# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 00:51:25 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-allothreonine
#   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
 2BK  2BK  N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-allothreonine  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_2BK
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
 2BK  C    C  C     0   0.523   3.9025  -1.6267   1.2694
 2BK  CG   C  CH3   0  -0.693   4.7319  -1.5229  -1.8783
 2BK  N1   N  N     0  -0.409  -1.4379   3.3363   0.5020
 2BK  C2   C  CR6   0   0.128  -0.1177   3.3929   0.5468
 2BK  C2A  C  CH3   0  -0.719   0.5315   4.7111   0.8363
 2BK  C3   C  CR6   0   0.264   0.6685   2.2523   0.3201
 2BK  O3   O  OH1   0  -0.650   2.0007   2.3821   0.3690
 2BK  C4   C  CR6   0   0.030   0.0451   1.0352   0.0387
 2BK  C4A  C  CH2   0  -0.343   0.8802  -0.1771  -0.2912
 2BK  C5   C  CR6   0  -0.075  -1.3523   1.0007   0.0112
 2BK  C5A  C  CH2   0  -0.216  -2.0558  -0.2948  -0.2798
 2BK  C6   C  CR16  0  -0.145  -2.0414   2.1789   0.2484
 2BK  P    P  P     0   1.460  -4.4307  -1.2343  -0.7853
 2BK  O1P  O  O     0  -0.708  -4.0841  -2.6298  -0.4603
 2BK  O2P  O  OH1   0  -0.738  -4.4383  -1.0370  -2.3701
 2BK  O3P  O  OH1   0  -0.728  -5.7911  -0.6418  -0.2090
 2BK  O4P  O  O2    0  -0.593  -3.4648  -0.1099  -0.1859
 2BK  N    N  NH1   0  -0.678   2.0815  -0.2255   0.5345
 2BK  CA   C  CH1   0  -0.161   3.0718  -1.1897   0.0798
 2BK  CB   C  CH1   0   0.013   3.9471  -0.5428  -1.0224
 2BK  OB   O  OH1   0  -0.658   4.7560   0.4758  -0.4804
 2BK  O    O  OH1   0  -0.581   4.7363  -2.6039   0.9554
 2BK  OT   O  O     0  -0.428   3.8177  -1.1512   2.3727
 2BK  H1   H  HCH3  0   0.239   4.0856  -2.3155  -2.2551
 2BK  H2   H  HCH3  0   0.245   5.1515  -1.0000  -2.7376
 2BK  H3   H  HCH3  0   0.237   5.5532  -1.9904  -1.3362
 2BK  H4   H  HCH3  0   0.244   1.1467   4.6676   1.7371
 2BK  H5   H  HCH3  0   0.244   1.1855   5.0280   0.0218
 2BK  H6   H  HCH3  0   0.244  -0.2297   5.4754   0.9790
 2BK  H7   H  HOH1  0   0.478   2.3756   1.4600   0.4495
 2BK  H8   H  HCH2  0   0.264   0.3005  -1.1021  -0.2064
 2BK  H9   H  HCH2  0   0.277   1.1764  -0.1059  -1.3423
 2BK  H10  H  HCH2  0   0.256  -1.7786  -0.6502  -1.2782
 2BK  H11  H  HCH2  0   0.264  -1.7473  -1.0625   0.4356
 2BK  H12  H  HCR6  0   0.253  -3.1232   2.2036   0.2335
 2BK  H13  H  HOH1  0   0.497  -4.7094  -0.1640  -2.6852
 2BK  H14  H  HOH1  0   0.506  -6.5609  -1.2057  -0.3650
 2BK  H15  H  HNH1  0   0.387   1.8142  -0.4176   1.4930
 2BK  H17  H  HCH1  0   0.279   2.5939  -2.0880  -0.3390
 2BK  H18  H  HCH1  0   0.248   3.2432  -0.0347  -1.6884
 2BK  H19  H  HOH1  0   0.452   5.5939   0.0973  -0.1930
 2BK  H20  H  HOH1  0   0.489   5.2761  -2.8429   1.7245

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
 2BK  OT   C    double    1.204  0.020  1.204
 2BK  O1P  P    double    1.474  0.020  1.474
 2BK  C    O    single    1.322  0.020  1.322
 2BK  C    CA   single    1.515  0.020  1.515
 2BK  O2P  P    single    1.597  0.020  1.597
 2BK  P    O4P  single    1.599  0.020  1.599
 2BK  P    O3P  single    1.592  0.020  1.592
 2BK  CA   N    single    1.455  0.020  1.455
 2BK  CA   CB   single    1.549  0.020  1.549
 2BK  N    C4A  single    1.459  0.020  1.459
 2BK  O4P  C5A  single    1.424  0.020  1.424
 2BK  C4A  C4   single    1.509  0.020  1.509
 2BK  O3   C3   single    1.339  0.020  1.339
 2BK  CB   OB   single    1.409  0.020  1.409
 2BK  CB   CG   single    1.519  0.020  1.519
 2BK  C4   C3   aromatic  1.396  0.020  1.396
 2BK  C4   C5   aromatic  1.398  0.020  1.398
 2BK  C3   C2   aromatic  1.404  0.020  1.404
 2BK  C5A  C5   single    1.503  0.020  1.503
 2BK  C5   C6   aromatic  1.385  0.020  1.385
 2BK  C2   C2A  single    1.498  0.020  1.498
 2BK  C2   N1   aromatic  1.322  0.020  1.322
 2BK  C6   N1   aromatic  1.330  0.020  1.330
 2BK  CG   H1   single    0.970  0.020  1.090
 2BK  CG   H2   single    0.970  0.020  1.090
 2BK  CG   H3   single    0.970  0.020  1.090
 2BK  C2A  H4   single    0.970  0.020  1.090
 2BK  C2A  H5   single    0.970  0.020  1.090
 2BK  C2A  H6   single    0.970  0.020  1.090
 2BK  O3   H7   single    0.850  0.020  0.980
 2BK  C4A  H8   single    0.970  0.020  1.090
 2BK  C4A  H9   single    0.970  0.020  1.090
 2BK  C5A  H10  single    0.970  0.020  1.090
 2BK  C5A  H11  single    0.970  0.020  1.090
 2BK  C6   H12  single    0.930  0.020  1.080
 2BK  O2P  H13  single    0.850  0.020  0.980
 2BK  O3P  H14  single    0.850  0.020  0.980
 2BK  N    H15  single    0.890  0.020  1.040
 2BK  CA   H17  single    0.970  0.020  1.090
 2BK  CB   H18  single    0.970  0.020  1.090
 2BK  OB   H19  single    0.850  0.020  0.980
 2BK  O    H20  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
 2BK  OT   C    O    123.62  3.000
 2BK  O    C    CA   111.86  3.000
 2BK  OT   C    CA   124.52  3.000
 2BK  H3   CG   H2   107.93  3.000
 2BK  H3   CG   H1   107.88  3.000
 2BK  H2   CG   H1   107.73  3.000
 2BK  H3   CG   CB   112.70  3.000
 2BK  H2   CG   CB   109.48  3.000
 2BK  H1   CG   CB   110.95  3.000
 2BK  C6   N1   C2   119.79  3.000
 2BK  C3   C2   C2A  120.24  3.000
 2BK  C2A  C2   N1   118.49  3.000
 2BK  C3   C2   N1   121.26  3.000
 2BK  H6   C2A  H5   108.25  3.000
 2BK  H6   C2A  H4   108.30  3.000
 2BK  H5   C2A  H4   106.83  3.000
 2BK  H6   C2A  C2   109.90  3.000
 2BK  H5   C2A  C2   111.78  3.000
 2BK  H4   C2A  C2   111.63  3.000
 2BK  C4   C3   O3   122.41  3.000
 2BK  C4   C3   C2   119.40  3.000
 2BK  O3   C3   C2   118.19  3.000
 2BK  H7   O3   C3   106.67  3.000
 2BK  C5   C4   C4A  121.95  3.000
 2BK  C5   C4   C3   118.15  3.000
 2BK  C4A  C4   C3   119.83  3.000
 2BK  H9   C4A  H8   105.82  3.000
 2BK  H9   C4A  N    108.85  3.000
 2BK  H8   C4A  N    111.36  3.000
 2BK  H9   C4A  C4   107.91  3.000
 2BK  H8   C4A  C4   111.64  3.000
 2BK  N    C4A  C4   111.03  3.000
 2BK  C6   C5   C5A  122.24  3.000
 2BK  C6   C5   C4   118.22  3.000
 2BK  C5A  C5   C4   119.54  3.000
 2BK  H11  C5A  H10  107.28  3.000
 2BK  H11  C5A  O4P  109.09  3.000
 2BK  H10  C5A  O4P  110.64  3.000
 2BK  H11  C5A  C5   110.27  3.000
 2BK  H10  C5A  C5   109.74  3.000
 2BK  O4P  C5A  C5   109.79  3.000
 2BK  H12  C6   C5   120.95  3.000
 2BK  H12  C6   N1   115.88  3.000
 2BK  C5   C6   N1   123.17  3.000
 2BK  O4P  P    O3P   96.82  3.000
 2BK  O3P  P    O2P  108.01  3.000
 2BK  O4P  P    O2P  106.74  3.000
 2BK  O3P  P    O1P  118.26  3.000
 2BK  O4P  P    O1P  116.17  3.000
 2BK  O2P  P    O1P  109.68  3.000
 2BK  H13  O2P  P    115.86  3.000
 2BK  H14  O3P  P    113.89  3.000
 2BK  P    O4P  C5A  118.80  3.000
 2BK  H15  N    CA   110.46  3.000
 2BK  H15  N    C4A  108.94  3.000
 2BK  CA   N    C4A  113.93  3.000
 2BK  H17  CA   CB   108.39  3.000
 2BK  H17  CA   N    111.37  3.000
 2BK  CB   CA   N    109.29  3.000
 2BK  H17  CA   C    107.54  3.000
 2BK  CB   CA   C    111.67  3.000
 2BK  N    CA   C    108.60  3.000
 2BK  H18  CB   OB   105.53  3.000
 2BK  H18  CB   CA   105.27  3.000
 2BK  OB   CB   CA   110.64  3.000
 2BK  H18  CB   CG   106.79  3.000
 2BK  OB   CB   CG   112.73  3.000
 2BK  CA   CB   CG   115.04  3.000
 2BK  H19  OB   CB   109.27  3.000
 2BK  H20  O    C    110.17  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
 2BK  CONST_01  C4   C3   C2   N1      0.00   0.0  0
 2BK  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 2BK  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 2BK  CONST_04  C5   C6   N1   C2      0.00   0.0  0
 2BK  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 2BK  CONST_06  C6   N1   C2   C3      0.00   0.0  0
 2BK  CONST_07  O3   C3   C2   N1    180.00   0.0  0
 2BK  CONST_08  C5A  C5   C6   N1    180.00   0.0  0
 2BK  CONST_09  C4A  C4   C3   C2    180.00   0.0  0
 2BK  CONST_10  C4   C3   C2   C2A   180.00   0.0  0
 2BK  CONST_11  C6   N1   C2   C2A   180.00   0.0  0
 2BK  CONST_12  C5A  C5   C4   C3    180.00   0.0  0
 2BK  CONST_13  C5   C4   C3   O3    180.00   0.0  0
 2BK  CONST_14  C6   C5   C4   C4A   180.00   0.0  0
 2BK  CONST_15  H12  C6   N1   C2    180.00   0.0  0
 2BK  CONST_16  H20  O    C    CA    180.00   0.0  0
 2BK  Var_01    N    C4A  C4   C3     38.75  30.0  1
 2BK  Var_02    O4P  C5A  C5   C4    176.91  30.0  1
 2BK  Var_03    H4   C2A  C2   N1    120.37  30.0  2
 2BK  Var_04    CA   N    C4A  C4   -167.23  30.0  1
 2BK  Var_05    O1P  P    O4P  C5A    45.28  30.0  2

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
 2BK  chir_01  CA  C   N   CB  negativ
 2BK  chir_02  CB  OB  CA  CG  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
 2BK  plan-1  N1   0.020
 2BK  plan-1  C2   0.020
 2BK  plan-1  C2A  0.020
 2BK  plan-1  C3   0.020
 2BK  plan-1  O3   0.020
 2BK  plan-1  C4   0.020
 2BK  plan-1  C4A  0.020
 2BK  plan-1  C5   0.020
 2BK  plan-1  C5A  0.020
 2BK  plan-1  C6   0.020
 2BK  plan-1  H12  0.020
 2BK  plan-2  C    0.020
 2BK  plan-2  CA   0.020
 2BK  plan-2  O    0.020
 2BK  plan-2  OT   0.020
 2BK  plan-2  H20  0.020

