# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 16:51:23 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[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
 PY6  PY6  N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-norleucine  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_PY6
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
 PY6  N1    N  N     0  -0.407  -3.6546  -0.2134  -1.0098
 PY6  C2    C  CR6   0   0.121  -3.7222   0.3168   0.2010
 PY6  C2A   C  CH3   0  -0.783  -5.0518   0.3327   0.8944
 PY6  C3    C  CR6   0   0.265  -2.5838   0.8490   0.8222
 PY6  O3    O  OH1   0  -0.614  -2.6264   1.3866   2.0542
 PY6  C4    C  CR6   0   0.066  -1.3630   0.8384   0.1545
 PY6  C4A   C  CH2   0  -0.351  -0.1290   1.3935   0.8137
 PY6  C5    C  CR6   0  -0.063  -1.3186   0.2611  -1.1163
 PY6  C6    C  CR16  0  -0.131  -2.4936  -0.2455  -1.6516
 PY6  C5A   C  CH2   0  -0.218  -0.0229   0.2301  -1.8796
 PY6  O4P   O  O2    0  -0.592  -0.1393  -0.6765  -2.9720
 PY6  P     P  P     0   1.460   0.9792  -0.6594  -4.1148
 PY6  O1P   O  O     0  -0.705   2.3793  -0.6423  -3.6544
 PY6  O2P   O  OH1   0  -0.728   0.4582  -1.9414  -4.9018
 PY6  O3P   O  OH1   0  -0.739   0.6926   0.6256  -5.0192
 PY6  N     N  NH1   0  -0.573   0.4498   0.3972   1.6955
 PY6  CA    C  CH1   0  -0.189   1.6281   0.8316   2.4025
 PY6  C     C  C     0   0.523   2.8283   1.1896   1.5318
 PY6  O     O  O     0  -0.441   3.6113   2.0698   1.7915
 PY6  CB    C  CH2   0  -0.442   2.0681  -0.2336   3.4151
 PY6  CG    C  CH2   0  -0.404   1.0605  -0.4252   4.5413
 PY6  CD    C  CH2   0  -0.423   1.4729  -1.5225   5.5142
 PY6  CE    C  CH3   0  -0.661   0.4860  -1.6870   6.6621
 PY6  OXT   O  OH1   0  -0.591   2.9516   0.3934   0.4762
 PY6  H2A1  H  HCH3  0   0.254  -5.3680   1.3454   1.1586
 PY6  H2A2  H  HCH3  0   0.270  -5.8130  -0.0875   0.2414
 PY6  H2A3  H  HCH3  0   0.260  -5.0406  -0.2582   1.8138
 PY6  HO3   H  HOH1  0   0.485  -3.5291   1.4197   2.3893
 PY6  H4A1  H  HCH2  0   0.260  -0.3912   2.2685   1.4117
 PY6  H4A2  H  HCH2  0   0.226   0.5629   1.7613   0.0427
 PY6  H6    H  HCR6  0   0.256  -2.5084  -0.6979  -2.6349
 PY6  H5A1  H  HCH2  0   0.260   0.2131   1.2385  -2.2377
 PY6  H5A2  H  HCH2  0   0.255   0.8006  -0.0877  -1.2361
 PY6  HOP2  H  HOH1  0   0.506   1.0382  -2.2253  -5.6215
 PY6  HOP3  H  HOH1  0   0.497  -0.1868   0.6713  -5.4187
 PY6  HN2   H  HNH1  0   0.352   0.6262  -0.4678   1.1987
 PY6  HA    H  HCH1  0   0.265   1.3776   1.7443   2.9529
 PY6  HB1   H  HCH2  0   0.241   3.0347   0.0514   3.8397
 PY6  HB2   H  HCH2  0   0.231   2.2295  -1.1819   2.8910
 PY6  HG1   H  HCH2  0   0.225   0.0796  -0.6550   4.1183
 PY6  HG2   H  HCH2  0   0.212   0.9485   0.5193   5.0847
 PY6  HD1   H  HCH2  0   0.212   2.4661  -1.2999   5.9165
 PY6  HD2   H  HCH2  0   0.213   1.5705  -2.4685   4.9728
 PY6  HE1   H  HCH3  0   0.226   0.7973  -2.4747   7.3491
 PY6  HE2   H  HCH3  0   0.216   0.3967  -0.7635   7.2371
 PY6  HE3   H  HCH3  0   0.216  -0.5093  -1.9431   6.2943
 PY6  HXT   H  HOH1  0   0.482   3.7382   0.6347  -0.0356

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
 PY6  N1   C2    aromatic  1.323  0.020  1.323
 PY6  N1   C6    aromatic  1.327  0.020  1.327
 PY6  C2   C2A   single    1.500  0.020  1.500
 PY6  C2   C3    aromatic  1.402  0.020  1.402
 PY6  C2A  H2A1  single    0.970  0.020  1.090
 PY6  C2A  H2A2  single    0.970  0.020  1.090
 PY6  C2A  H2A3  single    0.970  0.020  1.090
 PY6  C3   O3    single    1.345  0.020  1.345
 PY6  C3   C4    aromatic  1.391  0.020  1.391
 PY6  O3   HO3   single    0.850  0.020  0.980
 PY6  C4   C4A   single    1.505  0.020  1.505
 PY6  C4   C5    aromatic  1.396  0.020  1.396
 PY6  C4A  N     single    1.451  0.020  1.451
 PY6  C4A  H4A1  single    0.970  0.020  1.090
 PY6  C4A  H4A2  single    0.970  0.020  1.090
 PY6  C5   C6    aromatic  1.387  0.020  1.387
 PY6  C5   C5A   single    1.504  0.020  1.504
 PY6  C6   H6    single    0.930  0.020  1.080
 PY6  C5A  O4P   single    1.424  0.020  1.424
 PY6  C5A  H5A1  single    0.970  0.020  1.090
 PY6  C5A  H5A2  single    0.970  0.020  1.090
 PY6  O4P  P     single    1.599  0.020  1.599
 PY6  P    O1P   double    1.474  0.020  1.474
 PY6  P    O2P   single    1.592  0.020  1.592
 PY6  P    O3P   single    1.597  0.020  1.597
 PY6  O2P  HOP2  single    0.850  0.020  0.980
 PY6  O3P  HOP3  single    0.850  0.020  0.980
 PY6  N    CA    single    1.441  0.020  1.441
 PY6  N    HN2   single    0.890  0.020  1.040
 PY6  CA   C     single    1.525  0.020  1.525
 PY6  CA   CB    single    1.534  0.020  1.534
 PY6  CA   HA    single    0.970  0.020  1.090
 PY6  C    O     double    1.206  0.020  1.206
 PY6  C    OXT   single    1.328  0.020  1.328
 PY6  CB   CG    single    1.523  0.020  1.523
 PY6  CB   HB1   single    0.970  0.020  1.090
 PY6  CB   HB2   single    0.970  0.020  1.090
 PY6  CG   CD    single    1.523  0.020  1.523
 PY6  CG   HG1   single    0.970  0.020  1.090
 PY6  CG   HG2   single    0.970  0.020  1.090
 PY6  CD   CE    single    1.523  0.020  1.523
 PY6  CD   HD1   single    0.970  0.020  1.090
 PY6  CD   HD2   single    0.970  0.020  1.090
 PY6  CE   HE1   single    0.970  0.020  1.090
 PY6  CE   HE2   single    0.970  0.020  1.090
 PY6  CE   HE3   single    0.970  0.020  1.090
 PY6  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
 PY6  C6    N1   C2    119.79  3.000
 PY6  C3    C2   C2A   120.74  3.000
 PY6  C3    C2   N1    121.06  3.000
 PY6  C2A   C2   N1    118.20  3.000
 PY6  H2A3  C2A  H2A2  107.66  3.000
 PY6  H2A3  C2A  H2A1  107.48  3.000
 PY6  H2A2  C2A  H2A1  107.50  3.000
 PY6  H2A3  C2A  C2    111.97  3.000
 PY6  H2A2  C2A  C2    109.81  3.000
 PY6  H2A1  C2A  C2    112.21  3.000
 PY6  C4    C3   O3    118.06  3.000
 PY6  C4    C3   C2    119.80  3.000
 PY6  O3    C3   C2    122.14  3.000
 PY6  HO3   O3   C3    111.22  3.000
 PY6  C5    C4   C4A   121.66  3.000
 PY6  C5    C4   C3    117.89  3.000
 PY6  C4A   C4   C3    120.42  3.000
 PY6  H4A2  C4A  H4A1  105.49  3.000
 PY6  H4A2  C4A  N     113.89  3.000
 PY6  H4A1  C4A  N     108.26  3.000
 PY6  H4A2  C4A  C4    109.41  3.000
 PY6  H4A1  C4A  C4    109.79  3.000
 PY6  N     C4A  C4    109.88  3.000
 PY6  C5A   C5   C6    121.76  3.000
 PY6  C5A   C5   C4    119.85  3.000
 PY6  C6    C5   C4    118.37  3.000
 PY6  H6    C6   C5    120.98  3.000
 PY6  H6    C6   N1    115.95  3.000
 PY6  C5    C6   N1    123.07  3.000
 PY6  H5A2  C5A  H5A1  107.33  3.000
 PY6  H5A2  C5A  O4P   109.16  3.000
 PY6  H5A1  C5A  O4P   110.65  3.000
 PY6  H5A2  C5A  C5    110.88  3.000
 PY6  H5A1  C5A  C5    109.42  3.000
 PY6  O4P   C5A  C5    109.38  3.000
 PY6  P     O4P  C5A   118.95  3.000
 PY6  O3P   P    O2P   108.01  3.000
 PY6  O3P   P    O1P   109.75  3.000
 PY6  O2P   P    O1P   118.33  3.000
 PY6  O3P   P    O4P   106.72  3.000
 PY6  O2P   P    O4P    96.65  3.000
 PY6  O1P   P    O4P   116.19  3.000
 PY6  HOP2  O2P  P     114.08  3.000
 PY6  HOP3  O3P  P     115.79  3.000
 PY6  HN2   N    CA    110.84  3.000
 PY6  HN2   N    C4A   110.96  3.000
 PY6  CA    N    C4A   114.67  3.000
 PY6  HA    CA   CB    108.22  3.000
 PY6  HA    CA   C     105.74  3.000
 PY6  CB    CA   C     108.30  3.000
 PY6  HA    CA   N     108.11  3.000
 PY6  CB    CA   N     110.42  3.000
 PY6  C     CA   N     115.72  3.000
 PY6  OXT   C    O     123.26  3.000
 PY6  OXT   C    CA    112.71  3.000
 PY6  O     C    CA    123.99  3.000
 PY6  HB2   CB   HB1   106.33  3.000
 PY6  HB2   CB   CG    110.02  3.000
 PY6  HB1   CB   CG    109.29  3.000
 PY6  HB2   CB   CA    109.12  3.000
 PY6  HB1   CB   CA    109.20  3.000
 PY6  CG    CB   CA    112.68  3.000
 PY6  HG2   CG   HG1   106.35  3.000
 PY6  HG2   CG   CD    109.39  3.000
 PY6  HG1   CG   CD    109.80  3.000
 PY6  HG2   CG   CB    109.02  3.000
 PY6  HG1   CG   CB    109.51  3.000
 PY6  CD    CG   CB    112.56  3.000
 PY6  HD2   CD   HD1   106.07  3.000
 PY6  HD2   CD   CE    109.71  3.000
 PY6  HD1   CD   CE    109.46  3.000
 PY6  HD2   CD   CG    109.32  3.000
 PY6  HD1   CD   CG    109.51  3.000
 PY6  CE    CD   CG    112.57  3.000
 PY6  HE3   CE   HE2   107.54  3.000
 PY6  HE3   CE   HE1   107.65  3.000
 PY6  HE2   CE   HE1   107.61  3.000
 PY6  HE3   CE   CD    111.24  3.000
 PY6  HE2   CE   CD    111.02  3.000
 PY6  HE1   CE   CD    111.59  3.000
 PY6  HXT   OXT  C     110.24  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
 PY6  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 PY6  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 PY6  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 PY6  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 PY6  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 PY6  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 PY6  CONST_07  O3    C3   C2   N1    180.00   0.0  0
 PY6  CONST_08  C5A   C5   C6   N1    180.00   0.0  0
 PY6  CONST_09  C4A   C4   C3   C2    180.00   0.0  0
 PY6  CONST_10  C6    N1   C2   C2A   180.00   0.0  0
 PY6  CONST_11  C4    C3   C2   C2A   180.00   0.0  0
 PY6  CONST_12  C5A   C5   C4   C3    180.00   0.0  0
 PY6  CONST_13  C5    C4   C3   O3    180.00   0.0  0
 PY6  CONST_14  C6    C5   C4   C4A   180.00   0.0  0
 PY6  CONST_15  H6    C6   N1   C2    180.00   0.0  0
 PY6  CONST_16  HXT   OXT  C    CA    180.00   0.0  0
 PY6  Var_01    N     C4A  C4   C3     82.31  30.0  2
 PY6  Var_02    O4P   C5A  C5   C4    165.82  30.0  2
 PY6  Var_03    H2A1  C2A  C2   N1   -121.66  30.0  2
 PY6  Var_04    CA    N    C4A  C4   -178.88  30.0  3
 PY6  Var_05    O1P   P    O4P  C5A    46.73  30.0  3
 PY6  Var_06    CD    CG   CB   CA    177.69  30.0  3
 PY6  Var_07    CE    CD   CG   CB    178.36  30.0  3
 PY6  Var_08    HE1   CE   CD   CG   -179.90  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
 PY6  chir_01  CA  N  C  CB  positiv

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
 PY6  plan-1  N1   0.020
 PY6  plan-1  C2   0.020
 PY6  plan-1  C2A  0.020
 PY6  plan-1  C3   0.020
 PY6  plan-1  O3   0.020
 PY6  plan-1  C4   0.020
 PY6  plan-1  C4A  0.020
 PY6  plan-1  C5   0.020
 PY6  plan-1  C6   0.020
 PY6  plan-1  C5A  0.020
 PY6  plan-1  H6   0.020
 PY6  plan-2  CA   0.020
 PY6  plan-2  C    0.020
 PY6  plan-2  O    0.020
 PY6  plan-2  OXT  0.020
 PY6  plan-2  HXT  0.020

