# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 21:14:55 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 3-chloro-4-(4-chloro-2-hydroxyphenoxy)-N-methylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1ccc(Oc2ccc(Cl)cc2O)c(Cl)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
 TN3  TN3  3-chloro-4-(4-chloro-2-hydroxyphenoxy)-N-methylbenzamide  ligand  31  20  .  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_TN3
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
 TN3  CL21  CL  CL    0  -0.098   1.7350   2.9491  -0.3945
 TN3  C14   C   CR6   0  -0.130   1.7026   1.2234  -0.3685
 TN3  C13   C   CR16  0  -0.245   2.8858   0.5111  -0.3205
 TN3  C10   C   CR6   0  -0.054   2.8654  -0.8813  -0.3129
 TN3  C11   C   C     0   0.529   4.1105  -1.7065  -0.2855
 TN3  O13   O   O     0  -0.491   4.1213  -2.8448  -0.7375
 TN3  N20   N   NH1   0  -0.639   5.1956  -1.1361   0.2557
 TN3  C12   C   CH3   0  -0.513   6.4601  -1.8281   0.3428
 TN3  C9    C   CR16  0  -0.258   1.6382  -1.5326  -0.3733
 TN3  C8    C   CR16  0  -0.336   0.4519  -0.8213  -0.4112
 TN3  C7    C   CR6   0   0.452   0.4726   0.5676  -0.4094
 TN3  O9    O   O2    0  -0.484  -0.6282   1.3451  -0.4780
 TN3  C5    C   CR6   0   0.240  -1.8628   0.7742  -0.3016
 TN3  C6    C   CR6   0   0.329  -2.2838   0.4513   0.9916
 TN3  O8    O   OH1   0  -0.608  -1.4184   0.6586   1.9915
 TN3  C1    C   CR16  0  -0.342  -3.5609  -0.0653   1.1739
 TN3  C4    C   CR16  0  -0.308  -2.6964   0.5833  -1.3851
 TN3  C3    C   CR16  0  -0.244  -3.9750   0.0714  -1.2090
 TN3  C2    C   CR6   0  -0.028  -4.3853  -0.2466   0.0738
 TN3  CL12  CL  CL    0  -0.120  -5.9744  -0.8878   0.3238
 TN3  H13   H   HCR6  0   0.282   3.8171   1.0622  -0.3109
 TN3  H20   H   HNH1  0   0.411   5.1070  -0.2649   0.7501
 TN3  H121  H   HCH3  0   0.251   7.2011  -1.1381   0.7358
 TN3  H122  H   HCH3  0   0.238   6.4087  -2.6941   1.0049
 TN3  H123  H   HCH3  0   0.242   6.7920  -2.1660  -0.6379
 TN3  H9    H   HCR6  0   0.271   1.6005  -2.6131  -0.3850
 TN3  H8    H   HCR6  0   0.293  -0.4867  -1.3580  -0.4563
 TN3  HO8   H   HOH1  0   0.486  -1.8002   0.3929   2.8365
 TN3  H1    H   HCR6  0   0.302  -3.9071  -0.3182   2.1685
 TN3  H4    H   HCR6  0   0.288  -2.3473   0.8415  -2.3764
 TN3  H3    H   HCR6  0   0.284  -4.6280  -0.0753  -2.0572

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
 TN3  CL21  C14   single    1.726  0.020  1.726
 TN3  C14   C13   aromatic  1.382  0.020  1.382
 TN3  C14   C7    aromatic  1.395  0.020  1.395
 TN3  C13   C10   aromatic  1.393  0.020  1.393
 TN3  C13   H13   single    0.930  0.020  1.080
 TN3  C10   C11   single    1.494  0.020  1.494
 TN3  C10   C9    aromatic  1.391  0.020  1.391
 TN3  C11   O13   double    1.225  0.020  1.225
 TN3  C11   N20   single    1.340  0.020  1.340
 TN3  N20   C12   single    1.444  0.020  1.444
 TN3  N20   H20   single    0.860  0.020  1.020
 TN3  C12   H121  single    0.970  0.020  1.090
 TN3  C12   H122  single    0.970  0.020  1.090
 TN3  C12   H123  single    0.970  0.020  1.090
 TN3  C9    C8    aromatic  1.384  0.020  1.384
 TN3  C9    H9    single    0.930  0.020  1.080
 TN3  C8    C7    aromatic  1.389  0.020  1.389
 TN3  C8    H8    single    0.930  0.020  1.080
 TN3  C7    O9    single    1.349  0.020  1.349
 TN3  O9    C5    single    1.372  0.020  1.372
 TN3  C5    C6    aromatic  1.398  0.020  1.398
 TN3  C5    C4    aromatic  1.380  0.020  1.380
 TN3  C6    O8    single    1.339  0.020  1.339
 TN3  C6    C1    aromatic  1.390  0.020  1.390
 TN3  O8    HO8   single    0.850  0.020  0.980
 TN3  C1    C2    aromatic  1.387  0.020  1.387
 TN3  C1    H1    single    0.930  0.020  1.080
 TN3  C4    C3    aromatic  1.388  0.020  1.388
 TN3  C4    H4    single    0.930  0.020  1.080
 TN3  C3    C2    aromatic  1.384  0.020  1.384
 TN3  C3    H3    single    0.930  0.020  1.080
 TN3  C2    CL12  single    1.732  0.020  1.732

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
 TN3  C7    C14  C13   120.92  3.000
 TN3  C7    C14  CL21  119.09  3.000
 TN3  C13   C14  CL21  119.99  3.000
 TN3  H13   C13  C10   121.44  3.000
 TN3  H13   C13  C14   118.34  3.000
 TN3  C10   C13  C14   120.21  3.000
 TN3  C9    C10  C11   118.53  3.000
 TN3  C9    C10  C13   118.75  3.000
 TN3  C11   C10  C13   122.70  3.000
 TN3  N20   C11  O13   122.51  3.000
 TN3  N20   C11  C10   116.56  3.000
 TN3  O13   C11  C10   120.93  3.000
 TN3  H20   N20  C12   117.56  3.000
 TN3  H20   N20  C11   119.73  3.000
 TN3  C12   N20  C11   121.97  3.000
 TN3  H123  C12  H122  108.33  3.000
 TN3  H123  C12  H121  108.36  3.000
 TN3  H122  C12  H121  108.46  3.000
 TN3  H123  C12  N20   111.18  3.000
 TN3  H122  C12  N20   112.06  3.000
 TN3  H121  C12  N20   108.35  3.000
 TN3  H9    C9   C8    118.91  3.000
 TN3  H9    C9   C10   119.95  3.000
 TN3  C8    C9   C10   121.13  3.000
 TN3  H8    C8   C7    120.59  3.000
 TN3  H8    C8   C9    119.33  3.000
 TN3  C7    C8   C9    120.08  3.000
 TN3  O9    C7   C8    124.33  3.000
 TN3  O9    C7   C14   116.75  3.000
 TN3  C8    C7   C14   118.91  3.000
 TN3  C5    O9   C7    119.20  3.000
 TN3  C4    C5   C6    120.82  3.000
 TN3  C4    C5   O9    120.01  3.000
 TN3  C6    C5   O9    119.10  3.000
 TN3  C1    C6   O8    123.63  3.000
 TN3  C1    C6   C5    118.95  3.000
 TN3  O8    C6   C5    117.42  3.000
 TN3  HO8   O8   C6    110.84  3.000
 TN3  H1    C1   C2    120.53  3.000
 TN3  H1    C1   C6    120.07  3.000
 TN3  C2    C1   C6    119.40  3.000
 TN3  H4    C4   C3    120.08  3.000
 TN3  H4    C4   C5    119.42  3.000
 TN3  C3    C4   C5    120.50  3.000
 TN3  H3    C3   C2    121.15  3.000
 TN3  H3    C3   C4    120.47  3.000
 TN3  C2    C3   C4    118.38  3.000
 TN3  CL12  C2   C3    119.41  3.000
 TN3  CL12  C2   C1    118.65  3.000
 TN3  C3    C2   C1    121.95  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
 TN3  CONST_01  C9    C10  C13  C14      0.00   0.0  0
 TN3  CONST_02  C9    C8   C7   C14      0.00   0.0  0
 TN3  CONST_03  C8    C7   C14  C13      0.00   0.0  0
 TN3  CONST_04  C8    C9   C10  C13      0.00   0.0  0
 TN3  CONST_05  C7    C14  C13  C10      0.00   0.0  0
 TN3  CONST_06  C7    C8   C9   C10      0.00   0.0  0
 TN3  CONST_07  C2    C1   C6   C5       0.00   0.0  0
 TN3  CONST_08  C2    C3   C4   C5       0.00   0.0  0
 TN3  CONST_09  C3    C4   C5   C6       0.00   0.0  0
 TN3  CONST_10  C3    C2   C1   C6       0.00   0.0  0
 TN3  CONST_11  C4    C5   C6   C1       0.00   0.0  0
 TN3  CONST_12  C4    C3   C2   C1       0.00   0.0  0
 TN3  CONST_13  C10   C13  C14  CL21   180.00   0.0  0
 TN3  CONST_14  C8    C7   C14  CL21   180.00   0.0  0
 TN3  CONST_15  C11   C10  C13  C14    180.00   0.0  0
 TN3  CONST_16  O9    C7   C14  C13    180.00   0.0  0
 TN3  CONST_17  C8    C9   C10  C11    180.00   0.0  0
 TN3  CONST_18  O9    C7   C8   C9     180.00   0.0  0
 TN3  CONST_19  C1    C6   C5   O9     180.00   0.0  0
 TN3  CONST_20  C3    C4   C5   O9     180.00   0.0  0
 TN3  CONST_21  CL12  C2   C1   C6     180.00   0.0  0
 TN3  CONST_22  C4    C5   C6   O8     180.00   0.0  0
 TN3  CONST_23  C2    C1   C6   O8     180.00   0.0  0
 TN3  CONST_24  CL12  C2   C3   C4     180.00   0.0  0
 TN3  CONST_25  H8    C8   C7   C14    180.00   0.0  0
 TN3  CONST_26  H9    C9   C10  C13    180.00   0.0  0
 TN3  CONST_27  H13   C13  C10  C9     180.00   0.0  0
 TN3  CONST_28  H1    C1   C6   C5     180.00   0.0  0
 TN3  CONST_29  H3    C3   C4   C5     180.00   0.0  0
 TN3  CONST_30  H4    C4   C5   C6     180.00   0.0  0
 TN3  CONST_31  C12   N20  C11  C10    180.00   0.0  0
 TN3  CONST_32  H20   N20  C11  C10      0.00   0.0  0
 TN3  CONST_33  C12   N20  C11  O13      0.00   0.0  0
 TN3  Var_01    C6    C5   O9   C7      77.00  30.0  2
 TN3  Var_02    O13   C11  C10  C13   -154.12  30.0  2
 TN3  Var_03    H121  C12  N20  C11    175.16  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
 TN3  plan-1  CL21  0.020
 TN3  plan-1  C14   0.020
 TN3  plan-1  C13   0.020
 TN3  plan-1  C10   0.020
 TN3  plan-1  C11   0.020
 TN3  plan-1  C9    0.020
 TN3  plan-1  C8    0.020
 TN3  plan-1  C7    0.020
 TN3  plan-1  O9    0.020
 TN3  plan-1  H13   0.020
 TN3  plan-1  H9    0.020
 TN3  plan-1  H8    0.020
 TN3  plan-2  O9    0.020
 TN3  plan-2  C5    0.020
 TN3  plan-2  C6    0.020
 TN3  plan-2  O8    0.020
 TN3  plan-2  C1    0.020
 TN3  plan-2  C4    0.020
 TN3  plan-2  C3    0.020
 TN3  plan-2  C2    0.020
 TN3  plan-2  CL12  0.020
 TN3  plan-2  H1    0.020
 TN3  plan-2  H4    0.020
 TN3  plan-2  H3    0.020
 TN3  plan-3  C10   0.020
 TN3  plan-3  C11   0.020
 TN3  plan-3  O13   0.020
 TN3  plan-3  N20   0.020
 TN3  plan-3  C12   0.020
 TN3  plan-3  H20   0.020

