# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 11:47:45 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 6-({4-[(R)-hydroxy(4-nitrophenoxy)phosphoryl]butanoyl}amino)hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCCNC(=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
 PNF  PNF  '6-({4-[(R)-hydroxy(4-nitrophenoxy)phosphoryl]butanoyl}amino)hexanoic acid'  ligand  48  27  .  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_PNF
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
 PNF  C1    C  CR6    0   0.437   0.6489   0.0723  -4.9875
 PNF  C2    C  CR16   0  -0.374  -0.4245   0.7054  -5.6283
 PNF  C3    C  CR16   0  -0.256  -0.6629   0.4817  -6.9685
 PNF  C4    C  CR6    0   0.224   0.1659  -0.3728  -7.6861
 PNF  C5    C  CR16   0  -0.256   1.2410  -1.0039  -7.0683
 PNF  C6    C  CR16   0  -0.349   1.4746  -0.7828  -5.7287
 PNF  P1    P  P      0   1.270  -0.1873   0.7181  -2.5103
 PNF  O1    O  O2     0  -0.622   0.9483   0.2460  -3.7029
 PNF  O2    O  OP    -1  -0.783  -0.3991   2.1976  -2.6451
 PNF  O3    O  O      0  -0.783  -1.3408  -0.2345  -2.6096
 PNF  C8    C  CH2    0  -0.709   0.8618   0.3394  -1.0734
 PNF  C9    C  CH2    0  -0.435   0.1089   0.6035   0.2285
 PNF  C10   C  CH2    0  -0.547   0.9588   0.2738   1.4556
 PNF  C11   C  C      0   0.531   0.2206   0.6006   2.7357
 PNF  N2    N  NH1    0  -0.626  -0.1490  -0.4545   3.4779
 PNF  O6    O  O      0  -0.512  -0.0447   1.7575   3.0424
 PNF  C12   C  CH2    0  -0.279  -0.8536  -0.3440   4.7360
 PNF  C13   C  CH2    0  -0.424   0.0741  -0.2695   5.9431
 PNF  C14   C  CH2    0  -0.418  -0.6970  -0.1816   7.2537
 PNF  C15   C  CH2    0  -0.402   0.2098  -0.1401   8.4784
 PNF  C16   C  CH2    0  -0.579  -0.5687  -0.0741   9.7820
 PNF  C17   C  C      0   0.409   0.2712  -0.0409  11.0710
 PNF  O7    O  O      0  -0.610   1.5026   0.1221  10.9616
 PNF  O8    O  OC    -1  -0.634  -0.3627  -0.1696  12.1405
 PNF  N1    N  N      1   0.326  -0.0884  -0.6032  -9.0863
 PNF  O4    O  O      0  -0.394   0.6579  -1.3405  -9.6925
 PNF  O5    O  O     -1  -0.394  -1.0383  -0.0510  -9.5973
 PNF  H21   H  HCR6   0   0.284  -1.0614   1.3935  -5.0912
 PNF  H31   H  HCR6   0   0.295  -1.4938   0.9809  -7.4452
 PNF  H51   H  HCR6   0   0.294   1.8907  -1.6686  -7.6189
 PNF  H61   H  HCR6   0   0.278   2.3056  -1.2727  -5.2387
 PNF  H81   H  HCH2   0   0.252   1.7651   0.9539  -1.1108
 PNF  H82   H  HCH2   0   0.251   1.1789  -0.7055  -1.1169
 PNF  H91   H  HCH2   0   0.235  -0.8040   0.0028   0.2507
 PNF  H92   H  HCH2   0   0.237  -0.1991   1.6500   0.2706
 PNF  H101  H  HCH2   0   0.256   1.8738   0.8712   1.4368
 PNF  H102  H  HCH2   0   0.245   1.2602  -0.7756   1.4232
 PNF  HN21  H  HNH1   0   0.398   0.1311  -1.3740   3.1798
 PNF  H121  H  HCH2   0   0.241  -1.5115  -1.2102   4.8272
 PNF  H122  H  HCH2   0   0.236  -1.4940   0.5379   4.6998
 PNF  H131  H  HCH2   0   0.220   0.7319   0.5990   5.8394
 PNF  H132  H  HCH2   0   0.215   0.7218  -1.1522   5.9552
 PNF  H141  H  HCH2   0   0.206  -1.3767  -1.0379   7.3333
 PNF  H142  H  HCH2   0   0.208  -1.3361   0.7088   7.2413
 PNF  H151  H  HCH2   0   0.203   0.8808   0.7199   8.4009
 PNF  H152  H  HCH2   0   0.201   0.8543  -1.0250   8.4760
 PNF  H161  H  HCH2   0   0.212  -1.2609  -0.9216   9.8420
 PNF  H162  H  HCH2   0   0.219  -1.2128   0.8146   9.7779

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
 PNF  C1   C2    aromatic  1.401  0.020  1.401
 PNF  C1   C6    aromatic  1.401  0.020  1.401
 PNF  C1   O1    single    1.330  0.020  1.330
 PNF  C2   C3    aromatic  1.379  0.020  1.379
 PNF  C2   H21   single    0.930  0.020  1.080
 PNF  C3   C4    aromatic  1.390  0.020  1.390
 PNF  C3   H31   single    0.930  0.020  1.080
 PNF  C4   C5    aromatic  1.391  0.020  1.391
 PNF  C4   N1    single    1.442  0.020  1.442
 PNF  C5   C6    aromatic  1.378  0.020  1.378
 PNF  C5   H51   single    0.930  0.020  1.080
 PNF  C6   H61   single    0.930  0.020  1.080
 PNF  P1   O1    single    1.713  0.020  1.713
 PNF  P1   O2    deloc     1.501  0.020  1.501
 PNF  P1   O3    deloc     1.499  0.020  1.499
 PNF  P1   C8    single    1.819  0.020  1.819
 PNF  C8   C9    single    1.527  0.020  1.527
 PNF  C8   H81   single    0.970  0.020  1.090
 PNF  C8   H82   single    0.970  0.020  1.090
 PNF  C9   C10   single    1.529  0.020  1.529
 PNF  C9   H91   single    0.970  0.020  1.090
 PNF  C9   H92   single    0.970  0.020  1.090
 PNF  C10  C11   single    1.513  0.020  1.513
 PNF  C10  H101  single    0.970  0.020  1.090
 PNF  C10  H102  single    0.970  0.020  1.090
 PNF  C11  N2    single    1.342  0.020  1.342
 PNF  C11  O6    double    1.226  0.020  1.226
 PNF  N2   C12   single    1.446  0.020  1.446
 PNF  N2   HN21  single    0.860  0.020  1.020
 PNF  C12  C13   single    1.524  0.020  1.524
 PNF  C12  H121  single    0.970  0.020  1.090
 PNF  C12  H122  single    0.970  0.020  1.090
 PNF  C13  C14   single    1.523  0.020  1.523
 PNF  C13  H131  single    0.970  0.020  1.090
 PNF  C13  H132  single    0.970  0.020  1.090
 PNF  C14  C15   single    1.524  0.020  1.524
 PNF  C14  H141  single    0.970  0.020  1.090
 PNF  C14  H142  single    0.970  0.020  1.090
 PNF  C15  C16   single    1.520  0.020  1.520
 PNF  C15  H151  single    0.970  0.020  1.090
 PNF  C15  H152  single    0.970  0.020  1.090
 PNF  C16  C17   single    1.539  0.020  1.539
 PNF  C16  H161  single    0.970  0.020  1.090
 PNF  C16  H162  single    0.970  0.020  1.090
 PNF  C17  O7    deloc     1.247  0.020  1.247
 PNF  C17  O8    deloc     1.250  0.020  1.250
 PNF  N1   O4    double    1.212  0.020  1.212
 PNF  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
 PNF  O1    C1   C6    117.25  3.000
 PNF  O1    C1   C2    123.71  3.000
 PNF  C6    C1   C2    119.03  3.000
 PNF  H21   C2   C3    118.97  3.000
 PNF  H21   C2   C1    120.79  3.000
 PNF  C3    C2   C1    120.22  3.000
 PNF  H31   C3   C4    120.99  3.000
 PNF  H31   C3   C2    119.13  3.000
 PNF  C4    C3   C2    119.88  3.000
 PNF  N1    C4   C5    119.67  3.000
 PNF  N1    C4   C3    119.64  3.000
 PNF  C5    C4   C3    120.69  3.000
 PNF  H51   C5   C6    119.49  3.000
 PNF  H51   C5   C4    121.17  3.000
 PNF  C6    C5   C4    119.34  3.000
 PNF  H61   C6   C5    119.87  3.000
 PNF  H61   C6   C1    119.30  3.000
 PNF  C5    C6   C1    120.83  3.000
 PNF  C8    P1   O3    111.34  3.000
 PNF  C8    P1   O2    110.95  3.000
 PNF  O3    P1   O2    120.79  3.000
 PNF  C8    P1   O1     96.33  3.000
 PNF  O3    P1   O1    106.79  3.000
 PNF  O2    P1   O1    107.62  3.000
 PNF  P1    O1   C1    123.98  3.000
 PNF  H82   C8   H81   107.24  3.000
 PNF  H82   C8   C9    110.02  3.000
 PNF  H81   C8   C9    109.84  3.000
 PNF  H82   C8   P1    109.57  3.000
 PNF  H81   C8   P1    109.43  3.000
 PNF  C9    C8   P1    110.68  3.000
 PNF  H92   C9   H91   106.89  3.000
 PNF  H92   C9   C10   109.43  3.000
 PNF  H91   C9   C10   109.24  3.000
 PNF  H92   C9   C8    109.74  3.000
 PNF  H91   C9   C8    109.52  3.000
 PNF  C10   C9   C8    111.90  3.000
 PNF  H102  C10  H101  107.08  3.000
 PNF  H102  C10  C11   111.54  3.000
 PNF  H101  C10  C11   107.75  3.000
 PNF  H102  C10  C9    109.68  3.000
 PNF  H101  C10  C9    109.50  3.000
 PNF  C11   C10  C9    111.17  3.000
 PNF  O6    C11  N2    122.96  3.000
 PNF  O6    C11  C10   121.40  3.000
 PNF  N2    C11  C10   115.62  3.000
 PNF  HN21  N2   C12   117.58  3.000
 PNF  HN21  N2   C11   118.55  3.000
 PNF  C12   N2   C11   123.73  3.000
 PNF  H122  C12  H121  106.89  3.000
 PNF  H122  C12  C13   110.13  3.000
 PNF  H121  C12  C13   109.84  3.000
 PNF  H122  C12  N2    108.61  3.000
 PNF  H121  C12  N2    107.80  3.000
 PNF  C13   C12  N2    113.34  3.000
 PNF  H132  C13  H131  106.58  3.000
 PNF  H132  C13  C14   109.66  3.000
 PNF  H131  C13  C14   109.88  3.000
 PNF  H132  C13  C12   109.23  3.000
 PNF  H131  C13  C12   109.24  3.000
 PNF  C14   C13  C12   112.09  3.000
 PNF  H142  C14  H141  105.90  3.000
 PNF  H142  C14  C15   109.49  3.000
 PNF  H141  C14  C15   109.38  3.000
 PNF  H142  C14  C13   109.41  3.000
 PNF  H141  C14  C13   109.35  3.000
 PNF  C15   C14  C13   113.06  3.000
 PNF  H152  C15  H151  105.92  3.000
 PNF  H152  C15  C16   109.79  3.000
 PNF  H151  C15  C16   109.94  3.000
 PNF  H152  C15  C14   109.05  3.000
 PNF  H151  C15  C14   109.24  3.000
 PNF  C16   C15  C14   112.68  3.000
 PNF  H162  C16  H161  104.81  3.000
 PNF  H162  C16  C17   107.82  3.000
 PNF  H161  C16  C17   108.40  3.000
 PNF  H162  C16  C15   109.42  3.000
 PNF  H161  C16  C15   109.68  3.000
 PNF  C17   C16  C15   116.09  3.000
 PNF  O8    C17  O7    126.11  3.000
 PNF  O8    C17  C16   115.96  3.000
 PNF  O7    C17  C16   117.92  3.000
 PNF  O5    N1   O4    123.31  3.000
 PNF  O5    N1   C4    118.36  3.000
 PNF  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
 PNF  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 PNF  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 PNF  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 PNF  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 PNF  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 PNF  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 PNF  CONST_07  N1    C4   C3   C2    180.00   0.0  0
 PNF  CONST_08  O1    C1   C2   C3    180.00   0.0  0
 PNF  CONST_09  O1    C1   C6   C5    180.00   0.0  0
 PNF  CONST_10  N1    C4   C5   C6    180.00   0.0  0
 PNF  CONST_11  H31   C3   C2   C1    180.00   0.0  0
 PNF  CONST_12  H51   C5   C6   C1    180.00   0.0  0
 PNF  CONST_13  H61   C6   C1   C2    180.00   0.0  0
 PNF  CONST_14  H21   C2   C3   C4    180.00   0.0  0
 PNF  CONST_15  O4    N1   C4   C3    180.00   0.0  0
 PNF  CONST_16  O5    N1   C4   C3      0.00   0.0  0
 PNF  CONST_17  O4    N1   C4   C5      0.00   0.0  0
 PNF  CONST_18  O5    N1   C4   C5    180.00   0.0  0
 PNF  CONST_19  C12   N2   C11  C10   180.00   0.0  0
 PNF  CONST_20  C12   N2   C11  O6      0.00   0.0  0
 PNF  CONST_21  HN21  N2   C11  C10     0.00   0.0  0
 PNF  Var_01    O2    P1   O1   C1    -78.39  30.0  1
 PNF  Var_02    C10   C9   C8   P1    179.13  30.0  3
 PNF  Var_03    C9    C8   P1   O1   -177.74  30.0  3
 PNF  Var_04    C11   C10  C9   C8    177.41  30.0  3
 PNF  Var_05    N2    C11  C10  C9    111.22  30.0  3
 PNF  Var_06    C13   C12  N2   C11   -90.90  30.0  3
 PNF  Var_07    C14   C13  C12  N2   -178.87  30.0  3
 PNF  Var_08    C15   C14  C13  C12   178.61  30.0  3
 PNF  Var_09    C16   C15  C14  C13  -179.12  30.0  3
 PNF  Var_10    C17   C16  C15  C14   179.50  30.0  3
 PNF  Var_11    O7    C17  C16  C15    10.01  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
 PNF  plan-1  C1    0.020
 PNF  plan-1  C2    0.020
 PNF  plan-1  C3    0.020
 PNF  plan-1  C4    0.020
 PNF  plan-1  C5    0.020
 PNF  plan-1  C6    0.020
 PNF  plan-1  O1    0.020
 PNF  plan-1  N1    0.020
 PNF  plan-1  H21   0.020
 PNF  plan-1  H31   0.020
 PNF  plan-1  H51   0.020
 PNF  plan-1  H61   0.020
 PNF  plan-2  C10   0.020
 PNF  plan-2  C11   0.020
 PNF  plan-2  N2    0.020
 PNF  plan-2  O6    0.020
 PNF  plan-2  C12   0.020
 PNF  plan-2  HN21  0.020
 PNF  plan-3  C4    0.020
 PNF  plan-3  N1    0.020
 PNF  plan-3  O4    0.020
 PNF  plan-3  O5    0.020
 PNF  plan-4  C16   0.020
 PNF  plan-4  C17   0.020
 PNF  plan-4  O7    0.020
 PNF  plan-4  O8    0.020

