# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Sep 27 11:09:52 2022
#   Inital geometry file: a 108 line input string
#   Ligand name: (2~{S},3~{R})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](O)[C@H](NCc1c(O)c(C)ncc1CO[P](O)(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
 F9X  F9X  "(2S,3R)-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-pentanoic acid"  ligand  45  24  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F9X
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
 F9X  P    P  P     0   1.468   -8.2108  -1.6703  16.5196
 F9X  O1P  O  OH1   0  -0.743   -9.5888  -2.3351  16.9714
 F9X  O2P  O  OH1   0  -0.745   -7.8322  -2.5660  15.2461
 F9X  O3P  O  O     0  -0.690   -8.1899  -0.2117  16.3136
 F9X  N1   N  N     0  -0.406   -4.1781  -3.6923  20.5438
 F9X  CA   C  CH1   0  -0.194  -10.1336  -1.3466  20.5853
 F9X  C    C  C     0   0.534  -10.0912   0.0996  20.1276
 F9X  O    O  O     0  -0.433  -10.4241   0.4888  19.0373
 F9X  CB   C  CH1   0   0.060  -11.1005  -1.5399  21.7635
 F9X  CG   C  CH2   0  -0.461  -12.4788  -0.9377  21.4921
 F9X  N    N  NH1   0  -0.607   -8.7568  -1.7451  20.8251
 F9X  OB   O  OH1   0  -0.661  -11.1755  -2.9321  21.9850
 F9X  C2   C  CR6   0   0.135   -4.8268  -3.5371  21.6889
 F9X  C2A  C  CH3   0  -0.780   -4.0299  -3.5564  22.9589
 F9X  C3   C  CR6   0   0.262   -6.2170  -3.3605  21.7146
 F9X  C4   C  CR6   0   0.093   -6.9463  -3.3412  20.5275
 F9X  C4A  C  CH2   0  -0.341   -8.4397  -3.1455  20.5848
 F9X  C5   C  CR6   0  -0.027   -6.2340  -3.4984  19.3369
 F9X  C5A  C  CH2   0  -0.292   -6.8898  -3.4667  17.9913
 F9X  C6   C  CR16  0  -0.134   -4.8594  -3.6716  19.4080
 F9X  O4P  O  O2    0  -0.580   -7.2331  -2.1022  17.6999
 F9X  OT   O  OH1   0  -0.591   -9.6114   0.9018  21.0725
 F9X  H1   H  HOH1  0   0.500  -10.3592  -2.0803  16.4453
 F9X  H2   H  HOH1  0   0.496   -7.1042  -2.2124  14.7155
 F9X  H3   H  HCH1  0   0.267  -10.5127  -1.9235  19.7374
 F9X  H4   H  HCH1  0   0.207  -10.6731  -1.0371  22.6440
 F9X  H5   H  HCH2  0   0.228  -12.3815   0.1435  21.3629
 F9X  H6   H  HCH2  0   0.227  -12.8722  -1.3311  20.5495
 F9X  H7   H  HNH1  0   0.358   -8.4675  -1.4729  21.7564
 F9X  H9   H  HOH1  0   0.455  -11.4885  -3.0857  22.8813
 F9X  H10  H  HCH3  0   0.237  -14.4170  -0.6954  22.4237
 F9X  H11  H  HCH3  0   0.223  -13.6903  -2.2620  22.7308
 F9X  H12  H  HCH3  0   0.223  -13.0920  -0.8315  23.5735
 F9X  H13  H  HCH3  0   0.270   -2.9773  -3.7065  22.7318
 F9X  H14  H  HCH3  0   0.258   -4.1177  -2.6188  23.5142
 F9X  H15  H  HCH3  0   0.258   -4.3426  -4.3627  23.6278
 F9X  H16  H  HCH2  0   0.246   -8.8893  -3.4289  19.6342
 F9X  H17  H  HCH2  0   0.234   -8.8605  -3.8249  21.3313
 F9X  H18  H  HCH2  0   0.257   -7.7778  -4.1020  17.9666
 F9X  H19  H  HCH2  0   0.267   -6.1974  -3.8355  17.2324
 F9X  H20  H  HCR6  0   0.257   -4.2836  -3.8006  18.4969
 F9X  H22  H  HOH1  0   0.480   -9.5621   1.8125  20.7437
 F9X  O3   O  OH1   0  -0.622   -6.9028  -3.1994  22.8637
 F9X  CD   C  CH3   0  -0.679  -13.4708  -1.1999  22.6180
 F9X  H21  H  HOH1  0   0.487   -6.3233  -3.2208  23.6334

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
 F9X  O3P  P    double    1.473  0.020  1.473
 F9X  O2P  P    single    1.602  0.020  1.602
 F9X  P    O1P  single    1.595  0.020  1.595
 F9X  P    O4P  single    1.592  0.020  1.592
 F9X  O4P  C5A  single    1.437  0.020  1.437
 F9X  C5A  C5   single    1.497  0.020  1.497
 F9X  C5   C6   aromatic  1.387  0.020  1.387
 F9X  C5   C4   aromatic  1.396  0.020  1.396
 F9X  C6   N1   aromatic  1.325  0.020  1.325
 F9X  C4A  C4   single    1.507  0.020  1.507
 F9X  C4A  N    single    1.456  0.020  1.456
 F9X  C4   C3   aromatic  1.393  0.020  1.393
 F9X  N1   C2   aromatic  1.325  0.020  1.325
 F9X  N    CA   single    1.453  0.020  1.453
 F9X  CA   C    single    1.518  0.020  1.518
 F9X  CA   CB   single    1.536  0.020  1.536
 F9X  C3   C2   aromatic  1.402  0.020  1.402
 F9X  C3   O3   single    1.348  0.020  1.348
 F9X  C2   C2A  single    1.499  0.020  1.499
 F9X  O    C    double    1.205  0.020  1.205
 F9X  CG   CB   single    1.528  0.020  1.528
 F9X  CG   CD   single    1.523  0.020  1.523
 F9X  C    OT   single    1.329  0.020  1.329
 F9X  CB   OB   single    1.412  0.020  1.412
 F9X  O1P  H1   single    0.850  0.020  0.980
 F9X  O2P  H2   single    0.850  0.020  0.980
 F9X  CA   H3   single    0.970  0.020  1.090
 F9X  CB   H4   single    0.970  0.020  1.090
 F9X  CG   H5   single    0.970  0.020  1.090
 F9X  CG   H6   single    0.970  0.020  1.090
 F9X  N    H7   single    0.890  0.020  1.040
 F9X  OB   H9   single    0.850  0.020  0.980
 F9X  CD   H10  single    0.970  0.020  1.090
 F9X  CD   H11  single    0.970  0.020  1.090
 F9X  CD   H12  single    0.970  0.020  1.090
 F9X  C2A  H13  single    0.970  0.020  1.090
 F9X  C2A  H14  single    0.970  0.020  1.090
 F9X  C2A  H15  single    0.970  0.020  1.090
 F9X  C4A  H16  single    0.970  0.020  1.090
 F9X  C4A  H17  single    0.970  0.020  1.090
 F9X  C5A  H18  single    0.970  0.020  1.090
 F9X  C5A  H19  single    0.970  0.020  1.090
 F9X  C6   H20  single    0.930  0.020  1.080
 F9X  O3   H21  single    0.850  0.020  0.980
 F9X  OT   H22  single    0.850  0.020  0.980

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
 F9X  O4P  P    O3P  111.31  3.000
 F9X  O4P  P    O2P  107.01  3.000
 F9X  O3P  P    O2P  116.04  3.000
 F9X  O4P  P    O1P  101.97  3.000
 F9X  O2P  P    O1P  101.32  3.000
 F9X  O3P  P    O1P  117.67  3.000
 F9X  H1   O1P  P    115.10  3.000
 F9X  H2   O2P  P    114.16  3.000
 F9X  C6   N1   C2   119.17  3.000
 F9X  H3   CA   N    108.17  3.000
 F9X  H3   CA   CB   108.07  3.000
 F9X  N    CA   CB   115.80  3.000
 F9X  H3   CA   C    106.18  3.000
 F9X  CB   CA   C    111.64  3.000
 F9X  N    CA   C    106.53  3.000
 F9X  OT   C    O    123.25  3.000
 F9X  OT   C    CA   111.77  3.000
 F9X  O    C    CA   124.97  3.000
 F9X  H4   CB   OB   110.23  3.000
 F9X  H4   CB   CG   108.20  3.000
 F9X  OB   CB   CG   111.63  3.000
 F9X  H4   CB   CA   108.16  3.000
 F9X  OB   CB   CA   106.13  3.000
 F9X  CG   CB   CA   112.44  3.000
 F9X  H6   CG   H5   106.60  3.000
 F9X  H6   CG   CD   109.91  3.000
 F9X  H5   CG   CD   108.40  3.000
 F9X  H6   CG   CB   109.60  3.000
 F9X  H5   CG   CB   109.30  3.000
 F9X  CD   CG   CB   112.84  3.000
 F9X  H7   N    C4A  110.37  3.000
 F9X  H7   N    CA   110.41  3.000
 F9X  C4A  N    CA   116.29  3.000
 F9X  H9   OB   CB   108.73  3.000
 F9X  C3   C2   C2A  120.87  3.000
 F9X  C2A  C2   N1   118.05  3.000
 F9X  C3   C2   N1   121.08  3.000
 F9X  H15  C2A  H14  107.39  3.000
 F9X  H15  C2A  H13  107.63  3.000
 F9X  H14  C2A  H13  107.59  3.000
 F9X  H15  C2A  C2   112.07  3.000
 F9X  H14  C2A  C2   112.12  3.000
 F9X  H13  C2A  C2   109.84  3.000
 F9X  O3   C3   C4   117.28  3.000
 F9X  O3   C3   C2   122.37  3.000
 F9X  C4   C3   C2   120.34  3.000
 F9X  C5   C4   C4A  123.54  3.000
 F9X  C4A  C4   C3   119.21  3.000
 F9X  C5   C4   C3   117.25  3.000
 F9X  H17  C4A  H16  105.98  3.000
 F9X  H17  C4A  C4   109.06  3.000
 F9X  H16  C4A  C4   110.00  3.000
 F9X  H17  C4A  N    113.64  3.000
 F9X  H16  C4A  N    107.73  3.000
 F9X  C4   C4A  N    110.30  3.000
 F9X  C6   C5   C5A  118.86  3.000
 F9X  C6   C5   C4   118.42  3.000
 F9X  C5A  C5   C4   122.71  3.000
 F9X  H19  C5A  H18  107.67  3.000
 F9X  H19  C5A  O4P  109.36  3.000
 F9X  H18  C5A  O4P  110.71  3.000
 F9X  H19  C5A  C5   109.87  3.000
 F9X  H18  C5A  C5   111.35  3.000
 F9X  O4P  C5A  C5   107.88  3.000
 F9X  H20  C6   C5   119.83  3.000
 F9X  H20  C6   N1   116.43  3.000
 F9X  C5   C6   N1   123.74  3.000
 F9X  C5A  O4P  P    123.68  3.000
 F9X  H22  OT   C    110.13  3.000
 F9X  H21  O3   C3   111.86  3.000
 F9X  H12  CD   H11  107.94  3.000
 F9X  H12  CD   H10  107.52  3.000
 F9X  H11  CD   H10  107.13  3.000
 F9X  H12  CD   CG   111.27  3.000
 F9X  H11  CD   CG   112.04  3.000
 F9X  H10  CD   CG   110.73  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
 F9X  CONST_01  C4   C5   C6   N1      0.00   0.0  0
 F9X  CONST_02  C4   C3   C2   N1      0.00   0.0  0
 F9X  CONST_03  C5   C6   N1   C2      0.00   0.0  0
 F9X  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 F9X  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 F9X  CONST_06  C6   N1   C2   C3      0.00   0.0  0
 F9X  CONST_07  C5A  C5   C6   N1    180.00   0.0  0
 F9X  CONST_08  O3   C3   C2   N1    180.00   0.0  0
 F9X  CONST_09  C4A  C4   C3   C2    180.00   0.0  0
 F9X  CONST_10  C6   N1   C2   C2A   180.00   0.0  0
 F9X  CONST_11  C4   C3   C2   C2A   180.00   0.0  0
 F9X  CONST_12  C5A  C5   C4   C3    180.00   0.0  0
 F9X  CONST_13  C6   C5   C4   C4A   180.00   0.0  0
 F9X  CONST_14  O3   C3   C4   C5    180.00   0.0  0
 F9X  CONST_15  H20  C6   N1   C2    180.00   0.0  0
 F9X  CONST_16  H20  C6   C5   C4    180.00   0.0  0
 F9X  CONST_17  H22  OT   C    CA    180.00   0.0  0
 F9X  CONST_18  H22  OT   C    O       0.00   0.0  0
 F9X  Var_01    C5   C4   C4A  N    -102.44  30.0  2
 F9X  Var_02    C3   C4   C4A  N      77.11  30.0  2
 F9X  Var_03    O4P  C5A  C5   C4     73.92  30.0  1
 F9X  Var_04    O4P  C5A  C5   C6   -105.12  30.0  1
 F9X  Var_05    H13  C2A  C2   N1     -0.14  30.0  2
 F9X  Var_06    H14  C2A  C2   N1    119.42  30.0  2
 F9X  Var_07    H15  C2A  C2   N1   -119.73  30.0  2
 F9X  Var_08    H16  C4A  C4   C3   -164.20  30.0  1
 F9X  Var_09    H17  C4A  C4   C3    -48.36  30.0  1
 F9X  Var_10    H13  C2A  C2   C3    179.83  30.0  2
 F9X  Var_11    H14  C2A  C2   C3    -60.61  30.0  2
 F9X  Var_12    H15  C2A  C2   C3     60.24  30.0  2
 F9X  Var_13    H18  C5A  C5   C4    -47.75  30.0  1
 F9X  Var_14    H19  C5A  C5   C4   -166.95  30.0  1
 F9X  Var_15    H16  C4A  C4   C5     16.25  30.0  1
 F9X  Var_16    H17  C4A  C4   C5    132.09  30.0  1
 F9X  Var_17    H18  C5A  C5   C6    133.20  30.0  1
 F9X  Var_18    H19  C5A  C5   C6     14.01  30.0  1
 F9X  Var_19    C5   C5A  O4P  P    -166.67  30.0  3
 F9X  Var_20    C4   C4A  N    CA    165.57  30.0  2
 F9X  Var_21    H7   N    C4A  C4    -67.67  30.0  3
 F9X  Var_22    C5A  O4P  P    O1P    63.61  30.0  3
 F9X  Var_23    C5A  O4P  P    O2P   -42.33  30.0  3
 F9X  Var_24    C5A  O4P  P    O3P  -170.07  30.0  3
 F9X  Var_25    H18  C5A  O4P  P     -44.59  30.0  3
 F9X  Var_26    H19  C5A  O4P  P      73.88  30.0  3
 F9X  Var_27    H16  C4A  N    CA     45.50  30.0  2
 F9X  Var_28    H17  C4A  N    CA    -71.60  30.0  2
 F9X  Var_29    H10  CD   CG   CB    175.85  30.0  3
 F9X  Var_30    H11  CD   CG   CB    -64.61  30.0  3
 F9X  Var_31    H12  CD   CG   CB     56.33  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
 F9X  chir_01  CA  N   C   CB  positiv
 F9X  chir_02  CB  OB  CA  CG  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
 F9X  plan-1  N1   0.020
 F9X  plan-1  C2   0.020
 F9X  plan-1  C2A  0.020
 F9X  plan-1  C3   0.020
 F9X  plan-1  C4   0.020
 F9X  plan-1  C4A  0.020
 F9X  plan-1  C5   0.020
 F9X  plan-1  C5A  0.020
 F9X  plan-1  C6   0.020
 F9X  plan-1  H20  0.020
 F9X  plan-1  O3   0.020
 F9X  plan-2  CA   0.020
 F9X  plan-2  C    0.020
 F9X  plan-2  O    0.020
 F9X  plan-2  OT   0.020
 F9X  plan-2  H22  0.020

