# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:51:02 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: 2,2-dichloro-N-[(1S,2S)-1,3-dihydroxy-1-(4-nitrophenyl)propan-2-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](NC(=O)C(Cl)Cl)[C@@H](O)c1ccc(cc1)[N+]([O-])=O
#
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
 LCL  LCL  2,2-dichloro-N-[(1S,2S)-1,3-dihydroxy-1-(4-nitrophenyl)propan-2-yl]acetamide  ligand  32  20  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LCL
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
 LCL  C1   C   CH1    0  -0.429  -1.8670  -1.5013   0.2335
 LCL  CL1  CL  CL     0  -0.059  -3.0013  -2.3569  -0.8235
 LCL  CL2  CL  CL     0  -0.052  -0.5991  -2.6017   0.7957
 LCL  C2   C   C      0   0.612  -1.2098  -0.3740  -0.5643
 LCL  O2   O   O      0  -0.439  -0.5711  -0.6087  -1.5666
 LCL  N2   N   NH1    0  -0.636  -1.4223   0.8371  -0.0340
 LCL  C3   C   CH1    0  -0.164  -0.9103   2.0631  -0.6102
 LCL  C4   C   CH2    0  -0.164  -2.0112   3.1196  -0.6074
 LCL  O4   O   OH1    0  -0.672  -2.5808   3.2242   0.6794
 LCL  C5   C   CH1    0  -0.009   0.3911   2.5286   0.0787
 LCL  O5   O   OH1    0  -0.652   0.2027   3.0323   1.3735
 LCL  C6   C   CR6    0   0.116   1.4141   1.4171   0.0345
 LCL  C7   C   CR16   0  -0.274   2.1883   1.2411  -1.1089
 LCL  C8   C   CR16   0  -0.255   3.0870   0.1970  -1.2092
 LCL  C9   C   CR6    0   0.237   3.2021  -0.6853  -0.1436
 LCL  N9   N   N      1   0.328   4.1355  -1.7942  -0.2371
 LCL  O9A  O   O     -1  -0.382   4.7937  -1.9024  -1.2458
 LCL  O9B  O   O      0  -0.382   4.2089  -2.5587   0.6969
 LCL  C10  C   CR16   0  -0.245   2.4498  -0.5294   1.0103
 LCL  C11  C   CR16   0  -0.308   1.5633   0.5297   1.0944
 LCL  H1   H   HCH1   0   0.364  -2.4189  -1.1594   1.1060
 LCL  H2   H   HNH1   0   0.412  -2.0537   0.9268   0.7487
 LCL  H3   H   HCH1   0   0.293  -0.6585   1.8679  -1.6541
 LCL  H4   H   HCH2   0   0.221  -1.5847   4.0736  -0.9384
 LCL  H5   H   HCH2   0   0.240  -2.7605   2.8263  -1.3480
 LCL  H6   H   HOH1   0   0.467  -3.5227   3.3880   0.5880
 LCL  H7   H   HCH1   0   0.265   0.7688   3.3616  -0.5237
 LCL  H8   H   HOH1   0   0.451  -0.4713   2.5277   1.8387
 LCL  H9   H   HCR6   0   0.267   2.0905   1.9311  -1.9380
 LCL  H10  H   HCR6   0   0.294   3.6828   0.0813  -2.1028
 LCL  H13  H   HCR6   0   0.293   2.5447  -1.2163   1.8382
 LCL  H14  H   HCR6   0   0.262   0.9896   0.6481   2.0036

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
 LCL  CL1  C1   single    1.771  0.020  1.771
 LCL  C1   CL2  single    1.770  0.020  1.770
 LCL  C1   C2   single    1.529  0.020  1.529
 LCL  C2   O2   double    1.212  0.020  1.212
 LCL  C2   N2   single    1.339  0.020  1.339
 LCL  N2   C3   single    1.448  0.020  1.448
 LCL  C4   C3   single    1.526  0.020  1.526
 LCL  C4   O4   single    1.411  0.020  1.411
 LCL  C3   C5   single    1.544  0.020  1.544
 LCL  C11  C10  aromatic  1.384  0.020  1.384
 LCL  C11  C6   aromatic  1.390  0.020  1.390
 LCL  C10  C9   aromatic  1.386  0.020  1.386
 LCL  C5   C6   single    1.511  0.020  1.511
 LCL  C5   O5   single    1.402  0.020  1.402
 LCL  C6   C7   aromatic  1.392  0.020  1.392
 LCL  O9B  N9   double    1.209  0.020  1.209
 LCL  C9   N9   single    1.452  0.020  1.452
 LCL  C9   C8   aromatic  1.388  0.020  1.388
 LCL  C7   C8   aromatic  1.381  0.020  1.381
 LCL  N9   O9A  single    1.209  0.020  1.209
 LCL  C1   H1   single    0.970  0.020  1.090
 LCL  N2   H2   single    0.860  0.020  1.020
 LCL  C3   H3   single    0.970  0.020  1.090
 LCL  C4   H4   single    0.970  0.020  1.090
 LCL  C4   H5   single    0.970  0.020  1.090
 LCL  O4   H6   single    0.850  0.020  0.980
 LCL  C5   H7   single    0.970  0.020  1.090
 LCL  O5   H8   single    0.850  0.020  0.980
 LCL  C7   H9   single    0.930  0.020  1.080
 LCL  C8   H10  single    0.930  0.020  1.080
 LCL  C10  H13  single    0.930  0.020  1.080
 LCL  C11  H14  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
 LCL  H1   C1   C2   113.88  3.000
 LCL  H1   C1   CL2  107.70  3.000
 LCL  C2   C1   CL2  108.43  3.000
 LCL  H1   C1   CL1  107.80  3.000
 LCL  C2   C1   CL1  108.66  3.000
 LCL  CL2  C1   CL1  110.36  3.000
 LCL  N2   C2   O2   125.92  3.000
 LCL  N2   C2   C1   113.07  3.000
 LCL  O2   C2   C1   121.02  3.000
 LCL  H2   N2   C3   117.02  3.000
 LCL  H2   N2   C2   119.12  3.000
 LCL  C3   N2   C2   123.50  3.000
 LCL  H3   C3   C5   106.63  3.000
 LCL  H3   C3   C4   106.98  3.000
 LCL  C5   C3   C4   113.48  3.000
 LCL  H3   C3   N2   108.10  3.000
 LCL  C5   C3   N2   112.06  3.000
 LCL  C4   C3   N2   109.29  3.000
 LCL  H5   C4   H4   107.19  3.000
 LCL  H5   C4   O4   111.15  3.000
 LCL  H4   C4   O4   111.58  3.000
 LCL  H5   C4   C3   107.90  3.000
 LCL  H4   C4   C3   108.75  3.000
 LCL  O4   C4   C3   110.14  3.000
 LCL  H6   O4   C4   108.77  3.000
 LCL  H7   C5   C6   108.05  3.000
 LCL  H7   C5   O5   106.33  3.000
 LCL  C6   C5   O5   112.47  3.000
 LCL  H7   C5   C3   105.94  3.000
 LCL  O5   C5   C3   114.02  3.000
 LCL  C6   C5   C3   109.61  3.000
 LCL  H8   O5   C5   110.63  3.000
 LCL  C11  C6   C7   119.06  3.000
 LCL  C7   C6   C5   119.57  3.000
 LCL  C11  C6   C5   121.32  3.000
 LCL  H9   C7   C8   118.99  3.000
 LCL  H9   C7   C6   119.87  3.000
 LCL  C8   C7   C6   121.14  3.000
 LCL  H10  C8   C9   121.42  3.000
 LCL  H10  C8   C7   119.99  3.000
 LCL  C9   C8   C7   118.59  3.000
 LCL  C10  C9   N9   119.22  3.000
 LCL  N9   C9   C8   119.28  3.000
 LCL  C10  C9   C8   121.50  3.000
 LCL  O9B  N9   O9A  123.68  3.000
 LCL  O9A  N9   C9   118.15  3.000
 LCL  O9B  N9   C9   118.16  3.000
 LCL  H13  C10  C11  119.77  3.000
 LCL  H13  C10  C9   121.26  3.000
 LCL  C11  C10  C9   118.97  3.000
 LCL  H14  C11  C10  118.34  3.000
 LCL  H14  C11  C6   120.93  3.000
 LCL  C10  C11  C6   120.73  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
 LCL  CONST_01  C9   C10  C11  C6     0.00   0.0  0
 LCL  CONST_02  C9   C8   C7   C6     0.00   0.0  0
 LCL  CONST_03  C10  C11  C6   C7     0.00   0.0  0
 LCL  CONST_04  C10  C9   C8   C7     0.00   0.0  0
 LCL  CONST_05  C11  C10  C9   C8     0.00   0.0  0
 LCL  CONST_06  C11  C6   C7   C8     0.00   0.0  0
 LCL  CONST_07  C10  C11  C6   C5   180.00   0.0  0
 LCL  CONST_08  C8   C7   C6   C5   180.00   0.0  0
 LCL  CONST_09  N9   C9   C8   C7   180.00   0.0  0
 LCL  CONST_10  C11  C10  C9   N9   180.00   0.0  0
 LCL  CONST_11  H13  C10  C11  C6   180.00   0.0  0
 LCL  CONST_12  H10  C8   C7   C6   180.00   0.0  0
 LCL  CONST_13  H14  C11  C6   C7   180.00   0.0  0
 LCL  CONST_14  H9   C7   C8   C9   180.00   0.0  0
 LCL  CONST_15  O9B  N9   C9   C8   180.00   0.0  0
 LCL  CONST_16  O9A  N9   C9   C8     0.00   0.0  0
 LCL  CONST_17  C10  C9   N9   O9A  180.00   0.0  0
 LCL  CONST_18  C10  C9   N9   O9B    0.00   0.0  0
 LCL  CONST_19  C3   N2   C2   C1   180.00   0.0  0
 LCL  CONST_20  C3   N2   C2   O2     0.00   0.0  0
 LCL  CONST_21  H2   N2   C2   C1     0.00   0.0  0
 LCL  Var_01    O2   C2   C1   CL1  -59.30  30.0  3

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
 LCL  chir_01  C3  N2  C4  C5  negativ
 LCL  chir_02  C5  O5  C3  C6  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
 LCL  plan-1  C5   0.020
 LCL  plan-1  C6   0.020
 LCL  plan-1  C7   0.020
 LCL  plan-1  C8   0.020
 LCL  plan-1  C9   0.020
 LCL  plan-1  N9   0.020
 LCL  plan-1  C10  0.020
 LCL  plan-1  C11  0.020
 LCL  plan-1  H9   0.020
 LCL  plan-1  H10  0.020
 LCL  plan-1  H13  0.020
 LCL  plan-1  H14  0.020
 LCL  plan-2  C1   0.020
 LCL  plan-2  C2   0.020
 LCL  plan-2  O2   0.020
 LCL  plan-2  N2   0.020
 LCL  plan-2  C3   0.020
 LCL  plan-2  H2   0.020
 LCL  plan-3  C9   0.020
 LCL  plan-3  N9   0.020
 LCL  plan-3  O9A  0.020
 LCL  plan-3  O9B  0.020

