# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 22:58:39 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: methyl (1~{R},2~{R},4~{S})-2-methyl-2,4,5,7,10-pentakis(oxidanyl)-6,11-bis(oxidanylidene)-3,4-dihydro-1~{H}-tetracene-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H]1c2cc3C(=O)c4c(O)ccc(O)c4C(=O)c3c(O)c2[C@@H](O)C[C@@]1(C)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
 5VD  5VD  'methyl (1~{R},2~{R},4~{S})-2-methyl-2,4,5,7,10-pentakis(oxidanyl)-6,11-bis(oxidanylidene)-3,4-dihydro-1~{H}-tetracene-1-carboxylate'  ligand  48  30  .  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_5VD
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
 5VD  C1   C  CR6   0   0.361   4.7194   0.8501   0.2983
 5VD  C2   C  CR16  0  -0.312   5.7602  -0.1013   0.2672
 5VD  O14  O  OH1   0  -0.669  -5.4077   0.0005  -0.1833
 5VD  C3   C  CR16  0  -0.312   5.4956  -1.4300   0.1028
 5VD  C8   C  CR6   0   0.387  -0.1184   1.8266   0.0286
 5VD  C4   C  CR6   0   0.363   4.1714  -1.8935  -0.0407
 5VD  C5   C  CR16  0  -0.363  -0.6409  -0.8832  -0.2298
 5VD  C6   C  CR6   0   0.145  -1.7035   0.0283  -0.2174
 5VD  C7   C  CR6   0  -0.070  -1.4468   1.3905  -0.1427
 5VD  C10  C  CH2   0  -0.498  -3.8898   1.8373  -0.5549
 5VD  CG   C  CR6   0   0.468   2.3154   1.3775   0.1867
 5VD  CD1  C  CR66  0  -0.179   0.9457   0.9131   0.0319
 5VD  CE1  C  CR66  0  -0.001   0.6614  -0.4527  -0.1223
 5VD  CZ   C  CR6   0   0.385   1.7557  -1.4434  -0.1566
 5VD  CE2  C  CR66  0  -0.204   3.1257  -0.9710  -0.0124
 5VD  CD2  C  CR66  0  -0.175   3.4016   0.4131   0.1584
 5VD  C9   C  CH1   0   0.001  -2.5391   2.4448  -0.2174
 5VD  C11  C  CT    0   0.226  -4.1515   0.5307   0.1842
 5VD  C12  C  CH1   0  -0.427  -3.1184  -0.4844  -0.3511
 5VD  O16  O  O     0  -0.533   2.5527   2.5917   0.3374
 5VD  O17  O  O     0  -0.451   1.5050  -2.6390  -0.3053
 5VD  O18  O  OH1   0  -0.611   5.0693   2.1198   0.4617
 5VD  O19  O  OH1   0  -0.613   3.9955  -3.1989  -0.1969
 5VD  C13  C  CH3   0  -0.696  -4.0871   0.7379   1.6963
 5VD  C14  C  C     0   0.592  -3.3107  -1.8305   0.3195
 5VD  O20  O  O     0  -0.438  -2.9195  -2.0996   1.4274
 5VD  O21  O  O2    0  -0.440  -3.9748  -2.6736  -0.4505
 5VD  C22  C  CH3   0  -0.428  -4.2760  -3.9617   0.0906
 5VD  O1   O  OH1   0  -0.665  -2.2708   3.4061  -1.2153
 5VD  O2   O  OH1   0  -0.628   0.0766   3.1301   0.1969
 5VD  H1   H  HCR6  0   0.295   6.7816   0.2397   0.3776
 5VD  H2   H  HOH1  0   0.452  -6.0956   0.5666   0.1839
 5VD  H3   H  HCR6  0   0.296   6.3056  -2.1475   0.0814
 5VD  H4   H  HCR6  0   0.268  -0.8274  -1.9422  -0.3404
 5VD  H5   H  HCH2  0   0.261  -4.6740   2.5615  -0.3161
 5VD  H6   H  HCH2  0   0.254  -3.9384   1.6495  -1.6320
 5VD  H7   H  HCH1  0   0.240  -2.6024   2.9276   0.7675
 5VD  H8   H  HCH1  0   0.314  -3.3246  -0.6055  -1.4205
 5VD  H9   H  HOH1  0   0.490   4.2541   2.6659   0.4684
 5VD  H10  H  HOH1  0   0.486   3.0287  -3.3621  -0.2850
 5VD  H11  H  HCH3  0   0.243  -4.7294   1.5766   1.9743
 5VD  H12  H  HCH3  0   0.254  -4.4350  -0.1401   2.2376
 5VD  H13  H  HCH3  0   0.238  -3.0827   0.9675   2.0517
 5VD  H14  H  HCH3  0   0.242  -4.9265  -3.8819   0.9611
 5VD  H15  H  HCH3  0   0.255  -4.7911  -4.5021  -0.6975
 5VD  H16  H  HCH3  0   0.242  -3.3696  -4.4995   0.3666
 5VD  H17  H  HOH1  0   0.458  -1.5416   3.9568  -0.9124
 5VD  H18  H  HOH1  0   0.496   1.0456   3.2898   0.2917

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
 5VD  O19  C4   single    1.326  0.020  1.326
 5VD  C3   C4   aromatic  1.410  0.020  1.410
 5VD  C3   C2   aromatic  1.365  0.020  1.365
 5VD  C4   CE2  aromatic  1.395  0.020  1.395
 5VD  C2   C1   aromatic  1.410  0.020  1.410
 5VD  O17  CZ   double    1.231  0.020  1.231
 5VD  CE2  CZ   single    1.456  0.020  1.456
 5VD  CE2  CD2  aromatic  1.422  0.020  1.422
 5VD  C1   CD2  aromatic  1.395  0.020  1.395
 5VD  C1   O18  single    1.327  0.020  1.327
 5VD  CZ   CE1  single    1.477  0.020  1.477
 5VD  CD2  CG   single    1.453  0.020  1.453
 5VD  CE1  C5   aromatic  1.376  0.020  1.376
 5VD  CE1  CD1  aromatic  1.404  0.020  1.404
 5VD  C22  O21  single    1.429  0.020  1.429
 5VD  CG   CD1  single    1.454  0.020  1.454
 5VD  CG   O16  double    1.246  0.020  1.246
 5VD  C5   C6   aromatic  1.400  0.020  1.400
 5VD  CD1  C8   aromatic  1.402  0.020  1.402
 5VD  O21  C14  single    1.321  0.020  1.321
 5VD  O20  C14  double    1.205  0.020  1.205
 5VD  C14  C12  single    1.516  0.020  1.516
 5VD  C6   C12  single    1.511  0.020  1.511
 5VD  C6   C7   aromatic  1.388  0.020  1.388
 5VD  C12  C11  single    1.544  0.020  1.544
 5VD  C8   C7   aromatic  1.409  0.020  1.409
 5VD  C8   O2   single    1.329  0.020  1.329
 5VD  C7   C9   single    1.520  0.020  1.520
 5VD  C11  C13  single    1.528  0.020  1.528
 5VD  C11  C10  single    1.524  0.020  1.524
 5VD  C11  O14  single    1.412  0.020  1.412
 5VD  C9   C10  single    1.519  0.020  1.519
 5VD  C9   O1   single    1.411  0.020  1.411
 5VD  C2   H1   single    0.930  0.020  1.080
 5VD  O14  H2   single    0.850  0.020  0.980
 5VD  C3   H3   single    0.930  0.020  1.080
 5VD  C5   H4   single    0.930  0.020  1.080
 5VD  C10  H5   single    0.970  0.020  1.090
 5VD  C10  H6   single    0.970  0.020  1.090
 5VD  C9   H7   single    0.970  0.020  1.090
 5VD  C12  H8   single    0.970  0.020  1.090
 5VD  O18  H9   single    0.850  0.020  0.980
 5VD  O19  H10  single    0.850  0.020  0.980
 5VD  C13  H11  single    0.970  0.020  1.090
 5VD  C13  H12  single    0.970  0.020  1.090
 5VD  C13  H13  single    0.970  0.020  1.090
 5VD  C22  H14  single    0.970  0.020  1.090
 5VD  C22  H15  single    0.970  0.020  1.090
 5VD  C22  H16  single    0.970  0.020  1.090
 5VD  O1   H17  single    0.850  0.020  0.980
 5VD  O2   H18  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
 5VD  O18  C1   CD2  124.12  3.000
 5VD  O18  C1   C2   116.97  3.000
 5VD  CD2  C1   C2   118.91  3.000
 5VD  H1   C2   C3   120.14  3.000
 5VD  H1   C2   C1   118.78  3.000
 5VD  C3   C2   C1   121.08  3.000
 5VD  H2   O14  C11  108.38  3.000
 5VD  H3   C3   C4   118.87  3.000
 5VD  H3   C3   C2   120.18  3.000
 5VD  C4   C3   C2   120.95  3.000
 5VD  O2   C8   CD1  121.83  3.000
 5VD  O2   C8   C7   117.23  3.000
 5VD  CD1  C8   C7   120.94  3.000
 5VD  O19  C4   CE2  123.63  3.000
 5VD  CE2  C4   C3   118.98  3.000
 5VD  O19  C4   C3   117.38  3.000
 5VD  H4   C5   CE1  118.54  3.000
 5VD  H4   C5   C6   120.51  3.000
 5VD  CE1  C5   C6   120.94  3.000
 5VD  C12  C6   C7   120.72  3.000
 5VD  C7   C6   C5   119.93  3.000
 5VD  C12  C6   C5   119.28  3.000
 5VD  C9   C7   C6   123.03  3.000
 5VD  C9   C7   C8   117.97  3.000
 5VD  C6   C7   C8   118.99  3.000
 5VD  H6   C10  H5   107.26  3.000
 5VD  H6   C10  C11  108.82  3.000
 5VD  H5   C10  C11  109.80  3.000
 5VD  H6   C10  C9   109.07  3.000
 5VD  H5   C10  C9   108.91  3.000
 5VD  C11  C10  C9   112.82  3.000
 5VD  O16  CG   CD2  120.45  3.000
 5VD  O16  CG   CD1  120.21  3.000
 5VD  CD2  CG   CD1  119.34  3.000
 5VD  CE1  CD1  CG   120.87  3.000
 5VD  CG   CD1  C8   120.45  3.000
 5VD  CE1  CD1  C8   118.67  3.000
 5VD  CZ   CE1  CD1  120.35  3.000
 5VD  CD1  CE1  C5   120.32  3.000
 5VD  CZ   CE1  C5   119.33  3.000
 5VD  O17  CZ   CE2  121.25  3.000
 5VD  CE2  CZ   CE1  118.51  3.000
 5VD  O17  CZ   CE1  120.24  3.000
 5VD  CD2  CE2  CZ   120.68  3.000
 5VD  CD2  CE2  C4   120.06  3.000
 5VD  CZ   CE2  C4   119.26  3.000
 5VD  CE2  CD2  CG   120.23  3.000
 5VD  CG   CD2  C1   119.75  3.000
 5VD  CE2  CD2  C1   120.01  3.000
 5VD  H7   C9   O1   110.21  3.000
 5VD  H7   C9   C10  108.89  3.000
 5VD  O1   C9   C10  106.52  3.000
 5VD  H7   C9   C7   107.59  3.000
 5VD  O1   C9   C7   111.75  3.000
 5VD  C10  C9   C7   111.87  3.000
 5VD  C13  C11  C12  113.83  3.000
 5VD  C13  C11  C10  110.89  3.000
 5VD  C12  C11  C10  106.30  3.000
 5VD  C10  C11  O14  110.39  3.000
 5VD  C13  C11  O14  110.25  3.000
 5VD  C12  C11  O14  104.96  3.000
 5VD  H8   C12  C14  108.03  3.000
 5VD  H8   C12  C11  106.57  3.000
 5VD  C14  C12  C11  110.21  3.000
 5VD  H8   C12  C6   107.46  3.000
 5VD  C11  C12  C6   111.89  3.000
 5VD  C14  C12  C6   112.39  3.000
 5VD  H9   O18  C1   108.32  3.000
 5VD  H10  O19  C4   107.69  3.000
 5VD  H13  C13  H12  107.60  3.000
 5VD  H13  C13  H11  107.28  3.000
 5VD  H12  C13  H11  107.74  3.000
 5VD  H13  C13  C11  112.97  3.000
 5VD  H12  C13  C11  111.68  3.000
 5VD  H11  C13  C11  109.34  3.000
 5VD  O21  C14  O20  123.82  3.000
 5VD  O20  C14  C12  124.30  3.000
 5VD  O21  C14  C12  111.88  3.000
 5VD  C22  O21  C14  117.42  3.000
 5VD  H16  C22  H15  109.45  3.000
 5VD  H16  C22  H14  109.30  3.000
 5VD  H15  C22  H14  109.46  3.000
 5VD  H16  C22  O21  111.44  3.000
 5VD  H15  C22  O21  105.89  3.000
 5VD  H14  C22  O21  111.24  3.000
 5VD  H17  O1   C9   108.13  3.000
 5VD  H18  O2   C8   108.37  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
 5VD  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 5VD  CONST_02  C4   CE2  CD2  C1     0.00   0.0  0
 5VD  CONST_03  CE2  C4   C3   C2     0.00   0.0  0
 5VD  CONST_04  CE2  CD2  C1   C2     0.00   0.0  0
 5VD  CONST_05  CD2  CE2  C4   C3     0.00   0.0  0
 5VD  CONST_06  CD2  C1   C2   C3     0.00   0.0  0
 5VD  CONST_07  C5   CE1  CD1  C8     0.00   0.0  0
 5VD  CONST_08  C5   C6   C7   C8     0.00   0.0  0
 5VD  CONST_09  CD1  CE1  C5   C6     0.00   0.0  0
 5VD  CONST_10  CD1  C8   C7   C6     0.00   0.0  0
 5VD  CONST_11  CE1  C5   C6   C7     0.00   0.0  0
 5VD  CONST_12  CE1  CD1  C8   C7     0.00   0.0  0
 5VD  CONST_13  O19  C4   C3   C2   180.00   0.0  0
 5VD  CONST_14  O18  C1   C2   C3   180.00   0.0  0
 5VD  CONST_15  O2   C8   C7   C6   180.00   0.0  0
 5VD  CONST_16  O18  C1   CD2  CG     0.00   0.0  0
 5VD  CONST_17  O2   C8   CD1  CG     0.00   0.0  0
 5VD  CONST_18  O2   C8   CD1  CE1  180.00   0.0  0
 5VD  CONST_19  O19  C4   CE2  CZ     0.00   0.0  0
 5VD  CONST_20  O18  C1   CD2  CE2  180.00   0.0  0
 5VD  CONST_21  O19  C4   CE2  CD2  180.00   0.0  0
 5VD  CONST_22  O2   C8   C7   C9     0.00   0.0  0
 5VD  CONST_23  H3   C3   C2   C1   180.00   0.0  0
 5VD  CONST_24  H1   C2   C3   C4   180.00   0.0  0
 5VD  CONST_25  H4   C5   C6   C7   180.00   0.0  0
 5VD  Var_01    H14  C22  O21  C14   62.73  30.0  3

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
 5VD  chir_01  C9   C7   C10  O1   positiv
 5VD  chir_02  C11  C12  C13  C10  negativ
 5VD  chir_03  C12  C11  C6   C14  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
 5VD  plan-1  C1   0.020
 5VD  plan-1  C2   0.020
 5VD  plan-1  C3   0.020
 5VD  plan-1  C8   0.020
 5VD  plan-1  C4   0.020
 5VD  plan-1  C5   0.020
 5VD  plan-1  C6   0.020
 5VD  plan-1  C7   0.020
 5VD  plan-1  CG   0.020
 5VD  plan-1  CD1  0.020
 5VD  plan-1  CE1  0.020
 5VD  plan-1  CZ   0.020
 5VD  plan-1  CE2  0.020
 5VD  plan-1  CD2  0.020
 5VD  plan-1  C9   0.020
 5VD  plan-1  C12  0.020
 5VD  plan-1  O16  0.020
 5VD  plan-1  O17  0.020
 5VD  plan-1  O18  0.020
 5VD  plan-1  O19  0.020
 5VD  plan-1  O2   0.020
 5VD  plan-1  H1   0.020
 5VD  plan-1  H3   0.020
 5VD  plan-1  H4   0.020
 5VD  plan-2  C12  0.020
 5VD  plan-2  C14  0.020
 5VD  plan-2  O20  0.020
 5VD  plan-2  O21  0.020

