# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 00:02:02 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (3R)-3,6,8-trihydroxy-3-methyl-3,4-dihydrotetraphene-1,7,12(2H)-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(O)CC(=O)c2c(C1)cc(O)c3C(=O)c4c(O)cccc4C(=O)c23
#
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
 2V4  2V4  (3R)-3,6,8-trihydroxy-3-methyl-3,4-dihydrotetraphene-1,7,12(2H)-trione  ligand  39  25  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2V4
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
 2V4  OAC  O  O     0  -0.347  -0.0987  -2.2296   0.7578
 2V4  CAS  C  CR6   0   0.284  -0.6429  -1.2770   0.2506
 2V4  CAX  C  CR66  0  -0.026   0.1188  -0.0455  -0.1081
 2V4  CAR  C  CR6   0  -0.048   1.4807  -0.0855  -0.3856
 2V4  CAN  C  C     0   0.348   2.1725  -1.3118  -0.8618
 2V4  OAB  O  O     0  -0.395   1.5766  -2.1779  -1.4635
 2V4  CAL  C  CH2   0  -0.557   3.6709  -1.3868  -0.6869
 2V4  CAY  C  CT    0   0.161   4.2959  -0.1816   0.0109
 2V4  CAA  C  CH3   0  -0.671   5.8108  -0.1948  -0.1415
 2V4  OAG  O  OH1   0  -0.668   3.9251  -0.1563   1.3777
 2V4  CAM  C  CH2   0  -0.500   3.6962   1.0795  -0.6014
 2V4  CAQ  C  CR6   0   0.134   2.2123   1.1160  -0.3888
 2V4  CAK  C  CR16  0  -0.420   1.5716   2.3213  -0.1944
 2V4  CAP  C  CR6   0   0.406   0.1897   2.3809  -0.0224
 2V4  OAF  O  OH1   0  -0.606  -0.3664   3.5733   0.1031
 2V4  CAW  C  CR66  0  -0.201  -0.5506   1.1782   0.0330
 2V4  CAT  C  CR6   0   0.486  -2.0072   1.2276   0.1409
 2V4  OAD  O  O     0  -0.516  -2.5870   2.3212   0.2410
 2V4  CAV  C  CR66  0  -0.160  -2.7747  -0.0063   0.0583
 2V4  CAU  C  CR66  0  -0.011  -2.1123  -1.2449   0.0697
 2V4  CAJ  C  CR16  0  -0.312  -2.8158  -2.4278  -0.0131
 2V4  CAH  C  CR16  0  -0.222  -4.2048  -2.3819  -0.1371
 2V4  CAI  C  CR16  0  -0.330  -4.8801  -1.1812  -0.1378
 2V4  CAO  C  CR6   0   0.387  -4.1791   0.0254  -0.0247
 2V4  OAE  O  OH1   0  -0.610  -4.8834   1.1494  -0.0045
 2V4  H1   H  HCH2  0   0.290   3.9065  -2.3117  -0.1491
 2V4  H2   H  HCH2  0   0.278   4.1029  -1.5100  -1.6848
 2V4  H3   H  HCH3  0   0.231   6.1077  -0.1407  -1.1894
 2V4  H4   H  HCH3  0   0.243   6.2556   0.6536   0.3805
 2V4  H5   H  HCH3  0   0.238   6.2357  -1.1115   0.2737
 2V4  H6   H  HOH1  0   0.449   4.2676  -0.9505   1.8021
 2V4  H7   H  HCH2  0   0.276   4.1519   1.9727  -0.1688
 2V4  H8   H  HCH2  0   0.281   3.9180   1.1012  -1.6732
 2V4  H9   H  HCR6  0   0.281   2.1394   3.2437  -0.1944
 2V4  H10  H  HOH1  0   0.492  -1.3368   3.4543   0.2051
 2V4  H11  H  HCR6  0   0.276  -2.2997  -3.3774   0.0028
 2V4  H12  H  HCR6  0   0.282  -4.7651  -3.3029  -0.2266
 2V4  H13  H  HCR6  0   0.287  -5.9592  -1.1557  -0.2172
 2V4  H14  H  HOH1  0   0.490  -4.2683   1.9045   0.0973

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
 2V4  OAE  CAO  single    1.327  0.020  1.327
 2V4  CAI  CAO  aromatic  1.400  0.020  1.400
 2V4  CAI  CAH  aromatic  1.378  0.020  1.378
 2V4  CAO  CAV  aromatic  1.407  0.020  1.407
 2V4  CAH  CAJ  aromatic  1.395  0.020  1.395
 2V4  CAV  CAT  single    1.456  0.020  1.456
 2V4  CAV  CAU  aromatic  1.405  0.020  1.405
 2V4  OAD  CAT  double    1.242  0.020  1.242
 2V4  CAJ  CAU  aromatic  1.379  0.020  1.379
 2V4  CAT  CAW  single    1.461  0.020  1.461
 2V4  CAU  CAS  single    1.481  0.020  1.481
 2V4  OAF  CAP  single    1.322  0.020  1.322
 2V4  CAW  CAP  aromatic  1.413  0.020  1.413
 2V4  CAW  CAX  aromatic  1.402  0.020  1.402
 2V4  CAS  OAC  double    1.209  0.020  1.209
 2V4  CAS  CAX  single    1.492  0.020  1.492
 2V4  CAP  CAK  aromatic  1.394  0.020  1.394
 2V4  CAX  CAR  aromatic  1.391  0.020  1.391
 2V4  CAK  CAQ  aromatic  1.379  0.020  1.379
 2V4  CAR  CAQ  aromatic  1.407  0.020  1.407
 2V4  CAR  CAN  single    1.486  0.020  1.486
 2V4  OAB  CAN  double    1.211  0.020  1.211
 2V4  CAQ  CAM  single    1.499  0.020  1.499
 2V4  CAN  CAL  single    1.510  0.020  1.510
 2V4  CAM  CAY  single    1.525  0.020  1.525
 2V4  CAL  CAY  single    1.526  0.020  1.526
 2V4  CAY  CAA  single    1.523  0.020  1.523
 2V4  CAY  OAG  single    1.417  0.020  1.417
 2V4  CAL  H1   single    0.970  0.020  1.090
 2V4  CAL  H2   single    0.970  0.020  1.090
 2V4  CAA  H3   single    0.970  0.020  1.090
 2V4  CAA  H4   single    0.970  0.020  1.090
 2V4  CAA  H5   single    0.970  0.020  1.090
 2V4  OAG  H6   single    0.850  0.020  0.980
 2V4  CAM  H7   single    0.970  0.020  1.090
 2V4  CAM  H8   single    0.970  0.020  1.090
 2V4  CAK  H9   single    0.930  0.020  1.080
 2V4  OAF  H10  single    0.850  0.020  0.980
 2V4  CAJ  H11  single    0.930  0.020  1.080
 2V4  CAH  H12  single    0.930  0.020  1.080
 2V4  CAI  H13  single    0.930  0.020  1.080
 2V4  OAE  H14  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
 2V4  CAU  CAS  CAX  117.35  3.000
 2V4  CAX  CAS  OAC  121.44  3.000
 2V4  CAU  CAS  OAC  121.01  3.000
 2V4  CAW  CAX  CAR  120.85  3.000
 2V4  CAR  CAX  CAS  121.63  3.000
 2V4  CAW  CAX  CAS  116.91  3.000
 2V4  CAQ  CAR  CAN  117.51  3.000
 2V4  CAN  CAR  CAX  122.92  3.000
 2V4  CAQ  CAR  CAX  119.03  3.000
 2V4  CAL  CAN  OAB  120.66  3.000
 2V4  CAL  CAN  CAR  117.75  3.000
 2V4  OAB  CAN  CAR  121.34  3.000
 2V4  H2   CAL  H1   105.53  3.000
 2V4  H2   CAL  CAY  110.13  3.000
 2V4  H1   CAL  CAY  110.74  3.000
 2V4  H2   CAL  CAN  106.96  3.000
 2V4  H1   CAL  CAN  108.19  3.000
 2V4  CAY  CAL  CAN  114.83  3.000
 2V4  CAM  CAY  OAG  105.65  3.000
 2V4  OAG  CAY  CAA  110.93  3.000
 2V4  CAM  CAY  CAA  111.00  3.000
 2V4  OAG  CAY  CAL  110.36  3.000
 2V4  CAA  CAY  CAL  110.78  3.000
 2V4  CAM  CAY  CAL  107.96  3.000
 2V4  H5   CAA  H4   108.19  3.000
 2V4  H5   CAA  H3   107.52  3.000
 2V4  H4   CAA  H3   108.07  3.000
 2V4  H5   CAA  CAY  110.87  3.000
 2V4  H4   CAA  CAY  110.55  3.000
 2V4  H3   CAA  CAY  111.51  3.000
 2V4  H6   OAG  CAY  108.50  3.000
 2V4  H8   CAM  H7   106.68  3.000
 2V4  H8   CAM  CAQ  109.81  3.000
 2V4  H7   CAM  CAQ  109.69  3.000
 2V4  H8   CAM  CAY  109.26  3.000
 2V4  H7   CAM  CAY  110.68  3.000
 2V4  CAQ  CAM  CAY  110.64  3.000
 2V4  CAK  CAQ  CAM  120.07  3.000
 2V4  CAM  CAQ  CAR  119.62  3.000
 2V4  CAK  CAQ  CAR  120.31  3.000
 2V4  H9   CAK  CAP  118.90  3.000
 2V4  H9   CAK  CAQ  120.06  3.000
 2V4  CAP  CAK  CAQ  121.03  3.000
 2V4  CAW  CAP  OAF  122.93  3.000
 2V4  CAW  CAP  CAK  119.19  3.000
 2V4  OAF  CAP  CAK  117.87  3.000
 2V4  H10  OAF  CAP  108.42  3.000
 2V4  CAT  CAW  CAP  119.75  3.000
 2V4  CAP  CAW  CAX  119.26  3.000
 2V4  CAT  CAW  CAX  120.86  3.000
 2V4  CAV  CAT  OAD  120.33  3.000
 2V4  OAD  CAT  CAW  120.07  3.000
 2V4  CAV  CAT  CAW  119.52  3.000
 2V4  CAO  CAV  CAU  119.41  3.000
 2V4  CAU  CAV  CAT  119.89  3.000
 2V4  CAO  CAV  CAT  120.70  3.000
 2V4  CAJ  CAU  CAV  121.02  3.000
 2V4  CAJ  CAU  CAS  119.67  3.000
 2V4  CAV  CAU  CAS  119.21  3.000
 2V4  H11  CAJ  CAH  120.37  3.000
 2V4  H11  CAJ  CAU  120.61  3.000
 2V4  CAH  CAJ  CAU  119.02  3.000
 2V4  H12  CAH  CAI  119.22  3.000
 2V4  H12  CAH  CAJ  119.67  3.000
 2V4  CAI  CAH  CAJ  121.11  3.000
 2V4  H13  CAI  CAO  119.00  3.000
 2V4  H13  CAI  CAH  120.62  3.000
 2V4  CAO  CAI  CAH  120.38  3.000
 2V4  OAE  CAO  CAI  117.75  3.000
 2V4  CAI  CAO  CAV  119.01  3.000
 2V4  OAE  CAO  CAV  123.23  3.000
 2V4  H14  OAE  CAO  108.75  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
 2V4  CONST_01  CAK  CAP  CAW  CAX     0.00   0.0  0
 2V4  CONST_02  CAK  CAQ  CAR  CAX     0.00   0.0  0
 2V4  CONST_03  CAP  CAW  CAX  CAR     0.00   0.0  0
 2V4  CONST_04  CAP  CAK  CAQ  CAR     0.00   0.0  0
 2V4  CONST_05  CAW  CAP  CAK  CAQ     0.00   0.0  0
 2V4  CONST_06  CAW  CAX  CAR  CAQ     0.00   0.0  0
 2V4  CONST_07  CAH  CAI  CAO  CAV     0.00   0.0  0
 2V4  CONST_08  CAH  CAJ  CAU  CAV     0.00   0.0  0
 2V4  CONST_09  CAI  CAO  CAV  CAU     0.00   0.0  0
 2V4  CONST_10  CAI  CAH  CAJ  CAU     0.00   0.0  0
 2V4  CONST_11  CAO  CAI  CAH  CAJ     0.00   0.0  0
 2V4  CONST_12  CAO  CAV  CAU  CAJ     0.00   0.0  0
 2V4  CONST_13  OAF  CAP  CAW  CAX   180.00   0.0  0
 2V4  CONST_14  OAF  CAP  CAK  CAQ   180.00   0.0  0
 2V4  CONST_15  CAT  CAW  CAP  OAF     0.00   0.0  0
 2V4  CONST_16  OAE  CAO  CAV  CAT     0.00   0.0  0
 2V4  CONST_17  OAE  CAO  CAV  CAU   180.00   0.0  0
 2V4  CONST_18  OAE  CAO  CAI  CAH   180.00   0.0  0
 2V4  CONST_19  H11  CAJ  CAU  CAS     0.00   0.0  0
 2V4  CONST_20  H9   CAK  CAQ  CAR   180.00   0.0  0
 2V4  CONST_21  H13  CAI  CAO  CAV   180.00   0.0  0
 2V4  CONST_22  H12  CAH  CAJ  CAU   180.00   0.0  0
 2V4  Var_01    CAL  CAN  CAR  CAX  -159.74  30.0  1
 2V4  Var_02    CAY  CAM  CAQ  CAR   -33.69  30.0  1
 2V4  Var_03    CAY  CAL  CAN  CAR     1.74  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
 2V4  chir_01  CAY  CAL  CAM  OAG  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
 2V4  plan-1  CAR  0.020
 2V4  plan-1  CAN  0.020
 2V4  plan-1  OAB  0.020
 2V4  plan-1  CAL  0.020
 2V4  plan-2  OAC  0.020
 2V4  plan-2  CAS  0.020
 2V4  plan-2  CAX  0.020
 2V4  plan-2  CAR  0.020
 2V4  plan-2  CAN  0.020
 2V4  plan-2  CAM  0.020
 2V4  plan-2  CAQ  0.020
 2V4  plan-2  CAK  0.020
 2V4  plan-2  CAP  0.020
 2V4  plan-2  OAF  0.020
 2V4  plan-2  CAW  0.020
 2V4  plan-2  CAT  0.020
 2V4  plan-2  OAD  0.020
 2V4  plan-2  CAV  0.020
 2V4  plan-2  CAU  0.020
 2V4  plan-2  CAJ  0.020
 2V4  plan-2  CAH  0.020
 2V4  plan-2  CAI  0.020
 2V4  plan-2  CAO  0.020
 2V4  plan-2  OAE  0.020
 2V4  plan-2  H9   0.020
 2V4  plan-2  H11  0.020
 2V4  plan-2  H12  0.020
 2V4  plan-2  H13  0.020

