# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 16:20:02 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C=C2[C@@H](NC(=O)c3c(O)c4OCOc4cc23)[C@H](O)[C@@H]1O
#
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
 3KF  3KF  (2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one  ligand  35  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3KF
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
 3KF  C1   C  CR56  0   0.343   2.7197   1.3162  -0.5256
 3KF  C2   C  CR56  0   0.216   3.3031   0.1084  -0.2043
 3KF  C3   C  CR6   0   0.279   2.5517  -1.0137   0.0740
 3KF  C4   C  CR6   0  -0.283   1.1466  -0.8600  -0.0128
 3KF  C5   C  CR6   0   0.154   0.5680   0.3823  -0.3275
 3KF  C6   C  CR16  0  -0.446   1.3554   1.5003  -0.5938
 3KF  C7   C  C     0   0.048  -0.8981   0.4493  -0.2974
 3KF  C8   C  C1    0  -0.341  -1.5776   1.4993   0.1604
 3KF  C9   C  CH1   0   0.011  -3.0671   1.5013   0.3389
 3KF  O1   O  O     0  -0.483   4.6566   0.2221  -0.2459
 3KF  C10  C  CH1   0   0.013  -3.5549   0.0694   0.5311
 3KF  C11  C  CH1   0  -0.025  -3.0897  -0.7951  -0.6312
 3KF  C12  C  CH1   0  -0.127  -1.5642  -0.8262  -0.7265
 3KF  C13  C  C     0   0.601   0.3020  -2.0231   0.3035
 3KF  O3   O  OH1   0  -0.666  -3.5562  -0.3005  -1.8629
 3KF  O4   O  OH1   0  -0.675  -4.9571  -0.0116   0.5838
 3KF  O5   O  OH1   0  -0.676  -3.4430   2.2307   1.4893
 3KF  O6   O  OH1   0  -0.624   3.1508  -2.1556   0.3985
 3KF  C    C  CH2   0   0.066   4.9105   1.6139  -0.3562
 3KF  N    N  NH1   0  -0.659  -1.0142  -1.9050   0.0808
 3KF  O    O  O     0  -0.481   3.6880   2.2219  -0.7676
 3KF  H1   H  HCR6  0   0.273   0.9203   2.4537  -0.8589
 3KF  H2   H  H     0   0.266  -1.0459   2.3952   0.4657
 3KF  H3   H  HCH1  0   0.238  -3.5470   1.9254  -0.5533
 3KF  H4   H  HCH1  0   0.222  -3.0980  -0.3230   1.4529
 3KF  H5   H  HCH1  0   0.252  -3.4486  -1.8226  -0.4674
 3KF  H6   H  HCH1  0   0.286  -1.3145  -1.0131  -1.7801
 3KF  H7   H  HOH1  0   0.456  -4.5119  -0.1944  -1.8018
 3KF  H8   H  HOH1  0   0.454  -5.2717   0.6275   1.2324
 3KF  H9   H  HOH1  0   0.461  -3.4675   3.1661   1.2663
 3KF  H10  H  HOH1  0   0.480   2.4270  -2.7900   0.6305
 3KF  H11  H  HCH2  0   0.237   5.2104   2.0215   0.6153
 3KF  H12  H  HCH2  0   0.252   5.6803   1.7936  -1.1050
 3KF  H13  H  HNH1  0   0.408  -1.5622  -2.7493   0.1780
 3KF  O2   O  O     0  -0.529   0.7911  -3.0678   0.7603

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
 3KF  O2   C13  double    1.241  0.020  1.241
 3KF  O6   C3   single    1.330  0.020  1.330
 3KF  O5   C9   single    1.413  0.020  1.413
 3KF  C13  N    single    1.340  0.020  1.340
 3KF  C13  C4   single    1.472  0.020  1.472
 3KF  C3   C4   aromatic  1.416  0.020  1.416
 3KF  C3   C2   aromatic  1.379  0.020  1.379
 3KF  N    C12  single    1.455  0.020  1.455
 3KF  C4   C5   aromatic  1.406  0.020  1.406
 3KF  C2   O1   single    1.359  0.020  1.359
 3KF  C2   C1   aromatic  1.379  0.020  1.379
 3KF  C11  O3   single    1.407  0.020  1.407
 3KF  C11  C12  single    1.529  0.020  1.529
 3KF  C11  C10  single    1.521  0.020  1.521
 3KF  O1   C    single    1.419  0.020  1.419
 3KF  C5   C7   single    1.468  0.020  1.468
 3KF  C5   C6   aromatic  1.393  0.020  1.393
 3KF  C8   C7   double    1.332  0.020  1.332
 3KF  C8   C9   single    1.500  0.020  1.500
 3KF  C1   C6   aromatic  1.378  0.020  1.378
 3KF  C1   O    single    1.348  0.020  1.348
 3KF  C7   C12  single    1.502  0.020  1.502
 3KF  C9   C10  single    1.525  0.020  1.525
 3KF  C    O    single    1.426  0.020  1.426
 3KF  C10  O4   single    1.406  0.020  1.406
 3KF  C6   H1   single    0.930  0.020  1.080
 3KF  C8   H2   single    0.930  0.020  1.080
 3KF  C9   H3   single    0.970  0.020  1.090
 3KF  C10  H4   single    0.970  0.020  1.090
 3KF  C11  H5   single    0.970  0.020  1.090
 3KF  C12  H6   single    0.970  0.020  1.090
 3KF  O3   H7   single    0.850  0.020  0.980
 3KF  O4   H8   single    0.850  0.020  0.980
 3KF  O5   H9   single    0.850  0.020  0.980
 3KF  O6   H10  single    0.850  0.020  0.980
 3KF  C    H11  single    0.970  0.020  1.090
 3KF  C    H12  single    0.970  0.020  1.090
 3KF  N    H13  single    0.890  0.020  1.040

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
 3KF  O    C1   C6   127.77  3.000
 3KF  O    C1   C2   109.05  3.000
 3KF  C6   C1   C2   123.17  3.000
 3KF  O1   C2   C3   128.10  3.000
 3KF  O1   C2   C1   109.93  3.000
 3KF  C3   C2   C1   121.95  3.000
 3KF  O6   C3   C4   123.72  3.000
 3KF  C4   C3   C2   116.10  3.000
 3KF  O6   C3   C2   120.17  3.000
 3KF  C13  C4   C5   120.67  3.000
 3KF  C5   C4   C3   121.19  3.000
 3KF  C13  C4   C3   118.06  3.000
 3KF  C7   C5   C6   122.12  3.000
 3KF  C6   C5   C4   121.28  3.000
 3KF  C7   C5   C4   116.54  3.000
 3KF  H1   C6   C5   121.82  3.000
 3KF  H1   C6   C1   121.89  3.000
 3KF  C5   C6   C1   116.28  3.000
 3KF  C12  C7   C8   122.79  3.000
 3KF  C12  C7   C5   113.48  3.000
 3KF  C8   C7   C5   123.55  3.000
 3KF  H2   C8   C9   116.85  3.000
 3KF  H2   C8   C7   119.83  3.000
 3KF  C9   C8   C7   123.27  3.000
 3KF  H3   C9   O5   110.23  3.000
 3KF  H3   C9   C10  108.98  3.000
 3KF  O5   C9   C10  107.28  3.000
 3KF  H3   C9   C8   109.74  3.000
 3KF  C10  C9   C8   109.35  3.000
 3KF  O5   C9   C8   111.21  3.000
 3KF  C    O1   C2   105.23  3.000
 3KF  H4   C10  O4   111.22  3.000
 3KF  H4   C10  C11  108.07  3.000
 3KF  O4   C10  C11  107.51  3.000
 3KF  H4   C10  C9   107.91  3.000
 3KF  O4   C10  C9   112.21  3.000
 3KF  C11  C10  C9   109.85  3.000
 3KF  H5   C11  O3   110.51  3.000
 3KF  H5   C11  C12  108.40  3.000
 3KF  O3   C11  C12  106.47  3.000
 3KF  H5   C11  C10  108.49  3.000
 3KF  C12  C11  C10  111.36  3.000
 3KF  O3   C11  C10  111.57  3.000
 3KF  H6   C12  N    108.66  3.000
 3KF  H6   C12  C11  106.86  3.000
 3KF  N    C12  C11  110.95  3.000
 3KF  H6   C12  C7   108.52  3.000
 3KF  C11  C12  C7   114.05  3.000
 3KF  N    C12  C7   107.67  3.000
 3KF  N    C13  O2   121.50  3.000
 3KF  N    C13  C4   117.28  3.000
 3KF  O2   C13  C4   121.22  3.000
 3KF  H7   O3   C11  108.19  3.000
 3KF  H8   O4   C10  108.23  3.000
 3KF  H9   O5   C9   108.67  3.000
 3KF  H10  O6   C3   106.15  3.000
 3KF  H12  C    H11  110.79  3.000
 3KF  H12  C    O    109.72  3.000
 3KF  H11  C    O    109.38  3.000
 3KF  H12  C    O1   109.99  3.000
 3KF  H11  C    O1   110.18  3.000
 3KF  O    C    O1   106.69  3.000
 3KF  H13  N    C13  116.28  3.000
 3KF  H13  N    C12  117.86  3.000
 3KF  C13  N    C12  121.92  3.000
 3KF  C    O    C1   106.12  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
 3KF  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 3KF  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 3KF  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 3KF  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 3KF  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 3KF  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 3KF  CONST_07  C12  N    C13  C4      0.00   0.0  0
 3KF  CONST_08  O6   C3   C2   C1    180.00   0.0  0
 3KF  CONST_09  O6   C3   C4   C5    180.00   0.0  0
 3KF  CONST_10  O6   C3   C2   O1      0.00   0.0  0
 3KF  CONST_11  O6   C3   C4   C13     0.00   0.0  0
 3KF  CONST_12  C12  N    C13  O2    180.00   0.0  0
 3KF  CONST_13  H1   C6   C1   C2    180.00   0.0  0
 3KF  CONST_14  H13  N    C13  C4    180.00   0.0  0
 3KF  Var_01    O1   C    O    C1     16.72  30.0  1
 3KF  Var_02    O    C    O1   C2    -16.79  30.0  1
 3KF  Var_03    N    C13  C4   C3   -173.11  30.0  1
 3KF  Var_04    C8   C7   C5   C4    141.39  30.0  1
 3KF  Var_05    C9   C8   C7   C5   -172.58  30.0  1

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
 3KF  chir_01  C9   O5  C8   C10  negativ
 3KF  chir_02  C10  O4  C9   C11  positiv
 3KF  chir_03  C11  O3  C10  C12  positiv
 3KF  chir_04  C12  N   C11  C7   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
 3KF  plan-1  C4   0.020
 3KF  plan-1  C12  0.020
 3KF  plan-1  C13  0.020
 3KF  plan-1  N    0.020
 3KF  plan-1  H13  0.020
 3KF  plan-1  O2   0.020
 3KF  plan-2  C1   0.020
 3KF  plan-2  C2   0.020
 3KF  plan-2  C3   0.020
 3KF  plan-2  C4   0.020
 3KF  plan-2  C5   0.020
 3KF  plan-2  C6   0.020
 3KF  plan-2  C7   0.020
 3KF  plan-2  O1   0.020
 3KF  plan-2  C13  0.020
 3KF  plan-2  O6   0.020
 3KF  plan-2  O    0.020
 3KF  plan-2  H1   0.020

