# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 15:51:15 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: N-{4-[(R)-hydroxy(4-nitrophenoxy)phosphoryl]butanoyl}-D-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
 PNE  PNE  N-{4-[(R)-hydroxy(4-nitrophenoxy)phosphoryl]butanoyl}-D-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_PNE
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
 PNE  P1    P  P      0   1.389  -3.7221  -4.8423  3.7301
 PNE  O1    O  O2     0  -0.610  -3.9831  -3.6591  4.8309
 PNE  O2    O  OH1    0  -0.738  -4.5578  -6.0521  4.3651
 PNE  O3    O  O      0  -0.694  -4.0815  -4.4795  2.3399
 PNE  C8    C  CH2    0  -0.728  -1.9937  -5.1854  4.0589
 PNE  C9    C  CH2    0  -0.437  -1.0662  -4.0308  3.6814
 PNE  C10   C  CH2    0  -0.579   0.3775  -4.3925  3.9928
 PNE  C11   C  C      0   0.575   1.3515  -3.2718  3.6964
 PNE  N2    N  NH1    0  -0.641   2.6199  -3.6760  3.4979
 PNE  O6    O  O      0  -0.496   1.0171  -2.0967  3.6621
 PNE  C12   C  CH1    0  -0.201   3.7167  -2.7587  3.3267
 PNE  C1L   C  CH3    0  -0.655   4.3084  -2.3048  4.6650
 PNE  C13   C  C      0   0.549   4.7762  -3.4131  2.4629
 PNE  O7    O  O      0  -0.434   4.7759  -4.5729  2.1377
 PNE  O8    O  OH1    0  -0.587   5.7207  -2.5506  2.1250
 PNE  C1    C  CR6    0   0.429  -5.1692  -3.1030  5.1738
 PNE  C2    C  CR16   0  -0.329  -5.1818  -2.3826  6.3660
 PNE  C6    C  CR16   0  -0.361  -6.3244  -3.2090  4.4030
 PNE  C4    C  CR6    0   0.241  -7.4924  -1.8895  6.0240
 PNE  C5    C  CR16   0  -0.254  -7.4894  -2.6024  4.8345
 PNE  C3    C  CR16   0  -0.256  -6.3418  -1.7711  6.7935
 PNE  N1    N  N      1   0.329  -8.7159  -1.2543  6.4700
 PNE  O4    O  O      0  -0.382  -8.6864  -0.6221  7.5005
 PNE  O5    O  O     -1  -0.383  -9.7080  -1.3876  5.7913
 PNE  HO2   H  HOH1   0   0.500  -5.0855  -6.5497  3.7260
 PNE  HC81  H  HCH2   0   0.293  -1.8851  -5.4459  5.1146
 PNE  HC82  H  HCH2   0   0.294  -1.7411  -6.0820  3.4856
 PNE  HC91  H  HCH2   0   0.251  -1.1730  -3.8036  2.6190
 PNE  HC92  H  HCH2   0   0.251  -1.3459  -3.1306  4.2291
 PNE  H101  H  HCH2   0   0.279   0.4754  -4.6358  5.0564
 PNE  H102  H  HCH2   0   0.264   0.6717  -5.2946  3.4501
 PNE  HN2   H  HNH1   0   0.401   2.8347  -4.6583  3.5746
 PNE  H12   H  HCH1   0   0.295   3.3499  -1.8797  2.7906
 PNE  H1L1  H  HCH3   0   0.247   5.1007  -1.5721  4.5242
 PNE  H1L2  H  HCH3   0   0.253   3.5269  -1.8419  5.2652
 PNE  H1L3  H  HCH3   0   0.239   4.7109  -3.1513  5.2216
 PNE  HO8   H  HOH1   0   0.488   6.4066  -2.9919  1.6015
 PNE  HC2   H  HCR6   0   0.293  -4.2781  -2.3040  6.9552
 PNE  HC6   H  HCR6   0   0.298  -6.3328  -3.7398  3.4619
 PNE  HC5   H  HCR6   0   0.305  -8.3814  -2.6890  4.2318
 PNE  HC3   H  HCR6   0   0.303  -6.3389  -1.2144  7.7190

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
 PNE  P1   O1    single    1.637  0.020  1.637
 PNE  P1   O2    single    1.602  0.020  1.602
 PNE  P1   O3    double    1.481  0.020  1.481
 PNE  P1   C8    single    1.793  0.020  1.793
 PNE  O1   C1    single    1.354  0.020  1.354
 PNE  O2   HO2   single    0.850  0.020  0.980
 PNE  C8   C9    single    1.528  0.020  1.528
 PNE  C8   HC81  single    0.970  0.020  1.090
 PNE  C8   HC82  single    0.970  0.020  1.090
 PNE  C9   C10   single    1.521  0.020  1.521
 PNE  C9   HC91  single    0.970  0.020  1.090
 PNE  C9   HC92  single    0.970  0.020  1.090
 PNE  C10  C11   single    1.514  0.020  1.514
 PNE  C10  H101  single    0.970  0.020  1.090
 PNE  C10  H102  single    0.970  0.020  1.090
 PNE  C11  N2    single    1.346  0.020  1.346
 PNE  C11  O6    double    1.222  0.020  1.222
 PNE  N2   C12   single    1.440  0.020  1.440
 PNE  N2   HN2   single    0.860  0.020  1.020
 PNE  C12  C1L   single    1.532  0.020  1.532
 PNE  C12  C13   single    1.516  0.020  1.516
 PNE  C12  H12   single    0.970  0.020  1.090
 PNE  C1L  H1L1  single    0.970  0.020  1.090
 PNE  C1L  H1L2  single    0.970  0.020  1.090
 PNE  C1L  H1L3  single    0.970  0.020  1.090
 PNE  C13  O7    double    1.205  0.020  1.205
 PNE  C13  O8    single    1.323  0.020  1.323
 PNE  O8   HO8   single    0.850  0.020  0.980
 PNE  C1   C2    aromatic  1.393  0.020  1.393
 PNE  C1   C6    aromatic  1.393  0.020  1.393
 PNE  C2   C3    aromatic  1.379  0.020  1.379
 PNE  C2   HC2   single    0.930  0.020  1.080
 PNE  C6   C5    aromatic  1.383  0.020  1.383
 PNE  C6   HC6   single    0.930  0.020  1.080
 PNE  C4   C5    aromatic  1.387  0.020  1.387
 PNE  C4   C3    aromatic  1.389  0.020  1.389
 PNE  C4   N1    single    1.449  0.020  1.449
 PNE  C5   HC5   single    0.930  0.020  1.080
 PNE  C3   HC3   single    0.930  0.020  1.080
 PNE  N1   O4    double    1.209  0.020  1.209
 PNE  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
 PNE  C8    P1   O3    116.94  3.000
 PNE  C8    P1   O2    106.60  3.000
 PNE  O3    P1   O2    115.50  3.000
 PNE  C8    P1   O1     99.72  3.000
 PNE  O3    P1   O1    114.55  3.000
 PNE  O2    P1   O1    101.31  3.000
 PNE  C1    O1   P1    127.36  3.000
 PNE  HO2   O2   P1    114.30  3.000
 PNE  HC82  C8   HC81  106.74  3.000
 PNE  HC82  C8   C9    110.47  3.000
 PNE  HC81  C8   C9    111.00  3.000
 PNE  HC82  C8   P1    106.46  3.000
 PNE  HC81  C8   P1    108.59  3.000
 PNE  C9    C8   P1    113.28  3.000
 PNE  HC92  C9   HC91  106.98  3.000
 PNE  HC92  C9   C10   109.70  3.000
 PNE  HC91  C9   C10   109.98  3.000
 PNE  HC92  C9   C8    110.12  3.000
 PNE  HC91  C9   C8    109.77  3.000
 PNE  C10   C9   C8    110.24  3.000
 PNE  H102  C10  H101  105.94  3.000
 PNE  H102  C10  C11   109.91  3.000
 PNE  H101  C10  C11   107.28  3.000
 PNE  H102  C10  C9    110.49  3.000
 PNE  H101  C10  C9    109.67  3.000
 PNE  C11   C10  C9    113.24  3.000
 PNE  O6    C11  N2    122.85  3.000
 PNE  O6    C11  C10   122.76  3.000
 PNE  N2    C11  C10   114.38  3.000
 PNE  HN2   N2   C12   117.85  3.000
 PNE  HN2   N2   C11   118.83  3.000
 PNE  C12   N2   C11   122.95  3.000
 PNE  H12   C12  C13   107.60  3.000
 PNE  H12   C12  C1L   108.65  3.000
 PNE  C13   C12  C1L   110.84  3.000
 PNE  H12   C12  N2    108.36  3.000
 PNE  C13   C12  N2    108.98  3.000
 PNE  C1L   C12  N2    112.27  3.000
 PNE  H1L3  C1L  H1L2  108.28  3.000
 PNE  H1L3  C1L  H1L1  108.66  3.000
 PNE  H1L2  C1L  H1L1  107.92  3.000
 PNE  H1L3  C1L  C12   111.01  3.000
 PNE  H1L2  C1L  C12   109.29  3.000
 PNE  H1L1  C1L  C12   111.57  3.000
 PNE  O8    C13  O7    123.98  3.000
 PNE  O8    C13  C12   111.30  3.000
 PNE  O7    C13  C12   124.71  3.000
 PNE  HO8   O8   C13   110.27  3.000
 PNE  C6    C1   C2    120.36  3.000
 PNE  C6    C1   O1    123.72  3.000
 PNE  C2    C1   O1    115.92  3.000
 PNE  HC2   C2   C3    120.11  3.000
 PNE  HC2   C2   C1    119.75  3.000
 PNE  C3    C2   C1    120.14  3.000
 PNE  HC6   C6   C5    118.74  3.000
 PNE  HC6   C6   C1    121.72  3.000
 PNE  C5    C6   C1    119.53  3.000
 PNE  N1    C4   C3    119.44  3.000
 PNE  N1    C4   C5    119.42  3.000
 PNE  C3    C4   C5    121.14  3.000
 PNE  HC5   C5   C4    121.20  3.000
 PNE  HC5   C5   C6    119.12  3.000
 PNE  C4    C5   C6    119.67  3.000
 PNE  HC3   C3   C4    121.38  3.000
 PNE  HC3   C3   C2    119.46  3.000
 PNE  C4    C3   C2    119.15  3.000
 PNE  O5    N1   O4    123.77  3.000
 PNE  O5    N1   C4    118.14  3.000
 PNE  O4    N1   C4    118.09  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
 PNE  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 PNE  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 PNE  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 PNE  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 PNE  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 PNE  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 PNE  CONST_07  C3   C2   C1   O1    180.00   0.0  0
 PNE  CONST_08  C5   C6   C1   O1    180.00   0.0  0
 PNE  CONST_09  N1   C4   C3   C2    180.00   0.0  0
 PNE  CONST_10  N1   C4   C5   C6    180.00   0.0  0
 PNE  CONST_11  HC3  C3   C2   C1    180.00   0.0  0
 PNE  CONST_12  HC5  C5   C6   C1    180.00   0.0  0
 PNE  CONST_13  HC6  C6   C1   C2    180.00   0.0  0
 PNE  CONST_14  HC2  C2   C1   C6    180.00   0.0  0
 PNE  CONST_15  O4   N1   C4   C5    180.00   0.0  0
 PNE  CONST_16  O5   N1   C4   C5      0.00   0.0  0
 PNE  CONST_17  O4   N1   C4   C3      0.00   0.0  0
 PNE  CONST_18  O5   N1   C4   C3    180.00   0.0  0
 PNE  CONST_19  C12  N2   C11  C10   180.00   0.0  0
 PNE  CONST_20  C12  N2   C11  O6      0.00   0.0  0
 PNE  CONST_21  HN2  N2   C11  C10     0.00   0.0  0
 PNE  CONST_22  HO8  O8   C13  C12   180.00   0.0  0
 PNE  Var_01    C2   C1   O1   P1    163.51  30.0  2
 PNE  Var_02    C10  C9   C8   P1    179.79  30.0  3
 PNE  Var_03    C9   C8   P1   O1    -67.27  30.0  3
 PNE  Var_04    C11  C10  C9   C8   -177.66  30.0  3
 PNE  Var_05    N2   C11  C10  C9   -157.48  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
 PNE  chir_02  C12  N2  C1L  C13  negativ
 PNE  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
 PNE  plan-1  O1   0.020
 PNE  plan-1  C1   0.020
 PNE  plan-1  C2   0.020
 PNE  plan-1  C6   0.020
 PNE  plan-1  C4   0.020
 PNE  plan-1  C5   0.020
 PNE  plan-1  C3   0.020
 PNE  plan-1  N1   0.020
 PNE  plan-1  HC2  0.020
 PNE  plan-1  HC6  0.020
 PNE  plan-1  HC5  0.020
 PNE  plan-1  HC3  0.020
 PNE  plan-2  C10  0.020
 PNE  plan-2  C11  0.020
 PNE  plan-2  N2   0.020
 PNE  plan-2  O6   0.020
 PNE  plan-2  C12  0.020
 PNE  plan-2  HN2  0.020
 PNE  plan-3  C4   0.020
 PNE  plan-3  N1   0.020
 PNE  plan-3  O4   0.020
 PNE  plan-3  O5   0.020
 PNE  plan-4  C12  0.020
 PNE  plan-4  C13  0.020
 PNE  plan-4  O7   0.020
 PNE  plan-4  O8   0.020
 PNE  plan-4  HO8  0.020

