# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 07:42:04 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: N-{4-[(R)-hydroxy(4-nitrophenoxy)phosphoryl]butanoyl}glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNC(=O)CCC[P@](O)(=O)Oc1ccc(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
 PGG  PGG  N-{4-[(R)-hydroxy(4-nitrophenoxy)phosphoryl]butanoyl}glycine  ligand  38  23  .  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_PGG
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
 PGG  C1    C  CR6    0   0.395   0.7386   0.0475  -3.1385
 PGG  C2    C  CR16   0  -0.320   0.7197   1.2352  -3.8581
 PGG  C3    C  CR16   0  -0.260   0.5231   1.2036  -5.2259
 PGG  C4    C  CR6    0   0.250   0.3408  -0.0215  -5.8521
 PGG  C5    C  CR16   0  -0.261   0.3607  -1.2123  -5.1395
 PGG  C6    C  CR16   0  -0.308   0.5583  -1.1759  -3.7718
 PGG  P1    P  P      0   1.378  -0.2601  -0.0789  -0.7270
 PGG  O1    O  O2     0  -0.618   0.9701   0.0971  -1.7933
 PGG  O2    O  OH1    0  -0.739  -1.1787   1.2182  -0.9368
 PGG  O3    O  O      0  -0.686  -1.0657  -1.3017  -0.9328
 PGG  C8    C  CH2    0  -0.758   0.6133   0.0888   0.8312
 PGG  C9    C  CH2    0  -0.437  -0.3479   0.0466   2.0203
 PGG  C10   C  CH2    0  -0.576   0.4154   0.1865   3.3274
 PGG  C11   C  C      0   0.574  -0.4872   0.1675   4.5436
 PGG  N2    N  NH1    0  -0.651   0.1443  -0.0575   5.7076
 PGG  O6    O  O      0  -0.497  -1.6929   0.3599   4.4826
 PGG  C12   C  CH2    0  -0.370  -0.5508  -0.0491   6.9636
 PGG  C13   C  C      0   0.520   0.4264  -0.1553   8.1054
 PGG  O7    O  OH1    0  -0.585  -0.2000  -0.1275   9.2689
 PGG  O8    O  O      0  -0.435   1.6202  -0.2552   7.9782
 PGG  N1    N  N      1   0.330   0.1279  -0.0575  -7.2883
 PGG  O4    O  O      0  -0.379  -0.0241  -1.1353  -7.8141
 PGG  O5    O  O     -1  -0.379   0.1124   0.9923  -7.8870
 PGG  H21   H  HCR6   0   0.293   0.8713   2.1801  -3.3541
 PGG  H31   H  HCR6   0   0.305   0.5098   2.1274  -5.7852
 PGG  H51   H  HCR6   0   0.304   0.2228  -2.1633  -5.6326
 PGG  H61   H  HCR6   0   0.295   0.5885  -2.0953  -3.2042
 PGG  HO21  H  HOH1   0   0.497  -0.7600   2.0713  -0.7591
 PGG  H81   H  HCH2   0   0.296   1.1829   1.0220   0.8224
 PGG  H82   H  HCH2   0   0.300   1.3377  -0.7271   0.8914
 PGG  H91   H  HCH2   0   0.252  -0.9031  -0.8934   2.0120
 PGG  H92   H  HCH2   0   0.250  -1.0814   0.8493   1.9352
 PGG  H101  H  HCH2   0   0.280   0.9703   1.1308   3.3370
 PGG  H102  H  HCH2   0   0.267   1.1667  -0.6031   3.4168
 PGG  HN21  H  HNH1   0   0.405   1.1405  -0.2132   5.7165
 PGG  H121  H  HCH2   0   0.289  -1.2610  -0.8790   7.0397
 PGG  H122  H  HCH2   0   0.289  -1.1348   0.8675   7.0878
 PGG  HO71  H  HOH1   0   0.490   0.4352  -0.2043   9.9969

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
 PGG  C1   C2    aromatic  1.389  0.020  1.389
 PGG  C1   C6    aromatic  1.389  0.020  1.389
 PGG  C1   O1    single    1.366  0.020  1.366
 PGG  C2   C3    aromatic  1.382  0.020  1.382
 PGG  C2   H21   single    0.930  0.020  1.080
 PGG  C3   C4    aromatic  1.388  0.020  1.388
 PGG  C3   H31   single    0.930  0.020  1.080
 PGG  C4   C5    aromatic  1.388  0.020  1.388
 PGG  C4   N1    single    1.452  0.020  1.452
 PGG  C5   C6    aromatic  1.382  0.020  1.382
 PGG  C5   H51   single    0.930  0.020  1.080
 PGG  C6   H61   single    0.930  0.020  1.080
 PGG  P1   O1    single    1.637  0.020  1.637
 PGG  P1   O2    single    1.603  0.020  1.603
 PGG  P1   O3    double    1.479  0.020  1.479
 PGG  P1   C8    single    1.794  0.020  1.794
 PGG  O2   HO21  single    0.850  0.020  0.980
 PGG  C8   C9    single    1.530  0.020  1.530
 PGG  C8   H81   single    0.970  0.020  1.090
 PGG  C8   H82   single    0.970  0.020  1.090
 PGG  C9   C10   single    1.520  0.020  1.520
 PGG  C9   H91   single    0.970  0.020  1.090
 PGG  C9   H92   single    0.970  0.020  1.090
 PGG  C10  C11   single    1.515  0.020  1.515
 PGG  C10  H101  single    0.970  0.020  1.090
 PGG  C10  H102  single    0.970  0.020  1.090
 PGG  C11  N2    single    1.343  0.020  1.343
 PGG  C11  O6    double    1.222  0.020  1.222
 PGG  N2   C12   single    1.436  0.020  1.436
 PGG  N2   HN21  single    0.860  0.020  1.020
 PGG  C12  C13   single    1.507  0.020  1.507
 PGG  C12  H121  single    0.970  0.020  1.090
 PGG  C12  H122  single    0.970  0.020  1.090
 PGG  C13  O7    single    1.322  0.020  1.322
 PGG  C13  O8    double    1.205  0.020  1.205
 PGG  O7   HO71  single    0.850  0.020  0.980
 PGG  N1   O4    double    1.209  0.020  1.209
 PGG  N1   O5    single    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
 PGG  O1    C1   C6    120.19  3.000
 PGG  O1    C1   C2    118.79  3.000
 PGG  C6    C1   C2    121.01  3.000
 PGG  H21   C2   C3    120.07  3.000
 PGG  H21   C2   C1    120.25  3.000
 PGG  C3    C2   C1    119.67  3.000
 PGG  H31   C3   C4    121.31  3.000
 PGG  H31   C3   C2    119.65  3.000
 PGG  C4    C3   C2    119.04  3.000
 PGG  N1    C4   C5    119.24  3.000
 PGG  N1    C4   C3    119.17  3.000
 PGG  C5    C4   C3    121.59  3.000
 PGG  H51   C5   C6    119.55  3.000
 PGG  H51   C5   C4    121.28  3.000
 PGG  C6    C5   C4    119.17  3.000
 PGG  H61   C6   C5    120.07  3.000
 PGG  H61   C6   C1    120.40  3.000
 PGG  C5    C6   C1    119.52  3.000
 PGG  C8    P1   O3    117.60  3.000
 PGG  C8    P1   O2    108.48  3.000
 PGG  O3    P1   O2    109.80  3.000
 PGG  C8    P1   O1    100.94  3.000
 PGG  O3    P1   O1    114.05  3.000
 PGG  O2    P1   O1    104.97  3.000
 PGG  P1    O1   C1    120.67  3.000
 PGG  HO21  O2   P1    116.21  3.000
 PGG  H82   C8   H81   107.00  3.000
 PGG  H82   C8   C9    110.68  3.000
 PGG  H81   C8   C9    110.92  3.000
 PGG  H82   C8   P1    107.51  3.000
 PGG  H81   C8   P1    109.05  3.000
 PGG  C9    C8   P1    111.51  3.000
 PGG  H92   C9   H91   106.92  3.000
 PGG  H92   C9   C10   109.69  3.000
 PGG  H91   C9   C10   109.94  3.000
 PGG  H92   C9   C8    109.98  3.000
 PGG  H91   C9   C8    109.72  3.000
 PGG  C10   C9   C8    110.51  3.000
 PGG  H102  C10  H101  105.89  3.000
 PGG  H102  C10  C11   109.56  3.000
 PGG  H101  C10  C11   107.80  3.000
 PGG  H102  C10  C9    110.42  3.000
 PGG  H101  C10  C9    109.95  3.000
 PGG  C11   C10  C9    112.96  3.000
 PGG  O6    C11  N2    122.23  3.000
 PGG  O6    C11  C10   123.07  3.000
 PGG  N2    C11  C10   114.69  3.000
 PGG  HN21  N2   C12   118.14  3.000
 PGG  HN21  N2   C11   119.87  3.000
 PGG  C12   N2   C11   121.97  3.000
 PGG  H122  C12  H121  106.32  3.000
 PGG  H122  C12  C13   108.62  3.000
 PGG  H121  C12  C13   108.34  3.000
 PGG  H122  C12  N2    111.27  3.000
 PGG  H121  C12  N2    111.74  3.000
 PGG  C13   C12  N2    110.40  3.000
 PGG  O8    C13  O7    124.36  3.000
 PGG  O8    C13  C12   124.65  3.000
 PGG  O7    C13  C12   110.99  3.000
 PGG  HO71  O7   C13   110.42  3.000
 PGG  O5    N1   O4    123.88  3.000
 PGG  O5    N1   C4    118.04  3.000
 PGG  O4    N1   C4    118.08  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
 PGG  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 PGG  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 PGG  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 PGG  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 PGG  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 PGG  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 PGG  CONST_07  N1    C4   C3   C2    180.00   0.0  0
 PGG  CONST_08  O1    C1   C2   C3    180.00   0.0  0
 PGG  CONST_09  O1    C1   C6   C5    180.00   0.0  0
 PGG  CONST_10  N1    C4   C5   C6    180.00   0.0  0
 PGG  CONST_11  H31   C3   C2   C1    180.00   0.0  0
 PGG  CONST_12  H51   C5   C6   C1    180.00   0.0  0
 PGG  CONST_13  H61   C6   C1   C2    180.00   0.0  0
 PGG  CONST_14  H21   C2   C3   C4    180.00   0.0  0
 PGG  CONST_15  O4    N1   C4   C3    180.00   0.0  0
 PGG  CONST_16  O5    N1   C4   C3      0.00   0.0  0
 PGG  CONST_17  O4    N1   C4   C5      0.00   0.0  0
 PGG  CONST_18  O5    N1   C4   C5    180.00   0.0  0
 PGG  CONST_19  C12   N2   C11  C10   180.00   0.0  0
 PGG  CONST_20  C12   N2   C11  O6      0.00   0.0  0
 PGG  CONST_21  HN21  N2   C11  C10     0.00   0.0  0
 PGG  CONST_22  HO71  O7   C13  C12   180.00   0.0  0
 PGG  Var_01    O2    P1   O1   C1    -66.72  30.0  2
 PGG  Var_02    C10   C9   C8   P1    179.84  30.0  3
 PGG  Var_03    C9    C8   P1   O1    176.47  30.0  3
 PGG  Var_04    C11   C10  C9   C8    179.35  30.0  3
 PGG  Var_05    N2    C11  C10  C9    163.67  30.0  3
 PGG  Var_06    C13   C12  N2   C11  -172.83  30.0  3
 PGG  Var_07    O7    C13  C12  N2    179.02  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
 PGG  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
 PGG  plan-1  C1    0.020
 PGG  plan-1  C2    0.020
 PGG  plan-1  C3    0.020
 PGG  plan-1  C4    0.020
 PGG  plan-1  C5    0.020
 PGG  plan-1  C6    0.020
 PGG  plan-1  O1    0.020
 PGG  plan-1  N1    0.020
 PGG  plan-1  H21   0.020
 PGG  plan-1  H31   0.020
 PGG  plan-1  H51   0.020
 PGG  plan-1  H61   0.020
 PGG  plan-2  C10   0.020
 PGG  plan-2  C11   0.020
 PGG  plan-2  N2    0.020
 PGG  plan-2  O6    0.020
 PGG  plan-2  C12   0.020
 PGG  plan-2  HN21  0.020
 PGG  plan-3  C4    0.020
 PGG  plan-3  N1    0.020
 PGG  plan-3  O4    0.020
 PGG  plan-3  O5    0.020
 PGG  plan-4  C12   0.020
 PGG  plan-4  C13   0.020
 PGG  plan-4  O7    0.020
 PGG  plan-4  O8    0.020
 PGG  plan-4  HO71  0.020

