# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 21:57:37 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: N-(4-{(S)-hydroxy[(4-nitrobenzyl)oxy]phosphoryl}butanoyl)glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNC(=O)CCC[P@@](O)(=O)OCc1ccc(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
 PNB  PNB  N-(4-{(S)-hydroxy[(4-nitrobenzyl)oxy]phosphoryl}butanoyl)glycine  ligand  41  24  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PNB
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
 PNB  N1    N  N      1   0.330   2.1531   0.7582  -6.7544
 PNB  O4    O  O      0  -0.380   3.2292   1.1781  -6.3980
 PNB  O5    O  O     -1  -0.380   1.8407   0.6045  -7.9119
 PNB  C1    C  CR6    0   0.061  -0.6721  -0.2374  -3.7815
 PNB  C2    C  CR16   0  -0.280  -0.9782  -0.4000  -5.1310
 PNB  C3    C  CR16   0  -0.253  -0.0631  -0.0731  -6.1132
 PNB  C4    C  CR6    0   0.240   1.1783   0.4178  -5.7319
 PNB  C5    C  CR16   0  -0.249   1.5085   0.5872  -4.3964
 PNB  C6    C  CR16   0  -0.286   0.5775   0.2588  -3.4254
 PNB  O1    O  O2     0  -0.598  -1.1181  -0.7991  -1.4939
 PNB  P1    P  P      0   1.392  -1.8087  -0.2814  -0.1313
 PNB  O2    O  O      0  -0.709  -2.3042   1.1151  -0.1668
 PNB  O3    O  OH1    0  -0.749  -3.0448  -1.2698   0.1538
 PNB  C8    C  CH2    0  -0.754  -0.5176  -0.6505   1.0646
 PNB  C9    C  CH2    0  -0.434  -0.9363  -0.3128   2.4936
 PNB  C10   C  CH2    0  -0.567   0.2049  -0.5891   3.4652
 PNB  C11   C  C      0   0.571  -0.1915  -0.3505   4.9052
 PNB  O6    O  O      0  -0.500  -1.2813  -0.6866   5.3483
 PNB  N2    N  NH1    0  -0.648   0.7460   0.2291   5.6707
 PNB  C12   C  CH2    0  -0.373   0.5419   0.4747   7.0705
 PNB  C13   C  C      0   0.521   1.8261   0.9296   7.7150
 PNB  O7    O  O      0  -0.435   2.8672   1.0852   7.1296
 PNB  O8    O  OH1    0  -0.585   1.6584   1.1421   9.0088
 PNB  H2    H  HCR6   0   0.277  -1.9440  -0.7922  -5.4234
 PNB  H3    H  HCR6   0   0.299  -0.3197  -0.2090  -7.1535
 PNB  H5    H  HCR6   0   0.299   2.4742   0.9700  -4.1010
 PNB  H6    H  HCR6   0   0.272   0.8434   0.3935  -2.3867
 PNB  H71   H  HCH2   0   0.268  -2.2559  -1.4795  -3.0676
 PNB  H72   H  HCH2   0   0.263  -2.4496   0.2361  -2.7176
 PNB  HO3   H  HOH1   0   0.492  -2.8277  -2.2101   0.2032
 PNB  H81   H  HCH2   0   0.290   0.3649  -0.0736   0.7756
 PNB  H82   H  HCH2   0   0.291  -0.2452  -1.7058   0.9808
 PNB  H91   H  HCH2   0   0.249  -1.8086  -0.9017   2.7793
 PNB  H92   H  HCH2   0   0.251  -1.2253   0.7384   2.5578
 PNB  H101  H  HCH2   0   0.258   1.0798   0.0060   3.1941
 PNB  H102  H  HCH2   0   0.275   0.5084  -1.6378   3.3819
 PNB  HN2   H  HNH1   0   0.405   1.6173   0.5251   5.2595
 PNB  H121  H  HCH2   0   0.291   0.1954  -0.4277   7.5818
 PNB  H122  H  HCH2   0   0.289  -0.2221   1.2402   7.2431
 PNB  HO8   H  HOH1   0   0.490   2.4886   1.4386   9.4118
 PNB  C7    C  CH2    0  -0.192  -1.7198  -0.5785  -2.7618

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
 PNB  N1   O4    double    1.209  0.020  1.209
 PNB  N1   O5    single    1.209  0.020  1.209
 PNB  N1   C4    single    1.453  0.020  1.453
 PNB  C1   C2    aromatic  1.393  0.020  1.393
 PNB  C1   C6    aromatic  1.391  0.020  1.391
 PNB  C1   C7    single    1.501  0.020  1.501
 PNB  C2   C3    aromatic  1.382  0.020  1.382
 PNB  C2   H2    single    0.930  0.020  1.080
 PNB  C3   C4    aromatic  1.388  0.020  1.388
 PNB  C3   H3    single    0.930  0.020  1.080
 PNB  C4   C5    aromatic  1.386  0.020  1.386
 PNB  C5   C6    aromatic  1.385  0.020  1.385
 PNB  C5   H5    single    0.930  0.020  1.080
 PNB  C6   H6    single    0.930  0.020  1.080
 PNB  C7   O1    single    1.421  0.020  1.421
 PNB  C7   H71   single    0.970  0.020  1.090
 PNB  C7   H72   single    0.970  0.020  1.090
 PNB  O1   P1    single    1.613  0.020  1.613
 PNB  P1   O2    double    1.482  0.020  1.482
 PNB  P1   O3    single    1.608  0.020  1.608
 PNB  P1   C8    single    1.798  0.020  1.798
 PNB  O3   HO3   single    0.850  0.020  0.980
 PNB  C8   C9    single    1.527  0.020  1.527
 PNB  C8   H81   single    0.970  0.020  1.090
 PNB  C8   H82   single    0.970  0.020  1.090
 PNB  C9   C10   single    1.524  0.020  1.524
 PNB  C9   H91   single    0.970  0.020  1.090
 PNB  C9   H92   single    0.970  0.020  1.090
 PNB  C10  C11   single    1.513  0.020  1.513
 PNB  C10  H101  single    0.970  0.020  1.090
 PNB  C10  H102  single    0.970  0.020  1.090
 PNB  C11  O6    double    1.224  0.020  1.224
 PNB  C11  N2    single    1.342  0.020  1.342
 PNB  N2   C12   single    1.436  0.020  1.436
 PNB  N2   HN2   single    0.860  0.020  1.020
 PNB  C12  C13   single    1.507  0.020  1.507
 PNB  C12  H121  single    0.970  0.020  1.090
 PNB  C12  H122  single    0.970  0.020  1.090
 PNB  C13  O7    double    1.205  0.020  1.205
 PNB  C13  O8    single    1.322  0.020  1.322
 PNB  O8   HO8   single    0.850  0.020  0.980

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
 PNB  C4    N1   O5    118.08  3.000
 PNB  C4    N1   O4    118.11  3.000
 PNB  O5    N1   O4    123.82  3.000
 PNB  C7    C1   C6    122.29  3.000
 PNB  C7    C1   C2    118.56  3.000
 PNB  C6    C1   C2    119.14  3.000
 PNB  H2    C2   C3    118.98  3.000
 PNB  H2    C2   C1    119.99  3.000
 PNB  C3    C2   C1    121.03  3.000
 PNB  H3    C3   C4    121.43  3.000
 PNB  H3    C3   C2    119.84  3.000
 PNB  C4    C3   C2    118.73  3.000
 PNB  C5    C4   C3    121.39  3.000
 PNB  C5    C4   N1    119.31  3.000
 PNB  C3    C4   N1    119.30  3.000
 PNB  H5    C5   C6    119.57  3.000
 PNB  H5    C5   C4    121.32  3.000
 PNB  C6    C5   C4    119.11  3.000
 PNB  H6    C6   C5    118.62  3.000
 PNB  H6    C6   C1    120.77  3.000
 PNB  C5    C6   C1    120.61  3.000
 PNB  P1    O1   C7    121.52  3.000
 PNB  C8    P1   O3    107.93  3.000
 PNB  C8    P1   O2    116.70  3.000
 PNB  O3    P1   O2    109.05  3.000
 PNB  C8    P1   O1    100.87  3.000
 PNB  O3    P1   O1    106.36  3.000
 PNB  O2    P1   O1    115.17  3.000
 PNB  HO3   O3   P1    115.75  3.000
 PNB  H82   C8   H81   106.74  3.000
 PNB  H82   C8   C9    110.71  3.000
 PNB  H81   C8   C9    110.61  3.000
 PNB  H82   C8   P1    109.03  3.000
 PNB  H81   C8   P1    107.19  3.000
 PNB  C9    C8   P1    112.34  3.000
 PNB  H92   C9   H91   107.02  3.000
 PNB  H92   C9   C10   109.59  3.000
 PNB  H91   C9   C10   109.51  3.000
 PNB  H92   C9   C8    109.90  3.000
 PNB  H91   C9   C8    110.18  3.000
 PNB  C10   C9   C8    110.56  3.000
 PNB  H102  C10  H101  106.31  3.000
 PNB  H102  C10  C11   107.22  3.000
 PNB  H101  C10  C11   111.11  3.000
 PNB  H102  C10  C9    109.44  3.000
 PNB  H101  C10  C9    110.05  3.000
 PNB  C11   C10  C9    112.47  3.000
 PNB  N2    C11  O6    122.30  3.000
 PNB  N2    C11  C10   115.35  3.000
 PNB  O6    C11  C10   122.34  3.000
 PNB  HN2   N2   C12   118.06  3.000
 PNB  HN2   N2   C11   119.87  3.000
 PNB  C12   N2   C11   122.05  3.000
 PNB  H122  C12  H121  106.39  3.000
 PNB  H122  C12  C13   108.42  3.000
 PNB  H121  C12  C13   108.61  3.000
 PNB  H122  C12  N2    111.86  3.000
 PNB  H121  C12  N2    111.09  3.000
 PNB  C13   C12  N2    110.33  3.000
 PNB  O8    C13  O7    124.37  3.000
 PNB  O8    C13  C12   111.04  3.000
 PNB  O7    C13  C12   124.59  3.000
 PNB  HO8   O8   C13   110.34  3.000
 PNB  H72   C7   H71   107.33  3.000
 PNB  H72   C7   O1    111.22  3.000
 PNB  H71   C7   O1    109.26  3.000
 PNB  H72   C7   C1    108.88  3.000
 PNB  H71   C7   C1    109.87  3.000
 PNB  O1    C7   C1    110.24  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
 PNB  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 PNB  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 PNB  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 PNB  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 PNB  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 PNB  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 PNB  CONST_07  C2   C3   C4   N1    180.00   0.0  0
 PNB  CONST_08  C6   C5   C4   N1    180.00   0.0  0
 PNB  CONST_09  C7   C1   C2   C3    180.00   0.0  0
 PNB  CONST_10  C7   C1   C6   C5    180.00   0.0  0
 PNB  CONST_11  H3   C3   C2   C1    180.00   0.0  0
 PNB  CONST_12  H5   C5   C6   C1    180.00   0.0  0
 PNB  CONST_13  H6   C6   C1   C2    180.00   0.0  0
 PNB  CONST_14  H2   C2   C3   C4    180.00   0.0  0
 PNB  CONST_15  C3   C4   N1   O4    180.00   0.0  0
 PNB  CONST_16  C5   C4   N1   O4      0.00   0.0  0
 PNB  CONST_17  C3   C4   N1   O5      0.00   0.0  0
 PNB  CONST_18  C5   C4   N1   O5    180.00   0.0  0
 PNB  CONST_19  C12  N2   C11  C10   180.00   0.0  0
 PNB  CONST_20  C12  N2   C11  O6      0.00   0.0  0
 PNB  CONST_21  HN2  N2   C11  C10     0.00   0.0  0
 PNB  CONST_22  HO8  O8   C13  C12   180.00   0.0  0
 PNB  Var_01    O1   C7   C1   C2    159.92  30.0  2
 PNB  Var_02    O2   P1   O1   C7    -46.45  30.0  3
 PNB  Var_03    C9   C8   P1   O1   -177.33  30.0  3
 PNB  Var_04    C10  C9   C8   P1   -177.77  30.0  3
 PNB  Var_05    C11  C10  C9   C8   -176.45  30.0  3
 PNB  Var_06    O6   C11  C10  C9     40.84  30.0  3
 PNB  Var_07    C13  C12  N2   C11   171.10  30.0  3
 PNB  Var_08    O7   C13  C12  N2      1.16  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
 PNB  chir_01  P1  O2  O3  C8  both

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
 PNB  plan-1  N1   0.020
 PNB  plan-1  C1   0.020
 PNB  plan-1  C2   0.020
 PNB  plan-1  C3   0.020
 PNB  plan-1  C4   0.020
 PNB  plan-1  C5   0.020
 PNB  plan-1  C6   0.020
 PNB  plan-1  H2   0.020
 PNB  plan-1  H3   0.020
 PNB  plan-1  H5   0.020
 PNB  plan-1  H6   0.020
 PNB  plan-1  C7   0.020
 PNB  plan-2  C10  0.020
 PNB  plan-2  C11  0.020
 PNB  plan-2  O6   0.020
 PNB  plan-2  N2   0.020
 PNB  plan-2  C12  0.020
 PNB  plan-2  HN2  0.020
 PNB  plan-3  N1   0.020
 PNB  plan-3  O4   0.020
 PNB  plan-3  O5   0.020
 PNB  plan-3  C4   0.020
 PNB  plan-4  C12  0.020
 PNB  plan-4  C13  0.020
 PNB  plan-4  O7   0.020
 PNB  plan-4  O8   0.020
 PNB  plan-4  HO8  0.020

