# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 18:59:12 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 2,2-dichloro-N-[(1R,2R)-2-hydroxy-1-(hydroxymethyl)-2-(4-nitrophenyl)ethyl]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
 CLM  CLM  2,2-dichloro-N-[(1R,2R)-2-hydroxy-1-(hydroxymethyl)-2-(4-nitrophenyl)ethyl]acetamide  ligand  32  20  .  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_CLM
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
 CLM  C1   C   CH1    0  -0.430   1.4915  -0.3664   1.8358
 CLM  CL1  CL  CL     0  -0.051   2.6074  -0.8764   0.5618
 CLM  CL2  CL  CL     0  -0.060   2.3478   0.5822   3.0637
 CLM  C2   C   C      0   0.611   0.4067   0.5135   1.2130
 CLM  O2   O   O      0  -0.438   0.6927   1.5101   0.5867
 CLM  N2   N   NH1    0  -0.638  -0.8315   0.0587   1.4434
 CLM  C3   C   CH1    0  -0.155  -2.0277   0.7083   0.9501
 CLM  C4   C   CH2    0  -0.177  -3.0784   0.7550   2.0599
 CLM  O4   O   OH1    0  -0.670  -3.2627  -0.5090   2.6619
 CLM  C5   C   CH1    0  -0.015  -2.5470   0.0504  -0.3463
 CLM  O5   O   OH1    0  -0.652  -3.1285  -1.2094  -0.1464
 CLM  C6   C   CR6    0   0.120  -1.4493   0.0265  -1.3841
 CLM  C7   C   CR16   0  -0.312  -0.6202  -1.0799  -1.5345
 CLM  C8   C   CR16   0  -0.244   0.4264  -1.0620  -2.4393
 CLM  C9   C   CR6    0   0.236   0.6297   0.0741  -3.2072
 CLM  N9   N   N      1   0.328   1.7224   0.0980  -4.1640
 CLM  O9A  O   O     -1  -0.382   1.8927   1.1064  -4.8094
 CLM  O9B  O   O      0  -0.382   2.4159  -0.8875  -4.2635
 CLM  C10  C   CR16   0  -0.253  -0.1916   1.1871  -3.0881
 CLM  C11  C   CR16   0  -0.276  -1.2255   1.1514  -2.1727
 CLM  H1   H   HCH1   0   0.364   1.1064  -1.2624   2.3172
 CLM  HN2  H   HNH1   0   0.410  -0.9541  -0.7397   2.0490
 CLM  H3   H   HCH1   0   0.290  -1.7742   1.7402   0.7010
 CLM  H41  H   HCH2   0   0.230  -4.0225   1.1043   1.6314
 CLM  H42  H   HCH2   0   0.244  -2.7655   1.5002   2.7952
 CLM  HO4  H   HOH1   0   0.466  -2.9858  -0.4572   3.5796
 CLM  H5   H   HCH1   0   0.266  -3.3478   0.7004  -0.7149
 CLM  HO5  H   HOH1   0   0.450  -2.6219  -1.7171   0.4950
 CLM  H7   H   HCR6   0   0.265  -0.7774  -1.9748  -0.9475
 CLM  H8   H   HCR6   0   0.294   1.0670  -1.9263  -2.5354
 CLM  H10  H   HCR6   0   0.294  -0.0376   2.0665  -3.6959
 CLM  H11  H   HCR6   0   0.267  -1.8699   2.0164  -2.0747

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
 CLM  C1   CL1  single    1.769  0.020  1.769
 CLM  C1   CL2  single    1.772  0.020  1.772
 CLM  C1   C2   single    1.529  0.020  1.529
 CLM  C1   H1   single    0.970  0.020  1.090
 CLM  C2   O2   double    1.211  0.020  1.211
 CLM  C2   N2   single    1.339  0.020  1.339
 CLM  N2   C3   single    1.448  0.020  1.448
 CLM  N2   HN2  single    0.860  0.020  1.020
 CLM  C3   C4   single    1.529  0.020  1.529
 CLM  C3   C5   single    1.544  0.020  1.544
 CLM  C3   H3   single    0.970  0.020  1.090
 CLM  C4   O4   single    1.412  0.020  1.412
 CLM  C4   H41  single    0.970  0.020  1.090
 CLM  C4   H42  single    0.970  0.020  1.090
 CLM  O4   HO4  single    0.850  0.020  0.980
 CLM  C5   O5   single    1.402  0.020  1.402
 CLM  C5   C6   single    1.511  0.020  1.511
 CLM  C5   H5   single    0.970  0.020  1.090
 CLM  O5   HO5  single    0.850  0.020  0.980
 CLM  C6   C7   aromatic  1.391  0.020  1.391
 CLM  C6   C11  aromatic  1.392  0.020  1.392
 CLM  C7   C8   aromatic  1.384  0.020  1.384
 CLM  C7   H7   single    0.930  0.020  1.080
 CLM  C8   C9   aromatic  1.386  0.020  1.386
 CLM  C8   H8   single    0.930  0.020  1.080
 CLM  C9   N9   single    1.453  0.020  1.453
 CLM  C9   C10  aromatic  1.388  0.020  1.388
 CLM  N9   O9A  single    1.209  0.020  1.209
 CLM  N9   O9B  double    1.209  0.020  1.209
 CLM  C10  C11  aromatic  1.381  0.020  1.381
 CLM  C10  H10  single    0.930  0.020  1.080
 CLM  C11  H11  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
 CLM  H1   C1   C2   113.77  3.000
 CLM  H1   C1   CL2  107.78  3.000
 CLM  C2   C1   CL2  108.48  3.000
 CLM  H1   C1   CL1  107.74  3.000
 CLM  C2   C1   CL1  108.67  3.000
 CLM  CL2  C1   CL1  110.40  3.000
 CLM  N2   C2   O2   125.92  3.000
 CLM  N2   C2   C1   112.98  3.000
 CLM  O2   C2   C1   121.10  3.000
 CLM  HN2  N2   C3   117.31  3.000
 CLM  HN2  N2   C2   118.95  3.000
 CLM  C3   N2   C2   123.57  3.000
 CLM  H3   C3   C5   106.82  3.000
 CLM  H3   C3   C4   107.24  3.000
 CLM  C5   C3   C4   113.04  3.000
 CLM  H3   C3   N2   108.06  3.000
 CLM  C5   C3   N2   111.89  3.000
 CLM  C4   C3   N2   109.52  3.000
 CLM  H42  C4   H41  107.03  3.000
 CLM  H42  C4   O4   111.16  3.000
 CLM  H41  C4   O4   109.89  3.000
 CLM  H42  C4   C3   108.21  3.000
 CLM  H41  C4   C3   108.57  3.000
 CLM  O4   C4   C3   111.82  3.000
 CLM  HO4  O4   C4   108.76  3.000
 CLM  H5   C5   C6   108.03  3.000
 CLM  H5   C5   O5   106.14  3.000
 CLM  C6   C5   O5   112.65  3.000
 CLM  H5   C5   C3   106.00  3.000
 CLM  C6   C5   C3   109.83  3.000
 CLM  O5   C5   C3   113.75  3.000
 CLM  HO5  O5   C5   110.54  3.000
 CLM  C11  C6   C7   119.07  3.000
 CLM  C11  C6   C5   119.55  3.000
 CLM  C7   C6   C5   121.34  3.000
 CLM  H7   C7   C8   118.39  3.000
 CLM  H7   C7   C6   120.85  3.000
 CLM  C8   C7   C6   120.76  3.000
 CLM  H8   C8   C9   121.30  3.000
 CLM  H8   C8   C7   119.77  3.000
 CLM  C9   C8   C7   118.93  3.000
 CLM  C10  C9   N9   119.23  3.000
 CLM  C10  C9   C8   121.52  3.000
 CLM  N9   C9   C8   119.25  3.000
 CLM  O9B  N9   O9A  123.70  3.000
 CLM  O9B  N9   C9   118.18  3.000
 CLM  O9A  N9   C9   118.12  3.000
 CLM  H10  C10  C11  120.04  3.000
 CLM  H10  C10  C9   121.34  3.000
 CLM  C11  C10  C9   118.61  3.000
 CLM  H11  C11  C10  118.99  3.000
 CLM  H11  C11  C6   119.91  3.000
 CLM  C10  C11  C6   121.11  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
 CLM  CONST_01  C9   C8   C7   C6     0.00   0.0  0
 CLM  CONST_02  C9   C10  C11  C6     0.00   0.0  0
 CLM  CONST_03  C10  C11  C6   C7     0.00   0.0  0
 CLM  CONST_04  C10  C9   C8   C7     0.00   0.0  0
 CLM  CONST_05  C11  C6   C7   C8     0.00   0.0  0
 CLM  CONST_06  C11  C10  C9   C8     0.00   0.0  0
 CLM  CONST_07  C8   C7   C6   C5   180.00   0.0  0
 CLM  CONST_08  C10  C11  C6   C5   180.00   0.0  0
 CLM  CONST_09  N9   C9   C8   C7   180.00   0.0  0
 CLM  CONST_10  C11  C10  C9   N9   180.00   0.0  0
 CLM  CONST_11  H8   C8   C7   C6   180.00   0.0  0
 CLM  CONST_12  H10  C10  C11  C6   180.00   0.0  0
 CLM  CONST_13  H11  C11  C6   C7   180.00   0.0  0
 CLM  CONST_14  H7   C7   C8   C9   180.00   0.0  0
 CLM  CONST_15  O9A  N9   C9   C8   180.00   0.0  0
 CLM  CONST_16  O9B  N9   C9   C8     0.00   0.0  0
 CLM  CONST_17  C10  C9   N9   O9A    0.00   0.0  0
 CLM  CONST_18  C10  C9   N9   O9B  180.00   0.0  0
 CLM  CONST_19  C3   N2   C2   C1   180.00   0.0  0
 CLM  CONST_20  C3   N2   C2   O2     0.00   0.0  0
 CLM  CONST_21  HN2  N2   C2   C1     0.00   0.0  0
 CLM  Var_01    O2   C2   C1   CL1  -56.35  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
 CLM  chir_01  C3  N2  C4  C5  positiv
 CLM  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
 CLM  plan-1  C5   0.020
 CLM  plan-1  C6   0.020
 CLM  plan-1  C7   0.020
 CLM  plan-1  C8   0.020
 CLM  plan-1  C9   0.020
 CLM  plan-1  N9   0.020
 CLM  plan-1  C10  0.020
 CLM  plan-1  C11  0.020
 CLM  plan-1  H7   0.020
 CLM  plan-1  H8   0.020
 CLM  plan-1  H10  0.020
 CLM  plan-1  H11  0.020
 CLM  plan-2  C1   0.020
 CLM  plan-2  C2   0.020
 CLM  plan-2  O2   0.020
 CLM  plan-2  N2   0.020
 CLM  plan-2  C3   0.020
 CLM  plan-2  HN2  0.020
 CLM  plan-3  C9   0.020
 CLM  plan-3  N9   0.020
 CLM  plan-3  O9A  0.020
 CLM  plan-3  O9B  0.020

