# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 09:04:16 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: [6-methyl-5-oxidanyl-4-[(~{E})-[(1~{R})-1-phenylethyl]iminomethyl]pyridin-3-yl]methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N=Cc1c(O)c(C)ncc1CO[P](O)(O)=O)c2ccccc2
#
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
 6DF  6DF  '[6-methyl-5-oxidanyl-4-[(~{E})-[(1~{R})-1-phenylethyl]iminomethyl]pyridin-3-yl]methyl dihydrogen phosphate'  ligand  43  24  .  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_6DF
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
 6DF  N1   N  N     0  -0.403  27.1460  33.5824  21.5361
 6DF  C2   C  CR6   0   0.131  27.8753  32.7595  20.8019
 6DF  N2   N  N     0  -0.308  26.5888  32.5083  16.6322
 6DF  C3   C  CR6   0   0.266  27.4850  32.3871  19.5026
 6DF  C4   C  CR6   0   0.054  26.2949  32.8886  18.9780
 6DF  C5   C  CR6   0   0.008  25.5359  33.7451  19.7841
 6DF  C6   C  CR16  0  -0.136  26.0114  34.0621  21.0430
 6DF  C7   C  CH1   0  -0.169  26.0858  32.1562  15.3192
 6DF  C8   C  CH3   0  -0.722  24.6151  31.7578  15.2101
 6DF  C9   C  CR6   0   0.126  26.9603  31.0664  14.7326
 6DF  C10  C  CR16  0  -0.302  27.4366  30.0198  15.5167
 6DF  C11  C  CR16  0  -0.242  28.1869  28.9982  14.9486
 6DF  C12  C  CR16  0  -0.270  28.4719  29.0097  13.5894
 6DF  C13  C  CR16  0  -0.242  28.0024  30.0519  12.8008
 6DF  O2P  O  O     0  -0.701  21.9959  33.6248  17.1004
 6DF  P    P  P     0   1.460  21.8771  33.4856  18.5662
 6DF  O3P  O  OH1   0  -0.740  21.1943  34.7292  19.3039
 6DF  O1P  O  OH1   0  -0.727  21.1393  32.1812  19.1051
 6DF  O4P  O  O2    0  -0.583  23.2288  33.3158  19.3985
 6DF  C5'  C  CH2   0  -0.300  24.2414  34.3330  19.3160
 6DF  C2'  C  CH3   0  -0.789  29.1447  32.2218  21.3906
 6DF  O3   O  OH1   0  -0.597  28.2174  31.5414  18.7647
 6DF  C4'  C  C1    0  -0.098  25.8146  32.5257  17.6279
 6DF  C14  C  CR16  0  -0.306  27.2528  31.0717  13.3715
 6DF  H1   H  HCR6  0   0.263  25.4509  34.7365  21.6816
 6DF  H2   H  HCH1  0   0.262  26.2347  33.0511  14.7042
 6DF  H3   H  HCH3  0   0.248  23.9453  32.5434  15.5622
 6DF  H4   H  HCH3  0   0.255  24.3734  31.5630  14.1654
 6DF  H5   H  HCH3  0   0.232  24.3987  30.8472  15.7728
 6DF  H6   H  HCR6  0   0.249  27.2317  30.0025  16.5795
 6DF  H7   H  HCR6  0   0.253  28.5537  28.1919  15.5711
 6DF  H8   H  HCR6  0   0.253  29.0581  28.2139  13.1483
 6DF  H9   H  HCR6  0   0.254  28.2233  30.0748  11.7413
 6DF  H10  H  HOH1  0   0.500  20.6165  35.2588  18.7390
 6DF  H11  H  HOH1  0   0.504  20.4951  31.8117  18.4867
 6DF  H12  H  HCH2  0   0.260  24.3285  34.7045  18.2913
 6DF  H13  H  HCH2  0   0.275  23.9619  35.1758  19.9511
 6DF  H14  H  HCH3  0   0.276  29.2807  32.6125  22.3960
 6DF  H15  H  HCH3  0   0.259  29.1348  31.1305  21.4607
 6DF  H16  H  HCH3  0   0.264  30.0206  32.5057  20.8017
 6DF  H17  H  HOH1  0   0.487  28.9596  31.1931  19.2715
 6DF  H18  H  H     0   0.251  24.7502  32.2950  17.5557
 6DF  H19  H  HCR6  0   0.248  26.8913  31.8841  12.7510

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
 6DF  C13  C12  aromatic  1.389  0.020  1.389
 6DF  C13  C14  aromatic  1.388  0.020  1.388
 6DF  C12  C11  aromatic  1.389  0.020  1.389
 6DF  C14  C9   aromatic  1.392  0.020  1.392
 6DF  C9   C10  aromatic  1.392  0.020  1.392
 6DF  C9   C7   single    1.515  0.020  1.515
 6DF  C11  C10  aromatic  1.389  0.020  1.389
 6DF  C8   C7   single    1.528  0.020  1.528
 6DF  C7   N2   single    1.449  0.020  1.449
 6DF  N2   C4'  double    1.261  0.020  1.261
 6DF  O2P  P    double    1.477  0.020  1.477
 6DF  C4'  C4   single    1.478  0.020  1.478
 6DF  O3   C3   single    1.340  0.020  1.340
 6DF  P    O3P  single    1.599  0.020  1.599
 6DF  P    O1P  single    1.593  0.020  1.593
 6DF  P    O4P  single    1.596  0.020  1.596
 6DF  C4   C3   aromatic  1.394  0.020  1.394
 6DF  C4   C5   aromatic  1.400  0.020  1.400
 6DF  C5'  O4P  single    1.438  0.020  1.438
 6DF  C5'  C5   single    1.497  0.020  1.497
 6DF  C3   C2   aromatic  1.407  0.020  1.407
 6DF  C5   C6   aromatic  1.383  0.020  1.383
 6DF  C2   C2'  single    1.499  0.020  1.499
 6DF  C2   N1   aromatic  1.322  0.020  1.322
 6DF  C6   N1   aromatic  1.327  0.020  1.327
 6DF  C6   H1   single    0.930  0.020  1.080
 6DF  C7   H2   single    0.970  0.020  1.090
 6DF  C8   H3   single    0.970  0.020  1.090
 6DF  C8   H4   single    0.970  0.020  1.090
 6DF  C8   H5   single    0.970  0.020  1.090
 6DF  C10  H6   single    0.930  0.020  1.080
 6DF  C11  H7   single    0.930  0.020  1.080
 6DF  C12  H8   single    0.930  0.020  1.080
 6DF  C13  H9   single    0.930  0.020  1.080
 6DF  O3P  H10  single    0.850  0.020  0.980
 6DF  O1P  H11  single    0.850  0.020  0.980
 6DF  C5'  H12  single    0.970  0.020  1.090
 6DF  C5'  H13  single    0.970  0.020  1.090
 6DF  C2'  H14  single    0.970  0.020  1.090
 6DF  C2'  H15  single    0.970  0.020  1.090
 6DF  C2'  H16  single    0.970  0.020  1.090
 6DF  O3   H17  single    0.850  0.020  0.980
 6DF  C4'  H18  single    0.930  0.020  1.080
 6DF  C14  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
 6DF  C6   N1   C2   119.36  3.000
 6DF  C2'  C2   C3   120.18  3.000
 6DF  C2'  C2   N1   118.18  3.000
 6DF  C3   C2   N1   121.64  3.000
 6DF  C4'  N2   C7   120.36  3.000
 6DF  O3   C3   C4   119.10  3.000
 6DF  C4   C3   C2   119.29  3.000
 6DF  O3   C3   C2   121.60  3.000
 6DF  C4'  C4   C5   120.00  3.000
 6DF  C5   C4   C3   117.80  3.000
 6DF  C4'  C4   C3   122.20  3.000
 6DF  C5'  C5   C6   119.49  3.000
 6DF  C6   C5   C4   118.56  3.000
 6DF  C5'  C5   C4   121.95  3.000
 6DF  H1   C6   C5   120.05  3.000
 6DF  H1   C6   N1   116.60  3.000
 6DF  C5   C6   N1   123.34  3.000
 6DF  H2   C7   C9   106.95  3.000
 6DF  H2   C7   C8   107.68  3.000
 6DF  C9   C7   C8   109.90  3.000
 6DF  H2   C7   N2   105.24  3.000
 6DF  C8   C7   N2   117.52  3.000
 6DF  C9   C7   N2   108.97  3.000
 6DF  H5   C8   H4   107.51  3.000
 6DF  H5   C8   H3   108.21  3.000
 6DF  H4   C8   H3   107.57  3.000
 6DF  H5   C8   C7   111.81  3.000
 6DF  H4   C8   C7   109.18  3.000
 6DF  H3   C8   C7   112.35  3.000
 6DF  C14  C9   C10  118.80  3.000
 6DF  C10  C9   C7   121.35  3.000
 6DF  C14  C9   C7   119.80  3.000
 6DF  H6   C10  C11  119.47  3.000
 6DF  H6   C10  C9   120.02  3.000
 6DF  C11  C10  C9   120.50  3.000
 6DF  H7   C11  C12  119.96  3.000
 6DF  H7   C11  C10  119.71  3.000
 6DF  C12  C11  C10  120.33  3.000
 6DF  H8   C12  C13  120.23  3.000
 6DF  H8   C12  C11  120.26  3.000
 6DF  C13  C12  C11  119.51  3.000
 6DF  H9   C13  C14  119.80  3.000
 6DF  H9   C13  C12  120.17  3.000
 6DF  C14  C13  C12  120.02  3.000
 6DF  O4P  P    O1P   97.40  3.000
 6DF  O4P  P    O3P  101.76  3.000
 6DF  O1P  P    O3P  106.44  3.000
 6DF  O4P  P    O2P  117.34  3.000
 6DF  O1P  P    O2P  116.76  3.000
 6DF  O3P  P    O2P  114.76  3.000
 6DF  H10  O3P  P    114.33  3.000
 6DF  H11  O1P  P    113.92  3.000
 6DF  C5'  O4P  P    119.42  3.000
 6DF  H13  C5'  H12  107.65  3.000
 6DF  H13  C5'  O4P  109.42  3.000
 6DF  H12  C5'  O4P  110.50  3.000
 6DF  H13  C5'  C5   110.04  3.000
 6DF  H12  C5'  C5   110.95  3.000
 6DF  O4P  C5'  C5   108.26  3.000
 6DF  H16  C2'  H15  107.51  3.000
 6DF  H16  C2'  H14  107.74  3.000
 6DF  H15  C2'  H14  107.49  3.000
 6DF  H16  C2'  C2   111.95  3.000
 6DF  H15  C2'  C2   112.06  3.000
 6DF  H14  C2'  C2   109.89  3.000
 6DF  H17  O3   C3   111.06  3.000
 6DF  H18  C4'  C4   115.41  3.000
 6DF  H18  C4'  N2   122.91  3.000
 6DF  C4   C4'  N2   121.66  3.000
 6DF  H19  C14  C13  119.67  3.000
 6DF  H19  C14  C9   119.49  3.000
 6DF  C13  C14  C9   120.84  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
 6DF  CONST_01  C4   C3   C2   N1     0.00   0.0  0
 6DF  CONST_02  C4   C5   C6   N1     0.00   0.0  0
 6DF  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 6DF  CONST_04  C5   C6   N1   C2     0.00   0.0  0
 6DF  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 6DF  CONST_06  C6   N1   C2   C3     0.00   0.0  0
 6DF  CONST_07  C12  C13  C14  C9     0.00   0.0  0
 6DF  CONST_08  C12  C11  C10  C9     0.00   0.0  0
 6DF  CONST_09  C13  C14  C9   C10    0.00   0.0  0
 6DF  CONST_10  C13  C12  C11  C10    0.00   0.0  0
 6DF  CONST_11  C14  C13  C12  C11    0.00   0.0  0
 6DF  CONST_12  C14  C9   C10  C11    0.00   0.0  0
 6DF  CONST_13  O3   C3   C2   N1   180.00   0.0  0
 6DF  CONST_14  C5'  C5   C6   N1   180.00   0.0  0
 6DF  CONST_15  C4'  C4   C3   C2   180.00   0.0  0
 6DF  CONST_16  C5'  C5   C4   C3   180.00   0.0  0
 6DF  CONST_17  C2'  C2   C3   C4   180.00   0.0  0
 6DF  CONST_18  O3   C3   C4   C5   180.00   0.0  0
 6DF  CONST_19  C4'  C4   C5   C6   180.00   0.0  0
 6DF  CONST_20  C2'  C2   N1   C6   180.00   0.0  0
 6DF  CONST_21  C13  C14  C9   C7   180.00   0.0  0
 6DF  CONST_22  C11  C10  C9   C7   180.00   0.0  0
 6DF  CONST_23  H1   C6   N1   C2   180.00   0.0  0
 6DF  CONST_24  H9   C13  C14  C9   180.00   0.0  0
 6DF  CONST_25  H7   C11  C10  C9   180.00   0.0  0
 6DF  CONST_26  H19  C14  C9   C10  180.00   0.0  0
 6DF  CONST_27  H8   C12  C11  C10  180.00   0.0  0
 6DF  CONST_28  H6   C10  C11  C12  180.00   0.0  0
 6DF  Var_01    C3   C4   C4'  N2   -44.75  30.0  2
 6DF  Var_02    O4P  C5'  C5   C4    76.82  30.0  2
 6DF  Var_03    H14  C2'  C2   N1     0.13  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
 6DF  chir_01  C7  C9  C8  N2  negativ

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
 6DF  plan-1  N1   0.020
 6DF  plan-1  C2   0.020
 6DF  plan-1  C3   0.020
 6DF  plan-1  C4   0.020
 6DF  plan-1  C5   0.020
 6DF  plan-1  C6   0.020
 6DF  plan-1  C5'  0.020
 6DF  plan-1  C2'  0.020
 6DF  plan-1  O3   0.020
 6DF  plan-1  C4'  0.020
 6DF  plan-1  H1   0.020
 6DF  plan-2  C7   0.020
 6DF  plan-2  C9   0.020
 6DF  plan-2  C10  0.020
 6DF  plan-2  C11  0.020
 6DF  plan-2  C12  0.020
 6DF  plan-2  C13  0.020
 6DF  plan-2  C14  0.020
 6DF  plan-2  H6   0.020
 6DF  plan-2  H7   0.020
 6DF  plan-2  H8   0.020
 6DF  plan-2  H9   0.020
 6DF  plan-2  H19  0.020
 6DF  plan-3  N2   0.020
 6DF  plan-3  C4   0.020
 6DF  plan-3  C7   0.020
 6DF  plan-3  C4'  0.020
 6DF  plan-3  H18  0.020

