# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 02:11:54 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (3R)-2,3-dihydroxy-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-aspartic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN[C@@](O)([C@@H](O)C(O)=O)C(O)=O)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
 CBA  CBA  '(3R)-2,3-dihydroxy-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-aspartic acid'  ligand  43  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CBA
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
 CBA  N1    N  N     0  -0.407   2.9328   0.6515   2.7965
 CBA  C2    C  CR6   0   0.130   3.2826   0.7355   1.5258
 CBA  C2A   C  CH3   0  -0.719   4.6921   1.1213   1.1972
 CBA  C3    C  CR6   0   0.255   2.3682   0.4634   0.4933
 CBA  O3    O  OH1   0  -0.644   2.8229   0.5509  -0.7635
 CBA  C4    C  CR6   0   0.026   1.0575   0.1073   0.8154
 CBA  C4A   C  CH2   0  -0.327   0.0388  -0.2392  -0.2445
 CBA  C5    C  CR6   0  -0.070   0.7181   0.0196   2.1712
 CBA  C5A   C  CH2   0  -0.215  -0.6747  -0.3928   2.5600
 CBA  C6    C  CR16  0  -0.145   1.6896   0.3025   3.1151
 CBA  P     P  P     0   1.460  -2.1862  -0.5729   4.6822
 CBA  O1P   O  O     0  -0.707  -3.1806  -1.4980   4.1096
 CBA  O2P   O  OH1   0  -0.728  -1.6530  -0.8619   6.1542
 CBA  O3P   O  OH1   0  -0.739  -2.7525   0.9198   4.6435
 CBA  O4P   O  O2    0  -0.592  -0.7539  -0.5362   3.9729
 CBA  N     N  NH1   0  -0.697   0.2957   0.4689  -1.4963
 CBA  CA    C  CT    0   0.289  -0.3618  -0.0529  -2.6648
 CBA  OA    O  OH1   0  -0.640  -1.7406  -0.2059  -2.5487
 CBA  CB    C  CH1   0  -0.104  -0.0352   0.9135  -3.8536
 CBA  OB    O  OH1   0  -0.630   1.3167   1.1789  -4.0174
 CBA  C     C  C     0   0.516   0.1593  -1.4665  -2.9805
 CBA  O     O  O     0  -0.403  -0.5532  -2.3831  -3.2795
 CBA  OT    O  OH1   0  -0.579   1.4775  -1.5268  -2.9167
 CBA  CG    C  C     0   0.517  -0.6364   0.3512  -5.1363
 CBA  OD1   O  O     0  -0.433  -0.0172  -0.4006  -5.8462
 CBA  OD2   O  OH1   0  -0.569  -1.8625   0.7690  -5.3670
 CBA  H2A1  H  HCH3  0   0.246   5.2173   0.3209   0.6721
 CBA  H2A2  H  HCH3  0   0.244   4.7288   2.0000   0.5510
 CBA  H2A3  H  HCH3  0   0.245   5.2381   1.3435   2.1117
 CBA  HO3   H  HOH1  0   0.483   2.0430   0.5050  -1.3685
 CBA  H4A1  H  HCH2  0   0.285   0.0852  -1.3187  -0.4210
 CBA  H4A2  H  HCH2  0   0.270  -0.9719  -0.0382   0.1186
 CBA  H5A1  H  HCH2  0   0.256  -1.3919   0.3564   2.2056
 CBA  H5A2  H  HCH2  0   0.266  -0.9373  -1.3426   2.0854
 CBA  H6    H  HCR6  0   0.255   1.4698   0.2493   4.1734
 CBA  HOP2  H  HOH1  0   0.506  -2.3479  -1.0846   6.7883
 CBA  HOP3  H  HOH1  0   0.497  -2.1967   1.5931   5.0585
 CBA  HN    H  HNH1  0   0.394   0.0712   1.4532  -1.3812
 CBA  HOA   H  HOH1  0   0.464  -2.1467   0.6531  -2.3805
 CBA  HB    H  HCH1  0   0.303  -0.5162   1.8683  -3.6133
 CBA  HOB   H  HOH1  0   0.457   1.7604   0.4147  -4.4043
 CBA  HOT   H  HOH1  0   0.495   1.7851  -2.4142  -3.1608
 CBA  HOD2  H  HOH1  0   0.490  -2.2163   0.3609  -6.1731

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
 CBA  N1   C2    aromatic  1.321  0.020  1.321
 CBA  N1   C6    aromatic  1.330  0.020  1.330
 CBA  C2   C2A   single    1.498  0.020  1.498
 CBA  C2   C3    aromatic  1.406  0.020  1.406
 CBA  C2A  H2A1  single    0.970  0.020  1.090
 CBA  C2A  H2A2  single    0.970  0.020  1.090
 CBA  C2A  H2A3  single    0.970  0.020  1.090
 CBA  C3   O3    single    1.339  0.020  1.339
 CBA  C3   C4    aromatic  1.396  0.020  1.396
 CBA  O3   HO3   single    0.850  0.020  0.980
 CBA  C4   C4A   single    1.510  0.020  1.510
 CBA  C4   C5    aromatic  1.400  0.020  1.400
 CBA  C4A  N     single    1.461  0.020  1.461
 CBA  C4A  H4A1  single    0.970  0.020  1.090
 CBA  C4A  H4A2  single    0.970  0.020  1.090
 CBA  C5   C5A   single    1.504  0.020  1.504
 CBA  C5   C6    aromatic  1.384  0.020  1.384
 CBA  C5A  O4P   single    1.422  0.020  1.422
 CBA  C5A  H5A1  single    0.970  0.020  1.090
 CBA  C5A  H5A2  single    0.970  0.020  1.090
 CBA  C6   H6    single    0.930  0.020  1.080
 CBA  P    O1P   double    1.474  0.020  1.474
 CBA  P    O2P   single    1.592  0.020  1.592
 CBA  P    O3P   single    1.597  0.020  1.597
 CBA  P    O4P   single    1.599  0.020  1.599
 CBA  O2P  HOP2  single    0.850  0.020  0.980
 CBA  O3P  HOP3  single    0.850  0.020  0.980
 CBA  N    CA    single    1.439  0.020  1.439
 CBA  N    HN    single    0.890  0.020  1.040
 CBA  CA   OA    single    1.392  0.020  1.392
 CBA  CA   CB    single    1.566  0.020  1.566
 CBA  CA   C     single    1.539  0.020  1.539
 CBA  OA   HOA   single    0.850  0.020  0.980
 CBA  CB   OB    single    1.387  0.020  1.387
 CBA  CB   CG    single    1.524  0.020  1.524
 CBA  CB   HB    single    0.970  0.020  1.090
 CBA  OB   HOB   single    0.850  0.020  0.980
 CBA  C    O     double    1.199  0.020  1.199
 CBA  C    OT    single    1.321  0.020  1.321
 CBA  OT   HOT   single    0.850  0.020  0.980
 CBA  CG   OD1   double    1.205  0.020  1.205
 CBA  CG   OD2   single    1.316  0.020  1.316
 CBA  OD2  HOD2  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
 CBA  C6    N1   C2    119.66  3.000
 CBA  C3    C2   C2A   120.05  3.000
 CBA  C3    C2   N1    121.48  3.000
 CBA  C2A   C2   N1    118.47  3.000
 CBA  H2A3  C2A  H2A2  108.44  3.000
 CBA  H2A3  C2A  H2A1  108.21  3.000
 CBA  H2A2  C2A  H2A1  106.81  3.000
 CBA  H2A3  C2A  C2    109.90  3.000
 CBA  H2A2  C2A  C2    111.65  3.000
 CBA  H2A1  C2A  C2    111.68  3.000
 CBA  C4    C3   O3    123.50  3.000
 CBA  C4    C3   C2    119.38  3.000
 CBA  O3    C3   C2    117.12  3.000
 CBA  HO3   O3   C3    107.67  3.000
 CBA  C5    C4   C4A   120.10  3.000
 CBA  C5    C4   C3    117.84  3.000
 CBA  C4A   C4   C3    122.00  3.000
 CBA  H4A2  C4A  H4A1  105.91  3.000
 CBA  H4A2  C4A  N     111.00  3.000
 CBA  H4A1  C4A  N     109.41  3.000
 CBA  H4A2  C4A  C4    110.40  3.000
 CBA  H4A1  C4A  C4    108.10  3.000
 CBA  N     C4A  C4    111.80  3.000
 CBA  C6    C5   C5A   122.00  3.000
 CBA  C6    C5   C4    118.52  3.000
 CBA  C5A   C5   C4    119.47  3.000
 CBA  H5A2  C5A  H5A1  107.23  3.000
 CBA  H5A2  C5A  O4P   109.28  3.000
 CBA  H5A1  C5A  O4P   110.71  3.000
 CBA  H5A2  C5A  C5    110.38  3.000
 CBA  H5A1  C5A  C5    109.57  3.000
 CBA  O4P   C5A  C5    109.64  3.000
 CBA  H6    C6   C5    120.96  3.000
 CBA  H6    C6   N1    115.92  3.000
 CBA  C5    C6   N1    123.12  3.000
 CBA  O4P   P    O3P   106.59  3.000
 CBA  O4P   P    O2P    96.57  3.000
 CBA  O3P   P    O2P   108.11  3.000
 CBA  O4P   P    O1P   116.52  3.000
 CBA  O3P   P    O1P   109.75  3.000
 CBA  O2P   P    O1P   118.11  3.000
 CBA  HOP2  O2P  P     114.06  3.000
 CBA  HOP3  O3P  P     115.89  3.000
 CBA  P     O4P  C5A   119.53  3.000
 CBA  HN    N    CA    110.02  3.000
 CBA  HN    N    C4A   109.49  3.000
 CBA  CA    N    C4A   116.09  3.000
 CBA  C     CA   CB    109.90  3.000
 CBA  C     CA   OA    104.57  3.000
 CBA  CB    CA   OA    109.73  3.000
 CBA  C     CA   N     110.18  3.000
 CBA  CB    CA   N     107.30  3.000
 CBA  OA    CA   N     115.13  3.000
 CBA  HOA   OA   CA    109.49  3.000
 CBA  HB    CB   CG    109.45  3.000
 CBA  HB    CB   OB    106.67  3.000
 CBA  CG    CB   OB    110.83  3.000
 CBA  HB    CB   CA    106.24  3.000
 CBA  CG    CB   CA    109.19  3.000
 CBA  OB    CB   CA    114.25  3.000
 CBA  HOB   OB   CB    110.12  3.000
 CBA  OT    C    O     124.77  3.000
 CBA  OT    C    CA    111.70  3.000
 CBA  O     C    CA    123.51  3.000
 CBA  HOT   OT   C     110.24  3.000
 CBA  OD2   CG   OD1   125.00  3.000
 CBA  OD2   CG   CB    113.45  3.000
 CBA  OD1   CG   CB    121.55  3.000
 CBA  HOD2  OD2  CG    110.60  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
 CBA  CONST_01  C4    C3   C2   N1     0.00   0.0  0
 CBA  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 CBA  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 CBA  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 CBA  CONST_05  C6    N1   C2   C3     0.00   0.0  0
 CBA  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 CBA  CONST_07  O3    C3   C2   N1   180.00   0.0  0
 CBA  CONST_08  C5A   C5   C6   N1   180.00   0.0  0
 CBA  CONST_09  C4A   C4   C3   C2   180.00   0.0  0
 CBA  CONST_10  C6    N1   C2   C2A  180.00   0.0  0
 CBA  CONST_11  C4    C3   C2   C2A  180.00   0.0  0
 CBA  CONST_12  C5A   C5   C4   C3   180.00   0.0  0
 CBA  CONST_13  C5    C4   C3   O3   180.00   0.0  0
 CBA  CONST_14  C6    C5   C4   C4A  180.00   0.0  0
 CBA  CONST_15  H6    C6   N1   C2   180.00   0.0  0
 CBA  CONST_16  HOT   OT   C    CA   180.00   0.0  0
 CBA  CONST_17  HOD2  OD2  CG   CB   180.00   0.0  0
 CBA  Var_01    N     C4A  C4   C3   -29.79  30.0  2
 CBA  Var_02    O4P   C5A  C5   C4   174.50  30.0  2
 CBA  Var_03    H2A1  C2A  C2   N1   116.73  30.0  2
 CBA  Var_04    CA    N    C4A  C4   163.14  30.0  3
 CBA  Var_05    O1P   P    O4P  C5A   49.55  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
 CBA  chir_01  CA  OA  CB  C   positiv
 CBA  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
 CBA  plan-1  N1    0.020
 CBA  plan-1  C2    0.020
 CBA  plan-1  C2A   0.020
 CBA  plan-1  C3    0.020
 CBA  plan-1  O3    0.020
 CBA  plan-1  C4    0.020
 CBA  plan-1  C4A   0.020
 CBA  plan-1  C5    0.020
 CBA  plan-1  C5A   0.020
 CBA  plan-1  C6    0.020
 CBA  plan-1  H6    0.020
 CBA  plan-2  CA    0.020
 CBA  plan-2  C     0.020
 CBA  plan-2  O     0.020
 CBA  plan-2  OT    0.020
 CBA  plan-2  HOT   0.020
 CBA  plan-3  CB    0.020
 CBA  plan-3  CG    0.020
 CBA  plan-3  OD1   0.020
 CBA  plan-3  OD2   0.020
 CBA  plan-3  HOD2  0.020

