# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 16:15:48 2022
#   Inital geometry file: a 120 line input string
#   Ligand name: (3~{S})-3-[(9,9-dimethylfluoren-2-yl)methyl]-2-oxidanylidene-pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)c2ccccc2c3ccc(C[C@@H](CC(O)=O)C(=O)C(O)=O)cc13
#
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
 QVZ  QVZ  "3-((9,9-dimethyl-9H-fluoren-2-yl)methyl)-2-oxoglutarate"
  ligand  44  26  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QVZ
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
 QVZ  C10  C  CR16   0  -0.384  19.1471  24.3886  31.9944
 QVZ  C13  C  CR5    0  -0.233  18.3030  24.9903  34.3769
 QVZ  C15  C  CR16   0  -0.257  21.1182  25.7710  37.4942
 QVZ  C17  C  CR16   0  -0.328  18.7884  25.6257  36.8625
 QVZ  C01  C  C      0   0.279  21.1411  25.9926  28.8286
 QVZ  C02  C  CH1    0  -0.338  19.8425  25.2181  28.8327
 QVZ  C04  C  CH2    0  -0.554  18.6446  26.0610  29.2462
 QVZ  C05  C  CR6    0   0.130  20.2421  24.2133  31.1464
 QVZ  C06  C  CR16   0  -0.320  21.5300  24.3430  31.6730
 QVZ  C07  C  CR16   0  -0.338  21.7395  24.6501  33.0123
 QVZ  C08  C  CR56   0   0.083  20.6386  24.8410  33.8357
 QVZ  C09  C  CR56   0   0.146  19.3477  24.7096  33.3207
 QVZ  C11  C  CR56   0   0.103  20.5324  25.1971  35.2490
 QVZ  C12  C  CR56   0   0.124  19.1751  25.2920  35.5778
 QVZ  C14  C  CR16   0  -0.351  21.5116  25.4350  36.2041
 QVZ  C16  C  CR16   0  -0.259  19.7689  25.8654  37.8222
 QVZ  C18  C  CH3    0  -0.626  17.4467  26.1993  33.9829
 QVZ  C19  C  CH3    0  -0.627  17.4134  23.7692  34.6245
 QVZ  O02  O  OC    -1  -0.581  23.4477  25.4472  28.8587
 QVZ  O03  O  O      0  -0.578  22.1805  24.6545  27.1880
 QVZ  O04  O  O      0  -0.603  17.1285  24.6733  28.0460
 QVZ  O05  O  OC    -1  -0.611  16.4458  25.5082  29.9948
 QVZ  H08  H  HCR6   0   0.245  18.1426  24.3030  31.5958
 QVZ  H10  H  HCR6   0   0.251  21.8679  25.9607  38.2517
 QVZ  H12  H  HCR6   0   0.246  17.7396  25.7022  37.1254
 QVZ  H01  H  HCH1   0   0.253  19.6849  24.8696  27.8086
 QVZ  H02  H  HCH2   0   0.255  19.1246  23.3286  29.5569
 QVZ  H03  H  HCH2   0   0.255  20.8486  23.3531  29.2825
 QVZ  H04  H  HCH2   0   0.210  18.7587  26.4300  30.2668
 QVZ  H05  H  HCH2   0   0.231  18.6154  26.9520  28.6082
 QVZ  H06  H  HCR6   0   0.245  22.3847  24.2153  31.0196
 QVZ  H07  H  HCR6   0   0.240  22.7487  24.7457  33.3954
 QVZ  H09  H  HCR6   0   0.245  22.5634  25.3626  35.9541
 QVZ  H11  H  HCR6   0   0.250  19.4797  26.1281  38.8317
 QVZ  H14  H  HCH3   0   0.234  16.7180  26.4259  34.7625
 QVZ  H13  H  HCH3   0   0.231  18.0626  27.0852  33.8236
 QVZ  H15  H  HCH3   0   0.231  16.9015  25.9972  33.0590
 QVZ  H18  H  HCH3   0   0.234  16.6994  23.9680  35.4255
 QVZ  H16  H  HCH3   0   0.235  16.8450  23.5189  33.7270
 QVZ  H17  H  HCH3   0   0.231  18.0049  22.8975  34.9062
 QVZ  C03  C  CH2    0  -0.545  20.0201  23.9393  29.6856
 QVZ  C20  C  C      0   0.344  22.3848  25.2873  28.2384
 QVZ  C21  C  C      0   0.411  17.2903  25.3417  29.0877
 QVZ  O01  O  O      0  -0.408  21.2257  27.1302  29.2390

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
 QVZ  O03  C20  deloc     1.243  0.020  1.243
 QVZ  O04  C21  deloc     1.248  0.020  1.248
 QVZ  C20  O02  deloc     1.241  0.020  1.241
 QVZ  C20  C01  single    1.547  0.020  1.547
 QVZ  C02  C01  single    1.512  0.020  1.512
 QVZ  C02  C04  single    1.522  0.020  1.522
 QVZ  C02  C03  single    1.547  0.020  1.547
 QVZ  C21  C04  single    1.542  0.020  1.542
 QVZ  C21  O05  deloc     1.250  0.020  1.250
 QVZ  C01  O01  double    1.212  0.020  1.212
 QVZ  C03  C05  single    1.503  0.020  1.503
 QVZ  C05  C06  aromatic  1.397  0.020  1.397
 QVZ  C05  C10  aromatic  1.396  0.020  1.396
 QVZ  C06  C07  aromatic  1.390  0.020  1.390
 QVZ  C10  C09  aromatic  1.379  0.020  1.379
 QVZ  C07  C08  aromatic  1.388  0.020  1.388
 QVZ  C09  C08  aromatic  1.396  0.020  1.396
 QVZ  C09  C13  single    1.512  0.020  1.512
 QVZ  C08  C11  aromatic  1.461  0.020  1.461
 QVZ  C18  C13  single    1.533  0.020  1.533
 QVZ  C13  C19  single    1.531  0.020  1.531
 QVZ  C13  C12  single    1.515  0.020  1.515
 QVZ  C11  C12  aromatic  1.400  0.020  1.400
 QVZ  C11  C14  aromatic  1.388  0.020  1.388
 QVZ  C12  C17  aromatic  1.383  0.020  1.383
 QVZ  C14  C15  aromatic  1.390  0.020  1.390
 QVZ  C17  C16  aromatic  1.393  0.020  1.393
 QVZ  C15  C16  aromatic  1.392  0.020  1.392
 QVZ  C10  H08  single    0.930  0.020  1.080
 QVZ  C15  H10  single    0.930  0.020  1.080
 QVZ  C17  H12  single    0.930  0.020  1.080
 QVZ  C02  H01  single    0.970  0.020  1.090
 QVZ  C03  H02  single    0.970  0.020  1.090
 QVZ  C03  H03  single    0.970  0.020  1.090
 QVZ  C04  H04  single    0.970  0.020  1.090
 QVZ  C04  H05  single    0.970  0.020  1.090
 QVZ  C06  H06  single    0.930  0.020  1.080
 QVZ  C07  H07  single    0.930  0.020  1.080
 QVZ  C14  H09  single    0.930  0.020  1.080
 QVZ  C16  H11  single    0.930  0.020  1.080
 QVZ  C18  H14  single    0.970  0.020  1.090
 QVZ  C18  H13  single    0.970  0.020  1.090
 QVZ  C18  H15  single    0.970  0.020  1.090
 QVZ  C19  H18  single    0.970  0.020  1.090
 QVZ  C19  H16  single    0.970  0.020  1.090
 QVZ  C19  H17  single    0.970  0.020  1.090

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
 QVZ  H08  C10  C09  120.44  3.000
 QVZ  H08  C10  C05  119.58  3.000
 QVZ  C09  C10  C05  119.95  3.000
 QVZ  C19  C13  C18  110.24  3.000
 QVZ  C19  C13  C12  111.43  3.000
 QVZ  C18  C13  C12  111.61  3.000
 QVZ  C12  C13  C09  101.13  3.000
 QVZ  C19  C13  C09  111.49  3.000
 QVZ  C18  C13  C09  110.66  3.000
 QVZ  H10  C15  C16  119.65  3.000
 QVZ  H10  C15  C14  119.72  3.000
 QVZ  C16  C15  C14  120.63  3.000
 QVZ  H12  C17  C16  120.12  3.000
 QVZ  H12  C17  C12  120.87  3.000
 QVZ  C16  C17  C12  119.01  3.000
 QVZ  O01  C01  C02  122.66  3.000
 QVZ  O01  C01  C20  120.06  3.000
 QVZ  C02  C01  C20  117.26  3.000
 QVZ  H01  C02  C04  108.52  3.000
 QVZ  H01  C02  C03  105.63  3.000
 QVZ  C04  C02  C03  113.47  3.000
 QVZ  H01  C02  C01  106.54  3.000
 QVZ  C03  C02  C01  109.04  3.000
 QVZ  C04  C02  C01  113.15  3.000
 QVZ  H05  C04  H04  105.79  3.000
 QVZ  H05  C04  C02  108.24  3.000
 QVZ  H04  C04  C02  111.04  3.000
 QVZ  H05  C04  C21  107.22  3.000
 QVZ  H04  C04  C21  110.23  3.000
 QVZ  C02  C04  C21  113.90  3.000
 QVZ  C06  C05  C03  121.29  3.000
 QVZ  C06  C05  C10  118.84  3.000
 QVZ  C03  C05  C10  119.83  3.000
 QVZ  H06  C06  C07  119.22  3.000
 QVZ  H06  C06  C05  119.26  3.000
 QVZ  C07  C06  C05  121.51  3.000
 QVZ  H07  C07  C08  121.12  3.000
 QVZ  H07  C07  C06  120.03  3.000
 QVZ  C08  C07  C06  118.84  3.000
 QVZ  C11  C08  C09  108.21  3.000
 QVZ  C11  C08  C07  131.68  3.000
 QVZ  C09  C08  C07  120.11  3.000
 QVZ  C08  C09  C13  111.33  3.000
 QVZ  C13  C09  C10  127.92  3.000
 QVZ  C08  C09  C10  120.74  3.000
 QVZ  C14  C11  C12  120.71  3.000
 QVZ  C14  C11  C08  130.98  3.000
 QVZ  C12  C11  C08  108.31  3.000
 QVZ  C11  C12  C17  120.39  3.000
 QVZ  C17  C12  C13  128.59  3.000
 QVZ  C11  C12  C13  111.01  3.000
 QVZ  H09  C14  C11  120.96  3.000
 QVZ  H09  C14  C15  120.34  3.000
 QVZ  C11  C14  C15  118.70  3.000
 QVZ  H11  C16  C17  119.76  3.000
 QVZ  H11  C16  C15  119.68  3.000
 QVZ  C17  C16  C15  120.56  3.000
 QVZ  H15  C18  H13  107.99  3.000
 QVZ  H15  C18  H14  108.03  3.000
 QVZ  H13  C18  H14  108.23  3.000
 QVZ  H15  C18  C13  110.52  3.000
 QVZ  H13  C18  C13  111.27  3.000
 QVZ  H14  C18  C13  110.68  3.000
 QVZ  H17  C19  H16  108.16  3.000
 QVZ  H17  C19  H18  108.11  3.000
 QVZ  H16  C19  H18  107.74  3.000
 QVZ  H17  C19  C13  111.36  3.000
 QVZ  H16  C19  C13  110.65  3.000
 QVZ  H18  C19  C13  110.70  3.000
 QVZ  H03  C03  H02  106.17  3.000
 QVZ  H03  C03  C05  110.16  3.000
 QVZ  H02  C03  C05  109.75  3.000
 QVZ  H03  C03  C02  109.10  3.000
 QVZ  H02  C03  C02  107.65  3.000
 QVZ  C05  C03  C02  113.71  3.000
 QVZ  O03  C20  O02  128.95  3.000
 QVZ  O02  C20  C01  116.05  3.000
 QVZ  O03  C20  C01  114.98  3.000
 QVZ  O05  C21  O04  126.10  3.000
 QVZ  O05  C21  C04  117.17  3.000
 QVZ  O04  C21  C04  116.71  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
 QVZ  CONST_01  C07  C06  C05  C10     0.00   0.0  0
 QVZ  CONST_02  C07  C08  C09  C10     0.00   0.0  0
 QVZ  CONST_03  C11  C08  C09  C10   180.00   0.0  0
 QVZ  CONST_04  C12  C13  C09  C10   180.00   0.0  0
 QVZ  CONST_05  C08  C11  C14  C15   180.00   0.0  0
 QVZ  CONST_06  C12  C11  C14  C15     0.00   0.0  0
 QVZ  CONST_07  C12  C17  C16  C15     0.00   0.0  0
 QVZ  CONST_08  C09  C13  C12  C17   180.00   0.0  0
 QVZ  CONST_09  C08  C11  C12  C17   180.00   0.0  0
 QVZ  CONST_10  C14  C11  C12  C17     0.00   0.0  0
 QVZ  CONST_11  C14  C15  C16  C17     0.00   0.0  0
 QVZ  CONST_12  C08  C07  C06  C05     0.00   0.0  0
 QVZ  CONST_13  C08  C09  C10  C05     0.00   0.0  0
 QVZ  CONST_14  C09  C10  C05  C06     0.00   0.0  0
 QVZ  CONST_15  C09  C08  C07  C06     0.00   0.0  0
 QVZ  CONST_16  C11  C08  C07  C06   180.00   0.0  0
 QVZ  CONST_17  C12  C11  C08  C07   180.00   0.0  0
 QVZ  CONST_18  C14  C11  C08  C07     0.00   0.0  0
 QVZ  CONST_19  C12  C13  C09  C08     0.00   0.0  0
 QVZ  CONST_20  C12  C11  C08  C09     0.00   0.0  0
 QVZ  CONST_21  C14  C11  C08  C09   180.00   0.0  0
 QVZ  CONST_22  C11  C12  C13  C09     0.00   0.0  0
 QVZ  CONST_23  C16  C17  C12  C11     0.00   0.0  0
 QVZ  CONST_24  C16  C15  C14  C11     0.00   0.0  0
 QVZ  CONST_25  C07  C06  C05  C03   180.00   0.0  0
 QVZ  CONST_26  C09  C10  C05  C03   180.00   0.0  0
 QVZ  CONST_27  H06  C06  C05  C10   180.00   0.0  0
 QVZ  CONST_28  H08  C10  C09  C13     0.00   0.0  0
 QVZ  CONST_29  H12  C17  C12  C13     0.00   0.0  0
 QVZ  CONST_30  H12  C17  C16  C15   180.00   0.0  0
 QVZ  CONST_31  H10  C15  C16  C17   180.00   0.0  0
 QVZ  CONST_32  H07  C07  C06  C05   180.00   0.0  0
 QVZ  CONST_33  H08  C10  C05  C06   180.00   0.0  0
 QVZ  CONST_34  H06  C06  C07  C08   180.00   0.0  0
 QVZ  CONST_35  H08  C10  C09  C08   180.00   0.0  0
 QVZ  CONST_36  H09  C14  C11  C08     0.00   0.0  0
 QVZ  CONST_37  H07  C07  C08  C09   180.00   0.0  0
 QVZ  CONST_38  H07  C07  C08  C11     0.00   0.0  0
 QVZ  CONST_39  H12  C17  C12  C11   180.00   0.0  0
 QVZ  CONST_40  H10  C15  C14  C11   180.00   0.0  0
 QVZ  CONST_41  H09  C14  C11  C12   180.00   0.0  0
 QVZ  CONST_42  H11  C16  C17  C12   180.00   0.0  0
 QVZ  CONST_43  H11  C16  C15  C14   180.00   0.0  0
 QVZ  CONST_44  H09  C14  C15  C16   180.00   0.0  0
 QVZ  Var_01    C18  C13  C09  C10   -60.66  30.0  1
 QVZ  Var_02    C19  C13  C09  C10    62.42  30.0  1
 QVZ  Var_03    C18  C13  C12  C17    62.32  30.0  1
 QVZ  Var_04    C19  C13  C12  C17   -61.41  30.0  1
 QVZ  Var_05    C18  C13  C09  C08   117.97  30.0  1
 QVZ  Var_06    C19  C13  C09  C08  -118.94  30.0  1
 QVZ  Var_07    C18  C13  C12  C11  -117.64  30.0  1
 QVZ  Var_08    C19  C13  C12  C11   118.63  30.0  1
 QVZ  Var_09    C02  C03  C05  C10    85.74  30.0  2
 QVZ  Var_10    C06  C05  C03  C02   -92.05  30.0  2
 QVZ  Var_11    H02  C03  C05  C10   -34.89  30.0  2
 QVZ  Var_12    H03  C03  C05  C10  -151.44  30.0  2
 QVZ  Var_13    H02  C03  C05  C06   147.32  30.0  2
 QVZ  Var_14    H03  C03  C05  C06    30.76  30.0  2
 QVZ  Var_15    H14  C18  C13  C09  -177.82  30.0  3
 QVZ  Var_16    H13  C18  C13  C09   -57.43  30.0  3
 QVZ  Var_17    H15  C18  C13  C09    62.54  30.0  3
 QVZ  Var_18    H18  C19  C13  C09   176.97  30.0  3
 QVZ  Var_19    H16  C19  C13  C09   -63.66  30.0  3
 QVZ  Var_20    H17  C19  C13  C09    56.67  30.0  3
 QVZ  Var_21    H14  C18  C13  C12   -66.02  30.0  3
 QVZ  Var_22    H13  C18  C13  C12    54.36  30.0  3
 QVZ  Var_23    H15  C18  C13  C12   174.33  30.0  3
 QVZ  Var_24    H18  C19  C13  C12    64.80  30.0  3
 QVZ  Var_25    H16  C19  C13  C12  -175.83  30.0  3
 QVZ  Var_26    H17  C19  C13  C12   -55.50  30.0  3
 QVZ  Var_27    H18  C19  C13  C18   -59.70  30.0  3
 QVZ  Var_28    H16  C19  C13  C18    59.67  30.0  3
 QVZ  Var_29    H17  C19  C13  C18   179.99  30.0  3
 QVZ  Var_30    H14  C18  C13  C19    58.37  30.0  3
 QVZ  Var_31    H13  C18  C13  C19   178.76  30.0  3
 QVZ  Var_32    H15  C18  C13  C19   -61.27  30.0  3
 QVZ  Var_33    O03  C20  C01  C02    42.61  30.0  3
 QVZ  Var_34    O02  C20  C01  C02  -138.60  30.0  3
 QVZ  Var_35    O04  C21  C04  C02   -42.37  30.0  2
 QVZ  Var_36    O05  C21  C04  C02   139.38  30.0  2
 QVZ  Var_37    O03  C20  C01  O01  -135.92  30.0  3
 QVZ  Var_38    O02  C20  C01  O01    42.87  30.0  3
 QVZ  Var_39    H04  C04  C21  O04  -167.96  30.0  3
 QVZ  Var_40    H05  C04  C21  O04    77.34  30.0  3
 QVZ  Var_41    H04  C04  C21  O05    13.79  30.0  3
 QVZ  Var_42    H05  C04  C21  O05  -100.91  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
 QVZ  chir_01  C02  C01  C04  C03  positiv

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
 QVZ  plan-1  C01  0.020
 QVZ  plan-1  C02  0.020
 QVZ  plan-1  C20  0.020
 QVZ  plan-1  O01  0.020
 QVZ  plan-2  C10  0.020
 QVZ  plan-2  C13  0.020
 QVZ  plan-2  C15  0.020
 QVZ  plan-2  C17  0.020
 QVZ  plan-2  C05  0.020
 QVZ  plan-2  C06  0.020
 QVZ  plan-2  C07  0.020
 QVZ  plan-2  C08  0.020
 QVZ  plan-2  C09  0.020
 QVZ  plan-2  C11  0.020
 QVZ  plan-2  C12  0.020
 QVZ  plan-2  C14  0.020
 QVZ  plan-2  C16  0.020
 QVZ  plan-2  H08  0.020
 QVZ  plan-2  H10  0.020
 QVZ  plan-2  H12  0.020
 QVZ  plan-2  H06  0.020
 QVZ  plan-2  H07  0.020
 QVZ  plan-2  H09  0.020
 QVZ  plan-2  H11  0.020
 QVZ  plan-2  C03  0.020
 QVZ  plan-3  C01  0.020
 QVZ  plan-3  O02  0.020
 QVZ  plan-3  O03  0.020
 QVZ  plan-3  C20  0.020
 QVZ  plan-4  C04  0.020
 QVZ  plan-4  O04  0.020
 QVZ  plan-4  O05  0.020
 QVZ  plan-4  C21  0.020

