# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 08:21:26 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (3~{R})-3-(4-chlorophenyl)-3-(1-methylbenzotriazol-5-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nnc2cc(ccc12)[C@H](CC(O)=O)c3ccc(Cl)cc3
#
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
 J6N  J6N  '(3~{R})-3-(4-chlorophenyl)-3-(1-methylbenzotriazol-5-yl)propanoic acid'  ligand  36  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 OK
;

data_comp_J6N
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
 J6N  N3   N   N     0  -0.064  -4.1564   2.3439  -0.9857
 J6N  C5   C   CR56  0   0.147  -2.4925   0.9981  -0.9034
 J6N  C6   C   CR16  0  -0.351  -1.4263   0.1414  -1.1923
 J6N  C7   C   CR6   0   0.170  -0.7654  -0.4526  -0.1389
 J6N  C8   C   CR16  0  -0.321  -1.1743  -0.1881   1.1913
 J6N  C10  C   CR56  0   0.376  -2.8746   1.2414   0.4154
 J6N  C13  C   CH2   0  -0.582   0.4239  -2.6269   0.4326
 J6N  C20  C   CR6   0  -0.059   4.0762   0.8771  -0.1328
 J6N  C22  C   CR16  0  -0.191   3.5636   0.5480  -1.3751
 J6N  N2   N   NR5   0  -0.375  -3.9177   2.0947   0.2956
 J6N  N4   N   N     0  -0.333  -3.3234   1.7089  -1.7201
 J6N  C9   C   CR16  0  -0.275  -2.2213   0.6505   1.4978
 J6N  C11  C   CH1   0  -0.438   0.4157  -1.3609  -0.4238
 J6N  O15  O   O     0  -0.434  -1.5181  -3.4369  -0.7317
 J6N  O16  O   OH1   0  -0.592  -1.0513  -4.2396   1.2961
 J6N  C17  C   CR6   0   0.220   1.7151  -0.5927  -0.2980
 J6N  C18  C   CR16  0  -0.324   2.2586  -0.2505   0.9383
 J6N  C19  C   CR16  0  -0.191   3.4331   0.4805   1.0296
 J6N  C23  C   CR16  0  -0.332   2.3868  -0.1840  -1.4456
 J6N  H27  H   HCR6  0   0.263  -1.1330  -0.0498  -2.2171
 J6N  H28  H   HCR6  0   0.260  -0.6532  -0.6613   2.0133
 J6N  H31  H   HCH2  0   0.314   1.2709  -3.2530   0.1327
 J6N  H30  H   HCH2  0   0.275   0.5777  -2.4161   1.4916
 J6N  H34  H   HCR6  0   0.280   4.0708   0.8521  -2.2807
 J6N  H24  H   HCH3  0   0.267  -5.3214   1.8924   1.8327
 J6N  H25  H   HCH3  0   0.266  -4.1070   3.1647   2.0732
 J6N  H26  H   HCH3  0   0.279  -5.4044   3.3925   0.8899
 J6N  H29  H   HCR6  0   0.284  -2.5166   0.8299   2.5227
 J6N  H12  H   HCH1  0   0.285   0.3305  -1.6769  -1.4658
 J6N  H1   H   HOH1  0   0.481  -1.8316  -4.7910   1.1329
 J6N  H32  H   HCR6  0   0.257   1.7774  -0.5537   1.8594
 J6N  H33  H   HCR6  0   0.281   3.8406   0.7344   1.9987
 J6N  H35  H   HCR6  0   0.262   1.9869  -0.4360  -2.4204
 J6N  C1   C   CH3   0  -0.531  -4.7349   2.6651   1.3386
 J6N  C14  C   C     0   0.557  -0.8211  -3.4539   0.2510
 J6N  CL   CL  CL    0  -0.131   5.5458   1.7913  -0.0258

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
 J6N  O15  C14  double    1.205  0.020  1.205
 J6N  O16  C14  single    1.328  0.020  1.328
 J6N  C14  C13  single    1.506  0.020  1.506
 J6N  C13  C11  single    1.528  0.020  1.528
 J6N  C11  C17  single    1.515  0.020  1.515
 J6N  C11  C7   single    1.517  0.020  1.517
 J6N  C18  C17  aromatic  1.393  0.020  1.393
 J6N  C18  C19  aromatic  1.386  0.020  1.386
 J6N  C17  C23  aromatic  1.391  0.020  1.391
 J6N  C7   C6   aromatic  1.378  0.020  1.378
 J6N  C7   C8   aromatic  1.417  0.020  1.417
 J6N  C6   C5   aromatic  1.398  0.020  1.398
 J6N  C8   C9   aromatic  1.376  0.020  1.376
 J6N  C19  C20  aromatic  1.386  0.020  1.386
 J6N  C23  C22  aromatic  1.388  0.020  1.388
 J6N  C5   N4   aromatic  1.365  0.020  1.365
 J6N  C5   C10  aromatic  1.394  0.020  1.394
 J6N  N4   N3   aromatic  1.279  0.020  1.279
 J6N  C9   C10  aromatic  1.396  0.020  1.396
 J6N  C20  C22  aromatic  1.384  0.020  1.384
 J6N  C20  CL   single    1.734  0.020  1.734
 J6N  C10  N2   aromatic  1.353  0.020  1.353
 J6N  N3   N2   aromatic  1.327  0.020  1.327
 J6N  N2   C1   single    1.443  0.020  1.443
 J6N  C6   H27  single    0.930  0.020  1.080
 J6N  C8   H28  single    0.930  0.020  1.080
 J6N  C13  H31  single    0.970  0.020  1.090
 J6N  C13  H30  single    0.970  0.020  1.090
 J6N  C22  H34  single    0.930  0.020  1.080
 J6N  C1   H24  single    0.970  0.020  1.090
 J6N  C1   H25  single    0.970  0.020  1.090
 J6N  C1   H26  single    0.970  0.020  1.090
 J6N  C9   H29  single    0.930  0.020  1.080
 J6N  C11  H12  single    0.970  0.020  1.090
 J6N  O16  H1   single    0.850  0.020  0.980
 J6N  C18  H32  single    0.930  0.020  1.080
 J6N  C19  H33  single    0.930  0.020  1.080
 J6N  C23  H35  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
 J6N  N4   N3   N2   110.12  3.000
 J6N  N4   C5   C10  107.95  3.000
 J6N  C10  C5   C6   120.76  3.000
 J6N  N4   C5   C6   131.29  3.000
 J6N  H27  C6   C7   121.16  3.000
 J6N  H27  C6   C5   120.68  3.000
 J6N  C7   C6   C5   118.16  3.000
 J6N  C11  C7   C8   120.86  3.000
 J6N  C8   C7   C6   119.92  3.000
 J6N  C11  C7   C6   119.20  3.000
 J6N  H28  C8   C9   117.62  3.000
 J6N  H28  C8   C7   119.51  3.000
 J6N  C9   C8   C7   122.86  3.000
 J6N  C9   C10  N2   134.16  3.000
 J6N  N2   C10  C5   103.74  3.000
 J6N  C9   C10  C5   122.10  3.000
 J6N  H30  C13  H31  105.50  3.000
 J6N  H30  C13  C14  109.87  3.000
 J6N  H31  C13  C14  107.00  3.000
 J6N  H30  C13  C11  112.63  3.000
 J6N  H31  C13  C11  108.92  3.000
 J6N  C14  C13  C11  112.52  3.000
 J6N  CL   C20  C19  119.49  3.000
 J6N  CL   C20  C22  119.65  3.000
 J6N  C19  C20  C22  120.86  3.000
 J6N  H34  C22  C23  120.23  3.000
 J6N  H34  C22  C20  120.74  3.000
 J6N  C23  C22  C20  119.03  3.000
 J6N  C1   N2   C10  128.47  3.000
 J6N  C1   N2   N3   121.46  3.000
 J6N  C10  N2   N3   110.04  3.000
 J6N  C5   N4   N3   108.15  3.000
 J6N  H29  C9   C10  122.47  3.000
 J6N  H29  C9   C8   121.33  3.000
 J6N  C10  C9   C8   116.20  3.000
 J6N  H12  C11  C17  107.03  3.000
 J6N  H12  C11  C13  107.17  3.000
 J6N  C17  C11  C13  111.65  3.000
 J6N  H12  C11  C7   106.96  3.000
 J6N  C17  C11  C7   110.41  3.000
 J6N  C13  C11  C7   113.25  3.000
 J6N  H1   O16  C14  110.10  3.000
 J6N  C23  C17  C18  118.14  3.000
 J6N  C23  C17  C11  119.65  3.000
 J6N  C18  C17  C11  122.20  3.000
 J6N  H32  C18  C19  117.92  3.000
 J6N  H32  C18  C17  120.85  3.000
 J6N  C19  C18  C17  121.23  3.000
 J6N  H33  C19  C18  120.14  3.000
 J6N  H33  C19  C20  120.62  3.000
 J6N  C18  C19  C20  119.25  3.000
 J6N  H35  C23  C17  119.72  3.000
 J6N  H35  C23  C22  118.78  3.000
 J6N  C17  C23  C22  121.50  3.000
 J6N  H26  C1   H25  109.11  3.000
 J6N  H26  C1   H24  109.33  3.000
 J6N  H25  C1   H24  109.29  3.000
 J6N  H26  C1   N2   108.39  3.000
 J6N  H25  C1   N2   110.05  3.000
 J6N  H24  C1   N2   110.65  3.000
 J6N  O16  C14  O15  123.37  3.000
 J6N  O16  C14  C13  111.93  3.000
 J6N  O15  C14  C13  124.68  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
 J6N  CONST_01  C6   C5   N4   N3   180.00   0.0  0
 J6N  CONST_02  C10  C5   N4   N3     0.00   0.0  0
 J6N  CONST_03  C5   C10  N2   N3     0.00   0.0  0
 J6N  CONST_04  C9   C10  N2   N3   180.00   0.0  0
 J6N  CONST_05  C8   C7   C6   C5     0.00   0.0  0
 J6N  CONST_06  N2   N3   N4   C5     0.00   0.0  0
 J6N  CONST_07  C8   C9   C10  C5     0.00   0.0  0
 J6N  CONST_08  C9   C8   C7   C6     0.00   0.0  0
 J6N  CONST_09  C9   C10  C5   C6     0.00   0.0  0
 J6N  CONST_10  N2   C10  C5   C6   180.00   0.0  0
 J6N  CONST_11  N4   C5   C6   C7   180.00   0.0  0
 J6N  CONST_12  C10  C5   C6   C7     0.00   0.0  0
 J6N  CONST_13  C10  C9   C8   C7     0.00   0.0  0
 J6N  CONST_14  N2   C10  C9   C8   180.00   0.0  0
 J6N  CONST_15  N4   N3   N2   C10    0.00   0.0  0
 J6N  CONST_16  C17  C18  C19  C20    0.00   0.0  0
 J6N  CONST_17  C17  C23  C22  C20    0.00   0.0  0
 J6N  CONST_18  C18  C17  C23  C22    0.00   0.0  0
 J6N  CONST_19  C18  C19  C20  C22    0.00   0.0  0
 J6N  CONST_20  N4   C5   C10  N2     0.00   0.0  0
 J6N  CONST_21  C9   C10  C5   N4   180.00   0.0  0
 J6N  CONST_22  C23  C17  C18  C19    0.00   0.0  0
 J6N  CONST_23  C23  C22  C20  C19    0.00   0.0  0
 J6N  CONST_24  C11  C7   C6   C5   180.00   0.0  0
 J6N  CONST_25  C1   N2   C10  C5   180.00   0.0  0
 J6N  CONST_26  C11  C17  C23  C22  180.00   0.0  0
 J6N  CONST_27  C9   C10  N2   C1     0.00   0.0  0
 J6N  CONST_28  N4   N3   N2   C1   180.00   0.0  0
 J6N  CONST_29  C11  C7   C8   C9   180.00   0.0  0
 J6N  CONST_30  C19  C18  C17  C11  180.00   0.0  0
 J6N  CONST_31  CL   C20  C19  C18  180.00   0.0  0
 J6N  CONST_32  C23  C22  C20  CL   180.00   0.0  0
 J6N  CONST_33  H29  C9   C10  C5   180.00   0.0  0
 J6N  CONST_34  H28  C8   C7   C6   180.00   0.0  0
 J6N  CONST_35  H27  C6   C7   C8   180.00   0.0  0
 J6N  CONST_36  H32  C18  C19  C20  180.00   0.0  0
 J6N  CONST_37  H35  C23  C22  C20  180.00   0.0  0
 J6N  CONST_38  H33  C19  C20  C22  180.00   0.0  0
 J6N  CONST_39  H34  C22  C23  C17  180.00   0.0  0
 J6N  CONST_40  H1   O16  C14  C13  180.00   0.0  0
 J6N  Var_01    H24  C1   N2   N3   111.35  30.0  2
 J6N  Var_02    O15  C14  C13  C11   24.79  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 J6N  chir_01  C11  C13  C17  C7  positiv

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
 J6N  plan-1  C20  0.020
 J6N  plan-1  C22  0.020
 J6N  plan-1  C11  0.020
 J6N  plan-1  C17  0.020
 J6N  plan-1  C18  0.020
 J6N  plan-1  C19  0.020
 J6N  plan-1  C23  0.020
 J6N  plan-1  H34  0.020
 J6N  plan-1  H32  0.020
 J6N  plan-1  H33  0.020
 J6N  plan-1  H35  0.020
 J6N  plan-1  CL   0.020
 J6N  plan-2  N3   0.020
 J6N  plan-2  C5   0.020
 J6N  plan-2  C6   0.020
 J6N  plan-2  C7   0.020
 J6N  plan-2  C8   0.020
 J6N  plan-2  C10  0.020
 J6N  plan-2  N2   0.020
 J6N  plan-2  N4   0.020
 J6N  plan-2  C9   0.020
 J6N  plan-2  C11  0.020
 J6N  plan-2  H27  0.020
 J6N  plan-2  H28  0.020
 J6N  plan-2  H29  0.020
 J6N  plan-2  C1   0.020
 J6N  plan-3  C13  0.020
 J6N  plan-3  O15  0.020
 J6N  plan-3  O16  0.020
 J6N  plan-3  H1   0.020
 J6N  plan-3  C14  0.020

