# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 05:52:04 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: ~{N}-(4-carbamimidoylphenyl)-3-ethoxy-2-oxidanyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1cccc(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
 J2Q  J2Q  ~{N}-(4-carbamimidoylphenyl)-3-ethoxy-2-oxidanyl-benzamide  ligand  39  22  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J2Q
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
 J2Q  C10  C  CR16  0  -0.380   4.3281   1.4920  -0.3344
 J2Q  C17  C  C     0   0.625   0.3889  -0.1576  -0.2140
 J2Q  C21  C  CR6   0   0.377  -2.0263   0.3613  -0.1675
 J2Q  C22  C  CR16  0  -0.286  -2.5607  -0.8406  -0.6324
 J2Q  C24  C  CR16  0  -0.284  -3.9287  -1.0490  -0.5742
 J2Q  C26  C  CR6   0  -0.005  -4.7946  -0.0898  -0.0569
 J2Q  C01  C  CH3   0  -0.682   7.3693  -1.4644   0.4329
 J2Q  C05  C  CH2   0  -0.190   6.4710  -0.2816   0.1608
 J2Q  O08  O  O2    0  -0.465   5.1251  -0.7376   0.1724
 J2Q  C09  C  CR6   0   0.337   4.1457   0.1488  -0.0713
 J2Q  C12  C  CR16  0  -0.255   3.2294   2.3188  -0.5842
 J2Q  C14  C  CR16  0  -0.327   1.9554   1.8080  -0.5549
 J2Q  C16  C  CR6   0  -0.193   1.7383   0.4484  -0.2735
 J2Q  O18  O  O     0  -0.515   0.2438  -1.3816  -0.1492
 J2Q  N19  N  NH1   0  -0.769  -0.6657   0.6857  -0.2165
 J2Q  C27  C  CR16  0  -0.268  -4.2509   1.1087   0.4004
 J2Q  C29  C  CR16  0  -0.334  -2.8882   1.3326   0.3420
 J2Q  C31  C  C     0   0.329  -6.2609  -0.3440  -0.0222
 J2Q  N32  N  NH2   0  -0.804  -6.9200   0.2432   1.0175
 J2Q  N35  N  N     0  -0.642  -6.9039  -1.0176  -0.8979
 J2Q  C37  C  CR6   0   0.269   2.8396  -0.3909  -0.0525
 J2Q  O38  O  OH1   0  -0.620   2.7369  -1.6960   0.1874
 J2Q  H1   H  HCR6  0   0.289   5.3208   1.9202  -0.3606
 J2Q  H2   H  HCR6  0   0.280  -1.9330  -1.6133  -1.0457
 J2Q  H3   H  HCR6  0   0.266  -4.3180  -1.9940  -0.9318
 J2Q  H4   H  HCH3  0   0.238   8.4075  -1.1335   0.4323
 J2Q  H5   H  HCH3  0   0.236   7.1602  -1.9103   1.4052
 J2Q  H6   H  HCH3  0   0.236   7.2607  -2.2307  -0.3343
 J2Q  H7   H  HCH2  0   0.225   6.6133   0.4924   0.9227
 J2Q  H8   H  HCH2  0   0.225   6.7112   0.1635  -0.8109
 J2Q  H9   H  HCR6  0   0.265   3.3915   3.3646  -0.8047
 J2Q  H10  H  HCR6  0   0.257   1.1312   2.4733  -0.7754
 J2Q  H11  H  HNH1  0   0.431  -0.4690   1.6680  -0.1071
 J2Q  H12  H  HCR6  0   0.268  -4.8899   1.8876   0.7957
 J2Q  H13  H  HCR6  0   0.278  -2.4886   2.2745   0.6980
 J2Q  H14  H  HNH2  0   0.392  -6.4228   0.3756   1.8824
 J2Q  H15  H  HNH2  0   0.384  -7.8861  -0.0191   1.1342
 J2Q  H16  H  H     0   0.332  -6.2948  -1.2947  -1.6586
 J2Q  H17  H  HOH1  0   0.480   1.7789  -1.9210   0.1104

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
 J2Q  N35  C31  double    1.278  0.020  1.278
 J2Q  C31  N32  single    1.364  0.020  1.364
 J2Q  C31  C26  single    1.489  0.020  1.489
 J2Q  C24  C26  aromatic  1.392  0.020  1.392
 J2Q  C24  C22  aromatic  1.385  0.020  1.385
 J2Q  C26  C27  aromatic  1.393  0.020  1.393
 J2Q  C22  C21  aromatic  1.395  0.020  1.395
 J2Q  C27  C29  aromatic  1.382  0.020  1.382
 J2Q  C21  C29  aromatic  1.395  0.020  1.395
 J2Q  C21  N19  single    1.400  0.020  1.400
 J2Q  N19  C17  single    1.350  0.020  1.350
 J2Q  O38  C37  single    1.331  0.020  1.331
 J2Q  C17  O18  double    1.234  0.020  1.234
 J2Q  C17  C16  single    1.480  0.020  1.480
 J2Q  C37  C16  aromatic  1.402  0.020  1.402
 J2Q  C37  C09  aromatic  1.413  0.020  1.413
 J2Q  O08  C05  single    1.421  0.020  1.421
 J2Q  O08  C09  single    1.343  0.020  1.343
 J2Q  C05  C01  single    1.510  0.020  1.510
 J2Q  C16  C14  aromatic  1.405  0.020  1.405
 J2Q  C09  C10  aromatic  1.381  0.020  1.381
 J2Q  C14  C12  aromatic  1.373  0.020  1.373
 J2Q  C10  C12  aromatic  1.398  0.020  1.398
 J2Q  C10  H1   single    0.930  0.020  1.080
 J2Q  C22  H2   single    0.930  0.020  1.080
 J2Q  C24  H3   single    0.930  0.020  1.080
 J2Q  C01  H4   single    0.970  0.020  1.090
 J2Q  C01  H5   single    0.970  0.020  1.090
 J2Q  C01  H6   single    0.970  0.020  1.090
 J2Q  C05  H7   single    0.970  0.020  1.090
 J2Q  C05  H8   single    0.970  0.020  1.090
 J2Q  C12  H9   single    0.930  0.020  1.080
 J2Q  C14  H10  single    0.930  0.020  1.080
 J2Q  N19  H11  single    0.860  0.020  1.020
 J2Q  C27  H12  single    0.930  0.020  1.080
 J2Q  C29  H13  single    0.930  0.020  1.080
 J2Q  N32  H14  single    0.890  0.020  1.040
 J2Q  N32  H15  single    0.890  0.020  1.040
 J2Q  N35  H16  single    0.890  0.020  1.040
 J2Q  O38  H17  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
 J2Q  H1   C10  C12  118.89  3.000
 J2Q  H1   C10  C09  120.73  3.000
 J2Q  C12  C10  C09  120.38  3.000
 J2Q  N19  C17  O18  121.85  3.000
 J2Q  O18  C17  C16  121.01  3.000
 J2Q  N19  C17  C16  117.14  3.000
 J2Q  C29  C21  N19  116.88  3.000
 J2Q  N19  C21  C22  124.09  3.000
 J2Q  C29  C21  C22  119.00  3.000
 J2Q  H2   C22  C24  118.91  3.000
 J2Q  H2   C22  C21  121.48  3.000
 J2Q  C24  C22  C21  119.60  3.000
 J2Q  H3   C24  C26  120.03  3.000
 J2Q  H3   C24  C22  118.20  3.000
 J2Q  C26  C24  C22  121.77  3.000
 J2Q  C31  C26  C27  121.58  3.000
 J2Q  C27  C26  C24  118.16  3.000
 J2Q  C31  C26  C24  120.26  3.000
 J2Q  H6   C01  H5   108.73  3.000
 J2Q  H6   C01  H4   107.94  3.000
 J2Q  H5   C01  H4   107.91  3.000
 J2Q  H6   C01  C05  111.39  3.000
 J2Q  H5   C01  C05  111.54  3.000
 J2Q  H4   C01  C05  109.20  3.000
 J2Q  H8   C05  H7   107.54  3.000
 J2Q  H8   C05  O08  110.20  3.000
 J2Q  H7   C05  O08  110.13  3.000
 J2Q  H8   C05  C01  110.34  3.000
 J2Q  H7   C05  C01  110.54  3.000
 J2Q  O08  C05  C01  108.09  3.000
 J2Q  C09  O08  C05  118.51  3.000
 J2Q  C37  C09  O08  114.80  3.000
 J2Q  O08  C09  C10  125.46  3.000
 J2Q  C37  C09  C10  119.74  3.000
 J2Q  H9   C12  C14  120.23  3.000
 J2Q  H9   C12  C10  119.40  3.000
 J2Q  C14  C12  C10  120.37  3.000
 J2Q  H10  C14  C16  121.20  3.000
 J2Q  H10  C14  C12  118.28  3.000
 J2Q  C16  C14  C12  120.50  3.000
 J2Q  C37  C16  C14  119.30  3.000
 J2Q  C14  C16  C17  123.02  3.000
 J2Q  C37  C16  C17  117.68  3.000
 J2Q  H11  N19  C21  114.32  3.000
 J2Q  H11  N19  C17  117.14  3.000
 J2Q  C21  N19  C17  127.91  3.000
 J2Q  H12  C27  C29  118.75  3.000
 J2Q  H12  C27  C26  120.56  3.000
 J2Q  C29  C27  C26  120.68  3.000
 J2Q  H13  C29  C27  119.38  3.000
 J2Q  H13  C29  C21  119.84  3.000
 J2Q  C27  C29  C21  120.78  3.000
 J2Q  N35  C31  N32  120.40  3.000
 J2Q  N32  C31  C26  114.85  3.000
 J2Q  N35  C31  C26  124.71  3.000
 J2Q  H15  N32  H14  114.10  3.000
 J2Q  H15  N32  C31  116.07  3.000
 J2Q  H14  N32  C31  118.23  3.000
 J2Q  H16  N35  C31  110.86  3.000
 J2Q  O38  C37  C16  123.69  3.000
 J2Q  C16  C37  C09  119.68  3.000
 J2Q  O38  C37  C09  116.63  3.000
 J2Q  H17  O38  C37  106.52  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
 J2Q  CONST_01  C16  C37  C09  C10     0.00   0.0  0
 J2Q  CONST_02  C16  C14  C12  C10     0.00   0.0  0
 J2Q  CONST_03  C26  C24  C22  C21     0.00   0.0  0
 J2Q  CONST_04  C26  C27  C29  C21     0.00   0.0  0
 J2Q  CONST_05  C27  C26  C24  C22     0.00   0.0  0
 J2Q  CONST_06  C27  C29  C21  C22     0.00   0.0  0
 J2Q  CONST_07  C29  C27  C26  C24     0.00   0.0  0
 J2Q  CONST_08  C29  C21  C22  C24     0.00   0.0  0
 J2Q  CONST_09  C14  C16  C37  C09     0.00   0.0  0
 J2Q  CONST_10  C14  C12  C10  C09     0.00   0.0  0
 J2Q  CONST_11  C37  C16  C14  C12     0.00   0.0  0
 J2Q  CONST_12  C37  C09  C10  C12     0.00   0.0  0
 J2Q  CONST_13  O38  C37  C09  C10   180.00   0.0  0
 J2Q  CONST_14  C09  C37  C16  C17   180.00   0.0  0
 J2Q  CONST_15  C12  C14  C16  C17   180.00   0.0  0
 J2Q  CONST_16  C31  C26  C24  C22   180.00   0.0  0
 J2Q  CONST_17  N19  C21  C22  C24   180.00   0.0  0
 J2Q  CONST_18  C16  C37  C09  O08   180.00   0.0  0
 J2Q  CONST_19  C12  C10  C09  O08   180.00   0.0  0
 J2Q  CONST_20  O38  C37  C16  C14   180.00   0.0  0
 J2Q  CONST_21  C27  C29  C21  N19   180.00   0.0  0
 J2Q  CONST_22  C31  C26  C27  C29   180.00   0.0  0
 J2Q  CONST_23  H10  C14  C12  C10   180.00   0.0  0
 J2Q  CONST_24  H3   C24  C22  C21   180.00   0.0  0
 J2Q  CONST_25  H12  C27  C29  C21   180.00   0.0  0
 J2Q  CONST_26  H13  C29  C21  C22   180.00   0.0  0
 J2Q  CONST_27  H2   C22  C24  C26   180.00   0.0  0
 J2Q  CONST_28  H9   C12  C10  C09   180.00   0.0  0
 J2Q  CONST_29  H1   C10  C12  C14   180.00   0.0  0
 J2Q  CONST_30  C16  C17  N19  C21   180.00   0.0  0
 J2Q  CONST_34  O18  C17  N19  C21     0.00   0.0  0
 J2Q  CONST_35  H16  N35  C31  C26     0.00   0.0  0
 J2Q  CONST_37  H15  N32  C31  C26   180.00   0.0  0
 J2Q  Var_01    N35  C31  C26  C24   -33.56  30.0  2
 J2Q  Var_02    C37  C09  O08  C05   179.45  30.0  2
 J2Q  Var_03    N19  C17  C16  C14   -10.98  30.0  2
 J2Q  Var_04    H7   C05  O08  C09    60.24  30.0  3
 J2Q  Var_05    H4   C01  C05  O08  -179.76  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
 J2Q  plan-1  C21  0.020
 J2Q  plan-1  C22  0.020
 J2Q  plan-1  C24  0.020
 J2Q  plan-1  C26  0.020
 J2Q  plan-1  N19  0.020
 J2Q  plan-1  C27  0.020
 J2Q  plan-1  C29  0.020
 J2Q  plan-1  C31  0.020
 J2Q  plan-1  H2   0.020
 J2Q  plan-1  H3   0.020
 J2Q  plan-1  H12  0.020
 J2Q  plan-1  H13  0.020
 J2Q  plan-2  C10  0.020
 J2Q  plan-2  C17  0.020
 J2Q  plan-2  O08  0.020
 J2Q  plan-2  C09  0.020
 J2Q  plan-2  C12  0.020
 J2Q  plan-2  C14  0.020
 J2Q  plan-2  C16  0.020
 J2Q  plan-2  C37  0.020
 J2Q  plan-2  O38  0.020
 J2Q  plan-2  H1   0.020
 J2Q  plan-2  H9   0.020
 J2Q  plan-2  H10  0.020
 J2Q  plan-3  C17  0.020
 J2Q  plan-3  C21  0.020
 J2Q  plan-3  C16  0.020
 J2Q  plan-3  O18  0.020
 J2Q  plan-3  N19  0.020
 J2Q  plan-3  H11  0.020
 J2Q  plan-4  C26  0.020
 J2Q  plan-4  C31  0.020
 J2Q  plan-4  N32  0.020
 J2Q  plan-4  N35  0.020
 J2Q  plan-4  H14  0.020
 J2Q  plan-4  H15  0.020
 J2Q  plan-4  H16  0.020

