# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 30 22:39:47 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 6-[(phenylcarbamoyl)amino]naphthalene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc2cc(NC(=O)Nc3ccccc3)ccc2c1
#
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
 1U2  1U2  6-[(phenylcarbamoyl)amino]naphthalene-2-carboximidamide  ligand  39  23  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1U2
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
 1U2  O    O  O     0  -0.490  -2.3388  -1.1620  -0.3197
 1U2  C8   C  C     0   0.715  -2.4056  -0.0076   0.0583
 1U2  N4   N  NH1   0  -0.783  -3.5754   0.6872   0.1965
 1U2  C9   C  CR6   0   0.368  -4.8644   0.2072  -0.0557
 1U2  C14  C  CR16  0  -0.339  -5.9139   0.7697   0.6732
 1U2  C13  C  CR16  0  -0.247  -7.2219   0.3710   0.4497
 1U2  C12  C  CR16  0  -0.273  -7.5072  -0.6027  -0.4980
 1U2  C11  C  CR16  0  -0.250  -6.4645  -1.1573  -1.2269
 1U2  C10  C  CR16  0  -0.301  -5.1508  -0.7584  -1.0215
 1U2  N3   N  NH1   0  -0.786  -1.3090   0.7456   0.3986
 1U2  C7   C  CR6   0   0.387   0.0162   0.3083   0.3611
 1U2  C6   C  CR16  0  -0.420   0.9988   1.2081   0.0225
 1U2  C15  C  CR16  0  -0.291   0.3757  -1.0146   0.7278
 1U2  C16  C  CR16  0  -0.309   1.6865  -1.3950   0.7201
 1U2  C17  C  CR66  0   0.123   2.7159  -0.4911   0.3695
 1U2  C5   C  CR66  0   0.136   2.3588   0.8361   0.0248
 1U2  C4   C  CR16  0  -0.307   3.3871   1.7426  -0.3255
 1U2  C3   C  CR16  0  -0.282   4.6952   1.3473  -0.3393
 1U2  C18  C  CR16  0  -0.360   4.0741  -0.8686   0.3614
 1U2  C2   C  CR6   0   0.000   5.0575   0.0240   0.0136
 1U2  C1   C  C     0   0.331   6.4847  -0.4033   0.0193
 1U2  N2   N  NH2   0  -0.805   7.2610   0.1867  -0.9335
 1U2  N1   N  N     0  -0.642   6.9948  -1.2261   0.8542
 1U2  H8   H  HNH1  0   0.411  -3.5363   1.5627   0.6966
 1U2  H13  H  HCR6  0   0.268  -5.7039   1.5239   1.4226
 1U2  H12  H  HCR6  0   0.259  -8.0179   0.8208   1.0287
 1U2  H11  H  HCR6  0   0.254  -8.5268  -0.9214  -0.6685
 1U2  H10  H  HCR6  0   0.257  -6.6690  -1.9093  -1.9783
 1U2  H9   H  HCR6  0   0.269  -4.3664  -1.1934  -1.6203
 1U2  H7   H  HNH1  0   0.414  -1.4321   1.7457   0.4599
 1U2  H6   H  HCR6  0   0.267   0.7327   2.2205  -0.2601
 1U2  H14  H  HCR6  0   0.273  -0.3815  -1.7215   1.0289
 1U2  H15  H  HCR6  0   0.261   1.9500  -2.4062   1.0050
 1U2  H5   H  HCR6  0   0.259   3.1265   2.7614  -0.5851
 1U2  H4   H  HCR6  0   0.263   5.4646   2.0620  -0.6024
 1U2  H16  H  HCR6  0   0.262   4.3272  -1.8911   0.6180
 1U2  H3   H  HNH2  0   0.393   6.8263   0.4630  -1.7980
 1U2  H2   H  HNH2  0   0.385   8.1914  -0.1845  -1.0411
 1U2  H1   H  H     0   0.332   6.3153  -1.4865   1.5592

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
 1U2  C16  C15  aromatic  1.365  0.020  1.365
 1U2  C16  C17  aromatic  1.414  0.020  1.414
 1U2  C15  C7   aromatic  1.419  0.020  1.419
 1U2  N1   C1   double    1.278  0.020  1.278
 1U2  C11  C10  aromatic  1.388  0.020  1.388
 1U2  C11  C12  aromatic  1.388  0.020  1.388
 1U2  C18  C17  aromatic  1.410  0.020  1.410
 1U2  C18  C2   aromatic  1.373  0.020  1.373
 1U2  C10  C9   aromatic  1.395  0.020  1.395
 1U2  C17  C5   aromatic  1.417  0.020  1.417
 1U2  O    C8   double    1.217  0.020  1.217
 1U2  C1   N2   single    1.363  0.020  1.363
 1U2  C1   C2   single    1.490  0.020  1.490
 1U2  C12  C13  aromatic  1.388  0.020  1.388
 1U2  C8   N3   single    1.373  0.020  1.373
 1U2  C8   N4   single    1.368  0.020  1.368
 1U2  C2   C3   aromatic  1.417  0.020  1.417
 1U2  C7   N3   single    1.396  0.020  1.396
 1U2  C7   C6   aromatic  1.375  0.020  1.375
 1U2  C9   N4   single    1.398  0.020  1.398
 1U2  C9   C14  aromatic  1.396  0.020  1.396
 1U2  C5   C6   aromatic  1.410  0.020  1.410
 1U2  C5   C4   aromatic  1.415  0.020  1.415
 1U2  C13  C14  aromatic  1.385  0.020  1.385
 1U2  C3   C4   aromatic  1.367  0.020  1.367
 1U2  N4   H8   single    0.860  0.020  1.020
 1U2  C14  H13  single    0.930  0.020  1.080
 1U2  C13  H12  single    0.930  0.020  1.080
 1U2  C12  H11  single    0.930  0.020  1.080
 1U2  C11  H10  single    0.930  0.020  1.080
 1U2  C10  H9   single    0.930  0.020  1.080
 1U2  N3   H7   single    0.860  0.020  1.020
 1U2  C6   H6   single    0.930  0.020  1.080
 1U2  C15  H14  single    0.930  0.020  1.080
 1U2  C16  H15  single    0.930  0.020  1.080
 1U2  C4   H5   single    0.930  0.020  1.080
 1U2  C3   H4   single    0.930  0.020  1.080
 1U2  C18  H16  single    0.930  0.020  1.080
 1U2  N2   H3   single    0.890  0.020  1.040
 1U2  N2   H2   single    0.890  0.020  1.040
 1U2  N1   H1   single    0.890  0.020  1.040

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
 1U2  N3   C8   N4   112.30  3.000
 1U2  N4   C8   O    124.09  3.000
 1U2  N3   C8   O    123.62  3.000
 1U2  H8   N4   C9   115.02  3.000
 1U2  H8   N4   C8   117.24  3.000
 1U2  C9   N4   C8   126.57  3.000
 1U2  C10  C9   C14  119.07  3.000
 1U2  C14  C9   N4   117.42  3.000
 1U2  C10  C9   N4   123.47  3.000
 1U2  H13  C14  C13  119.65  3.000
 1U2  H13  C14  C9   119.71  3.000
 1U2  C13  C14  C9   120.63  3.000
 1U2  H12  C13  C12  120.36  3.000
 1U2  H12  C13  C14  119.24  3.000
 1U2  C12  C13  C14  120.39  3.000
 1U2  H11  C12  C11  120.51  3.000
 1U2  H11  C12  C13  120.52  3.000
 1U2  C11  C12  C13  118.97  3.000
 1U2  H10  C11  C10  118.75  3.000
 1U2  H10  C11  C12  120.02  3.000
 1U2  C10  C11  C12  121.23  3.000
 1U2  H9   C10  C11  119.36  3.000
 1U2  H9   C10  C9   120.94  3.000
 1U2  C11  C10  C9   119.70  3.000
 1U2  H7   N3   C7   115.33  3.000
 1U2  H7   N3   C8   117.45  3.000
 1U2  C7   N3   C8   125.42  3.000
 1U2  C15  C7   C6   119.53  3.000
 1U2  C6   C7   N3   118.69  3.000
 1U2  C15  C7   N3   121.71  3.000
 1U2  H6   C6   C5   118.92  3.000
 1U2  H6   C6   C7   120.00  3.000
 1U2  C5   C6   C7   121.08  3.000
 1U2  H14  C15  C16  119.54  3.000
 1U2  H14  C15  C7   120.35  3.000
 1U2  C16  C15  C7   120.11  3.000
 1U2  H15  C16  C17  119.00  3.000
 1U2  H15  C16  C15  119.50  3.000
 1U2  C17  C16  C15  121.49  3.000
 1U2  C18  C17  C5   119.48  3.000
 1U2  C5   C17  C16  118.40  3.000
 1U2  C18  C17  C16  122.12  3.000
 1U2  C4   C5   C17  118.50  3.000
 1U2  C4   C5   C6   122.11  3.000
 1U2  C17  C5   C6   119.38  3.000
 1U2  H5   C4   C3   119.99  3.000
 1U2  H5   C4   C5   119.15  3.000
 1U2  C3   C4   C5   120.86  3.000
 1U2  H4   C3   C2   119.70  3.000
 1U2  H4   C3   C4   119.46  3.000
 1U2  C2   C3   C4   120.83  3.000
 1U2  H16  C18  C2   120.39  3.000
 1U2  H16  C18  C17  118.43  3.000
 1U2  C2   C18  C17  121.17  3.000
 1U2  C1   C2   C18  119.92  3.000
 1U2  C1   C2   C3   120.92  3.000
 1U2  C18  C2   C3   119.16  3.000
 1U2  N1   C1   N2   120.51  3.000
 1U2  N2   C1   C2   114.75  3.000
 1U2  N1   C1   C2   124.71  3.000
 1U2  H2   N2   H3   114.10  3.000
 1U2  H2   N2   C1   116.18  3.000
 1U2  H3   N2   C1   118.24  3.000
 1U2  H1   N1   C1   110.62  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
 1U2  CONST_01  C12  C11  C10  C9     0.00   0.0  0
 1U2  CONST_02  C12  C13  C14  C9     0.00   0.0  0
 1U2  CONST_03  C11  C10  C9   C14    0.00   0.0  0
 1U2  CONST_04  C11  C12  C13  C14    0.00   0.0  0
 1U2  CONST_05  C10  C11  C12  C13    0.00   0.0  0
 1U2  CONST_06  C10  C9   C14  C13    0.00   0.0  0
 1U2  CONST_07  C17  C16  C15  C7     0.00   0.0  0
 1U2  CONST_08  C17  C5   C6   C7     0.00   0.0  0
 1U2  CONST_09  C4   C5   C6   C7   180.00   0.0  0
 1U2  CONST_10  C16  C15  C7   C6     0.00   0.0  0
 1U2  CONST_11  C16  C17  C5   C6     0.00   0.0  0
 1U2  CONST_12  C18  C17  C5   C6   180.00   0.0  0
 1U2  CONST_13  C3   C4   C5   C6   180.00   0.0  0
 1U2  CONST_14  C18  C17  C16  C15  180.00   0.0  0
 1U2  CONST_15  C5   C17  C16  C15    0.00   0.0  0
 1U2  CONST_16  C5   C6   C7   C15    0.00   0.0  0
 1U2  CONST_17  C2   C18  C17  C16  180.00   0.0  0
 1U2  CONST_18  C4   C5   C17  C16  180.00   0.0  0
 1U2  CONST_19  C3   C2   C18  C17    0.00   0.0  0
 1U2  CONST_20  C3   C4   C5   C17    0.00   0.0  0
 1U2  CONST_21  C2   C18  C17  C5     0.00   0.0  0
 1U2  CONST_22  C2   C3   C4   C5     0.00   0.0  0
 1U2  CONST_23  C18  C17  C5   C4     0.00   0.0  0
 1U2  CONST_24  C18  C2   C3   C4     0.00   0.0  0
 1U2  CONST_25  C11  C10  C9   N4   180.00   0.0  0
 1U2  CONST_26  C13  C14  C9   N4   180.00   0.0  0
 1U2  CONST_27  C16  C15  C7   N3   180.00   0.0  0
 1U2  CONST_28  C5   C6   C7   N3   180.00   0.0  0
 1U2  CONST_29  C1   C2   C18  C17  180.00   0.0  0
 1U2  CONST_30  C1   C2   C3   C4   180.00   0.0  0
 1U2  CONST_31  H10  C11  C10  C9   180.00   0.0  0
 1U2  CONST_32  H12  C13  C14  C9   180.00   0.0  0
 1U2  CONST_33  H9   C10  C9   C14  180.00   0.0  0
 1U2  CONST_34  H11  C12  C13  C14  180.00   0.0  0
 1U2  CONST_35  H13  C14  C13  C12  180.00   0.0  0
 1U2  CONST_36  H15  C16  C15  C7   180.00   0.0  0
 1U2  CONST_37  H14  C15  C7   C6   180.00   0.0  0
 1U2  CONST_38  H5   C4   C5   C6     0.00   0.0  0
 1U2  CONST_39  H6   C6   C7   C15  180.00   0.0  0
 1U2  CONST_40  H16  C18  C17  C16    0.00   0.0  0
 1U2  CONST_41  H4   C3   C4   C5   180.00   0.0  0
 1U2  CONST_48  C7   N3   C8   O      0.00   0.0  0
 1U2  CONST_49  C9   N4   C8   O      0.00   0.0  0
 1U2  CONST_50  C7   N3   C8   N4   180.00   0.0  0
 1U2  CONST_51  N3   C8   N4   C9   180.00   0.0  0
 1U2  CONST_52  H1   N1   C1   C2     0.00   0.0  0
 1U2  CONST_54  H2   N2   C1   C2   180.00   0.0  0
 1U2  Var_01    N1   C1   C2   C3   144.38  30.0  2

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
 1U2  plan-1  N4   0.020
 1U2  plan-1  C9   0.020
 1U2  plan-1  C14  0.020
 1U2  plan-1  C13  0.020
 1U2  plan-1  C12  0.020
 1U2  plan-1  C11  0.020
 1U2  plan-1  C10  0.020
 1U2  plan-1  H13  0.020
 1U2  plan-1  H12  0.020
 1U2  plan-1  H11  0.020
 1U2  plan-1  H10  0.020
 1U2  plan-1  H9   0.020
 1U2  plan-2  N3   0.020
 1U2  plan-2  C7   0.020
 1U2  plan-2  C6   0.020
 1U2  plan-2  C15  0.020
 1U2  plan-2  C16  0.020
 1U2  plan-2  C17  0.020
 1U2  plan-2  C5   0.020
 1U2  plan-2  C4   0.020
 1U2  plan-2  C3   0.020
 1U2  plan-2  C18  0.020
 1U2  plan-2  C2   0.020
 1U2  plan-2  C1   0.020
 1U2  plan-2  H6   0.020
 1U2  plan-2  H14  0.020
 1U2  plan-2  H15  0.020
 1U2  plan-2  H5   0.020
 1U2  plan-2  H4   0.020
 1U2  plan-2  H16  0.020
 1U2  plan-3  O    0.020
 1U2  plan-3  C8   0.020
 1U2  plan-3  N4   0.020
 1U2  plan-3  C9   0.020
 1U2  plan-3  N3   0.020
 1U2  plan-3  C7   0.020
 1U2  plan-3  H8   0.020
 1U2  plan-3  H7   0.020
 1U2  plan-4  C2   0.020
 1U2  plan-4  C1   0.020
 1U2  plan-4  N2   0.020
 1U2  plan-4  N1   0.020
 1U2  plan-4  H3   0.020
 1U2  plan-4  H2   0.020
 1U2  plan-4  H1   0.020

