# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:09:36 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: (3alpha,8alpha,14beta)-3-[2-(diethylamino)ethoxy]androst-5-en-17-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC)CCO[C@H]1CC[C@]2(C)[C@H]3CC[C@@]4(C)[C@@H](CCC4=O)[C@@H]3CC=C2C1
#
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
 MKM  MKM  (3alpha,8alpha,14beta)-3-[2-(diethylamino)ethoxy]androst-5-en-17-one  ligand  69  28  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MKM
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
 MKM  N    N  NT    0  -0.401   6.4759  -0.0226   0.3433
 MKM  C1   C  CH2   0  -0.471   1.7309   1.2602  -0.2804
 MKM  C10  C  CH1   0  -0.188  -2.0691   0.4411   0.0964
 MKM  C11  C  CH1   0  -0.202  -4.2918  -0.6255   0.4425
 MKM  C12  C  CT    0  -0.205  -5.0221   0.6313  -0.0349
 MKM  C13  C  CH2   0  -0.403  -4.2080   1.8532   0.3549
 MKM  C14  C  CH2   0  -0.453  -2.8012   1.7509  -0.2402
 MKM  C15  C  CH2   0  -0.456  -5.3421  -1.7330   0.3399
 MKM  C16  C  CH2   0  -0.568  -6.6144  -1.0307   0.8343
 MKM  C17  C  C     0   0.432  -6.3639   0.4590   0.6439
 MKM  C18  C  CH3   0  -0.679  -0.7424   0.6109  -2.0800
 MKM  C19  C  CH3   0  -0.666  -5.3357   0.6176  -1.5426
 MKM  C2   C  CH1   0   0.110   2.2510  -0.1233   0.0611
 MKM  C20  C  CH2   0  -0.148   4.3199  -1.2587   0.2743
 MKM  C21  C  CH2   0  -0.317   5.7713  -1.1913  -0.1534
 MKM  C22  C  CH2   0  -0.284   6.9210  -0.2119   1.7148
 MKM  C23  C  CH3   0  -0.665   7.1790   1.0942   2.4489
 MKM  C24  C  CH2   0  -0.284   7.5616   0.3725  -0.5397
 MKM  C25  C  CH3   0  -0.659   7.0751   1.0800  -1.7944
 MKM  C3   C  CH2   0  -0.549   1.4031  -1.1791  -0.6488
 MKM  C4   C  C     0   0.215  -0.0634  -1.0247  -0.3426
 MKM  C5   C  CT    0  -0.127  -0.6685   0.3519  -0.5654
 MKM  C6   C  CH2   0  -0.432   0.2600   1.3924   0.0971
 MKM  C7   C  C1    0  -0.331  -0.7706  -2.0659   0.0940
 MKM  C8   C  CH2   0  -0.452  -2.2360  -2.0449   0.3728
 MKM  C9   C  CH1   0  -0.237  -2.9230  -0.8070  -0.1887
 MKM  O1   O  O2    0  -0.490   3.6107  -0.1920  -0.3058
 MKM  H2   H  HCH2  0   0.238   2.3104   2.0182   0.2527
 MKM  H3   H  HCH2  0   0.222   1.8712   1.4510  -1.3495
 MKM  H4   H  HCH1  0   0.211  -1.8980   0.4415   1.1834
 MKM  H5   H  HCH1  0   0.225  -4.1124  -0.4749   1.5197
 MKM  H6   H  HCH2  0   0.231  -4.6841   2.7762   0.0143
 MKM  H7   H  HCH2  0   0.225  -4.1455   1.9134   1.4465
 MKM  H8   H  HCH2  0   0.240  -2.2137   2.5997   0.1162
 MKM  H9   H  HCH2  0   0.227  -2.8712   1.8731  -1.3229
 MKM  H10  H  HCH2  0   0.231  -5.4551  -2.0809  -0.6895
 MKM  H11  H  HCH2  0   0.249  -5.0907  -2.6036   0.9458
 MKM  H12  H  HCH2  0   0.278  -7.5283  -1.3388   0.3225
 MKM  H13  H  HCH2  0   0.277  -6.7788  -1.2118   1.9002
 MKM  H14  H  HCH3  0   0.230  -0.9493   1.6589  -2.3006
 MKM  H15  H  HCH3  0   0.237   0.1939   0.3604  -2.5776
 MKM  H16  H  HCH3  0   0.233  -1.5223   0.0058  -2.5458
 MKM  H17  H  HCH3  0   0.244  -5.9563  -0.2302  -1.8359
 MKM  H18  H  HCH3  0   0.244  -5.8715   1.5270  -1.8198
 MKM  H19  H  HCH3  0   0.245  -4.4310   0.5738  -2.1474
 MKM  H20  H  HCH1  0   0.190   2.1522  -0.2748   1.1493
 MKM  H21  H  HCH2  0   0.199   3.9243  -2.2323  -0.0443
 MKM  H22  H  HCH2  0   0.194   4.2281  -1.2303   1.3700
 MKM  H23  H  HCH2  0   0.235   5.7966  -1.1934  -1.2450
 MKM  H24  H  HCH2  0   0.203   6.2618  -2.1287   0.1575
 MKM  H25  H  HCH2  0   0.225   6.1404  -0.7497   2.2568
 MKM  H26  H  HCH2  0   0.191   7.8159  -0.8558   1.7623
 MKM  H27  H  HCH3  0   0.225   7.4365   0.8965   3.4900
 MKM  H28  H  HCH3  0   0.222   8.0015   1.6659   2.0173
 MKM  H29  H  HCH3  0   0.221   6.2883   1.7228   2.4326
 MKM  H30  H  HCH2  0   0.226   8.2151   1.0582   0.0019
 MKM  H31  H  HCH2  0   0.190   8.1935  -0.4891  -0.8152
 MKM  H32  H  HCH3  0   0.221   6.4579   0.4384  -2.4240
 MKM  H33  H  HCH3  0   0.220   6.4858   1.9590  -1.5327
 MKM  H34  H  HCH3  0   0.222   7.9236   1.4063  -2.3971
 MKM  H35  H  HCH2  0   0.230   1.5790  -1.0840  -1.7271
 MKM  H36  H  HCH2  0   0.246   1.7209  -2.1865  -0.3699
 MKM  H38  H  HCH2  0   0.222   0.1654   1.2998   1.1847
 MKM  H39  H  HCH2  0   0.237  -0.0797   2.3992  -0.1553
 MKM  H40  H  H     0   0.222  -0.2590  -3.0112   0.2562
 MKM  H42  H  HCH2  0   0.240  -2.6962  -2.9491  -0.0365
 MKM  H43  H  HCH2  0   0.225  -2.4024  -2.1021   1.4570
 MKM  H44  H  HCH1  0   0.221  -3.0321  -0.9355  -1.2727
 MKM  O2   O  O     0  -0.401  -7.1137   1.3447   0.9790

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
 MKM  C8   C7   single  1.492  0.020  1.492
 MKM  C8   C9   single  1.523  0.020  1.523
 MKM  C7   C4   double  1.332  0.020  1.332
 MKM  C15  C16  single  1.535  0.020  1.535
 MKM  C15  C11  single  1.530  0.020  1.530
 MKM  C16  C17  single  1.523  0.020  1.523
 MKM  C23  C22  single  1.520  0.020  1.520
 MKM  C22  N    single  1.454  0.020  1.454
 MKM  C11  C9   single  1.518  0.020  1.518
 MKM  C11  C12  single  1.530  0.020  1.530
 MKM  C9   C10  single  1.539  0.020  1.539
 MKM  C4   C3   single  1.506  0.020  1.506
 MKM  C4   C5   single  1.520  0.020  1.520
 MKM  N    C21  single  1.452  0.020  1.452
 MKM  N    C24  single  1.454  0.020  1.454
 MKM  C21  C20  single  1.515  0.020  1.515
 MKM  C3   C2   single  1.529  0.020  1.529
 MKM  C17  C12  single  1.514  0.020  1.514
 MKM  C17  O2   double  1.208  0.020  1.208
 MKM  C20  O1   single  1.406  0.020  1.406
 MKM  C10  C5   single  1.552  0.020  1.552
 MKM  C10  C14  single  1.538  0.020  1.538
 MKM  C12  C19  single  1.540  0.020  1.540
 MKM  C12  C13  single  1.519  0.020  1.519
 MKM  C25  C24  single  1.520  0.020  1.520
 MKM  C5   C18  single  1.538  0.020  1.538
 MKM  C5   C6   single  1.544  0.020  1.544
 MKM  C2   O1   single  1.410  0.020  1.410
 MKM  C2   C1   single  1.517  0.020  1.517
 MKM  C13  C14  single  1.531  0.020  1.531
 MKM  C6   C1   single  1.524  0.020  1.524
 MKM  C1   H2   single  0.970  0.020  1.090
 MKM  C1   H3   single  0.970  0.020  1.090
 MKM  C10  H4   single  0.970  0.020  1.090
 MKM  C11  H5   single  0.970  0.020  1.090
 MKM  C13  H6   single  0.970  0.020  1.090
 MKM  C13  H7   single  0.970  0.020  1.090
 MKM  C14  H8   single  0.970  0.020  1.090
 MKM  C14  H9   single  0.970  0.020  1.090
 MKM  C15  H10  single  0.970  0.020  1.090
 MKM  C15  H11  single  0.970  0.020  1.090
 MKM  C16  H12  single  0.970  0.020  1.090
 MKM  C16  H13  single  0.970  0.020  1.090
 MKM  C18  H14  single  0.970  0.020  1.090
 MKM  C18  H15  single  0.970  0.020  1.090
 MKM  C18  H16  single  0.970  0.020  1.090
 MKM  C19  H17  single  0.970  0.020  1.090
 MKM  C19  H18  single  0.970  0.020  1.090
 MKM  C19  H19  single  0.970  0.020  1.090
 MKM  C2   H20  single  0.970  0.020  1.090
 MKM  C20  H21  single  0.970  0.020  1.090
 MKM  C20  H22  single  0.970  0.020  1.090
 MKM  C21  H23  single  0.970  0.020  1.090
 MKM  C21  H24  single  0.970  0.020  1.090
 MKM  C22  H25  single  0.970  0.020  1.090
 MKM  C22  H26  single  0.970  0.020  1.090
 MKM  C23  H27  single  0.970  0.020  1.090
 MKM  C23  H28  single  0.970  0.020  1.090
 MKM  C23  H29  single  0.970  0.020  1.090
 MKM  C24  H30  single  0.970  0.020  1.090
 MKM  C24  H31  single  0.970  0.020  1.090
 MKM  C25  H32  single  0.970  0.020  1.090
 MKM  C25  H33  single  0.970  0.020  1.090
 MKM  C25  H34  single  0.970  0.020  1.090
 MKM  C3   H35  single  0.970  0.020  1.090
 MKM  C3   H36  single  0.970  0.020  1.090
 MKM  C6   H38  single  0.970  0.020  1.090
 MKM  C6   H39  single  0.970  0.020  1.090
 MKM  C7   H40  single  0.930  0.020  1.080
 MKM  C8   H42  single  0.970  0.020  1.090
 MKM  C8   H43  single  0.970  0.020  1.090
 MKM  C9   H44  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
 MKM  C24  N    C22  112.30  3.000
 MKM  C24  N    C21  111.91  3.000
 MKM  C22  N    C21  111.49  3.000
 MKM  H3   C1   H2   106.71  3.000
 MKM  H3   C1   C6   110.50  3.000
 MKM  H2   C1   C6   109.31  3.000
 MKM  H3   C1   C2   109.56  3.000
 MKM  H2   C1   C2   109.93  3.000
 MKM  C6   C1   C2   110.74  3.000
 MKM  H4   C10  C9   105.64  3.000
 MKM  H4   C10  C5   106.32  3.000
 MKM  C9   C10  C5   112.04  3.000
 MKM  H4   C10  C14  106.85  3.000
 MKM  C5   C10  C14  112.67  3.000
 MKM  C9   C10  C14  112.71  3.000
 MKM  H5   C11  C9   106.01  3.000
 MKM  H5   C11  C15  106.03  3.000
 MKM  C9   C11  C15  120.30  3.000
 MKM  H5   C11  C12  105.69  3.000
 MKM  C9   C11  C12  113.50  3.000
 MKM  C15  C11  C12  104.25  3.000
 MKM  C19  C12  C17  104.92  3.000
 MKM  C19  C12  C13  111.56  3.000
 MKM  C17  C12  C13  116.85  3.000
 MKM  C13  C12  C11  108.95  3.000
 MKM  C19  C12  C11  113.29  3.000
 MKM  C17  C12  C11  100.93  3.000
 MKM  H7   C13  H6   106.80  3.000
 MKM  H7   C13  C14  109.80  3.000
 MKM  H6   C13  C14  109.60  3.000
 MKM  H7   C13  C12  109.31  3.000
 MKM  H6   C13  C12  111.46  3.000
 MKM  C14  C13  C12  109.82  3.000
 MKM  H9   C14  H8   105.73  3.000
 MKM  H9   C14  C13  108.61  3.000
 MKM  H8   C14  C13  108.39  3.000
 MKM  H9   C14  C10  110.05  3.000
 MKM  H8   C14  C10  109.54  3.000
 MKM  C13  C14  C10  114.16  3.000
 MKM  H11  C15  H10  107.05  3.000
 MKM  H11  C15  C16  112.18  3.000
 MKM  H10  C15  C16  111.31  3.000
 MKM  H11  C15  C11  112.50  3.000
 MKM  H10  C15  C11  111.39  3.000
 MKM  C16  C15  C11  102.49  3.000
 MKM  H13  C16  H12  106.52  3.000
 MKM  H13  C16  C17  107.98  3.000
 MKM  H12  C16  C17  110.80  3.000
 MKM  H13  C16  C15  111.27  3.000
 MKM  H12  C16  C15  114.44  3.000
 MKM  C17  C16  C15  105.72  3.000
 MKM  O2   C17  C16  125.49  3.000
 MKM  O2   C17  C12  126.25  3.000
 MKM  C16  C17  C12  108.26  3.000
 MKM  H16  C18  H15  106.95  3.000
 MKM  H16  C18  H14  108.11  3.000
 MKM  H15  C18  H14  106.95  3.000
 MKM  H16  C18  C5   111.17  3.000
 MKM  H15  C18  C5   111.70  3.000
 MKM  H14  C18  C5   111.71  3.000
 MKM  H19  C19  H18  107.48  3.000
 MKM  H19  C19  H17  106.98  3.000
 MKM  H18  C19  H17  107.46  3.000
 MKM  H19  C19  C12  112.02  3.000
 MKM  H18  C19  C12  109.96  3.000
 MKM  H17  C19  C12  112.71  3.000
 MKM  H20  C2   O1   109.65  3.000
 MKM  H20  C2   C3   108.27  3.000
 MKM  O1   C2   C3   112.36  3.000
 MKM  H20  C2   C1   108.46  3.000
 MKM  O1   C2   C1   108.45  3.000
 MKM  C3   C2   C1   109.58  3.000
 MKM  H22  C20  H21  106.36  3.000
 MKM  H22  C20  O1   110.44  3.000
 MKM  H21  C20  O1   111.80  3.000
 MKM  H22  C20  C21  111.10  3.000
 MKM  H21  C20  C21  107.62  3.000
 MKM  O1   C20  C21  109.46  3.000
 MKM  H24  C21  H23  105.66  3.000
 MKM  H24  C21  C20  107.99  3.000
 MKM  H23  C21  C20  107.72  3.000
 MKM  H24  C21  N    111.83  3.000
 MKM  H23  C21  N    109.41  3.000
 MKM  C20  C21  N    113.84  3.000
 MKM  H26  C22  H25  105.73  3.000
 MKM  H26  C22  C23  110.06  3.000
 MKM  H25  C22  C23  107.75  3.000
 MKM  H26  C22  N    111.39  3.000
 MKM  H25  C22  N    108.26  3.000
 MKM  C23  C22  N    113.29  3.000
 MKM  H29  C23  H28  107.94  3.000
 MKM  H29  C23  H27  108.16  3.000
 MKM  H28  C23  H27  107.14  3.000
 MKM  H29  C23  C22  110.45  3.000
 MKM  H28  C23  C22  112.78  3.000
 MKM  H27  C23  C22  110.20  3.000
 MKM  H31  C24  H30  105.76  3.000
 MKM  H31  C24  C25  109.91  3.000
 MKM  H30  C24  C25  107.99  3.000
 MKM  H31  C24  N    111.54  3.000
 MKM  H30  C24  N    108.46  3.000
 MKM  C25  C24  N    112.87  3.000
 MKM  H34  C25  H33  108.17  3.000
 MKM  H34  C25  H32  107.30  3.000
 MKM  H33  C25  H32  107.88  3.000
 MKM  H34  C25  C24  110.26  3.000
 MKM  H33  C25  C24  110.49  3.000
 MKM  H32  C25  C24  112.57  3.000
 MKM  H36  C3   H35  106.51  3.000
 MKM  H36  C3   C4   109.02  3.000
 MKM  H35  C3   C4   110.32  3.000
 MKM  H36  C3   C2   110.91  3.000
 MKM  H35  C3   C2   107.92  3.000
 MKM  C4   C3   C2   112.01  3.000
 MKM  C7   C4   C5   122.99  3.000
 MKM  C5   C4   C3   116.79  3.000
 MKM  C7   C4   C3   120.22  3.000
 MKM  C6   C5   C4   107.94  3.000
 MKM  C6   C5   C18  109.75  3.000
 MKM  C4   C5   C18  108.41  3.000
 MKM  C6   C5   C10  108.73  3.000
 MKM  C18  C5   C10  111.52  3.000
 MKM  C4   C5   C10  110.42  3.000
 MKM  H39  C6   H38  106.29  3.000
 MKM  H39  C6   C5   109.57  3.000
 MKM  H38  C6   C5   108.48  3.000
 MKM  H39  C6   C1   108.84  3.000
 MKM  H38  C6   C1   108.78  3.000
 MKM  C5   C6   C1   114.56  3.000
 MKM  H40  C7   C8   116.53  3.000
 MKM  H40  C7   C4   118.60  3.000
 MKM  C8   C7   C4   124.86  3.000
 MKM  H43  C8   H42  105.22  3.000
 MKM  H43  C8   C9   109.75  3.000
 MKM  H42  C8   C9   110.13  3.000
 MKM  H43  C8   C7   109.42  3.000
 MKM  H42  C8   C7   109.37  3.000
 MKM  C9   C8   C7   112.69  3.000
 MKM  H44  C9   C8   108.30  3.000
 MKM  H44  C9   C11  109.58  3.000
 MKM  C8   C9   C11  110.52  3.000
 MKM  H44  C9   C10  109.47  3.000
 MKM  C11  C9   C10  109.05  3.000
 MKM  C8   C9   C10  109.91  3.000
 MKM  C20  O1   C2   114.58  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
 MKM  Var_01  C12  C13  C14  C10   -53.34  30.0  1
 MKM  Var_02  C17  C16  C15  C11    21.98  30.0  1
 MKM  Var_03  C15  C16  C17  C12     3.86  30.0  1
 MKM  Var_04  C7   C4   C3   C2   -128.00  30.0  1
 MKM  Var_05  C5   C6   C1   C2    -57.34  30.0  1
 MKM  Var_06  C8   C7   C4   C3   -177.27  30.0  1
 MKM  Var_07  C9   C8   C7   C4     13.19  30.0  1
 MKM  Var_08  C21  C20  O1   C2   -177.84  30.0  1
 MKM  Var_09  O1   C20  C21  N      65.38  30.0  3
 MKM  Var_10  C22  N    C21  C20    81.44  30.0  2
 MKM  Var_11  C23  C22  N    C21  -158.29  30.0  2
 MKM  Var_12  C25  C24  N    C21    75.91  30.0  3
 MKM  Var_13  H27  C23  C22  N     175.75  30.0  3
 MKM  Var_14  H32  C25  C24  N     -63.39  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
 MKM  chir_01  C10  C9   C5   C14  negativ
 MKM  chir_02  C11  C15  C9   C12  negativ
 MKM  chir_03  C12  C13  C17  C11  positiv
 MKM  chir_04  C2   C3   O1   C1   negativ
 MKM  chir_05  C5   C10  C4   C6   positiv
 MKM  chir_06  C9   C10  C11  C8   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
 MKM  plan-1  C12  0.020
 MKM  plan-1  C16  0.020
 MKM  plan-1  C17  0.020
 MKM  plan-1  O2   0.020

