# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 08:05:15 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: N-hydroxy-4-({[(thiophen-3-yl)methyl]amino}methyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)c1ccc(CNCc2cscc2)cc1
#
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
 LSL  LSL  "N-hydroxy-4-({[(thiophen-3-yl)methyl]amino}methyl)benzamide"
  ligand  32  18  .  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_LSL
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
 LSL  C10  C  CR15  0  -0.529  -51.2074   5.1188  -3.9306
 LSL  C13  C  CR15  0  -0.202  -49.1096   4.6918  -3.0629
 LSL  C15  C  CR16  0  -0.251  -48.1047  -0.8050  -7.2664
 LSL  C02  C  CR6   0  -0.066  -46.9755  -1.0006  -6.4766
 LSL  C03  C  CR16  0  -0.266  -46.6227  -0.0191  -5.5518
 LSL  C04  C  CR16  0  -0.275  -47.3762   1.1374  -5.4320
 LSL  C05  C  CR6   0   0.089  -48.4989   1.3437  -6.2303
 LSL  C06  C  CH2   0  -0.313  -49.3428   2.5800  -6.0784
 LSL  C08  C  CH2   0  -0.360  -49.3236   4.9576  -5.6203
 LSL  C09  C  CR5   0   0.167  -49.8930   4.9267  -4.2334
 LSL  C12  C  CR15  0  -0.459  -49.8436   4.7206  -1.9193
 LSL  C14  C  CR16  0  -0.300  -48.8465   0.3593  -7.1513
 LSL  N07  N  NH1   0  -0.593  -48.5362   3.7684  -5.8934
 LSL  N17  N  NH1   0  -0.378  -44.8967  -2.1683  -6.4187
 LSL  O16  O  O     0  -0.462  -46.7678  -3.3300  -6.9194
 LSL  O18  O  OH1   0  -0.536  -44.1123  -3.2775  -6.3584
 LSL  S11  S  S2    0   0.198  -51.4998   5.0286  -2.2427
 LSL  H1   H  HCR5  0   0.288  -52.0198   5.3052  -4.6174
 LSL  H2   H  HCR5  0   0.258  -48.0442   4.5098  -3.0828
 LSL  H3   H  HCR6  0   0.259  -48.3980  -1.5582  -7.9857
 LSL  H4   H  HCR6  0   0.260  -45.7735  -0.1550  -4.8933
 LSL  H5   H  HCR6  0   0.252  -47.0910   1.8866  -4.7053
 LSL  H6   H  HCH2  0   0.221  -50.0333   2.6576  -6.9318
 LSL  H7   H  HCH2  0   0.250  -49.9775   2.4586  -5.1942
 LSL  H8   H  HCH2  0   0.253  -48.6577   5.8190  -5.7166
 LSL  H9   H  HCH2  0   0.216  -50.1387   5.1125  -6.3424
 LSL  H10  H  HCR5  0   0.290  -49.5010   4.5798  -0.9056
 LSL  H11  H  HCR6  0   0.254  -49.7109   0.5033  -7.7888
 LSL  H12  H  HNH1  0   0.355  -47.9801   3.9261  -6.7245
 LSL  H14  H  HNH1  0   0.420  -44.4278  -1.2980  -6.2145
 LSL  H15  H  HOH1  0   0.476  -43.7974  -3.4401  -7.2582
 LSL  C01  C  C     0   0.485  -46.2226  -2.2811  -6.6201

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
 LSL  O16  C01  double    1.219  0.020  1.219
 LSL  C15  C14  aromatic  1.385  0.020  1.385
 LSL  C15  C02  aromatic  1.392  0.020  1.392
 LSL  C14  C05  aromatic  1.392  0.020  1.392
 LSL  C01  C02  single    1.492  0.020  1.492
 LSL  C01  N17  single    1.346  0.020  1.346
 LSL  O18  N17  single    1.360  0.020  1.360
 LSL  C02  C03  aromatic  1.394  0.020  1.394
 LSL  C05  C06  single    1.505  0.020  1.505
 LSL  C05  C04  aromatic  1.393  0.020  1.393
 LSL  N07  C08  single    1.452  0.020  1.452
 LSL  N07  C06  single    1.448  0.020  1.448
 LSL  C08  C09  single    1.500  0.020  1.500
 LSL  C03  C04  aromatic  1.386  0.020  1.386
 LSL  C09  C10  aromatic  1.362  0.020  1.362
 LSL  C09  C13  aromatic  1.428  0.020  1.428
 LSL  C10  S11  aromatic  1.715  0.020  1.715
 LSL  C13  C12  aromatic  1.359  0.020  1.359
 LSL  S11  C12  aromatic  1.715  0.020  1.715
 LSL  C10  H1   single    0.930  0.020  1.080
 LSL  C13  H2   single    0.930  0.020  1.080
 LSL  C15  H3   single    0.930  0.020  1.080
 LSL  C03  H4   single    0.930  0.020  1.080
 LSL  C04  H5   single    0.930  0.020  1.080
 LSL  C06  H6   single    0.970  0.020  1.090
 LSL  C06  H7   single    0.970  0.020  1.090
 LSL  C08  H8   single    0.970  0.020  1.090
 LSL  C08  H9   single    0.970  0.020  1.090
 LSL  C12  H10  single    0.930  0.020  1.080
 LSL  C14  H11  single    0.930  0.020  1.080
 LSL  N07  H12  single    0.890  0.020  1.040
 LSL  N17  H14  single    0.860  0.020  1.020
 LSL  O18  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
 LSL  H1   C10  S11  120.43  3.000
 LSL  H1   C10  C09  127.49  3.000
 LSL  S11  C10  C09  112.07  3.000
 LSL  H2   C13  C12  123.45  3.000
 LSL  H2   C13  C09  123.60  3.000
 LSL  C12  C13  C09  112.95  3.000
 LSL  H3   C15  C14  119.68  3.000
 LSL  H3   C15  C02  119.95  3.000
 LSL  C14  C15  C02  120.37  3.000
 LSL  C03  C02  C01  122.70  3.000
 LSL  C03  C02  C15  118.87  3.000
 LSL  C01  C02  C15  118.38  3.000
 LSL  H4   C03  C04  118.59  3.000
 LSL  H4   C03  C02  120.89  3.000
 LSL  C04  C03  C02  120.50  3.000
 LSL  H5   C04  C05  119.65  3.000
 LSL  H5   C04  C03  119.52  3.000
 LSL  C05  C04  C03  120.82  3.000
 LSL  C14  C05  C06  120.51  3.000
 LSL  C06  C05  C04  121.06  3.000
 LSL  C14  C05  C04  118.40  3.000
 LSL  H7   C06  H6   105.68  3.000
 LSL  H7   C06  N07  108.10  3.000
 LSL  H6   C06  N07  113.00  3.000
 LSL  H7   C06  C05  108.38  3.000
 LSL  H6   C06  C05  109.36  3.000
 LSL  N07  C06  C05  112.01  3.000
 LSL  H9   C08  H8   106.41  3.000
 LSL  H9   C08  N07  113.19  3.000
 LSL  H8   C08  N07  107.37  3.000
 LSL  H9   C08  C09  109.19  3.000
 LSL  H8   C08  C09  109.21  3.000
 LSL  N07  C08  C09  111.28  3.000
 LSL  C08  C09  C13  123.59  3.000
 LSL  C13  C09  C10  111.73  3.000
 LSL  C08  C09  C10  124.68  3.000
 LSL  H10  C12  S11  120.47  3.000
 LSL  H10  C12  C13  128.03  3.000
 LSL  S11  C12  C13  111.50  3.000
 LSL  H11  C14  C05  119.63  3.000
 LSL  H11  C14  C15  119.34  3.000
 LSL  C05  C14  C15  121.03  3.000
 LSL  H12  N07  C08  108.95  3.000
 LSL  H12  N07  C06  109.20  3.000
 LSL  C08  N07  C06  113.20  3.000
 LSL  H14  N17  O18  115.24  3.000
 LSL  H14  N17  C01  124.06  3.000
 LSL  O18  N17  C01  120.43  3.000
 LSL  H15  O18  N17  106.49  3.000
 LSL  C12  S11  C10   91.74  3.000
 LSL  O16  C01  N17  123.32  3.000
 LSL  N17  C01  C02  114.25  3.000
 LSL  O16  C01  C02  122.42  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
 LSL  CONST_01  C12  C13  C09  C10     0.00   0.0  0
 LSL  CONST_02  C13  C12  S11  C10     0.00   0.0  0
 LSL  CONST_03  S11  C10  C09  C13     0.00   0.0  0
 LSL  CONST_04  C04  C05  C14  C15     0.00   0.0  0
 LSL  CONST_05  C04  C03  C02  C15     0.00   0.0  0
 LSL  CONST_06  C05  C14  C15  C02     0.00   0.0  0
 LSL  CONST_07  C05  C04  C03  C02     0.00   0.0  0
 LSL  CONST_08  C14  C15  C02  C03     0.00   0.0  0
 LSL  CONST_09  C14  C05  C04  C03     0.00   0.0  0
 LSL  CONST_10  C12  S11  C10  C09     0.00   0.0  0
 LSL  CONST_11  S11  C12  C13  C09     0.00   0.0  0
 LSL  CONST_12  C06  C05  C14  C15   180.00   0.0  0
 LSL  CONST_13  C14  C15  C02  C01   180.00   0.0  0
 LSL  CONST_14  C04  C03  C02  C01   180.00   0.0  0
 LSL  CONST_15  C06  C05  C04  C03   180.00   0.0  0
 LSL  CONST_16  S11  C10  C09  C08   180.00   0.0  0
 LSL  CONST_17  C12  C13  C09  C08   180.00   0.0  0
 LSL  CONST_18  H2   C13  C09  C10   180.00   0.0  0
 LSL  CONST_19  H10  C12  S11  C10   180.00   0.0  0
 LSL  CONST_20  H1   C10  C09  C13   180.00   0.0  0
 LSL  CONST_21  H4   C03  C02  C15   180.00   0.0  0
 LSL  CONST_22  H11  C14  C15  C02   180.00   0.0  0
 LSL  CONST_23  H5   C04  C03  C02   180.00   0.0  0
 LSL  CONST_24  H3   C15  C02  C03   180.00   0.0  0
 LSL  CONST_25  H11  C14  C05  C04   180.00   0.0  0
 LSL  CONST_26  H3   C15  C14  C05   180.00   0.0  0
 LSL  CONST_27  H4   C03  C04  C05   180.00   0.0  0
 LSL  CONST_28  H10  C12  C13  C09   180.00   0.0  0
 LSL  CONST_29  H1   C10  S11  C12   180.00   0.0  0
 LSL  CONST_30  H5   C04  C05  C14   180.00   0.0  0
 LSL  CONST_31  H2   C13  C12  S11   180.00   0.0  0
 LSL  CONST_32  O18  N17  C01  C02   180.00   0.0  0
 LSL  CONST_33  H14  N17  C01  C02     0.00   0.0  0
 LSL  CONST_34  O18  N17  C01  O16     0.00   0.0  0
 LSL  CONST_35  H14  N17  C01  O16   180.00   0.0  0
 LSL  Var_01    N07  C08  C09  C10  -128.20  30.0  2
 LSL  Var_02    N07  C08  C09  C13    51.91  30.0  2
 LSL  Var_03    O16  C01  C02  C15   -31.10  30.0  2
 LSL  Var_04    N17  C01  C02  C15   147.59  30.0  2
 LSL  Var_05    O16  C01  C02  C03   146.45  30.0  2
 LSL  Var_06    N17  C01  C02  C03   -34.86  30.0  2
 LSL  Var_07    N07  C06  C05  C04    41.59  30.0  2
 LSL  Var_08    N07  C06  C05  C14  -140.19  30.0  2
 LSL  Var_09    H8   C08  C09  C10   113.45  30.0  2
 LSL  Var_10    H9   C08  C09  C10    -2.54  30.0  2
 LSL  Var_11    H8   C08  C09  C13   -66.45  30.0  2
 LSL  Var_12    H9   C08  C09  C13   177.57  30.0  2
 LSL  Var_13    H6   C06  C05  C04   167.66  30.0  2
 LSL  Var_14    H7   C06  C05  C04   -77.59  30.0  2
 LSL  Var_15    H6   C06  C05  C14   -14.12  30.0  2
 LSL  Var_16    H7   C06  C05  C14   100.64  30.0  2
 LSL  Var_17    C08  N07  C06  C05  -174.62  30.0  1
 LSL  Var_18    C09  C08  N07  C06    72.80  30.0  3
 LSL  Var_19    H12  N07  C06  C05    63.82  30.0  1
 LSL  Var_20    H12  N07  C08  C09  -165.49  30.0  1
 LSL  Var_21    H8   C08  N07  C06  -167.74  30.0  3
 LSL  Var_22    H9   C08  N07  C06   -50.61  30.0  3
 LSL  Var_23    H6   C06  N07  C08    61.32  30.0  3
 LSL  Var_24    H7   C06  N07  C08   -55.28  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
 LSL  plan-1  C10  0.020
 LSL  plan-1  C13  0.020
 LSL  plan-1  C08  0.020
 LSL  plan-1  C09  0.020
 LSL  plan-1  C12  0.020
 LSL  plan-1  S11  0.020
 LSL  plan-1  H1   0.020
 LSL  plan-1  H2   0.020
 LSL  plan-1  H10  0.020
 LSL  plan-2  C15  0.020
 LSL  plan-2  C02  0.020
 LSL  plan-2  C03  0.020
 LSL  plan-2  C04  0.020
 LSL  plan-2  C05  0.020
 LSL  plan-2  C06  0.020
 LSL  plan-2  C14  0.020
 LSL  plan-2  H3   0.020
 LSL  plan-2  H4   0.020
 LSL  plan-2  H5   0.020
 LSL  plan-2  H11  0.020
 LSL  plan-2  C01  0.020
 LSL  plan-3  C02  0.020
 LSL  plan-3  N17  0.020
 LSL  plan-3  O16  0.020
 LSL  plan-3  O18  0.020
 LSL  plan-3  H14  0.020
 LSL  plan-3  C01  0.020

