# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 02:15:04 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 4-{[(2R,3R)-2-[(dichloroacetyl)amino]-3-hydroxy-3-(4-nitrophenyl)propyl]oxy}-4-oxobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]([C@@H](COC(=O)CCC(O)=O)NC(=O)C(Cl)Cl)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
 CL8  CL8  '4-{[(2R,3R)-2-[(dichloroacetyl)amino]-3-hydroxy-3-(4-nitrophenyl)propyl]oxy}-4-oxobutanoic acid'  ligand  42  27  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CL8
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
 CL8  C1    C   CH1    0  -0.416  39.6021  37.9676  -10.3287
 CL8  CL1   CL  CL     0  -0.055  40.7017  37.0718   -9.2973
 CL8  CL2   CL  CL     0  -0.089  38.2938  36.8844  -10.9020
 CL8  C2    C   C      0   0.630  40.3256  38.5000  -11.5693
 CL8  O2    O   O      0  -0.437  41.3713  38.0289  -11.9495
 CL8  N2    N   NH1    0  -0.641  39.6205  39.4488  -12.2170
 CL8  C3    C   CH1    0  -0.162  40.1386  40.1191  -13.3886
 CL8  C4    C   CH2    0  -0.197  39.8411  41.6183  -13.3477
 CL8  C5    C   CH1    0  -0.017  39.5278  39.5105  -14.6709
 CL8  O5    O   OH1    0  -0.652  38.1293  39.5867  -14.6704
 CL8  C6    C   C      0   0.131  40.0482  38.1046  -14.8628
 CL8  C7    C   C1     0  -0.274  41.3442  37.9224  -15.3401
 CL8  C8    C   C1     0  -0.254  41.8853  36.6599  -15.4743
 CL8  C9    C   C      0   0.236  41.1100  35.5628  -15.1211
 CL8  N9    N   N      1   0.329  41.6675  34.2283  -15.2493
 CL8  O9A   O   O     -1  -0.383  40.9705  33.2867  -14.9492
 CL8  O9B   O   O      0  -0.382  42.8037  34.1212  -15.6493
 CL8  C10   C   C1     0  -0.249  39.8138  35.7138  -14.6553
 CL8  C11   C   C1     0  -0.312  39.2875  36.9887  -14.5362
 CL8  O4    O   O2     0  -0.460  40.0659  42.2255  -12.0823
 CL8  O15   O   O      0  -0.573  40.8798  40.4720   -9.6558
 CL8  C15   C   C      0   0.451  41.8248  40.9109   -8.9664
 CL8  O16   O   OC    -1  -0.616  42.4112  40.3348   -8.0333
 CL8  C14   C   CH2    0  -0.589  42.3168  42.3259   -9.3254
 CL8  C13   C   CH2    0  -0.554  41.4016  43.0376  -10.3088
 CL8  C12   C   C      0   0.619  41.3133  42.3055  -11.6174
 CL8  O12   O   O      0  -0.470  42.2706  41.9099  -12.2368
 CL8  H1    H   HCH1   0   0.354  39.1429  38.7576   -9.7429
 CL8  H2    H   HNH1   0   0.411  38.8705  39.8949  -11.7108
 CL8  H3    H   HCH1   0   0.289  41.2159  39.9690  -13.4220
 CL8  H41C  H   HCH2   0   0.257  40.4244  42.1097  -14.1300
 CL8  H42C  H   HCH2   0   0.257  38.7863  41.7992  -13.5515
 CL8  H5    H   HCH1   0   0.272  39.8692  40.1136  -15.5193
 CL8  HA    H   HOH1   0   0.450  37.7946  39.2393  -13.8349
 CL8  H7    H   H      0   0.267  41.9449  38.7816  -15.6136
 CL8  H11   H   H      0   0.256  38.2702  37.0892  -14.1854
 CL8  H8    H   H      0   0.294  42.8916  36.5406  -15.8482
 CL8  H10   H   H      0   0.294  39.2112  34.8576  -14.3896
 CL8  H141  H   HCH2   0   0.240  42.4068  42.9246   -8.4155
 CL8  H142  H   HCH2   0   0.235  43.3306  42.2580   -9.7321
 CL8  H131  H   HCH2   0   0.247  40.4093  43.1800   -9.8822
 CL8  H132  H   HCH2   0   0.263  41.7962  44.0350  -10.5311

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
 CL8  C1   CL1   single    1.754  0.020  1.754
 CL8  C1   CL2   single    1.793  0.020  1.793
 CL8  C1   C2    single    1.532  0.020  1.532
 CL8  C2   O2    double    1.208  0.020  1.208
 CL8  C2   N2    single    1.348  0.020  1.348
 CL8  N2   C3    single    1.446  0.020  1.446
 CL8  C3   C4    single    1.529  0.020  1.529
 CL8  C3   C5    single    1.545  0.020  1.545
 CL8  C4   O4    single    1.421  0.020  1.421
 CL8  C5   O5    single    1.401  0.020  1.401
 CL8  C5   C6    single    1.511  0.020  1.511
 CL8  C6   C7    aromatic  1.393  0.020  1.393
 CL8  C6   C11   aromatic  1.389  0.020  1.389
 CL8  C7   C8    aromatic  1.380  0.020  1.380
 CL8  C8   C9    aromatic  1.389  0.020  1.389
 CL8  C9   N9    single    1.452  0.020  1.452
 CL8  C9   C10   aromatic  1.386  0.020  1.386
 CL8  N9   O9A   single    1.209  0.020  1.209
 CL8  N9   O9B   double    1.209  0.020  1.209
 CL8  C10  C11   aromatic  1.384  0.020  1.384
 CL8  O4   C12   single    1.334  0.020  1.334
 CL8  O15  C15   deloc     1.249  0.020  1.249
 CL8  C15  O16   deloc     1.244  0.020  1.244
 CL8  C15  C14   single    1.540  0.020  1.540
 CL8  C14  C13   single    1.520  0.020  1.520
 CL8  C13  C12   single    1.502  0.020  1.502
 CL8  C12  O12   double    1.207  0.020  1.207
 CL8  C1   H1    single    0.970  0.020  1.090
 CL8  N2   H2    single    0.890  0.020  1.040
 CL8  C3   H3    single    0.970  0.020  1.090
 CL8  C4   H41C  single    0.970  0.020  1.090
 CL8  C4   H42C  single    0.970  0.020  1.090
 CL8  C5   H5    single    0.970  0.020  1.090
 CL8  O5   HA    single    0.850  0.020  0.980
 CL8  C7   H7    single    0.930  0.020  1.080
 CL8  C11  H11   single    0.930  0.020  1.080
 CL8  C8   H8    single    0.930  0.020  1.080
 CL8  C10  H10   single    0.930  0.020  1.080
 CL8  C14  H141  single    0.970  0.020  1.090
 CL8  C14  H142  single    0.970  0.020  1.090
 CL8  C13  H131  single    0.970  0.020  1.090
 CL8  C13  H132  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
 CL8  H1    C1   C2    112.58  3.000
 CL8  H1    C1   CL2   107.68  3.000
 CL8  C2    C1   CL2   107.20  3.000
 CL8  H1    C1   CL1   108.64  3.000
 CL8  C2    C1   CL1   110.96  3.000
 CL8  CL2   C1   CL1   109.70  3.000
 CL8  N2    C2   O2    125.17  3.000
 CL8  N2    C2   C1    112.75  3.000
 CL8  O2    C2   C1    121.88  3.000
 CL8  H2    N2   C3    117.90  3.000
 CL8  H2    N2   C2    117.33  3.000
 CL8  C3    N2   C2    121.89  3.000
 CL8  H3    C3   C5    108.15  3.000
 CL8  H3    C3   C4    109.19  3.000
 CL8  C5    C3   C4    109.36  3.000
 CL8  H3    C3   N2    108.40  3.000
 CL8  C5    C3   N2    110.38  3.000
 CL8  C4    C3   N2    111.30  3.000
 CL8  H42C  C4   H41C  107.95  3.000
 CL8  H42C  C4   O4    104.40  3.000
 CL8  H41C  C4   O4    111.15  3.000
 CL8  H42C  C4   C3    110.26  3.000
 CL8  H41C  C4   C3    108.54  3.000
 CL8  O4    C4   C3    114.33  3.000
 CL8  H5    C5   C6    107.85  3.000
 CL8  H5    C5   O5    106.35  3.000
 CL8  C6    C5   O5    113.23  3.000
 CL8  H5    C5   C3    107.62  3.000
 CL8  C6    C5   C3    109.61  3.000
 CL8  O5    C5   C3    111.90  3.000
 CL8  HA    O5   C5    109.10  3.000
 CL8  C11   C6   C7    119.00  3.000
 CL8  C11   C6   C5    121.92  3.000
 CL8  C7    C6   C5    119.04  3.000
 CL8  H7    C7   C8    118.92  3.000
 CL8  H7    C7   C6    119.91  3.000
 CL8  C8    C7   C6    121.18  3.000
 CL8  H8    C8   C9    121.38  3.000
 CL8  H8    C8   C7    120.00  3.000
 CL8  C9    C8   C7    118.62  3.000
 CL8  C10   C9   N9    119.28  3.000
 CL8  C10   C9   C8    121.44  3.000
 CL8  N9    C9   C8    119.28  3.000
 CL8  O9B   N9   O9A   123.69  3.000
 CL8  O9B   N9   C9    118.13  3.000
 CL8  O9A   N9   C9    118.19  3.000
 CL8  H10   C10  C11   119.79  3.000
 CL8  H10   C10  C9    121.21  3.000
 CL8  C11   C10  C9    119.00  3.000
 CL8  H11   C11  C10   118.12  3.000
 CL8  H11   C11  C6    121.13  3.000
 CL8  C10   C11  C6    120.75  3.000
 CL8  C12   O4   C4    118.94  3.000
 CL8  C14   C15  O16   116.73  3.000
 CL8  C14   C15  O15   115.83  3.000
 CL8  O16   C15  O15   127.44  3.000
 CL8  H142  C14  H141  105.49  3.000
 CL8  H142  C14  C13   110.26  3.000
 CL8  H141  C14  C13   109.37  3.000
 CL8  H142  C14  C15   108.99  3.000
 CL8  H141  C14  C15   109.60  3.000
 CL8  C13   C14  C15   112.86  3.000
 CL8  H132  C13  H131  106.77  3.000
 CL8  H132  C13  C12   106.75  3.000
 CL8  H131  C13  C12   110.57  3.000
 CL8  H132  C13  C14   109.92  3.000
 CL8  H131  C13  C14   110.87  3.000
 CL8  C12   C13  C14   111.77  3.000
 CL8  O12   C12  C13   124.07  3.000
 CL8  O12   C12  O4    122.91  3.000
 CL8  C13   C12  O4    112.83  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
 CL8  CONST_01  C9    C8   C7   C6     0.00   0.0  0
 CL8  CONST_02  C9    C10  C11  C6     0.00   0.0  0
 CL8  CONST_03  C10   C11  C6   C7     0.00   0.0  0
 CL8  CONST_04  C10   C9   C8   C7     0.00   0.0  0
 CL8  CONST_05  C11   C6   C7   C8     0.00   0.0  0
 CL8  CONST_06  C11   C10  C9   C8     0.00   0.0  0
 CL8  CONST_07  C8    C7   C6   C5   180.00   0.0  0
 CL8  CONST_08  C10   C11  C6   C5   180.00   0.0  0
 CL8  CONST_09  N9    C9   C8   C7   180.00   0.0  0
 CL8  CONST_10  C11   C10  C9   N9   180.00   0.0  0
 CL8  CONST_11  H8    C8   C7   C6   180.00   0.0  0
 CL8  CONST_12  H10   C10  C11  C6   180.00   0.0  0
 CL8  CONST_13  H11   C11  C6   C7   180.00   0.0  0
 CL8  CONST_14  H7    C7   C8   C9   180.00   0.0  0
 CL8  CONST_15  O9A   N9   C9   C8   180.00   0.0  0
 CL8  CONST_16  O9B   N9   C9   C8     0.00   0.0  0
 CL8  CONST_17  C10   C9   N9   O9A    0.00   0.0  0
 CL8  CONST_18  C10   C9   N9   O9B  180.00   0.0  0
 CL8  CONST_19  C3    N2   C2   C1   180.00   0.0  0
 CL8  CONST_20  C3    N2   C2   O2     0.00   0.0  0
 CL8  Var_01    O2    C2   C1   CL1   19.88  30.0  3
 CL8  Var_02    C13   C12  O4   C4   176.82  30.0  3
 CL8  Var_03    C14   C13  C12  O4   136.09  30.0  1
 CL8  Var_04    C13   C14  C15  O15    9.90  30.0  3
 CL8  Var_05    C12   C13  C14  C15  -61.57  30.0  3
 CL8  Var_06    H41C  C4   O4   C12  -56.43  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
 CL8  chir_01  C3  N2  C4  C5  positiv
 CL8  chir_02  C5  O5  C3  C6  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
 CL8  plan-1  C5   0.020
 CL8  plan-1  C6   0.020
 CL8  plan-1  C7   0.020
 CL8  plan-1  C8   0.020
 CL8  plan-1  C9   0.020
 CL8  plan-1  N9   0.020
 CL8  plan-1  C10  0.020
 CL8  plan-1  C11  0.020
 CL8  plan-1  H7   0.020
 CL8  plan-1  H11  0.020
 CL8  plan-1  H8   0.020
 CL8  plan-1  H10  0.020
 CL8  plan-2  C1   0.020
 CL8  plan-2  C2   0.020
 CL8  plan-2  O2   0.020
 CL8  plan-2  N2   0.020
 CL8  plan-2  C3   0.020
 CL8  plan-2  H2   0.020
 CL8  plan-3  C9   0.020
 CL8  plan-3  N9   0.020
 CL8  plan-3  O9A  0.020
 CL8  plan-3  O9B  0.020
 CL8  plan-4  O15  0.020
 CL8  plan-4  C15  0.020
 CL8  plan-4  O16  0.020
 CL8  plan-4  C14  0.020
 CL8  plan-5  O4   0.020
 CL8  plan-5  C13  0.020
 CL8  plan-5  C12  0.020
 CL8  plan-5  O12  0.020

