# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 19:55:45 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: 6-[(2~{R})-2-methyl-4-(1-methylindol-5-yl)carbonyl-piperazin-1-yl]sulfonyl-3~{H}-1,3-benzoxazol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CN(CCN1[S](=O)(=O)c2ccc3NC(=O)Oc3c2)C(=O)c4ccc5n(C)ccc5c4
#
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
 SYW  SYW  6-[(2~{R})-2-methyl-4-(1-methylindol-5-yl)carbonyl-piperazin-1-yl]sulfonyl-3~{H}-1,3-benzoxazol-2-one  ligand  54  32  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SYW
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
 SYW  C23  C  CR6   0  -0.085  -10.5900   8.9842  -22.8094
 SYW  C29  C  CR15  0  -0.025  -11.1437  13.5026  -23.0983
 SYW  C28  C  CH3   0  -0.529  -13.1180  13.1535  -24.6039
 SYW  C26  C  CR56  0   0.370  -11.6888  11.4020  -23.5580
 SYW  C25  C  CR16  0  -0.300  -12.2833  10.2325  -24.0293
 SYW  C11  C  CR6   0  -0.209  -10.9628   4.3105  -17.2434
 SYW  C20  C  CR16  0  -0.324  -11.3699   5.3727  -16.4317
 SYW  C21  C  C     0   0.517   -9.9296   7.6781  -22.5160
 SYW  C12  C  CR16  0  -0.248   -9.8655   3.5152  -16.9319
 SYW  C16  C  CR5   0   0.652   -9.7987   6.3789  -13.4135
 SYW  C14  C  CR56  0   0.350   -9.5036   4.8076  -14.9885
 SYW  C13  C  CR16  0  -0.282   -9.1106   3.7553  -15.7893
 SYW  C02  C  CH1   0  -0.120  -10.0396   4.8710  -20.5172
 SYW  C03  C  CH2   0  -0.298  -10.2048   5.3167  -21.9674
 SYW  N04  N  NT    0  -0.463  -10.7131   6.6708  -22.0571
 SYW  C05  C  CH2   0  -0.305  -11.9854   6.8450  -21.3839
 SYW  C06  C  CH2   0  -0.294  -11.8825   6.4100  -19.9271
 SYW  N07  N  N     0  -0.590  -11.3481   5.0551  -19.8740
 SYW  S08  S  S     0   1.385  -11.8643   3.9935  -18.7365
 SYW  O09  O  OS    0  -0.644  -11.4872   2.6660  -19.1915
 SYW  O10  O  OS    0  -0.645  -13.2614   4.2963  -18.4742
 SYW  N15  N  NR15  0  -0.733   -9.0271   5.3274  -13.8108
 SYW  O17  O  O     0  -0.426   -9.7041   7.0781  -12.4464
 SYW  O18  O  O     0  -0.459  -10.7771   6.5367  -14.3549
 SYW  C19  C  CR56  0   0.335  -10.6073   5.5887  -15.3151
 SYW  O22  O  O     0  -0.480   -8.7357   7.5323  -22.7397
 SYW  C24  C  CR16  0  -0.278  -11.7296   9.0320  -23.6364
 SYW  N27  N  NR5   0  -0.515  -12.0260  12.7042  -23.7754
 SYW  C30  C  CR15  0  -0.424  -10.2260  12.7413  -22.4356
 SYW  C31  C  CR56  0   0.079  -10.5520  11.3798  -22.7171
 SYW  C32  C  CR16  0  -0.374   -9.9929  10.1508  -22.3631
 SYW  H1   H  HCR5  0   0.284  -11.2426  14.5762  -23.1439
 SYW  H2   H  HCH3  0   0.266  -13.1760  14.2376  -24.5605
 SYW  H3   H  HCH3  0   0.253  -12.9694  12.8557  -25.6420
 SYW  H4   H  HCH3  0   0.254  -14.0650  12.7425  -24.2549
 SYW  H5   H  HCR6  0   0.267  -13.1459  10.2546  -24.6831
 SYW  H6   H  HCR6  0   0.306  -12.2326   5.9856  -16.6570
 SYW  H7   H  HCR6  0   0.292   -9.5856   2.6965  -17.5794
 SYW  H8   H  HCR6  0   0.292   -8.2605   3.1356  -15.5420
 SYW  H12  H  HCH1  0   0.282   -9.8237   3.8031  -20.5399
 SYW  H13  H  HCH2  0   0.264  -10.9180   4.6501  -22.4617
 SYW  H14  H  HCH2  0   0.271   -9.2556   5.2425  -22.4916
 SYW  H15  H  HCH2  0   0.284  -12.2986   7.8851  -21.4151
 SYW  H16  H  HCH2  0   0.252  -12.7501   6.2463  -21.8867
 SYW  H17  H  HCH2  0   0.249  -11.2514   7.1086  -19.3692
 SYW  H18  H  HCH2  0   0.284  -12.8770   6.4354  -19.4884
 SYW  H19  H  HNR5  0   0.440   -8.2339   4.9929  -13.2834
 SYW  H20  H  HCR6  0   0.260  -12.1706   8.1088  -23.9913
 SYW  H21  H  HCR5  0   0.247   -9.4172  13.1077  -21.8242
 SYW  H22  H  HCR6  0   0.249   -9.1074  10.1109  -21.7402
 SYW  C01  C  CH3   0  -0.661   -8.9020   5.5947  -19.8076
 SYW  H9   H  HCH3  0   0.247   -8.7876   5.2489  -18.7814
 SYW  H10  H  HCH3  0   0.243   -7.9656   5.3959  -20.3283
 SYW  H11  H  HCH3  0   0.236   -9.0435   6.6748  -19.7831

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
 SYW  C28  N27  single    1.443  0.020  1.443
 SYW  C25  C24  aromatic  1.379  0.020  1.379
 SYW  C25  C26  aromatic  1.394  0.020  1.394
 SYW  C24  C23  aromatic  1.409  0.020  1.409
 SYW  N27  C26  aromatic  1.363  0.020  1.363
 SYW  N27  C29  aromatic  1.369  0.020  1.369
 SYW  C26  C31  aromatic  1.414  0.020  1.414
 SYW  C29  C30  aromatic  1.364  0.020  1.364
 SYW  C23  C21  single    1.493  0.020  1.493
 SYW  C23  C32  aromatic  1.384  0.020  1.384
 SYW  O22  C21  double    1.223  0.020  1.223
 SYW  C21  N04  single    1.356  0.020  1.356
 SYW  C31  C32  aromatic  1.396  0.020  1.396
 SYW  C31  C30  aromatic  1.428  0.020  1.428
 SYW  N04  C03  single    1.449  0.020  1.449
 SYW  N04  C05  single    1.450  0.020  1.450
 SYW  C03  C02  single    1.526  0.020  1.526
 SYW  C05  C06  single    1.524  0.020  1.524
 SYW  C02  N07  single    1.470  0.020  1.470
 SYW  C02  C01  single    1.524  0.020  1.524
 SYW  C06  N07  single    1.457  0.020  1.457
 SYW  N07  S08  single    1.639  0.020  1.639
 SYW  O09  S08  double    1.453  0.020  1.453
 SYW  S08  O10  double    1.453  0.020  1.453
 SYW  S08  C11  single    1.773  0.020  1.773
 SYW  C11  C12  aromatic  1.391  0.020  1.391
 SYW  C11  C20  aromatic  1.397  0.020  1.397
 SYW  C12  C13  aromatic  1.390  0.020  1.390
 SYW  C20  C19  aromatic  1.369  0.020  1.369
 SYW  C13  C14  aromatic  1.379  0.020  1.379
 SYW  C19  C14  aromatic  1.391  0.020  1.391
 SYW  C19  O18  single    1.360  0.020  1.360
 SYW  C14  N15  single    1.373  0.020  1.373
 SYW  O18  C16  single    1.367  0.020  1.367
 SYW  N15  C16  single    1.363  0.020  1.363
 SYW  C16  O17  double    1.197  0.020  1.197
 SYW  C29  H1   single    0.930  0.020  1.080
 SYW  C28  H2   single    0.970  0.020  1.090
 SYW  C28  H3   single    0.970  0.020  1.090
 SYW  C28  H4   single    0.970  0.020  1.090
 SYW  C25  H5   single    0.930  0.020  1.080
 SYW  C20  H6   single    0.930  0.020  1.080
 SYW  C12  H7   single    0.930  0.020  1.080
 SYW  C13  H8   single    0.930  0.020  1.080
 SYW  C01  H9   single    0.970  0.020  1.090
 SYW  C01  H10  single    0.970  0.020  1.090
 SYW  C01  H11  single    0.970  0.020  1.090
 SYW  C02  H12  single    0.970  0.020  1.090
 SYW  C03  H13  single    0.970  0.020  1.090
 SYW  C03  H14  single    0.970  0.020  1.090
 SYW  C05  H15  single    0.970  0.020  1.090
 SYW  C05  H16  single    0.970  0.020  1.090
 SYW  C06  H17  single    0.970  0.020  1.090
 SYW  C06  H18  single    0.970  0.020  1.090
 SYW  N15  H19  single    0.860  0.020  1.020
 SYW  C24  H20  single    0.930  0.020  1.080
 SYW  C30  H21  single    0.930  0.020  1.080
 SYW  C32  H22  single    0.930  0.020  1.080

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
 SYW  C32  C23  C24  120.62  3.000
 SYW  C32  C23  C21  118.89  3.000
 SYW  C24  C23  C21  120.20  3.000
 SYW  H1   C29  C30  129.60  3.000
 SYW  H1   C29  N27  120.01  3.000
 SYW  C30  C29  N27  110.39  3.000
 SYW  H4   C28  H3   108.69  3.000
 SYW  H4   C28  H2   108.49  3.000
 SYW  H3   C28  H2   108.53  3.000
 SYW  H4   C28  N27  110.88  3.000
 SYW  H3   C28  N27  111.02  3.000
 SYW  H2   C28  N27  109.16  3.000
 SYW  C31  C26  N27  107.98  3.000
 SYW  C31  C26  C25  122.06  3.000
 SYW  N27  C26  C25  129.96  3.000
 SYW  H5   C25  C24  120.64  3.000
 SYW  H5   C25  C26  121.79  3.000
 SYW  C24  C25  C26  117.56  3.000
 SYW  S08  C11  C12  119.19  3.000
 SYW  C12  C11  C20  122.31  3.000
 SYW  S08  C11  C20  118.49  3.000
 SYW  H6   C20  C19  121.64  3.000
 SYW  H6   C20  C11  122.81  3.000
 SYW  C19  C20  C11  115.55  3.000
 SYW  O22  C21  N04  122.49  3.000
 SYW  N04  C21  C23  117.44  3.000
 SYW  O22  C21  C23  120.01  3.000
 SYW  H7   C12  C13  118.86  3.000
 SYW  H7   C12  C11  120.23  3.000
 SYW  C13  C12  C11  120.91  3.000
 SYW  O18  C16  O17  123.06  3.000
 SYW  O17  C16  N15  129.87  3.000
 SYW  O18  C16  N15  107.07  3.000
 SYW  C19  C14  N15  105.32  3.000
 SYW  N15  C14  C13  133.47  3.000
 SYW  C19  C14  C13  121.20  3.000
 SYW  H8   C13  C14  121.92  3.000
 SYW  H8   C13  C12  121.07  3.000
 SYW  C14  C13  C12  117.01  3.000
 SYW  H12  C02  N07  107.96  3.000
 SYW  H12  C02  C03  106.73  3.000
 SYW  N07  C02  C03  106.43  3.000
 SYW  H12  C02  C01  109.10  3.000
 SYW  N07  C02  C01  113.67  3.000
 SYW  C03  C02  C01  112.62  3.000
 SYW  H14  C03  H13  108.05  3.000
 SYW  H14  C03  N04  109.89  3.000
 SYW  H13  C03  N04  108.22  3.000
 SYW  H14  C03  C02  110.11  3.000
 SYW  H13  C03  C02  108.78  3.000
 SYW  N04  C03  C02  111.69  3.000
 SYW  C05  N04  C03  113.03  3.000
 SYW  C05  N04  C21  125.09  3.000
 SYW  C03  N04  C21  120.82  3.000
 SYW  H16  C05  H15  108.01  3.000
 SYW  H16  C05  C06  109.31  3.000
 SYW  H15  C05  C06  108.67  3.000
 SYW  H16  C05  N04  109.53  3.000
 SYW  H15  C05  N04  110.76  3.000
 SYW  C06  C05  N04  110.51  3.000
 SYW  H18  C06  H17  107.87  3.000
 SYW  H18  C06  N07  110.02  3.000
 SYW  H17  C06  N07  111.31  3.000
 SYW  H18  C06  C05  108.50  3.000
 SYW  H17  C06  C05  110.13  3.000
 SYW  N07  C06  C05  108.96  3.000
 SYW  S08  N07  C06  120.79  3.000
 SYW  S08  N07  C02  120.19  3.000
 SYW  C06  N07  C02  115.28  3.000
 SYW  O10  S08  O09  119.75  3.000
 SYW  O10  S08  N07  107.04  3.000
 SYW  O09  S08  N07  107.02  3.000
 SYW  O10  S08  C11  107.43  3.000
 SYW  O09  S08  C11  107.17  3.000
 SYW  N07  S08  C11  107.97  3.000
 SYW  H19  N15  C14  126.55  3.000
 SYW  H19  N15  C16  123.23  3.000
 SYW  C14  N15  C16  110.22  3.000
 SYW  C19  O18  C16  108.44  3.000
 SYW  O18  C19  C14  108.95  3.000
 SYW  O18  C19  C20  128.03  3.000
 SYW  C14  C19  C20  123.01  3.000
 SYW  H20  C24  C25  119.03  3.000
 SYW  H20  C24  C23  119.52  3.000
 SYW  C25  C24  C23  121.44  3.000
 SYW  C26  N27  C28  125.21  3.000
 SYW  C26  N27  C29  108.60  3.000
 SYW  C28  N27  C29  126.18  3.000
 SYW  H21  C30  C31  127.39  3.000
 SYW  H21  C30  C29  126.19  3.000
 SYW  C31  C30  C29  106.42  3.000
 SYW  C32  C31  C30  134.27  3.000
 SYW  C30  C31  C26  106.61  3.000
 SYW  C32  C31  C26  119.11  3.000
 SYW  H22  C32  C31  120.37  3.000
 SYW  H22  C32  C23  120.45  3.000
 SYW  C31  C32  C23  119.18  3.000
 SYW  H11  C01  H10  107.65  3.000
 SYW  H11  C01  H9   107.89  3.000
 SYW  H10  C01  H9   107.59  3.000
 SYW  H11  C01  C02  112.61  3.000
 SYW  H10  C01  C02  109.42  3.000
 SYW  H9   C01  C02  111.50  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
 SYW  CONST_01  C26  C25  C24  C23    0.00   0.0  0
 SYW  CONST_02  C26  C31  C32  C23    0.00   0.0  0
 SYW  CONST_03  C30  C31  C32  C23  180.00   0.0  0
 SYW  CONST_04  C25  C26  N27  C29  180.00   0.0  0
 SYW  CONST_05  C31  C26  N27  C29    0.00   0.0  0
 SYW  CONST_06  C26  C31  C30  C29    0.00   0.0  0
 SYW  CONST_07  C32  C31  C30  C29  180.00   0.0  0
 SYW  CONST_08  C30  C29  N27  C26    0.00   0.0  0
 SYW  CONST_09  C32  C23  C24  C25    0.00   0.0  0
 SYW  CONST_10  C32  C31  C26  C25    0.00   0.0  0
 SYW  CONST_11  C30  C31  C26  C25  180.00   0.0  0
 SYW  CONST_12  C14  C13  C12  C11    0.00   0.0  0
 SYW  CONST_13  C14  C19  C20  C11    0.00   0.0  0
 SYW  CONST_14  C13  C12  C11  C20    0.00   0.0  0
 SYW  CONST_15  C13  C14  C19  C20    0.00   0.0  0
 SYW  CONST_16  C19  C20  C11  C12    0.00   0.0  0
 SYW  CONST_17  C19  C14  C13  C12    0.00   0.0  0
 SYW  CONST_18  N27  C26  C25  C24  180.00   0.0  0
 SYW  CONST_19  C31  C26  C25  C24    0.00   0.0  0
 SYW  CONST_20  C31  C32  C23  C24    0.00   0.0  0
 SYW  CONST_21  C32  C31  C26  N27  180.00   0.0  0
 SYW  CONST_22  C30  C31  C26  N27    0.00   0.0  0
 SYW  CONST_23  C31  C30  C29  N27    0.00   0.0  0
 SYW  CONST_24  C25  C26  N27  C28    0.00   0.0  0
 SYW  CONST_25  C31  C26  N27  C28  180.00   0.0  0
 SYW  CONST_26  C30  C29  N27  C28  180.00   0.0  0
 SYW  CONST_27  C21  C23  C24  C25  180.00   0.0  0
 SYW  CONST_28  C31  C32  C23  C21  180.00   0.0  0
 SYW  CONST_29  S08  C11  C12  C13  180.00   0.0  0
 SYW  CONST_30  C19  C20  C11  S08  180.00   0.0  0
 SYW  CONST_31  C03  N04  C21  C23  180.00   0.0  0
 SYW  CONST_33  H5   C25  C24  C23  180.00   0.0  0
 SYW  CONST_34  H20  C24  C25  C26  180.00   0.0  0
 SYW  CONST_35  H1   C29  N27  C26  180.00   0.0  0
 SYW  CONST_36  H22  C32  C31  C26  180.00   0.0  0
 SYW  CONST_37  H21  C30  C31  C26  180.00   0.0  0
 SYW  CONST_38  H8   C13  C12  C11  180.00   0.0  0
 SYW  CONST_39  H7   C12  C11  C20  180.00   0.0  0
 SYW  CONST_40  H6   C20  C11  C12  180.00   0.0  0
 SYW  CONST_41  O22  C21  N04  C03    0.00   0.0  0
 SYW  Var_01    C05  N04  C03  C02  -57.79  30.0  1
 SYW  Var_02    C05  C06  N07  C02   57.36  30.0  1
 SYW  Var_03    C06  C05  N04  C03   55.63  30.0  1
 SYW  Var_04    N07  C06  C05  N04  -53.23  30.0  1
 SYW  Var_05    C02  N07  S08  C11   74.71  30.0  2
 SYW  Var_06    N07  S08  C11  C20   80.04  30.0  2
 SYW  Var_07    C24  C23  C21  N04  -51.72  30.0  1
 SYW  Var_08    H2   C28  N27  C29   -3.57  30.0  2

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
 SYW  chir_01  C02  C03  N07  C01  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
 SYW  plan-1  C11  0.020
 SYW  plan-1  C20  0.020
 SYW  plan-1  C12  0.020
 SYW  plan-1  C16  0.020
 SYW  plan-1  C14  0.020
 SYW  plan-1  C13  0.020
 SYW  plan-1  S08  0.020
 SYW  plan-1  N15  0.020
 SYW  plan-1  O17  0.020
 SYW  plan-1  O18  0.020
 SYW  plan-1  C19  0.020
 SYW  plan-1  H6   0.020
 SYW  plan-1  H7   0.020
 SYW  plan-1  H8   0.020
 SYW  plan-1  H19  0.020
 SYW  plan-2  C23  0.020
 SYW  plan-2  C29  0.020
 SYW  plan-2  C28  0.020
 SYW  plan-2  C26  0.020
 SYW  plan-2  C25  0.020
 SYW  plan-2  C21  0.020
 SYW  plan-2  C24  0.020
 SYW  plan-2  N27  0.020
 SYW  plan-2  C30  0.020
 SYW  plan-2  C31  0.020
 SYW  plan-2  C32  0.020
 SYW  plan-2  H1   0.020
 SYW  plan-2  H5   0.020
 SYW  plan-2  H20  0.020
 SYW  plan-2  H21  0.020
 SYW  plan-2  H22  0.020
 SYW  plan-3  C23  0.020
 SYW  plan-3  C21  0.020
 SYW  plan-3  C03  0.020
 SYW  plan-3  N04  0.020
 SYW  plan-3  C05  0.020
 SYW  plan-3  O22  0.020

