# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 23:48:14 2021
#   Inital geometry file: a 88 line input string
#   Ligand name: 2-{[1-(3,5-dimethylphenyl)-1H-imidazol-2-yl]sulfanyl}-N-hydroxyacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)cc(c1)n2ccnc2SCC(=O)NO
#
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
 DJM  DJM  2-{[1-(3,5-dimethylphenyl)-1H-imidazol-2-yl]sulfanyl}-N-hydroxyacetamide  ligand  34  19  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DJM
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
 DJM  C01  C  CH3   0  -0.724  -128.9325  222.9876  228.9571
 DJM  C02  C  CR6   0   0.116  -127.4766  222.6253  228.9168
 DJM  C03  C  CR16  0  -0.339  -127.0766  221.2930  228.9749
 DJM  C04  C  CR6   0   0.113  -125.7340  220.9249  228.9678
 DJM  C05  C  CH3   0  -0.723  -125.3375  219.4811  229.0728
 DJM  C06  C  CR16  0  -0.322  -124.7683  221.9243  228.8990
 DJM  C07  C  CR6   0   0.316  -125.1585  223.2522  228.8239
 DJM  C08  C  CR16  0  -0.327  -126.4985  223.6099  228.8279
 DJM  C10  C  CR15  0  -0.102  -124.0156  225.2919  229.6405
 DJM  C11  C  CR15  0  -0.217  -122.9888  226.0488  229.1562
 DJM  C13  C  CR5   0   0.232  -123.2711  224.4741  227.7505
 DJM  C15  C  CH2   0  -0.704  -124.6710  223.5721  225.5258
 DJM  C16  C  C     0   0.542  -125.0194  225.0202  225.2769
 DJM  N09  N  NR5   0  -0.502  -124.1769  224.2710  228.7456
 DJM  N12  N  N     0  -0.419  -122.5407  225.5343  227.9765
 DJM  N18  N  NH1   0  -0.362  -124.6867  225.4435  224.0427
 DJM  O17  O  O     0  -0.450  -125.5514  225.7146  226.1203
 DJM  O19  O  OH1   0  -0.542  -124.7222  226.7760  223.7611
 DJM  H1   H  HCH3  0   0.251  -129.3193  222.9203  229.9758
 DJM  H2   H  HCH3  0   0.246  -129.1045  224.0049  228.6087
 DJM  H3   H  HCH3  0   0.247  -129.5281  222.3134  228.3419
 DJM  H4   H  HCR6  0   0.246  -127.8342  220.5183  229.0263
 DJM  H5   H  HCH3  0   0.252  -125.3674  219.1458  230.1114
 DJM  H6   H  HCH3  0   0.247  -126.0140  218.8402  228.5081
 DJM  H7   H  HCH3  0   0.246  -124.3261  219.3129  228.7056
 DJM  H8   H  HCR6  0   0.262  -123.7157  221.6699  228.9060
 DJM  H9   H  HCR6  0   0.262  -126.7756  224.6533  228.7422
 DJM  H10  H  HCR5  0   0.300  -124.6224  225.3720  230.5267
 DJM  H11  H  HCR5  0   0.260  -122.5551  226.9335  229.5950
 DJM  H12  H  HCH2  0   0.317  -125.4547  223.1009  226.1166
 DJM  H13  H  HCH2  0   0.320  -124.5480  222.9985  224.6060
 DJM  H14  H  HNH1  0   0.418  -124.0792  224.9043  223.4417
 DJM  H15  H  HOH1  0   0.480  -125.5390  226.9216  223.2668
 DJM  S14  S  S2    0   0.060  -123.0613  223.4270  226.3698

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
 DJM  O19  N18  single    1.362  0.020  1.362
 DJM  N18  C16  single    1.347  0.020  1.347
 DJM  C16  O17  double    1.215  0.020  1.215
 DJM  C16  C15  single    1.510  0.020  1.510
 DJM  C15  S14  single    1.823  0.020  1.823
 DJM  S14  C13  single    1.746  0.020  1.746
 DJM  C13  N12  aromatic  1.307  0.020  1.307
 DJM  C13  N09  aromatic  1.361  0.020  1.361
 DJM  C05  C04  single    1.501  0.020  1.501
 DJM  N12  C11  aromatic  1.363  0.020  1.363
 DJM  C04  C06  aromatic  1.391  0.020  1.391
 DJM  C04  C03  aromatic  1.392  0.020  1.392
 DJM  C06  C07  aromatic  1.386  0.020  1.386
 DJM  C07  N09  single    1.417  0.020  1.417
 DJM  C07  C08  aromatic  1.387  0.020  1.387
 DJM  C03  C02  aromatic  1.392  0.020  1.392
 DJM  N09  C10  aromatic  1.367  0.020  1.367
 DJM  C02  C08  aromatic  1.391  0.020  1.391
 DJM  C02  C01  single    1.501  0.020  1.501
 DJM  C11  C10  aromatic  1.365  0.020  1.365
 DJM  C01  H1   single    0.970  0.020  1.090
 DJM  C01  H2   single    0.970  0.020  1.090
 DJM  C01  H3   single    0.970  0.020  1.090
 DJM  C03  H4   single    0.930  0.020  1.080
 DJM  C05  H5   single    0.970  0.020  1.090
 DJM  C05  H6   single    0.970  0.020  1.090
 DJM  C05  H7   single    0.970  0.020  1.090
 DJM  C06  H8   single    0.930  0.020  1.080
 DJM  C08  H9   single    0.930  0.020  1.080
 DJM  C10  H10  single    0.930  0.020  1.080
 DJM  C11  H11  single    0.930  0.020  1.080
 DJM  C15  H12  single    0.970  0.020  1.090
 DJM  C15  H13  single    0.970  0.020  1.090
 DJM  N18  H14  single    0.890  0.020  1.040
 DJM  O19  H15  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
 DJM  H3   C01  H2   108.12  3.000
 DJM  H3   C01  H1   107.16  3.000
 DJM  H2   C01  H1   107.47  3.000
 DJM  H3   C01  C02  111.45  3.000
 DJM  H2   C01  C02  111.72  3.000
 DJM  H1   C01  C02  110.73  3.000
 DJM  C08  C02  C03  118.57  3.000
 DJM  C08  C02  C01  120.87  3.000
 DJM  C03  C02  C01  120.56  3.000
 DJM  H4   C03  C04  119.01  3.000
 DJM  H4   C03  C02  118.99  3.000
 DJM  C04  C03  C02  121.99  3.000
 DJM  C06  C04  C05  120.73  3.000
 DJM  C06  C04  C03  118.67  3.000
 DJM  C05  C04  C03  120.58  3.000
 DJM  H7   C05  H6   108.12  3.000
 DJM  H7   C05  H5   107.39  3.000
 DJM  H6   C05  H5   107.17  3.000
 DJM  H7   C05  C04  111.74  3.000
 DJM  H6   C05  C04  111.44  3.000
 DJM  H5   C05  C04  110.77  3.000
 DJM  H8   C06  C07  119.94  3.000
 DJM  H8   C06  C04  120.37  3.000
 DJM  C07  C06  C04  119.69  3.000
 DJM  N09  C07  C08  118.95  3.000
 DJM  C08  C07  C06  121.26  3.000
 DJM  N09  C07  C06  119.79  3.000
 DJM  H9   C08  C07  119.70  3.000
 DJM  H9   C08  C02  120.48  3.000
 DJM  C07  C08  C02  119.80  3.000
 DJM  H10  C10  N09  121.85  3.000
 DJM  H10  C10  C11  132.43  3.000
 DJM  N09  C10  C11  105.70  3.000
 DJM  H11  C11  N12  121.98  3.000
 DJM  H11  C11  C10  127.82  3.000
 DJM  N12  C11  C10  110.20  3.000
 DJM  S14  C13  N12  123.79  3.000
 DJM  N12  C13  N09  111.51  3.000
 DJM  S14  C13  N09  124.67  3.000
 DJM  H13  C15  H12  108.13  3.000
 DJM  H13  C15  S14  104.41  3.000
 DJM  H12  C15  S14  110.48  3.000
 DJM  H13  C15  C16  113.03  3.000
 DJM  H12  C15  C16  109.78  3.000
 DJM  S14  C15  C16  110.87  3.000
 DJM  O17  C16  N18  124.38  3.000
 DJM  O17  C16  C15  122.32  3.000
 DJM  N18  C16  C15  113.30  3.000
 DJM  C13  N09  C10  106.78  3.000
 DJM  C10  N09  C07  125.63  3.000
 DJM  C13  N09  C07  127.50  3.000
 DJM  C13  N12  C11  105.79  3.000
 DJM  H14  N18  O19  114.50  3.000
 DJM  H14  N18  C16  121.73  3.000
 DJM  O19  N18  C16  119.37  3.000
 DJM  H15  O19  N18  105.98  3.000
 DJM  C15  S14  C13  102.26  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
 DJM  CONST_01  C06  C04  C03  C02     0.00   0.0  0
 DJM  CONST_02  C06  C07  C08  C02     0.00   0.0  0
 DJM  CONST_03  N09  C07  C08  C02   180.00   0.0  0
 DJM  CONST_04  C07  C06  C04  C03     0.00   0.0  0
 DJM  CONST_05  C07  C08  C02  C03     0.00   0.0  0
 DJM  CONST_06  N09  C07  C06  C04   180.00   0.0  0
 DJM  CONST_07  C08  C07  C06  C04     0.00   0.0  0
 DJM  CONST_08  C08  C02  C03  C04     0.00   0.0  0
 DJM  CONST_11  N12  C13  N09  C07   180.00   0.0  0
 DJM  CONST_12  C11  C10  N09  C07   180.00   0.0  0
 DJM  CONST_15  N12  C13  N09  C10     0.00   0.0  0
 DJM  CONST_16  C13  N12  C11  C10     0.00   0.0  0
 DJM  CONST_17  N09  C13  N12  C11     0.00   0.0  0
 DJM  CONST_18  C13  N09  C10  C11     0.00   0.0  0
 DJM  CONST_19  N12  C11  C10  N09     0.00   0.0  0
 DJM  CONST_20  C04  C03  C02  C01   180.00   0.0  0
 DJM  CONST_21  C07  C08  C02  C01   180.00   0.0  0
 DJM  CONST_22  C05  C04  C03  C02   180.00   0.0  0
 DJM  CONST_23  C07  C06  C04  C05   180.00   0.0  0
 DJM  CONST_24  S14  C13  N09  C07     0.00   0.0  0
 DJM  CONST_25  S14  C13  N09  C10   180.00   0.0  0
 DJM  CONST_26  S14  C13  N12  C11   180.00   0.0  0
 DJM  CONST_27  H8   C06  C04  C03   180.00   0.0  0
 DJM  CONST_28  H9   C08  C02  C03   180.00   0.0  0
 DJM  CONST_29  H4   C03  C04  C06   180.00   0.0  0
 DJM  CONST_30  H10  C10  N09  C07     0.00   0.0  0
 DJM  CONST_31  H11  C11  N12  C13   180.00   0.0  0
 DJM  CONST_32  O19  N18  C16  C15   180.00   0.0  0
 DJM  CONST_33  O19  N18  C16  O17     0.00   0.0  0
 DJM  CONST_34  H14  N18  C16  C15     0.00   0.0  0
 DJM  Var_01    N12  C13  S14  C15  -118.76  30.0  2
 DJM  Var_02    H5   C05  C04  C03   -80.67  30.0  2
 DJM  Var_03    H1   C01  C02  C03    77.37  30.0  2
 DJM  Var_04    C16  C15  S14  C13    53.10  30.0  1
 DJM  Var_05    S14  C15  C16  N18    96.03  30.0  3

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
 DJM  plan-1  C07  0.020
 DJM  plan-1  C10  0.020
 DJM  plan-1  C11  0.020
 DJM  plan-1  C13  0.020
 DJM  plan-1  N09  0.020
 DJM  plan-1  N12  0.020
 DJM  plan-1  H10  0.020
 DJM  plan-1  H11  0.020
 DJM  plan-1  S14  0.020
 DJM  plan-2  C01  0.020
 DJM  plan-2  C02  0.020
 DJM  plan-2  C03  0.020
 DJM  plan-2  C04  0.020
 DJM  plan-2  C05  0.020
 DJM  plan-2  C06  0.020
 DJM  plan-2  C07  0.020
 DJM  plan-2  C08  0.020
 DJM  plan-2  N09  0.020
 DJM  plan-2  H4   0.020
 DJM  plan-2  H8   0.020
 DJM  plan-2  H9   0.020
 DJM  plan-3  C15  0.020
 DJM  plan-3  C16  0.020
 DJM  plan-3  N18  0.020
 DJM  plan-3  O17  0.020
 DJM  plan-3  O19  0.020
 DJM  plan-3  H14  0.020

