# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 23:44:28 2020
#   Inital geometry file: a 161 line input string
#   Ligand name: (14beta,17alpha,25R)-3-oxocholest-4-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]2[C@@H]3CCC4=CC(=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
 DL4  DL4  '(14beta,17alpha,25R)-3-oxocholest-4-en-26-oic acid'  ligand  71  30  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DL4
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
 DL4  O3    O  OC    -1  -0.627  -9.8223   0.0938   0.8497
 DL4  C27   C  C      0   0.423  -8.6714  -0.2831   1.1593
 DL4  O2    O  O      0  -0.605  -8.3852  -1.0383   2.1100
 DL4  C25   C  CH1    0  -0.373  -7.5200   0.2506   0.2743
 DL4  C26   C  CH3    0  -0.659  -7.8130  -0.0539  -1.1953
 DL4  C24   C  CH2    0  -0.389  -6.1408  -0.2456   0.6995
 DL4  C23   C  CH2    0  -0.428  -4.9799   0.4560   0.0011
 DL4  C22   C  CH2    0  -0.404  -3.6259  -0.0456   0.4920
 DL4  C20   C  CH1    0  -0.233  -2.4046   0.5709  -0.2050
 DL4  C21   C  CH3    0  -0.672  -2.3124   2.0620   0.1092
 DL4  C17   C  CR15   0  -0.162  -1.1379  -0.2055   0.1823
 DL4  C16   C  CH2    0  -0.446  -1.2151  -1.6984  -0.2396
 DL4  C15   C  CH2    0  -0.450   0.2242  -2.1588  -0.5410
 DL4  C14   C  CR15   0  -0.173   1.0777  -0.9943  -0.0542
 DL4  C8    C  CH1    0  -0.237   2.5259  -0.9142  -0.5080
 DL4  C7    C  CH2    0  -0.419   3.2867  -2.1911  -0.1799
 DL4  C6    C  CH2    0  -0.510   4.7590  -2.0736  -0.5555
 DL4  C13   C  CR5    0  -0.055   0.2333   0.2512  -0.3766
 DL4  C18   C  CH3    0  -0.687   0.1283   0.5054  -1.8839
 DL4  C12   C  CH2    0  -0.409   0.8988   1.4364   0.3256
 DL4  C11   C  CH2    0  -0.448   2.3771   1.5708  -0.0526
 DL4  C9    C  CH1    0  -0.179   3.1871   0.2916   0.1771
 DL4  C10   C  CT     0  -0.148   4.6947   0.4625  -0.1726
 DL4  C1    C  CH2    0  -0.448   5.2967   1.5279   0.7548
 DL4  C19   C  CH3    0  -0.669   4.8980   0.8695  -1.6432
 DL4  C5    C  C      0   0.260   5.4012  -0.8612   0.0420
 DL4  C4    C  C1     0  -0.465   6.5706  -0.9723   0.6954
 DL4  C3    C  C      0   0.404   7.3494   0.1709   1.1649
 DL4  O1    O  O      0  -0.441   8.3942   0.0251   1.7766
 DL4  C2    C  CH2    0  -0.573   6.8170   1.5233   0.7820
 DL4  H25   H  HCH1   0   0.206  -7.5274   1.3447   0.3861
 DL4  H26   H  HCH3   0   0.222  -8.7856   0.3372  -1.4885
 DL4  H26A  H  HCH3   0   0.216  -7.0670   0.3840  -1.8596
 DL4  H26B  H  HCH3   0   0.205  -7.8168  -1.1321  -1.3771
 DL4  H24   H  HCH2   0   0.205  -6.0276  -0.1091   1.7784
 DL4  H24A  H  HCH2   0   0.192  -6.0667  -1.3256   0.5268
 DL4  H23   H  HCH2   0   0.206  -5.0373   0.3051  -1.0820
 DL4  H23A  H  HCH2   0   0.206  -5.0755   1.5351   0.1601
 DL4  H22   H  HCH2   0   0.199  -3.5412   0.1241   1.5728
 DL4  H22A  H  HCH2   0   0.226  -3.6113  -1.1314   0.3611
 DL4  H20   H  HCH1   0   0.201  -2.5491   0.4558  -1.2879
 DL4  H21   H  HCH3   0   0.210  -2.0504   2.2242   1.1576
 DL4  H21A  H  HCH3   0   0.227  -1.5620   2.5651  -0.4985
 DL4  H21B  H  HCH3   0   0.233  -3.2584   2.5700  -0.0788
 DL4  H17   H  HCR5   0   0.202  -1.0539  -0.1594   1.2777
 DL4  H16   H  HCH2   0   0.229  -1.6670  -2.3059   0.5449
 DL4  H16A  H  HCH2   0   0.218  -1.8560  -1.8068  -1.1188
 DL4  H15   H  HCH2   0   0.230   0.4745  -3.0955  -0.0403
 DL4  H15A  H  HCH2   0   0.216   0.3747  -2.3279  -1.6109
 DL4  H14   H  HCR5   0   0.206   1.1045  -1.0626   1.0454
 DL4  H8    H  HCH1   0   0.214   2.5515  -0.7771  -1.5970
 DL4  H7    H  HCH2   0   0.217   3.1992  -2.4035   0.8915
 DL4  H7A   H  HCH2   0   0.243   2.8492  -3.0438  -0.7039
 DL4  H6    H  HCH2   0   0.254   5.3073  -2.9714  -0.2649
 DL4  H6A   H  HCH2   0   0.251   4.8430  -1.9989  -1.6461
 DL4  H18   H  HCH3   0   0.232  -0.3146  -0.3372  -2.4176
 DL4  H18A  H  HCH3   0   0.231  -0.4992   1.3750  -2.0871
 DL4  H18B  H  HCH3   0   0.231   1.0955   0.7015  -2.3469
 DL4  H12   H  HCH2   0   0.226   0.4024   2.3789   0.0903
 DL4  H12A  H  HCH2   0   0.210   0.8090   1.3001   1.4097
 DL4  H11   H  HCH2   0   0.221   2.4547   1.8740  -1.1001
 DL4  H11A  H  HCH2   0   0.239   2.8031   2.3947   0.5243
 DL4  H9    H  HCH1   0   0.214   3.1521   0.0819   1.2574
 DL4  H1    H  HCH2   0   0.248   4.9489   2.5184   0.4598
 DL4  H1A   H  HCH2   0   0.239   4.9288   1.3591   1.7723
 DL4  H19   H  HCH3   0   0.242   4.5026   1.8679  -1.8287
 DL4  H19A  H  HCH3   0   0.241   5.9570   0.8854  -1.9066
 DL4  H19B  H  HCH3   0   0.239   4.4027   0.1882  -2.3352
 DL4  H4    H  H      0   0.247   7.0135  -1.9529   0.8410
 DL4  H2    H  HCH2   0   0.265   7.2217   1.7657  -0.2076
 DL4  H2A   H  HCH2   0   0.265   7.2000   2.2803   1.4680

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
 DL4  C27  O3    deloc   1.250  0.020  1.250
 DL4  O2   C27   deloc   1.247  0.020  1.247
 DL4  C27  C25   single  1.547  0.020  1.547
 DL4  C24  C25   single  1.526  0.020  1.526
 DL4  C25  C26   single  1.529  0.020  1.529
 DL4  C25  H25   single  0.970  0.020  1.090
 DL4  C26  H26   single  0.970  0.020  1.090
 DL4  C26  H26A  single  0.970  0.020  1.090
 DL4  C26  H26B  single  0.970  0.020  1.090
 DL4  C23  C24   single  1.526  0.020  1.526
 DL4  C24  H24   single  0.970  0.020  1.090
 DL4  C24  H24A  single  0.970  0.020  1.090
 DL4  C22  C23   single  1.525  0.020  1.525
 DL4  C23  H23   single  0.970  0.020  1.090
 DL4  C23  H23A  single  0.970  0.020  1.090
 DL4  C20  C22   single  1.535  0.020  1.535
 DL4  C22  H22   single  0.970  0.020  1.090
 DL4  C22  H22A  single  0.970  0.020  1.090
 DL4  C17  C20   single  1.535  0.020  1.535
 DL4  C21  C20   single  1.527  0.020  1.527
 DL4  C20  H20   single  0.970  0.020  1.090
 DL4  C21  H21   single  0.970  0.020  1.090
 DL4  C21  H21A  single  0.970  0.020  1.090
 DL4  C21  H21B  single  0.970  0.020  1.090
 DL4  C13  C17   single  1.549  0.020  1.549
 DL4  C17  C16   single  1.553  0.020  1.553
 DL4  C17  H17   single  0.970  0.020  1.090
 DL4  C15  C16   single  1.541  0.020  1.541
 DL4  C16  H16   single  0.970  0.020  1.090
 DL4  C16  H16A  single  0.970  0.020  1.090
 DL4  C14  C15   single  1.524  0.020  1.524
 DL4  C15  H15   single  0.970  0.020  1.090
 DL4  C15  H15A  single  0.970  0.020  1.090
 DL4  C8   C14   single  1.520  0.020  1.520
 DL4  C14  C13   single  1.539  0.020  1.539
 DL4  C14  H14   single  0.970  0.020  1.090
 DL4  C9   C8    single  1.536  0.020  1.536
 DL4  C7   C8    single  1.522  0.020  1.522
 DL4  C8   H8    single  0.970  0.020  1.090
 DL4  C6   C7    single  1.524  0.020  1.524
 DL4  C7   H7    single  0.970  0.020  1.090
 DL4  C7   H7A   single  0.970  0.020  1.090
 DL4  C5   C6    single  1.496  0.020  1.496
 DL4  C6   H6    single  0.970  0.020  1.090
 DL4  C6   H6A   single  0.970  0.020  1.090
 DL4  C12  C13   single  1.530  0.020  1.530
 DL4  C13  C18   single  1.532  0.020  1.532
 DL4  C18  H18   single  0.970  0.020  1.090
 DL4  C18  H18A  single  0.970  0.020  1.090
 DL4  C18  H18B  single  0.970  0.020  1.090
 DL4  C11  C12   single  1.532  0.020  1.532
 DL4  C12  H12   single  0.970  0.020  1.090
 DL4  C12  H12A  single  0.970  0.020  1.090
 DL4  C9   C11   single  1.531  0.020  1.531
 DL4  C11  H11   single  0.970  0.020  1.090
 DL4  C11  H11A  single  0.970  0.020  1.090
 DL4  C10  C9    single  1.557  0.020  1.557
 DL4  C9   H9    single  0.970  0.020  1.090
 DL4  C1   C10   single  1.535  0.020  1.535
 DL4  C5   C10   single  1.516  0.020  1.516
 DL4  C10  C19   single  1.539  0.020  1.539
 DL4  C2   C1    single  1.521  0.020  1.521
 DL4  C1   H1    single  0.970  0.020  1.090
 DL4  C1   H1A   single  0.970  0.020  1.090
 DL4  C19  H19   single  0.970  0.020  1.090
 DL4  C19  H19A  single  0.970  0.020  1.090
 DL4  C19  H19B  single  0.970  0.020  1.090
 DL4  C4   C5    double  1.344  0.020  1.344
 DL4  C3   C4    single  1.461  0.020  1.461
 DL4  C4   H4    single  0.930  0.020  1.080
 DL4  O1   C3    double  1.219  0.020  1.219
 DL4  C3   C2    single  1.503  0.020  1.503
 DL4  C2   H2    single  0.970  0.020  1.090
 DL4  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
 DL4  C25   C27  O2    118.30  3.000
 DL4  C25   C27  O3    116.07  3.000
 DL4  O2    C27  O3    125.63  3.000
 DL4  H25   C25  C24   107.54  3.000
 DL4  H25   C25  C26   107.12  3.000
 DL4  C24   C25  C26   112.10  3.000
 DL4  H25   C25  C27   106.26  3.000
 DL4  C26   C25  C27   109.78  3.000
 DL4  C24   C25  C27   113.64  3.000
 DL4  H26B  C26  H26A  107.27  3.000
 DL4  H26B  C26  H26   107.84  3.000
 DL4  H26A  C26  H26   107.63  3.000
 DL4  H26B  C26  C25   110.90  3.000
 DL4  H26A  C26  C25   111.98  3.000
 DL4  H26   C26  C25   111.01  3.000
 DL4  H24A  C24  H24   105.76  3.000
 DL4  H24A  C24  C23   109.24  3.000
 DL4  H24   C24  C23   108.40  3.000
 DL4  H24A  C24  C25   109.73  3.000
 DL4  H24   C24  C25   109.14  3.000
 DL4  C23   C24  C25   114.24  3.000
 DL4  H23A  C23  H23   105.95  3.000
 DL4  H23A  C23  C22   110.78  3.000
 DL4  H23   C23  C22   108.64  3.000
 DL4  H23A  C23  C24   108.69  3.000
 DL4  H23   C23  C24   110.46  3.000
 DL4  C22   C23  C24   112.14  3.000
 DL4  H22A  C22  H22   105.69  3.000
 DL4  H22A  C22  C20   109.49  3.000
 DL4  H22   C22  C20   108.88  3.000
 DL4  H22A  C22  C23   107.45  3.000
 DL4  H22   C22  C23   109.55  3.000
 DL4  C20   C22  C23   115.34  3.000
 DL4  H20   C20  C17   107.71  3.000
 DL4  H20   C20  C21   108.25  3.000
 DL4  C17   C20  C21   113.09  3.000
 DL4  H20   C20  C22   107.50  3.000
 DL4  C21   C20  C22   110.29  3.000
 DL4  C17   C20  C22   109.80  3.000
 DL4  H21B  C21  H21A  106.65  3.000
 DL4  H21B  C21  H21   107.72  3.000
 DL4  H21A  C21  H21   107.55  3.000
 DL4  H21B  C21  C20   111.54  3.000
 DL4  H21A  C21  C20   112.22  3.000
 DL4  H21   C21  C20   110.91  3.000
 DL4  H17   C17  C13   106.22  3.000
 DL4  H17   C17  C16   108.35  3.000
 DL4  C13   C17  C16   103.26  3.000
 DL4  H17   C17  C20   107.04  3.000
 DL4  C16   C17  C20   112.11  3.000
 DL4  C13   C17  C20   119.34  3.000
 DL4  H16A  C16  H16   106.28  3.000
 DL4  H16A  C16  C15   111.14  3.000
 DL4  H16   C16  C15   111.18  3.000
 DL4  H16A  C16  C17   110.05  3.000
 DL4  H16   C16  C17   111.14  3.000
 DL4  C15   C16  C17   107.09  3.000
 DL4  H15A  C15  H15   106.54  3.000
 DL4  H15A  C15  C14   110.71  3.000
 DL4  H15   C15  C14   112.40  3.000
 DL4  H15A  C15  C16   111.47  3.000
 DL4  H15   C15  C16   112.40  3.000
 DL4  C14   C15  C16   103.44  3.000
 DL4  H14   C14  C13   105.81  3.000
 DL4  H14   C14  C8    106.15  3.000
 DL4  C13   C14  C8    114.68  3.000
 DL4  H14   C14  C15   106.56  3.000
 DL4  C13   C14  C15   104.14  3.000
 DL4  C8    C14  C15   118.60  3.000
 DL4  H8    C8   C9    109.53  3.000
 DL4  H8    C8   C7    107.88  3.000
 DL4  C9    C8   C7    110.31  3.000
 DL4  H8    C8   C14   108.97  3.000
 DL4  C7    C8   C14   111.57  3.000
 DL4  C9    C8   C14   108.56  3.000
 DL4  H7A   C7   H7    106.61  3.000
 DL4  H7A   C7   C6    109.20  3.000
 DL4  H7    C7   C6    109.45  3.000
 DL4  H7A   C7   C8    110.57  3.000
 DL4  H7    C7   C8    109.48  3.000
 DL4  C6    C7   C8    111.41  3.000
 DL4  H6A   C6   H6    106.41  3.000
 DL4  H6A   C6   C5    108.00  3.000
 DL4  H6    C6   C5    110.16  3.000
 DL4  H6A   C6   C7    108.93  3.000
 DL4  H6    C6   C7    110.88  3.000
 DL4  C5    C6   C7    112.25  3.000
 DL4  C12   C13  C18   110.66  3.000
 DL4  C18   C13  C14   112.21  3.000
 DL4  C12   C13  C14   106.98  3.000
 DL4  C18   C13  C17   110.07  3.000
 DL4  C12   C13  C17   116.60  3.000
 DL4  C14   C13  C17    99.87  3.000
 DL4  H18B  C18  H18A  106.72  3.000
 DL4  H18B  C18  H18   106.93  3.000
 DL4  H18A  C18  H18   106.90  3.000
 DL4  H18B  C18  C13   112.76  3.000
 DL4  H18A  C18  C13   110.78  3.000
 DL4  H18   C18  C13   112.39  3.000
 DL4  H12A  C12  H12   106.46  3.000
 DL4  H12A  C12  C11   109.52  3.000
 DL4  H12   C12  C11   108.06  3.000
 DL4  H12A  C12  C13   108.78  3.000
 DL4  H12   C12  C13   111.86  3.000
 DL4  C11   C12  C13   112.00  3.000
 DL4  H11A  C11  H11   105.62  3.000
 DL4  H11A  C11  C9    110.15  3.000
 DL4  H11   C11  C9    109.74  3.000
 DL4  H11A  C11  C12   108.20  3.000
 DL4  H11   C11  C12   109.23  3.000
 DL4  C9    C11  C12   113.58  3.000
 DL4  H9    C9   C10   105.79  3.000
 DL4  H9    C9   C11   106.82  3.000
 DL4  C10   C9   C11   112.75  3.000
 DL4  H9    C9   C8    105.92  3.000
 DL4  C10   C9   C8    113.75  3.000
 DL4  C11   C9   C8    111.16  3.000
 DL4  C5    C10  C19   107.73  3.000
 DL4  C19   C10  C1    109.98  3.000
 DL4  C5    C10  C1    109.74  3.000
 DL4  C19   C10  C9    111.80  3.000
 DL4  C5    C10  C9    108.88  3.000
 DL4  C1    C10  C9    108.67  3.000
 DL4  H1A   C1   H1    106.51  3.000
 DL4  H1A   C1   C2    108.59  3.000
 DL4  H1    C1   C2    109.06  3.000
 DL4  H1A   C1   C10   108.82  3.000
 DL4  H1    C1   C10   109.99  3.000
 DL4  C2    C1   C10   113.62  3.000
 DL4  H19B  C19  H19A  107.26  3.000
 DL4  H19B  C19  H19   107.44  3.000
 DL4  H19A  C19  H19   107.32  3.000
 DL4  H19B  C19  C10   112.41  3.000
 DL4  H19A  C19  C10   111.26  3.000
 DL4  H19   C19  C10   110.91  3.000
 DL4  C4    C5   C10   123.13  3.000
 DL4  C4    C5   C6    120.03  3.000
 DL4  C10   C5   C6    116.81  3.000
 DL4  H4    C4   C3    116.50  3.000
 DL4  H4    C4   C5    119.65  3.000
 DL4  C3    C4   C5    123.73  3.000
 DL4  C2    C3   O1    122.61  3.000
 DL4  C2    C3   C4    115.69  3.000
 DL4  O1    C3   C4    121.63  3.000
 DL4  H2A   C2   H2    106.53  3.000
 DL4  H2A   C2   C3    109.86  3.000
 DL4  H2    C2   C3    107.35  3.000
 DL4  H2A   C2   C1    111.11  3.000
 DL4  H2    C2   C1    110.63  3.000
 DL4  C3    C2   C1    111.19  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
 DL4  Var_01  C14  C15  C16  C17    9.28  30.0  1
 DL4  Var_02  C5   C6   C7   C8    53.10  30.0  1
 DL4  Var_03  C10  C5   C6   C7   -51.08  30.0  1
 DL4  Var_04  C3   C4   C5   C6   172.16  30.0  1
 DL4  Var_05  C9   C11  C12  C13  -54.13  30.0  1
 DL4  Var_06  C3   C2   C1   C10  -56.10  30.0  1
 DL4  Var_07  C4   C3   C2   C1    34.42  30.0  1
 DL4  Var_08  C2   C3   C4   C5    -4.50  30.0  1
 DL4  Var_09  C22  C23  C24  C25  178.23  30.0  2
 DL4  Var_10  C20  C22  C23  C24  177.58  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
 DL4  chir_01  C25  C27  C24  C26  negativ
 DL4  chir_02  C20  C22  C17  C21  positiv
 DL4  chir_03  C17  C16  C13  C20  negativ
 DL4  chir_04  C14  C13  C8   C15  positiv
 DL4  chir_05  C8   C14  C9   C7   negativ
 DL4  chir_06  C13  C12  C14  C17  negativ
 DL4  chir_07  C9   C8   C11  C10  positiv
 DL4  chir_08  C10  C5   C1   C9   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
 DL4  plan-1  C4   0.020
 DL4  plan-1  C3   0.020
 DL4  plan-1  O1   0.020
 DL4  plan-1  C2   0.020
 DL4  plan-2  O3   0.020
 DL4  plan-2  C27  0.020
 DL4  plan-2  O2   0.020
 DL4  plan-2  C25  0.020

