# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 14:35:11 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: {2-[5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]ethyl}phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CC[P](O)(O)=O)c(CO)c1O
#
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
 5B0  5B0  '{2-[5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]ethyl}phosphonic acid'  ligand  30  16  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5B0
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
 5B0  OAE   O  OH1   0  -0.744   4.0104   0.4868  -1.5589
 5B0  PAP   P  P     0   1.376   3.3719   0.3766  -0.0884
 5B0  OAF   O  OH1   0  -0.753   3.6716  -1.1161   0.4384
 5B0  OAC   O  O     0  -0.717   3.8608   1.3491   0.9178
 5B0  CAJ   C  CH2   0  -0.752   1.6122   0.4582  -0.4667
 5B0  CAI   C  CH2   0  -0.567   0.7452   0.2666   0.7836
 5B0  CAN   C  CR6   0   0.045  -0.7157   0.4102   0.4599
 5B0  CAH   C  CR16  0  -0.146  -1.3274   1.6447   0.6388
 5B0  NAK   N  N     0  -0.404  -2.5977   1.8880   0.3549
 5B0  CAL   C  CR6   0   0.119  -3.3543   0.9121  -0.1260
 5B0  CAA   C  CH3   0  -0.784  -4.7876   1.2178  -0.4466
 5B0  CAM   C  CR6   0   0.281  -2.8300  -0.3700  -0.3329
 5B0  OAD   O  OH1   0  -0.619  -3.5803  -1.3796  -0.8119
 5B0  CAO   C  CR6   0   0.025  -1.4891  -0.6322  -0.0525
 5B0  C1    C  CH2   0  -0.225  -0.9509  -2.0200  -0.2568
 5B0  O2    O  OH1   0  -0.664  -1.4150  -2.8294   0.8033
 5B0  HAE   H  HOH1  0   0.494   4.9741   0.5678  -1.5687
 5B0  HAF   H  HOH1  0   0.489   3.4578  -1.8277  -0.1789
 5B0  HAJ1  H  HCH2  0   0.301   1.4128   1.4364  -0.9100
 5B0  HAJ2  H  HCH2  0   0.289   1.3728  -0.2856  -1.2306
 5B0  HAI1  H  HCH2  0   0.269   0.9467  -0.7021   1.2433
 5B0  HAI2  H  HCH2  0   0.276   1.0152   1.0198   1.5259
 5B0  HAH   H  HCR6  0   0.250  -0.7551   2.4759   1.0390
 5B0  HAA1  H  HCH3  0   0.256  -5.0054   1.0870  -1.5101
 5B0  HAA2  H  HCH3  0   0.257  -5.4813   0.5829   0.1101
 5B0  HAA3  H  HCH3  0   0.271  -5.0087   2.2517  -0.1924
 5B0  HAD   H  HOH1  0   0.486  -4.4672  -1.0804  -1.0409
 5B0  H11C  H  HCH2  0   0.223  -1.2788  -2.4003  -1.2305
 5B0  H12C  H  HCH2  0   0.209   0.1430  -2.0008  -0.2898
 5B0  H2    H  HOH1  0   0.458  -1.1609  -3.7374   0.6112

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
 5B0  OAE  PAP   single    1.607  0.020  1.607
 5B0  PAP  OAF   single    1.611  0.020  1.611
 5B0  PAP  OAC   double    1.482  0.020  1.482
 5B0  PAP  CAJ   single    1.802  0.020  1.802
 5B0  CAJ  CAI   single    1.534  0.020  1.534
 5B0  CAI  CAN   single    1.503  0.020  1.503
 5B0  CAN  CAH   aromatic  1.389  0.020  1.389
 5B0  CAN  CAO   aromatic  1.395  0.020  1.395
 5B0  CAH  NAK   aromatic  1.324  0.020  1.324
 5B0  NAK  CAL   aromatic  1.325  0.020  1.325
 5B0  CAL  CAA   single    1.500  0.020  1.500
 5B0  CAL  CAM   aromatic  1.401  0.020  1.401
 5B0  CAM  OAD   single    1.346  0.020  1.346
 5B0  CAM  CAO   aromatic  1.395  0.020  1.395
 5B0  CAO  C1    single    1.503  0.020  1.503
 5B0  C1   O2    single    1.412  0.020  1.412
 5B0  OAE  HAE   single    0.850  0.020  0.980
 5B0  OAF  HAF   single    0.850  0.020  0.980
 5B0  CAJ  HAJ1  single    0.970  0.020  1.090
 5B0  CAJ  HAJ2  single    0.970  0.020  1.090
 5B0  CAI  HAI1  single    0.970  0.020  1.090
 5B0  CAI  HAI2  single    0.970  0.020  1.090
 5B0  CAH  HAH   single    0.930  0.020  1.080
 5B0  CAA  HAA1  single    0.970  0.020  1.090
 5B0  CAA  HAA2  single    0.970  0.020  1.090
 5B0  CAA  HAA3  single    0.970  0.020  1.090
 5B0  OAD  HAD   single    0.850  0.020  0.980
 5B0  C1   H11C  single    0.970  0.020  1.090
 5B0  C1   H12C  single    0.970  0.020  1.090
 5B0  O2   H2    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
 5B0  HAE   OAE  PAP   114.26  3.000
 5B0  CAJ   PAP  OAC   115.79  3.000
 5B0  CAJ   PAP  OAF   106.99  3.000
 5B0  OAC   PAP  OAF   108.94  3.000
 5B0  CAJ   PAP  OAE   101.12  3.000
 5B0  OAC   PAP  OAE   116.43  3.000
 5B0  OAF   PAP  OAE   106.79  3.000
 5B0  HAF   OAF  PAP   115.62  3.000
 5B0  HAJ2  CAJ  HAJ1  106.62  3.000
 5B0  HAJ2  CAJ  CAI   111.17  3.000
 5B0  HAJ1  CAJ  CAI   109.85  3.000
 5B0  HAJ2  CAJ  PAP   109.26  3.000
 5B0  HAJ1  CAJ  PAP   107.69  3.000
 5B0  CAI   CAJ  PAP   112.04  3.000
 5B0  HAI2  CAI  HAI1  106.29  3.000
 5B0  HAI2  CAI  CAN   108.72  3.000
 5B0  HAI1  CAI  CAN   110.80  3.000
 5B0  HAI2  CAI  CAJ   109.17  3.000
 5B0  HAI1  CAI  CAJ   110.49  3.000
 5B0  CAN   CAI  CAJ   111.22  3.000
 5B0  CAO   CAN  CAH   117.84  3.000
 5B0  CAO   CAN  CAI   123.12  3.000
 5B0  CAH   CAN  CAI   119.02  3.000
 5B0  HAH   CAH  NAK   116.37  3.000
 5B0  HAH   CAH  CAN   119.71  3.000
 5B0  NAK   CAH  CAN   123.92  3.000
 5B0  CAL   NAK  CAH   119.35  3.000
 5B0  CAM   CAL  CAA   120.84  3.000
 5B0  CAM   CAL  NAK   120.94  3.000
 5B0  CAA   CAL  NAK   118.22  3.000
 5B0  HAA3  CAA  HAA2  107.71  3.000
 5B0  HAA3  CAA  HAA1  107.50  3.000
 5B0  HAA2  CAA  HAA1  107.43  3.000
 5B0  HAA3  CAA  CAL   109.76  3.000
 5B0  HAA2  CAA  CAL   112.28  3.000
 5B0  HAA1  CAA  CAL   111.95  3.000
 5B0  CAO   CAM  OAD   117.80  3.000
 5B0  CAO   CAM  CAL   120.15  3.000
 5B0  OAD   CAM  CAL   122.05  3.000
 5B0  HAD   OAD  CAM   111.39  3.000
 5B0  C1    CAO  CAM   119.38  3.000
 5B0  C1    CAO  CAN   122.78  3.000
 5B0  CAM   CAO  CAN   117.79  3.000
 5B0  H12C  C1   H11C  106.17  3.000
 5B0  H12C  C1   O2    111.17  3.000
 5B0  H11C  C1   O2    111.71  3.000
 5B0  H12C  C1   CAO   110.23  3.000
 5B0  H11C  C1   CAO   109.52  3.000
 5B0  O2    C1   CAO   108.03  3.000
 5B0  H2    O2   C1    107.70  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
 5B0  CONST_01  CAL   NAK  CAH  CAN    0.00   0.0  0
 5B0  CONST_02  CAL   CAM  CAO  CAN    0.00   0.0  0
 5B0  CONST_03  CAM   CAO  CAN  CAH    0.00   0.0  0
 5B0  CONST_04  CAM   CAL  NAK  CAH    0.00   0.0  0
 5B0  CONST_05  CAO   CAN  CAH  NAK    0.00   0.0  0
 5B0  CONST_06  CAO   CAM  CAL  NAK    0.00   0.0  0
 5B0  CONST_07  NAK   CAH  CAN  CAI  180.00   0.0  0
 5B0  CONST_08  CAM   CAO  CAN  CAI  180.00   0.0  0
 5B0  CONST_09  OAD   CAM  CAO  CAN  180.00   0.0  0
 5B0  CONST_10  C1    CAO  CAN  CAH  180.00   0.0  0
 5B0  CONST_11  CAA   CAL  NAK  CAH  180.00   0.0  0
 5B0  CONST_12  OAD   CAM  CAL  NAK  180.00   0.0  0
 5B0  CONST_13  C1    CAO  CAM  CAL  180.00   0.0  0
 5B0  CONST_14  CAO   CAM  CAL  CAA  180.00   0.0  0
 5B0  CONST_15  HAH   CAH  NAK  CAL  180.00   0.0  0
 5B0  Var_01    CAH   CAN  CAI  CAJ  -94.74  30.0  2
 5B0  Var_02    O2    C1   CAO  CAN  102.06  30.0  2
 5B0  Var_03    HAA1  CAA  CAL  NAK  117.55  30.0  2
 5B0  Var_04    CAN   CAI  CAJ  PAP  177.00  30.0  3
 5B0  Var_05    CAI   CAJ  PAP  OAE  175.70  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
 5B0  plan-1  CAI  0.020
 5B0  plan-1  CAN  0.020
 5B0  plan-1  CAH  0.020
 5B0  plan-1  NAK  0.020
 5B0  plan-1  CAL  0.020
 5B0  plan-1  CAA  0.020
 5B0  plan-1  CAM  0.020
 5B0  plan-1  OAD  0.020
 5B0  plan-1  CAO  0.020
 5B0  plan-1  C1   0.020
 5B0  plan-1  HAH  0.020

