# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 22:41:32 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-threonine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[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
 2BO  2BO  N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-threonine  ligand  42  23  .  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_2BO
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
 2BO  N1   N  N     0  -0.406   0.9320  -3.6185   0.4819
 2BO  C2   C  CR6   0   0.123  -0.3689  -3.7543   0.2827
 2BO  C2A  C  CH3   0  -0.785  -1.0070  -5.0662   0.6313
 2BO  C3   C  CR6   0   0.269  -1.1340  -2.7003  -0.2357
 2BO  O3   O  OH1   0  -0.611  -2.4579  -2.8096  -0.4430
 2BO  C4   C  CR6   0   0.051  -0.5201  -1.4937  -0.5590
 2BO  C4A  C  CH2   0  -0.338  -1.3429  -0.3448  -1.0741
 2BO  C5   C  CR6   0  -0.068   0.8520  -1.3749  -0.3287
 2BO  C5A  C  CH2   0  -0.218   1.5528  -0.0838  -0.6547
 2BO  C6   C  CR16  0  -0.133   1.5290  -2.4698   0.1884
 2BO  P    P  P     0   1.457   3.7360   1.1819   0.0226
 2BO  O1P  O  O     0  -0.706   3.6435   2.2253  -1.0141
 2BO  O2P  O  OH1   0  -0.728   5.1473   0.4854   0.2647
 2BO  O3P  O  OH1   0  -0.737   3.2258   1.7631   1.4197
 2BO  O4P  O  O2    0  -0.592   2.9128  -0.1621  -0.2424
 2BO  N    N  NH1   0  -0.587  -2.0187   0.3071   0.0374
 2BO  CA   C  CH1   0  -0.221  -2.7780   1.4731  -0.3352
 2BO  CB   C  CH1   0   0.026  -3.9413   1.6998   0.6539
 2BO  OB   O  OH1   0  -0.667  -3.4401   1.9201   1.9551
 2BO  C    C  C     0   0.542  -1.9155   2.7244  -0.4302
 2BO  O    O  OH1   0  -0.592  -2.5766   3.7466  -0.9565
 2BO  OT   O  O     0  -0.432  -0.7687   2.7939  -0.0638
 2BO  CG   C  CH3   0  -0.690  -4.9328   0.5505   0.6017
 2BO  H1   H  HCH3  0   0.256  -1.7999  -4.9520   1.3744
 2BO  H2   H  HCH3  0   0.258  -1.4440  -5.5568  -0.2424
 2BO  H3   H  HCH3  0   0.271  -0.2610  -5.7393   1.0468
 2BO  H4   H  HOH1  0   0.484  -2.7768  -3.6894  -0.2138
 2BO  H5   H  HCH2  0   0.229  -0.7121   0.3396  -1.6559
 2BO  H6   H  HCH2  0   0.260  -2.0993  -0.7145  -1.7684
 2BO  H7   H  HCH2  0   0.268   1.5168   0.1073  -1.7305
 2BO  H8   H  HCH2  0   0.250   1.0403   0.7497  -0.1629
 2BO  H9   H  HCR6  0   0.257   2.5925  -2.4271   0.3834
 2BO  H10  H  HOH1  0   0.505   5.8874   1.1043   0.3254
 2BO  H11  H  HOH1  0   0.497   3.3006   1.1660   2.1766
 2BO  H12  H  HNH1  0   0.351  -1.3414   0.5440   0.7525
 2BO  H14  H  HCH1  0   0.281  -3.2211   1.3045  -1.3227
 2BO  H15  H  HCH1  0   0.243  -4.4591   2.6200   0.3743
 2BO  H16  H  HOH1  0   0.446  -3.1352   1.0760   2.3060
 2BO  H17  H  HOH1  0   0.483  -2.0150   4.5363  -0.9777
 2BO  H18  H  HCH3  0   0.235  -4.4434  -0.4013   0.8114
 2BO  H19  H  HCH3  0   0.238  -5.7318   0.7055   1.3272
 2BO  H20  H  HCH3  0   0.229  -5.3892   0.4807  -0.3864

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
 2BO  OT   C    double    1.206  0.020  1.206
 2BO  O1P  P    double    1.474  0.020  1.474
 2BO  C    O    single    1.326  0.020  1.326
 2BO  C    CA   single    1.523  0.020  1.523
 2BO  O2P  P    single    1.592  0.020  1.592
 2BO  P    O4P  single    1.598  0.020  1.598
 2BO  P    O3P  single    1.597  0.020  1.597
 2BO  CA   N    single    1.440  0.020  1.440
 2BO  CA   CB   single    1.544  0.020  1.544
 2BO  N    C4A  single    1.455  0.020  1.455
 2BO  O4P  C5A  single    1.423  0.020  1.423
 2BO  C4A  C4   single    1.504  0.020  1.504
 2BO  O3   C3   single    1.345  0.020  1.345
 2BO  CB   CG   single    1.519  0.020  1.519
 2BO  CB   OB   single    1.412  0.020  1.412
 2BO  C4   C3   aromatic  1.392  0.020  1.392
 2BO  C4   C5   aromatic  1.396  0.020  1.396
 2BO  C3   C2   aromatic  1.402  0.020  1.402
 2BO  C5A  C5   single    1.505  0.020  1.505
 2BO  C5   C6   aromatic  1.387  0.020  1.387
 2BO  C2   C2A  single    1.500  0.020  1.500
 2BO  C2   N1   aromatic  1.323  0.020  1.323
 2BO  C6   N1   aromatic  1.327  0.020  1.327
 2BO  C2A  H1   single    0.970  0.020  1.090
 2BO  C2A  H2   single    0.970  0.020  1.090
 2BO  C2A  H3   single    0.970  0.020  1.090
 2BO  O3   H4   single    0.850  0.020  0.980
 2BO  C4A  H5   single    0.970  0.020  1.090
 2BO  C4A  H6   single    0.970  0.020  1.090
 2BO  C5A  H7   single    0.970  0.020  1.090
 2BO  C5A  H8   single    0.970  0.020  1.090
 2BO  C6   H9   single    0.930  0.020  1.080
 2BO  O2P  H10  single    0.850  0.020  0.980
 2BO  O3P  H11  single    0.850  0.020  0.980
 2BO  N    H12  single    0.890  0.020  1.040
 2BO  CA   H14  single    0.970  0.020  1.090
 2BO  CB   H15  single    0.970  0.020  1.090
 2BO  OB   H16  single    0.850  0.020  0.980
 2BO  O    H17  single    0.850  0.020  0.980
 2BO  CG   H18  single    0.970  0.020  1.090
 2BO  CG   H19  single    0.970  0.020  1.090
 2BO  CG   H20  single    0.970  0.020  1.090

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
 2BO  C6   N1   C2   119.85  3.000
 2BO  C3   C2   C2A  120.76  3.000
 2BO  C2A  C2   N1   118.23  3.000
 2BO  C3   C2   N1   121.01  3.000
 2BO  H3   C2A  H2   107.58  3.000
 2BO  H3   C2A  H1   107.62  3.000
 2BO  H2   C2A  H1   107.48  3.000
 2BO  H3   C2A  C2   109.78  3.000
 2BO  H2   C2A  C2   112.14  3.000
 2BO  H1   C2A  C2   112.04  3.000
 2BO  C4   C3   O3   117.97  3.000
 2BO  C4   C3   C2   119.81  3.000
 2BO  O3   C3   C2   122.23  3.000
 2BO  H4   O3   C3   111.31  3.000
 2BO  C5   C4   C4A  121.94  3.000
 2BO  C5   C4   C3   117.96  3.000
 2BO  C4A  C4   C3   120.03  3.000
 2BO  H6   C4A  H5   105.81  3.000
 2BO  H6   C4A  N    108.41  3.000
 2BO  H5   C4A  N    113.10  3.000
 2BO  H6   C4A  C4   109.77  3.000
 2BO  H5   C4A  C4   110.09  3.000
 2BO  N    C4A  C4   109.55  3.000
 2BO  C6   C5   C5A  122.05  3.000
 2BO  C6   C5   C4   118.29  3.000
 2BO  C5A  C5   C4   119.66  3.000
 2BO  H8   C5A  H7   107.07  3.000
 2BO  H8   C5A  O4P  111.03  3.000
 2BO  H7   C5A  O4P  109.03  3.000
 2BO  H8   C5A  C5   109.75  3.000
 2BO  H7   C5A  C5   110.35  3.000
 2BO  O4P  C5A  C5   109.57  3.000
 2BO  H9   C6   C5   121.04  3.000
 2BO  H9   C6   N1   115.87  3.000
 2BO  C5   C6   N1   123.09  3.000
 2BO  O4P  P    O3P  106.65  3.000
 2BO  O3P  P    O2P  108.02  3.000
 2BO  O4P  P    O2P   96.54  3.000
 2BO  O3P  P    O1P  109.74  3.000
 2BO  O4P  P    O1P  116.52  3.000
 2BO  O2P  P    O1P  118.18  3.000
 2BO  H10  O2P  P    114.08  3.000
 2BO  H11  O3P  P    115.81  3.000
 2BO  P    O4P  C5A  119.60  3.000
 2BO  H12  N    CA   110.23  3.000
 2BO  H12  N    C4A  109.48  3.000
 2BO  CA   N    C4A  114.20  3.000
 2BO  H14  CA   C    107.42  3.000
 2BO  H14  CA   CB   107.18  3.000
 2BO  C    CA   CB   110.25  3.000
 2BO  H14  CA   N    108.78  3.000
 2BO  CB   CA   N    110.51  3.000
 2BO  C    CA   N    112.51  3.000
 2BO  H15  CB   CG   108.61  3.000
 2BO  H15  CB   OB   105.83  3.000
 2BO  CG   CB   OB   112.43  3.000
 2BO  H15  CB   CA   108.48  3.000
 2BO  OB   CB   CA   110.24  3.000
 2BO  CG   CB   CA   111.02  3.000
 2BO  H16  OB   CB   108.13  3.000
 2BO  OT   C    O    123.38  3.000
 2BO  O    C    CA   112.08  3.000
 2BO  OT   C    CA   124.54  3.000
 2BO  H17  O    C    110.36  3.000
 2BO  H20  CG   H19  107.78  3.000
 2BO  H20  CG   H18  107.82  3.000
 2BO  H19  CG   H18  108.96  3.000
 2BO  H20  CG   CB   110.66  3.000
 2BO  H19  CG   CB   110.37  3.000
 2BO  H18  CG   CB   111.15  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
 2BO  CONST_01  C4   C3   C2   N1     0.00   0.0  0
 2BO  CONST_02  C4   C5   C6   N1     0.00   0.0  0
 2BO  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 2BO  CONST_04  C5   C6   N1   C2     0.00   0.0  0
 2BO  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 2BO  CONST_06  C6   N1   C2   C3     0.00   0.0  0
 2BO  CONST_07  O3   C3   C2   N1   180.00   0.0  0
 2BO  CONST_08  C5A  C5   C6   N1   180.00   0.0  0
 2BO  CONST_09  C4A  C4   C3   C2   180.00   0.0  0
 2BO  CONST_10  C4   C3   C2   C2A  180.00   0.0  0
 2BO  CONST_11  C6   N1   C2   C2A  180.00   0.0  0
 2BO  CONST_12  C5A  C5   C4   C3   180.00   0.0  0
 2BO  CONST_13  C5   C4   C3   O3   180.00   0.0  0
 2BO  CONST_14  C6   C5   C4   C4A  180.00   0.0  0
 2BO  CONST_15  H9   C6   N1   C2   180.00   0.0  0
 2BO  CONST_16  H17  O    C    CA   180.00   0.0  0
 2BO  Var_01    N    C4A  C4   C3    78.59  30.0  2
 2BO  Var_02    O4P  C5A  C5   C4   175.52  30.0  2
 2BO  Var_03    H1   C2A  C2   N1   121.19  30.0  2
 2BO  Var_04    CA   N    C4A  C4   176.65  30.0  1
 2BO  Var_05    O1P  P    O4P  C5A  -47.74  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
 2BO  chir_01  CA  C   N   CB  negativ
 2BO  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
 2BO  plan-1  N1   0.020
 2BO  plan-1  C2   0.020
 2BO  plan-1  C2A  0.020
 2BO  plan-1  C3   0.020
 2BO  plan-1  O3   0.020
 2BO  plan-1  C4   0.020
 2BO  plan-1  C4A  0.020
 2BO  plan-1  C5   0.020
 2BO  plan-1  C5A  0.020
 2BO  plan-1  C6   0.020
 2BO  plan-1  H9   0.020
 2BO  plan-2  CA   0.020
 2BO  plan-2  C    0.020
 2BO  plan-2  O    0.020
 2BO  plan-2  OT   0.020
 2BO  plan-2  H17  0.020

