# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 22:28:32 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: N-{4-[(R)-hydroxy(4-nitrophenoxy)phosphoryl]butanoyl}-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)CCC[P@](O)(=O)Oc1ccc(cc1)[N+]([O-])=O)C(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
 PDE  PDE  N-{4-[(R)-hydroxy(4-nitrophenoxy)phosphoryl]butanoyl}-L-alanine  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_PDE
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
 PDE  P1    P  P      0   1.377   1.0267   0.3508   0.0638
 PDE  O1    O  O2     0  -0.618   2.1049  -0.6367  -0.6726
 PDE  O2    O  OH1    0  -0.738   1.0974  -0.0393   1.6163
 PDE  O3    O  O      0  -0.687   1.3111   1.7928  -0.1030
 PDE  C8    C  CH2    0  -0.759  -0.5113  -0.2724  -0.6184
 PDE  C9    C  CH2    0  -0.437  -1.7254   0.4691  -0.0597
 PDE  C10   C  CH2    0  -0.576  -3.0058  -0.0589  -0.6901
 PDE  C11   C  C      0   0.576  -4.2404   0.6826  -0.2236
 PDE  N2    N  NH1    0  -0.643  -5.3651  -0.0544  -0.2090
 PDE  O6    O  O      0  -0.497  -4.2180   1.8639   0.0910
 PDE  C12   C  CH1    0  -0.199  -6.6602   0.5000   0.0928
 PDE  C1D   C  CH3    0  -0.654  -7.3186   1.1392  -1.1344
 PDE  C13   C  C      0   0.549  -7.5393  -0.5941   0.6640
 PDE  O7    O  O      0  -0.434  -7.2591  -1.7656   0.6680
 PDE  O8    O  OH1    0  -0.586  -8.6710  -0.1026   1.1402
 PDE  C1    C  CR6    0   0.397   3.4446  -0.5356  -0.4303
 PDE  C2    C  CR16   0  -0.322   4.0557  -1.5181   0.3382
 PDE  C6    C  CR16   0  -0.310   4.1828   0.5082  -0.9747
 PDE  C4    C  CR6    0   0.250   6.1511  -0.4218   0.0110
 PDE  C5    C  CR16   0  -0.261   5.5464   0.5652  -0.7551
 PDE  C3    C  CR16   0  -0.260   5.4192  -1.4661   0.5585
 PDE  N1    N  N      1   0.330   7.5842  -0.3638   0.2397
 PDE  O4    O  O      0  -0.379   8.2020   0.5505  -0.2536
 PDE  O5    O  O     -1  -0.379   8.0887  -1.2327   0.9116
 PDE  HO2   H  HOH1   0   0.497   0.8525  -0.9473   1.8396
 PDE  HC81  H  HCH2   0   0.296  -0.5805  -1.3451  -0.4200
 PDE  HC82  H  HCH2   0   0.300  -0.4570  -0.1520  -1.7037
 PDE  HC91  H  HCH2   0   0.254  -1.6304   1.5369  -0.2569
 PDE  HC92  H  HCH2   0   0.251  -1.7728   0.3479   1.0248
 PDE  H101  H  HCH2   0   0.262  -3.1086  -1.1300  -0.5009
 PDE  H102  H  HCH2   0   0.279  -2.9525   0.0540  -1.7783
 PDE  HN2   H  HNH1   0   0.401  -5.3199  -1.0187  -0.4992
 PDE  H12   H  HCH1   0   0.294  -6.5373   1.2654   0.8632
 PDE  H1D1  H  HCH3   0   0.253  -6.6713   1.9242  -1.5216
 PDE  H1D2  H  HCH3   0   0.238  -7.4721   0.4017  -1.9222
 PDE  H1D3  H  HCH3   0   0.247  -8.2776   1.5904  -0.8861
 PDE  HO8   H  HOH1   0   0.488  -9.2367  -0.8183   1.4676
 PDE  HC2   H  HCR6   0   0.293   3.4712  -2.3284   0.7522
 PDE  HC6   H  HCR6   0   0.295   3.7013   1.2634  -1.5797
 PDE  HC5   H  HCR6   0   0.305   6.1196   1.3749  -1.1819
 PDE  HC3   H  HCR6   0   0.305   5.8939  -2.2335   1.1517

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
 PDE  P1   O1    single    1.637  0.020  1.637
 PDE  P1   O2    single    1.602  0.020  1.602
 PDE  P1   O3    double    1.479  0.020  1.479
 PDE  P1   C8    single    1.794  0.020  1.794
 PDE  O1   C1    single    1.365  0.020  1.365
 PDE  O2   HO2   single    0.850  0.020  0.980
 PDE  C8   C9    single    1.528  0.020  1.528
 PDE  C8   HC81  single    0.970  0.020  1.090
 PDE  C8   HC82  single    0.970  0.020  1.090
 PDE  C9   C10   single    1.522  0.020  1.522
 PDE  C9   HC91  single    0.970  0.020  1.090
 PDE  C9   HC92  single    0.970  0.020  1.090
 PDE  C10  C11   single    1.514  0.020  1.514
 PDE  C10  H101  single    0.970  0.020  1.090
 PDE  C10  H102  single    0.970  0.020  1.090
 PDE  C11  N2    single    1.345  0.020  1.345
 PDE  C11  O6    double    1.223  0.020  1.223
 PDE  N2   C12   single    1.441  0.020  1.441
 PDE  N2   HN2   single    0.860  0.020  1.020
 PDE  C12  C1D   single    1.532  0.020  1.532
 PDE  C12  C13   single    1.515  0.020  1.515
 PDE  C12  H12   single    0.970  0.020  1.090
 PDE  C1D  H1D1  single    0.970  0.020  1.090
 PDE  C1D  H1D2  single    0.970  0.020  1.090
 PDE  C1D  H1D3  single    0.970  0.020  1.090
 PDE  C13  O7    double    1.205  0.020  1.205
 PDE  C13  O8    single    1.323  0.020  1.323
 PDE  O8   HO8   single    0.850  0.020  0.980
 PDE  C1   C2    aromatic  1.389  0.020  1.389
 PDE  C1   C6    aromatic  1.390  0.020  1.390
 PDE  C2   C3    aromatic  1.382  0.020  1.382
 PDE  C2   HC2   single    0.930  0.020  1.080
 PDE  C6   C5    aromatic  1.382  0.020  1.382
 PDE  C6   HC6   single    0.930  0.020  1.080
 PDE  C4   C5    aromatic  1.388  0.020  1.388
 PDE  C4   C3    aromatic  1.388  0.020  1.388
 PDE  C4   N1    single    1.452  0.020  1.452
 PDE  C5   HC5   single    0.930  0.020  1.080
 PDE  C3   HC3   single    0.930  0.020  1.080
 PDE  N1   O4    double    1.209  0.020  1.209
 PDE  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
 PDE  C8    P1   O3    117.43  3.000
 PDE  C8    P1   O2    108.76  3.000
 PDE  O3    P1   O2    109.76  3.000
 PDE  C8    P1   O1    100.60  3.000
 PDE  O3    P1   O1    114.25  3.000
 PDE  O2    P1   O1    105.06  3.000
 PDE  C1    O1   P1    121.46  3.000
 PDE  HO2   O2   P1    116.19  3.000
 PDE  HC82  C8   HC81  106.94  3.000
 PDE  HC82  C8   C9    110.42  3.000
 PDE  HC81  C8   C9    111.07  3.000
 PDE  HC82  C8   P1    107.25  3.000
 PDE  HC81  C8   P1    109.04  3.000
 PDE  C9    C8   P1    111.93  3.000
 PDE  HC92  C9   HC91  106.98  3.000
 PDE  HC92  C9   C10   109.66  3.000
 PDE  HC91  C9   C10   109.77  3.000
 PDE  HC92  C9   C8    110.09  3.000
 PDE  HC91  C9   C8    109.87  3.000
 PDE  C10   C9   C8    110.40  3.000
 PDE  H102  C10  H101  106.12  3.000
 PDE  H102  C10  C11   107.18  3.000
 PDE  H101  C10  C11   110.49  3.000
 PDE  H102  C10  C9    109.57  3.000
 PDE  H101  C10  C9    110.34  3.000
 PDE  C11   C10  C9    112.87  3.000
 PDE  O6    C11  N2    122.82  3.000
 PDE  O6    C11  C10   122.52  3.000
 PDE  N2    C11  C10   114.65  3.000
 PDE  HN2   N2   C12   117.95  3.000
 PDE  HN2   N2   C11   118.92  3.000
 PDE  C12   N2   C11   122.90  3.000
 PDE  H12   C12  C13   107.77  3.000
 PDE  H12   C12  C1D   108.70  3.000
 PDE  C13   C12  C1D   110.72  3.000
 PDE  H12   C12  N2    108.43  3.000
 PDE  C13   C12  N2    108.83  3.000
 PDE  C1D   C12  N2    112.27  3.000
 PDE  H1D3  C1D  H1D2  108.74  3.000
 PDE  H1D3  C1D  H1D1  107.82  3.000
 PDE  H1D2  C1D  H1D1  108.33  3.000
 PDE  H1D3  C1D  C12   111.64  3.000
 PDE  H1D2  C1D  C12   110.92  3.000
 PDE  H1D1  C1D  C12   109.28  3.000
 PDE  O8    C13  O7    124.01  3.000
 PDE  O8    C13  C12   111.34  3.000
 PDE  O7    C13  C12   124.64  3.000
 PDE  HO8   O8   C13   110.28  3.000
 PDE  C6    C1   C2    120.96  3.000
 PDE  C6    C1   O1    120.49  3.000
 PDE  C2    C1   O1    118.53  3.000
 PDE  HC2   C2   C3    120.03  3.000
 PDE  HC2   C2   C1    120.26  3.000
 PDE  C3    C2   C1    119.71  3.000
 PDE  HC6   C6   C5    119.97  3.000
 PDE  HC6   C6   C1    120.50  3.000
 PDE  C5    C6   C1    119.52  3.000
 PDE  N1    C4   C3    119.23  3.000
 PDE  N1    C4   C5    119.24  3.000
 PDE  C3    C4   C5    121.54  3.000
 PDE  HC5   C5   C4    121.33  3.000
 PDE  HC5   C5   C6    119.45  3.000
 PDE  C4    C5   C6    119.22  3.000
 PDE  HC3   C3   C4    121.31  3.000
 PDE  HC3   C3   C2    119.63  3.000
 PDE  C4    C3   C2    119.06  3.000
 PDE  O5    N1   O4    123.87  3.000
 PDE  O5    N1   C4    118.08  3.000
 PDE  O4    N1   C4    118.05  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
 PDE  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 PDE  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 PDE  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 PDE  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 PDE  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 PDE  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 PDE  CONST_07  C3   C2   C1   O1    180.00   0.0  0
 PDE  CONST_08  C5   C6   C1   O1    180.00   0.0  0
 PDE  CONST_09  N1   C4   C3   C2    180.00   0.0  0
 PDE  CONST_10  N1   C4   C5   C6    180.00   0.0  0
 PDE  CONST_11  HC3  C3   C2   C1    180.00   0.0  0
 PDE  CONST_12  HC5  C5   C6   C1    180.00   0.0  0
 PDE  CONST_13  HC6  C6   C1   C2    180.00   0.0  0
 PDE  CONST_14  HC2  C2   C1   C6    180.00   0.0  0
 PDE  CONST_15  O4   N1   C4   C5      0.00   0.0  0
 PDE  CONST_16  O5   N1   C4   C5    180.00   0.0  0
 PDE  CONST_17  O4   N1   C4   C3    180.00   0.0  0
 PDE  CONST_18  O5   N1   C4   C3      0.00   0.0  0
 PDE  CONST_19  C12  N2   C11  C10   180.00   0.0  0
 PDE  CONST_20  C12  N2   C11  O6      0.00   0.0  0
 PDE  CONST_21  HN2  N2   C11  C10     0.00   0.0  0
 PDE  CONST_22  HO8  O8   C13  C12   180.00   0.0  0
 PDE  Var_01    C2   C1   O1   P1    106.93  30.0  2
 PDE  Var_02    C10  C9   C8   P1    178.37  30.0  3
 PDE  Var_03    C9   C8   P1   O1    178.61  30.0  3
 PDE  Var_04    C11  C10  C9   C8   -177.30  30.0  3
 PDE  Var_05    N2   C11  C10  C9   -150.29  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
 PDE  chir_02  C12  N2  C1D  C13  negativ
 PDE  chir_03  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
 PDE  plan-1  O1   0.020
 PDE  plan-1  C1   0.020
 PDE  plan-1  C2   0.020
 PDE  plan-1  C6   0.020
 PDE  plan-1  C4   0.020
 PDE  plan-1  C5   0.020
 PDE  plan-1  C3   0.020
 PDE  plan-1  N1   0.020
 PDE  plan-1  HC2  0.020
 PDE  plan-1  HC6  0.020
 PDE  plan-1  HC5  0.020
 PDE  plan-1  HC3  0.020
 PDE  plan-2  C10  0.020
 PDE  plan-2  C11  0.020
 PDE  plan-2  N2   0.020
 PDE  plan-2  O6   0.020
 PDE  plan-2  C12  0.020
 PDE  plan-2  HN2  0.020
 PDE  plan-3  C4   0.020
 PDE  plan-3  N1   0.020
 PDE  plan-3  O4   0.020
 PDE  plan-3  O5   0.020
 PDE  plan-4  C12  0.020
 PDE  plan-4  C13  0.020
 PDE  plan-4  O7   0.020
 PDE  plan-4  O8   0.020
 PDE  plan-4  HO8  0.020

