# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 03:57:40 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (2,5-dimethylbenzene-1,4-diyl)dimethanediyl bis(N-carbamimidoylcarbamimidothioate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(CSC(=N)NC(N)=N)c(C)cc1CSC(=N)NC(N)=N
#
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
 C1A  C1A  '(2,5-dimethylbenzene-1,4-diyl)dimethanediyl bis(N-carbamimidoylcarbamimidothioate)'  ligand  46  24  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C1A
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
 C1A  C1    C  CH3   0  -0.746  -1.2280  -1.3252   2.2831
 C1A  C2    C  CR6   0   0.081  -0.6057  -0.6526   1.0940
 C1A  C3    C  CR16  0  -0.327   0.6222  -0.0113   1.2116
 C1A  C4    C  CR6   0   0.069   1.2389   0.6283   0.1414
 C1A  C5    C  CH2   0  -0.632   2.5742   1.2818   0.3437
 C1A  S1    S  S2    0   0.061   3.8309   0.0356  -0.1083
 C1A  C6    C  C     0   0.327   5.2961   0.9942   0.1639
 C1A  N1    N  N     0  -0.644   5.1831   2.2288   0.4428
 C1A  N2    N  NH1   0  -0.691   6.5043   0.3347   0.1001
 C1A  C7    C  C     0   0.577   6.7639  -0.9802  -0.2532
 C1A  N3    N  N     0  -0.677   5.8669  -1.6766  -0.8269
 C1A  N4    N  NH2   0  -0.833   8.0535  -1.3436   0.0273
 C1A  C8    C  CR6   0   0.080   0.6170   0.6236  -1.1117
 C1A  C9    C  CH3   0  -0.746   1.2404   1.2946  -2.3012
 C1A  C10   C  CR16  0  -0.327  -0.6114  -0.0170  -1.2292
 C1A  C11   C  CR6   0   0.069  -1.2286  -0.6557  -0.1588
 C1A  C12   C  CH2   0  -0.632  -2.5657  -1.3056  -0.3605
 C1A  S2    S  S2    0   0.062  -3.8178  -0.0613   0.1094
 C1A  C13   C  C     0   0.327  -5.2868  -1.0105  -0.1732
 C1A  N5    N  N     0  -0.644  -5.1787  -2.2382  -0.4829
 C1A  N6    N  NH1   0  -0.691  -6.4937  -0.3520  -0.0810
 C1A  C14   C  C     0   0.578  -6.7498   0.9558   0.2999
 C1A  N7    N  N     0  -0.677  -5.8403   1.6495   0.8567
 C1A  N8    N  NH2   0  -0.834  -8.0499   1.3156   0.0642
 C1A  H51   H  HCH2  0   0.284   2.6981   2.1631  -0.2831
 C1A  H52   H  HCH2  0   0.287   2.7173   1.5830   1.3805
 C1A  HN1   H  H     0   0.338   6.0861   2.6671   0.6017
 C1A  HN2   H  HNH1  0   0.411   7.3075   0.9136   0.2991
 C1A  HN3   H  H     0   0.338   6.1648  -2.6362  -0.9552
 C1A  HN41  H  HNH2  0   0.396   8.4873  -0.9370   0.8417
 C1A  HN42  H  HNH2  0   0.398   8.2634  -2.3230  -0.0771
 C1A  H91   H  HCH3  0   0.243   2.2488   0.9225  -2.4912
 C1A  H92   H  HCH3  0   0.251   0.6480   1.1281  -3.1998
 C1A  H93   H  HCH3  0   0.247   1.3217   2.3740  -2.1558
 C1A  H10   H  HCR6  0   0.242  -1.1055  -0.0272  -2.1951
 C1A  H121  H  HCH2  0   0.287  -2.7143  -1.5970  -1.3994
 C1A  H122  H  HCH2  0   0.284  -2.6882  -2.1923   0.2590
 C1A  HN5   H  H     0   0.338  -6.0843  -2.6700  -0.6458
 C1A  HN6   H  HNH1  0   0.411  -7.2993  -0.9293  -0.2746
 C1A  HN7   H  H     0   0.338  -6.1414   2.6040   1.0126
 C1A  HN81  H  HNH2  0   0.396  -8.5065   0.9185  -0.7426
 C1A  HN82  H  HNH2  0   0.397  -8.2604   2.2927   0.1874
 C1A  H1    H  HCH3  0   0.243  -2.2335  -0.9486   2.4787
 C1A  H20   H  HCH3  0   0.247  -1.3157  -2.4036   2.1334
 C1A  H21   H  HCH3  0   0.251  -0.6311  -1.1659   3.1800
 C1A  H31   H  HCR6  0   0.242   1.1163  -0.0008   2.1776

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
 C1A  C1   C2    single    1.501  0.020  1.501
 C1A  C2   C3    aromatic  1.390  0.020  1.390
 C1A  C2   C11   aromatic  1.399  0.020  1.399
 C1A  C3   C4    aromatic  1.391  0.020  1.391
 C1A  C4   C5    single    1.500  0.020  1.500
 C1A  C4   C8    aromatic  1.399  0.020  1.399
 C1A  C5   S1    single    1.827  0.020  1.827
 C1A  C5   H51   single    0.970  0.020  1.090
 C1A  C5   H52   single    0.970  0.020  1.090
 C1A  S1   C6    single    1.772  0.020  1.772
 C1A  C6   N1    double    1.271  0.020  1.271
 C1A  C6   N2    single    1.378  0.020  1.378
 C1A  N1   HN1   single    0.890  0.020  1.040
 C1A  N2   C7    single    1.386  0.020  1.386
 C1A  N2   HN2   single    0.860  0.020  1.020
 C1A  C7   N3    double    1.272  0.020  1.272
 C1A  C7   N4    single    1.369  0.020  1.369
 C1A  N3   HN3   single    0.890  0.020  1.040
 C1A  N4   HN41  single    0.890  0.020  1.040
 C1A  N4   HN42  single    0.890  0.020  1.040
 C1A  C8   C9    single    1.501  0.020  1.501
 C1A  C8   C10   aromatic  1.390  0.020  1.390
 C1A  C9   H91   single    0.970  0.020  1.090
 C1A  C9   H92   single    0.970  0.020  1.090
 C1A  C9   H93   single    0.970  0.020  1.090
 C1A  C10  C11   aromatic  1.391  0.020  1.391
 C1A  C10  H10   single    0.930  0.020  1.080
 C1A  C11  C12   single    1.500  0.020  1.500
 C1A  C12  S2    single    1.827  0.020  1.827
 C1A  C12  H121  single    0.970  0.020  1.090
 C1A  C12  H122  single    0.970  0.020  1.090
 C1A  S2   C13   single    1.772  0.020  1.772
 C1A  C13  N5    double    1.271  0.020  1.271
 C1A  C13  N6    single    1.378  0.020  1.378
 C1A  N5   HN5   single    0.890  0.020  1.040
 C1A  N6   C14   single    1.386  0.020  1.386
 C1A  N6   HN6   single    0.860  0.020  1.020
 C1A  C14  N7    double    1.272  0.020  1.272
 C1A  C14  N8    single    1.369  0.020  1.369
 C1A  N7   HN7   single    0.890  0.020  1.040
 C1A  N8   HN81  single    0.890  0.020  1.040
 C1A  N8   HN82  single    0.890  0.020  1.040
 C1A  C1   H1    single    0.970  0.020  1.090
 C1A  C1   H20   single    0.970  0.020  1.090
 C1A  C1   H21   single    0.970  0.020  1.090
 C1A  C3   H31   single    0.930  0.020  1.080

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
 C1A  H21   C1   H20   107.54  3.000
 C1A  H21   C1   H1    107.87  3.000
 C1A  H20   C1   H1    106.94  3.000
 C1A  H21   C1   C2    111.07  3.000
 C1A  H20   C1   C2    111.54  3.000
 C1A  H1    C1   C2    111.66  3.000
 C1A  C11   C2   C3    118.03  3.000
 C1A  C11   C2   C1    121.58  3.000
 C1A  C3    C2   C1    120.38  3.000
 C1A  H31   C3   C4    118.60  3.000
 C1A  H31   C3   C2    118.81  3.000
 C1A  C4    C3   C2    122.59  3.000
 C1A  C8    C4   C5    121.19  3.000
 C1A  C8    C4   C3    119.38  3.000
 C1A  C5    C4   C3    119.42  3.000
 C1A  H52   C5   H51   108.02  3.000
 C1A  H52   C5   S1    109.50  3.000
 C1A  H51   C5   S1    109.36  3.000
 C1A  H52   C5   C4    111.45  3.000
 C1A  H51   C5   C4    112.10  3.000
 C1A  S1    C5   C4    106.37  3.000
 C1A  C6    S1   C5     99.31  3.000
 C1A  N2    C6   N1    123.58  3.000
 C1A  N2    C6   S1    117.33  3.000
 C1A  N1    C6   S1    119.06  3.000
 C1A  HN1   N1   C6    111.98  3.000
 C1A  HN2   N2   C7    116.43  3.000
 C1A  HN2   N2   C6    114.46  3.000
 C1A  C7    N2   C6    129.05  3.000
 C1A  N4    C7   N3    127.68  3.000
 C1A  N4    C7   N2    112.09  3.000
 C1A  N3    C7   N2    120.14  3.000
 C1A  HN3   N3   C7    111.61  3.000
 C1A  HN42  N4   HN41  112.71  3.000
 C1A  HN42  N4   C7    115.68  3.000
 C1A  HN41  N4   C7    117.63  3.000
 C1A  C10   C8   C9    120.39  3.000
 C1A  C10   C8   C4    118.03  3.000
 C1A  C9    C8   C4    121.58  3.000
 C1A  H93   C9   H92   107.55  3.000
 C1A  H93   C9   H91   106.94  3.000
 C1A  H92   C9   H91   107.87  3.000
 C1A  H93   C9   C8    111.54  3.000
 C1A  H92   C9   C8    111.08  3.000
 C1A  H91   C9   C8    111.66  3.000
 C1A  H10   C10  C11   118.60  3.000
 C1A  H10   C10  C8    118.81  3.000
 C1A  C11   C10  C8    122.59  3.000
 C1A  C12   C11  C10   119.40  3.000
 C1A  C12   C11  C2    121.21  3.000
 C1A  C10   C11  C2    119.37  3.000
 C1A  H122  C12  H121  108.03  3.000
 C1A  H122  C12  S2    109.35  3.000
 C1A  H121  C12  S2    109.52  3.000
 C1A  H122  C12  C11   112.12  3.000
 C1A  H121  C12  C11   111.45  3.000
 C1A  S2    C12  C11   106.33  3.000
 C1A  C13   S2   C12    99.34  3.000
 C1A  N6    C13  N5    123.53  3.000
 C1A  N6    C13  S2    117.36  3.000
 C1A  N5    C13  S2    119.08  3.000
 C1A  HN5   N5   C13   111.95  3.000
 C1A  HN6   N6   C14   116.41  3.000
 C1A  HN6   N6   C13   114.37  3.000
 C1A  C14   N6   C13   129.13  3.000
 C1A  N8    C14  N7    127.65  3.000
 C1A  N8    C14  N6    112.09  3.000
 C1A  N7    C14  N6    120.18  3.000
 C1A  HN7   N7   C14   111.63  3.000
 C1A  HN82  N8   HN81  112.66  3.000
 C1A  HN82  N8   C14   115.61  3.000
 C1A  HN81  N8   C14   117.65  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
 C1A  CONST_01  C8    C4   C3   C2     0.00   0.0  0
 C1A  CONST_02  C8    C10  C11  C2     0.00   0.0  0
 C1A  CONST_03  C10   C11  C2   C3     0.00   0.0  0
 C1A  CONST_04  C10   C8   C4   C3     0.00   0.0  0
 C1A  CONST_05  C11   C2   C3   C4     0.00   0.0  0
 C1A  CONST_06  C11   C10  C8   C4     0.00   0.0  0
 C1A  CONST_07  C4    C3   C2   C1   180.00   0.0  0
 C1A  CONST_08  C10   C11  C2   C1   180.00   0.0  0
 C1A  CONST_09  C5    C4   C3   C2   180.00   0.0  0
 C1A  CONST_10  C12   C11  C2   C3   180.00   0.0  0
 C1A  CONST_11  C9    C8   C4   C3   180.00   0.0  0
 C1A  CONST_12  C10   C8   C4   C5   180.00   0.0  0
 C1A  CONST_13  C12   C11  C10  C8   180.00   0.0  0
 C1A  CONST_14  C11   C10  C8   C9   180.00   0.0  0
 C1A  CONST_15  H10   C10  C11  C2   180.00   0.0  0
 C1A  CONST_16  H31   C3   C4   C8   180.00   0.0  0
 C1A  CONST_17  C7    N2   C6   S1     0.00   0.0  0
 C1A  CONST_18  N3    C7   N2   C6     0.00   0.0  0
 C1A  CONST_19  N4    C7   N2   C6   180.00   0.0  0
 C1A  CONST_20  C7    N2   C6   N1   180.00   0.0  0
 C1A  CONST_21  C14   N6   C13  S2     0.00   0.0  0
 C1A  CONST_22  N7    C14  N6   C13    0.00   0.0  0
 C1A  CONST_23  N8    C14  N6   C13  180.00   0.0  0
 C1A  CONST_24  C14   N6   C13  N5   180.00   0.0  0
 C1A  CONST_25  HN1   N1   C6   S1   180.00   0.0  0
 C1A  CONST_26  HN2   N2   C6   S1   180.00   0.0  0
 C1A  CONST_27  HN3   N3   C7   N2   180.00   0.0  0
 C1A  CONST_29  HN42  N4   C7   N2   180.00   0.0  0
 C1A  CONST_30  HN5   N5   C13  S2   180.00   0.0  0
 C1A  CONST_31  HN6   N6   C13  S2   180.00   0.0  0
 C1A  CONST_32  HN7   N7   C14  N6   180.00   0.0  0
 C1A  CONST_34  HN82  N8   C14  N6   180.00   0.0  0
 C1A  Var_01    S2    C12  C11  C2    84.94  30.0  2
 C1A  Var_02    S1    C5   C4   C3    92.97  30.0  2
 C1A  Var_03    H1    C1   C2   C3   124.38  30.0  2
 C1A  Var_04    H91   C9   C8   C4    55.63  30.0  2
 C1A  Var_05    N1    C6   S1   C5    -6.56  30.0  3
 C1A  Var_06    N5    C13  S2   C12    5.79  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
 C1A  plan-1  C1    0.020
 C1A  plan-1  C2    0.020
 C1A  plan-1  C3    0.020
 C1A  plan-1  C4    0.020
 C1A  plan-1  C5    0.020
 C1A  plan-1  C8    0.020
 C1A  plan-1  C9    0.020
 C1A  plan-1  C10   0.020
 C1A  plan-1  C11   0.020
 C1A  plan-1  C12   0.020
 C1A  plan-1  H10   0.020
 C1A  plan-1  H31   0.020
 C1A  plan-2  S1    0.020
 C1A  plan-2  C6    0.020
 C1A  plan-2  N1    0.020
 C1A  plan-2  N2    0.020
 C1A  plan-2  C7    0.020
 C1A  plan-2  N3    0.020
 C1A  plan-2  N4    0.020
 C1A  plan-2  HN1   0.020
 C1A  plan-2  HN2   0.020
 C1A  plan-2  HN3   0.020
 C1A  plan-2  HN41  0.020
 C1A  plan-2  HN42  0.020
 C1A  plan-3  S2    0.020
 C1A  plan-3  C13   0.020
 C1A  plan-3  N5    0.020
 C1A  plan-3  N6    0.020
 C1A  plan-3  C14   0.020
 C1A  plan-3  N7    0.020
 C1A  plan-3  N8    0.020
 C1A  plan-3  HN5   0.020
 C1A  plan-3  HN6   0.020
 C1A  plan-3  HN7   0.020
 C1A  plan-3  HN81  0.020
 C1A  plan-3  HN82  0.020

