# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 20:01:00 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  43  27  .  2021-08-08  2021-08-08  
;
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  -0.431  38.5280  37.5335  -10.7620
 CL8  CL1   CL  CL     0  -0.054  39.0948  37.4048   -9.0936
 CL8  CL2   CL  CL     0  -0.052  38.2176  35.9244  -11.4401
 CL8  C2    C   C      0   0.615  39.6146  38.2003  -11.6078
 CL8  O2    O   O      0  -0.428  40.7535  37.7937  -11.6010
 CL8  N2    N   NH1    0  -0.643  39.1554  39.2315  -12.3341
 CL8  C3    C   CH1    0  -0.170  39.9918  40.0091  -13.2241
 CL8  C4    C   CH2    0  -0.194  39.7089  41.4949  -13.0396
 CL8  C5    C   CH1    0  -0.025  39.7969  39.5906  -14.6959
 CL8  O5    O   OH1    0  -0.650  38.5229  39.9146  -15.1796
 CL8  C6    C   CR6    0   0.127  40.1592  38.1313  -14.8525
 CL8  C7    C   CR16   0  -0.273  41.5034  37.7740  -14.9276
 CL8  C8    C   CR16   0  -0.253  41.8883  36.4500  -14.9975
 CL8  C9    C   CR6    0   0.238  40.9049  35.4700  -14.9870
 CL8  N9    N   N      1   0.329  41.2944  34.0714  -15.0505
 CL8  O9A   O   O     -1  -0.380  40.4218  33.2350  -15.0333
 CL8  O9B   O   O      0  -0.380  42.4733  33.8118  -15.1166
 CL8  C10   C   CR16   0  -0.244  39.5604  35.7959  -14.9216
 CL8  C11   C   CR16   0  -0.323  39.1955  37.1301  -14.8612
 CL8  O4    O   O2     0  -0.459  39.9961  41.9057  -11.7052
 CL8  O15   O   O      0  -0.439  43.3736  40.6013   -9.6958
 CL8  C15   C   C      0   0.550  43.7312  41.7519   -9.6709
 CL8  O16   O   OH1    0  -0.596  45.0071  42.1216   -9.6942
 CL8  C14   C   CH2    0  -0.584  42.8058  42.9334   -9.5643
 CL8  C13   C   CH2    0  -0.587  41.3804  42.5940   -9.9440
 CL8  C12   C   C      0   0.614  41.2554  42.2028  -11.3902
 CL8  O12   O   O      0  -0.443  42.1665  42.1701  -12.1770
 CL8  H1    H   HCH1   0   0.365  37.5846  38.0747  -10.7524
 CL8  H2    H   HNH1   0   0.418  38.1993  39.5252  -12.2001
 CL8  H3    H   HCH1   0   0.297  41.0316  39.8074  -12.9618
 CL8  H41C  H   HCH2   0   0.265  40.2794  42.0772  -13.7646
 CL8  H42C  H   HCH2   0   0.271  38.6523  41.7148  -13.1878
 CL8  H5    H   HCH1   0   0.281  40.5001  40.1807  -15.2907
 CL8  HA    H   HOH1   0   0.455  37.8431  39.4759  -14.6572
 CL8  H7    H   HCR6   0   0.270  42.2672  38.5416  -14.9301
 CL8  H11   H   HCR6   0   0.264  38.1395  37.3599  -14.8203
 CL8  H8    H   HCR6   0   0.296  42.9362  36.1960  -15.0594
 CL8  H10   H   HCR6   0   0.297  38.7968  35.0326  -14.9149
 CL8  H16   H   HOH1   0   0.478  45.5786  41.3395   -9.7201
 CL8  H141  H   HCH2   0   0.305  42.8298  43.2737   -8.5248
 CL8  H142  H   HCH2   0   0.282  43.1896  43.7632  -10.1591
 CL8  H131  H   HCH2   0   0.287  40.9875  41.7855   -9.3237
 CL8  H132  H   HCH2   0   0.302  40.7319  43.4537   -9.7598

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    1.767  0.020  1.767
 CL8  C1   CL2   single    1.773  0.020  1.773
 CL8  C1   C2    single    1.530  0.020  1.530
 CL8  C2   O2    double    1.209  0.020  1.209
 CL8  C2   N2    single    1.342  0.020  1.342
 CL8  N2   C3    single    1.448  0.020  1.448
 CL8  C3   C4    single    1.524  0.020  1.524
 CL8  C3   C5    single    1.542  0.020  1.542
 CL8  C4   O4    single    1.425  0.020  1.425
 CL8  C5   O5    single    1.401  0.020  1.401
 CL8  C5   C6    single    1.512  0.020  1.512
 CL8  C6   C7    aromatic  1.393  0.020  1.393
 CL8  C6   C11   aromatic  1.390  0.020  1.390
 CL8  C7   C8    aromatic  1.381  0.020  1.381
 CL8  C8   C9    aromatic  1.388  0.020  1.388
 CL8  C9   N9    single    1.453  0.020  1.453
 CL8  C9   C10   aromatic  1.385  0.020  1.385
 CL8  N9   O9A   single    1.209  0.020  1.209
 CL8  N9   O9B   double    1.209  0.020  1.209
 CL8  C10  C11   aromatic  1.385  0.020  1.385
 CL8  O4   C12   single    1.332  0.020  1.332
 CL8  O15  C15   double    1.205  0.020  1.205
 CL8  C15  O16   single    1.329  0.020  1.329
 CL8  C15  C14   single    1.505  0.020  1.505
 CL8  C14  C13   single    1.514  0.020  1.514
 CL8  C13  C12   single    1.503  0.020  1.503
 CL8  C12  O12   double    1.204  0.020  1.204
 CL8  C1   H1    single    0.970  0.020  1.090
 CL8  N2   H2    single    0.860  0.020  1.020
 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  O16  H16   single    0.850  0.020  0.980
 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    113.83  3.000
 CL8  H1    C1   CL2   107.65  3.000
 CL8  C2    C1   CL2   107.96  3.000
 CL8  H1    C1   CL1   107.83  3.000
 CL8  C2    C1   CL1   109.02  3.000
 CL8  CL2   C1   CL1   110.56  3.000
 CL8  N2    C2   O2    125.70  3.000
 CL8  N2    C2   C1    113.02  3.000
 CL8  O2    C2   C1    121.28  3.000
 CL8  H2    N2   C3    118.21  3.000
 CL8  H2    N2   C2    118.41  3.000
 CL8  C3    N2   C2    123.20  3.000
 CL8  H3    C3   C5    107.44  3.000
 CL8  H3    C3   C4    109.15  3.000
 CL8  C5    C3   C4    110.90  3.000
 CL8  H3    C3   N2    107.67  3.000
 CL8  C5    C3   N2    111.58  3.000
 CL8  C4    C3   N2    109.99  3.000
 CL8  H42C  C4   H41C  108.00  3.000
 CL8  H42C  C4   O4    105.35  3.000
 CL8  H41C  C4   O4    111.28  3.000
 CL8  H42C  C4   C3    111.13  3.000
 CL8  H41C  C4   C3    110.05  3.000
 CL8  O4    C4   C3    110.92  3.000
 CL8  H5    C5   C6    108.08  3.000
 CL8  H5    C5   O5    105.79  3.000
 CL8  C6    C5   O5    113.92  3.000
 CL8  H5    C5   C3    106.93  3.000
 CL8  C6    C5   C3    109.30  3.000
 CL8  O5    C5   C3    112.44  3.000
 CL8  HA    O5   C5    110.45  3.000
 CL8  C11   C6   C7    118.95  3.000
 CL8  C11   C6   C5    122.00  3.000
 CL8  C7    C6   C5    118.98  3.000
 CL8  H7    C7   C8    118.89  3.000
 CL8  H7    C7   C6    119.93  3.000
 CL8  C8    C7   C6    121.18  3.000
 CL8  H8    C8   C9    121.45  3.000
 CL8  H8    C8   C7    119.93  3.000
 CL8  C9    C8   C7    118.63  3.000
 CL8  C10   C9   N9    119.26  3.000
 CL8  C10   C9   C8    121.46  3.000
 CL8  N9    C9   C8    119.28  3.000
 CL8  O9B   N9   O9A   123.79  3.000
 CL8  O9B   N9   C9    118.06  3.000
 CL8  O9A   N9   C9    118.15  3.000
 CL8  H10   C10  C11   119.64  3.000
 CL8  H10   C10  C9    121.37  3.000
 CL8  C11   C10  C9    118.99  3.000
 CL8  H11   C11  C10   117.63  3.000
 CL8  H11   C11  C6    121.59  3.000
 CL8  C10   C11  C6    120.78  3.000
 CL8  C12   O4   C4    118.44  3.000
 CL8  C14   C15  O16   111.92  3.000
 CL8  C14   C15  O15   124.66  3.000
 CL8  O16   C15  O15   123.38  3.000
 CL8  H16   O16  C15   110.02  3.000
 CL8  H142  C14  H141  105.89  3.000
 CL8  H142  C14  C13   111.41  3.000
 CL8  H141  C14  C13   109.19  3.000
 CL8  H142  C14  C15   110.02  3.000
 CL8  H141  C14  C15   107.35  3.000
 CL8  C13   C14  C15   112.66  3.000
 CL8  H132  C13  H131  105.85  3.000
 CL8  H132  C13  C12   108.52  3.000
 CL8  H131  C13  C12   108.89  3.000
 CL8  H132  C13  C14   109.89  3.000
 CL8  H131  C13  C14   111.24  3.000
 CL8  C12   C13  C14   112.21  3.000
 CL8  O12   C12  C13   124.93  3.000
 CL8  O12   C12  O4    123.70  3.000
 CL8  C13   C12  O4    111.36  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  CONST_21  H2    N2   C2   C1      0.00   0.0  0
 CL8  CONST_22  H16   O16  C15  O15     0.00   0.0  0
 CL8  Var_01    O2    C2   C1   CL1    51.66  30.0  3
 CL8  Var_02    C13   C12  O4   C4   -179.11  30.0  3
 CL8  Var_03    C14   C13  C12  O4    179.89  30.0  2
 CL8  Var_04    C13   C14  C15  O15   -18.97  30.0  3
 CL8  Var_05    C12   C13  C14  C15   -64.55  30.0  3
 CL8  Var_06    H41C  C4   O4   C12   -39.82  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-4  H16  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

