# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 23:04:54 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: N-[2-chloro-5-(trifluoromethyl)phenyl]imidodicarbonimidic diamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)NC(=N)Nc1cc(ccc1Cl)C(F)(F)F
#
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
 RJ1  RJ1  'N-[2-chloro-5-(trifluoromethyl)phenyl]imidodicarbonimidic diamide'  ligand  27  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RJ1
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
 RJ1  C1    C   CR6   0  -0.162   2.3423   0.1787   0.0169
 RJ1  C2    C   CR16  0  -0.323   2.4852   1.5469   0.1798
 RJ1  C3    C   CR16  0  -0.197   1.3417   2.3248   0.2609
 RJ1  C4    C   CR6   0  -0.159   0.0917   1.7427   0.1808
 RJ1  C5    C   CR6   0   0.480  -0.0770   0.3556   0.0160
 RJ1  C6    C   CR16  0  -0.367   1.0889  -0.4112  -0.0694
 RJ1  CL7   CL  CL    0  -0.106  -1.2956   2.7732   0.2925
 RJ1  C8    C   CT    0   1.049   3.5447  -0.7022  -0.1217
 RJ1  F9    F   F     0  -0.310   3.4080  -1.8533   0.5493
 RJ1  F10   F   F     0  -0.315   3.7694  -1.0331  -1.4031
 RJ1  F11   F   F     0  -0.305   4.6603  -0.1183   0.3271
 RJ1  N12   N   NH1   0  -0.797  -1.3554  -0.1571  -0.0387
 RJ1  C13   C   C     0   0.653  -1.7301  -1.4572  -0.2439
 RJ1  N14   N   NH1   0  -0.745  -3.1039  -1.6799  -0.1823
 RJ1  C15   C   C     0   0.639  -4.1371  -0.8050   0.1024
 RJ1  N16   N   NH2   0  -0.836  -5.3588  -1.4099   0.1014
 RJ1  N17   N   N     0  -0.707  -0.9009  -2.3985  -0.4798
 RJ1  N18   N   N     0  -0.738  -3.9038   0.4401   0.2805
 RJ1  H2    H   HCR6  0   0.275   3.4535   2.0213   0.2475
 RJ1  H3    H   HCR6  0   0.287   1.4255   3.3952   0.3871
 RJ1  H6    H   HCR6  0   0.320   0.9783  -1.4761  -0.2031
 RJ1  HN12  H   HNH1  0   0.455  -2.1569   0.4779   0.1133
 RJ1  HN14  H   HNH1  0   0.416  -3.3711  -2.6244  -0.4116
 RJ1  HN16  H   HNH2  0   0.401  -5.4126  -2.3902   0.3281
 RJ1  HN1A  H   HNH2  0   0.402  -6.1197  -0.8727   0.4834
 RJ1  HN17  H   H     0   0.341  -1.3680  -3.2900  -0.5922
 RJ1  HN18  H   H     0   0.350  -4.7364   0.9650   0.5119

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
 RJ1  C8   C1    single    1.497  0.020  1.497
 RJ1  C1   C6    aromatic  1.388  0.020  1.388
 RJ1  C1   C2    aromatic  1.385  0.020  1.385
 RJ1  C2   C3    aromatic  1.385  0.020  1.385
 RJ1  C2   H2    single    0.930  0.020  1.080
 RJ1  C3   C4    aromatic  1.381  0.020  1.381
 RJ1  C3   H3    single    0.930  0.020  1.080
 RJ1  C5   C4    aromatic  1.407  0.020  1.407
 RJ1  C4   CL7   single    1.732  0.020  1.732
 RJ1  C6   C5    aromatic  1.398  0.020  1.398
 RJ1  C5   N12   single    1.378  0.020  1.378
 RJ1  C6   H6    single    0.930  0.020  1.080
 RJ1  F11  C8    single    1.337  0.020  1.337
 RJ1  F9   C8    single    1.339  0.020  1.339
 RJ1  C8   F10   single    1.342  0.020  1.342
 RJ1  N12  C13   single    1.369  0.020  1.369
 RJ1  N12  HN12  single    0.860  0.020  1.020
 RJ1  C13  N17   double    1.276  0.020  1.276
 RJ1  C13  N14   single    1.393  0.020  1.393
 RJ1  N14  C15   single    1.383  0.020  1.383
 RJ1  N14  HN14  single    0.860  0.020  1.020
 RJ1  N18  C15   double    1.279  0.020  1.279
 RJ1  C15  N16   single    1.363  0.020  1.363
 RJ1  N16  HN16  single    0.890  0.020  1.040
 RJ1  N16  HN1A  single    0.890  0.020  1.040
 RJ1  N17  HN17  single    0.890  0.020  1.040
 RJ1  N18  HN18  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
 RJ1  C8    C1   C6    118.00  3.000
 RJ1  C6    C1   C2    121.35  3.000
 RJ1  C8    C1   C2    120.61  3.000
 RJ1  H2    C2   C3    119.31  3.000
 RJ1  H2    C2   C1    122.24  3.000
 RJ1  C3    C2   C1    118.44  3.000
 RJ1  H3    C3   C4    119.61  3.000
 RJ1  H3    C3   C2    119.92  3.000
 RJ1  C4    C3   C2    120.47  3.000
 RJ1  CL7   C4   C5    119.87  3.000
 RJ1  CL7   C4   C3    118.07  3.000
 RJ1  C5    C4   C3    122.06  3.000
 RJ1  N12   C5   C6    124.54  3.000
 RJ1  N12   C5   C4    118.85  3.000
 RJ1  C6    C5   C4    116.60  3.000
 RJ1  H6    C6   C5    117.60  3.000
 RJ1  H6    C6   C1    121.32  3.000
 RJ1  C5    C6   C1    121.08  3.000
 RJ1  F11   C8   F10   106.77  3.000
 RJ1  F10   C8   F9    106.47  3.000
 RJ1  F11   C8   F9    107.00  3.000
 RJ1  F10   C8   C1    111.58  3.000
 RJ1  F9    C8   C1    112.17  3.000
 RJ1  F11   C8   C1    112.47  3.000
 RJ1  HN12  N12  C13   113.16  3.000
 RJ1  HN12  N12  C5    118.99  3.000
 RJ1  C13   N12  C5    127.82  3.000
 RJ1  N17   C13  N14   122.07  3.000
 RJ1  N14   C13  N12   114.54  3.000
 RJ1  N17   C13  N12   123.39  3.000
 RJ1  HN14  N14  C15   116.19  3.000
 RJ1  HN14  N14  C13   113.65  3.000
 RJ1  C15   N14  C13   130.13  3.000
 RJ1  N18   C15  N16   126.54  3.000
 RJ1  N16   C15  N14   112.86  3.000
 RJ1  N18   C15  N14   120.53  3.000
 RJ1  HN1A  N16  HN16  113.16  3.000
 RJ1  HN1A  N16  C15   116.13  3.000
 RJ1  HN16  N16  C15   118.64  3.000
 RJ1  HN17  N17  C13   111.72  3.000
 RJ1  HN18  N18  C15   112.77  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
 RJ1  CONST_01  C4    C5   C6   C1     0.00   0.0  0
 RJ1  CONST_02  C4    C3   C2   C1     0.00   0.0  0
 RJ1  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 RJ1  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 RJ1  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 RJ1  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 RJ1  CONST_07  N12   C5   C6   C1   180.00   0.0  0
 RJ1  CONST_08  CL7   C4   C3   C2   180.00   0.0  0
 RJ1  CONST_09  C8    C1   C2   C3   180.00   0.0  0
 RJ1  CONST_10  N12   C5   C4   C3   180.00   0.0  0
 RJ1  CONST_11  C8    C1   C6   C5   180.00   0.0  0
 RJ1  CONST_12  CL7   C4   C5   C6   180.00   0.0  0
 RJ1  CONST_13  H3    C3   C2   C1   180.00   0.0  0
 RJ1  CONST_14  H6    C6   C1   C2   180.00   0.0  0
 RJ1  CONST_15  H2    C2   C3   C4   180.00   0.0  0
 RJ1  CONST_16  C13   N12  C5   C4   180.00   0.0  0
 RJ1  CONST_17  C13   N12  C5   C6     0.00   0.0  0
 RJ1  CONST_18  HN12  N12  C5   C4     0.00   0.0  0
 RJ1  CONST_19  N17   C13  N12  C5     0.00   0.0  0
 RJ1  CONST_20  N14   C13  N12  C5   180.00   0.0  0
 RJ1  CONST_21  C15   N14  C13  N12    0.00   0.0  0
 RJ1  CONST_22  N18   C15  N14  C13    0.00   0.0  0
 RJ1  CONST_23  N16   C15  N14  C13  180.00   0.0  0
 RJ1  CONST_24  N17   C13  N14  C15  180.00   0.0  0
 RJ1  CONST_25  HN17  N17  C13  N12  180.00   0.0  0
 RJ1  CONST_26  HN14  N14  C13  N12  180.00   0.0  0
 RJ1  CONST_27  HN18  N18  C15  N14  180.00   0.0  0
 RJ1  CONST_29  HN1A  N16  C15  N14  180.00   0.0  0
 RJ1  Var_01    F11   C8   C1   C2    19.07  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
 RJ1  plan-1  C1    0.020
 RJ1  plan-1  C2    0.020
 RJ1  plan-1  C3    0.020
 RJ1  plan-1  C4    0.020
 RJ1  plan-1  C5    0.020
 RJ1  plan-1  C6    0.020
 RJ1  plan-1  CL7   0.020
 RJ1  plan-1  C8    0.020
 RJ1  plan-1  N12   0.020
 RJ1  plan-1  H2    0.020
 RJ1  plan-1  H3    0.020
 RJ1  plan-1  H6    0.020
 RJ1  plan-2  C5    0.020
 RJ1  plan-2  N12   0.020
 RJ1  plan-2  C13   0.020
 RJ1  plan-2  N14   0.020
 RJ1  plan-2  C15   0.020
 RJ1  plan-2  N16   0.020
 RJ1  plan-2  N17   0.020
 RJ1  plan-2  N18   0.020
 RJ1  plan-2  HN12  0.020
 RJ1  plan-2  HN14  0.020
 RJ1  plan-2  HN16  0.020
 RJ1  plan-2  HN1A  0.020
 RJ1  plan-2  HN17  0.020
 RJ1  plan-2  HN18  0.020

