# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 06:08:12 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (3-chloranyl-4-phenyl-phenyl)methyl-methyl-azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[NH2+]Cc1ccc(c(Cl)c1)c2ccccc2
#
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
 RKN  RKN  (3-chloranyl-4-phenyl-phenyl)methyl-methyl-azanium  ligand  31  16  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RKN
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
 RKN  C1   C   CH2   0  -0.391   3.7975   0.3478   0.5920
 RKN  C2   C   CR6   0   0.060   2.3079   0.3511   0.4378
 RKN  C3   C   CR16  0  -0.256   1.6347   1.5317   0.1461
 RKN  C4   C   CR16  0  -0.296   0.2613   1.5239  -0.0183
 RKN  C5   C   CR6   0   0.153  -0.4844   0.3507   0.1002
 RKN  C6   C   CR6   0  -0.107   0.2110  -0.8207   0.4010
 RKN  C10  C   CR16  0  -0.242  -4.0787   1.3690   0.5483
 RKN  C11  C   CR16  0  -0.260  -4.7148   0.6030  -0.4185
 RKN  C13  C   CR16  0  -0.281  -2.5979  -0.3589  -1.0421
 RKN  CL   CL  CL    0  -0.115  -0.6382  -2.3127   0.6307
 RKN  C7   C   CR16  0  -0.219   1.5870  -0.8285   0.5681
 RKN  N    N   NT2   1  -0.634   4.4650   0.1396  -0.7274
 RKN  C    C   CH3   0  -0.531   5.9431   0.2119  -0.6638
 RKN  C8   C   CR6   0   0.059  -1.9521   0.4059  -0.0717
 RKN  C12  C   CR16  0  -0.243  -3.9702  -0.2582  -1.2153
 RKN  C9   C   CR16  0  -0.290  -2.7043   1.2734   0.7182
 RKN  H1   H   HCH2  0   0.320   4.1611   1.2970   0.9813
 RKN  H2   H   HCH2  0   0.321   4.1415  -0.4515   1.2452
 RKN  H3   H   HCR6  0   0.273   2.1815   2.4616   0.0506
 RKN  H4   H   HCR6  0   0.272  -0.2526   2.4467  -0.2538
 RKN  H6   H   HCR6  0   0.260  -5.7857   0.6789  -0.5549
 RKN  H7   H   HCR6  0   0.257  -2.0248  -1.0221  -1.6771
 RKN  H8   H   HCR6  0   0.288   2.0936  -1.7523   0.8173
 RKN  H9   H   HNT2  0   0.474   4.1884  -0.7661  -1.1095
 RKN  H10  H   HNT2  0   0.473   4.1239   0.8318  -1.3960
 RKN  H11  H   HCH3  0   0.290   6.3000  -0.5439   0.0283
 RKN  H12  H   HCH3  0   0.297   6.3410   0.0290  -1.6563
 RKN  H13  H   HCH3  0   0.291   6.2284   1.2010  -0.3217
 RKN  H14  H   HCR6  0   0.260  -4.4596  -0.8494  -1.9784
 RKN  H15  H   HCR6  0   0.258  -2.2133   1.8697   1.4777
 RKN  H5   H   HCR6  0   0.260  -4.6517   2.0421   1.1724

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
 RKN  C4   C3   aromatic  1.383  0.020  1.383
 RKN  C4   C5   aromatic  1.395  0.020  1.395
 RKN  C3   C2   aromatic  1.390  0.020  1.390
 RKN  C10  C11  aromatic  1.388  0.020  1.388
 RKN  C10  C9   aromatic  1.388  0.020  1.388
 RKN  C11  C12  aromatic  1.390  0.020  1.390
 RKN  C9   C8   aromatic  1.394  0.020  1.394
 RKN  C12  C13  aromatic  1.387  0.020  1.387
 RKN  C8   C13  aromatic  1.394  0.020  1.394
 RKN  C8   C5   single    1.479  0.020  1.479
 RKN  C5   C6   aromatic  1.395  0.020  1.395
 RKN  C2   C1   single    1.498  0.020  1.498
 RKN  C2   C7   aromatic  1.389  0.020  1.389
 RKN  C1   N    single    1.493  0.020  1.493
 RKN  C6   C7   aromatic  1.386  0.020  1.386
 RKN  C6   CL   single    1.732  0.020  1.732
 RKN  N    C    single    1.481  0.020  1.481
 RKN  C1   H1   single    0.970  0.020  1.090
 RKN  C1   H2   single    0.970  0.020  1.090
 RKN  C3   H3   single    0.930  0.020  1.080
 RKN  C4   H4   single    0.930  0.020  1.080
 RKN  C10  H5   single    0.930  0.020  1.080
 RKN  C11  H6   single    0.930  0.020  1.080
 RKN  C13  H7   single    0.930  0.020  1.080
 RKN  C7   H8   single    0.930  0.020  1.080
 RKN  N    H9   single    0.890  0.020  1.040
 RKN  N    H10  single    0.890  0.020  1.040
 RKN  C    H11  single    0.970  0.020  1.090
 RKN  C    H12  single    0.970  0.020  1.090
 RKN  C    H13  single    0.970  0.020  1.090
 RKN  C12  H14  single    0.930  0.020  1.080
 RKN  C9   H15  single    0.930  0.020  1.080

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
 RKN  H2   C1   H1   108.68  3.000
 RKN  H2   C1   N    106.66  3.000
 RKN  H1   C1   N    106.76  3.000
 RKN  H2   C1   C2   112.20  3.000
 RKN  H1   C1   C2   111.54  3.000
 RKN  N    C1   C2   110.73  3.000
 RKN  C7   C2   C3   119.33  3.000
 RKN  C7   C2   C1   120.32  3.000
 RKN  C3   C2   C1   120.35  3.000
 RKN  H3   C3   C4   119.71  3.000
 RKN  H3   C3   C2   120.22  3.000
 RKN  C4   C3   C2   120.07  3.000
 RKN  H4   C4   C5   118.80  3.000
 RKN  H4   C4   C3   119.51  3.000
 RKN  C5   C4   C3   121.69  3.000
 RKN  C8   C5   C6   123.44  3.000
 RKN  C6   C5   C4   117.26  3.000
 RKN  C8   C5   C4   119.29  3.000
 RKN  C7   C6   CL   117.77  3.000
 RKN  CL   C6   C5   120.50  3.000
 RKN  C7   C6   C5   121.70  3.000
 RKN  H5   C10  C9   119.77  3.000
 RKN  H5   C10  C11  120.16  3.000
 RKN  C9   C10  C11  120.07  3.000
 RKN  H6   C11  C12  120.09  3.000
 RKN  H6   C11  C10  120.18  3.000
 RKN  C12  C11  C10  119.73  3.000
 RKN  H7   C13  C12  119.68  3.000
 RKN  H7   C13  C8   119.95  3.000
 RKN  C12  C13  C8   120.36  3.000
 RKN  H8   C7   C6   119.80  3.000
 RKN  H8   C7   C2   120.24  3.000
 RKN  C6   C7   C2   119.95  3.000
 RKN  H10  N    H9   105.42  3.000
 RKN  H10  N    C    109.17  3.000
 RKN  H9   N    C    109.25  3.000
 RKN  H10  N    C1   109.56  3.000
 RKN  H9   N    C1   109.47  3.000
 RKN  C    N    C1   113.66  3.000
 RKN  H13  C    H12  110.23  3.000
 RKN  H13  C    H11  110.33  3.000
 RKN  H12  C    H11  110.21  3.000
 RKN  H13  C    N    108.69  3.000
 RKN  H12  C    N    108.57  3.000
 RKN  H11  C    N    108.76  3.000
 RKN  C9   C8   C13  119.07  3.000
 RKN  C13  C8   C5   121.35  3.000
 RKN  C9   C8   C5   119.54  3.000
 RKN  H14  C12  C13  119.72  3.000
 RKN  H14  C12  C11  120.04  3.000
 RKN  C13  C12  C11  120.24  3.000
 RKN  H15  C9   C8   119.70  3.000
 RKN  H15  C9   C10  119.78  3.000
 RKN  C8   C9   C10  120.52  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
 RKN  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 RKN  CONST_02  C5   C6   C7   C2     0.00   0.0  0
 RKN  CONST_03  C8   C5   C4   C3   180.00   0.0  0
 RKN  CONST_04  C6   C5   C4   C3     0.00   0.0  0
 RKN  CONST_05  C6   C7   C2   C3     0.00   0.0  0
 RKN  CONST_06  C7   C2   C3   C4     0.00   0.0  0
 RKN  CONST_09  C7   C6   C5   C4     0.00   0.0  0
 RKN  CONST_10  C10  C9   C8   C5   180.00   0.0  0
 RKN  CONST_11  C12  C13  C8   C5   180.00   0.0  0
 RKN  CONST_14  C13  C12  C11  C10    0.00   0.0  0
 RKN  CONST_15  C13  C8   C9   C10    0.00   0.0  0
 RKN  CONST_16  C8   C9   C10  C11    0.00   0.0  0
 RKN  CONST_17  C8   C13  C12  C11    0.00   0.0  0
 RKN  CONST_18  C8   C5   C6   C7   180.00   0.0  0
 RKN  CONST_19  C9   C10  C11  C12    0.00   0.0  0
 RKN  CONST_20  C9   C8   C13  C12    0.00   0.0  0
 RKN  CONST_21  C4   C3   C2   C1   180.00   0.0  0
 RKN  CONST_22  C6   C7   C2   C1   180.00   0.0  0
 RKN  CONST_23  CL   C6   C7   C2   180.00   0.0  0
 RKN  CONST_24  CL   C6   C5   C4   180.00   0.0  0
 RKN  CONST_25  C8   C5   C6   CL     0.00   0.0  0
 RKN  CONST_26  H4   C4   C3   C2   180.00   0.0  0
 RKN  CONST_27  H8   C7   C2   C3   180.00   0.0  0
 RKN  CONST_28  H3   C3   C4   C5   180.00   0.0  0
 RKN  CONST_29  H15  C9   C8   C5     0.00   0.0  0
 RKN  CONST_30  H7   C13  C8   C5     0.00   0.0  0
 RKN  CONST_31  H14  C12  C11  C10  180.00   0.0  0
 RKN  CONST_32  H6   C11  C12  C13  180.00   0.0  0
 RKN  CONST_33  H5   C10  C9   C8   180.00   0.0  0
 RKN  Var_01    N    C1   C2   C3   -87.92  30.0  2
 RKN  Var_02    C    N    C1   C2   176.28  30.0  3
 RKN  Var_03    H11  C    N    C1    58.86  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
 RKN  plan-1  C1   0.020
 RKN  plan-1  C2   0.020
 RKN  plan-1  C3   0.020
 RKN  plan-1  C4   0.020
 RKN  plan-1  C5   0.020
 RKN  plan-1  C6   0.020
 RKN  plan-1  CL   0.020
 RKN  plan-1  C7   0.020
 RKN  plan-1  C8   0.020
 RKN  plan-1  H3   0.020
 RKN  plan-1  H4   0.020
 RKN  plan-1  H8   0.020
 RKN  plan-2  C5   0.020
 RKN  plan-2  C10  0.020
 RKN  plan-2  C11  0.020
 RKN  plan-2  C13  0.020
 RKN  plan-2  C8   0.020
 RKN  plan-2  C12  0.020
 RKN  plan-2  C9   0.020
 RKN  plan-2  H6   0.020
 RKN  plan-2  H7   0.020
 RKN  plan-2  H14  0.020
 RKN  plan-2  H15  0.020
 RKN  plan-2  H5   0.020

