# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 19:53:03 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 6-({2-[(5-chloro-2-methoxyphenyl)amino]-2-oxoethyl}sulfanyl)pyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(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
 1E7  1E7  '6-({2-[(5-chloro-2-methoxyphenyl)amino]-2-oxoethyl}sulfanyl)pyridine-3-carboxylic acid'  ligand  35  23  .  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_1E7
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
 1E7  C1   C   C      0   0.572   0.9718  -0.6230   0.0360
 1E7  N2   N   NH1    0  -0.738   1.8731   0.3865   0.0045
 1E7  C3   C   CR6    0   0.288   3.2676   0.3130   0.0057
 1E7  O4   O   O      0  -0.456   1.2504  -1.8060   0.0762
 1E7  C6   C   CH2    0  -0.698  -0.4611  -0.1342   0.0125
 1E7  S7   S   S2     0   0.068  -1.5348  -1.5729   0.1975
 1E7  C10  C   CR6    0   0.086  -3.1236  -0.8165   0.1162
 1E7  C11  C   CR16   0  -0.294  -4.2372  -1.6546   0.2059
 1E7  C12  C   CR16   0  -0.168  -5.4885  -1.0777   0.1419
 1E7  C13  C   CR6    0  -0.200  -5.6154   0.3026  -0.0110
 1E7  C14  C   CR16   0  -0.083  -4.4378   1.0300  -0.0889
 1E7  N15  N   N      0  -0.422  -3.2200   0.4934  -0.0268
 1E7  C19  C   C      0   0.400  -6.9753   0.9743  -0.0867
 1E7  O20  O   O      0  -0.591  -7.9652   0.2248   0.0112
 1E7  O21  O   OC    -1  -0.592  -6.9792   2.2101  -0.2384
 1E7  C23  C   CR16   0  -0.276   3.9893  -0.8714  -0.0580
 1E7  C24  C   CR6    0  -0.051   5.3778  -0.8268  -0.0550
 1E7  C25  C   CR16   0  -0.223   6.0653   0.3659   0.0072
 1E7  C26  C   CR16   0  -0.385   5.3449   1.5540   0.0691
 1E7  C27  C   CR6    0   0.341   3.9603   1.5409   0.0709
 1E7  O31  O   O2     0  -0.481   3.1845   2.6381   0.1326
 1E7  CL3  CL  CL     0  -0.135   6.2558  -2.3222  -0.1356
 1E7  C33  C   CH3    0  -0.434   3.8034   3.9091   0.2061
 1E7  H1   H   HNH1   0   0.427   1.4961   1.3234  -0.0103
 1E7  H2   H   HCH2   0   0.316  -0.6355   0.5839   0.8151
 1E7  H3   H   HCH2   0   0.321  -0.6681   0.3761  -0.9301
 1E7  H4   H   HCR6   0   0.273  -4.1191  -2.7245   0.3194
 1E7  H5   H   HCR6   0   0.262  -6.3730  -1.6971   0.2075
 1E7  H6   H   HCR6   0   0.258  -4.4744   2.1069  -0.2053
 1E7  H8   H   HCR6   0   0.303   3.4809  -1.8195  -0.1106
 1E7  H9   H   HCR6   0   0.281   7.1458   0.3909   0.0080
 1E7  H10  H   HCR6   0   0.295   5.8911   2.4858   0.1187
 1E7  H11  H   HCH3   0   0.235   4.4272   4.0009   1.0981
 1E7  H12  H   HCH3   0   0.235   4.4124   4.1120  -0.6778
 1E7  H13  H   HCH3   0   0.266   3.0006   4.6391   0.2588

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
 1E7  S7   C6   single    1.805  0.020  1.805
 1E7  S7   C10  single    1.762  0.020  1.762
 1E7  C6   C1   single    1.514  0.020  1.514
 1E7  C11  C10  aromatic  1.397  0.020  1.397
 1E7  C11  C12  aromatic  1.379  0.020  1.379
 1E7  C10  N15  aromatic  1.321  0.020  1.321
 1E7  C12  C13  aromatic  1.395  0.020  1.395
 1E7  N15  C14  aromatic  1.332  0.020  1.332
 1E7  C13  C14  aromatic  1.386  0.020  1.386
 1E7  C13  C19  single    1.519  0.020  1.519
 1E7  O20  C19  deloc     1.245  0.020  1.245
 1E7  C1   O4   double    1.216  0.020  1.216
 1E7  C1   N2   single    1.354  0.020  1.354
 1E7  C19  O21  deloc     1.245  0.020  1.245
 1E7  N2   C3   single    1.396  0.020  1.396
 1E7  C3   C23  aromatic  1.388  0.020  1.388
 1E7  C3   C27  aromatic  1.411  0.020  1.411
 1E7  O31  C27  single    1.345  0.020  1.345
 1E7  O31  C33  single    1.416  0.020  1.416
 1E7  C23  C24  aromatic  1.389  0.020  1.389
 1E7  C27  C26  aromatic  1.385  0.020  1.385
 1E7  C24  C25  aromatic  1.378  0.020  1.378
 1E7  C24  CL3  single    1.736  0.020  1.736
 1E7  C26  C25  aromatic  1.391  0.020  1.391
 1E7  N2   H1   single    0.860  0.020  1.020
 1E7  C6   H2   single    0.970  0.020  1.090
 1E7  C6   H3   single    0.970  0.020  1.090
 1E7  C11  H4   single    0.930  0.020  1.080
 1E7  C12  H5   single    0.930  0.020  1.080
 1E7  C14  H6   single    0.930  0.020  1.080
 1E7  C23  H8   single    0.930  0.020  1.080
 1E7  C25  H9   single    0.930  0.020  1.080
 1E7  C26  H10  single    0.930  0.020  1.080
 1E7  C33  H11  single    0.970  0.020  1.090
 1E7  C33  H12  single    0.970  0.020  1.090
 1E7  C33  H13  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
 1E7  C6   C1   O4   122.10  3.000
 1E7  O4   C1   N2   125.01  3.000
 1E7  C6   C1   N2   112.89  3.000
 1E7  H1   N2   C3   114.94  3.000
 1E7  H1   N2   C1   116.33  3.000
 1E7  C3   N2   C1   128.73  3.000
 1E7  C27  C3   C23  119.28  3.000
 1E7  C27  C3   N2   116.38  3.000
 1E7  C23  C3   N2   124.33  3.000
 1E7  H3   C6   H2   107.29  3.000
 1E7  H3   C6   S7   110.39  3.000
 1E7  H2   C6   S7   110.75  3.000
 1E7  H3   C6   C1   110.10  3.000
 1E7  H2   C6   C1   110.63  3.000
 1E7  S7   C6   C1   107.70  3.000
 1E7  C10  S7   C6   100.92  3.000
 1E7  N15  C10  C11  122.94  3.000
 1E7  N15  C10  S7   119.77  3.000
 1E7  C11  C10  S7   117.29  3.000
 1E7  H4   C11  C12  121.15  3.000
 1E7  H4   C11  C10  120.86  3.000
 1E7  C12  C11  C10  117.99  3.000
 1E7  H5   C12  C13  119.93  3.000
 1E7  H5   C12  C11  119.96  3.000
 1E7  C13  C12  C11  120.11  3.000
 1E7  C19  C13  C14  121.72  3.000
 1E7  C19  C13  C12  121.65  3.000
 1E7  C14  C13  C12  116.63  3.000
 1E7  H6   C14  N15  115.86  3.000
 1E7  H6   C14  C13  119.91  3.000
 1E7  N15  C14  C13  124.23  3.000
 1E7  C14  N15  C10  118.11  3.000
 1E7  O21  C19  O20  127.18  3.000
 1E7  O21  C19  C13  116.60  3.000
 1E7  O20  C19  C13  116.21  3.000
 1E7  H8   C23  C24  120.01  3.000
 1E7  H8   C23  C3   120.51  3.000
 1E7  C24  C23  C3   119.48  3.000
 1E7  CL3  C24  C25  119.69  3.000
 1E7  CL3  C24  C23  118.54  3.000
 1E7  C25  C24  C23  121.77  3.000
 1E7  H9   C25  C26  119.87  3.000
 1E7  H9   C25  C24  121.25  3.000
 1E7  C26  C25  C24  118.87  3.000
 1E7  H10  C26  C27  120.88  3.000
 1E7  H10  C26  C25  118.46  3.000
 1E7  C27  C26  C25  120.66  3.000
 1E7  O31  C27  C26  124.69  3.000
 1E7  C26  C27  C3   119.93  3.000
 1E7  O31  C27  C3   115.38  3.000
 1E7  C33  O31  C27  118.85  3.000
 1E7  H13  C33  H12  109.05  3.000
 1E7  H13  C33  H11  109.03  3.000
 1E7  H12  C33  H11  109.07  3.000
 1E7  H13  C33  O31  106.42  3.000
 1E7  H12  C33  O31  111.62  3.000
 1E7  H11  C33  O31  111.56  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
 1E7  CONST_01  C25  C24  C23  C3      0.00   0.0  0
 1E7  CONST_02  C25  C26  C27  C3      0.00   0.0  0
 1E7  CONST_03  C13  C12  C11  C10     0.00   0.0  0
 1E7  CONST_04  C13  C14  N15  C10     0.00   0.0  0
 1E7  CONST_05  C14  N15  C10  C11     0.00   0.0  0
 1E7  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 1E7  CONST_07  N15  C10  C11  C12     0.00   0.0  0
 1E7  CONST_08  N15  C14  C13  C12     0.00   0.0  0
 1E7  CONST_09  C26  C27  C3   C23     0.00   0.0  0
 1E7  CONST_10  C26  C25  C24  C23     0.00   0.0  0
 1E7  CONST_11  C27  C3   C23  C24     0.00   0.0  0
 1E7  CONST_12  C27  C26  C25  C24     0.00   0.0  0
 1E7  CONST_13  C24  C23  C3   N2    180.00   0.0  0
 1E7  CONST_14  C26  C27  C3   N2    180.00   0.0  0
 1E7  CONST_15  CL3  C24  C23  C3    180.00   0.0  0
 1E7  CONST_16  C12  C11  C10  S7    180.00   0.0  0
 1E7  CONST_17  C14  N15  C10  S7    180.00   0.0  0
 1E7  CONST_18  C19  C13  C12  C11   180.00   0.0  0
 1E7  CONST_19  C19  C13  C14  N15   180.00   0.0  0
 1E7  CONST_20  O31  C27  C3   C23   180.00   0.0  0
 1E7  CONST_21  O31  C27  C26  C25   180.00   0.0  0
 1E7  CONST_22  CL3  C24  C25  C26   180.00   0.0  0
 1E7  CONST_23  H10  C26  C27  C3    180.00   0.0  0
 1E7  CONST_24  H5   C12  C11  C10   180.00   0.0  0
 1E7  CONST_25  H6   C14  N15  C10   180.00   0.0  0
 1E7  CONST_26  H4   C11  C12  C13   180.00   0.0  0
 1E7  CONST_27  H9   C25  C24  C23   180.00   0.0  0
 1E7  CONST_28  H8   C23  C24  C25   180.00   0.0  0
 1E7  CONST_29  C23  C3   N2   C1      0.00   0.0  0
 1E7  CONST_30  C27  C3   N2   C1    180.00   0.0  0
 1E7  CONST_31  H1   N2   C3   C23   180.00   0.0  0
 1E7  CONST_32  C6   C1   N2   C3    180.00   0.0  0
 1E7  CONST_33  O4   C1   N2   C3      0.00   0.0  0
 1E7  Var_01    C11  C10  S7   C6    179.00  30.0  2
 1E7  Var_02    O20  C19  C13  C12     0.82  30.0  2
 1E7  Var_03    H2   C6   S7   C10    59.94  30.0  3
 1E7  Var_04    H11  C33  O31  C27   -60.53  30.0  3
 1E7  Var_05    S7   C6   C1   N2   -175.36  30.0  1

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
 1E7  plan-1  N2   0.020
 1E7  plan-1  C3   0.020
 1E7  plan-1  C23  0.020
 1E7  plan-1  C24  0.020
 1E7  plan-1  C25  0.020
 1E7  plan-1  C26  0.020
 1E7  plan-1  C27  0.020
 1E7  plan-1  O31  0.020
 1E7  plan-1  CL3  0.020
 1E7  plan-1  H8   0.020
 1E7  plan-1  H9   0.020
 1E7  plan-1  H10  0.020
 1E7  plan-2  S7   0.020
 1E7  plan-2  C10  0.020
 1E7  plan-2  C11  0.020
 1E7  plan-2  C12  0.020
 1E7  plan-2  C13  0.020
 1E7  plan-2  C14  0.020
 1E7  plan-2  N15  0.020
 1E7  plan-2  C19  0.020
 1E7  plan-2  H4   0.020
 1E7  plan-2  H5   0.020
 1E7  plan-2  H6   0.020
 1E7  plan-3  C1   0.020
 1E7  plan-3  N2   0.020
 1E7  plan-3  C3   0.020
 1E7  plan-3  O4   0.020
 1E7  plan-3  C6   0.020
 1E7  plan-3  H1   0.020
 1E7  plan-4  C13  0.020
 1E7  plan-4  C19  0.020
 1E7  plan-4  O20  0.020
 1E7  plan-4  O21  0.020

