MSI  S1    S  S     0   1.374  -1.6120   1.6202   0.0869
 MSI  N1    N  NR5   0  -0.611   0.4165  -0.7232   5.1064
 MSI  N2    N  N     0  -0.584  -1.8879   0.3359  -0.8987
 MSI  O4    O  OS    0  -0.644  -2.8929   2.2609   0.3255
 MSI  O5    O  OS    0  -0.645  -0.5144   2.3725  -0.4986
 MSI  C2    C  CR5   0   0.464   1.7630  -0.8064   4.9093
 MSI  C3    C  CR5   0   0.265   2.0264  -0.2310   3.4966
 MSI  C4    C  CR16  0  -0.270   0.3166   0.7184   1.8070
 MSI  C5    C  CR6   0  -0.206  -1.0422   0.9652   1.6310
 MSI  C6    C  CR16  0  -0.221  -1.9600   0.6689   2.6386
 MSI  C7    C  CR16  0  -0.295  -1.5593   0.0955   3.8386
 MSI  C8    C  CR56  0   0.461  -0.2118  -0.1660   4.0030
 MSI  C9    C  CR56  0  -0.068   0.7099   0.1471   2.9973
 MSI  C20   C  CH1   0  -0.116  -0.7337  -0.3591  -1.5055
 MSI  C10   C  CH2   0  -0.471  -1.1553  -1.8340  -1.5201
 MSI  C11   C  CH2   0  -0.459  -2.1688  -1.9409  -0.3889
 MSI  C12   C  CH2   0  -0.307  -2.9314  -0.6335  -0.5121
 MSI  C13   C  CH2   0  -0.156  -0.4738   0.2144  -2.8861
 MSI  C14   C  CR6   0   0.390   0.9919  -0.2290  -4.7026
 MSI  C15   C  CR16  0  -0.347   2.0379  -0.9997  -5.2141
 MSI  C16   C  CR16  0  -0.241   2.5162  -0.7596  -6.4902
 MSI  C17   C  CR16  0  -0.281   1.9640   0.2469  -7.2769
 MSI  C18   C  CR16  0  -0.241   0.9266   1.0087  -6.7643
 MSI  C19   C  CR16  0  -0.380   0.4346   0.7812  -5.4830
 MSI  HC4   H  HCR6  0   0.302   1.0506   0.9728   1.0532
 MSI  HC6   H  HCR6  0   0.305  -3.0087   0.8960   2.5029
 MSI  HC7   H  HCR6  0   0.303  -2.2887  -0.1198   4.6064
 MSI  H20   H  HCH1  0   0.269   0.1626  -0.2486  -0.8859
 MSI  H101  H  HCH2  0   0.268  -0.3001  -2.4958  -1.3961
 MSI  H102  H  HCH2  0   0.246  -1.6293  -2.0824  -2.4730
 MSI  H111  H  HCH2  0   0.238  -1.6629  -1.9896   0.5787
 MSI  H112  H  HCH2  0   0.262  -2.8174  -2.8115  -0.4746
 MSI  H121  H  HCH2  0   0.269  -3.4412  -0.3422   0.4052
 MSI  H122  H  HCH2  0   0.269  -3.6843  -0.6806  -1.3005
 MSI  H131  H  HCH2  0   0.227  -1.3846   0.1240  -3.4904
 MSI  H132  H  HCH2  0   0.245  -0.2121   1.2743  -2.8204
 MSI  HC15  H  HCR6  0   0.261   2.4691  -1.7831  -4.6032
 MSI  HC16  H  HCR6  0   0.257   3.3276  -1.3648  -6.8742
 MSI  HC17  H  HCR6  0   0.253   2.3388   0.4309  -8.2748
 MSI  HC18  H  HCR6  0   0.259   0.4841   1.7952  -7.3621
 MSI  HC19  H  HCR6  0   0.280  -0.3756   1.3959  -5.1148
 MSI  HC11  H  HCH3  0   0.279   0.4402  -1.5663   6.9954
 MSI  HC12  H  HCH3  0   0.268  -0.7598  -0.2847   6.7811
 MSI  HC13  H  HCH3  0   0.268  -1.0297  -1.8885   6.0689
 MSI  C1    C  CH3   0  -0.545  -0.2775  -1.1365   6.3034
 MSI  O1    O  O2    0  -0.478   0.5869  -0.5290  -3.4509
 MSI  O2    O  O     0  -0.394   2.5968  -1.2334   5.6644
 MSI  O3    O  O     0  -0.322   3.1136  -0.1503   2.9957

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
 MSI  S1   N2    single    1.642  0.020  1.642
 MSI  S1   O4    double    1.452  0.020  1.452
 MSI  S1   O5    double    1.454  0.020  1.454
 MSI  S1   C5    single    1.771  0.020  1.771
 MSI  N1   C2    single    1.363  0.020  1.363
 MSI  N1   C8    single    1.387  0.020  1.387
 MSI  N1   C1    single    1.444  0.020  1.444
 MSI  N2   C20   single    1.478  0.020  1.478
 MSI  N2   C12   single    1.476  0.020  1.476
 MSI  O1   C13   single    1.413  0.020  1.413
 MSI  O1   C14   single    1.349  0.020  1.349
 MSI  O2   C2    double    1.203  0.020  1.203
 MSI  O3   C3    double    1.200  0.020  1.200
 MSI  C2   C3    single    1.548  0.020  1.548
 MSI  C3   C9    single    1.458  0.020  1.458
 MSI  C4   C5    aromatic  1.392  0.020  1.392
 MSI  C4   C9    aromatic  1.378  0.020  1.378
 MSI  C4   HC4   single    0.930  0.020  1.080
 MSI  C5   C6    aromatic  1.395  0.020  1.395
 MSI  C6   C7    aromatic  1.389  0.020  1.389
 MSI  C6   HC6   single    0.930  0.020  1.080
 MSI  C7   C8    aromatic  1.382  0.020  1.382
 MSI  C7   HC7   single    0.930  0.020  1.080
 MSI  C8   C9    aromatic  1.400  0.020  1.400
 MSI  C20  C10   single    1.534  0.020  1.534
 MSI  C20  C13   single    1.517  0.020  1.517
 MSI  C20  H20   single    0.970  0.020  1.090
 MSI  C10  C11   single    1.523  0.020  1.523
 MSI  C10  H101  single    0.970  0.020  1.090
 MSI  C10  H102  single    0.970  0.020  1.090
 MSI  C11  C12   single    1.519  0.020  1.519
 MSI  C11  H111  single    0.970  0.020  1.090
 MSI  C11  H112  single    0.970  0.020  1.090
 MSI  C12  H121  single    0.970  0.020  1.090
 MSI  C12  H122  single    0.970  0.020  1.090
 MSI  C13  H131  single    0.970  0.020  1.090
 MSI  C13  H132  single    0.970  0.020  1.090
 MSI  C14  C15   aromatic  1.396  0.020  1.396
 MSI  C14  C19   aromatic  1.393  0.020  1.393
 MSI  C15  C16   aromatic  1.384  0.020  1.384
 MSI  C15  HC15  single    0.930  0.020  1.080
 MSI  C16  C17   aromatic  1.392  0.020  1.392
 MSI  C16  HC16  single    0.930  0.020  1.080
 MSI  C17  C18   aromatic  1.385  0.020  1.385
 MSI  C17  HC17  single    0.930  0.020  1.080
 MSI  C18  C19   aromatic  1.391  0.020  1.391
 MSI  C18  HC18  single    0.930  0.020  1.080
 MSI  C19  HC19  single    0.930  0.020  1.080
 MSI  C1   HC11  single    0.970  0.020  1.090
 MSI  C1   HC12  single    0.970  0.020  1.090
 MSI  C1   HC13  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
 MSI  C5    S1   O5    107.43  3.000
 MSI  C5    S1   O4    107.68  3.000
 MSI  O5    S1   O4    120.26  3.000
 MSI  C5    S1   N2    106.74  3.000
 MSI  O5    S1   N2    106.85  3.000
 MSI  O4    S1   N2    107.19  3.000
 MSI  C1    N1   C8    123.84  3.000
 MSI  C1    N1   C2    125.24  3.000
 MSI  C8    N1   C2    110.91  3.000
 MSI  C12   N2   C20   110.55  3.000
 MSI  C12   N2   S1    118.38  3.000
 MSI  C20   N2   S1    118.88  3.000
 MSI  C3    C2   O2    125.92  3.000
 MSI  C3    C2   N1    106.10  3.000
 MSI  O2    C2   N1    127.98  3.000
 MSI  C9    C3   C2    104.79  3.000
 MSI  C9    C3   O3    131.14  3.000
 MSI  C2    C3   O3    124.07  3.000
 MSI  HC4   C4   C9    120.37  3.000
 MSI  HC4   C4   C5    122.15  3.000
 MSI  C9    C4   C5    117.48  3.000
 MSI  C6    C5   C4    120.88  3.000
 MSI  C6    C5   S1    119.78  3.000
 MSI  C4    C5   S1    119.32  3.000
 MSI  HC6   C6   C7    118.34  3.000
 MSI  HC6   C6   C5    120.19  3.000
 MSI  C7    C6   C5    121.47  3.000
 MSI  HC7   C7   C8    122.39  3.000
 MSI  HC7   C7   C6    120.09  3.000
 MSI  C8    C7   C6    117.52  3.000
 MSI  C9    C8   C7    120.94  3.000
 MSI  C9    C8   N1    111.31  3.000
 MSI  C7    C8   N1    127.75  3.000
 MSI  C8    C9   C4    121.71  3.000
 MSI  C8    C9   C3    106.89  3.000
 MSI  C4    C9   C3    131.40  3.000
 MSI  H20   C20  C13   109.66  3.000
 MSI  H20   C20  C10   109.10  3.000
 MSI  C13   C20  C10   113.69  3.000
 MSI  H20   C20  N2    111.07  3.000
 MSI  C13   C20  N2    109.25  3.000
 MSI  C10   C20  N2    103.97  3.000
 MSI  H102  C10  H101  107.58  3.000
 MSI  H102  C10  C11   110.07  3.000
 MSI  H101  C10  C11   113.30  3.000
 MSI  H102  C10  C20   110.25  3.000
 MSI  H101  C10  C20   111.57  3.000
 MSI  C11   C10  C20   104.09  3.000
 MSI  H112  C11  H111  108.05  3.000
 MSI  H112  C11  C12   112.50  3.000
 MSI  H111  C11  C12   110.03  3.000
 MSI  H112  C11  C10   113.21  3.000
 MSI  H111  C11  C10   110.66  3.000
 MSI  C12   C11  C10   102.33  3.000
 MSI  H122  C12  H121  107.29  3.000
 MSI  H122  C12  C11   111.59  3.000
 MSI  H121  C12  C11   113.39  3.000
 MSI  H122  C12  N2    109.09  3.000
 MSI  H121  C12  N2    112.08  3.000
 MSI  C11   C12  N2    103.40  3.000
 MSI  H132  C13  H131  108.16  3.000
 MSI  H132  C13  C20   110.64  3.000
 MSI  H131  C13  C20   109.14  3.000
 MSI  H132  C13  O1    110.75  3.000
 MSI  H131  C13  O1    111.09  3.000
 MSI  C20   C13  O1    107.06  3.000
 MSI  C19   C14  C15   119.66  3.000
 MSI  C19   C14  O1    124.12  3.000
 MSI  C15   C14  O1    116.23  3.000
 MSI  HC15  C15  C16   120.54  3.000
 MSI  HC15  C15  C14   119.39  3.000
 MSI  C16   C15  C14   120.06  3.000
 MSI  HC16  C16  C17   120.08  3.000
 MSI  HC16  C16  C15   119.28  3.000
 MSI  C17   C16  C15   120.64  3.000
 MSI  HC17  C17  C18   120.48  3.000
 MSI  HC17  C17  C16   120.47  3.000
 MSI  C18   C17  C16   119.06  3.000
 MSI  HC18  C18  C19   118.87  3.000
 MSI  HC18  C18  C17   120.09  3.000
 MSI  C19   C18  C17   121.04  3.000
 MSI  HC19  C19  C18   119.04  3.000
 MSI  HC19  C19  C14   121.41  3.000
 MSI  C18   C19  C14   119.54  3.000
 MSI  HC13  C1   HC12  109.18  3.000
 MSI  HC13  C1   HC11  108.69  3.000
 MSI  HC12  C1   HC11  108.83  3.000
 MSI  HC13  C1   N1    110.55  3.000
 MSI  HC12  C1   N1    110.64  3.000
 MSI  HC11  C1   N1    108.91  3.000
 MSI  C14   O1   C13   118.63  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
 MSI  CONST_01  C7    C6   C5   C4      0.00   0.0  0
 MSI  CONST_02  C7    C8   C9   C4      0.00   0.0  0
 MSI  CONST_03  C8    C9   C4   C5      0.00   0.0  0
 MSI  CONST_04  C8    C7   C6   C5      0.00   0.0  0
 MSI  CONST_05  C9    C4   C5   C6      0.00   0.0  0
 MSI  CONST_06  C9    C8   C7   C6      0.00   0.0  0
 MSI  CONST_07  C17   C16  C15  C14     0.00   0.0  0
 MSI  CONST_08  C17   C18  C19  C14     0.00   0.0  0
 MSI  CONST_09  C18   C19  C14  C15     0.00   0.0  0
 MSI  CONST_10  C18   C17  C16  C15     0.00   0.0  0
 MSI  CONST_11  C19   C14  C15  C16     0.00   0.0  0
 MSI  CONST_12  C19   C18  C17  C16     0.00   0.0  0
 MSI  CONST_13  C8    N1   C2   C3      0.00   0.0  0
 MSI  CONST_14  C9    C4   C5   S1    180.00   0.0  0
 MSI  CONST_15  C7    C6   C5   S1    180.00   0.0  0
 MSI  CONST_16  C16   C15  C14  O1    180.00   0.0  0
 MSI  CONST_17  C18   C19  C14  O1    180.00   0.0  0
 MSI  CONST_18  C8    N1   C2   O2    180.00   0.0  0
 MSI  CONST_19  C1    N1   C2   C3    180.00   0.0  0
 MSI  CONST_20  HC7   C7   C8   N1      0.00   0.0  0
 MSI  CONST_21  HC4   C4   C9   C3      0.00   0.0  0
 MSI  CONST_22  HC6   C6   C5   C4    180.00   0.0  0
 MSI  CONST_23  HC16  C16  C15  C14   180.00   0.0  0
 MSI  CONST_24  HC18  C18  C19  C14   180.00   0.0  0
 MSI  CONST_25  HC19  C19  C14  C15   180.00   0.0  0
 MSI  CONST_26  HC17  C17  C16  C15   180.00   0.0  0
 MSI  CONST_27  HC15  C15  C16  C17   180.00   0.0  0
 MSI  CONST_28  C1    N1   C2   O2      0.00   0.0  0
 MSI  Var_01    C10   C11  C12  N2    -36.81  30.0  1
 MSI  Var_02    C11   C12  N2   C20    21.90  30.0  1
 MSI  Var_03    C12   C11  C10  C20    38.56  30.0  1
 MSI  Var_04    C4    C5   S1   N2     87.27  30.0  2
 MSI  Var_05    C20   N2   S1   C5    -75.76  30.0  3
 MSI  Var_06    C15   C14  O1   C13  -179.64  30.0  2
 MSI  Var_07    HC11  C1   N1   C2     -2.73  30.0  3
 MSI  Var_08    H131  C13  O1   C14    59.48  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
 MSI  chir_01  C20  N2  C10  C13  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
 MSI  plan-1  C14   0.020
 MSI  plan-1  C15   0.020
 MSI  plan-1  C16   0.020
 MSI  plan-1  C17   0.020
 MSI  plan-1  C18   0.020
 MSI  plan-1  C19   0.020
 MSI  plan-1  HC15  0.020
 MSI  plan-1  HC16  0.020
 MSI  plan-1  HC17  0.020
 MSI  plan-1  HC18  0.020
 MSI  plan-1  HC19  0.020
 MSI  plan-1  O1    0.020
 MSI  plan-2  S1    0.020
 MSI  plan-2  N1    0.020
 MSI  plan-2  C2    0.020
 MSI  plan-2  C3    0.020
 MSI  plan-2  C4    0.020
 MSI  plan-2  C5    0.020
 MSI  plan-2  C6    0.020
 MSI  plan-2  C7    0.020
 MSI  plan-2  C8    0.020
 MSI  plan-2  C9    0.020
 MSI  plan-2  HC4   0.020
 MSI  plan-2  HC6   0.020
 MSI  plan-2  HC7   0.020
 MSI  plan-2  C1    0.020
 MSI  plan-2  O2    0.020
 MSI  plan-2  O3    0.020

