# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 22:54:27 2022
#   Inital geometry file: a 153 line input string
#   Ligand name: (2S)-2-({3,5-dicyano-4-ethyl-6-[4-(2-hydroxyethyl)-1,4-diazepan-1-yl]pyridin-2-yl}sulfanyl)-2-phenylacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1c(C#N)c(S[C@H](C(N)=O)c2ccccc2)nc(N3CCCN(CCO)CC3)c1C#N
#
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
 IO5  IO5  "(2S)-2-({3,5-dicyano-4-ethyl-6-[4-(2-hydroxyethyl)-1,4-diazepan-1-yl]pyridin-2-yl}sulfanyl)-2-phenylacetamide"
  ligand  61  33  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IO5
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
 IO5  C01  C  CH3   0  -0.658  -44.1698   -7.5737  31.9597
 IO5  C02  C  CH2   0  -0.550  -45.0542   -7.8042  30.7327
 IO5  C03  C  CR6   0   0.338  -44.7108   -9.0922  30.0470
 IO5  C04  C  CR6   0  -0.207  -45.3454  -10.2888  30.3863
 IO5  C05  C  CSP   0   0.015  -46.2165  -10.2722  31.5066
 IO5  C07  C  CR6   0   0.594  -44.9810  -11.4963  29.7128
 IO5  C09  C  CH2   0  -0.312  -47.0313  -12.7190  30.2859
 IO5  C10  C  CH2   0  -0.489  -47.8287  -13.8087  29.5808
 IO5  C11  C  CH2   0  -0.282  -47.6760  -13.8582  28.0617
 IO5  C13  C  CH2   0  -0.287  -45.2834  -14.2137  27.9117
 IO5  C14  C  CH2   0  -0.360  -45.0249  -13.8910  29.3775
 IO5  C15  C  CH2   0  -0.300  -46.7249  -15.1119  26.2298
 IO5  C16  C  CH2   0  -0.151  -46.0510  -16.4423  25.9277
 IO5  C19  C  CR6   0   0.110  -43.2933  -10.3956  28.6020
 IO5  C21  C  CH1   0  -0.635  -41.8541  -12.2116  27.1002
 IO5  C22  C  CR6   0   0.156  -40.9434  -12.3585  25.9057
 IO5  C23  C  CR16  0  -0.306  -41.4650  -12.7771  24.6861
 IO5  C24  C  CR16  0  -0.237  -40.6377  -12.9215  23.5808
 IO5  C25  C  CR16  0  -0.258  -39.2815  -12.6450  23.6862
 IO5  C26  C  CR16  0  -0.236  -38.7559  -12.2247  24.9017
 IO5  C27  C  CR16  0  -0.271  -39.5814  -12.0814  26.0072
 IO5  C28  C  C     0   0.577  -41.3385  -13.0253  28.2916
 IO5  C31  C  CR6   0  -0.101  -43.6852   -9.1371  29.1036
 IO5  C32  C  CSP   0  -0.031  -42.9981   -7.9635  28.7061
 IO5  N06  N  NS    0  -0.247  -46.8784  -10.2198  32.4508
 IO5  N08  N  NT    0  -0.472  -45.6417  -12.6552  29.8452
 IO5  N12  N  NT    0  -0.421  -46.6037  -14.7405  27.6293
 IO5  N18  N  N     0  -0.494  -43.9132  -11.5037  28.9030
 IO5  N29  N  NH2   0  -0.801  -41.5706  -14.3389  28.1693
 IO5  N33  N  NS    0  -0.236  -42.4259   -7.0167  28.3770
 IO5  O17  O  OH1   0  -0.669  -46.2567  -16.7251  24.5614
 IO5  O30  O  O     0  -0.454  -40.7474  -12.5210  29.2269
 IO5  S20  S  S2    0   0.160  -41.9461  -10.4463  27.4880
 IO5  H1   H  HCH3  0   0.249  -44.4343   -6.6288  32.4323
 IO5  H2   H  HCH3  0   0.241  -44.2965   -8.3650  32.6976
 IO5  H3   H  HCH3  0   0.239  -43.1157   -7.5297  31.6875
 IO5  H4   H  HCH2  0   0.277  -44.9311   -6.9767  30.0324
 IO5  H5   H  HCH2  0   0.275  -46.1039   -7.8028  31.0264
 IO5  H6   H  HCH2  0   0.263  -47.0972  -12.8674  31.3662
 IO5  H7   H  HCH2  0   0.260  -47.5037  -11.7644  30.0532
 IO5  H8   H  HCH2  0   0.265  -48.8740  -13.6094  29.8261
 IO5  H9   H  HCH2  0   0.246  -47.6101  -14.7957  29.9920
 IO5  H10  H  HCH2  0   0.202  -47.5685  -12.8354  27.6608
 IO5  H11  H  HCH2  0   0.244  -48.6044  -14.2525  27.6468
 IO5  H12  H  HCH2  0   0.241  -44.5417  -14.9616  27.6252
 IO5  H13  H  HCH2  0   0.212  -45.0657  -13.3149  27.3115
 IO5  H14  H  HCH2  0   0.271  -45.3723  -14.7046  30.0146
 IO5  H15  H  HCH2  0   0.283  -43.9514  -13.8158  29.5275
 IO5  H16  H  HCH2  0   0.199  -46.3241  -14.3348  25.5580
 IO5  H17  H  HCH2  0   0.234  -47.7856  -15.2146  25.9894
 IO5  H18  H  HCH2  0   0.191  -46.4904  -17.2099  26.5771
 IO5  H19  H  HCH2  0   0.194  -44.9810  -16.3996  26.1648
 IO5  H20  H  HCH1  0   0.352  -42.8575  -12.5505  26.8354
 IO5  H21  H  HCR6  0   0.261  -42.5234  -12.9926  24.6002
 IO5  H22  H  HCR6  0   0.261  -41.0545  -13.2504  22.6377
 IO5  H23  H  HCR6  0   0.260  -38.6355  -12.7566  22.8252
 IO5  H24  H  HCR6  0   0.261  -37.6994  -12.0080  24.9901
 IO5  H25  H  HCR6  0   0.261  -39.1595  -11.7554  26.9506
 IO5  H27  H  HNH2  0   0.406  -41.2229  -14.9815  28.8629
 IO5  H28  H  HNH2  0   0.416  -42.0495  -14.7296  27.3750
 IO5  H29  H  HOH1  0   0.452  -45.8294  -17.5618  24.3598

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
 IO5  C24  C23  aromatic  1.388  0.020  1.388
 IO5  C24  C25  aromatic  1.388  0.020  1.388
 IO5  C23  C22  aromatic  1.391  0.020  1.391
 IO5  C25  C26  aromatic  1.389  0.020  1.389
 IO5  O17  C16  single    1.410  0.020  1.410
 IO5  C22  C21  single    1.509  0.020  1.509
 IO5  C22  C27  aromatic  1.394  0.020  1.394
 IO5  C26  C27  aromatic  1.387  0.020  1.387
 IO5  C16  C15  single    1.522  0.020  1.522
 IO5  C21  C28  single    1.532  0.020  1.532
 IO5  C21  S20  single    1.810  0.020  1.810
 IO5  N29  C28  single    1.340  0.020  1.340
 IO5  C15  N12  single    1.453  0.020  1.453
 IO5  C28  O30  double    1.216  0.020  1.216
 IO5  S20  C19  single    1.749  0.020  1.749
 IO5  N33  C32  triple    1.154  0.020  1.154
 IO5  C13  N12  single    1.449  0.020  1.449
 IO5  C13  C14  single    1.523  0.020  1.523
 IO5  N12  C11  single    1.454  0.020  1.454
 IO5  C32  C31  single    1.417  0.020  1.417
 IO5  C19  C31  aromatic  1.410  0.020  1.410
 IO5  C19  N18  aromatic  1.305  0.020  1.305
 IO5  C31  C03  aromatic  1.394  0.020  1.394
 IO5  C11  C10  single    1.528  0.020  1.528
 IO5  N18  C07  aromatic  1.340  0.020  1.340
 IO5  C14  N08  single    1.458  0.020  1.458
 IO5  C03  C02  single    1.499  0.020  1.499
 IO5  C03  C04  aromatic  1.396  0.020  1.396
 IO5  C07  N08  single    1.341  0.020  1.341
 IO5  C07  C04  aromatic  1.430  0.020  1.430
 IO5  C02  C01  single    1.530  0.020  1.530
 IO5  N08  C09  single    1.459  0.020  1.459
 IO5  C04  C05  single    1.419  0.020  1.419
 IO5  C10  C09  single    1.523  0.020  1.523
 IO5  C05  N06  triple    1.154  0.020  1.154
 IO5  C01  H1   single    0.970  0.020  1.090
 IO5  C01  H2   single    0.970  0.020  1.090
 IO5  C01  H3   single    0.970  0.020  1.090
 IO5  C02  H4   single    0.970  0.020  1.090
 IO5  C02  H5   single    0.970  0.020  1.090
 IO5  C09  H6   single    0.970  0.020  1.090
 IO5  C09  H7   single    0.970  0.020  1.090
 IO5  C10  H8   single    0.970  0.020  1.090
 IO5  C10  H9   single    0.970  0.020  1.090
 IO5  C11  H10  single    0.970  0.020  1.090
 IO5  C11  H11  single    0.970  0.020  1.090
 IO5  C13  H12  single    0.970  0.020  1.090
 IO5  C13  H13  single    0.970  0.020  1.090
 IO5  C14  H14  single    0.970  0.020  1.090
 IO5  C14  H15  single    0.970  0.020  1.090
 IO5  C15  H16  single    0.970  0.020  1.090
 IO5  C15  H17  single    0.970  0.020  1.090
 IO5  C16  H18  single    0.970  0.020  1.090
 IO5  C16  H19  single    0.970  0.020  1.090
 IO5  C21  H20  single    0.970  0.020  1.090
 IO5  C23  H21  single    0.930  0.020  1.080
 IO5  C24  H22  single    0.930  0.020  1.080
 IO5  C25  H23  single    0.930  0.020  1.080
 IO5  C26  H24  single    0.930  0.020  1.080
 IO5  C27  H25  single    0.930  0.020  1.080
 IO5  N29  H27  single    0.860  0.020  1.020
 IO5  N29  H28  single    0.860  0.020  1.020
 IO5  O17  H29  single    0.850  0.020  0.980

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
 IO5  H3   C01  H2   108.12  3.000
 IO5  H3   C01  H1   107.96  3.000
 IO5  H2   C01  H1   107.94  3.000
 IO5  H3   C01  C02  111.40  3.000
 IO5  H2   C01  C02  111.50  3.000
 IO5  H1   C01  C02  109.78  3.000
 IO5  H5   C02  H4   106.30  3.000
 IO5  H5   C02  C03  110.18  3.000
 IO5  H4   C02  C03  109.40  3.000
 IO5  H5   C02  C01  109.90  3.000
 IO5  H4   C02  C01  109.59  3.000
 IO5  C03  C02  C01  111.34  3.000
 IO5  C31  C03  C04  118.11  3.000
 IO5  C04  C03  C02  121.40  3.000
 IO5  C31  C03  C02  120.38  3.000
 IO5  C07  C04  C05  122.56  3.000
 IO5  C05  C04  C03  117.44  3.000
 IO5  C07  C04  C03  119.56  3.000
 IO5  N06  C05  C04  180.00  3.000
 IO5  N18  C07  N08  116.59  3.000
 IO5  N08  C07  C04  123.91  3.000
 IO5  N18  C07  C04  119.50  3.000
 IO5  H7   C09  H6   107.69  3.000
 IO5  H7   C09  N08  108.05  3.000
 IO5  H6   C09  N08  111.23  3.000
 IO5  H7   C09  C10  107.50  3.000
 IO5  H6   C09  C10  109.21  3.000
 IO5  N08  C09  C10  112.95  3.000
 IO5  H9   C10  H8   105.79  3.000
 IO5  H9   C10  C11  108.99  3.000
 IO5  H8   C10  C11  108.97  3.000
 IO5  H9   C10  C09  111.57  3.000
 IO5  H8   C10  C09  105.46  3.000
 IO5  C11  C10  C09  115.54  3.000
 IO5  H11  C11  H10  106.25  3.000
 IO5  H11  C11  N12  107.17  3.000
 IO5  H10  C11  N12  112.48  3.000
 IO5  H11  C11  C10  107.75  3.000
 IO5  H10  C11  C10  109.93  3.000
 IO5  N12  C11  C10  112.89  3.000
 IO5  H13  C13  H12  106.35  3.000
 IO5  H13  C13  N12  111.72  3.000
 IO5  H12  C13  N12  108.59  3.000
 IO5  H13  C13  C14  108.52  3.000
 IO5  H12  C13  C14  106.41  3.000
 IO5  N12  C13  C14  114.78  3.000
 IO5  H15  C14  H14  106.60  3.000
 IO5  H15  C14  N08  108.36  3.000
 IO5  H14  C14  N08  108.07  3.000
 IO5  H15  C14  C13  108.37  3.000
 IO5  H14  C14  C13  110.50  3.000
 IO5  N08  C14  C13  114.61  3.000
 IO5  H17  C15  H16  106.57  3.000
 IO5  H17  C15  N12  108.48  3.000
 IO5  H16  C15  N12  112.11  3.000
 IO5  H17  C15  C16  107.71  3.000
 IO5  H16  C15  C16  109.53  3.000
 IO5  N12  C15  C16  112.20  3.000
 IO5  H19  C16  H18  106.85  3.000
 IO5  H19  C16  O17  111.07  3.000
 IO5  H18  C16  O17  112.01  3.000
 IO5  H19  C16  C15  110.80  3.000
 IO5  H18  C16  C15  108.47  3.000
 IO5  O17  C16  C15  107.64  3.000
 IO5  S20  C19  N18  119.22  3.000
 IO5  N18  C19  C31  122.94  3.000
 IO5  S20  C19  C31  117.81  3.000
 IO5  H20  C21  S20  107.94  3.000
 IO5  H20  C21  C28  109.45  3.000
 IO5  S20  C21  C28  111.62  3.000
 IO5  H20  C21  C22  109.41  3.000
 IO5  S20  C21  C22  107.17  3.000
 IO5  C28  C21  C22  111.15  3.000
 IO5  C27  C22  C23  119.35  3.000
 IO5  C27  C22  C21  120.84  3.000
 IO5  C23  C22  C21  119.80  3.000
 IO5  H21  C23  C24  119.89  3.000
 IO5  H21  C23  C22  119.71  3.000
 IO5  C24  C23  C22  120.40  3.000
 IO5  H22  C24  C25  120.20  3.000
 IO5  H22  C24  C23  119.73  3.000
 IO5  C25  C24  C23  120.07  3.000
 IO5  H23  C25  C26  120.10  3.000
 IO5  H23  C25  C24  120.15  3.000
 IO5  C26  C25  C24  119.76  3.000
 IO5  H24  C26  C27  119.68  3.000
 IO5  H24  C26  C25  120.10  3.000
 IO5  C27  C26  C25  120.22  3.000
 IO5  H25  C27  C26  119.55  3.000
 IO5  H25  C27  C22  120.25  3.000
 IO5  C26  C27  C22  120.20  3.000
 IO5  O30  C28  N29  124.14  3.000
 IO5  O30  C28  C21  122.78  3.000
 IO5  N29  C28  C21  113.05  3.000
 IO5  C32  C31  C19  120.30  3.000
 IO5  C19  C31  C03  118.28  3.000
 IO5  C32  C31  C03  121.33  3.000
 IO5  N33  C32  C31  180.00  3.000
 IO5  C14  N08  C09  117.56  3.000
 IO5  C09  N08  C07  122.48  3.000
 IO5  C14  N08  C07  119.50  3.000
 IO5  C15  N12  C13  110.89  3.000
 IO5  C13  N12  C11  113.16  3.000
 IO5  C15  N12  C11  112.33  3.000
 IO5  C19  N18  C07  120.87  3.000
 IO5  H28  N29  H27  117.39  3.000
 IO5  H28  N29  C28  122.35  3.000
 IO5  H27  N29  C28  120.19  3.000
 IO5  H29  O17  C16  108.24  3.000
 IO5  C21  S20  C19  101.77  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
 IO5  CONST_01  N18  C19  C31  C03     0.00   0.0  0
 IO5  CONST_02  N18  C07  C04  C03     0.00   0.0  0
 IO5  CONST_03  C19  C31  C03  C04     0.00   0.0  0
 IO5  CONST_04  C19  N18  C07  C04     0.00   0.0  0
 IO5  CONST_05  C31  C19  N18  C07     0.00   0.0  0
 IO5  CONST_06  C31  C03  C04  C07     0.00   0.0  0
 IO5  CONST_07  C25  C24  C23  C22     0.00   0.0  0
 IO5  CONST_08  C25  C26  C27  C22     0.00   0.0  0
 IO5  CONST_09  C26  C25  C24  C23     0.00   0.0  0
 IO5  CONST_10  C26  C27  C22  C23     0.00   0.0  0
 IO5  CONST_11  C27  C22  C23  C24     0.00   0.0  0
 IO5  CONST_12  C27  C26  C25  C24     0.00   0.0  0
 IO5  CONST_13  N08  C07  C04  C03   180.00   0.0  0
 IO5  CONST_14  N08  C07  N18  C19   180.00   0.0  0
 IO5  CONST_15  C19  C31  C03  C02   180.00   0.0  0
 IO5  CONST_16  C07  C04  C03  C02   180.00   0.0  0
 IO5  CONST_17  S20  C19  C31  C03   180.00   0.0  0
 IO5  CONST_18  C32  C31  C03  C04   180.00   0.0  0
 IO5  CONST_19  C31  C03  C04  C05   180.00   0.0  0
 IO5  CONST_22  S20  C19  N18  C07   180.00   0.0  0
 IO5  CONST_23  C24  C23  C22  C21   180.00   0.0  0
 IO5  CONST_24  C26  C27  C22  C21   180.00   0.0  0
 IO5  CONST_25  N18  C19  C31  C32   180.00   0.0  0
 IO5  CONST_26  H22  C24  C23  C22   180.00   0.0  0
 IO5  CONST_27  H24  C26  C27  C22   180.00   0.0  0
 IO5  CONST_28  H23  C25  C24  C23   180.00   0.0  0
 IO5  CONST_29  H25  C27  C22  C23   180.00   0.0  0
 IO5  CONST_30  H24  C26  C25  C24   180.00   0.0  0
 IO5  CONST_31  H21  C23  C24  C25   180.00   0.0  0
 IO5  CONST_32  H25  C27  C26  C25   180.00   0.0  0
 IO5  CONST_33  H22  C24  C25  C26   180.00   0.0  0
 IO5  CONST_34  H21  C23  C22  C27   180.00   0.0  0
 IO5  CONST_35  H23  C25  C26  C27   180.00   0.0  0
 IO5  CONST_36  H27  N29  C28  C21   180.00   0.0  0
 IO5  CONST_37  H28  N29  C28  C21     0.00   0.0  0
 IO5  CONST_38  H27  N29  C28  O30     0.00   0.0  0
 IO5  CONST_39  H28  N29  C28  O30   180.00   0.0  0
 IO5  Var_01    C31  C03  C02  C01   -85.59  30.0  2
 IO5  Var_02    C04  C03  C02  C01    90.53  30.0  2
 IO5  Var_03    C31  C19  S20  C21  -178.51  30.0  2
 IO5  Var_04    N18  C19  S20  C21    -0.44  30.0  2
 IO5  Var_05    H4   C02  C03  C04  -148.19  30.0  2
 IO5  Var_06    H5   C02  C03  C04   -31.68  30.0  2
 IO5  Var_07    H4   C02  C03  C31    35.69  30.0  2
 IO5  Var_08    H5   C02  C03  C31   152.21  30.0  2
 IO5  Var_09    O17  C16  C15  N12   178.44  30.0  1
 IO5  Var_10    H1   C01  C02  C03   179.50  30.0  3
 IO5  Var_11    H2   C01  C02  C03   -60.93  30.0  3
 IO5  Var_12    H3   C01  C02  C03    59.97  30.0  3
 IO5  Var_13    H18  C16  C15  N12    57.06  30.0  1
 IO5  Var_14    H19  C16  C15  N12   -59.93  30.0  1
 IO5  Var_15    H16  C15  C16  O17   -56.39  30.0  3
 IO5  Var_16    H17  C15  C16  O17    59.13  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
 IO5  chir_01  C21  C22  C28  S20  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
 IO5  plan-1  C02  0.020
 IO5  plan-1  C03  0.020
 IO5  plan-1  C04  0.020
 IO5  plan-1  C05  0.020
 IO5  plan-1  C07  0.020
 IO5  plan-1  C19  0.020
 IO5  plan-1  C31  0.020
 IO5  plan-1  C32  0.020
 IO5  plan-1  N06  0.020
 IO5  plan-1  N08  0.020
 IO5  plan-1  N18  0.020
 IO5  plan-1  N33  0.020
 IO5  plan-1  S20  0.020
 IO5  plan-2  C21  0.020
 IO5  plan-2  C22  0.020
 IO5  plan-2  C23  0.020
 IO5  plan-2  C24  0.020
 IO5  plan-2  C25  0.020
 IO5  plan-2  C26  0.020
 IO5  plan-2  C27  0.020
 IO5  plan-2  H21  0.020
 IO5  plan-2  H22  0.020
 IO5  plan-2  H23  0.020
 IO5  plan-2  H24  0.020
 IO5  plan-2  H25  0.020
 IO5  plan-3  C21  0.020
 IO5  plan-3  C28  0.020
 IO5  plan-3  N29  0.020
 IO5  plan-3  O30  0.020
 IO5  plan-3  H27  0.020
 IO5  plan-3  H28  0.020

