# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 19:31:28 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  36  23  .  2022-03-23  2022-03-23
;
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   0.413   0.6993  -0.0160  -3.1358
 PGG  C2    C  CR16   0  -0.333   0.6561   1.1889  -3.8385
 PGG  C3    C  CR16   0  -0.262   0.4450   1.1928  -5.2031
 PGG  C4    C  CR6    0   0.234   0.2624  -0.0158  -5.8647
 PGG  C5    C  CR16   0  -0.263   0.2947  -1.2246  -5.1795
 PGG  C6    C  CR16   0  -0.330   0.5067  -1.2200  -3.8151
 PGG  P1    P  P      0   1.263  -0.3986   0.0136  -0.7555
 PGG  O1    O  O2     0  -0.643   0.9405  -0.0155  -1.8150
 PGG  O2    O  OP    -1  -0.780  -1.0950   1.3281  -0.9583
 PGG  O3    O  O      0  -0.780  -1.1504  -1.2716  -0.9492
 PGG  C8    C  CH2    0  -0.726   0.5477  -0.0039   0.7970
 PGG  C9    C  CH2    0  -0.428  -0.3877   0.0024   2.0054
 PGG  C10   C  CH2    0  -0.570   0.3893  -0.0142   3.3116
 PGG  C11   C  C      0   0.554  -0.4925  -0.0126   4.5477
 PGG  N2    N  NH1    0  -0.633   0.1711  -0.0203   5.7087
 PGG  O6    O  O      0  -0.515  -1.7174  -0.0052   4.4865
 PGG  C12   C  CH2    0  -0.408  -0.4628  -0.0195   7.0012
 PGG  C13   C  C      0   0.396   0.5803  -0.0226   8.1370
 PGG  O7    O  OC    -1  -0.612   0.1089  -0.0233   9.2875
 PGG  O8    O  O      0  -0.601   1.7824  -0.0243   7.8088
 PGG  N1    N  N      1   0.328   0.0342  -0.0149  -7.2934
 PGG  O4    O  O      0  -0.389  -0.1234  -1.0785  -7.8496
 PGG  O5    O  O     -1  -0.389   0.0097   1.0499  -7.8688
 PGG  H21   H  HCR6   0   0.277   0.8039   2.1217  -3.3121
 PGG  H31   H  HCR6   0   0.295   0.4181   2.1311  -5.7379
 PGG  H51   H  HCR6   0   0.295   0.1512  -2.1630  -5.6952
 PGG  H61   H  HCR6   0   0.277   0.5389  -2.1531  -3.2698
 PGG  H81   H  HCH2   0   0.247   1.2093   0.8661   0.8310
 PGG  H82   H  HCH2   0   0.247   1.1861  -0.8914   0.8233
 PGG  H91   H  HCH2   0   0.229  -1.0508  -0.8639   1.9571
 PGG  H92   H  HCH2   0   0.229  -1.0283   0.8861   1.9659
 PGG  H101  H  HCH2   0   0.259   1.0603   0.8500   3.3592
 PGG  H102  H  HCH2   0   0.260   1.0408  -0.8938   3.3478
 PGG  HN21  H  HNH1   0   0.384   1.1807  -0.0242   5.7271
 PGG  H121  H  HCH2   0   0.236  -1.1121  -0.8932   7.1175
 PGG  H122  H  HCH2   0   0.236  -1.1080   0.8570   7.1182

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  1.396  0.020  1.396
 PGG  C1   C6    aromatic  1.396  0.020  1.396
 PGG  C1   O1    single    1.343  0.020  1.343
 PGG  C2   C3    aromatic  1.381  0.020  1.381
 PGG  C2   H21   single    0.930  0.020  1.080
 PGG  C3   C4    aromatic  1.390  0.020  1.390
 PGG  C3   H31   single    0.930  0.020  1.080
 PGG  C4   C5    aromatic  1.390  0.020  1.390
 PGG  C4   N1    single    1.447  0.020  1.447
 PGG  C5   C6    aromatic  1.381  0.020  1.381
 PGG  C5   H51   single    0.930  0.020  1.080
 PGG  C6   H61   single    0.930  0.020  1.080
 PGG  P1   O1    single    1.708  0.020  1.708
 PGG  P1   O2    deloc     1.501  0.020  1.501
 PGG  P1   O3    deloc     1.501  0.020  1.501
 PGG  P1   C8    single    1.818  0.020  1.818
 PGG  C8   C9    single    1.528  0.020  1.528
 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    1.518  0.020  1.518
 PGG  C10  H101  single    0.970  0.020  1.090
 PGG  C10  H102  single    0.970  0.020  1.090
 PGG  C11  N2    single    1.337  0.020  1.337
 PGG  C11  O6    double    1.226  0.020  1.226
 PGG  N2   C12   single    1.440  0.020  1.440
 PGG  N2   HN21  single    0.860  0.020  1.020
 PGG  C12  C13   single    1.542  0.020  1.542
 PGG  C12  H121  single    0.970  0.020  1.090
 PGG  C12  H122  single    0.970  0.020  1.090
 PGG  C13  O7    deloc     1.243  0.020  1.243
 PGG  C13  O8    deloc     1.246  0.020  1.246
 PGG  N1   O4    double    1.211  0.020  1.211
 PGG  N1   O5    single    1.211  0.020  1.211

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    120.26  3.000
 PGG  O1    C1   C2    120.04  3.000
 PGG  C6    C1   C2    119.70  3.000
 PGG  H21   C2   C3    119.97  3.000
 PGG  H21   C2   C1    119.70  3.000
 PGG  C3    C2   C1    120.32  3.000
 PGG  H31   C3   C4    121.09  3.000
 PGG  H31   C3   C2    119.69  3.000
 PGG  C4    C3   C2    119.21  3.000
 PGG  N1    C4   C5    119.41  3.000
 PGG  N1    C4   C3    119.35  3.000
 PGG  C5    C4   C3    121.24  3.000
 PGG  H51   C5   C6    119.67  3.000
 PGG  H51   C5   C4    121.13  3.000
 PGG  C6    C5   C4    119.20  3.000
 PGG  H61   C6   C5    120.01  3.000
 PGG  H61   C6   C1    119.66  3.000
 PGG  C5    C6   C1    120.33  3.000
 PGG  C8    P1   O3    111.26  3.000
 PGG  C8    P1   O2    111.42  3.000
 PGG  O3    P1   O2    119.98  3.000
 PGG  C8    P1   O1     96.98  3.000
 PGG  O3    P1   O1    107.34  3.000
 PGG  O2    P1   O1    107.14  3.000
 PGG  P1    O1   C1    118.00  3.000
 PGG  H82   C8   H81   106.97  3.000
 PGG  H82   C8   C9    109.98  3.000
 PGG  H81   C8   C9    110.03  3.000
 PGG  H82   C8   P1    109.40  3.000
 PGG  H81   C8   P1    109.50  3.000
 PGG  C9    C8   P1    110.89  3.000
 PGG  H92   C9   H91   106.51  3.000
 PGG  H92   C9   C10   109.86  3.000
 PGG  H91   C9   C10   109.86  3.000
 PGG  H92   C9   C8    109.50  3.000
 PGG  H91   C9   C8    109.48  3.000
 PGG  C10   C9   C8    111.50  3.000
 PGG  H102  C10  H101  105.54  3.000
 PGG  H102  C10  C11   108.63  3.000
 PGG  H101  C10  C11   108.64  3.000
 PGG  H102  C10  C9    109.95  3.000
 PGG  H101  C10  C9    109.99  3.000
 PGG  C11   C10  C9    113.75  3.000
 PGG  O6    C11  N2    122.61  3.000
 PGG  O6    C11  C10   122.64  3.000
 PGG  N2    C11  C10   114.75  3.000
 PGG  HN21  N2   C12   115.08  3.000
 PGG  HN21  N2   C11   120.79  3.000
 PGG  C12   N2   C11   124.13  3.000
 PGG  H122  C12  H121  106.14  3.000
 PGG  H122  C12  C13   108.76  3.000
 PGG  H121  C12  C13   108.75  3.000
 PGG  H122  C12  N2    110.84  3.000
 PGG  H121  C12  N2    110.86  3.000
 PGG  C13   C12  N2    111.32  3.000
 PGG  O8    C13  O7    127.55  3.000
 PGG  O8    C13  C12   117.29  3.000
 PGG  O7    C13  C12   115.16  3.000
 PGG  O5    N1   O4    123.49  3.000
 PGG  O5    N1   C4    118.24  3.000
 PGG  O4    N1   C4    118.27  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  Var_01    O2    P1   O1   C1    -65.17  30.0  1
 PGG  Var_02    C10   C9   C8   P1    179.91  30.0  3
 PGG  Var_03    C9    C8   P1   O1   -179.41  30.0  3
 PGG  Var_04    C11   C10  C9   C8   -179.84  30.0  3
 PGG  Var_05    N2    C11  C10  C9   -179.68  30.0  3
 PGG  Var_06    C13   C12  N2   C11  -179.71  30.0  3
 PGG  Var_07    O7    C13  C12  N2   -179.94  30.0  3

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

