# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 16:05:44 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: N-[(1R,2R)-2-hydroxy-1-(hydroxymethyl)-2-(4-nitrophenyl)ethyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H](CO)[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
 CLC  CLC  N-[(1R,2R)-2-hydroxy-1-(hydroxymethyl)-2-(4-nitrophenyl)ethyl]acetamide  ligand  32  18  .  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_CLC
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
 CLC  O1    O  O      0  -0.480   1.8406  -1.1587  -0.8642
 CLC  O2    O  OH1    0  -0.671  -1.1580   0.5281  -4.3131
 CLC  N2    N  NH1    0  -0.634   0.6691   0.1772  -2.2646
 CLC  O4    O  OH1    0  -0.653  -2.0976   1.2493  -1.6755
 CLC  C11   C  C      0   0.518   1.7748  -0.1617  -1.5637
 CLC  C12   C  CH3    0  -0.782   2.9165   0.8150  -1.7070
 CLC  C21   C  CH2    0  -0.161  -1.0754  -0.7346  -3.6909
 CLC  C50   C  CH1    0  -0.008  -1.5991  -0.0021  -1.2871
 CLC  C22   C  CH1    0  -0.151  -0.5567  -0.5867  -2.2650
 CLC  C1    C  CR6    0   0.123  -1.0293   0.0123   0.1129
 CLC  C2    C  CR16   0  -0.309  -0.4820   1.1649   0.6663
 CLC  C3    C  CR16   0  -0.253   0.0919   1.1428   1.9257
 CLC  C4    C  CR6    0   0.236   0.1016  -0.0463   2.6385
 CLC  C5    C  CR16   0  -0.254  -0.4524  -1.2077   2.1169
 CLC  C6    C  CR16   0  -0.269  -1.0120  -1.1651   0.8553
 CLC  N4    N  N      1   0.329   0.6962  -0.0765   3.9629
 CLC  O5    O  O     -1  -0.383   0.6795  -1.1216   4.5713
 CLC  O6    O  O      0  -0.383   1.1806   0.9437   4.3954
 CLC  HA    H  HOH1   0   0.463  -1.0782   0.4047  -5.2625
 CLC  H2    H  HNH1   0   0.398   0.7266   0.9643  -2.8923
 CLC  H4    H  HOH1   0   0.448  -1.3854   1.7946  -2.0236
 CLC  H121  H  HCH3   0   0.260   3.8144   0.4225  -1.2375
 CLC  H122  H  HCH3   0   0.261   3.1308   1.0298  -2.7541
 CLC  H123  H  HCH3   0   0.264   2.6594   1.7610  -1.2274
 CLC  H211  H  HCH2   0   0.229  -0.3854  -1.3946  -4.2267
 CLC  H212  H  HCH2   0   0.210  -2.0491  -1.2398  -3.6635
 CLC  H50   H  HCH1   0   0.259  -2.4533  -0.6879  -1.2943
 CLC  H22   H  HCH1   0   0.282  -0.3259  -1.5949  -1.9139
 CLC  HB    H  HCR6   0   0.257  -0.4999   2.1016   0.1263
 CLC  H3    H  HCR6   0   0.294   0.5167   2.0465   2.3375
 CLC  H5    H  HCR6   0   0.293  -0.4503  -2.1312   2.6771
 CLC  H6    H  HCR6   0   0.265  -1.4427  -2.0691   0.4427

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
 CLC  O1   C11   double    1.220  0.020  1.220
 CLC  O2   C21   single    1.410  0.020  1.410
 CLC  O2   HA    single    0.850  0.020  0.980
 CLC  N2   C11   single    1.352  0.020  1.352
 CLC  N2   C22   single    1.444  0.020  1.444
 CLC  N2   H2    single    0.860  0.020  1.020
 CLC  O4   C50   single    1.402  0.020  1.402
 CLC  O4   H4    single    0.850  0.020  0.980
 CLC  C11  C12   single    1.509  0.020  1.509
 CLC  C12  H121  single    0.970  0.020  1.090
 CLC  C12  H122  single    0.970  0.020  1.090
 CLC  C12  H123  single    0.970  0.020  1.090
 CLC  C21  C22   single    1.525  0.020  1.525
 CLC  C21  H211  single    0.970  0.020  1.090
 CLC  C21  H212  single    0.970  0.020  1.090
 CLC  C50  C22   single    1.544  0.020  1.544
 CLC  C50  C1    single    1.512  0.020  1.512
 CLC  C50  H50   single    0.970  0.020  1.090
 CLC  C22  H22   single    0.970  0.020  1.090
 CLC  C1   C2    aromatic  1.391  0.020  1.391
 CLC  C1   C6    aromatic  1.392  0.020  1.392
 CLC  C2   C3    aromatic  1.384  0.020  1.384
 CLC  C2   HB    single    0.930  0.020  1.080
 CLC  C3   C4    aromatic  1.386  0.020  1.386
 CLC  C3   H3    single    0.930  0.020  1.080
 CLC  C4   C5    aromatic  1.388  0.020  1.388
 CLC  C4   N4    single    1.452  0.020  1.452
 CLC  C5   C6    aromatic  1.381  0.020  1.381
 CLC  C5   H5    single    0.930  0.020  1.080
 CLC  C6   H6    single    0.930  0.020  1.080
 CLC  N4   O5    single    1.209  0.020  1.209
 CLC  N4   O6    double    1.209  0.020  1.209

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
 CLC  HA    O2   C21   108.43  3.000
 CLC  H2    N2   C22   117.46  3.000
 CLC  H2    N2   C11   118.14  3.000
 CLC  C22   N2   C11   124.16  3.000
 CLC  H4    O4   C50   110.05  3.000
 CLC  C12   C11  N2    114.02  3.000
 CLC  C12   C11  O1    122.86  3.000
 CLC  N2    C11  O1    123.11  3.000
 CLC  H123  C12  H122  107.32  3.000
 CLC  H123  C12  H121  108.54  3.000
 CLC  H122  C12  H121  108.88  3.000
 CLC  H123  C12  C11   109.94  3.000
 CLC  H122  C12  C11   111.56  3.000
 CLC  H121  C12  C11   110.51  3.000
 CLC  H212  C21  H211  107.09  3.000
 CLC  H212  C21  C22   108.86  3.000
 CLC  H211  C21  C22   107.56  3.000
 CLC  H212  C21  O2    111.80  3.000
 CLC  H211  C21  O2    111.14  3.000
 CLC  C22   C21  O2    110.23  3.000
 CLC  H50   C50  C1    107.82  3.000
 CLC  H50   C50  C22   106.57  3.000
 CLC  C1    C50  C22   109.61  3.000
 CLC  H50   C50  O4    106.24  3.000
 CLC  C1    C50  O4    112.47  3.000
 CLC  C22   C50  O4    113.74  3.000
 CLC  H22   C22  C50   106.77  3.000
 CLC  H22   C22  C21   106.44  3.000
 CLC  C50   C22  C21   113.53  3.000
 CLC  H22   C22  N2    107.99  3.000
 CLC  C50   C22  N2    111.87  3.000
 CLC  C21   C22  N2    109.90  3.000
 CLC  C6    C1   C2    118.94  3.000
 CLC  C6    C1   C50   119.38  3.000
 CLC  C2    C1   C50   121.65  3.000
 CLC  HB    C2   C3    118.36  3.000
 CLC  HB    C2   C1    120.85  3.000
 CLC  C3    C2   C1    120.79  3.000
 CLC  H3    C3   C4    121.26  3.000
 CLC  H3    C3   C2    119.77  3.000
 CLC  C4    C3   C2    118.97  3.000
 CLC  N4    C4   C5    119.25  3.000
 CLC  N4    C4   C3    119.32  3.000
 CLC  C5    C4   C3    121.43  3.000
 CLC  H5    C5   C6    120.07  3.000
 CLC  H5    C5   C4    121.30  3.000
 CLC  C6    C5   C4    118.63  3.000
 CLC  H6    C6   C5    118.92  3.000
 CLC  H6    C6   C1    119.86  3.000
 CLC  C5    C6   C1    121.23  3.000
 CLC  O6    N4   O5    123.68  3.000
 CLC  O6    N4   C4    118.21  3.000
 CLC  O5    N4   C4    118.11  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
 CLC  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 CLC  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 CLC  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 CLC  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 CLC  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 CLC  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 CLC  CONST_07  C3    C2   C1   C50  180.00   0.0  0
 CLC  CONST_08  C5    C6   C1   C50  180.00   0.0  0
 CLC  CONST_09  N4    C4   C3   C2   180.00   0.0  0
 CLC  CONST_10  N4    C4   C5   C6   180.00   0.0  0
 CLC  CONST_11  H3    C3   C2   C1   180.00   0.0  0
 CLC  CONST_12  H5    C5   C6   C1   180.00   0.0  0
 CLC  CONST_13  H6    C6   C1   C2   180.00   0.0  0
 CLC  CONST_14  HB    C2   C3   C4   180.00   0.0  0
 CLC  CONST_15  O5    N4   C4   C3   180.00   0.0  0
 CLC  CONST_16  O6    N4   C4   C3     0.00   0.0  0
 CLC  CONST_17  O5    N4   C4   C5     0.00   0.0  0
 CLC  CONST_18  O6    N4   C4   C5   180.00   0.0  0
 CLC  CONST_19  C22   N2   C11  O1     0.00   0.0  0
 CLC  CONST_20  C22   N2   C11  C12  180.00   0.0  0
 CLC  CONST_21  H2    N2   C11  O1   180.00   0.0  0
 CLC  Var_01    H121  C12  C11  O1     8.69  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
 CLC  chir_01  C50  O4  C22  C1   negativ
 CLC  chir_02  C22  N2  C50  C21  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
 CLC  plan-1  C50  0.020
 CLC  plan-1  C1   0.020
 CLC  plan-1  C2   0.020
 CLC  plan-1  C3   0.020
 CLC  plan-1  C4   0.020
 CLC  plan-1  C5   0.020
 CLC  plan-1  C6   0.020
 CLC  plan-1  N4   0.020
 CLC  plan-1  HB   0.020
 CLC  plan-1  H3   0.020
 CLC  plan-1  H5   0.020
 CLC  plan-1  H6   0.020
 CLC  plan-2  O1   0.020
 CLC  plan-2  N2   0.020
 CLC  plan-2  C11  0.020
 CLC  plan-2  C12  0.020
 CLC  plan-2  C22  0.020
 CLC  plan-2  H2   0.020
 CLC  plan-3  C4   0.020
 CLC  plan-3  N4   0.020
 CLC  plan-3  O5   0.020
 CLC  plan-3  O6   0.020

