# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:30:47 2022
#   Inital geometry file: a 143 line input string
#   Ligand name: (5beta,9beta)-3-oxocholan-24-oic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CCC(O)=O)[C@H]1CC[C@H]2[C@@H]3CC[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
 3KL  3KL  '(5beta,9beta)-3-oxocholan-24-oic acid'  ligand  64  27  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3KL
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
 3KL  C2   C  CH2    0  -0.562  -4.6262   1.6927  -1.2324
 3KL  C3   C  C      0   0.420  -5.3372   0.4543  -1.7000
 3KL  O3   O  O      0  -0.412  -6.3079   0.4882  -2.4267
 3KL  C4   C  CH2    0  -0.561  -4.7396  -0.8332  -1.2057
 3KL  C5   C  CH1    0  -0.222  -4.4532  -0.8429   0.3071
 3KL  C6   C  CH2    0  -0.431  -3.7515  -2.1413   0.7030
 3KL  C1   C  CH2    0  -0.436  -4.4144   1.6492   0.2802
 3KL  C7   C  CH2    0  -0.430  -2.3100  -2.1944   0.2134
 3KL  C8   C  CH1    0  -0.219  -1.5076  -0.9764   0.6604
 3KL  C9   C  CH1    0  -0.196  -2.2151   0.3361   0.2712
 3KL  C10  C  CT     0  -0.063  -3.6730   0.4028   0.7885
 3KL  C11  C  CH2    0  -0.435  -1.3649   1.5443   0.6734
 3KL  C12  C  CH2    0  -0.410   0.0667   1.4935   0.1320
 3KL  C13  C  CT     0  -0.051   0.7834   0.1982   0.5147
 3KL  C14  C  CH1    0  -0.172  -0.1136  -0.9662   0.0525
 3KL  C15  C  CH2    0  -0.447   0.7680  -2.1955   0.2222
 3KL  C16  C  CH2    0  -0.449   2.1746  -1.6825  -0.1425
 3KL  C17  C  CH1    0  -0.159   2.0824  -0.1365  -0.2623
 3KL  C18  C  CH3    0  -0.685   1.0562   0.1617   2.0223
 3KL  C19  C  CH3    0  -0.673  -3.7117   0.4671   2.3209
 3KL  C20  C  CH1    0  -0.230   3.3952   0.5529   0.1404
 3KL  C21  C  CH3    0  -0.671   3.3199   2.0748   0.0450
 3KL  C22  C  CH2    0  -0.398   4.5545   0.0183  -0.7131
 3KL  C23  C  CH2    0  -0.592   5.9358   0.4799  -0.2727
 3KL  C24  C  C      0   0.413   7.1200  -0.2068  -0.9793
 3KL  OT1  O  OC    -1  -0.633   8.2295   0.3562  -0.8602
 3KL  OT2  O  O      0  -0.611   6.9009  -1.2711  -1.5922
 3KL  H1   H  HCH2   0   0.259  -3.6614   1.7452  -1.7496
 3KL  H2   H  HCH2   0   0.261  -5.1911   2.5798  -1.5223
 3KL  H3   H  HCH2   0   0.259  -5.4007  -1.6633  -1.4634
 3KL  H4   H  HCH2   0   0.260  -3.8147  -0.9829  -1.7737
 3KL  H5   H  HCH1   0   0.231  -5.4277  -0.8208   0.8099
 3KL  H6   H  HCH2   0   0.229  -3.7685  -2.2417   1.7925
 3KL  H7   H  HCH2   0   0.228  -4.3134  -2.9958   0.3145
 3KL  H8   H  HCH2   0   0.245  -3.9017   2.5591   0.5974
 3KL  H9   H  HCH2   0   0.235  -5.3949   1.6819   0.7678
 3KL  H10  H  HCH2   0   0.235  -1.8370  -3.1071   0.5850
 3KL  H11  H  HCH2   0   0.208  -2.2785  -2.2675  -0.8800
 3KL  H12  H  HCH1   0   0.205  -1.4181  -1.0278   1.7524
 3KL  H13  H  HCH1   0   0.207  -2.2479   0.3361  -0.8280
 3KL  H14  H  HCH2   0   0.228  -1.8272   2.4666   0.3133
 3KL  H15  H  HCH2   0   0.218  -1.3387   1.6329   1.7632
 3KL  H16  H  HCH2   0   0.207   0.0462   1.5754  -0.9614
 3KL  H17  H  HCH2   0   0.222   0.6007   2.3728   0.4968
 3KL  H18  H  HCH1   0   0.203  -0.2555  -0.8200  -1.0305
 3KL  H19  H  HCH2   0   0.213   0.7328  -2.5551   1.2545
 3KL  H20  H  HCH2   0   0.227   0.4519  -3.0290  -0.4073
 3KL  H21  H  HCH2   0   0.217   2.9023  -1.9604   0.6242
 3KL  H22  H  HCH2   0   0.228   2.5279  -2.1286  -1.0728
 3KL  H23  H  HCH1   0   0.200   1.8920   0.1191  -1.3150
 3KL  H24  H  HCH3   0   0.230   0.1435   0.1736   2.6183
 3KL  H25  H  HCH3   0   0.230   1.6202  -0.7239   2.3213
 3KL  H26  H  HCH3   0   0.228   1.6406   1.0312   2.3298
 3KL  H27  H  HCH3   0   0.233  -3.0741  -0.2767   2.7964
 3KL  H28  H  HCH3   0   0.231  -3.3938   1.4456   2.6851
 3KL  H29  H  HCH3   0   0.228  -4.7295   0.3060   2.6832
 3KL  H30  H  HCH1   0   0.198   3.6078   0.2835   1.1844
 3KL  H31  H  HCH3   0   0.226   2.6020   2.5013   0.7430
 3KL  H32  H  HCH3   0   0.232   4.2821   2.5384   0.2662
 3KL  H33  H  HCH3   0   0.207   3.0285   2.3888  -0.9608
 3KL  H34  H  HCH2   0   0.224   4.5489  -1.0714  -0.6954
 3KL  H35  H  HCH2   0   0.192   4.3826   0.2999  -1.7595
 3KL  H36  H  HCH2   0   0.213   6.0511   1.5600  -0.3922
 3KL  H37  H  HCH2   0   0.217   6.0443   0.2984   0.8051

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
 3KL  OT2  C24  deloc   1.248  0.020  1.248
 3KL  OT1  C24  deloc   1.250  0.020  1.250
 3KL  C24  C23  single  1.541  0.020  1.541
 3KL  C23  C22  single  1.522  0.020  1.522
 3KL  C22  C20  single  1.536  0.020  1.536
 3KL  C20  C21  single  1.527  0.020  1.527
 3KL  C20  C17  single  1.537  0.020  1.537
 3KL  C16  C17  single  1.553  0.020  1.553
 3KL  C16  C15  single  1.541  0.020  1.541
 3KL  C17  C13  single  1.550  0.020  1.550
 3KL  C15  C14  single  1.522  0.020  1.522
 3KL  C14  C13  single  1.541  0.020  1.541
 3KL  C14  C8   single  1.521  0.020  1.521
 3KL  C13  C12  single  1.529  0.020  1.529
 3KL  C13  C18  single  1.533  0.020  1.533
 3KL  C12  C11  single  1.531  0.020  1.531
 3KL  C7   C8   single  1.526  0.020  1.526
 3KL  C7   C6   single  1.523  0.020  1.523
 3KL  C8   C9   single  1.541  0.020  1.541
 3KL  C4   C3   single  1.503  0.020  1.503
 3KL  C4   C5   single  1.540  0.020  1.540
 3KL  O3   C3   double  1.213  0.020  1.213
 3KL  C3   C2   single  1.503  0.020  1.503
 3KL  C9   C11  single  1.531  0.020  1.531
 3KL  C9   C10  single  1.548  0.020  1.548
 3KL  C2   C1   single  1.528  0.020  1.528
 3KL  C6   C5   single  1.528  0.020  1.528
 3KL  C5   C10  single  1.547  0.020  1.547
 3KL  C10  C1   single  1.537  0.020  1.537
 3KL  C10  C19  single  1.534  0.020  1.534
 3KL  C2   H1   single  0.970  0.020  1.090
 3KL  C2   H2   single  0.970  0.020  1.090
 3KL  C4   H3   single  0.970  0.020  1.090
 3KL  C4   H4   single  0.970  0.020  1.090
 3KL  C5   H5   single  0.970  0.020  1.090
 3KL  C6   H6   single  0.970  0.020  1.090
 3KL  C6   H7   single  0.970  0.020  1.090
 3KL  C1   H8   single  0.970  0.020  1.090
 3KL  C1   H9   single  0.970  0.020  1.090
 3KL  C7   H10  single  0.970  0.020  1.090
 3KL  C7   H11  single  0.970  0.020  1.090
 3KL  C8   H12  single  0.970  0.020  1.090
 3KL  C9   H13  single  0.970  0.020  1.090
 3KL  C11  H14  single  0.970  0.020  1.090
 3KL  C11  H15  single  0.970  0.020  1.090
 3KL  C12  H16  single  0.970  0.020  1.090
 3KL  C12  H17  single  0.970  0.020  1.090
 3KL  C14  H18  single  0.970  0.020  1.090
 3KL  C15  H19  single  0.970  0.020  1.090
 3KL  C15  H20  single  0.970  0.020  1.090
 3KL  C16  H21  single  0.970  0.020  1.090
 3KL  C16  H22  single  0.970  0.020  1.090
 3KL  C17  H23  single  0.970  0.020  1.090
 3KL  C18  H24  single  0.970  0.020  1.090
 3KL  C18  H25  single  0.970  0.020  1.090
 3KL  C18  H26  single  0.970  0.020  1.090
 3KL  C19  H27  single  0.970  0.020  1.090
 3KL  C19  H28  single  0.970  0.020  1.090
 3KL  C19  H29  single  0.970  0.020  1.090
 3KL  C20  H30  single  0.970  0.020  1.090
 3KL  C21  H31  single  0.970  0.020  1.090
 3KL  C21  H32  single  0.970  0.020  1.090
 3KL  C21  H33  single  0.970  0.020  1.090
 3KL  C22  H34  single  0.970  0.020  1.090
 3KL  C22  H35  single  0.970  0.020  1.090
 3KL  C23  H36  single  0.970  0.020  1.090
 3KL  C23  H37  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
 3KL  H2   C2   H1   106.95  3.000
 3KL  H2   C2   C1   110.98  3.000
 3KL  H1   C2   C1   110.28  3.000
 3KL  H2   C2   C3   110.02  3.000
 3KL  H1   C2   C3   108.01  3.000
 3KL  C1   C2   C3   110.50  3.000
 3KL  C4   C3   O3   122.62  3.000
 3KL  O3   C3   C2   122.83  3.000
 3KL  C4   C3   C2   114.55  3.000
 3KL  H4   C4   H3   106.54  3.000
 3KL  H4   C4   C5   110.58  3.000
 3KL  H3   C4   C5   109.85  3.000
 3KL  H4   C4   C3   106.39  3.000
 3KL  H3   C4   C3   109.45  3.000
 3KL  C5   C4   C3   113.74  3.000
 3KL  H5   C5   C10  106.81  3.000
 3KL  H5   C5   C6   107.84  3.000
 3KL  C10  C5   C6   111.84  3.000
 3KL  H5   C5   C4   106.56  3.000
 3KL  C10  C5   C4   113.24  3.000
 3KL  C6   C5   C4   110.20  3.000
 3KL  H7   C6   H6   105.90  3.000
 3KL  H7   C6   C7   110.16  3.000
 3KL  H6   C6   C7   109.36  3.000
 3KL  H7   C6   C5   109.62  3.000
 3KL  H6   C6   C5   109.19  3.000
 3KL  C7   C6   C5   112.39  3.000
 3KL  H9   C1   H8   105.44  3.000
 3KL  H9   C1   C10  107.99  3.000
 3KL  H8   C1   C10  110.70  3.000
 3KL  H9   C1   C2   108.40  3.000
 3KL  H8   C1   C2   109.21  3.000
 3KL  C10  C1   C2   114.67  3.000
 3KL  H11  C7   H10  105.72  3.000
 3KL  H11  C7   C8   109.29  3.000
 3KL  H10  C7   C8   109.84  3.000
 3KL  H11  C7   C6   110.50  3.000
 3KL  H10  C7   C6   109.23  3.000
 3KL  C8   C7   C6   112.07  3.000
 3KL  H12  C8   C14  108.87  3.000
 3KL  H12  C8   C9   109.20  3.000
 3KL  C14  C8   C9   108.31  3.000
 3KL  H12  C8   C7   107.29  3.000
 3KL  C9   C8   C7   111.38  3.000
 3KL  C14  C8   C7   111.74  3.000
 3KL  H13  C9   C11  106.21  3.000
 3KL  H13  C9   C10  107.81  3.000
 3KL  C11  C9   C10  113.65  3.000
 3KL  H13  C9   C8   105.43  3.000
 3KL  C10  C9   C8   112.62  3.000
 3KL  C11  C9   C8   110.54  3.000
 3KL  C19  C10  C9   111.05  3.000
 3KL  C19  C10  C1   106.51  3.000
 3KL  C9   C10  C1   112.25  3.000
 3KL  C19  C10  C5   109.39  3.000
 3KL  C1   C10  C5   107.88  3.000
 3KL  C9   C10  C5   109.65  3.000
 3KL  H15  C11  H14  105.67  3.000
 3KL  H15  C11  C12  109.43  3.000
 3KL  H14  C11  C12  107.88  3.000
 3KL  H15  C11  C9   109.81  3.000
 3KL  H14  C11  C9   110.15  3.000
 3KL  C12  C11  C9   113.59  3.000
 3KL  H17  C12  H16  106.39  3.000
 3KL  H17  C12  C13  111.68  3.000
 3KL  H16  C12  C13  108.75  3.000
 3KL  H17  C12  C11  108.21  3.000
 3KL  H16  C12  C11  109.42  3.000
 3KL  C13  C12  C11  112.20  3.000
 3KL  C18  C13  C17  109.80  3.000
 3KL  C18  C13  C14  112.38  3.000
 3KL  C17  C13  C14  100.04  3.000
 3KL  C18  C13  C12  110.47  3.000
 3KL  C14  C13  C12  106.99  3.000
 3KL  C17  C13  C12  116.76  3.000
 3KL  H18  C14  C15  106.93  3.000
 3KL  H18  C14  C13  105.63  3.000
 3KL  C15  C14  C13  103.87  3.000
 3KL  H18  C14  C8   106.00  3.000
 3KL  C13  C14  C8   114.76  3.000
 3KL  C15  C14  C8   118.74  3.000
 3KL  H20  C15  H19  106.50  3.000
 3KL  H20  C15  C16  112.47  3.000
 3KL  H19  C15  C16  111.23  3.000
 3KL  H20  C15  C14  112.63  3.000
 3KL  H19  C15  C14  110.61  3.000
 3KL  C16  C15  C14  103.50  3.000
 3KL  H22  C16  H21  106.18  3.000
 3KL  H22  C16  C17  111.13  3.000
 3KL  H21  C16  C17  110.29  3.000
 3KL  H22  C16  C15  111.19  3.000
 3KL  H21  C16  C15  110.93  3.000
 3KL  C17  C16  C15  107.18  3.000
 3KL  H23  C17  C20  107.13  3.000
 3KL  H23  C17  C16  108.39  3.000
 3KL  C20  C17  C16  112.06  3.000
 3KL  H23  C17  C13  106.53  3.000
 3KL  C16  C17  C13  103.06  3.000
 3KL  C20  C17  C13  119.19  3.000
 3KL  H26  C18  H25  107.00  3.000
 3KL  H26  C18  H24  106.59  3.000
 3KL  H25  C18  H24  106.95  3.000
 3KL  H26  C18  C13  110.70  3.000
 3KL  H25  C18  C13  112.38  3.000
 3KL  H24  C18  C13  112.87  3.000
 3KL  H29  C19  H28  107.04  3.000
 3KL  H29  C19  H27  107.46  3.000
 3KL  H28  C19  H27  107.23  3.000
 3KL  H29  C19  C10  110.40  3.000
 3KL  H28  C19  C10  111.32  3.000
 3KL  H27  C19  C10  113.12  3.000
 3KL  H30  C20  C22  107.26  3.000
 3KL  H30  C20  C21  108.26  3.000
 3KL  C22  C20  C21  110.46  3.000
 3KL  H30  C20  C17  107.71  3.000
 3KL  C21  C20  C17  112.87  3.000
 3KL  C22  C20  C17  110.07  3.000
 3KL  H33  C21  H32  107.43  3.000
 3KL  H33  C21  H31  107.56  3.000
 3KL  H32  C21  H31  106.58  3.000
 3KL  H33  C21  C20  110.91  3.000
 3KL  H32  C21  C20  111.56  3.000
 3KL  H31  C21  C20  112.52  3.000
 3KL  H35  C22  H34  105.74  3.000
 3KL  H35  C22  C23  109.90  3.000
 3KL  H34  C22  C23  107.66  3.000
 3KL  H35  C22  C20  108.82  3.000
 3KL  H34  C22  C20  109.58  3.000
 3KL  C23  C22  C20  114.76  3.000
 3KL  H37  C23  H36  105.08  3.000
 3KL  H37  C23  C24  107.49  3.000
 3KL  H36  C23  C24  108.02  3.000
 3KL  H37  C23  C22  108.88  3.000
 3KL  H36  C23  C22  111.35  3.000
 3KL  C24  C23  C22  115.46  3.000
 3KL  OT2  C24  OT1  125.95  3.000
 3KL  OT1  C24  C23  115.97  3.000
 3KL  OT2  C24  C23  118.07  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
 3KL  Var_01  C5   C4   C3   C2    48.12  30.0  1
 3KL  Var_02  C10  C1   C2   C3    55.39  30.0  1
 3KL  Var_03  C1   C2   C3   C4   -49.74  30.0  1
 3KL  Var_04  C8   C7   C6   C5    53.96  30.0  1
 3KL  Var_05  C13  C12  C11  C9   -54.43  30.0  1
 3KL  Var_06  C17  C16  C15  C14    9.71  30.0  1
 3KL  Var_07  C24  C23  C22  C20  171.27  30.0  1
 3KL  Var_08  OT2  C24  C23  C22  -16.77  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
 3KL  chir_01  C5   C4   C6   C10  negativ
 3KL  chir_02  C8   C14  C7   C9   positiv
 3KL  chir_03  C9   C10  C11  C8   negativ
 3KL  chir_04  C10  C5   C1   C9   positiv
 3KL  chir_05  C13  C14  C12  C17  positiv
 3KL  chir_06  C14  C15  C13  C8   positiv
 3KL  chir_07  C17  C20  C16  C13  negativ
 3KL  chir_08  C20  C17  C21  C22  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
 3KL  plan-1  C2   0.020
 3KL  plan-1  C3   0.020
 3KL  plan-1  O3   0.020
 3KL  plan-1  C4   0.020
 3KL  plan-2  C23  0.020
 3KL  plan-2  C24  0.020
 3KL  plan-2  OT1  0.020
 3KL  plan-2  OT2  0.020

