# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 05:26:21 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: N-(3,5-dimethoxyphenyl)imidodicarbonimidic diamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(NC(=N)NC(N)=N)cc(OC)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
 RJ6  RJ6  'N-(3,5-dimethoxyphenyl)imidodicarbonimidic diamide'  ligand  32  17  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RJ6
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
 RJ6  C1    C  CR6   0   0.430   2.4734   0.8978  -0.2834
 RJ6  C2    C  CR16  0  -0.552   2.5319  -0.4687  -0.0099
 RJ6  C3    C  CR6   0   0.438   1.3804  -1.1066   0.4491
 RJ6  C4    C  CR16  0  -0.451   0.1914  -0.4061   0.6331
 RJ6  C5    C  CR6   0   0.371   0.1464   0.9526   0.3287
 RJ6  C6    C  CR16  0  -0.458   1.2875   1.6076  -0.1273
 RJ6  O7    O  O2    0  -0.474   3.5257   1.6082  -0.7267
 RJ6  C8    C  CH3   0  -0.439   4.7533   0.9440  -0.9550
 RJ6  O9    O  O2    0  -0.474   1.3371  -2.4138   0.7621
 RJ6  C10   C  CH3   0  -0.439   2.5127  -3.1887   0.6322
 RJ6  N11   N  NH1   0  -0.774  -1.0129   1.7064   0.5063
 RJ6  C12   C  C     0   0.574  -2.3364   1.3006   0.4140
 RJ6  N13   N  NH1   0  -0.697  -2.5116   0.2456  -0.4556
 RJ6  C14   C  C     0   0.548  -3.5793  -0.6329  -0.5636
 RJ6  N15   N  NH2   0  -0.841  -3.2550  -1.6892  -1.3889
 RJ6  N16   N  N     0  -0.644  -3.2977   1.8797   1.0118
 RJ6  N17   N  N     0  -0.653  -4.7054  -0.4173  -0.0128
 RJ6  H2    H  HCR6  0   0.300   3.4492  -1.0223  -0.1472
 RJ6  H4    H  HCR6  0   0.274  -0.6676  -0.9222   1.0397
 RJ6  H6    H  HCR6  0   0.268   1.2557   2.6621  -0.3719
 RJ6  H8    H  HCH3  0   0.262   5.4426   1.6943  -1.3341
 RJ6  H8A   H  HCH3  0   0.230   5.1659   0.5200  -0.0363
 RJ6  H8B   H  HCH3  0   0.230   4.6549   0.1488  -1.6977
 RJ6  H10   H  HCH3  0   0.230   2.8629  -3.2299  -0.4022
 RJ6  H10A  H  HCH3  0   0.230   3.3216  -2.8140   1.2644
 RJ6  H10B  H  HCH3  0   0.262   2.2550  -4.1946   0.9540
 RJ6  HN11  H  HNH1  0   0.407  -0.8807   2.6814   0.7244
 RJ6  HN13  H  HNH1  0   0.413  -1.7409   0.0614  -1.0786
 RJ6  HN15  H  HNH2  0   0.386  -2.3164  -2.0535  -1.3222
 RJ6  HN1A  H  HNH2  0   0.392  -3.9391  -2.4274  -1.4308
 RJ6  HN16  H  H     0   0.328  -2.9297   2.5752   1.6518
 RJ6  HN17  H  H     0   0.324  -5.3205  -1.2086  -0.1680

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
 RJ6  C6   C1    aromatic  1.391  0.020  1.391
 RJ6  C1   C2    aromatic  1.395  0.020  1.395
 RJ6  C1   O7    single    1.345  0.020  1.345
 RJ6  C3   C2    aromatic  1.394  0.020  1.394
 RJ6  C2   H2    single    0.930  0.020  1.080
 RJ6  C4   C3    aromatic  1.392  0.020  1.392
 RJ6  C3   O9    single    1.345  0.020  1.345
 RJ6  C5   C4    aromatic  1.393  0.020  1.393
 RJ6  C4   H4    single    0.930  0.020  1.080
 RJ6  N11  C5    single    1.394  0.020  1.394
 RJ6  C5   C6    aromatic  1.393  0.020  1.393
 RJ6  C6   H6    single    0.930  0.020  1.080
 RJ6  C8   O7    single    1.414  0.020  1.414
 RJ6  C8   H8    single    0.970  0.020  1.090
 RJ6  C8   H8A   single    0.970  0.020  1.090
 RJ6  C8   H8B   single    0.970  0.020  1.090
 RJ6  C10  O9    single    1.414  0.020  1.414
 RJ6  C10  H10   single    0.970  0.020  1.090
 RJ6  C10  H10A  single    0.970  0.020  1.090
 RJ6  C10  H10B  single    0.970  0.020  1.090
 RJ6  C12  N11   single    1.387  0.020  1.387
 RJ6  N11  HN11  single    0.860  0.020  1.020
 RJ6  N13  C12   single    1.378  0.020  1.378
 RJ6  C12  N16   double    1.272  0.020  1.272
 RJ6  C14  N13   single    1.387  0.020  1.387
 RJ6  N13  HN13  single    0.860  0.020  1.020
 RJ6  N17  C14   double    1.272  0.020  1.272
 RJ6  C14  N15   single    1.379  0.020  1.379
 RJ6  N15  HN15  single    0.890  0.020  1.040
 RJ6  N15  HN1A  single    0.890  0.020  1.040
 RJ6  N16  HN16  single    0.890  0.020  1.040
 RJ6  N17  HN17  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
 RJ6  O7    C1   C6    115.76  3.000
 RJ6  O7    C1   C2    123.32  3.000
 RJ6  C6    C1   C2    120.91  3.000
 RJ6  H2    C2   C3    120.59  3.000
 RJ6  H2    C2   C1    120.85  3.000
 RJ6  C3    C2   C1    118.57  3.000
 RJ6  O9    C3   C4    115.52  3.000
 RJ6  O9    C3   C2    123.23  3.000
 RJ6  C4    C3   C2    121.25  3.000
 RJ6  H4    C4   C5    121.46  3.000
 RJ6  H4    C4   C3    119.21  3.000
 RJ6  C5    C4   C3    119.30  3.000
 RJ6  N11   C5   C6    117.96  3.000
 RJ6  C6    C5   C4    120.25  3.000
 RJ6  N11   C5   C4    121.76  3.000
 RJ6  H6    C6   C5    120.52  3.000
 RJ6  H6    C6   C1    119.78  3.000
 RJ6  C5    C6   C1    119.70  3.000
 RJ6  C8    O7   C1    118.97  3.000
 RJ6  H8B   C8   H8A   108.85  3.000
 RJ6  H8B   C8   H8    108.81  3.000
 RJ6  H8A   C8   H8    108.76  3.000
 RJ6  H8B   C8   O7    111.92  3.000
 RJ6  H8A   C8   O7    111.98  3.000
 RJ6  H8    C8   O7    106.41  3.000
 RJ6  C10   O9   C3    118.98  3.000
 RJ6  H10B  C10  H10A  108.75  3.000
 RJ6  H10B  C10  H10   108.74  3.000
 RJ6  H10A  C10  H10   108.86  3.000
 RJ6  H10B  C10  O9    106.43  3.000
 RJ6  H10A  C10  O9    111.98  3.000
 RJ6  H10   C10  O9    111.97  3.000
 RJ6  HN11  N11  C12   114.99  3.000
 RJ6  HN11  N11  C5    116.20  3.000
 RJ6  C12   N11  C5    128.80  3.000
 RJ6  N16   C12  N13   123.30  3.000
 RJ6  N16   C12  N11   123.83  3.000
 RJ6  N13   C12  N11   112.77  3.000
 RJ6  HN13  N13  C14   115.13  3.000
 RJ6  HN13  N13  C12   115.64  3.000
 RJ6  C14   N13  C12   129.19  3.000
 RJ6  N17   C14  N15   126.67  3.000
 RJ6  N15   C14  N13   110.53  3.000
 RJ6  N17   C14  N13   122.71  3.000
 RJ6  HN1A  N15  HN15  111.71  3.000
 RJ6  HN1A  N15  C14   115.25  3.000
 RJ6  HN15  N15  C14   117.11  3.000
 RJ6  HN16  N16  C12   109.55  3.000
 RJ6  HN17  N17  C14   109.78  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
 RJ6  CONST_01  C4    C5   C6   C1     0.00   0.0  0
 RJ6  CONST_02  C4    C3   C2   C1     0.00   0.0  0
 RJ6  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 RJ6  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 RJ6  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 RJ6  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 RJ6  CONST_07  N11   C5   C6   C1   180.00   0.0  0
 RJ6  CONST_08  O9    C3   C2   C1   180.00   0.0  0
 RJ6  CONST_09  O7    C1   C2   C3   180.00   0.0  0
 RJ6  CONST_10  N11   C5   C4   C3   180.00   0.0  0
 RJ6  CONST_11  O9    C3   C4   C5   180.00   0.0  0
 RJ6  CONST_12  O7    C1   C6   C5   180.00   0.0  0
 RJ6  CONST_13  H6    C6   C1   C2   180.00   0.0  0
 RJ6  CONST_14  H4    C4   C3   C2   180.00   0.0  0
 RJ6  CONST_15  H2    C2   C3   C4   180.00   0.0  0
 RJ6  CONST_22  N17   C14  N13  C12    0.00   0.0  0
 RJ6  CONST_23  N15   C14  N13  C12  180.00   0.0  0
 RJ6  CONST_26  HN16  N16  C12  N11    0.00   0.0  0
 RJ6  CONST_27  HN17  N17  C14  N13  180.00   0.0  0
 RJ6  CONST_29  HN1A  N15  C14  N13  180.00   0.0  0
 RJ6  Var_01    H8    C8   O7   C1   178.26  30.0  3
 RJ6  Var_02    H10   C10  O9   C3   -62.45  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
 RJ6  plan-1  C1    0.020
 RJ6  plan-1  C2    0.020
 RJ6  plan-1  C3    0.020
 RJ6  plan-1  C4    0.020
 RJ6  plan-1  C5    0.020
 RJ6  plan-1  C6    0.020
 RJ6  plan-1  O7    0.020
 RJ6  plan-1  O9    0.020
 RJ6  plan-1  N11   0.020
 RJ6  plan-1  H2    0.020
 RJ6  plan-1  H4    0.020
 RJ6  plan-1  H6    0.020
 RJ6  plan-2  C5    0.020
 RJ6  plan-2  N11   0.020
 RJ6  plan-2  C12   0.020
 RJ6  plan-2  N13   0.020
 RJ6  plan-2  C14   0.020
 RJ6  plan-2  N15   0.020
 RJ6  plan-2  N16   0.020
 RJ6  plan-2  N17   0.020
 RJ6  plan-2  HN11  0.020
 RJ6  plan-2  HN13  0.020
 RJ6  plan-2  HN15  0.020
 RJ6  plan-2  HN1A  0.020
 RJ6  plan-2  HN16  0.020
 RJ6  plan-2  HN17  0.020

