# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 18:28:45 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  39  24  .  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_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   1.270   0.9352  -0.1476   0.4743
 PDE  O1    O  O2     0  -0.621   2.1478  -0.5267  -0.6768
 PDE  O2    O  OP    -1  -0.784   0.8227  -1.3088   1.4183
 PDE  O3    O  O      0  -0.784   1.2443   1.2271   0.9873
 PDE  C8    C  CH2    0  -0.709  -0.4547  -0.1247  -0.6979
 PDE  C9    C  CH2    0  -0.435  -1.7541   0.2353   0.0192
 PDE  C10   C  CH2    0  -0.554  -2.9490   0.2566  -0.9300
 PDE  C11   C  C      0   0.548  -4.1991   0.7769  -0.2489
 PDE  N2    N  NH1    0  -0.631  -5.2909   0.0187  -0.3800
 PDE  O6    O  O      0  -0.522  -4.1882   1.8342   0.3762
 PDE  C12   C  CH1    0  -0.203  -6.5730   0.3202   0.2158
 PDE  C1D   C  CH3    0  -0.657  -7.3156   1.4144  -0.5501
 PDE  C13   C  C      0   0.416  -7.4338  -0.9649   0.2733
 PDE  O7    O  O      0  -0.600  -7.0004  -1.9741  -0.3175
 PDE  O8    O  OC    -1  -0.606  -8.5050  -0.8596   0.8951
 PDE  C1    C  CR6    0   0.438   3.4529  -0.4662  -0.4276
 PDE  C2    C  CR16   0  -0.380   4.0055  -0.5617   0.8570
 PDE  C6    C  CR16   0  -0.348   4.3097  -0.3136  -1.5256
 PDE  C4    C  CR6    0   0.223   6.2051  -0.3395  -0.0692
 PDE  C5    C  CR16   0  -0.256   5.6750  -0.2533  -1.3528
 PDE  C3    C  CR16   0  -0.254   5.3722  -0.4967   1.0325
 PDE  N1    N  N      1   0.326   7.6321  -0.2687   0.1204
 PDE  O4    O  O      0  -0.394   8.3370  -0.1512  -0.8583
 PDE  O5    O  O     -1  -0.394   8.0664  -0.3291   1.2500
 PDE  HC81  H  HCH2   0   0.250  -0.5431  -1.1044  -1.1753
 PDE  HC82  H  HCH2   0   0.250  -0.2565   0.6036  -1.4885
 PDE  HC91  H  HCH2   0   0.234  -1.6519   1.2153   0.4882
 PDE  HC92  H  HCH2   0   0.234  -1.9421  -0.4817   0.8224
 PDE  H101  H  HCH2   0   0.244  -3.1113  -0.7365  -1.3560
 PDE  H102  H  HCH2   0   0.255  -2.7306   0.9241  -1.7694
 PDE  HN2   H  HNH1   0   0.382  -5.2383  -0.8792  -0.8393
 PDE  H12   H  HCH1   0   0.234  -6.4110   0.6649   1.2420
 PDE  H1D1  H  HCH3   0   0.230  -6.7199   2.3247  -0.6099
 PDE  H1D2  H  HCH3   0   0.217  -7.5441   1.0899  -1.5670
 PDE  H1D3  H  HCH3   0   0.226  -8.2528   1.6575  -0.0520
 PDE  HC2   H  HCR6   0   0.286   3.3743  -0.7132   1.7207
 PDE  HC6   H  HCR6   0   0.278   3.8896  -0.2410  -2.5203
 PDE  HC5   H  HCR6   0   0.294   6.3146  -0.1324  -2.2150
 PDE  HC3   H  HCR6   0   0.295   5.7784  -0.5756   2.0306

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    1.714  0.020  1.714
 PDE  P1   O2    deloc     1.501  0.020  1.501
 PDE  P1   O3    deloc     1.500  0.020  1.500
 PDE  P1   C8    single    1.818  0.020  1.818
 PDE  O1   C1    single    1.330  0.020  1.330
 PDE  C8   C9    single    1.527  0.020  1.527
 PDE  C8   HC81  single    0.970  0.020  1.090
 PDE  C8   HC82  single    0.970  0.020  1.090
 PDE  C9   C10   single    1.526  0.020  1.526
 PDE  C9   HC91  single    0.970  0.020  1.090
 PDE  C9   HC92  single    0.970  0.020  1.090
 PDE  C10  C11   single    1.516  0.020  1.516
 PDE  C10  H101  single    0.970  0.020  1.090
 PDE  C10  H102  single    0.970  0.020  1.090
 PDE  C11  N2    single    1.336  0.020  1.336
 PDE  C11  O6    double    1.228  0.020  1.228
 PDE  N2   C12   single    1.446  0.020  1.446
 PDE  N2   HN2   single    0.860  0.020  1.020
 PDE  C12  C1D   single    1.528  0.020  1.528
 PDE  C12  C13   single    1.548  0.020  1.548
 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    deloc     1.247  0.020  1.247
 PDE  C13  O8    deloc     1.243  0.020  1.243
 PDE  C1   C2    aromatic  1.402  0.020  1.402
 PDE  C1   C6    aromatic  1.401  0.020  1.401
 PDE  C2   C3    aromatic  1.379  0.020  1.379
 PDE  C2   HC2   single    0.930  0.020  1.080
 PDE  C6   C5    aromatic  1.378  0.020  1.378
 PDE  C6   HC6   single    0.930  0.020  1.080
 PDE  C4   C5    aromatic  1.391  0.020  1.391
 PDE  C4   C3    aromatic  1.390  0.020  1.390
 PDE  C4   N1    single    1.441  0.020  1.441
 PDE  C5   HC5   single    0.930  0.020  1.080
 PDE  C3   HC3   single    0.930  0.020  1.080
 PDE  N1   O4    double    1.212  0.020  1.212
 PDE  N1   O5    single    1.212  0.020  1.212

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    111.51  3.000
 PDE  C8    P1   O2    110.97  3.000
 PDE  O3    P1   O2    120.64  3.000
 PDE  C8    P1   O1     96.35  3.000
 PDE  O3    P1   O1    106.66  3.000
 PDE  O2    P1   O1    107.71  3.000
 PDE  C1    O1   P1    123.93  3.000
 PDE  HC82  C8   HC81  107.21  3.000
 PDE  HC82  C8   C9    109.69  3.000
 PDE  HC81  C8   C9    110.33  3.000
 PDE  HC82  C8   P1    109.64  3.000
 PDE  HC81  C8   P1    109.39  3.000
 PDE  C9    C8   P1    110.53  3.000
 PDE  HC92  C9   HC91  106.82  3.000
 PDE  HC92  C9   C10   109.36  3.000
 PDE  HC91  C9   C10   109.15  3.000
 PDE  HC92  C9   C8    109.68  3.000
 PDE  HC91  C9   C8    109.50  3.000
 PDE  C10   C9   C8    112.17  3.000
 PDE  H102  C10  H101  106.56  3.000
 PDE  H102  C10  C11   107.45  3.000
 PDE  H101  C10  C11   111.39  3.000
 PDE  H102  C10  C9    109.22  3.000
 PDE  H101  C10  C9    110.25  3.000
 PDE  C11   C10  C9    111.78  3.000
 PDE  O6    C11  N2    123.08  3.000
 PDE  O6    C11  C10   121.12  3.000
 PDE  N2    C11  C10   115.80  3.000
 PDE  HN2   N2   C12   114.78  3.000
 PDE  HN2   N2   C11   120.45  3.000
 PDE  C12   N2   C11   124.48  3.000
 PDE  H12   C12  C13   108.00  3.000
 PDE  H12   C12  C1D   108.44  3.000
 PDE  C13   C12  C1D   110.05  3.000
 PDE  H12   C12  N2    108.72  3.000
 PDE  C13   C12  N2    109.60  3.000
 PDE  C1D   C12  N2    111.94  3.000
 PDE  H1D3  C1D  H1D2  108.20  3.000
 PDE  H1D3  C1D  H1D1  108.01  3.000
 PDE  H1D2  C1D  H1D1  108.16  3.000
 PDE  H1D3  C1D  C12   110.42  3.000
 PDE  H1D2  C1D  C12   110.84  3.000
 PDE  H1D1  C1D  C12   111.11  3.000
 PDE  O8    C13  O7    127.23  3.000
 PDE  O8    C13  C12   115.31  3.000
 PDE  O7    C13  C12   117.45  3.000
 PDE  C6    C1   C2    118.98  3.000
 PDE  C6    C1   O1    117.27  3.000
 PDE  C2    C1   O1    123.75  3.000
 PDE  HC2   C2   C3    118.93  3.000
 PDE  HC2   C2   C1    120.79  3.000
 PDE  C3    C2   C1    120.27  3.000
 PDE  HC6   C6   C5    119.81  3.000
 PDE  HC6   C6   C1    119.36  3.000
 PDE  C5    C6   C1    120.83  3.000
 PDE  N1    C4   C3    119.64  3.000
 PDE  N1    C4   C5    119.70  3.000
 PDE  C3    C4   C5    120.66  3.000
 PDE  HC5   C5   C4    121.18  3.000
 PDE  HC5   C5   C6    119.44  3.000
 PDE  C4    C5   C6    119.38  3.000
 PDE  HC3   C3   C4    121.01  3.000
 PDE  HC3   C3   C2    119.11  3.000
 PDE  C4    C3   C2    119.88  3.000
 PDE  O5    N1   O4    123.32  3.000
 PDE  O5    N1   C4    118.36  3.000
 PDE  O4    N1   C4    118.33  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  Var_01    C2   C1   O1   P1     23.76  30.0  2
 PDE  Var_02    C10  C9   C8   P1   -179.63  30.0  3
 PDE  Var_03    C9   C8   P1   O1   -178.47  30.0  3
 PDE  Var_04    C11  C10  C9   C8   -173.05  30.0  3
 PDE  Var_05    N2   C11  C10  C9   -129.48  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
 PDE  chir_02  C12  N2  C1D  C13  negativ

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

