# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 12:56:53 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 6-({2-[(5-chloro-4-{[(2S)-2,3-dihydroxypropyl]oxy}-2-methoxyphenyl)amino]-2-oxoethyl}sulfanyl)pyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(OC[C@@H](O)CO)c(Cl)cc1NC(=O)CSc2ccc(cn2)C(O)=O
#
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
 1E6  1E6  '6-({2-[(5-chloro-4-{[(2S)-2,3-dihydroxypropyl]oxy}-2-methoxyphenyl)amino]-2-oxoethyl}sulfanyl)pyridine-3-carboxylic acid'  ligand  47  29  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1E6
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
 1E6  C1   C   C      0   0.399  -8.9526  -0.9158   0.4863
 1E6  C2   C   C      0  -0.200  -7.5813  -0.3910   0.0941
 1E6  O3   O   OC    -1  -0.592  -8.9797  -1.7880   1.3748
 1E6  O4   O   O      0  -0.591  -9.9244  -0.4243  -0.1172
 1E6  C5   C   C1     0  -0.084  -6.4263  -0.8465   0.7107
 1E6  N6   N   N      0  -0.422  -5.1983  -0.4259   0.4096
 1E6  C7   C   C      0   0.086  -5.0678   0.4845  -0.5392
 1E6  C8   C   C1     0  -0.294  -6.1566   1.0190  -1.2321
 1E6  C9   C   C1     0  -0.169  -7.4188   0.5700  -0.9033
 1E6  S10  S   S2     0   0.064  -3.4636   1.0677  -0.9759
 1E6  C11  C   CH2    0  -0.694  -2.4305   0.0800   0.1251
 1E6  C12  C   C      0   0.551  -0.9860   0.4504  -0.1324
 1E6  N15  N   NH1    0  -0.725  -0.1134  -0.1785   0.6837
 1E6  C16  C   CR6    0   0.200   1.2846  -0.0549   0.5522
 1E6  C17  C   CR16   0  -0.217   1.9232   1.1386   0.8439
 1E6  C18  C   CR6    0  -0.209   3.2922   1.2588   0.7066
 1E6  C19  C   CR6    0   0.503   4.0618   0.1715   0.2882
 1E6  C20  C   CR16   0  -0.557   3.4246  -1.0333  -0.0005
 1E6  C21  C   CR6    0   0.414   2.0414  -1.1480   0.1165
 1E6  O22  O   O2     0  -0.452   5.3800   0.3662   0.1927
 1E6  C23  C   CH2    0  -0.203   6.2132  -0.7148  -0.1860
 1E6  C24  C   CH1    0  -0.040   7.6523  -0.2270  -0.1459
 1E6  C27  C   CH2    0  -0.164   8.5689  -1.3153  -0.6834
 1E6  O28  O   OH1    0  -0.667   9.8795  -0.8099  -0.7460
 1E6  CL3  CL  CL     0  -0.117   4.0721   2.7604   1.0643
 1E6  O37  O   O2     0  -0.457   1.3589  -2.2658  -0.1605
 1E6  C38  C   CH3    0  -0.443   2.0610  -3.4033  -0.6277
 1E6  O43  O   O      0  -0.462  -0.6569   1.2457  -0.9922
 1E6  O44  O   OH1    0  -0.653   8.0250   0.2131   1.1356
 1E6  H2   H   H      0   0.258  -6.4900  -1.5931   1.4932
 1E6  H3   H   H      0   0.273  -6.0124   1.7631  -2.0050
 1E6  H4   H   H      0   0.262  -8.2830   0.9625  -1.4228
 1E6  H5   H   HCH2   0   0.314  -2.6912   0.2668   1.1677
 1E6  H6   H   HCH2   0   0.315  -2.5840  -0.9843  -0.0612
 1E6  H7   H   HNH1   0   0.413  -0.4703  -0.8776   1.3186
 1E6  H8   H   HCR6   0   0.286   1.3427   1.9823   1.1919
 1E6  H9   H   HCR6   0   0.316   4.0060  -1.8814  -0.3314
 1E6  H10  H   HCH2   0   0.234   6.0783  -1.5599   0.5007
 1E6  H11  H   HCH2   0   0.238   5.9622  -1.0582  -1.1953
 1E6  H12  H   HCH1   0   0.242   7.7357   0.6470  -0.8008
 1E6  H13  H   HCH2   0   0.199   8.5069  -2.1981  -0.0300
 1E6  H14  H   HCH2   0   0.204   8.2047  -1.6262  -1.6712
 1E6  H15  H   HOH1   0   0.457  10.4565  -1.5180  -1.0452
 1E6  H16  H   HCH3   0   0.235   2.7695  -3.7787   0.1147
 1E6  H17  H   HCH3   0   0.267   1.3120  -4.1680  -0.8156
 1E6  H18  H   HCH3   0   0.235   2.5946  -3.1959  -1.5582
 1E6  H19  H   HOH1   0   0.445   8.0238  -0.5424   1.7338

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
 1E6  S10  C11  single    1.804  0.020  1.804
 1E6  S10  C7   single    1.762  0.020  1.762
 1E6  C11  C12  single    1.513  0.020  1.513
 1E6  C7   C8   aromatic  1.397  0.020  1.397
 1E6  C7   N6   aromatic  1.321  0.020  1.321
 1E6  C8   C9   aromatic  1.379  0.020  1.379
 1E6  N6   C5   aromatic  1.332  0.020  1.332
 1E6  C9   C2   aromatic  1.395  0.020  1.395
 1E6  C5   C2   aromatic  1.386  0.020  1.386
 1E6  C2   C1   single    1.520  0.020  1.520
 1E6  O4   C1   deloc     1.245  0.020  1.245
 1E6  C1   O3   deloc     1.245  0.020  1.245
 1E6  C12  O43  double    1.217  0.020  1.217
 1E6  C12  N15  single    1.350  0.020  1.350
 1E6  N15  C16  single    1.410  0.020  1.410
 1E6  O37  C38  single    1.416  0.020  1.416
 1E6  O37  C21  single    1.339  0.020  1.339
 1E6  C16  C21  aromatic  1.399  0.020  1.399
 1E6  C16  C17  aromatic  1.385  0.020  1.385
 1E6  C21  C20  aromatic  1.393  0.020  1.393
 1E6  C17  C18  aromatic  1.381  0.020  1.381
 1E6  C20  C19  aromatic  1.393  0.020  1.393
 1E6  C18  C19  aromatic  1.396  0.020  1.396
 1E6  C18  CL3  single    1.729  0.020  1.729
 1E6  C19  O22  single    1.336  0.020  1.336
 1E6  O22  C23  single    1.416  0.020  1.416
 1E6  C23  C24  single    1.520  0.020  1.520
 1E6  O28  C27  single    1.406  0.020  1.406
 1E6  C24  C27  single    1.521  0.020  1.521
 1E6  C24  O44  single    1.405  0.020  1.405
 1E6  C5   H2   single    0.930  0.020  1.080
 1E6  C8   H3   single    0.930  0.020  1.080
 1E6  C9   H4   single    0.930  0.020  1.080
 1E6  C11  H5   single    0.970  0.020  1.090
 1E6  C11  H6   single    0.970  0.020  1.090
 1E6  N15  H7   single    0.860  0.020  1.020
 1E6  C17  H8   single    0.930  0.020  1.080
 1E6  C20  H9   single    0.930  0.020  1.080
 1E6  C23  H10  single    0.970  0.020  1.090
 1E6  C23  H11  single    0.970  0.020  1.090
 1E6  C24  H12  single    0.970  0.020  1.090
 1E6  C27  H13  single    0.970  0.020  1.090
 1E6  C27  H14  single    0.970  0.020  1.090
 1E6  O28  H15  single    0.850  0.020  0.980
 1E6  C38  H16  single    0.970  0.020  1.090
 1E6  C38  H17  single    0.970  0.020  1.090
 1E6  C38  H18  single    0.970  0.020  1.090
 1E6  O44  H19  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
 1E6  O4   C1   O3   127.25  3.000
 1E6  O3   C1   C2   116.46  3.000
 1E6  O4   C1   C2   116.29  3.000
 1E6  C9   C2   C5   116.58  3.000
 1E6  C5   C2   C1   121.57  3.000
 1E6  C9   C2   C1   121.85  3.000
 1E6  H2   C5   N6   115.78  3.000
 1E6  H2   C5   C2   119.91  3.000
 1E6  N6   C5   C2   124.31  3.000
 1E6  C7   N6   C5   118.08  3.000
 1E6  S10  C7   C8   117.39  3.000
 1E6  C8   C7   N6   122.88  3.000
 1E6  S10  C7   N6   119.73  3.000
 1E6  H3   C8   C9   121.05  3.000
 1E6  H3   C8   C7   120.89  3.000
 1E6  C9   C8   C7   118.06  3.000
 1E6  H4   C9   C8   119.89  3.000
 1E6  H4   C9   C2   120.02  3.000
 1E6  C8   C9   C2   120.10  3.000
 1E6  C11  S10  C7   100.89  3.000
 1E6  H6   C11  H5   107.25  3.000
 1E6  H6   C11  C12  110.12  3.000
 1E6  H5   C11  C12  110.42  3.000
 1E6  H6   C11  S10  110.44  3.000
 1E6  H5   C11  S10  110.65  3.000
 1E6  C12  C11  S10  107.98  3.000
 1E6  O43  C12  N15  123.84  3.000
 1E6  N15  C12  C11  113.58  3.000
 1E6  O43  C12  C11  122.58  3.000
 1E6  H7   N15  C16  118.04  3.000
 1E6  H7   N15  C12  118.31  3.000
 1E6  C16  N15  C12  122.93  3.000
 1E6  C21  C16  C17  119.31  3.000
 1E6  C17  C16  N15  120.89  3.000
 1E6  C21  C16  N15  119.80  3.000
 1E6  H8   C17  C18  119.74  3.000
 1E6  H8   C17  C16  119.51  3.000
 1E6  C18  C17  C16  120.75  3.000
 1E6  CL3  C18  C19  119.31  3.000
 1E6  CL3  C18  C17  120.13  3.000
 1E6  C19  C18  C17  120.55  3.000
 1E6  O22  C19  C20  124.23  3.000
 1E6  O22  C19  C18  116.86  3.000
 1E6  C20  C19  C18  118.91  3.000
 1E6  H9   C20  C21  119.71  3.000
 1E6  H9   C20  C19  119.75  3.000
 1E6  C21  C20  C19  120.54  3.000
 1E6  O37  C21  C20  123.90  3.000
 1E6  C20  C21  C16  119.93  3.000
 1E6  O37  C21  C16  116.17  3.000
 1E6  C23  O22  C19  119.23  3.000
 1E6  H11  C23  H10  107.88  3.000
 1E6  H11  C23  C24  110.00  3.000
 1E6  H10  C23  C24  110.31  3.000
 1E6  H11  C23  O22  110.54  3.000
 1E6  H10  C23  O22  110.37  3.000
 1E6  C24  C23  O22  107.76  3.000
 1E6  H12  C24  O44  105.97  3.000
 1E6  H12  C24  C27  108.29  3.000
 1E6  O44  C24  C27  112.74  3.000
 1E6  H12  C24  C23  108.20  3.000
 1E6  O44  C24  C23  112.06  3.000
 1E6  C27  C24  C23  109.36  3.000
 1E6  H14  C27  H13  106.77  3.000
 1E6  H14  C27  O28  111.78  3.000
 1E6  H13  C27  O28  111.56  3.000
 1E6  H14  C27  C24  108.70  3.000
 1E6  H13  C27  C24  109.29  3.000
 1E6  O28  C27  C24  108.68  3.000
 1E6  H15  O28  C27  107.97  3.000
 1E6  C38  O37  C21  119.09  3.000
 1E6  H18  C38  H17  108.84  3.000
 1E6  H18  C38  H16  109.10  3.000
 1E6  H17  C38  H16  108.82  3.000
 1E6  H18  C38  O37  111.76  3.000
 1E6  H17  C38  O37  106.29  3.000
 1E6  H16  C38  O37  111.92  3.000
 1E6  H19  O44  C24  108.67  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
 1E6  CONST_01  C7   C8   C9   C2      0.00   0.0  0
 1E6  CONST_02  C7   N6   C5   C2      0.00   0.0  0
 1E6  CONST_03  C8   C7   N6   C5      0.00   0.0  0
 1E6  CONST_04  C8   C9   C2   C5      0.00   0.0  0
 1E6  CONST_05  C9   C8   C7   N6      0.00   0.0  0
 1E6  CONST_06  C9   C2   C5   N6      0.00   0.0  0
 1E6  CONST_07  C19  C20  C21  C16     0.00   0.0  0
 1E6  CONST_08  C19  C18  C17  C16     0.00   0.0  0
 1E6  CONST_09  C20  C21  C16  C17     0.00   0.0  0
 1E6  CONST_10  C20  C19  C18  C17     0.00   0.0  0
 1E6  CONST_11  C21  C16  C17  C18     0.00   0.0  0
 1E6  CONST_12  C21  C20  C19  C18     0.00   0.0  0
 1E6  CONST_13  C8   C9   C2   C1    180.00   0.0  0
 1E6  CONST_14  N6   C5   C2   C1    180.00   0.0  0
 1E6  CONST_15  S10  C7   N6   C5    180.00   0.0  0
 1E6  CONST_16  S10  C7   C8   C9    180.00   0.0  0
 1E6  CONST_17  C20  C21  C16  N15   180.00   0.0  0
 1E6  CONST_18  C18  C17  C16  N15   180.00   0.0  0
 1E6  CONST_19  CL3  C18  C17  C16   180.00   0.0  0
 1E6  CONST_20  O37  C21  C16  C17   180.00   0.0  0
 1E6  CONST_21  O22  C19  C18  C17   180.00   0.0  0
 1E6  CONST_22  O37  C21  C20  C19   180.00   0.0  0
 1E6  CONST_23  CL3  C18  C19  C20   180.00   0.0  0
 1E6  CONST_24  O22  C19  C20  C21   180.00   0.0  0
 1E6  CONST_25  H3   C8   C9   C2    180.00   0.0  0
 1E6  CONST_26  H4   C9   C2   C5    180.00   0.0  0
 1E6  CONST_27  H2   C5   N6   C7    180.00   0.0  0
 1E6  CONST_28  H9   C20  C21  C16   180.00   0.0  0
 1E6  CONST_29  H8   C17  C18  C19   180.00   0.0  0
 1E6  CONST_33  C16  N15  C12  C11   180.00   0.0  0
 1E6  CONST_34  O43  C12  N15  C16     0.00   0.0  0
 1E6  Var_01    C9   C2   C1   O3    178.91  30.0  2
 1E6  Var_02    C12  C11  S10  C7    179.41  30.0  3
 1E6  Var_03    C24  C23  O22  C19  -177.28  30.0  3
 1E6  Var_04    H16  C38  O37  C21    63.18  30.0  3
 1E6  Var_05    O43  C12  C11  S10    -2.80  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
 1E6  chir_01  C24  C23  C27  O44  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
 1E6  plan-1  C1   0.020
 1E6  plan-1  C2   0.020
 1E6  plan-1  C5   0.020
 1E6  plan-1  N6   0.020
 1E6  plan-1  C7   0.020
 1E6  plan-1  C8   0.020
 1E6  plan-1  C9   0.020
 1E6  plan-1  S10  0.020
 1E6  plan-1  H2   0.020
 1E6  plan-1  H3   0.020
 1E6  plan-1  H4   0.020
 1E6  plan-2  N15  0.020
 1E6  plan-2  C16  0.020
 1E6  plan-2  C17  0.020
 1E6  plan-2  C18  0.020
 1E6  plan-2  C19  0.020
 1E6  plan-2  C20  0.020
 1E6  plan-2  C21  0.020
 1E6  plan-2  O22  0.020
 1E6  plan-2  CL3  0.020
 1E6  plan-2  O37  0.020
 1E6  plan-2  H8   0.020
 1E6  plan-2  H9   0.020
 1E6  plan-3  C11  0.020
 1E6  plan-3  C12  0.020
 1E6  plan-3  N15  0.020
 1E6  plan-3  C16  0.020
 1E6  plan-3  O43  0.020
 1E6  plan-3  H7   0.020
 1E6  plan-4  C1   0.020
 1E6  plan-4  C2   0.020
 1E6  plan-4  O3   0.020
 1E6  plan-4  O4   0.020

