# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 19:53:13 2021
#   Inital geometry file: a 161 line input string
#   Ligand name: (5beta,14beta,17alpha,25R)-3-oxocholest-7-en-26-oic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CCC[C@@H](C)C(O)=O)[C@H]1CC[C@H]2C3=CC[C@H]4CC(=O)CC[C@]4(C)[C@H]3CC[C@]12C
#
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
 DL7  DL7  '(5beta,14beta,17alpha,25R)-3-oxocholest-7-en-26-oic acid'  ligand  72  30  .  2021-08-08  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DL7
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
 DL7  O3    O  O     0  -0.443   -9.2592  -30.9781   2.7040
 DL7  C27   C  C     0   0.549   -8.8583  -31.8037   3.4867
 DL7  O2    O  OH1   0  -0.578   -9.6481  -32.7344   4.0154
 DL7  C25   C  CH1   0  -0.355   -7.4279  -31.8987   3.9607
 DL7  C26   C  CH3   0  -0.639   -7.0074  -30.5701   4.5868
 DL7  C24   C  CH2   0  -0.402   -6.5159  -32.2650   2.7848
 DL7  C23   C  CH2   0  -0.430   -6.8012  -33.6281   2.1645
 DL7  C22   C  CH2   0  -0.393   -5.8486  -33.9356   1.0134
 DL7  C20   C  CH1   0  -0.233   -5.9306  -35.3652   0.4600
 DL7  C21   C  CH3   0  -0.654   -7.3498  -35.6932   0.0081
 DL7  C17   C  CH1   0  -0.164   -4.8832  -35.5493  -0.6484
 DL7  C16   C  CH2   0  -0.438   -3.4416  -35.2710  -0.1448
 DL7  C15   C  CH2   0  -0.440   -2.4911  -36.1829  -0.9440
 DL7  C14   C  CH1   0  -0.251   -3.3849  -36.7684  -2.0257
 DL7  C8    C  CR6   0   0.203   -2.9457  -37.9735  -2.7984
 DL7  C7    C  CR16  0  -0.329   -1.7370  -38.5200  -2.6811
 DL7  C6    C  C     0  -0.429   -1.2273  -39.6027  -3.5772
 DL7  C13   C  CT    0  -0.059   -4.7610  -36.9253  -1.3470
 DL7  C18   C  CH3   0  -0.668   -4.7356  -38.0565  -0.3170
 DL7  C12   C  CH2   0  -0.406   -5.7625  -37.2079  -2.4660
 DL7  C11   C  CH2   0  -0.432   -5.3821  -38.4680  -3.2400
 DL7  C9    C  CR16  0  -0.252   -3.9601  -38.4359  -3.8257
 DL7  C10   C  CR6   0  -0.058   -3.5667  -39.7651  -4.5210
 DL7  C1    C  CH2   0  -0.422   -4.3351  -39.8807  -5.8435
 DL7  C19   C  CH3   0  -0.685   -3.8775  -40.9680  -3.6226
 DL7  C5    C  CR16  0  -0.239   -2.0628  -39.7010  -4.8436
 DL7  C4    C  CH2   0  -0.553   -1.5792  -40.8650  -5.7179
 DL7  C3    C  C     0   0.418   -2.4234  -41.0707  -6.9414
 DL7  O1    O  O     0  -0.442   -1.9485  -41.2301  -8.0505
 DL7  C2    C  CH2   0  -0.566   -3.9021  -41.0747  -6.6984
 DL7  HO2   H  HOH1  0   0.454  -10.5466  -32.6239   3.6738
 DL7  H25   H  HCH1  0   0.251   -7.3580  -32.6844   4.7170
 DL7  H26   H  HCH3  0   0.236   -7.6472  -30.2945   5.4254
 DL7  H26A  H  HCH3  0   0.232   -5.9874  -30.6453   4.9629
 DL7  H26B  H  HCH3  0   0.228   -7.0375  -29.7622   3.8562
 DL7  H24   H  HCH2  0   0.223   -6.5865  -31.4854   2.0199
 DL7  H24A  H  HCH2  0   0.227   -5.4839  -32.2447   3.1473
 DL7  H23   H  HCH2  0   0.212   -6.7143  -34.4036   2.9336
 DL7  H23A  H  HCH2  0   0.220   -7.8344  -33.6630   1.8094
 DL7  H22   H  HCH2  0   0.202   -6.0271  -33.2211   0.2004
 DL7  H22A  H  HCH2  0   0.224   -4.8293  -33.7438   1.3600
 DL7  H20   H  HCH1  0   0.203   -5.6753  -36.0456   1.2835
 DL7  H21   H  HCH3  0   0.230   -8.0726  -35.5193   0.8051
 DL7  H21A  H  HCH3  0   0.206   -7.6505  -35.0830  -0.8471
 DL7  H21B  H  HCH3  0   0.223   -7.4576  -36.7378  -0.2761
 DL7  H17   H  HCH1  0   0.200   -5.1131  -34.8195  -1.4380
 DL7  H16   H  HCH2  0   0.230   -3.1802  -34.2203  -0.2707
 DL7  H16A  H  HCH2  0   0.215   -3.3629  -35.4777   0.9259
 DL7  H15   H  HCH2  0   0.230   -1.6413  -35.6398  -1.3594
 DL7  H15A  H  HCH2  0   0.215   -2.0779  -36.9656  -0.3042
 DL7  H14   H  HCH1  0   0.221   -3.5306  -35.9763  -2.7789
 DL7  H7    H  HCR6  0   0.222   -1.0450  -38.1383  -1.9387
 DL7  H6    H  H     0   0.240   -0.1865  -39.3914  -3.8382
 DL7  H6A   H  H     0   0.224   -1.2020  -40.5661  -3.0530
 DL7  H18   H  HCH3  0   0.232   -4.3139  -38.9770  -0.7225
 DL7  H18A  H  HCH3  0   0.227   -4.1343  -37.7931   0.5542
 DL7  H18B  H  HCH3  0   0.224   -5.7391  -38.2898   0.0438
 DL7  H12   H  HCH2  0   0.231   -6.7783  -37.3336  -2.0898
 DL7  H12A  H  HCH2  0   0.205   -5.7898  -36.3460  -3.1433
 DL7  H11   H  HCH2  0   0.229   -5.4934  -39.3216  -2.5694
 DL7  H11A  H  HCH2  0   0.229   -6.1062  -38.6184  -4.0438
 DL7  H9    H  HCR6  0   0.218   -3.9705  -37.6577  -4.6063
 DL7  H1    H  HCH2  0   0.251   -5.4084  -39.9604  -5.6623
 DL7  H1A   H  HCH2  0   0.228   -4.1929  -38.9654  -6.4278
 DL7  H19   H  HCH3  0   0.217   -3.3958  -41.8859  -3.9621
 DL7  H19A  H  HCH3  0   0.251   -3.5507  -40.8028  -2.5955
 DL7  H19B  H  HCH3  0   0.235   -4.9473  -41.1744  -3.5947
 DL7  H5    H  HCR6  0   0.230   -1.9003  -38.7750  -5.4114
 DL7  H4    H  HCH2  0   0.257   -0.5366  -40.7175  -6.0062
 DL7  H4A   H  HCH2  0   0.254   -1.6116  -41.7965  -5.1402
 DL7  H2    H  HCH2  0   0.259   -4.1556  -42.0077  -6.1823
 DL7  H2A   H  HCH2  0   0.247   -4.4414  -41.0868  -7.6473

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
 DL7  O3   C27   double  1.206  0.020  1.206
 DL7  C27  C25   single  1.510  0.020  1.510
 DL7  C27  O2    single  1.330  0.020  1.330
 DL7  O2   HO2   single  0.850  0.020  0.980
 DL7  C24  C25   single  1.533  0.020  1.533
 DL7  C25  C26   single  1.528  0.020  1.528
 DL7  C25  H25   single  0.970  0.020  1.090
 DL7  C26  H26   single  0.970  0.020  1.090
 DL7  C26  H26A  single  0.970  0.020  1.090
 DL7  C26  H26B  single  0.970  0.020  1.090
 DL7  C23  C24   single  1.524  0.020  1.524
 DL7  C24  H24   single  0.970  0.020  1.090
 DL7  C24  H24A  single  0.970  0.020  1.090
 DL7  C22  C23   single  1.525  0.020  1.525
 DL7  C23  H23   single  0.970  0.020  1.090
 DL7  C23  H23A  single  0.970  0.020  1.090
 DL7  C20  C22   single  1.535  0.020  1.535
 DL7  C22  H22   single  0.970  0.020  1.090
 DL7  C22  H22A  single  0.970  0.020  1.090
 DL7  C17  C20   single  1.536  0.020  1.536
 DL7  C21  C20   single  1.525  0.020  1.525
 DL7  C20  H20   single  0.970  0.020  1.090
 DL7  C21  H21   single  0.970  0.020  1.090
 DL7  C21  H21A  single  0.970  0.020  1.090
 DL7  C21  H21B  single  0.970  0.020  1.090
 DL7  C13  C17   single  1.548  0.020  1.548
 DL7  C17  C16   single  1.552  0.020  1.552
 DL7  C17  H17   single  0.970  0.020  1.090
 DL7  C15  C16   single  1.541  0.020  1.541
 DL7  C16  H16   single  0.970  0.020  1.090
 DL7  C16  H16A  single  0.970  0.020  1.090
 DL7  C14  C15   single  1.521  0.020  1.521
 DL7  C15  H15   single  0.970  0.020  1.090
 DL7  C15  H15A  single  0.970  0.020  1.090
 DL7  C8   C14   single  1.497  0.020  1.497
 DL7  C14  C13   single  1.542  0.020  1.542
 DL7  C14  H14   single  0.970  0.020  1.090
 DL7  C9   C8    single  1.516  0.020  1.516
 DL7  C8   C7    double  1.332  0.020  1.332
 DL7  C6   C7    single  1.495  0.020  1.495
 DL7  C7   H7    single  0.930  0.020  1.080
 DL7  C5   C6    single  1.520  0.020  1.520
 DL7  C6   H6    single  0.970  0.020  1.090
 DL7  C6   H6A   single  0.970  0.020  1.090
 DL7  C12  C13   single  1.528  0.020  1.528
 DL7  C13  C18   single  1.530  0.020  1.530
 DL7  C18  H18   single  0.970  0.020  1.090
 DL7  C18  H18A  single  0.970  0.020  1.090
 DL7  C18  H18B  single  0.970  0.020  1.090
 DL7  C11  C12   single  1.527  0.020  1.527
 DL7  C12  H12   single  0.970  0.020  1.090
 DL7  C12  H12A  single  0.970  0.020  1.090
 DL7  C9   C11   single  1.538  0.020  1.538
 DL7  C11  H11   single  0.970  0.020  1.090
 DL7  C11  H11A  single  0.970  0.020  1.090
 DL7  C10  C9    single  1.551  0.020  1.551
 DL7  C9   H9    single  0.970  0.020  1.090
 DL7  C1   C10   single  1.534  0.020  1.534
 DL7  C5   C10   single  1.540  0.020  1.540
 DL7  C10  C19   single  1.533  0.020  1.533
 DL7  C2   C1    single  1.531  0.020  1.531
 DL7  C1   H1    single  0.970  0.020  1.090
 DL7  C1   H1A   single  0.970  0.020  1.090
 DL7  C19  H19   single  0.970  0.020  1.090
 DL7  C19  H19A  single  0.970  0.020  1.090
 DL7  C19  H19B  single  0.970  0.020  1.090
 DL7  C4   C5    single  1.534  0.020  1.534
 DL7  C5   H5    single  0.970  0.020  1.090
 DL7  C3   C4    single  1.501  0.020  1.501
 DL7  C4   H4    single  0.970  0.020  1.090
 DL7  C4   H4A   single  0.970  0.020  1.090
 DL7  O1   C3    double  1.217  0.020  1.217
 DL7  C3   C2    single  1.499  0.020  1.499
 DL7  C2   H2    single  0.970  0.020  1.090
 DL7  C2   H2A   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
 DL7  C25   C27  O2    113.18  3.000
 DL7  O2    C27  O3    122.65  3.000
 DL7  C25   C27  O3    124.17  3.000
 DL7  HO2   O2   C27   109.34  3.000
 DL7  H25   C25  C24   108.73  3.000
 DL7  H25   C25  C26   108.90  3.000
 DL7  C24   C25  C26   111.01  3.000
 DL7  H25   C25  C27   108.85  3.000
 DL7  C26   C25  C27   109.55  3.000
 DL7  C24   C25  C27   109.75  3.000
 DL7  H26B  C26  H26A  107.96  3.000
 DL7  H26B  C26  H26   108.18  3.000
 DL7  H26A  C26  H26   107.54  3.000
 DL7  H26B  C26  C25   111.24  3.000
 DL7  H26A  C26  C25   109.82  3.000
 DL7  H26   C26  C25   111.93  3.000
 DL7  H24A  C24  H24   106.21  3.000
 DL7  H24A  C24  C23   109.15  3.000
 DL7  H24   C24  C23   109.91  3.000
 DL7  H24A  C24  C25   107.62  3.000
 DL7  H24   C24  C25   109.12  3.000
 DL7  C23   C24  C25   114.49  3.000
 DL7  H23A  C23  H23   106.29  3.000
 DL7  H23A  C23  C22   109.79  3.000
 DL7  H23   C23  C22   109.73  3.000
 DL7  H23A  C23  C24   109.73  3.000
 DL7  H23   C23  C24   109.41  3.000
 DL7  C22   C23  C24   111.74  3.000
 DL7  H22A  C22  H22   105.81  3.000
 DL7  H22A  C22  C20   109.11  3.000
 DL7  H22   C22  C20   109.31  3.000
 DL7  H22A  C22  C23   107.91  3.000
 DL7  H22   C22  C23   109.05  3.000
 DL7  C20   C22  C23   115.23  3.000
 DL7  H20   C20  C17   107.95  3.000
 DL7  H20   C20  C21   107.77  3.000
 DL7  C17   C20  C21   113.26  3.000
 DL7  H20   C20  C22   107.11  3.000
 DL7  C21   C20  C22   110.91  3.000
 DL7  C17   C20  C22   109.59  3.000
 DL7  H21B  C21  H21A  107.73  3.000
 DL7  H21B  C21  H21   106.17  3.000
 DL7  H21A  C21  H21   107.50  3.000
 DL7  H21B  C21  C20   112.09  3.000
 DL7  H21A  C21  C20   111.58  3.000
 DL7  H21   C21  C20   111.47  3.000
 DL7  H17   C17  C13   106.40  3.000
 DL7  H17   C17  C16   107.95  3.000
 DL7  C13   C17  C16   103.44  3.000
 DL7  H17   C17  C20   107.23  3.000
 DL7  C16   C17  C20   112.19  3.000
 DL7  C13   C17  C20   119.08  3.000
 DL7  H16A  C16  H16   106.15  3.000
 DL7  H16A  C16  C15   110.59  3.000
 DL7  H16   C16  C15   111.26  3.000
 DL7  H16A  C16  C17   110.53  3.000
 DL7  H16   C16  C17   110.98  3.000
 DL7  C15   C16  C17   107.37  3.000
 DL7  H15A  C15  H15   106.57  3.000
 DL7  H15A  C15  C14   111.30  3.000
 DL7  H15   C15  C14   112.26  3.000
 DL7  H15A  C15  C16   110.72  3.000
 DL7  H15   C15  C16   112.55  3.000
 DL7  C14   C15  C16   103.55  3.000
 DL7  H14   C14  C13   104.82  3.000
 DL7  H14   C14  C8    105.33  3.000
 DL7  C13   C14  C8    114.01  3.000
 DL7  H14   C14  C15   106.68  3.000
 DL7  C13   C14  C15   104.51  3.000
 DL7  C8    C14  C15   120.31  3.000
 DL7  C9    C8   C7    122.81  3.000
 DL7  C7    C8   C14   123.44  3.000
 DL7  C9    C8   C14   113.51  3.000
 DL7  H7    C7   C6    116.60  3.000
 DL7  H7    C7   C8    119.68  3.000
 DL7  C6    C7   C8    123.63  3.000
 DL7  H6A   C6   H6    105.18  3.000
 DL7  H6A   C6   C5    110.72  3.000
 DL7  H6    C6   C5    109.67  3.000
 DL7  H6A   C6   C7    110.95  3.000
 DL7  H6    C6   C7    109.12  3.000
 DL7  C5    C6   C7    111.02  3.000
 DL7  C12   C13  C18   111.54  3.000
 DL7  C18   C13  C14   110.89  3.000
 DL7  C12   C13  C14   106.34  3.000
 DL7  C18   C13  C17   110.78  3.000
 DL7  C12   C13  C17   116.30  3.000
 DL7  C14   C13  C17   100.29  3.000
 DL7  H18B  C18  H18A  107.11  3.000
 DL7  H18B  C18  H18   107.34  3.000
 DL7  H18A  C18  H18   106.71  3.000
 DL7  H18B  C18  C13   111.42  3.000
 DL7  H18A  C18  C13   111.61  3.000
 DL7  H18   C18  C13   112.34  3.000
 DL7  H12A  C12  H12   106.29  3.000
 DL7  H12A  C12  C11   109.98  3.000
 DL7  H12   C12  C11   108.17  3.000
 DL7  H12A  C12  C13   108.86  3.000
 DL7  H12   C12  C13   112.28  3.000
 DL7  C11   C12  C13   111.13  3.000
 DL7  H11A  C11  H11   106.08  3.000
 DL7  H11A  C11  C9    109.60  3.000
 DL7  H11   C11  C9    110.16  3.000
 DL7  H11A  C11  C12   108.75  3.000
 DL7  H11   C11  C12   107.98  3.000
 DL7  C9    C11  C12   113.96  3.000
 DL7  H9    C9   C10   106.86  3.000
 DL7  H9    C9   C11   106.00  3.000
 DL7  C10   C9   C11   112.79  3.000
 DL7  H9    C9   C8    105.72  3.000
 DL7  C10   C9   C8    113.30  3.000
 DL7  C11   C9   C8    111.52  3.000
 DL7  C5    C10  C19   110.70  3.000
 DL7  C19   C10  C1    110.15  3.000
 DL7  C5    C10  C1    108.17  3.000
 DL7  C19   C10  C9    111.00  3.000
 DL7  C5    C10  C9    107.82  3.000
 DL7  C1    C10  C9    108.91  3.000
 DL7  H1A   C1   H1    106.10  3.000
 DL7  H1A   C1   C2    108.49  3.000
 DL7  H1    C1   C2    108.29  3.000
 DL7  H1A   C1   C10   109.39  3.000
 DL7  H1    C1   C10   110.79  3.000
 DL7  C2    C1   C10   113.48  3.000
 DL7  H19B  C19  H19A  107.38  3.000
 DL7  H19B  C19  H19   106.38  3.000
 DL7  H19A  C19  H19   106.75  3.000
 DL7  H19B  C19  C10   111.26  3.000
 DL7  H19A  C19  C10   111.86  3.000
 DL7  H19   C19  C10   112.85  3.000
 DL7  H5    C5   C4    107.36  3.000
 DL7  H5    C5   C10   106.73  3.000
 DL7  C4    C5   C10   113.32  3.000
 DL7  H5    C5   C6    107.15  3.000
 DL7  C4    C5   C6    110.53  3.000
 DL7  C10   C5   C6    111.41  3.000
 DL7  H4A   C4   H4    106.38  3.000
 DL7  H4A   C4   C3    107.25  3.000
 DL7  H4    C4   C3    109.91  3.000
 DL7  H4A   C4   C5    109.57  3.000
 DL7  H4    C4   C5    110.43  3.000
 DL7  C3    C4   C5    113.04  3.000
 DL7  C2    C3   O1    122.17  3.000
 DL7  C2    C3   C4    115.04  3.000
 DL7  O1    C3   C4    122.78  3.000
 DL7  H2A   C2   H2    106.59  3.000
 DL7  H2A   C2   C3    110.28  3.000
 DL7  H2    C2   C3    107.87  3.000
 DL7  H2A   C2   C1    110.75  3.000
 DL7  H2    C2   C1    109.61  3.000
 DL7  C3    C2   C1    111.57  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
 DL7  CONST_01  HO2  O2   C27  O3      0.00   0.0  0
 DL7  Var_01    C6   C7   C8   C14  -171.38   0.0  0
 DL7  Var_02    C14  C15  C16  C17     9.24  30.0  1
 DL7  Var_03    C5   C6   C7   C8     16.73  30.0  1
 DL7  Var_04    C9   C11  C12  C13   -55.95  30.0  1
 DL7  Var_05    C3   C2   C1   C10   -54.01  30.0  1
 DL7  Var_06    C4   C3   C2   C1     48.47  30.0  1
 DL7  Var_07    C2   C3   C4   C5    -47.14  30.0  1
 DL7  Var_08    C22  C23  C24  C25  -179.31  30.0  2
 DL7  Var_09    C20  C22  C23  C24   171.68  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
 DL7  chir_01  C25  C27  C24  C26  negativ
 DL7  chir_02  C20  C22  C17  C21  positiv
 DL7  chir_03  C17  C16  C13  C20  negativ
 DL7  chir_04  C14  C15  C8   C13  negativ
 DL7  chir_05  C13  C14  C12  C17  positiv
 DL7  chir_06  C9   C8   C11  C10  positiv
 DL7  chir_07  C10  C1   C5   C9   negativ
 DL7  chir_08  C5   C6   C10  C4   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
 DL7  plan-1  C4   0.020
 DL7  plan-1  C3   0.020
 DL7  plan-1  O1   0.020
 DL7  plan-1  C2   0.020
 DL7  plan-2  O3   0.020
 DL7  plan-2  C27  0.020
 DL7  plan-2  O2   0.020
 DL7  plan-2  C25  0.020
 DL7  plan-2  HO2  0.020
 DL7  plan-3  C14  0.020
 DL7  plan-3  C8   0.020
 DL7  plan-3  C7   0.020
 DL7  plan-3  C6   0.020
 DL7  plan-3  C9   0.020
 DL7  plan-3  H7   0.020

