# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:26:44 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: N-(7-carbamimidoylnaphthalen-1-yl)-3-hydroxy-2-methylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(O)cccc1C(=O)Nc2cccc3ccc(cc23)C(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
 709  709  N-(7-carbamimidoylnaphthalen-1-yl)-3-hydroxy-2-methylbenzamide  ligand  41  24  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_709
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
 709  C1    C  CR66  0   0.091  -3.1713   1.6954  -0.4745
 709  C2    C  CR16  0  -0.300  -4.3902   1.1236  -0.0458
 709  C3    C  CR16  0  -0.291  -4.4389  -0.1535   0.4367
 709  C4    C  CR6   0   0.055  -3.2629  -0.9354   0.5175
 709  C5    C  CR16  0  -0.347  -2.0710  -0.4064   0.0886
 709  C6    C  CR66  0   0.108  -1.9911   0.9080  -0.4189
 709  C7    C  CR6   0   0.317  -0.7695   1.4814  -0.8732
 709  C8    C  CR16  0  -0.291  -0.7380   2.7765  -1.3210
 709  C9    C  CR16  0  -0.263  -1.9099   3.5560  -1.3443
 709  C10   C  CR16  0  -0.318  -3.1039   3.0275  -0.9406
 709  C11   C  C     0   0.338  -3.2926  -2.3253   1.0536
 709  N12   N  NH2   0  -0.823  -4.3258  -2.5958   1.9039
 709  N13   N  N     0  -0.651  -2.4061  -3.1556   0.6566
 709  N14   N  NH1   0  -0.748   0.3971   0.6932  -0.8683
 709  C15   C  C     0   0.479   1.5480   1.0312  -0.2353
 709  C16   C  CR6   0  -0.081   2.6624   0.0524  -0.4307
 709  O17   O  O     0  -0.453   1.6810   2.0484   0.4203
 709  C18   C  CR16  0  -0.298   3.0003  -0.2991  -1.7373
 709  C19   C  CR16  0  -0.248   4.0884  -1.1229  -1.9676
 709  C20   C  CR16  0  -0.375   4.8310  -1.6012  -0.9014
 709  C21   C  CR6   0   0.341   4.4822  -1.2580   0.4012
 709  C22   C  CR6   0  -0.017   3.3852  -0.4264   0.6649
 709  C23   C  CH3   0  -0.718   3.0296  -0.1146   2.0911
 709  O24   O  OH1   0  -0.626   5.1822  -1.7064   1.4626
 709  H2    H  HCR6  0   0.262  -5.2953   1.7153  -0.1088
 709  H3    H  HCR6  0   0.262  -5.3910  -0.5671   0.7417
 709  H5    H  HCR6  0   0.244  -1.1797  -1.0142   0.1647
 709  H8    H  HCR6  0   0.271   0.1888   3.2013  -1.6816
 709  H9    H  HCR6  0   0.266  -1.8571   4.5754  -1.7027
 709  H10   H  HCR6  0   0.261  -4.0089   3.6210  -0.9749
 709  H121  H  HNH2  0   0.393  -4.3004  -3.4762   2.3943
 709  H122  H  HNH2  0   0.396  -4.7034  -1.8424   2.4552
 709  H13   H  H     0   0.325  -2.5107  -4.0529   1.1228
 709  H14   H  HNH1  0   0.418   0.3526  -0.2141  -1.3083
 709  H18   H  HCR6  0   0.263   2.4303   0.0889  -2.5717
 709  H19   H  HCR6  0   0.265   4.3659  -1.3894  -2.9785
 709  H20   H  HCR6  0   0.274   5.6853  -2.2445  -1.0804
 709  H231  H  HCH3  0   0.251   3.6538   0.6863   2.4921
 709  H232  H  HCH3  0   0.244   1.9942   0.1958   2.2025
 709  H233  H  HCH3  0   0.245   3.1755  -0.9851   2.7287
 709  H24   H  HOH1  0   0.477   5.9029  -2.2775   1.1738

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
 709  C1   C2    aromatic  1.413  0.020  1.413
 709  C1   C6    aromatic  1.420  0.020  1.420
 709  C1   C10   aromatic  1.413  0.020  1.413
 709  C2   C3    aromatic  1.366  0.020  1.366
 709  C2   H2    single    0.930  0.020  1.080
 709  C3   C4    aromatic  1.415  0.020  1.415
 709  C3   H3    single    0.930  0.020  1.080
 709  C4   C5    aromatic  1.373  0.020  1.373
 709  C4   C11   single    1.490  0.020  1.490
 709  C5   C6    aromatic  1.411  0.020  1.411
 709  C5   H5    single    0.930  0.020  1.080
 709  C6   C7    aromatic  1.424  0.020  1.424
 709  C7   C8    aromatic  1.371  0.020  1.371
 709  C7   N14   single    1.408  0.020  1.408
 709  C8   C9    aromatic  1.408  0.020  1.408
 709  C8   H8    single    0.930  0.020  1.080
 709  C9   C10   aromatic  1.367  0.020  1.367
 709  C9   H9    single    0.930  0.020  1.080
 709  C10  H10   single    0.930  0.020  1.080
 709  C11  N12   single    1.365  0.020  1.365
 709  C11  N13   double    1.278  0.020  1.278
 709  N12  H121  single    0.890  0.020  1.040
 709  N12  H122  single    0.890  0.020  1.040
 709  N13  H13   single    0.890  0.020  1.040
 709  N14  C15   single    1.356  0.020  1.356
 709  N14  H14   single    0.860  0.020  1.020
 709  C15  C16   single    1.496  0.020  1.496
 709  C15  O17   double    1.217  0.020  1.217
 709  C16  C18   aromatic  1.395  0.020  1.395
 709  C16  C22   aromatic  1.397  0.020  1.397
 709  C18  C19   aromatic  1.384  0.020  1.384
 709  C18  H18   single    0.930  0.020  1.080
 709  C19  C20   aromatic  1.385  0.020  1.385
 709  C19  H19   single    0.930  0.020  1.080
 709  C20  C21   aromatic  1.391  0.020  1.391
 709  C20  H20   single    0.930  0.020  1.080
 709  C21  C22   aromatic  1.402  0.020  1.402
 709  C21  O24   single    1.348  0.020  1.348
 709  C22  C23   single    1.503  0.020  1.503
 709  C23  H231  single    0.970  0.020  1.090
 709  C23  H232  single    0.970  0.020  1.090
 709  C23  H233  single    0.970  0.020  1.090
 709  O24  H24   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
 709  C10   C1   C6    119.74  3.000
 709  C10   C1   C2    121.52  3.000
 709  C6    C1   C2    118.74  3.000
 709  H2    C2   C3    120.10  3.000
 709  H2    C2   C1    118.82  3.000
 709  C3    C2   C1    121.08  3.000
 709  H3    C3   C4    120.28  3.000
 709  H3    C3   C2    119.23  3.000
 709  C4    C3   C2    120.48  3.000
 709  C11   C4   C5    119.29  3.000
 709  C11   C4   C3    121.30  3.000
 709  C5    C4   C3    119.41  3.000
 709  H5    C5   C6    120.14  3.000
 709  H5    C5   C4    118.49  3.000
 709  C6    C5   C4    121.36  3.000
 709  C7    C6   C5    122.57  3.000
 709  C7    C6   C1    118.51  3.000
 709  C5    C6   C1    118.91  3.000
 709  N14   C7   C8    120.73  3.000
 709  N14   C7   C6    118.97  3.000
 709  C8    C7   C6    120.30  3.000
 709  H8    C8   C9    119.37  3.000
 709  H8    C8   C7    119.99  3.000
 709  C9    C8   C7    120.63  3.000
 709  H9    C9   C10   120.32  3.000
 709  H9    C9   C8    119.12  3.000
 709  C10   C9   C8    120.55  3.000
 709  H10   C10  C9    120.59  3.000
 709  H10   C10  C1    119.16  3.000
 709  C9    C10  C1    120.25  3.000
 709  N13   C11  N12   126.14  3.000
 709  N13   C11  C4    118.72  3.000
 709  N12   C11  C4    115.09  3.000
 709  H122  N12  H121  113.36  3.000
 709  H122  N12  C11   118.46  3.000
 709  H121  N12  C11   117.19  3.000
 709  H13   N13  C11   111.08  3.000
 709  H14   N14  C15   117.70  3.000
 709  H14   N14  C7    117.72  3.000
 709  C15   N14  C7    124.42  3.000
 709  O17   C15  C16   122.38  3.000
 709  O17   C15  N14   123.52  3.000
 709  C16   C15  N14   114.09  3.000
 709  C22   C16  C18   121.54  3.000
 709  C22   C16  C15   120.47  3.000
 709  C18   C16  C15   117.89  3.000
 709  H18   C18  C19   119.94  3.000
 709  H18   C18  C16   120.29  3.000
 709  C19   C18  C16   119.76  3.000
 709  H19   C19  C20   119.80  3.000
 709  H19   C19  C18   120.25  3.000
 709  C20   C19  C18   119.95  3.000
 709  H20   C20  C21   119.90  3.000
 709  H20   C20  C19   120.03  3.000
 709  C21   C20  C19   120.08  3.000
 709  O24   C21  C22   117.10  3.000
 709  O24   C21  C20   121.65  3.000
 709  C22   C21  C20   121.25  3.000
 709  C23   C22  C21   119.14  3.000
 709  C23   C22  C16   123.42  3.000
 709  C21   C22  C16   117.43  3.000
 709  H233  C23  H232  107.22  3.000
 709  H233  C23  H231  107.14  3.000
 709  H232  C23  H231  107.31  3.000
 709  H233  C23  C22   110.99  3.000
 709  H232  C23  C22   112.46  3.000
 709  H231  C23  C22   111.44  3.000
 709  H24   O24  C21   110.46  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
 709  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 709  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 709  CONST_03  C8    C7   C6   C1     0.00   0.0  0
 709  CONST_04  C8    C9   C10  C1     0.00   0.0  0
 709  CONST_05  C5    C6   C1   C2     0.00   0.0  0
 709  CONST_06  C7    C6   C1   C2   180.00   0.0  0
 709  CONST_07  C9    C10  C1   C2   180.00   0.0  0
 709  CONST_08  C5    C4   C3   C2     0.00   0.0  0
 709  CONST_09  C6    C1   C2   C3     0.00   0.0  0
 709  CONST_10  C10   C1   C2   C3   180.00   0.0  0
 709  CONST_11  C6    C5   C4   C3     0.00   0.0  0
 709  CONST_12  C7    C6   C5   C4   180.00   0.0  0
 709  CONST_13  C10   C1   C6   C5   180.00   0.0  0
 709  CONST_14  C8    C7   C6   C5   180.00   0.0  0
 709  CONST_15  C9    C10  C1   C6     0.00   0.0  0
 709  CONST_16  C9    C8   C7   C6     0.00   0.0  0
 709  CONST_17  C10   C1   C6   C7     0.00   0.0  0
 709  CONST_18  C10   C9   C8   C7     0.00   0.0  0
 709  CONST_19  C20   C19  C18  C16    0.00   0.0  0
 709  CONST_20  C20   C21  C22  C16    0.00   0.0  0
 709  CONST_21  C21   C22  C16  C18    0.00   0.0  0
 709  CONST_22  C21   C20  C19  C18    0.00   0.0  0
 709  CONST_23  C22   C16  C18  C19    0.00   0.0  0
 709  CONST_24  C22   C21  C20  C19    0.00   0.0  0
 709  CONST_25  N14   C7   C6   C1   180.00   0.0  0
 709  CONST_26  C11   C4   C3   C2   180.00   0.0  0
 709  CONST_27  N14   C7   C6   C5     0.00   0.0  0
 709  CONST_28  C11   C4   C5   C6   180.00   0.0  0
 709  CONST_29  N14   C7   C8   C9   180.00   0.0  0
 709  CONST_30  C19   C18  C16  C15  180.00   0.0  0
 709  CONST_31  C21   C22  C16  C15  180.00   0.0  0
 709  CONST_32  O24   C21  C22  C16  180.00   0.0  0
 709  CONST_33  C23   C22  C16  C18  180.00   0.0  0
 709  CONST_34  O24   C21  C20  C19  180.00   0.0  0
 709  CONST_35  C23   C22  C21  C20  180.00   0.0  0
 709  CONST_36  H3    C3   C2   C1   180.00   0.0  0
 709  CONST_37  H5    C5   C6   C1   180.00   0.0  0
 709  CONST_38  H9    C9   C10  C1   180.00   0.0  0
 709  CONST_39  H10   C10  C1   C2     0.00   0.0  0
 709  CONST_40  H2    C2   C3   C4   180.00   0.0  0
 709  CONST_41  H8    C8   C7   C6   180.00   0.0  0
 709  CONST_42  H19   C19  C18  C16  180.00   0.0  0
 709  CONST_43  H20   C20  C19  C18  180.00   0.0  0
 709  CONST_44  H18   C18  C19  C20  180.00   0.0  0
 709  CONST_45  C16   C15  N14  C7   180.00   0.0  0
 709  CONST_49  O17   C15  N14  C7     0.00   0.0  0
 709  CONST_50  H121  N12  C11  C4   180.00   0.0  0
 709  CONST_52  H13   N13  C11  C4   180.00   0.0  0
 709  Var_01    N12   C11  C4   C3   -24.44  30.0  2
 709  Var_02    C18   C16  C15  N14   53.02  30.0  2
 709  Var_03    H231  C23  C22  C16  -99.71  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
 709  plan-1  C15   0.020
 709  plan-1  C16   0.020
 709  plan-1  C18   0.020
 709  plan-1  C19   0.020
 709  plan-1  C20   0.020
 709  plan-1  C21   0.020
 709  plan-1  C22   0.020
 709  plan-1  C23   0.020
 709  plan-1  O24   0.020
 709  plan-1  H18   0.020
 709  plan-1  H19   0.020
 709  plan-1  H20   0.020
 709  plan-2  C1    0.020
 709  plan-2  C2    0.020
 709  plan-2  C3    0.020
 709  plan-2  C4    0.020
 709  plan-2  C5    0.020
 709  plan-2  C6    0.020
 709  plan-2  C7    0.020
 709  plan-2  C8    0.020
 709  plan-2  C9    0.020
 709  plan-2  C10   0.020
 709  plan-2  C11   0.020
 709  plan-2  N14   0.020
 709  plan-2  H2    0.020
 709  plan-2  H3    0.020
 709  plan-2  H5    0.020
 709  plan-2  H8    0.020
 709  plan-2  H9    0.020
 709  plan-2  H10   0.020
 709  plan-3  C7    0.020
 709  plan-3  N14   0.020
 709  plan-3  C15   0.020
 709  plan-3  C16   0.020
 709  plan-3  O17   0.020
 709  plan-3  H14   0.020
 709  plan-4  C4    0.020
 709  plan-4  C11   0.020
 709  plan-4  N12   0.020
 709  plan-4  N13   0.020
 709  plan-4  H121  0.020
 709  plan-4  H122  0.020
 709  plan-4  H13   0.020

