# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 03:52:47 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 4-({[3-(aminomethyl)phenyl]carbamoyl}amino)benzenecarboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cccc(NC(=O)Nc2ccc(cc2)C(N)=N)c1
#
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
 2X1  2X1  4-({[3-(aminomethyl)phenyl]carbamoyl}amino)benzenecarboximidamide  ligand  38  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2X1
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
 2X1  C1   C  C     0   0.746   0.4355   0.4155   0.1100
 2X1  N3   N  NH1   0  -0.793   1.6625  -0.0885   0.4394
 2X1  N4   N  NH1   0  -0.795  -0.5743  -0.4779   0.3662
 2X1  C5   C  CR6   0  -0.009  -4.7387  -0.2310  -0.1660
 2X1  N6   N  NH2   0  -0.805  -6.7866   1.0257  -0.2973
 2X1  O7   O  O     0  -0.493   0.2565   1.5260  -0.3552
 2X1  C8   C  CR6   0   0.400   2.9129   0.5155   0.2772
 2X1  C9   C  CR16  0  -0.279  -4.1217  -1.3451   0.4005
 2X1  C10  C  CR16  0  -0.272  -3.9280   0.8307  -0.5558
 2X1  N11  N  N     0  -0.645  -6.9253  -1.2385  -0.6277
 2X1  C12  C  CR6   0   0.381  -1.9406  -0.3244   0.1642
 2X1  C13  C  CR16  0  -0.401   4.0209  -0.3350   0.3257
 2X1  C14  C  CR16  0  -0.346  -2.7533  -1.3909   0.5674
 2X1  C15  C  CR16  0  -0.304  -2.5499   0.7961  -0.4055
 2X1  C16  C  CR6   0   0.091   5.3135   0.1514   0.2032
 2X1  C18  C  CR16  0  -0.235   4.4074   2.3669  -0.0230
 2X1  C19  C  CR16  0  -0.328   3.1112   1.8856   0.1082
 2X1  C20  C  CH2   0  -0.330   6.5056  -0.7696   0.2947
 2X1  C21  C  CR16  0  -0.323   5.5022   1.5193   0.0165
 2X1  H1   H  HNH1  0   0.413   1.7045  -1.0514   0.7362
 2X1  H2   H  HNH1  0   0.416  -0.3115  -1.3651   0.7681
 2X1  H3   H  HNH2  0   0.391  -6.3694   1.7129   0.3080
 2X1  H4   H  HNH2  0   0.383  -7.7942   1.0445  -0.3066
 2X1  H5   H  HCR6  0   0.263  -4.7134  -2.1866   0.7387
 2X1  H6   H  HCR6  0   0.262  -4.3662   1.7091  -1.0120
 2X1  H7   H  H     0   0.330  -6.3413  -2.0569  -0.7545
 2X1  H8   H  HCR6  0   0.260   3.8731  -1.4014   0.4527
 2X1  H9   H  HCR6  0   0.275  -2.3047  -2.2671   1.0202
 2X1  H10  H  HCR6  0   0.284  -1.9679   1.6381  -0.7397
 2X1  H11  H  HNH2  0   0.345   6.0549  -2.1905  -1.0829
 2X1  H12  H  HNH2  0   0.357   6.9776  -2.7315   0.1310
 2X1  H14  H  HCR6  0   0.254   4.5568   3.4305  -0.1596
 2X1  H15  H  HCR6  0   0.271   2.2831   2.5737   0.0781
 2X1  H16  H  HCH2  0   0.216   7.3279  -0.3276  -0.2837
 2X1  H17  H  HCH2  0   0.244   6.8488  -0.7804   1.3337
 2X1  H18  H  HCR6  0   0.244   6.5031   1.9180  -0.0989
 2X1  C2   C  C     0   0.327  -6.2118  -0.2098  -0.3652
 2X1  N17  N  NH2   0  -0.796   6.1893  -2.1345  -0.0812

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
 2X1  N11  C2   double    1.279  0.020  1.279
 2X1  C2   N6   single    1.364  0.020  1.364
 2X1  C2   C5   single    1.487  0.020  1.487
 2X1  C10  C5   aromatic  1.392  0.020  1.392
 2X1  C10  C15  aromatic  1.387  0.020  1.387
 2X1  C5   C9   aromatic  1.394  0.020  1.394
 2X1  C15  C12  aromatic  1.397  0.020  1.397
 2X1  O7   C1   double    1.217  0.020  1.217
 2X1  C9   C14  aromatic  1.379  0.020  1.379
 2X1  C12  C14  aromatic  1.400  0.020  1.400
 2X1  C12  N4   single    1.390  0.020  1.390
 2X1  C1   N4   single    1.372  0.020  1.372
 2X1  C1   N3   single    1.367  0.020  1.367
 2X1  C19  C18  aromatic  1.389  0.020  1.389
 2X1  C19  C8   aromatic  1.395  0.020  1.395
 2X1  C18  C21  aromatic  1.385  0.020  1.385
 2X1  N3   C8   single    1.398  0.020  1.398
 2X1  C8   C13  aromatic  1.398  0.020  1.398
 2X1  C21  C16  aromatic  1.393  0.020  1.393
 2X1  C13  C16  aromatic  1.387  0.020  1.387
 2X1  C16  C20  single    1.509  0.020  1.509
 2X1  C20  N17  single    1.451  0.020  1.451
 2X1  N3   H1   single    0.860  0.020  1.020
 2X1  N4   H2   single    0.860  0.020  1.020
 2X1  N6   H3   single    0.890  0.020  1.040
 2X1  N6   H4   single    0.890  0.020  1.040
 2X1  C9   H5   single    0.930  0.020  1.080
 2X1  C10  H6   single    0.930  0.020  1.080
 2X1  N11  H7   single    0.890  0.020  1.040
 2X1  C13  H8   single    0.930  0.020  1.080
 2X1  C14  H9   single    0.930  0.020  1.080
 2X1  C15  H10  single    0.930  0.020  1.080
 2X1  N17  H11  single    0.890  0.020  1.040
 2X1  N17  H12  single    0.890  0.020  1.040
 2X1  C18  H14  single    0.930  0.020  1.080
 2X1  C19  H15  single    0.930  0.020  1.080
 2X1  C20  H16  single    0.970  0.020  1.090
 2X1  C20  H17  single    0.970  0.020  1.090
 2X1  C21  H18  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
 2X1  O7   C1   N4   123.85  3.000
 2X1  N4   C1   N3   112.06  3.000
 2X1  O7   C1   N3   124.09  3.000
 2X1  H1   N3   C8   114.17  3.000
 2X1  H1   N3   C1   117.41  3.000
 2X1  C8   N3   C1   128.00  3.000
 2X1  H2   N4   C12  114.28  3.000
 2X1  H2   N4   C1   117.08  3.000
 2X1  C12  N4   C1   128.63  3.000
 2X1  C10  C5   C9   117.76  3.000
 2X1  C9   C5   C2   120.30  3.000
 2X1  C10  C5   C2   121.93  3.000
 2X1  H4   N6   H3   114.04  3.000
 2X1  H4   N6   C2   115.96  3.000
 2X1  H3   N6   C2   118.27  3.000
 2X1  C19  C8   C13  119.30  3.000
 2X1  C13  C8   N3   116.24  3.000
 2X1  C19  C8   N3   124.45  3.000
 2X1  H5   C9   C14  118.59  3.000
 2X1  H5   C9   C5   120.41  3.000
 2X1  C14  C9   C5   120.99  3.000
 2X1  H6   C10  C15  117.92  3.000
 2X1  H6   C10  C5   120.09  3.000
 2X1  C15  C10  C5   121.98  3.000
 2X1  H7   N11  C2   110.72  3.000
 2X1  C15  C12  C14  118.38  3.000
 2X1  C14  C12  N4   116.40  3.000
 2X1  C15  C12  N4   125.22  3.000
 2X1  H8   C13  C16  118.86  3.000
 2X1  H8   C13  C8   119.64  3.000
 2X1  C16  C13  C8   121.50  3.000
 2X1  H9   C14  C12  119.74  3.000
 2X1  H9   C14  C9   119.22  3.000
 2X1  C12  C14  C9   121.05  3.000
 2X1  H10  C15  C12  121.21  3.000
 2X1  H10  C15  C10  118.95  3.000
 2X1  C12  C15  C10  119.85  3.000
 2X1  C21  C16  C20  120.02  3.000
 2X1  C20  C16  C13  121.12  3.000
 2X1  C21  C16  C13  118.85  3.000
 2X1  H14  C18  C21  119.71  3.000
 2X1  H14  C18  C19  118.76  3.000
 2X1  C21  C18  C19  121.53  3.000
 2X1  H15  C19  C18  119.57  3.000
 2X1  H15  C19  C8   121.45  3.000
 2X1  C18  C19  C8   118.99  3.000
 2X1  H17  C20  H16  105.62  3.000
 2X1  H17  C20  N17  107.77  3.000
 2X1  H16  C20  N17  113.92  3.000
 2X1  H17  C20  C16  108.14  3.000
 2X1  H16  C20  C16  108.29  3.000
 2X1  N17  C20  C16  112.72  3.000
 2X1  H18  C21  C18  120.13  3.000
 2X1  H18  C21  C16  120.04  3.000
 2X1  C18  C21  C16  119.83  3.000
 2X1  N11  C2   N6   120.23  3.000
 2X1  N6   C2   C5   115.07  3.000
 2X1  N11  C2   C5   124.66  3.000
 2X1  H12  N17  H11  106.17  3.000
 2X1  H12  N17  C20  109.33  3.000
 2X1  H11  N17  C20  109.72  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
 2X1  CONST_01  C12  C15  C10  C5     0.00   0.0  0
 2X1  CONST_02  C12  C14  C9   C5     0.00   0.0  0
 2X1  CONST_03  C21  C18  C19  C8     0.00   0.0  0
 2X1  CONST_04  C21  C16  C13  C8     0.00   0.0  0
 2X1  CONST_05  C15  C10  C5   C9     0.00   0.0  0
 2X1  CONST_06  C15  C12  C14  C9     0.00   0.0  0
 2X1  CONST_07  C14  C9   C5   C10    0.00   0.0  0
 2X1  CONST_08  C14  C12  C15  C10    0.00   0.0  0
 2X1  CONST_09  C18  C19  C8   C13    0.00   0.0  0
 2X1  CONST_10  C18  C21  C16  C13    0.00   0.0  0
 2X1  CONST_11  C19  C18  C21  C16    0.00   0.0  0
 2X1  CONST_12  C19  C8   C13  C16    0.00   0.0  0
 2X1  CONST_13  C15  C10  C5   C2   180.00   0.0  0
 2X1  CONST_14  C14  C9   C5   C2   180.00   0.0  0
 2X1  CONST_15  C18  C19  C8   N3   180.00   0.0  0
 2X1  CONST_16  C16  C13  C8   N3   180.00   0.0  0
 2X1  CONST_17  C10  C15  C12  N4   180.00   0.0  0
 2X1  CONST_18  C9   C14  C12  N4   180.00   0.0  0
 2X1  CONST_19  C20  C16  C13  C8   180.00   0.0  0
 2X1  CONST_20  C20  C16  C21  C18  180.00   0.0  0
 2X1  CONST_21  H10  C15  C10  C5   180.00   0.0  0
 2X1  CONST_22  H9   C14  C9   C5   180.00   0.0  0
 2X1  CONST_23  H14  C18  C19  C8   180.00   0.0  0
 2X1  CONST_24  H6   C10  C5   C9   180.00   0.0  0
 2X1  CONST_25  H5   C9   C5   C10  180.00   0.0  0
 2X1  CONST_26  H15  C19  C8   C13  180.00   0.0  0
 2X1  CONST_27  H18  C21  C16  C13  180.00   0.0  0
 2X1  CONST_28  H8   C13  C8   C19  180.00   0.0  0
 2X1  CONST_29  C15  C12  N4   C1     0.00   0.0  0
 2X1  CONST_30  C14  C12  N4   C1   180.00   0.0  0
 2X1  CONST_33  H1   N3   C8   C13    0.00   0.0  0
 2X1  CONST_34  H2   N4   C12  C14    0.00   0.0  0
 2X1  CONST_35  C12  N4   C1   O7     0.00   0.0  0
 2X1  CONST_36  C8   N3   C1   O7     0.00   0.0  0
 2X1  CONST_37  C12  N4   C1   N3   180.00   0.0  0
 2X1  CONST_38  C8   N3   C1   N4   180.00   0.0  0
 2X1  CONST_39  H7   N11  C2   C5     0.00   0.0  0
 2X1  CONST_41  H4   N6   C2   C5   180.00   0.0  0
 2X1  Var_01    C10  C5   C2   N6   -31.48  30.0  2
 2X1  Var_02    N17  C20  C16  C13   25.93  30.0  2
 2X1  Var_03    H11  N17  C20  C16   72.47  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
 2X1  plan-1  N4   0.020
 2X1  plan-1  C5   0.020
 2X1  plan-1  C9   0.020
 2X1  plan-1  C10  0.020
 2X1  plan-1  C12  0.020
 2X1  plan-1  C14  0.020
 2X1  plan-1  C15  0.020
 2X1  plan-1  H5   0.020
 2X1  plan-1  H6   0.020
 2X1  plan-1  H9   0.020
 2X1  plan-1  H10  0.020
 2X1  plan-1  C2   0.020
 2X1  plan-2  N3   0.020
 2X1  plan-2  C8   0.020
 2X1  plan-2  C13  0.020
 2X1  plan-2  C16  0.020
 2X1  plan-2  C18  0.020
 2X1  plan-2  C19  0.020
 2X1  plan-2  C20  0.020
 2X1  plan-2  C21  0.020
 2X1  plan-2  H8   0.020
 2X1  plan-2  H14  0.020
 2X1  plan-2  H15  0.020
 2X1  plan-2  H18  0.020
 2X1  plan-3  C1   0.020
 2X1  plan-3  N3   0.020
 2X1  plan-3  N4   0.020
 2X1  plan-3  O7   0.020
 2X1  plan-3  C8   0.020
 2X1  plan-3  C12  0.020
 2X1  plan-3  H1   0.020
 2X1  plan-3  H2   0.020
 2X1  plan-4  C5   0.020
 2X1  plan-4  N6   0.020
 2X1  plan-4  N11  0.020
 2X1  plan-4  H3   0.020
 2X1  plan-4  H4   0.020
 2X1  plan-4  H7   0.020
 2X1  plan-4  C2   0.020

