# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 13:11:36 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: ~{N}-(4-carbamimidoylphenyl)-3-methoxy-2-oxidanyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1O)C(=O)Nc2ccc(cc2)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
 J2W  J2W  ~{N}-(4-carbamimidoylphenyl)-3-methoxy-2-oxidanyl-benzamide  ligand  36  21  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_J2W
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
 J2W  C13  C  CR6   0  -0.180  -2.0779  -0.1941  -0.4150
 J2W  C21  C  CR16  0  -0.278   3.7687  -1.1613   0.7118
 J2W  C24  C  CR16  0  -0.272   3.6921   0.9163  -0.4608
 J2W  C26  C  CR16  0  -0.303   2.3082   0.8529  -0.5221
 J2W  C28  C  C     0   0.329   5.9332  -0.0292   0.1817
 J2W  C01  C  CH3   0  -0.433  -6.7428   0.3833   0.5085
 J2W  O05  O  O2    0  -0.491  -5.4080   0.8496   0.4589
 J2W  C06  C  CR6   0   0.314  -4.4474   0.0167   0.0101
 J2W  C07  C  CR16  0  -0.374  -4.6459  -1.2804  -0.4279
 J2W  C09  C  CR16  0  -0.261  -3.5624  -2.0420  -0.8605
 J2W  C11  C  CR16  0  -0.289  -2.2912  -1.5075  -0.8486
 J2W  C14  C  C     0   0.530  -0.7107   0.4026  -0.4760
 J2W  O15  O  O     0  -0.448  -0.4975   1.4992  -0.9564
 J2W  N16  N  NH1   0  -0.744   0.2564  -0.4083   0.0330
 J2W  C18  C  CR6   0   0.381   1.6394  -0.2335   0.0441
 J2W  C19  C  CR16  0  -0.343   2.3920  -1.2356   0.6651
 J2W  C23  C  CR6   0  -0.006   4.4468  -0.0818   0.1477
 J2W  N29  N  NH2   0  -0.806   6.4649   1.2267   0.2106
 J2W  N32  N  N     0  -0.643   6.6982  -1.0531   0.1419
 J2W  C34  C  CR6   0   0.276  -3.1549   0.5743   0.0127
 J2W  O35  O  OH1   0  -0.611  -2.9556   1.8262   0.4520
 J2W  H1   H  HCR6  0   0.265   4.3159  -1.9511   1.2107
 J2W  H2   H  HCR6  0   0.264   4.1847   1.7625  -0.9214
 J2W  H3   H  HCR6  0   0.286   1.7697   1.6468  -1.0111
 J2W  H4   H  HCH3  0   0.265  -7.3406   1.2005   0.9028
 J2W  H5   H  HCH3  0   0.234  -7.1161   0.1194  -0.4840
 J2W  H6   H  HCH3  0   0.234  -6.8436  -0.4817   1.1682
 J2W  H7   H  HCR6  0   0.289  -5.6372  -1.7131  -0.4412
 J2W  H8   H  HCR6  0   0.263  -3.7270  -3.0517  -1.2101
 J2W  H9   H  HCR6  0   0.268  -1.4570  -2.0989  -1.2041
 J2W  H10  H  HNH1  0   0.424  -0.0651  -1.2533   0.4816
 J2W  H11  H  HCR6  0   0.276   1.8901  -2.0831   1.1161
 J2W  H12  H  HNH2  0   0.392   5.9445   1.9540   0.6722
 J2W  H13  H  HNH2  0   0.384   7.4614   1.2811   0.3508
 J2W  H14  H  H     0   0.331   6.1581  -1.9006   0.0133
 J2W  H15  H  HOH1  0   0.477  -3.7940   2.2072   0.7437

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
 J2W  N32  C28  double    1.279  0.020  1.279
 J2W  C28  N29  single    1.364  0.020  1.364
 J2W  C28  C23  single    1.488  0.020  1.488
 J2W  C21  C23  aromatic  1.394  0.020  1.394
 J2W  C21  C19  aromatic  1.379  0.020  1.379
 J2W  C23  C24  aromatic  1.391  0.020  1.391
 J2W  C19  C18  aromatic  1.399  0.020  1.399
 J2W  C24  C26  aromatic  1.387  0.020  1.387
 J2W  C18  C26  aromatic  1.396  0.020  1.396
 J2W  C18  N16  single    1.394  0.020  1.394
 J2W  N16  C14  single    1.361  0.020  1.361
 J2W  O35  C34  single    1.342  0.020  1.342
 J2W  C14  O15  double    1.216  0.020  1.216
 J2W  C14  C13  single    1.493  0.020  1.493
 J2W  C34  C13  aromatic  1.391  0.020  1.391
 J2W  C34  C06  aromatic  1.408  0.020  1.408
 J2W  O05  C01  single    1.415  0.020  1.415
 J2W  O05  C06  single    1.348  0.020  1.348
 J2W  C13  C11  aromatic  1.399  0.020  1.399
 J2W  C06  C07  aromatic  1.383  0.020  1.383
 J2W  C11  C09  aromatic  1.379  0.020  1.379
 J2W  C07  C09  aromatic  1.393  0.020  1.393
 J2W  C21  H1   single    0.930  0.020  1.080
 J2W  C24  H2   single    0.930  0.020  1.080
 J2W  C26  H3   single    0.930  0.020  1.080
 J2W  C01  H4   single    0.970  0.020  1.090
 J2W  C01  H5   single    0.970  0.020  1.090
 J2W  C01  H6   single    0.970  0.020  1.090
 J2W  C07  H7   single    0.930  0.020  1.080
 J2W  C09  H8   single    0.930  0.020  1.080
 J2W  C11  H9   single    0.930  0.020  1.080
 J2W  N16  H10  single    0.860  0.020  1.020
 J2W  C19  H11  single    0.930  0.020  1.080
 J2W  N29  H12  single    0.890  0.020  1.040
 J2W  N29  H13  single    0.890  0.020  1.040
 J2W  N32  H14  single    0.890  0.020  1.040
 J2W  O35  H15  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
 J2W  C34  C13  C14  120.06  3.000
 J2W  C34  C13  C11  119.73  3.000
 J2W  C14  C13  C11  120.14  3.000
 J2W  H1   C21  C23  120.37  3.000
 J2W  H1   C21  C19  118.73  3.000
 J2W  C23  C21  C19  120.90  3.000
 J2W  H2   C24  C23  120.01  3.000
 J2W  H2   C24  C26  118.11  3.000
 J2W  C23  C24  C26  121.86  3.000
 J2W  H3   C26  C18  121.24  3.000
 J2W  H3   C26  C24  119.04  3.000
 J2W  C18  C26  C24  119.72  3.000
 J2W  N32  C28  N29  120.31  3.000
 J2W  N29  C28  C23  114.99  3.000
 J2W  N32  C28  C23  124.66  3.000
 J2W  H6   C01  H5   109.00  3.000
 J2W  H6   C01  H4   109.00  3.000
 J2W  H5   C01  H4   108.86  3.000
 J2W  H6   C01  O05  111.66  3.000
 J2W  H5   C01  O05  111.72  3.000
 J2W  H4   C01  O05  106.49  3.000
 J2W  C06  O05  C01  118.70  3.000
 J2W  C34  C06  C07  120.25  3.000
 J2W  C07  C06  O05  125.62  3.000
 J2W  C34  C06  O05  114.13  3.000
 J2W  H7   C07  C09  119.36  3.000
 J2W  H7   C07  C06  120.70  3.000
 J2W  C09  C07  C06  119.95  3.000
 J2W  H8   C09  C11  120.33  3.000
 J2W  H8   C09  C07  119.51  3.000
 J2W  C11  C09  C07  120.16  3.000
 J2W  H9   C11  C09  119.72  3.000
 J2W  H9   C11  C13  119.80  3.000
 J2W  C09  C11  C13  120.46  3.000
 J2W  N16  C14  O15  124.09  3.000
 J2W  O15  C14  C13  122.49  3.000
 J2W  N16  C14  C13  113.41  3.000
 J2W  H10  N16  C18  114.67  3.000
 J2W  H10  N16  C14  116.03  3.000
 J2W  C18  N16  C14  129.29  3.000
 J2W  C19  C18  N16  116.58  3.000
 J2W  N16  C18  C26  124.73  3.000
 J2W  C19  C18  C26  118.69  3.000
 J2W  H11  C19  C18  119.74  3.000
 J2W  H11  C19  C21  119.37  3.000
 J2W  C18  C19  C21  120.89  3.000
 J2W  C28  C23  C24  121.78  3.000
 J2W  C24  C23  C21  117.94  3.000
 J2W  C28  C23  C21  120.27  3.000
 J2W  H13  N29  H12  114.12  3.000
 J2W  H13  N29  C28  115.98  3.000
 J2W  H12  N29  C28  118.26  3.000
 J2W  H14  N32  C28  110.78  3.000
 J2W  O35  C34  C06  120.44  3.000
 J2W  C06  C34  C13  119.45  3.000
 J2W  O35  C34  C13  120.09  3.000
 J2W  H15  O35  C34  109.75  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
 J2W  CONST_01  C07  C06  C34  C13     0.00   0.0  0
 J2W  CONST_02  C07  C09  C11  C13     0.00   0.0  0
 J2W  CONST_03  C26  C24  C23  C21     0.00   0.0  0
 J2W  CONST_04  C26  C18  C19  C21     0.00   0.0  0
 J2W  CONST_05  C19  C21  C23  C24     0.00   0.0  0
 J2W  CONST_06  C19  C18  C26  C24     0.00   0.0  0
 J2W  CONST_07  C11  C13  C34  C06     0.00   0.0  0
 J2W  CONST_08  C11  C09  C07  C06     0.00   0.0  0
 J2W  CONST_09  C34  C13  C11  C09     0.00   0.0  0
 J2W  CONST_10  C34  C06  C07  C09     0.00   0.0  0
 J2W  CONST_11  C23  C21  C19  C18     0.00   0.0  0
 J2W  CONST_12  C23  C24  C26  C18     0.00   0.0  0
 J2W  CONST_13  O05  C06  C34  C13   180.00   0.0  0
 J2W  CONST_14  N16  C18  C19  C21   180.00   0.0  0
 J2W  CONST_15  N16  C18  C26  C24   180.00   0.0  0
 J2W  CONST_16  C28  C23  C24  C26   180.00   0.0  0
 J2W  CONST_17  C19  C21  C23  C28   180.00   0.0  0
 J2W  CONST_18  C09  C07  C06  O05   180.00   0.0  0
 J2W  CONST_19  C14  C13  C34  C06   180.00   0.0  0
 J2W  CONST_20  O35  C34  C06  C07   180.00   0.0  0
 J2W  CONST_21  C14  C13  C11  C09   180.00   0.0  0
 J2W  CONST_22  O35  C34  C13  C11   180.00   0.0  0
 J2W  CONST_23  H8   C09  C11  C13   180.00   0.0  0
 J2W  CONST_24  H2   C24  C23  C21   180.00   0.0  0
 J2W  CONST_25  H1   C21  C23  C24   180.00   0.0  0
 J2W  CONST_26  H11  C19  C18  C26   180.00   0.0  0
 J2W  CONST_27  H9   C11  C09  C07   180.00   0.0  0
 J2W  CONST_28  H7   C07  C09  C11   180.00   0.0  0
 J2W  CONST_29  H3   C26  C18  C19   180.00   0.0  0
 J2W  CONST_30  C18  N16  C14  C13   180.00   0.0  0
 J2W  CONST_31  C14  N16  C18  C26     0.00   0.0  0
 J2W  CONST_32  C19  C18  N16  C14   180.00   0.0  0
 J2W  CONST_33  H10  N16  C18  C26   180.00   0.0  0
 J2W  CONST_34  C18  N16  C14  O15     0.00   0.0  0
 J2W  CONST_35  H14  N32  C28  C23     0.00   0.0  0
 J2W  CONST_37  H13  N29  C28  C23   180.00   0.0  0
 J2W  Var_01    N32  C28  C23  C21    31.90  30.0  2
 J2W  Var_02    C34  C06  O05  C01  -179.45  30.0  2
 J2W  Var_03    N16  C14  C13  C11   -47.66  30.0  2
 J2W  Var_04    H4   C01  O05  C06   179.52  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
 J2W  plan-1  C21  0.020
 J2W  plan-1  C24  0.020
 J2W  plan-1  C26  0.020
 J2W  plan-1  C28  0.020
 J2W  plan-1  N16  0.020
 J2W  plan-1  C18  0.020
 J2W  plan-1  C19  0.020
 J2W  plan-1  C23  0.020
 J2W  plan-1  H1   0.020
 J2W  plan-1  H2   0.020
 J2W  plan-1  H3   0.020
 J2W  plan-1  H11  0.020
 J2W  plan-2  C13  0.020
 J2W  plan-2  O05  0.020
 J2W  plan-2  C06  0.020
 J2W  plan-2  C07  0.020
 J2W  plan-2  C09  0.020
 J2W  plan-2  C11  0.020
 J2W  plan-2  C14  0.020
 J2W  plan-2  C34  0.020
 J2W  plan-2  O35  0.020
 J2W  plan-2  H7   0.020
 J2W  plan-2  H8   0.020
 J2W  plan-2  H9   0.020
 J2W  plan-3  C13  0.020
 J2W  plan-3  C14  0.020
 J2W  plan-3  O15  0.020
 J2W  plan-3  N16  0.020
 J2W  plan-3  C18  0.020
 J2W  plan-3  H10  0.020
 J2W  plan-4  C28  0.020
 J2W  plan-4  C23  0.020
 J2W  plan-4  N29  0.020
 J2W  plan-4  N32  0.020
 J2W  plan-4  H12  0.020
 J2W  plan-4  H13  0.020
 J2W  plan-4  H14  0.020

