# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 01:41:43 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: [(4Z)-5-hydroxy-6-methyl-4-{[(E)-(pyridin-4-ylcarbonyl)diazenyl]methylidene}-1,4-dihydropyridin-3-yl]methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(O)C(=C/N=NC(=O)c2ccncc2)\C(=CN1)CO[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
 2B9  2B9  '[(4Z)-5-hydroxy-6-methyl-4-{[(E)-(pyridin-4-ylcarbonyl)diazenyl]methylidene}-1,4-dihydropyridin-3-yl]methyl dihydrogen phosphate'  ligand  40  25  .  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_2B9
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
 2B9  OAE  O  O     0  -0.704  -3.4881   3.2635  -0.9336
 2B9  PAY  P  P     0   1.467  -4.1689   2.3128  -0.0375
 2B9  OAF  O  OH1   0  -0.738  -4.0165   2.7915   1.4770
 2B9  OAC  O  OH1   0  -0.727  -5.7028   1.9835  -0.2977
 2B9  OAR  O  O2    0  -0.597  -3.6483   0.7980  -0.0949
 2B9  CAM  C  CH2   0  -0.209  -2.2548   0.5375  -0.0387
 2B9  CAW  C  CR6   0  -0.124  -2.0374  -0.9492   0.0069
 2B9  CAL  C  CR16  0   0.013  -3.1115  -1.7964   0.0255
 2B9  NAP  N  NR16  0  -0.609  -2.9169  -3.1180   0.0541
 2B9  CAT  C  CR6   0   0.264  -1.7090  -3.6974   0.0634
 2B9  CAA  C  CH3   0  -0.787  -1.6310  -5.1850   0.0930
 2B9  CAV  C  CR6   0   0.241  -0.5873  -2.8829   0.0454
 2B9  OAD  O  OH1   0  -0.579   0.6365  -3.4146   0.0526
 2B9  CAX  C  CR6   0   0.136  -0.7198  -1.4733   0.0205
 2B9  CAG  C  C1    0  -0.151   0.3848  -0.5566   0.0090
 2B9  NAN  N  N     0  -0.162   1.6277  -0.9292  -0.0002
 2B9  NAQ  N  N     0  -0.435   2.4938   0.0622  -0.0076
 2B9  CAS  C  C     0   0.429   3.7775  -0.3630  -0.0317
 2B9  OAB  O  O     0  -0.489   4.1986  -1.5160  -0.0563
 2B9  CAU  C  CR6   0   0.038   4.7611   0.7756  -0.0286
 2B9  CAJ  C  CR16  0  -0.347   6.1251   0.5047  -0.0579
 2B9  CAH  C  CR16  0  -0.064   7.0227   1.5607  -0.0532
 2B9  NAO  N  N     0  -0.403   6.6563   2.8371  -0.0219
 2B9  CAI  C  CR16  0  -0.063   5.3532   3.0950   0.0058
 2B9  CAK  C  CR16  0  -0.350   4.3750   2.1126   0.0037
 2B9  H1   H  HOH1  0   0.498  -4.4977   2.2755   2.1379
 2B9  H2   H  HOH1  0   0.508  -6.2570   2.7622  -0.4433
 2B9  H3   H  HCH2  0   0.272  -1.7591   0.9585  -0.9183
 2B9  H4   H  HCH2  0   0.267  -1.8113   1.0028   0.8481
 2B9  H5   H  HCR6  0   0.331  -4.1390  -1.4723   0.0181
 2B9  H6   H  HCH3  0   0.295  -2.6225  -5.6320   0.1041
 2B9  H7   H  HCH3  0   0.289  -1.1089  -5.5701  -0.7847
 2B9  H8   H  HCH3  0   0.289  -1.1048  -5.5349   0.9830
 2B9  H9   H  HOH1  0   0.490   0.6056  -4.3788   0.0618
 2B9  H10  H  H     0   0.211   0.1591   0.5089   0.0088
 2B9  H14  H  HCR6  0   0.262   6.4887  -0.5132  -0.0848
 2B9  H15  H  HCR6  0   0.261   8.0889   1.3641  -0.0760
 2B9  H16  H  HCR6  0   0.261   5.0677   4.1409   0.0313
 2B9  H17  H  HCR6  0   0.262   3.3297   2.3846   0.0274
 2B9  H18  H  HNR6  0   0.453  -3.7320  -3.7173   0.0688

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
 2B9  NAO  CAI  aromatic  1.329  0.020  1.329
 2B9  NAO  CAH  aromatic  1.328  0.020  1.328
 2B9  CAI  CAK  aromatic  1.386  0.020  1.386
 2B9  CAH  CAJ  aromatic  1.386  0.020  1.386
 2B9  CAK  CAU  aromatic  1.392  0.020  1.392
 2B9  CAJ  CAU  aromatic  1.391  0.020  1.391
 2B9  CAU  CAS  single    1.505  0.020  1.505
 2B9  CAS  NAQ  single    1.353  0.020  1.353
 2B9  CAS  OAB  double    1.228  0.020  1.228
 2B9  NAQ  NAN  double    1.316  0.020  1.316
 2B9  NAN  CAG  single    1.298  0.020  1.298
 2B9  CAG  CAX  double    1.435  0.020  1.435
 2B9  OAD  CAV  single    1.334  0.020  1.334
 2B9  CAX  CAV  single    1.416  0.020  1.416
 2B9  CAX  CAW  single    1.418  0.020  1.418
 2B9  CAV  CAT  double    1.386  0.020  1.386
 2B9  CAM  CAW  single    1.503  0.020  1.503
 2B9  CAM  OAR  single    1.419  0.020  1.419
 2B9  CAW  CAL  double    1.368  0.020  1.368
 2B9  CAT  CAA  single    1.490  0.020  1.490
 2B9  CAT  NAP  single    1.340  0.020  1.340
 2B9  OAE  PAY  double    1.473  0.020  1.473
 2B9  CAL  NAP  single    1.336  0.020  1.336
 2B9  OAC  PAY  single    1.590  0.020  1.590
 2B9  OAR  PAY  single    1.603  0.020  1.603
 2B9  PAY  OAF  single    1.596  0.020  1.596
 2B9  OAF  H1   single    0.850  0.020  0.980
 2B9  OAC  H2   single    0.850  0.020  0.980
 2B9  CAM  H3   single    0.970  0.020  1.090
 2B9  CAM  H4   single    0.970  0.020  1.090
 2B9  CAL  H5   single    0.930  0.020  1.080
 2B9  CAA  H6   single    0.970  0.020  1.090
 2B9  CAA  H7   single    0.970  0.020  1.090
 2B9  CAA  H8   single    0.970  0.020  1.090
 2B9  OAD  H9   single    0.850  0.020  0.980
 2B9  CAG  H10  single    0.930  0.020  1.080
 2B9  CAJ  H14  single    0.930  0.020  1.080
 2B9  CAH  H15  single    0.930  0.020  1.080
 2B9  CAI  H16  single    0.930  0.020  1.080
 2B9  CAK  H17  single    0.930  0.020  1.080
 2B9  NAP  H18  single    0.860  0.020  1.020

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
 2B9  OAR  PAY  OAC   96.41  3.000
 2B9  OAR  PAY  OAF  106.65  3.000
 2B9  OAC  PAY  OAF  108.03  3.000
 2B9  OAF  PAY  OAE  109.85  3.000
 2B9  OAR  PAY  OAE  115.98  3.000
 2B9  OAC  PAY  OAE  118.67  3.000
 2B9  H1   OAF  PAY  116.18  3.000
 2B9  H2   OAC  PAY  114.25  3.000
 2B9  CAM  OAR  PAY  119.41  3.000
 2B9  H4   CAM  H3   107.70  3.000
 2B9  H4   CAM  CAW  109.70  3.000
 2B9  H3   CAM  CAW  109.85  3.000
 2B9  H4   CAM  OAR  110.59  3.000
 2B9  H3   CAM  OAR  110.04  3.000
 2B9  CAW  CAM  OAR  108.96  3.000
 2B9  CAX  CAW  CAL  120.03  3.000
 2B9  CAL  CAW  CAM  119.95  3.000
 2B9  CAX  CAW  CAM  120.01  3.000
 2B9  H5   CAL  NAP  115.88  3.000
 2B9  H5   CAL  CAW  124.22  3.000
 2B9  NAP  CAL  CAW  119.90  3.000
 2B9  H18  NAP  CAT  118.04  3.000
 2B9  H18  NAP  CAL  117.96  3.000
 2B9  CAT  NAP  CAL  124.00  3.000
 2B9  CAV  CAT  CAA  122.99  3.000
 2B9  CAA  CAT  NAP  118.63  3.000
 2B9  CAV  CAT  NAP  118.38  3.000
 2B9  H8   CAA  H7   108.18  3.000
 2B9  H8   CAA  H6   107.43  3.000
 2B9  H7   CAA  H6   107.41  3.000
 2B9  H8   CAA  CAT  111.19  3.000
 2B9  H7   CAA  CAT  111.18  3.000
 2B9  H6   CAA  CAT  111.28  3.000
 2B9  CAX  CAV  OAD  118.85  3.000
 2B9  CAX  CAV  CAT  120.63  3.000
 2B9  OAD  CAV  CAT  120.53  3.000
 2B9  H9   OAD  CAV  111.65  3.000
 2B9  CAG  CAX  CAV  124.33  3.000
 2B9  CAV  CAX  CAW  117.06  3.000
 2B9  CAG  CAX  CAW  118.61  3.000
 2B9  H10  CAG  NAN  118.64  3.000
 2B9  H10  CAG  CAX  117.73  3.000
 2B9  NAN  CAG  CAX  123.63  3.000
 2B9  NAQ  NAN  CAG  114.46  3.000
 2B9  CAS  NAQ  NAN  112.82  3.000
 2B9  CAU  CAS  OAB  119.11  3.000
 2B9  OAB  CAS  NAQ  128.40  3.000
 2B9  CAU  CAS  NAQ  112.49  3.000
 2B9  CAK  CAU  CAJ  117.36  3.000
 2B9  CAJ  CAU  CAS  119.58  3.000
 2B9  CAK  CAU  CAS  123.07  3.000
 2B9  H14  CAJ  CAH  119.97  3.000
 2B9  H14  CAJ  CAU  120.91  3.000
 2B9  CAH  CAJ  CAU  119.12  3.000
 2B9  H15  CAH  NAO  116.48  3.000
 2B9  H15  CAH  CAJ  119.91  3.000
 2B9  NAO  CAH  CAJ  123.61  3.000
 2B9  CAI  NAO  CAH  117.23  3.000
 2B9  H16  CAI  CAK  119.85  3.000
 2B9  H16  CAI  NAO  116.48  3.000
 2B9  CAK  CAI  NAO  123.67  3.000
 2B9  H17  CAK  CAI  120.28  3.000
 2B9  H17  CAK  CAU  120.71  3.000
 2B9  CAI  CAK  CAU  119.01  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
 2B9  CONST_01  NAO  CAI  CAK  CAU     0.00   0.0  0
 2B9  CONST_02  NAO  CAH  CAJ  CAU     0.00   0.0  0
 2B9  CONST_03  CAI  NAO  CAH  CAJ     0.00   0.0  0
 2B9  CONST_04  CAI  CAK  CAU  CAJ     0.00   0.0  0
 2B9  CONST_05  CAK  CAI  NAO  CAH     0.00   0.0  0
 2B9  CONST_06  CAK  CAU  CAJ  CAH     0.00   0.0  0
 2B9  CONST_07  CAI  CAK  CAU  CAS   180.00   0.0  0
 2B9  CONST_08  CAH  CAJ  CAU  CAS   180.00   0.0  0
 2B9  CONST_09  H16  CAI  CAK  CAU   180.00   0.0  0
 2B9  CONST_10  H15  CAH  CAJ  CAU   180.00   0.0  0
 2B9  CONST_11  H17  CAK  CAU  CAJ   180.00   0.0  0
 2B9  CONST_12  H14  CAJ  CAH  NAO   180.00   0.0  0
 2B9  CONST_13  CAU  CAS  NAQ  NAN   180.00   0.0  0
 2B9  CONST_14  OAB  CAS  NAQ  NAN     0.00   0.0  0
 2B9  Var_01    CAX  CAW  CAM  OAR   177.83  30.0  3
 2B9  Var_02    NAN  CAG  CAX  CAW  -178.94  30.0  2
 2B9  Var_03    CAK  CAU  CAS  NAQ     0.36  30.0  2
 2B9  Var_04    H6   CAA  CAT  NAP    -0.01  30.0  3
 2B9  Var_05    CAW  CAM  OAR  PAY   175.30  30.0  1

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
 2B9  plan-1  CAM  0.020
 2B9  plan-1  CAW  0.020
 2B9  plan-1  CAL  0.020
 2B9  plan-1  NAP  0.020
 2B9  plan-1  CAT  0.020
 2B9  plan-1  CAA  0.020
 2B9  plan-1  CAV  0.020
 2B9  plan-1  OAD  0.020
 2B9  plan-1  CAX  0.020
 2B9  plan-1  CAG  0.020
 2B9  plan-1  H5   0.020
 2B9  plan-1  H18  0.020
 2B9  plan-2  CAS  0.020
 2B9  plan-2  CAU  0.020
 2B9  plan-2  CAJ  0.020
 2B9  plan-2  CAH  0.020
 2B9  plan-2  NAO  0.020
 2B9  plan-2  CAI  0.020
 2B9  plan-2  CAK  0.020
 2B9  plan-2  H14  0.020
 2B9  plan-2  H15  0.020
 2B9  plan-2  H16  0.020
 2B9  plan-2  H17  0.020
 2B9  plan-3  CAG  0.020
 2B9  plan-3  NAN  0.020
 2B9  plan-3  NAQ  0.020
 2B9  plan-3  CAS  0.020
 2B9  plan-3  OAB  0.020
 2B9  plan-3  CAU  0.020

