# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 22:46:21 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: trans-4-[({[(2-chlorobenzyl)oxy]carbonyl}amino)methyl]cyclohexanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CC[C@H](CC1)CNC(=O)OCc2ccccc2Cl
#
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
 4LB  4LB  'trans-4-[({[(2-chlorobenzyl)oxy]carbonyl}amino)methyl]cyclohexanecarboxylic acid'  ligand  41  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4LB
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
 4LB  C1   C   CR16   0  -0.227  -4.3667   2.7466  -0.5945
 4LB  C2   C   CR16   0  -0.276  -5.6974   2.6335  -0.2233
 4LB  C3   C   CR16   0  -0.197  -6.1692   1.4320   0.2837
 4LB  C9   C   C      0   0.767  -0.8053  -1.3364  -0.1035
 4LB  C12  C   CH2    0  -0.234   1.5708  -1.6821  -0.6064
 4LB  C13  C   CH1    0  -0.278   2.7866  -0.7630  -0.6119
 4LB  C15  C   CH2    0  -0.415   4.0699  -1.5904  -0.6290
 4LB  C16  C   CH2    0  -0.418   5.3124  -0.7067  -0.6268
 4LB  C19  C   CH2    0  -0.408   4.0399   1.0842   0.5732
 4LB  C20  C   CH2    0  -0.411   2.7990   0.1963   0.5757
 4LB  C21  C   C      0   0.426   6.6135   1.1112   0.5837
 4LB  C4   C   CR6    0  -0.093  -5.2990   0.3621   0.4096
 4LB  C5   C   CR6    0   0.101  -3.9576   0.4462   0.0416
 4LB  C6   C   CR16   0  -0.322  -3.5086   1.6633  -0.4632
 4LB  O8   O   O2     0  -0.495  -1.7840  -0.4376  -0.3067
 4LB  O10  O   O      0  -0.520  -0.9623  -2.3670   0.5198
 4LB  N11  N   NH1    0  -0.667   0.3371  -0.9287  -0.6707
 4LB  C17  C   CH1    0  -0.378   5.3240   0.2632   0.5562
 4LB  O22  O   OC    -1  -0.622   7.6869   0.4924   0.4207
 4LB  O23  O   O      0  -0.605   6.5028   2.3384   0.7798
 4LB  CL1  CL  CL     0  -0.125  -5.9131  -1.1300   1.0553
 4LB  H1   H   HCR6   0   0.264  -3.9890   3.6806  -0.9883
 4LB  H2   H   HCR6   0   0.268  -6.3723   3.4727  -0.3237
 4LB  H3   H   HCR6   0   0.281  -7.2045   1.3277   0.5787
 4LB  H4   H   HCH2   0   0.256  -2.9972  -1.0137   1.2717
 4LB  H5   H   HCH2   0   0.252  -3.4837  -1.6131  -0.3105
 4LB  H6   H   HCH2   0   0.236   1.6365  -2.3825  -1.4463
 4LB  H7   H   HCH2   0   0.235   1.5695  -2.2784   0.3077
 4LB  H8   H   HCH1   0   0.218   2.7622  -0.1662  -1.5354
 4LB  H9   H   HCH2   0   0.206   4.0856  -2.2395   0.2551
 4LB  H10  H   HCH2   0   0.224   4.0795  -2.2517  -1.5009
 4LB  H11  H   HCH2   0   0.222   6.2107  -1.3246  -0.6091
 4LB  H12  H   HCH2   0   0.200   5.3442  -0.1354  -1.5630
 4LB  H13  H   HCH2   0   0.197   4.0120   1.7360  -0.3069
 4LB  H14  H   HCH2   0   0.215   4.0214   1.7431   1.4429
 4LB  H15  H   HCH2   0   0.224   1.8992   0.8169   0.5739
 4LB  H16  H   HCH2   0   0.202   2.7697  -0.3905   1.5028
 4LB  H17  H   HCR6   0   0.264  -2.4748   1.7744  -0.7578
 4LB  H18  H   HNH1   0   0.399   0.3262  -0.0824  -1.2190
 4LB  H19  H   HCH1   0   0.209   5.3370  -0.3512   1.4706
 4LB  C7   C   CH2    0  -0.171  -3.0623  -0.7493   0.2125

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
 4LB  O23  C21  deloc     1.248  0.020  1.248
 4LB  O22  C21  deloc     1.250  0.020  1.250
 4LB  C21  C17  single    1.544  0.020  1.544
 4LB  C17  C19  single    1.524  0.020  1.524
 4LB  C17  C16  single    1.530  0.020  1.530
 4LB  C19  C20  single    1.526  0.020  1.526
 4LB  C16  C15  single    1.525  0.020  1.525
 4LB  C20  C13  single    1.527  0.020  1.527
 4LB  C15  C13  single    1.527  0.020  1.527
 4LB  C13  C12  single    1.524  0.020  1.524
 4LB  C12  N11  single    1.447  0.020  1.447
 4LB  N11  C9   single    1.339  0.020  1.339
 4LB  O10  C9   double    1.215  0.020  1.215
 4LB  C9   O8   single    1.344  0.020  1.344
 4LB  O8   C7   single    1.414  0.020  1.414
 4LB  C7   C5   single    1.503  0.020  1.503
 4LB  C5   C6   aromatic  1.392  0.020  1.392
 4LB  C5   C4   aromatic  1.393  0.020  1.393
 4LB  C6   C1   aromatic  1.388  0.020  1.388
 4LB  CL1  C4   single    1.738  0.020  1.738
 4LB  C4   C3   aromatic  1.385  0.020  1.385
 4LB  C1   C2   aromatic  1.386  0.020  1.386
 4LB  C3   C2   aromatic  1.387  0.020  1.387
 4LB  C1   H1   single    0.930  0.020  1.080
 4LB  C2   H2   single    0.930  0.020  1.080
 4LB  C3   H3   single    0.930  0.020  1.080
 4LB  C7   H4   single    0.970  0.020  1.090
 4LB  C7   H5   single    0.970  0.020  1.090
 4LB  C12  H6   single    0.970  0.020  1.090
 4LB  C12  H7   single    0.970  0.020  1.090
 4LB  C13  H8   single    0.970  0.020  1.090
 4LB  C15  H9   single    0.970  0.020  1.090
 4LB  C15  H10  single    0.970  0.020  1.090
 4LB  C16  H11  single    0.970  0.020  1.090
 4LB  C16  H12  single    0.970  0.020  1.090
 4LB  C19  H13  single    0.970  0.020  1.090
 4LB  C19  H14  single    0.970  0.020  1.090
 4LB  C20  H15  single    0.970  0.020  1.090
 4LB  C20  H16  single    0.970  0.020  1.090
 4LB  C6   H17  single    0.930  0.020  1.080
 4LB  N11  H18  single    0.860  0.020  1.020
 4LB  C17  H19  single    0.970  0.020  1.090

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
 4LB  H1   C1   C6   119.50  3.000
 4LB  H1   C1   C2   120.21  3.000
 4LB  C6   C1   C2   120.29  3.000
 4LB  H2   C2   C3   119.59  3.000
 4LB  H2   C2   C1   120.73  3.000
 4LB  C3   C2   C1   119.68  3.000
 4LB  H3   C3   C4   120.15  3.000
 4LB  H3   C3   C2   120.60  3.000
 4LB  C4   C3   C2   119.26  3.000
 4LB  N11  C9   O10  125.87  3.000
 4LB  O10  C9   O8   123.42  3.000
 4LB  N11  C9   O8   110.71  3.000
 4LB  H7   C12  H6   107.03  3.000
 4LB  H7   C12  N11  108.70  3.000
 4LB  H6   C12  N11  110.49  3.000
 4LB  H7   C12  C13  109.47  3.000
 4LB  H6   C12  C13  109.57  3.000
 4LB  N11  C12  C13  111.47  3.000
 4LB  H8   C13  C20  108.20  3.000
 4LB  H8   C13  C15  107.66  3.000
 4LB  C20  C13  C15  110.02  3.000
 4LB  H8   C13  C12  108.21  3.000
 4LB  C15  C13  C12  110.10  3.000
 4LB  C20  C13  C12  112.49  3.000
 4LB  H10  C15  H9   106.53  3.000
 4LB  H10  C15  C16  110.13  3.000
 4LB  H9   C15  C16  109.28  3.000
 4LB  H10  C15  C13  110.11  3.000
 4LB  H9   C15  C13  108.88  3.000
 4LB  C16  C15  C13  111.76  3.000
 4LB  H12  C16  H11  106.56  3.000
 4LB  H12  C16  C17  109.24  3.000
 4LB  H11  C16  C17  109.90  3.000
 4LB  H12  C16  C15  108.92  3.000
 4LB  H11  C16  C15  110.05  3.000
 4LB  C17  C16  C15  112.01  3.000
 4LB  H14  C19  H13  106.29  3.000
 4LB  H14  C19  C17  110.39  3.000
 4LB  H13  C19  C17  109.45  3.000
 4LB  H14  C19  C20  109.65  3.000
 4LB  H13  C19  C20  109.08  3.000
 4LB  C17  C19  C20  111.83  3.000
 4LB  H16  C20  H15  106.44  3.000
 4LB  H16  C20  C19  109.52  3.000
 4LB  H15  C20  C19  109.82  3.000
 4LB  H16  C20  C13  108.71  3.000
 4LB  H15  C20  C13  110.41  3.000
 4LB  C19  C20  C13  111.77  3.000
 4LB  O23  C21  O22  125.72  3.000
 4LB  O22  C21  C17  116.31  3.000
 4LB  O23  C21  C17  117.97  3.000
 4LB  CL1  C4   C5   119.35  3.000
 4LB  CL1  C4   C3   118.36  3.000
 4LB  C5   C4   C3   122.29  3.000
 4LB  C6   C5   C4   117.33  3.000
 4LB  C4   C5   C7   119.68  3.000
 4LB  C6   C5   C7   122.99  3.000
 4LB  H17  C6   C5   119.83  3.000
 4LB  H17  C6   C1   119.03  3.000
 4LB  C5   C6   C1   121.14  3.000
 4LB  C9   O8   C7   117.08  3.000
 4LB  H18  N11  C12  118.05  3.000
 4LB  H18  N11  C9   118.46  3.000
 4LB  C12  N11  C9   123.37  3.000
 4LB  H19  C17  C21  106.37  3.000
 4LB  H19  C17  C19  107.52  3.000
 4LB  C21  C17  C19  114.06  3.000
 4LB  H19  C17  C16  106.76  3.000
 4LB  C19  C17  C16  110.10  3.000
 4LB  C21  C17  C16  111.62  3.000
 4LB  H5   C7   H4   107.16  3.000
 4LB  H5   C7   O8   110.27  3.000
 4LB  H4   C7   O8   110.79  3.000
 4LB  H5   C7   C5   110.13  3.000
 4LB  H4   C7   C5   109.75  3.000
 4LB  O8   C7   C5   108.74  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
 4LB  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 4LB  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 4LB  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 4LB  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 4LB  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 4LB  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 4LB  CONST_07  C7   C5   C6   C1    180.00   0.0  0
 4LB  CONST_08  CL1  C4   C3   C2    180.00   0.0  0
 4LB  CONST_09  C7   C5   C4   C3    180.00   0.0  0
 4LB  CONST_10  CL1  C4   C5   C6    180.00   0.0  0
 4LB  CONST_11  H3   C3   C2   C1    180.00   0.0  0
 4LB  CONST_12  H17  C6   C1   C2    180.00   0.0  0
 4LB  CONST_13  H1   C1   C2   C3    180.00   0.0  0
 4LB  CONST_14  H2   C2   C3   C4    180.00   0.0  0
 4LB  Var_01    C17  C19  C20  C13   -56.31  30.0  1
 4LB  Var_02    C17  C16  C15  C13    55.74  30.0  1
 4LB  Var_03    O8   C7   C5   C4    176.39  30.0  2
 4LB  Var_04    C13  C12  N11  C9   -148.74  30.0  1
 4LB  Var_05    C5   C7   O8   C9    172.65  30.0  3
 4LB  Var_06    N11  C9   O8   C7    178.62  30.0  1

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
 4LB  chir_01  C13  C20  C15  C12  negativ
 4LB  chir_02  C17  C21  C19  C16  negativ

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
 4LB  plan-1  C1   0.020
 4LB  plan-1  C2   0.020
 4LB  plan-1  C3   0.020
 4LB  plan-1  C4   0.020
 4LB  plan-1  C5   0.020
 4LB  plan-1  C6   0.020
 4LB  plan-1  CL1  0.020
 4LB  plan-1  H1   0.020
 4LB  plan-1  H2   0.020
 4LB  plan-1  H3   0.020
 4LB  plan-1  H17  0.020
 4LB  plan-1  C7   0.020
 4LB  plan-2  C21  0.020
 4LB  plan-2  C17  0.020
 4LB  plan-2  O22  0.020
 4LB  plan-2  O23  0.020
 4LB  plan-3  C9   0.020
 4LB  plan-3  O8   0.020
 4LB  plan-3  O10  0.020
 4LB  plan-3  N11  0.020

