# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Sep 20 08:36:38 2022
#   Inital geometry file: a 97 line input string
#   Ligand name: N-(benzylcarbamothioyl)-L-histidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](Cc1c[nH]cn1)NC(=S)NCc2ccccc2
#
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
 95I  95I  "N-(benzylcarbamothioyl)-L-histidine"  ligand  37  21  .  2022-09-16  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_95I
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
 95I  C10  C  CR16  0  -0.292  -3.1800  23.5199  -25.7344
 95I  C13  C  C     0   0.536   1.7923  23.3657  -21.1244
 95I  C17  C  CR5   0   0.133   4.0514  21.5238  -21.7202
 95I  C20  C  CR15  0   0.085   5.0961  21.0748  -19.9141
 95I  C02  C  C     0   0.433   0.1411  23.8843  -23.6588
 95I  C04  C  CH2   0  -0.387  -1.4377  25.2060  -25.0282
 95I  C05  C  CR6   0   0.129  -2.0798  24.3073  -26.0563
 95I  C06  C  CR16  0  -0.294  -1.5695  24.2543  -27.3520
 95I  C07  C  CR16  0  -0.241  -2.1462  23.4301  -28.3069
 95I  C08  C  CR16  0  -0.265  -3.2467  22.6475  -27.9768
 95I  C09  C  CR16  0  -0.241  -3.7635  22.6962  -26.6898
 95I  C12  C  CH1   0  -0.136   1.9214  22.6755  -22.4757
 95I  C16  C  CH2   0  -0.563   3.3999  22.3590  -22.7666
 95I  C18  C  CR15  0  -0.116   4.1302  20.1603  -21.6503
 95I  N03  N  NH1   0  -0.607  -0.1173  24.7628  -24.6341
 95I  N11  N  NH1   0  -0.627   1.4293  23.5248  -23.5268
 95I  N19  N  NR15  0  -0.562   4.7977  19.8956  -20.4912
 95I  N21  N  N     0  -0.449   4.6605  22.0804  -20.6294
 95I  O15  O  OH1   0  -0.583   1.5225  22.5095  -20.1514
 95I  S01  S  S1    0  -0.418  -1.0481  23.2646  -22.6399
 95I  H1   H  HCR6  0   0.247  -3.5818  23.5518  -24.7293
 95I  H2   H  HCR5  0   0.276   5.6346  21.1437  -18.9815
 95I  H3   H  HCH2  0   0.276  -1.3237  26.2127  -25.4325
 95I  H4   H  HCH2  0   0.267  -2.0624  25.2794  -24.1396
 95I  H5   H  HCR6  0   0.251  -0.7168  24.8683  -27.6200
 95I  H6   H  HCR6  0   0.253  -1.7412  23.4021  -29.3104
 95I  H7   H  HCR6  0   0.254  -3.6999  22.0056  -28.7213
 95I  H8   H  HCR6  0   0.252  -4.6212  22.0905  -26.4263
 95I  H9   H  HCH1  0   0.283   1.3546  21.7430  -22.4572
 95I  H10  H  HCH2  0   0.262   3.9499  23.2983  -22.8694
 95I  H11  H  HCH2  0   0.279   3.4386  21.8518  -23.7324
 95I  H12  H  HCR5  0   0.284   3.7787  19.3841  -22.3090
 95I  H13  H  HNH1  0   0.406   0.6454  25.0626  -25.2244
 95I  H14  H  HNH1  0   0.408   2.1200  23.9786  -24.1079
 95I  H15  H  HNR5  0   0.419   5.0411  18.9830  -20.1393
 95I  H17  H  HOH1  0   0.477   1.5172  22.9695  -19.2980
 95I  O14  O  O     0  -0.430   1.9650  24.5451  -20.9583

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
 95I  C07  C08  aromatic  1.390  0.020  1.390
 95I  C07  C06  aromatic  1.387  0.020  1.387
 95I  C08  C09  aromatic  1.388  0.020  1.388
 95I  C06  C05  aromatic  1.394  0.020  1.394
 95I  C09  C10  aromatic  1.390  0.020  1.390
 95I  C05  C10  aromatic  1.391  0.020  1.391
 95I  C05  C04  single    1.509  0.020  1.509
 95I  C04  N03  single    1.447  0.020  1.447
 95I  N03  C02  single    1.338  0.020  1.338
 95I  C02  N11  single    1.344  0.020  1.344
 95I  C02  S01  double    1.684  0.020  1.684
 95I  N11  C12  single    1.438  0.020  1.438
 95I  C16  C17  single    1.489  0.020  1.489
 95I  C16  C12  single    1.540  0.020  1.540
 95I  N21  C17  aromatic  1.368  0.020  1.368
 95I  N21  C20  aromatic  1.309  0.020  1.309
 95I  C17  C18  aromatic  1.368  0.020  1.368
 95I  C12  C13  single    1.523  0.020  1.523
 95I  C20  N19  aromatic  1.346  0.020  1.346
 95I  C18  N19  aromatic  1.363  0.020  1.363
 95I  C13  O14  double    1.204  0.020  1.204
 95I  C13  O15  single    1.324  0.020  1.324
 95I  C10  H1   single    0.930  0.020  1.080
 95I  C20  H2   single    0.930  0.020  1.080
 95I  C04  H3   single    0.970  0.020  1.090
 95I  C04  H4   single    0.970  0.020  1.090
 95I  C06  H5   single    0.930  0.020  1.080
 95I  C07  H6   single    0.930  0.020  1.080
 95I  C08  H7   single    0.930  0.020  1.080
 95I  C09  H8   single    0.930  0.020  1.080
 95I  C12  H9   single    0.970  0.020  1.090
 95I  C16  H10  single    0.970  0.020  1.090
 95I  C16  H11  single    0.970  0.020  1.090
 95I  C18  H12  single    0.930  0.020  1.080
 95I  N03  H13  single    0.860  0.020  1.020
 95I  N11  H14  single    0.860  0.020  1.020
 95I  N19  H15  single    0.860  0.020  1.020
 95I  O15  H17  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
 95I  H1   C10  C09  119.98  3.000
 95I  H1   C10  C05  119.45  3.000
 95I  C09  C10  C05  120.57  3.000
 95I  O15  C13  O14  124.17  3.000
 95I  O15  C13  C12  112.10  3.000
 95I  O14  C13  C12  123.68  3.000
 95I  N21  C17  C18  109.84  3.000
 95I  C18  C17  C16  128.35  3.000
 95I  N21  C17  C16  121.80  3.000
 95I  H2   C20  N21  126.11  3.000
 95I  H2   C20  N19  122.48  3.000
 95I  N21  C20  N19  111.41  3.000
 95I  S01  C02  N11  121.27  3.000
 95I  S01  C02  N03  123.11  3.000
 95I  N11  C02  N03  115.62  3.000
 95I  H4   C04  H3   107.47  3.000
 95I  H4   C04  N03  108.77  3.000
 95I  H3   C04  N03  106.75  3.000
 95I  H4   C04  C05  110.62  3.000
 95I  H3   C04  C05  109.98  3.000
 95I  N03  C04  C05  113.04  3.000
 95I  C06  C05  C04  120.02  3.000
 95I  C04  C05  C10  121.08  3.000
 95I  C06  C05  C10  118.90  3.000
 95I  H5   C06  C07  119.55  3.000
 95I  H5   C06  C05  119.75  3.000
 95I  C07  C06  C05  120.70  3.000
 95I  H6   C07  C08  120.12  3.000
 95I  H6   C07  C06  119.87  3.000
 95I  C08  C07  C06  120.01  3.000
 95I  H7   C08  C09  120.18  3.000
 95I  H7   C08  C07  120.13  3.000
 95I  C09  C08  C07  119.69  3.000
 95I  H8   C09  C08  120.08  3.000
 95I  H8   C09  C10  119.79  3.000
 95I  C08  C09  C10  120.13  3.000
 95I  H9   C12  N11  109.84  3.000
 95I  H9   C12  C16  109.05  3.000
 95I  N11  C12  C16  108.17  3.000
 95I  H9   C12  C13  109.16  3.000
 95I  C16  C12  C13  110.01  3.000
 95I  N11  C12  C13  110.60  3.000
 95I  H11  C16  H10  107.35  3.000
 95I  H11  C16  C12  107.26  3.000
 95I  H10  C16  C12  108.92  3.000
 95I  H11  C16  C17  110.22  3.000
 95I  H10  C16  C17  109.14  3.000
 95I  C12  C16  C17  113.75  3.000
 95I  H12  C18  N19  122.67  3.000
 95I  H12  C18  C17  131.95  3.000
 95I  N19  C18  C17  105.38  3.000
 95I  H13  N03  C04  116.03  3.000
 95I  H13  N03  C02  118.37  3.000
 95I  C04  N03  C02  125.16  3.000
 95I  H14  N11  C12  116.86  3.000
 95I  H14  N11  C02  118.60  3.000
 95I  C12  N11  C02  123.89  3.000
 95I  H15  N19  C18  126.22  3.000
 95I  H15  N19  C20  126.14  3.000
 95I  C18  N19  C20  107.63  3.000
 95I  C20  N21  C17  105.75  3.000
 95I  H17  O15  C13  109.95  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
 95I  CONST_01  C07  C08  C09  C10     0.00   0.0  0
 95I  CONST_02  C07  C06  C05  C10     0.00   0.0  0
 95I  CONST_03  N19  C20  N21  C17     0.00   0.0  0
 95I  CONST_04  C20  N19  C18  C17     0.00   0.0  0
 95I  CONST_05  C18  C17  N21  C20     0.00   0.0  0
 95I  CONST_06  C08  C07  C06  C05     0.00   0.0  0
 95I  CONST_07  C08  C09  C10  C05     0.00   0.0  0
 95I  CONST_08  C09  C08  C07  C06     0.00   0.0  0
 95I  CONST_09  C09  C10  C05  C06     0.00   0.0  0
 95I  CONST_10  N21  C20  N19  C18     0.00   0.0  0
 95I  CONST_11  N21  C17  C18  N19     0.00   0.0  0
 95I  CONST_12  C16  C17  N21  C20   180.00   0.0  0
 95I  CONST_13  C07  C06  C05  C04   180.00   0.0  0
 95I  CONST_14  C09  C10  C05  C04   180.00   0.0  0
 95I  CONST_15  N19  C18  C17  C16   180.00   0.0  0
 95I  CONST_16  H7   C08  C09  C10   180.00   0.0  0
 95I  CONST_17  H5   C06  C05  C10   180.00   0.0  0
 95I  CONST_18  H2   C20  N21  C17   180.00   0.0  0
 95I  CONST_19  H15  N19  C18  C17   180.00   0.0  0
 95I  CONST_20  H12  C18  N19  C20   180.00   0.0  0
 95I  CONST_21  H6   C07  C06  C05   180.00   0.0  0
 95I  CONST_22  H8   C09  C10  C05   180.00   0.0  0
 95I  CONST_23  H7   C08  C07  C06   180.00   0.0  0
 95I  CONST_24  H1   C10  C05  C06   180.00   0.0  0
 95I  CONST_25  H8   C09  C08  C07   180.00   0.0  0
 95I  CONST_26  H5   C06  C07  C08   180.00   0.0  0
 95I  CONST_27  H1   C10  C09  C08   180.00   0.0  0
 95I  CONST_28  H6   C07  C08  C09   180.00   0.0  0
 95I  CONST_29  H2   C20  N19  C18   180.00   0.0  0
 95I  CONST_30  H12  C18  C17  N21   180.00   0.0  0
 95I  CONST_31  H15  N19  C20  N21   180.00   0.0  0
 95I  CONST_32  N11  C02  N03  C04   180.00   0.0  0
 95I  CONST_33  S01  C02  N03  C04     0.00   0.0  0
 95I  CONST_34  N03  C02  N11  C12   180.00   0.0  0
 95I  CONST_35  S01  C02  N11  C12     0.00   0.0  0
 95I  CONST_36  H17  O15  C13  C12   180.00   0.0  0
 95I  CONST_37  H14  N11  C02  N03     0.00   0.0  0
 95I  CONST_38  H13  N03  C02  N11     0.00   0.0  0
 95I  CONST_39  H17  O15  C13  O14     0.00   0.0  0
 95I  CONST_40  H13  N03  C02  S01   180.00   0.0  0
 95I  CONST_41  H14  N11  C02  S01   180.00   0.0  0
 95I  Var_01    N03  C04  C05  C10   111.06  30.0  2
 95I  Var_02    N03  C04  C05  C06   -68.79  30.0  2
 95I  Var_03    N21  C17  C16  C12   -88.61  30.0  2
 95I  Var_04    C18  C17  C16  C12    90.06  30.0  2
 95I  Var_05    H3   C04  C05  C10  -129.74  30.0  2
 95I  Var_06    H4   C04  C05  C10   -11.18  30.0  2
 95I  Var_07    H3   C04  C05  C06    50.40  30.0  2
 95I  Var_08    H4   C04  C05  C06   168.96  30.0  2
 95I  Var_09    H10  C16  C17  C18  -148.10  30.0  1
 95I  Var_10    H11  C16  C17  C18   -30.44  30.0  1
 95I  Var_11    H10  C16  C17  N21    33.24  30.0  1
 95I  Var_12    H11  C16  C17  N21   150.90  30.0  1
 95I  Var_13    C05  C04  N03  C02   -87.14  30.0  1
 95I  Var_14    H13  N03  C04  C05    85.02  30.0  3
 95I  Var_15    H3   C04  N03  C02   151.82  30.0  1
 95I  Var_16    H4   C04  N03  C02    36.13  30.0  1

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
 95I  chir_01  C12  N11  C16  C13  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
 95I  plan-1  C17  0.020
 95I  plan-1  C20  0.020
 95I  plan-1  C16  0.020
 95I  plan-1  C18  0.020
 95I  plan-1  N19  0.020
 95I  plan-1  N21  0.020
 95I  plan-1  H2   0.020
 95I  plan-1  H12  0.020
 95I  plan-1  H15  0.020
 95I  plan-2  C10  0.020
 95I  plan-2  C04  0.020
 95I  plan-2  C05  0.020
 95I  plan-2  C06  0.020
 95I  plan-2  C07  0.020
 95I  plan-2  C08  0.020
 95I  plan-2  C09  0.020
 95I  plan-2  H1   0.020
 95I  plan-2  H5   0.020
 95I  plan-2  H6   0.020
 95I  plan-2  H7   0.020
 95I  plan-2  H8   0.020
 95I  plan-3  C02  0.020
 95I  plan-3  C04  0.020
 95I  plan-3  C12  0.020
 95I  plan-3  N03  0.020
 95I  plan-3  N11  0.020
 95I  plan-3  S01  0.020
 95I  plan-3  H13  0.020
 95I  plan-3  H14  0.020
 95I  plan-4  C13  0.020
 95I  plan-4  C12  0.020
 95I  plan-4  O15  0.020
 95I  plan-4  H17  0.020
 95I  plan-4  O14  0.020

