# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 17:19:06 2022
#   Inital geometry file: a 157 line input string
#   Ligand name: (3alpha,8alpha,14beta,22S,23R)-17,23-epoxyveratraman-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CN[C@H]2[C@@H](C)[C@@]3(CC[C@H]4[C@@H]5CC=C6C[C@@H](O)CC[C@]6(C)[C@H]5CC4=C3C)O[C@@H]2C1
#
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
 CY8  CY8  (3alpha,8alpha,14beta,22S,23R)-17,23-epoxyveratraman-3-ol  ligand  71  30  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CY8
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
 CY8  O01  O  O2    0  -0.519   2.8560   0.1385  -0.7407
 CY8  O02  O  OH1   0  -0.677  -8.1369  -0.9767  -0.0985
 CY8  N03  N  NH1   0  -0.608   5.8358   0.0196   1.2356
 CY8  C04  C  CH1   0  -0.212  -2.5690   0.0506   0.4324
 CY8  C05  C  CH1   0  -0.231  -1.9516   1.0691  -0.5212
 CY8  C06  C  CH1   0  -0.269  -0.6251   1.3914   0.1578
 CY8  C07  C  CT    0  -0.140  -3.8417  -0.6041  -0.1218
 CY8  C08  C  CT    0   0.199   2.2379   0.6445   0.4649
 CY8  C09  C  C     0   0.096  -0.1719   0.0421   0.6568
 CY8  C10  C  CH2   0  -0.488  -1.3886  -0.8461   0.8330
 CY8  C11  C  CH2   0  -0.427   0.4592   2.0602  -0.6583
 CY8  C12  C  CH1   0  -0.335   3.3683   0.6215   1.5670
 CY8  C13  C  CH2   0  -0.461   1.7257   2.0582   0.1834
 CY8  C14  C  C     0   0.042   1.1066  -0.3229   0.7776
 CY8  C15  C  CH2   0  -0.455  -2.9037   2.2250  -0.7507
 CY8  C16  C  CH1   0  -0.057   4.4565  -0.1978   0.8693
 CY8  C17  C  C     0   0.206  -4.7250   0.4836  -0.7209
 CY8  C18  C  CH1   0   0.099   4.2498   0.2010  -0.5755
 CY8  C19  C  CH2   0  -0.428  -4.6000  -1.2742   1.0417
 CY8  C20  C  C1    0  -0.333  -4.3002   1.7243  -0.9707
 CY8  C22  C  CH2   0  -0.548  -6.1473   0.0883  -1.0175
 CY8  C23  C  CH2   0  -0.469  -6.0207  -1.7103   0.7033
 CY8  C24  C  CH2   0  -0.458   5.0483  -0.6942  -1.4926
 CY8  C25  C  CH1   0   0.089  -6.8299  -0.5299   0.2002
 CY8  C26  C  CH3   0  -0.666   3.8757   1.9758   2.0526
 CY8  C27  C  CH3   0  -0.753   1.4913  -1.7296   1.1373
 CY8  C28  C  CH1   0  -0.253   6.5211  -0.5872  -1.0709
 CY8  C29  C  CH2   0  -0.267   6.6858  -0.8507   0.4290
 CY8  C30  C  CH3   0  -0.657   7.3993  -1.5324  -1.8783
 CY8  H1   H  HOH1  0   0.446  -8.6517  -0.2202  -0.3967
 CY8  H2   H  HNH1  0   0.349   5.9775  -0.1981   2.2145
 CY8  H4   H  HCH1  0   0.226  -2.8732   0.6160   1.3246
 CY8  H5   H  HCH1  0   0.226  -1.7393   0.5850  -1.4846
 CY8  H6   H  HCH1  0   0.227  -0.8470   2.0373   1.0230
 CY8  H7   H  HCH2  0   0.245  -1.4852  -1.2372   1.8488
 CY8  H8   H  HCH2  0   0.241  -1.3102  -1.7149   0.1739
 CY8  H9   H  HCH2  0   0.213   0.6153   1.5186  -1.5966
 CY8  H10  H  HCH2  0   0.231   0.1776   3.0828  -0.9214
 CY8  H11  H  HCH1  0   0.244   2.9944   0.0897   2.4457
 CY8  H12  H  HCH2  0   0.224   1.4959   2.5584   1.1283
 CY8  H13  H  HCH2  0   0.238   2.5221   2.6387  -0.2883
 CY8  H14  H  HCH2  0   0.226  -2.8876   2.9016   0.1135
 CY8  H15  H  HCH2  0   0.237  -2.5923   2.8320  -1.6058
 CY8  H16  H  HCH1  0   0.217   4.1904  -1.2671   0.9530
 CY8  H17  H  HCH1  0   0.190   4.6089   1.2359  -0.7102
 CY8  H18  H  HCH2  0   0.238  -4.0236  -2.1331   1.3966
 CY8  H19  H  HCH2  0   0.223  -4.6441  -0.5693   1.8792
 CY8  H20  H  H     0   0.222  -5.0125   2.4389  -1.3749
 CY8  H24  H  HCH2  0   0.241  -6.7107   0.9616  -1.3605
 CY8  H25  H  HCH2  0   0.231  -6.1801  -0.6453  -1.8324
 CY8  H26  H  HCH2  0   0.221  -6.0173  -2.4999  -0.0553
 CY8  H27  H  HCH2  0   0.238  -6.4920  -2.1336   1.5946
 CY8  H28  H  HCH2  0   0.212   4.7064  -1.7314  -1.3926
 CY8  H29  H  HCH2  0   0.235   4.9367  -0.4114  -2.5431
 CY8  H30  H  HCH1  0   0.190  -6.8588   0.2318   0.9955
 CY8  H31  H  HCH3  0   0.231   3.0859   2.5491   2.5368
 CY8  H32  H  HCH3  0   0.237   4.6604   1.8273   2.7941
 CY8  H33  H  HCH3  0   0.220   4.2947   2.5908   1.2562
 CY8  H34  H  HCH3  0   0.235   2.1006  -1.7754   2.0427
 CY8  H35  H  HCH3  0   0.254   0.6187  -2.3576   1.3055
 CY8  H36  H  HCH3  0   0.236   2.0800  -2.1886   0.3405
 CY8  H37  H  HCH1  0   0.222   6.8503   0.4410  -1.2623
 CY8  H38  H  HCH2  0   0.231   7.7273  -0.6810   0.7127
 CY8  H39  H  HCH2  0   0.184   6.4744  -1.9180   0.6130
 CY8  H40  H  HCH3  0   0.230   7.2931  -1.3498  -2.9486
 CY8  H41  H  HCH3  0   0.228   8.4541  -1.4118  -1.6257
 CY8  H42  H  HCH3  0   0.217   7.1294  -2.5744  -1.6924
 CY8  C21  C  CH3   0  -0.671  -3.5264  -1.6433  -1.2070
 CY8  H21  H  HCH3  0   0.228  -3.0177  -2.5148  -0.7919
 CY8  H22  H  HCH3  0   0.236  -4.4293  -2.0135  -1.6921
 CY8  H23  H  HCH3  0   0.233  -2.8899  -1.2237  -1.9875

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
 CY8  N03  C29  single  1.460  0.020  1.460
 CY8  N03  C16  single  1.444  0.020  1.444
 CY8  C26  C12  single  1.526  0.020  1.526
 CY8  C29  C28  single  1.532  0.020  1.532
 CY8  C28  C30  single  1.522  0.020  1.522
 CY8  C28  C24  single  1.536  0.020  1.536
 CY8  C13  C11  single  1.521  0.020  1.521
 CY8  C13  C08  single  1.530  0.020  1.530
 CY8  C18  C16  single  1.513  0.020  1.513
 CY8  C18  C24  single  1.510  0.020  1.510
 CY8  C18  O01  single  1.405  0.020  1.405
 CY8  C11  C06  single  1.513  0.020  1.513
 CY8  C16  C12  single  1.530  0.020  1.530
 CY8  C12  C08  single  1.579  0.020  1.579
 CY8  C08  O01  single  1.446  0.020  1.446
 CY8  C08  C14  single  1.521  0.020  1.521
 CY8  C15  C05  single  1.515  0.020  1.515
 CY8  C15  C20  single  1.500  0.020  1.500
 CY8  C06  C05  single  1.525  0.020  1.525
 CY8  C06  C09  single  1.508  0.020  1.508
 CY8  C05  C04  single  1.526  0.020  1.526
 CY8  C20  C17  double  1.335  0.020  1.335
 CY8  C14  C09  double  1.335  0.020  1.335
 CY8  C14  C27  single  1.502  0.020  1.502
 CY8  C09  C10  single  1.517  0.020  1.517
 CY8  C04  C10  single  1.536  0.020  1.536
 CY8  C04  C07  single  1.535  0.020  1.535
 CY8  C17  C07  single  1.524  0.020  1.524
 CY8  C17  C22  single  1.506  0.020  1.506
 CY8  C07  C21  single  1.535  0.020  1.535
 CY8  C07  C19  single  1.542  0.020  1.542
 CY8  C22  C25  single  1.527  0.020  1.527
 CY8  C19  C23  single  1.524  0.020  1.524
 CY8  C25  O02  single  1.413  0.020  1.413
 CY8  C25  C23  single  1.517  0.020  1.517
 CY8  O02  H1   single  0.850  0.020  0.980
 CY8  N03  H2   single  0.890  0.020  1.040
 CY8  C04  H4   single  0.970  0.020  1.090
 CY8  C05  H5   single  0.970  0.020  1.090
 CY8  C06  H6   single  0.970  0.020  1.090
 CY8  C10  H7   single  0.970  0.020  1.090
 CY8  C10  H8   single  0.970  0.020  1.090
 CY8  C11  H9   single  0.970  0.020  1.090
 CY8  C11  H10  single  0.970  0.020  1.090
 CY8  C12  H11  single  0.970  0.020  1.090
 CY8  C13  H12  single  0.970  0.020  1.090
 CY8  C13  H13  single  0.970  0.020  1.090
 CY8  C15  H14  single  0.970  0.020  1.090
 CY8  C15  H15  single  0.970  0.020  1.090
 CY8  C16  H16  single  0.970  0.020  1.090
 CY8  C18  H17  single  0.970  0.020  1.090
 CY8  C19  H18  single  0.970  0.020  1.090
 CY8  C19  H19  single  0.970  0.020  1.090
 CY8  C20  H20  single  0.930  0.020  1.080
 CY8  C21  H21  single  0.970  0.020  1.090
 CY8  C21  H22  single  0.970  0.020  1.090
 CY8  C21  H23  single  0.970  0.020  1.090
 CY8  C22  H24  single  0.970  0.020  1.090
 CY8  C22  H25  single  0.970  0.020  1.090
 CY8  C23  H26  single  0.970  0.020  1.090
 CY8  C23  H27  single  0.970  0.020  1.090
 CY8  C24  H28  single  0.970  0.020  1.090
 CY8  C24  H29  single  0.970  0.020  1.090
 CY8  C25  H30  single  0.970  0.020  1.090
 CY8  C26  H31  single  0.970  0.020  1.090
 CY8  C26  H32  single  0.970  0.020  1.090
 CY8  C26  H33  single  0.970  0.020  1.090
 CY8  C27  H34  single  0.970  0.020  1.090
 CY8  C27  H35  single  0.970  0.020  1.090
 CY8  C27  H36  single  0.970  0.020  1.090
 CY8  C28  H37  single  0.970  0.020  1.090
 CY8  C29  H38  single  0.970  0.020  1.090
 CY8  C29  H39  single  0.970  0.020  1.090
 CY8  C30  H40  single  0.970  0.020  1.090
 CY8  C30  H41  single  0.970  0.020  1.090
 CY8  C30  H42  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
 CY8  C18  O01  C08  108.08  3.000
 CY8  H1   O02  C25  108.16  3.000
 CY8  H2   N03  C29  108.93  3.000
 CY8  H2   N03  C16  110.28  3.000
 CY8  C29  N03  C16  109.05  3.000
 CY8  H4   C04  C10  107.54  3.000
 CY8  H4   C04  C07  106.44  3.000
 CY8  C10  C04  C07  118.85  3.000
 CY8  H4   C04  C05  106.02  3.000
 CY8  C07  C04  C05  113.24  3.000
 CY8  C10  C04  C05  103.99  3.000
 CY8  H5   C05  C15  108.95  3.000
 CY8  H5   C05  C06  108.39  3.000
 CY8  C15  C05  C06  116.93  3.000
 CY8  H5   C05  C04  109.39  3.000
 CY8  C06  C05  C04  102.41  3.000
 CY8  C15  C05  C04  110.47  3.000
 CY8  H6   C06  C11  107.97  3.000
 CY8  H6   C06  C09  108.97  3.000
 CY8  C11  C06  C09  111.01  3.000
 CY8  H6   C06  C05  107.35  3.000
 CY8  C09  C06  C05  102.69  3.000
 CY8  C11  C06  C05  118.47  3.000
 CY8  C21  C07  C19  109.88  3.000
 CY8  C19  C07  C17  108.77  3.000
 CY8  C21  C07  C17  108.93  3.000
 CY8  C19  C07  C04  108.71  3.000
 CY8  C21  C07  C04  111.94  3.000
 CY8  C17  C07  C04  108.55  3.000
 CY8  C14  C08  C13  112.12  3.000
 CY8  C14  C08  C12  112.32  3.000
 CY8  C13  C08  C12  112.44  3.000
 CY8  C14  C08  O01  105.47  3.000
 CY8  C12  C08  O01  105.72  3.000
 CY8  C13  C08  O01  108.24  3.000
 CY8  C14  C09  C10  126.70  3.000
 CY8  C10  C09  C06  108.74  3.000
 CY8  C14  C09  C06  124.21  3.000
 CY8  H8   C10  H7   106.40  3.000
 CY8  H8   C10  C09  109.74  3.000
 CY8  H7   C10  C09  112.86  3.000
 CY8  H8   C10  C04  111.22  3.000
 CY8  H7   C10  C04  112.56  3.000
 CY8  C09  C10  C04  104.14  3.000
 CY8  H10  C11  H9   107.05  3.000
 CY8  H10  C11  C13  110.43  3.000
 CY8  H9   C11  C13  110.79  3.000
 CY8  H10  C11  C06  111.04  3.000
 CY8  H9   C11  C06  110.24  3.000
 CY8  C13  C11  C06  107.32  3.000
 CY8  H11  C12  C26  106.85  3.000
 CY8  H11  C12  C16  110.45  3.000
 CY8  C26  C12  C16  112.57  3.000
 CY8  H11  C12  C08  108.86  3.000
 CY8  C16  C12  C08  101.46  3.000
 CY8  C26  C12  C08  116.57  3.000
 CY8  H13  C13  H12  106.45  3.000
 CY8  H13  C13  C11  111.56  3.000
 CY8  H12  C13  C11  107.62  3.000
 CY8  H13  C13  C08  109.05  3.000
 CY8  H12  C13  C08  109.51  3.000
 CY8  C11  C13  C08  112.46  3.000
 CY8  C27  C14  C09  121.53  3.000
 CY8  C27  C14  C08  117.02  3.000
 CY8  C09  C14  C08  121.32  3.000
 CY8  H15  C15  H14  105.62  3.000
 CY8  H15  C15  C20  109.61  3.000
 CY8  H14  C15  C20  109.57  3.000
 CY8  H15  C15  C05  111.28  3.000
 CY8  H14  C15  C05  109.99  3.000
 CY8  C20  C15  C05  110.65  3.000
 CY8  H16  C16  C18  107.12  3.000
 CY8  H16  C16  C12  108.20  3.000
 CY8  C18  C16  C12  101.37  3.000
 CY8  H16  C16  N03  110.89  3.000
 CY8  C12  C16  N03  118.89  3.000
 CY8  C18  C16  N03  109.46  3.000
 CY8  C22  C17  C20  120.51  3.000
 CY8  C22  C17  C07  115.95  3.000
 CY8  C20  C17  C07  123.54  3.000
 CY8  H17  C18  C24  108.04  3.000
 CY8  H17  C18  C16  108.61  3.000
 CY8  C24  C18  C16  110.58  3.000
 CY8  H17  C18  O01  110.50  3.000
 CY8  C24  C18  O01  115.27  3.000
 CY8  C16  C18  O01  103.66  3.000
 CY8  H19  C19  H18  106.17  3.000
 CY8  H19  C19  C23  108.44  3.000
 CY8  H18  C19  C23  109.80  3.000
 CY8  H19  C19  C07  108.48  3.000
 CY8  H18  C19  C07  109.09  3.000
 CY8  C23  C19  C07  114.53  3.000
 CY8  H20  C20  C17  118.17  3.000
 CY8  H20  C20  C15  116.44  3.000
 CY8  C17  C20  C15  125.39  3.000
 CY8  H25  C22  H24  106.59  3.000
 CY8  H25  C22  C25  107.96  3.000
 CY8  H24  C22  C25  110.05  3.000
 CY8  H25  C22  C17  110.50  3.000
 CY8  H24  C22  C17  109.78  3.000
 CY8  C25  C22  C17  111.81  3.000
 CY8  H27  C23  H26  106.67  3.000
 CY8  H27  C23  C25  109.98  3.000
 CY8  H26  C23  C25  109.45  3.000
 CY8  H27  C23  C19  109.36  3.000
 CY8  H26  C23  C19  110.93  3.000
 CY8  C25  C23  C19  110.38  3.000
 CY8  H29  C24  H28  107.48  3.000
 CY8  H29  C24  C28  110.10  3.000
 CY8  H28  C24  C28  109.87  3.000
 CY8  H29  C24  C18  112.09  3.000
 CY8  H28  C24  C18  109.91  3.000
 CY8  C28  C24  C18  107.40  3.000
 CY8  H30  C25  C23  108.21  3.000
 CY8  H30  C25  C22  107.91  3.000
 CY8  C23  C25  C22  109.94  3.000
 CY8  H30  C25  O02  110.30  3.000
 CY8  C23  C25  O02  108.51  3.000
 CY8  C22  C25  O02  111.90  3.000
 CY8  H33  C26  H32  107.29  3.000
 CY8  H33  C26  H31  107.85  3.000
 CY8  H32  C26  H31  106.94  3.000
 CY8  H33  C26  C12  113.34  3.000
 CY8  H32  C26  C12  109.57  3.000
 CY8  H31  C26  C12  111.56  3.000
 CY8  H36  C27  H35  107.61  3.000
 CY8  H36  C27  H34  106.65  3.000
 CY8  H35  C27  H34  107.16  3.000
 CY8  H36  C27  C14  110.92  3.000
 CY8  H35  C27  C14  111.85  3.000
 CY8  H34  C27  C14  112.37  3.000
 CY8  H37  C28  C30  108.45  3.000
 CY8  H37  C28  C29  107.46  3.000
 CY8  C30  C28  C29  110.52  3.000
 CY8  H37  C28  C24  107.78  3.000
 CY8  C30  C28  C24  111.37  3.000
 CY8  C29  C28  C24  111.11  3.000
 CY8  H39  C29  H38  106.83  3.000
 CY8  H39  C29  C28  108.00  3.000
 CY8  H38  C29  C28  109.27  3.000
 CY8  H39  C29  N03  111.90  3.000
 CY8  H38  C29  N03  108.61  3.000
 CY8  C28  C29  N03  112.08  3.000
 CY8  H42  C30  H41  107.75  3.000
 CY8  H42  C30  H40  107.61  3.000
 CY8  H41  C30  H40  107.62  3.000
 CY8  H42  C30  C28  111.07  3.000
 CY8  H41  C30  C28  111.48  3.000
 CY8  H40  C30  C28  111.12  3.000
 CY8  H23  C21  H22  107.19  3.000
 CY8  H23  C21  H21  107.90  3.000
 CY8  H22  C21  H21  106.52  3.000
 CY8  H23  C21  C07  111.41  3.000
 CY8  H22  C21  C07  111.99  3.000
 CY8  H21  C21  C07  111.56  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
 CY8  Var_01  C08  C14  C09  C06     2.61   0.0  0
 CY8  Var_02  C15  C20  C17  C07     2.15   0.0  0
 CY8  Var_03  C10  C09  C14  C08   175.04   0.0  0
 CY8  Var_04  C06  C09  C10  C04    -0.70  30.0  1
 CY8  Var_05  C17  C20  C15  C05    13.53  30.0  1
 CY8  Var_06  C08  C13  C11  C06    64.37  30.0  1
 CY8  Var_07  C25  C22  C17  C07    52.69  30.0  1
 CY8  Var_08  C25  C23  C19  C07   -56.50  30.0  1
 CY8  Var_09  C28  C29  N03  C16    59.23  30.0  1
 CY8  Var_10  H20  C20  C17  C07  -178.39   0.0  0
 CY8  Var_11  H34  C27  C14  C08    61.68  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
 CY8  chir_01  C04  C05  C10  C07  positiv
 CY8  chir_02  C05  C04  C06  C15  positiv
 CY8  chir_03  C06  C11  C05  C09  negativ
 CY8  chir_04  C07  C19  C17  C04  negativ
 CY8  chir_05  C08  C13  C12  C14  negativ
 CY8  chir_06  C12  C08  C16  C26  negativ
 CY8  chir_07  C16  N03  C18  C12  positiv
 CY8  chir_08  C18  O01  C24  C16  positiv
 CY8  chir_09  C25  C22  O02  C23  negativ
 CY8  chir_10  C28  C29  C30  C24  negativ

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
 CY8  plan-1  C07  0.020
 CY8  plan-1  C15  0.020
 CY8  plan-1  C17  0.020
 CY8  plan-1  C20  0.020
 CY8  plan-1  C22  0.020
 CY8  plan-1  H20  0.020
 CY8  plan-2  C06  0.020
 CY8  plan-2  C08  0.020
 CY8  plan-2  C09  0.020
 CY8  plan-2  C10  0.020
 CY8  plan-2  C14  0.020
 CY8  plan-2  C27  0.020

