# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 02:30:11 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: [5-hydroxy-4-({(E)-[(4-hydroxy-2,2'-bipyridin-6-yl)methylidene]amino}methyl)-6-methylpyridin-3-yl]methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN=Cc2cc(O)cc(n2)c3ccccn3)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
 5B6  5B6  '[5-hydroxy-4-({(E)-[(4-hydroxy-2,2'-bipyridin-6-yl)methylidene]amino}methyl)-6-methylpyridin-3-yl]methyl dihydrogen phosphate'  ligand  49  30  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5B6
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
 5B6  O3   O  OH1   0  -0.728   5.2146   2.0936   2.0804
 5B6  P1   P  P     0   1.465   4.6240   2.0923   0.6023
 5B6  O4   O  O     0  -0.708   3.7047   3.1764   0.2120
 5B6  O2   O  OH1   0  -0.738   5.8495   2.0316  -0.4187
 5B6  O5   O  O2    0  -0.593   3.9932   0.6230   0.6587
 5B6  C9   C  CH2   0  -0.205   3.1327   0.1982  -0.3911
 5B6  C8   C  CR6   0  -0.074   2.7707  -1.2465  -0.1917
 5B6  C6   C  CR6   0   0.093   1.7940  -1.8324  -0.9988
 5B6  C5   C  CR6   0   0.271   1.4738  -3.1663  -0.7699
 5B6  O1   O  OH1   0  -0.617   0.5129  -3.7227  -1.5288
 5B6  C3   C  CR6   0   0.125   2.1510  -3.8858   0.2246
 5B6  C4   C  CH3   0  -0.785   1.8345  -5.3305   0.4733
 5B6  N2   N  N     0  -0.406   3.0839  -3.3106   0.9654
 5B6  C10  C  CR16  0  -0.133   3.3862  -2.0327   0.7709
 5B6  C7   C  CH2   0  -0.413   1.0630  -1.0500  -2.0622
 5B6  N1   N  N     0  -0.299  -0.2021  -0.5913  -1.5313
 5B6  C1   C  C1    0  -0.077  -0.4303   0.6491  -1.5647
 5B6  C2   C  CR6   0   0.208  -1.6790   1.2389  -1.0462
 5B6  N3   N  N     0  -0.460  -2.6163   0.4241  -0.5730
 5B6  C11  C  CR6   0   0.199  -3.7327   0.9617  -0.1035
 5B6  C12  C  CR16  0  -0.439  -3.9643   2.3351  -0.0807
 5B6  C13  C  CR6   0   0.473  -2.9813   3.1817  -0.5746
 5B6  O6   O  OH1   0  -0.609  -3.1014   4.5101  -0.5951
 5B6  C14  C  CR16  0  -0.410  -1.8081   2.6181  -1.0743
 5B6  C15  C  CR6   0   0.196  -4.7575   0.0193   0.4126
 5B6  N4   N  N     0  -0.432  -5.8786   0.5512   0.8924
 5B6  C19  C  CR16  0  -0.072  -6.8173  -0.2569   1.3611
 5B6  C18  C  CR16  0  -0.320  -6.6931  -1.6390   1.3784
 5B6  C17  C  CR16  0  -0.151  -5.5250  -2.1946   0.8794
 5B6  C16  C  CR16  0  -0.303  -4.5384  -1.3562   0.3874
 5B6  H1   H  HOH1  0   0.506   5.6039   2.9360   2.3513
 5B6  H2   H  HOH1  0   0.497   6.5358   1.3816  -0.2150
 5B6  H3   H  HCH2  0   0.252   2.2308   0.8157  -0.3954
 5B6  H4   H  HCH2  0   0.261   3.6214   0.3276  -1.3627
 5B6  H5   H  HOH1  0   0.488   0.4026  -4.6576  -1.3239
 5B6  H6   H  HCH3  0   0.257   2.0224  -5.9498  -0.4078
 5B6  H7   H  HCH3  0   0.272   2.4560  -5.7109   1.2803
 5B6  H8   H  HCH3  0   0.259   0.7903  -5.4791   0.7600
 5B6  H9   H  HCR6  0   0.258   4.1529  -1.6232   1.4155
 5B6  H10  H  HCH2  0   0.239   1.6849  -0.2288  -2.4390
 5B6  H11  H  HCH2  0   0.279   0.8603  -1.6967  -2.9182
 5B6  H12  H  H     0   0.231   0.2854   1.3675  -1.9814
 5B6  H13  H  HCR6  0   0.288  -4.8929   2.7231   0.3168
 5B6  H14  H  HOH1  0   0.484  -3.9498   4.7849  -0.2263
 5B6  H15  H  HCR6  0   0.283  -1.0178   3.2434  -1.4711
 5B6  H16  H  HCR6  0   0.265  -7.7147   0.2160   1.7437
 5B6  H17  H  HCR6  0   0.274  -7.4904  -2.2542   1.7717
 5B6  H18  H  HCR6  0   0.275  -5.3821  -3.2671   0.8725
 5B6  H19  H  HCR6  0   0.275  -3.6149  -1.7503  -0.0111

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
 5B6  O4   P1   double    1.474  0.020  1.474
 5B6  O3   P1   single    1.592  0.020  1.592
 5B6  P1   O5   single    1.600  0.020  1.600
 5B6  P1   O2   single    1.596  0.020  1.596
 5B6  C1   C2   single    1.475  0.020  1.475
 5B6  C1   N1   double    1.262  0.020  1.262
 5B6  C2   C14  aromatic  1.386  0.020  1.386
 5B6  C2   N3   aromatic  1.329  0.020  1.329
 5B6  C14  C13  aromatic  1.394  0.020  1.394
 5B6  C7   N1   single    1.447  0.020  1.447
 5B6  C7   C6   single    1.509  0.020  1.509
 5B6  N3   C11  aromatic  1.325  0.020  1.325
 5B6  O5   C9   single    1.422  0.020  1.422
 5B6  C13  O6   single    1.334  0.020  1.334
 5B6  C13  C12  aromatic  1.388  0.020  1.388
 5B6  C11  C12  aromatic  1.393  0.020  1.393
 5B6  C11  C15  single    1.485  0.020  1.485
 5B6  N4   C15  aromatic  1.330  0.020  1.330
 5B6  N4   C19  aromatic  1.324  0.020  1.324
 5B6  O1   C5   single    1.345  0.020  1.345
 5B6  C15  C16  aromatic  1.393  0.020  1.393
 5B6  C19  C18  aromatic  1.388  0.020  1.388
 5B6  C6   C5   aromatic  1.391  0.020  1.391
 5B6  C6   C8   aromatic  1.396  0.020  1.396
 5B6  C5   C3   aromatic  1.402  0.020  1.402
 5B6  C16  C17  aromatic  1.385  0.020  1.385
 5B6  C18  C17  aromatic  1.386  0.020  1.386
 5B6  C9   C8   single    1.503  0.020  1.503
 5B6  C8   C10  aromatic  1.387  0.020  1.387
 5B6  C3   C4   single    1.500  0.020  1.500
 5B6  C3   N2   aromatic  1.323  0.020  1.323
 5B6  C10  N2   aromatic  1.328  0.020  1.328
 5B6  O3   H1   single    0.850  0.020  0.980
 5B6  O2   H2   single    0.850  0.020  0.980
 5B6  C9   H3   single    0.970  0.020  1.090
 5B6  C9   H4   single    0.970  0.020  1.090
 5B6  O1   H5   single    0.850  0.020  0.980
 5B6  C4   H6   single    0.970  0.020  1.090
 5B6  C4   H7   single    0.970  0.020  1.090
 5B6  C4   H8   single    0.970  0.020  1.090
 5B6  C10  H9   single    0.930  0.020  1.080
 5B6  C7   H10  single    0.970  0.020  1.090
 5B6  C7   H11  single    0.970  0.020  1.090
 5B6  C1   H12  single    0.930  0.020  1.080
 5B6  C12  H13  single    0.930  0.020  1.080
 5B6  O6   H14  single    0.850  0.020  0.980
 5B6  C14  H15  single    0.930  0.020  1.080
 5B6  C19  H16  single    0.930  0.020  1.080
 5B6  C18  H17  single    0.930  0.020  1.080
 5B6  C17  H18  single    0.930  0.020  1.080
 5B6  C16  H19  single    0.930  0.020  1.080

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
 5B6  H1   O3   P1   114.23  3.000
 5B6  O5   P1   O2   106.88  3.000
 5B6  O2   P1   O4   109.72  3.000
 5B6  O5   P1   O4   116.03  3.000
 5B6  O2   P1   O3   108.01  3.000
 5B6  O5   P1   O3    96.57  3.000
 5B6  O4   P1   O3   118.47  3.000
 5B6  H2   O2   P1   115.83  3.000
 5B6  C9   O5   P1   119.13  3.000
 5B6  H4   C9   H3   107.34  3.000
 5B6  H4   C9   C8   109.80  3.000
 5B6  H3   C9   C8   110.17  3.000
 5B6  H4   C9   O5   110.46  3.000
 5B6  H3   C9   O5   109.47  3.000
 5B6  C8   C9   O5   109.57  3.000
 5B6  C10  C8   C6   118.29  3.000
 5B6  C10  C8   C9   122.02  3.000
 5B6  C6   C8   C9   119.69  3.000
 5B6  C7   C6   C5   120.11  3.000
 5B6  C5   C6   C8   117.93  3.000
 5B6  C7   C6   C8   121.92  3.000
 5B6  C3   C5   O1   122.22  3.000
 5B6  C3   C5   C6   119.85  3.000
 5B6  O1   C5   C6   117.93  3.000
 5B6  H5   O1   C5   111.30  3.000
 5B6  N2   C3   C4   118.35  3.000
 5B6  N2   C3   C5   120.98  3.000
 5B6  C4   C3   C5   120.67  3.000
 5B6  H8   C4   H7   107.69  3.000
 5B6  H8   C4   H6   107.37  3.000
 5B6  H7   C4   H6   107.56  3.000
 5B6  H8   C4   C3   112.10  3.000
 5B6  H7   C4   C3   109.85  3.000
 5B6  H6   C4   C3   112.07  3.000
 5B6  C10  N2   C3   119.81  3.000
 5B6  H9   C10  N2   115.99  3.000
 5B6  H9   C10  C8   120.89  3.000
 5B6  N2   C10  C8   123.11  3.000
 5B6  H11  C7   H10  106.22  3.000
 5B6  H11  C7   N1   108.25  3.000
 5B6  H10  C7   N1   112.61  3.000
 5B6  H11  C7   C6   109.59  3.000
 5B6  H10  C7   C6   110.83  3.000
 5B6  N1   C7   C6   109.23  3.000
 5B6  C1   N1   C7   117.40  3.000
 5B6  H12  C1   C2   115.10  3.000
 5B6  H12  C1   N1   122.42  3.000
 5B6  C2   C1   N1   122.47  3.000
 5B6  C14  C2   N3   123.49  3.000
 5B6  N3   C2   C1   118.49  3.000
 5B6  C14  C2   C1   118.02  3.000
 5B6  C11  N3   C2   118.14  3.000
 5B6  C15  C11  C12  120.35  3.000
 5B6  C15  C11  N3   116.56  3.000
 5B6  C12  C11  N3   123.09  3.000
 5B6  H13  C12  C13  121.31  3.000
 5B6  H13  C12  C11  120.15  3.000
 5B6  C13  C12  C11  118.53  3.000
 5B6  C14  C13  O6   118.22  3.000
 5B6  O6   C13  C12  123.30  3.000
 5B6  C14  C13  C12  118.48  3.000
 5B6  H14  O6   C13  110.91  3.000
 5B6  H15  C14  C13  120.79  3.000
 5B6  H15  C14  C2   120.94  3.000
 5B6  C13  C14  C2   118.27  3.000
 5B6  C16  C15  N4   122.26  3.000
 5B6  C16  C15  C11  120.79  3.000
 5B6  N4   C15  C11  116.95  3.000
 5B6  C19  N4   C15  118.75  3.000
 5B6  H16  C19  C18  120.27  3.000
 5B6  H16  C19  N4   116.45  3.000
 5B6  C18  C19  N4   123.28  3.000
 5B6  H17  C18  C17  121.62  3.000
 5B6  H17  C18  C19  120.35  3.000
 5B6  C17  C18  C19  118.03  3.000
 5B6  H18  C17  C16  120.24  3.000
 5B6  H18  C17  C18  120.72  3.000
 5B6  C16  C17  C18  119.04  3.000
 5B6  H19  C16  C17  121.27  3.000
 5B6  H19  C16  C15  120.09  3.000
 5B6  C17  C16  C15  118.64  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
 5B6  CONST_01  C3   C5   C6   C8      0.00   0.0  0
 5B6  CONST_02  C3   N2   C10  C8      0.00   0.0  0
 5B6  CONST_03  N2   C3   C5   C6      0.00   0.0  0
 5B6  CONST_04  N2   C10  C8   C6      0.00   0.0  0
 5B6  CONST_05  C10  C8   C6   C5      0.00   0.0  0
 5B6  CONST_06  C10  N2   C3   C5      0.00   0.0  0
 5B6  CONST_07  C12  C13  C14  C2      0.00   0.0  0
 5B6  CONST_08  C12  C11  N3   C2      0.00   0.0  0
 5B6  CONST_09  C15  C11  N3   C2    180.00   0.0  0
 5B6  CONST_10  C13  C14  C2   N3      0.00   0.0  0
 5B6  CONST_11  C13  C12  C11  N3      0.00   0.0  0
 5B6  CONST_12  N4   C15  C11  N3    180.00   0.0  0
 5B6  CONST_13  C16  C15  C11  N3      0.00   0.0  0
 5B6  CONST_14  C14  C2   N3   C11     0.00   0.0  0
 5B6  CONST_15  C14  C13  C12  C11     0.00   0.0  0
 5B6  CONST_16  C19  N4   C15  C11   180.00   0.0  0
 5B6  CONST_17  C17  C16  C15  C11   180.00   0.0  0
 5B6  CONST_18  N4   C15  C11  C12     0.00   0.0  0
 5B6  CONST_19  C16  C15  C11  C12   180.00   0.0  0
 5B6  CONST_20  C15  C11  C12  C13   180.00   0.0  0
 5B6  CONST_21  C18  C19  N4   C15     0.00   0.0  0
 5B6  CONST_22  C18  C17  C16  C15     0.00   0.0  0
 5B6  CONST_23  C17  C16  C15  N4      0.00   0.0  0
 5B6  CONST_24  C17  C18  C19  N4      0.00   0.0  0
 5B6  CONST_25  C16  C15  N4   C19     0.00   0.0  0
 5B6  CONST_26  C16  C17  C18  C19     0.00   0.0  0
 5B6  CONST_27  C5   C6   C8   C9    180.00   0.0  0
 5B6  CONST_28  N2   C10  C8   C9    180.00   0.0  0
 5B6  CONST_29  O1   C5   C6   C8    180.00   0.0  0
 5B6  CONST_30  C4   C3   C5   C6    180.00   0.0  0
 5B6  CONST_31  N2   C3   C5   O1    180.00   0.0  0
 5B6  CONST_32  C7   C6   C5   C3    180.00   0.0  0
 5B6  CONST_33  C10  N2   C3   C4    180.00   0.0  0
 5B6  CONST_34  C7   C6   C8   C10   180.00   0.0  0
 5B6  CONST_35  C13  C14  C2   C1    180.00   0.0  0
 5B6  CONST_36  C11  N3   C2   C1    180.00   0.0  0
 5B6  CONST_37  O6   C13  C14  C2    180.00   0.0  0
 5B6  CONST_38  O6   C13  C12  C11   180.00   0.0  0
 5B6  CONST_39  H9   C10  C8   C6    180.00   0.0  0
 5B6  CONST_40  H15  C14  C2   N3    180.00   0.0  0
 5B6  CONST_41  H13  C12  C11  N3    180.00   0.0  0
 5B6  CONST_42  H19  C16  C15  C11     0.00   0.0  0
 5B6  CONST_43  H16  C19  N4   C15   180.00   0.0  0
 5B6  CONST_44  H18  C17  C16  C15   180.00   0.0  0
 5B6  CONST_45  H17  C18  C19  N4    180.00   0.0  0
 5B6  Var_01    C6   C8   C9   O5    171.49  30.0  2
 5B6  Var_02    N1   C7   C6   C8    -96.62  30.0  3
 5B6  Var_03    C14  C2   C1   N1    177.15  30.0  2
 5B6  Var_04    H6   C4   C3   C5     60.74  30.0  2
 5B6  Var_05    C2   C1   N1   C7   -179.59   0.0  2
 5B6  Var_06    C8   C9   O5   P1    174.68  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
 5B6  plan-1  C9   0.020
 5B6  plan-1  C8   0.020
 5B6  plan-1  C6   0.020
 5B6  plan-1  C5   0.020
 5B6  plan-1  O1   0.020
 5B6  plan-1  C3   0.020
 5B6  plan-1  C4   0.020
 5B6  plan-1  N2   0.020
 5B6  plan-1  C10  0.020
 5B6  plan-1  C7   0.020
 5B6  plan-1  H9   0.020
 5B6  plan-2  C1   0.020
 5B6  plan-2  C2   0.020
 5B6  plan-2  N3   0.020
 5B6  plan-2  C11  0.020
 5B6  plan-2  C12  0.020
 5B6  plan-2  C13  0.020
 5B6  plan-2  O6   0.020
 5B6  plan-2  C14  0.020
 5B6  plan-2  C15  0.020
 5B6  plan-2  H13  0.020
 5B6  plan-2  H15  0.020
 5B6  plan-3  C11  0.020
 5B6  plan-3  C15  0.020
 5B6  plan-3  N4   0.020
 5B6  plan-3  C19  0.020
 5B6  plan-3  C18  0.020
 5B6  plan-3  C17  0.020
 5B6  plan-3  C16  0.020
 5B6  plan-3  H16  0.020
 5B6  plan-3  H17  0.020
 5B6  plan-3  H18  0.020
 5B6  plan-3  H19  0.020
 5B6  plan-4  C7   0.020
 5B6  plan-4  N1   0.020
 5B6  plan-4  C1   0.020
 5B6  plan-4  C2   0.020
 5B6  plan-4  H12  0.020

