# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 21:15:10 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-alloisoleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)[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
 ILP  ILP  N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-alloisoleucine  ligand  47  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 OK
;

data_comp_ILP
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
 ILP  P     P  P     0   1.458  -4.1317  -1.1811  -0.0608
 ILP  O1P   O  O     0  -0.704  -3.6596  -2.5771  -0.0530
 ILP  O2P   O  OH1   0  -0.728  -5.1781  -0.7439  -1.1781
 ILP  O3P   O  OH1   0  -0.739  -4.7492  -0.8130   1.3660
 ILP  O4P   O  O2    0  -0.592  -3.0371  -0.0619  -0.3848
 ILP  C5A   C  CH2   0  -0.222  -1.7984  -0.0764   0.3181
 ILP  C5    C  CR6   0  -0.064  -1.1344   1.2677   0.1942
 ILP  N1    N  N     0  -0.407  -1.2445   3.5765  -0.4004
 ILP  C6    C  CR16  0  -0.134  -1.8042   2.3768  -0.3012
 ILP  C2    C  CR6   0   0.122   0.0103   3.7506  -0.0180
 ILP  C2A   C  CH3   0  -0.783   0.6065   5.1211  -0.1444
 ILP  C3    C  CR6   0   0.264   0.7649   2.6851   0.4923
 ILP  O3    O  OH1   0  -0.611   2.0431   2.8358   0.8817
 ILP  C4    C  CR6   0   0.058   0.1883   1.4242   0.6123
 ILP  C4A   C  CH2   0  -0.340   0.9960   0.2711   1.1418
 ILP  N     N  NH1   0  -0.573   1.8315  -0.2755   0.0877
 ILP  CA    C  CH1   0  -0.200   2.6535  -1.3810   0.5045
 ILP  CB    C  CH1   0  -0.227   3.8394  -1.6076  -0.4601
 ILP  CG2   C  CH3   0  -0.684   3.3732  -1.9321  -1.8766
 ILP  CG1   C  CH2   0  -0.400   4.7717  -0.3950  -0.4219
 ILP  CD1   C  CH3   0  -0.673   6.0783  -0.6013  -1.1761
 ILP  C     C  C     0   0.532   1.8632  -2.6725   0.6831
 ILP  O     O  O     0  -0.437   0.7538  -2.8625   0.2478
 ILP  OXT   O  OH1   0  -0.590   2.5450  -3.5883   1.3600
 ILP  HOP2  H  HOH1  0   0.506  -5.8946  -1.3781  -1.3157
 ILP  HOP3  H  HOH1  0   0.496  -5.1486   0.0642   1.4401
 ILP  H5A1  H  HCH2  0   0.258  -1.9557  -0.3068   1.3776
 ILP  H5A2  H  HCH2  0   0.262  -1.1607  -0.8638  -0.0911
 ILP  HG    H  HCR6  0   0.256  -2.8315   2.3052  -0.6346
 ILP  H2A1  H  HCH3  0   0.255   0.9121   5.5283   0.8232
 ILP  H2A2  H  HCH3  0   0.258   1.4845   5.1286  -0.7950
 ILP  H2A3  H  HCH3  0   0.270  -0.1266   5.8033  -0.5681
 ILP  HO3   H  HOH1  0   0.484   2.3040   3.7632   0.8686
 ILP  H4A1  H  HCH2  0   0.257   1.6474   0.6211   1.9449
 ILP  H4A2  H  HCH2  0   0.225   0.3293  -0.4677   1.6058
 ILP  HN2   H  HNH1  0   0.351   1.2617  -0.5390  -0.7071
 ILP  HA    H  HCH1  0   0.275   3.0833  -1.1301   1.4811
 ILP  HB    H  HCH1  0   0.234   4.3996  -2.4668  -0.0774
 ILP  HG21  H  HCH3  0   0.222   2.8639  -1.0815  -2.3337
 ILP  HG22  H  HCH3  0   0.244   4.2186  -2.1831  -2.5170
 ILP  HG23  H  HCH3  0   0.234   2.6937  -2.7857  -1.9072
 ILP  HG11  H  HCH2  0   0.223   4.2426   0.4764  -0.8132
 ILP  HG12  H  HCH2  0   0.217   5.0001  -0.1658   0.6236
 ILP  HD11  H  HCH3  0   0.216   6.6218  -1.4702  -0.7991
 ILP  HD12  H  HCH3  0   0.222   5.9203  -0.7506  -2.2447
 ILP  HD13  H  HCH3  0   0.230   6.7302   0.2659  -1.0653
 ILP  HXT   H  HOH1  0   0.481   2.0324  -4.4085   1.4237

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
 ILP  P    O1P   double    1.474  0.020  1.474
 ILP  P    O2P   single    1.592  0.020  1.592
 ILP  P    O3P   single    1.598  0.020  1.598
 ILP  P    O4P   single    1.599  0.020  1.599
 ILP  O2P  HOP2  single    0.850  0.020  0.980
 ILP  O3P  HOP3  single    0.850  0.020  0.980
 ILP  O4P  C5A   single    1.424  0.020  1.424
 ILP  C5A  C5    single    1.504  0.020  1.504
 ILP  C5A  H5A1  single    0.970  0.020  1.090
 ILP  C5A  H5A2  single    0.970  0.020  1.090
 ILP  C5   C6    aromatic  1.387  0.020  1.387
 ILP  C5   C4    aromatic  1.396  0.020  1.396
 ILP  N1   C6    aromatic  1.328  0.020  1.328
 ILP  N1   C2    aromatic  1.323  0.020  1.323
 ILP  C6   HG    single    0.930  0.020  1.080
 ILP  C2   C2A   single    1.500  0.020  1.500
 ILP  C2   C3    aromatic  1.402  0.020  1.402
 ILP  C2A  H2A1  single    0.970  0.020  1.090
 ILP  C2A  H2A2  single    0.970  0.020  1.090
 ILP  C2A  H2A3  single    0.970  0.020  1.090
 ILP  C3   O3    single    1.345  0.020  1.345
 ILP  C3   C4    aromatic  1.392  0.020  1.392
 ILP  O3   HO3   single    0.850  0.020  0.980
 ILP  C4   C4A   single    1.504  0.020  1.504
 ILP  C4A  N     single    1.452  0.020  1.452
 ILP  C4A  H4A1  single    0.970  0.020  1.090
 ILP  C4A  H4A2  single    0.970  0.020  1.090
 ILP  N    CA    single    1.439  0.020  1.439
 ILP  N    HN2   single    0.890  0.020  1.040
 ILP  CA   CB    single    1.545  0.020  1.545
 ILP  CA   C     single    1.525  0.020  1.525
 ILP  CA   HA    single    0.970  0.020  1.090
 ILP  CB   CG2   single    1.526  0.020  1.526
 ILP  CB   CG1   single    1.530  0.020  1.530
 ILP  CB   HB    single    0.970  0.020  1.090
 ILP  CG2  HG21  single    0.970  0.020  1.090
 ILP  CG2  HG22  single    0.970  0.020  1.090
 ILP  CG2  HG23  single    0.970  0.020  1.090
 ILP  CG1  CD1   single    1.523  0.020  1.523
 ILP  CG1  HG11  single    0.970  0.020  1.090
 ILP  CG1  HG12  single    0.970  0.020  1.090
 ILP  CD1  HD11  single    0.970  0.020  1.090
 ILP  CD1  HD12  single    0.970  0.020  1.090
 ILP  CD1  HD13  single    0.970  0.020  1.090
 ILP  C    O     double    1.207  0.020  1.207
 ILP  C    OXT   single    1.327  0.020  1.327
 ILP  OXT  HXT   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
 ILP  O4P   P    O3P   106.52  3.000
 ILP  O4P   P    O2P    96.64  3.000
 ILP  O3P   P    O2P   108.02  3.000
 ILP  O4P   P    O1P   116.42  3.000
 ILP  O3P   P    O1P   109.71  3.000
 ILP  O2P   P    O1P   118.32  3.000
 ILP  HOP2  O2P  P     114.02  3.000
 ILP  HOP3  O3P  P     115.93  3.000
 ILP  C5A   O4P  P     119.23  3.000
 ILP  H5A2  C5A  H5A1  107.12  3.000
 ILP  H5A2  C5A  C5    110.82  3.000
 ILP  H5A1  C5A  C5    109.32  3.000
 ILP  H5A2  C5A  O4P   109.27  3.000
 ILP  H5A1  C5A  O4P   110.77  3.000
 ILP  C5    C5A  O4P   109.52  3.000
 ILP  C4    C5   C6    118.35  3.000
 ILP  C4    C5   C5A   119.58  3.000
 ILP  C6    C5   C5A   122.05  3.000
 ILP  C2    N1   C6    119.81  3.000
 ILP  HG    C6   N1    115.91  3.000
 ILP  HG    C6   C5    121.03  3.000
 ILP  N1    C6   C5    123.07  3.000
 ILP  C3    C2   C2A   120.74  3.000
 ILP  C3    C2   N1    121.04  3.000
 ILP  C2A   C2   N1    118.21  3.000
 ILP  H2A3  C2A  H2A2  107.78  3.000
 ILP  H2A3  C2A  H2A1  107.43  3.000
 ILP  H2A2  C2A  H2A1  107.45  3.000
 ILP  H2A3  C2A  C2    109.76  3.000
 ILP  H2A2  C2A  C2    112.07  3.000
 ILP  H2A1  C2A  C2    112.13  3.000
 ILP  C4    C3   O3    118.06  3.000
 ILP  C4    C3   C2    119.80  3.000
 ILP  O3    C3   C2    122.14  3.000
 ILP  HO3   O3   C3    111.18  3.000
 ILP  C4A   C4   C3    120.16  3.000
 ILP  C4A   C4   C5    121.89  3.000
 ILP  C3    C4   C5    117.92  3.000
 ILP  H4A2  C4A  H4A1  105.50  3.000
 ILP  H4A2  C4A  N     113.76  3.000
 ILP  H4A1  C4A  N     108.14  3.000
 ILP  H4A2  C4A  C4    109.79  3.000
 ILP  H4A1  C4A  C4    109.49  3.000
 ILP  N     C4A  C4    110.00  3.000
 ILP  HN2   N    CA    110.41  3.000
 ILP  HN2   N    C4A   110.11  3.000
 ILP  CA    N    C4A   114.06  3.000
 ILP  HA    CA   C     107.02  3.000
 ILP  HA    CA   CB    106.79  3.000
 ILP  C     CA   CB    110.29  3.000
 ILP  HA    CA   N     107.82  3.000
 ILP  C     CA   N     112.86  3.000
 ILP  CB    CA   N     111.73  3.000
 ILP  HB    CB   CG1   107.55  3.000
 ILP  HB    CB   CG2   108.29  3.000
 ILP  CG1   CB   CG2   112.20  3.000
 ILP  HB    CB   CA    106.83  3.000
 ILP  CG1   CB   CA    109.62  3.000
 ILP  CG2   CB   CA    112.09  3.000
 ILP  HG23  CG2  HG22  106.64  3.000
 ILP  HG23  CG2  HG21  107.89  3.000
 ILP  HG22  CG2  HG21  107.17  3.000
 ILP  HG23  CG2  CB    112.49  3.000
 ILP  HG22  CG2  CB    110.94  3.000
 ILP  HG21  CG2  CB    111.43  3.000
 ILP  HG12  CG1  HG11  106.04  3.000
 ILP  HG12  CG1  CD1   108.81  3.000
 ILP  HG11  CG1  CD1   110.27  3.000
 ILP  HG12  CG1  CB    108.48  3.000
 ILP  HG11  CG1  CB    109.16  3.000
 ILP  CD1   CG1  CB    113.77  3.000
 ILP  HD13  CD1  HD12  107.16  3.000
 ILP  HD13  CD1  HD11  107.46  3.000
 ILP  HD12  CD1  HD11  107.55  3.000
 ILP  HD13  CD1  CG1   110.79  3.000
 ILP  HD12  CD1  CG1   112.31  3.000
 ILP  HD11  CD1  CG1   111.34  3.000
 ILP  OXT   C    O     123.20  3.000
 ILP  OXT   C    CA    112.20  3.000
 ILP  O     C    CA    124.59  3.000
 ILP  HXT   OXT  C     110.22  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
 ILP  CONST_01  C2    N1   C6   C5      0.00   0.0  0
 ILP  CONST_02  C2    C3   C4   C5      0.00   0.0  0
 ILP  CONST_03  C4    C5   C6   N1      0.00   0.0  0
 ILP  CONST_04  C4    C3   C2   N1      0.00   0.0  0
 ILP  CONST_05  C3    C4   C5   C6      0.00   0.0  0
 ILP  CONST_06  C3    C2   N1   C6      0.00   0.0  0
 ILP  CONST_07  N1    C6   C5   C5A   180.00   0.0  0
 ILP  CONST_08  C3    C4   C5   C5A   180.00   0.0  0
 ILP  CONST_09  O3    C3   C4   C5    180.00   0.0  0
 ILP  CONST_10  O3    C3   C2   N1    180.00   0.0  0
 ILP  CONST_11  C4A   C4   C5   C6    180.00   0.0  0
 ILP  CONST_12  C2A   C2   N1   C6    180.00   0.0  0
 ILP  CONST_13  C4A   C4   C3   C2    180.00   0.0  0
 ILP  CONST_14  C4    C3   C2   C2A   180.00   0.0  0
 ILP  CONST_15  HG    C6   N1   C2    180.00   0.0  0
 ILP  CONST_16  HXT   OXT  C    CA    180.00   0.0  0
 ILP  Var_01    C6    C5   C5A  O4P    11.91  30.0  2
 ILP  Var_02    N     C4A  C4   C5     97.56  30.0  2
 ILP  Var_03    H2A1  C2A  C2   N1    118.67  30.0  2
 ILP  Var_04    C5    C5A  O4P  P    -161.79  30.0  3
 ILP  Var_05    CA    N    C4A  C4    179.49  30.0  3
 ILP  Var_06    HD11  CD1  CG1  CB    -56.91  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
 ILP  chir_01  CA  N   CB   C    positiv
 ILP  chir_02  CB  CA  CG2  CG1  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
 ILP  plan-1  C5A  0.020
 ILP  plan-1  C5   0.020
 ILP  plan-1  N1   0.020
 ILP  plan-1  C6   0.020
 ILP  plan-1  C2   0.020
 ILP  plan-1  C2A  0.020
 ILP  plan-1  C3   0.020
 ILP  plan-1  O3   0.020
 ILP  plan-1  C4   0.020
 ILP  plan-1  C4A  0.020
 ILP  plan-1  HG   0.020
 ILP  plan-2  CA   0.020
 ILP  plan-2  C    0.020
 ILP  plan-2  O    0.020
 ILP  plan-2  OXT  0.020
 ILP  plan-2  HXT  0.020

