# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 16:56:25 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: [6-methyl-5-oxidanyl-4-[(~{E})-2-oxidanylideneundecyliminomethyl]pyridin-3-yl]methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCC(=O)CN=Cc1c(O)c(C)ncc1CO[P](O)(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
 P89  P89  '[6-methyl-5-oxidanyl-4-[(~{E})-2-oxidanylideneundecyliminomethyl]pyridin-3-yl]methyl dihydrogen phosphate'  ligand  59  28  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_P89
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
 P89  CAA  C  CH3   0  -0.662  -12.7514   1.5846  -0.7559
 P89  CAD  C  CH2   0  -0.418  -11.4297   1.0489  -1.2887
 P89  CAE  C  CH2   0  -0.406  -10.3171   1.0691  -0.2475
 P89  CAF  C  CH2   0  -0.411   -8.9900   0.5369  -0.7727
 P89  CAG  C  CH2   0  -0.411   -7.8750   0.5585   0.2658
 P89  CAH  C  CH2   0  -0.412   -6.5494   0.0325  -0.2693
 P89  CAI  C  CH2   0  -0.414   -5.4279   0.0535   0.7618
 P89  CAJ  C  CH2   0  -0.416   -4.1047  -0.4501   0.1991
 P89  CAK  C  CH2   0  -0.565   -2.9900  -0.4276   1.2327
 P89  CAL  C  C     0   0.392   -1.6473  -0.8607   0.7121
 P89  OAC  O  O     0  -0.388   -1.4760  -1.3066  -0.3957
 P89  CA   C  CH2   0  -0.414   -0.4883  -0.6773   1.6785
 P89  N4A  N  N     0  -0.443    0.7014  -1.3081   1.1899
 P89  C4A  C  C1    0   0.060    1.6624  -0.5875   0.7762
 P89  C4   C  CR6   0  -0.021    2.8709  -1.1929   0.2225
 P89  C3   C  CR6   0   0.302    2.9598  -2.5850   0.0971
 P89  O3   O  OH1   0  -0.623    1.9879  -3.4053   0.4736
 P89  C2   C  CR6   0   0.132    4.1270  -3.1502  -0.4560
 P89  C2A  C  CH3   0  -0.721    4.2422  -4.6340  -0.6105
 P89  N1   N  N     0  -0.397    5.1258  -2.3896  -0.8505
 P89  C6   C  CR16  0  -0.144    5.0504  -1.0616  -0.7364
 P89  C5   C  CR6   0  -0.062    3.9559  -0.4084  -0.2085
 P89  C5A  C  CH2   0  -0.231    3.8911   1.0928  -0.1002
 P89  OP4  O  O2    0  -0.592    5.0496   1.7177  -0.6350
 P89  P    P  P     0   1.457    6.2336   2.2772   0.2846
 P89  OP2  O  OH1   0  -0.732    7.5625   1.5858  -0.2621
 P89  OP3  O  OH1   0  -0.729    6.2467   3.7843  -0.2395
 P89  OP1  O  O     0  -0.702    6.0868   2.0549   1.7341
 P89  H1   H  HCH3  0   0.226  -13.5343   1.5500  -1.5143
 P89  H2   H  HCH3  0   0.215  -13.0956   1.0010   0.1001
 P89  H3   H  HCH3  0   0.215  -12.6555   2.6215  -0.4279
 P89  H4   H  HCH2  0   0.209  -11.5698   0.0249  -1.6486
 P89  H5   H  HCH2  0   0.210  -11.1193   1.6349  -2.1596
 P89  H6   H  HCH2  0   0.205  -10.1803   2.0946   0.1137
 P89  H7   H  HCH2  0   0.205  -10.6262   0.4813   0.6243
 P89  H8   H  HCH2  0   0.206   -9.1278  -0.4885  -1.1333
 P89  H9   H  HCH2  0   0.206   -8.6827   1.1247  -1.6451
 P89  H10  H  HCH2  0   0.206   -7.7389   1.5831   0.6292
 P89  H11  H  HCH2  0   0.207   -8.1783  -0.0335   1.1366
 P89  H12  H  HCH2  0   0.208   -6.6856  -0.9917  -0.6334
 P89  H13  H  HCH2  0   0.208   -6.2493   0.6254  -1.1406
 P89  H14  H  HCH2  0   0.211   -5.2998   1.0745   1.1373
 P89  H15  H  HCH2  0   0.212   -5.7173  -0.5538   1.6265
 P89  H16  H  HCH2  0   0.224   -4.2335  -1.4676  -0.1794
 P89  H17  H  HCH2  0   0.223   -3.8208   0.1642  -0.6601
 P89  H18  H  HCH2  0   0.266   -2.8805   0.5730   1.6664
 P89  H19  H  HCH2  0   0.275   -3.2382  -1.0742   2.0828
 P89  H20  H  HCH2  0   0.265   -0.3625   0.4013   1.8444
 P89  H21  H  HCH2  0   0.291   -0.7653  -1.1116   2.6431
 P89  H22  H  H     0   0.262    1.6021   0.5016   0.8243
 P89  H23  H  HOH1  0   0.475    1.2475  -2.8461   0.8436
 P89  H24  H  HCH3  0   0.250    3.4897  -5.0225  -1.2994
 P89  H25  H  HCH3  0   0.249    5.2249  -4.8905  -0.9999
 P89  H26  H  HCH3  0   0.248    4.1004  -5.1527   0.3388
 P89  H27  H  HCR6  0   0.252    5.9137  -0.5157  -1.0915
 P89  H28  H  HCH2  0   0.279    3.0464   1.4761  -0.6754
 P89  H29  H  HCH2  0   0.261    3.7375   1.3932   0.9393
 P89  H30  H  HOH1  0   0.499    7.7759   1.7431  -1.1919
 P89  H31  H  HOH1  0   0.503    6.9422   4.3329   0.1483

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
 P89  C2A  C2   single    1.496  0.020  1.496
 P89  O3   C3   single    1.326  0.020  1.326
 P89  C2   C3   aromatic  1.410  0.020  1.410
 P89  C2   N1   aromatic  1.316  0.020  1.316
 P89  C3   C4   aromatic  1.401  0.020  1.401
 P89  N1   C6   aromatic  1.335  0.020  1.335
 P89  C4   C4A  single    1.461  0.020  1.461
 P89  C4   C5   aromatic  1.407  0.020  1.407
 P89  N4A  C4A  double    1.270  0.020  1.270
 P89  N4A  CA   single    1.433  0.020  1.433
 P89  OAC  CAL  double    1.206  0.020  1.206
 P89  C6   C5   aromatic  1.380  0.020  1.380
 P89  CAF  CAG  single    1.524  0.020  1.524
 P89  CAF  CAE  single    1.523  0.020  1.523
 P89  CAG  CAH  single    1.523  0.020  1.523
 P89  CAL  CA   single    1.520  0.020  1.520
 P89  CAL  CAK  single    1.504  0.020  1.504
 P89  CAH  CAI  single    1.524  0.020  1.524
 P89  CAJ  CAI  single    1.523  0.020  1.523
 P89  CAJ  CAK  single    1.520  0.020  1.520
 P89  C5   C5A  single    1.507  0.020  1.507
 P89  CAE  CAD  single    1.524  0.020  1.524
 P89  C5A  OP4  single    1.421  0.020  1.421
 P89  OP4  P    single    1.600  0.020  1.600
 P89  CAD  CAA  single    1.522  0.020  1.522
 P89  OP1  P    double    1.474  0.020  1.474
 P89  P    OP3  single    1.596  0.020  1.596
 P89  P    OP2  single    1.595  0.020  1.595
 P89  CAA  H1   single    0.970  0.020  1.090
 P89  CAA  H2   single    0.970  0.020  1.090
 P89  CAA  H3   single    0.970  0.020  1.090
 P89  CAD  H4   single    0.970  0.020  1.090
 P89  CAD  H5   single    0.970  0.020  1.090
 P89  CAE  H6   single    0.970  0.020  1.090
 P89  CAE  H7   single    0.970  0.020  1.090
 P89  CAF  H8   single    0.970  0.020  1.090
 P89  CAF  H9   single    0.970  0.020  1.090
 P89  CAG  H10  single    0.970  0.020  1.090
 P89  CAG  H11  single    0.970  0.020  1.090
 P89  CAH  H12  single    0.970  0.020  1.090
 P89  CAH  H13  single    0.970  0.020  1.090
 P89  CAI  H14  single    0.970  0.020  1.090
 P89  CAI  H15  single    0.970  0.020  1.090
 P89  CAJ  H16  single    0.970  0.020  1.090
 P89  CAJ  H17  single    0.970  0.020  1.090
 P89  CAK  H18  single    0.970  0.020  1.090
 P89  CAK  H19  single    0.970  0.020  1.090
 P89  CA   H20  single    0.970  0.020  1.090
 P89  CA   H21  single    0.970  0.020  1.090
 P89  C4A  H22  single    0.930  0.020  1.080
 P89  O3   H23  single    0.850  0.020  0.980
 P89  C2A  H24  single    0.970  0.020  1.090
 P89  C2A  H25  single    0.970  0.020  1.090
 P89  C2A  H26  single    0.970  0.020  1.090
 P89  C6   H27  single    0.930  0.020  1.080
 P89  C5A  H28  single    0.970  0.020  1.090
 P89  C5A  H29  single    0.970  0.020  1.090
 P89  OP2  H30  single    0.850  0.020  0.980
 P89  OP3  H31  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
 P89  H3   CAA  H2   107.45  3.000
 P89  H3   CAA  H1   107.59  3.000
 P89  H2   CAA  H1   107.58  3.000
 P89  H3   CAA  CAD  111.29  3.000
 P89  H2   CAA  CAD  111.10  3.000
 P89  H1   CAA  CAD  111.63  3.000
 P89  H5   CAD  H4   105.99  3.000
 P89  H5   CAD  CAE  109.23  3.000
 P89  H4   CAD  CAE  109.30  3.000
 P89  H5   CAD  CAA  109.65  3.000
 P89  H4   CAD  CAA  109.47  3.000
 P89  CAE  CAD  CAA  112.96  3.000
 P89  H7   CAE  H6   105.96  3.000
 P89  H7   CAE  CAF  109.43  3.000
 P89  H6   CAE  CAF  109.38  3.000
 P89  H7   CAE  CAD  109.29  3.000
 P89  H6   CAE  CAD  109.19  3.000
 P89  CAF  CAE  CAD  113.32  3.000
 P89  H9   CAF  H8   105.98  3.000
 P89  H9   CAF  CAG  109.25  3.000
 P89  H8   CAF  CAG  109.24  3.000
 P89  H9   CAF  CAE  109.35  3.000
 P89  H8   CAF  CAE  109.32  3.000
 P89  CAG  CAF  CAE  113.42  3.000
 P89  H11  CAG  H10  106.03  3.000
 P89  H11  CAG  CAH  109.48  3.000
 P89  H10  CAG  CAH  109.35  3.000
 P89  H11  CAG  CAF  109.35  3.000
 P89  H10  CAG  CAF  109.29  3.000
 P89  CAH  CAG  CAF  113.11  3.000
 P89  H13  CAH  H12  106.00  3.000
 P89  H13  CAH  CAI  109.21  3.000
 P89  H12  CAH  CAI  109.23  3.000
 P89  H13  CAH  CAG  109.32  3.000
 P89  H12  CAH  CAG  109.35  3.000
 P89  CAI  CAH  CAG  113.46  3.000
 P89  H15  CAI  H14  106.08  3.000
 P89  H15  CAI  CAJ  109.74  3.000
 P89  H14  CAI  CAJ  109.46  3.000
 P89  H15  CAI  CAH  109.39  3.000
 P89  H14  CAI  CAH  109.32  3.000
 P89  CAJ  CAI  CAH  112.63  3.000
 P89  H17  CAJ  H16  106.34  3.000
 P89  H17  CAJ  CAK  109.60  3.000
 P89  H16  CAJ  CAK  109.60  3.000
 P89  H17  CAJ  CAI  109.27  3.000
 P89  H16  CAJ  CAI  109.47  3.000
 P89  CAK  CAJ  CAI  112.38  3.000
 P89  H19  CAK  H18  104.73  3.000
 P89  H19  CAK  CAL  107.50  3.000
 P89  H18  CAK  CAL  108.10  3.000
 P89  H19  CAK  CAJ  110.63  3.000
 P89  H18  CAK  CAJ  110.84  3.000
 P89  CAL  CAK  CAJ  114.52  3.000
 P89  CA   CAL  OAC  121.34  3.000
 P89  CA   CAL  CAK  115.21  3.000
 P89  OAC  CAL  CAK  123.44  3.000
 P89  H21  CA   H20  106.61  3.000
 P89  H21  CA   N4A  109.66  3.000
 P89  H20  CA   N4A  112.88  3.000
 P89  H21  CA   CAL  108.64  3.000
 P89  H20  CA   CAL  107.56  3.000
 P89  N4A  CA   CAL  111.30  3.000
 P89  C4A  N4A  CA   119.31  3.000
 P89  H22  C4A  C4   118.41  3.000
 P89  H22  C4A  N4A  120.64  3.000
 P89  C4   C4A  N4A  120.94  3.000
 P89  C5   C4   C3   118.55  3.000
 P89  C5   C4   C4A  121.55  3.000
 P89  C3   C4   C4A  119.90  3.000
 P89  C2   C3   O3   118.03  3.000
 P89  C2   C3   C4   119.09  3.000
 P89  O3   C3   C4   122.88  3.000
 P89  H23  O3   C3   107.58  3.000
 P89  N1   C2   C2A  118.93  3.000
 P89  N1   C2   C3   120.94  3.000
 P89  C2A  C2   C3   120.12  3.000
 P89  H26  C2A  H25  108.47  3.000
 P89  H26  C2A  H24  106.87  3.000
 P89  H25  C2A  H24  108.24  3.000
 P89  H26  C2A  C2   111.82  3.000
 P89  H25  C2A  C2   109.90  3.000
 P89  H24  C2A  C2   111.41  3.000
 P89  C6   N1   C2   120.43  3.000
 P89  H27  C6   C5   121.33  3.000
 P89  H27  C6   N1   115.41  3.000
 P89  C5   C6   N1   123.27  3.000
 P89  C5A  C5   C6   122.24  3.000
 P89  C5A  C5   C4   120.04  3.000
 P89  C6   C5   C4   117.72  3.000
 P89  H29  C5A  H28  107.21  3.000
 P89  H29  C5A  OP4  110.60  3.000
 P89  H28  C5A  OP4  106.15  3.000
 P89  H29  C5A  C5   110.39  3.000
 P89  H28  C5A  C5   110.20  3.000
 P89  OP4  C5A  C5   112.09  3.000
 P89  P    OP4  C5A  122.73  3.000
 P89  OP1  P    OP3  117.80  3.000
 P89  OP3  P    OP2  106.86  3.000
 P89  OP1  P    OP2  110.78  3.000
 P89  OP2  P    OP4  105.54  3.000
 P89  OP3  P    OP4   98.48  3.000
 P89  OP1  P    OP4  116.03  3.000
 P89  H30  OP2  P    116.31  3.000
 P89  H31  OP3  P    114.20  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
 P89  CONST_01  N1   C2   C3   C4      0.00   0.0  0
 P89  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 P89  CONST_03  C6   N1   C2   C3      0.00   0.0  0
 P89  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 P89  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 P89  CONST_06  C5   C6   N1   C2      0.00   0.0  0
 P89  CONST_07  C2   C3   C4   C4A   180.00   0.0  0
 P89  CONST_08  C6   C5   C4   C4A   180.00   0.0  0
 P89  CONST_09  C2A  C2   C3   C4    180.00   0.0  0
 P89  CONST_10  C5A  C5   C4   C3    180.00   0.0  0
 P89  CONST_11  N1   C2   C3   O3    180.00   0.0  0
 P89  CONST_12  C5   C4   C3   O3    180.00   0.0  0
 P89  CONST_13  C6   N1   C2   C2A   180.00   0.0  0
 P89  CONST_14  C5A  C5   C6   N1    180.00   0.0  0
 P89  CONST_15  H27  C6   C5   C4    180.00   0.0  0
 P89  Var_01    C3   C4   C4A  N4A     2.37  30.0  2
 P89  Var_02    OP4  C5A  C5   C4   -177.48  30.0  2
 P89  Var_03    H24  C2A  C2   C3     63.16  30.0  2
 P89  Var_04    C4   C4A  N4A  CA   -177.60   0.0  2
 P89  Var_05    CAF  CAE  CAD  CAA  -179.90  30.0  1
 P89  Var_06    CAG  CAF  CAE  CAD   179.89  30.0  1
 P89  Var_07    CAH  CAG  CAF  CAE  -179.66  30.0  3
 P89  Var_08    CAI  CAH  CAG  CAF   179.87  30.0  3
 P89  Var_09    CAJ  CAI  CAH  CAG  -178.85  30.0  3
 P89  Var_10    CAK  CAJ  CAI  CAH  -179.96  30.0  1
 P89  Var_11    CAL  CAK  CAJ  CAI  -177.54  30.0  3
 P89  Var_12    OAC  CAL  CAK  CAJ    -6.44  30.0  1
 P89  Var_13    N4A  CA   CAL  CAK   170.63  30.0  3
 P89  Var_14    OP1  P    OP4  C5A     2.64  30.0  3
 P89  Var_15    H1   CAA  CAD  CAE  -179.36  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
 P89  plan-1  C4A  0.020
 P89  plan-1  C4   0.020
 P89  plan-1  C3   0.020
 P89  plan-1  O3   0.020
 P89  plan-1  C2   0.020
 P89  plan-1  C2A  0.020
 P89  plan-1  N1   0.020
 P89  plan-1  C6   0.020
 P89  plan-1  C5   0.020
 P89  plan-1  C5A  0.020
 P89  plan-1  H27  0.020
 P89  plan-2  CAK  0.020
 P89  plan-2  CAL  0.020
 P89  plan-2  OAC  0.020
 P89  plan-2  CA   0.020
 P89  plan-3  CA   0.020
 P89  plan-3  N4A  0.020
 P89  plan-3  C4A  0.020
 P89  plan-3  C4   0.020
 P89  plan-3  H22  0.020

