# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 10:48:52 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 2-[(1R,2R,3S,5R,6R,7S)-2-benzyl-6-hydroxytricyclo[3.3.1.1~3,7~]decan-2-yl]-1-(3-hydroxyazetidin-1-yl)ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CN(C1)C(=O)C[C@@]2(Cc3ccccc3)C4CC5CC2CC(C4)[C@@H]5O
#
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
 8KD  8KD  2-[(1R,2R,3S,5R,6R,7S)-2-benzyl-6-hydroxytricyclo[3.3.1.1~3,7~]decan-2-yl]-1-(3-hydroxyazetidin-1-yl)ethan-1-one  ligand  55  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8KD
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
 8KD  C13  C  CR16  0  -0.315   0.5382  -2.7178  -0.4693
 8KD  C18  C  CR16  0  -0.238   1.5989  -3.5172  -0.8747
 8KD  C15  C  C     0   0.541   1.3971   1.2639   0.4268
 8KD  C19  C  CR16  0  -0.275   2.8214  -3.4466  -0.2192
 8KD  C20  C  CR16  0  -0.242   2.9694  -2.5722   0.8483
 8KD  C21  C  CR16  0  -0.319   1.9081  -1.7680   1.2418
 8KD  C22  C  C     0  -0.272   3.9047   1.2391   0.6122
 8KD  C23  C  C     0  -0.025   4.5586   0.4287  -0.5218
 8KD  C24  C  C     0  -0.284   3.1753   0.3843  -1.2166
 8KD  C11  C  CH2   0  -0.536  -0.4636  -0.9551   1.0672
 8KD  C12  C  CH2   0  -0.603   0.2712   0.8789  -0.5023
 8KD  C1   C  CH1   0  -0.235  -1.8491  -0.3444  -1.0248
 8KD  C2   C  CT    0  -0.012  -0.9528   0.1825   0.1291
 8KD  C3   C  CH1   0  -0.229  -1.8401   1.1533   0.9535
 8KD  C4   C  CH2   0  -0.440  -3.0648   0.4187   1.5172
 8KD  C5   C  CH1   0  -0.262  -3.9216  -0.1337   0.3749
 8KD  C6   C  CH2   0  -0.453  -3.0829  -1.0791  -0.4893
 8KD  C7   C  CH2   0  -0.443  -2.3604   0.8094  -1.8991
 8KD  C8   C  CH1   0   0.094  -4.4166   1.0059  -0.5133
 8KD  C9   C  CH1   0  -0.290  -3.2040   1.7686  -1.0582
 8KD  C10  C  CH2   0  -0.438  -2.3594   2.3126   0.0954
 8KD  C14  C  CR6   0   0.150   0.6767  -1.8169   0.5884
 8KD  N16  N  N     0  -0.450   2.6285   1.0721  -0.0573
 8KD  O17  O  O     0  -0.502   1.2305   1.7705   1.5331
 8KD  O26  O  OH1   0  -0.680  -5.2843   1.8258   0.2416
 8KD  H44  H  HCR6  0   0.245  -0.4122  -2.8155  -0.9787
 8KD  H45  H  HCR6  0   0.253   1.4665  -4.2061  -1.6993
 8KD  H46  H  HCR6  0   0.252   3.6459  -4.0746  -0.5312
 8KD  H47  H  HCR6  0   0.253   3.9116  -2.5169   1.3794
 8KD  H48  H  HCR6  0   0.246   2.0348  -1.0910   2.0788
 8KD  H50  H  H     0   0.246   3.9529   0.7953   1.6083
 8KD  H49  H  H     0   0.247   4.2429   2.2772   0.6681
 8KD  H51  H  H     0   0.233   4.8753  -0.5657  -0.1943
 8KD  H52  H  H     0   0.250   3.1247   0.9685  -2.1388
 8KD  H53  H  H     0   0.252   2.7613  -0.6107  -1.3913
 8KD  H40  H  HCH2  0   0.253  -0.1668  -0.4973   2.0136
 8KD  H41  H  HCH2  0   0.256  -1.3002  -1.6085   1.3139
 8KD  H42  H  HCH2  0   0.283  -0.0297   1.8059  -0.9950
 8KD  H43  H  HCH2  0   0.266   0.6525   0.2449  -1.3065
 8KD  H27  H  HCH1  0   0.230  -1.2695  -1.0223  -1.6585
 8KD  H28  H  HCH1  0   0.237  -1.2508   1.5517   1.7810
 8KD  H29  H  HCH2  0   0.235  -2.7742  -0.3919   2.1897
 8KD  H30  H  HCH2  0   0.231  -3.6490   1.1131   2.1263
 8KD  H31  H  HCH1  0   0.228  -4.7838  -0.6756   0.7777
 8KD  H33  H  HCH2  0   0.232  -3.6745  -1.4359  -1.3387
 8KD  H32  H  HCH2  0   0.238  -2.8123  -1.9736   0.0760
 8KD  H34  H  HCH2  0   0.239  -1.5420   1.3471  -2.3823
 8KD  H35  H  HCH2  0   0.232  -2.9645   0.3941  -2.7126
 8KD  H36  H  HCH1  0   0.198  -4.9643   0.5724  -1.3660
 8KD  H37  H  HCH1  0   0.228  -3.5527   2.5960  -1.6881
 8KD  H39  H  HCH2  0   0.229  -2.9513   2.9860   0.7214
 8KD  H38  H  HCH2  0   0.230  -1.5402   2.9214  -0.2954
 8KD  H55  H  HOH1  0   0.444  -5.5219   2.5862  -0.2985
 8KD  O25  O  OH1   0  -0.663   5.5830   1.1195  -1.1665
 8KD  H54  H  HOH1  0   0.458   5.9625   0.5462  -1.8398

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
 8KD  O26  C8   single    1.412  0.020  1.412
 8KD  C5   C8   single    1.527  0.020  1.527
 8KD  C5   C4   single    1.531  0.020  1.531
 8KD  C5   C6   single    1.531  0.020  1.531
 8KD  C8   C9   single    1.533  0.020  1.533
 8KD  C4   C3   single    1.535  0.020  1.535
 8KD  C6   C1   single    1.533  0.020  1.533
 8KD  C9   C10  single    1.530  0.020  1.530
 8KD  C9   C7   single    1.529  0.020  1.529
 8KD  C10  C3   single    1.533  0.020  1.533
 8KD  C3   C2   single    1.552  0.020  1.552
 8KD  C1   C7   single    1.535  0.020  1.535
 8KD  C1   C2   single    1.553  0.020  1.553
 8KD  C11  C2   single    1.554  0.020  1.554
 8KD  C11  C14  single    1.507  0.020  1.507
 8KD  C2   C12  single    1.543  0.020  1.543
 8KD  C21  C14  aromatic  1.395  0.020  1.395
 8KD  C21  C20  aromatic  1.389  0.020  1.389
 8KD  C14  C13  aromatic  1.396  0.020  1.396
 8KD  C20  C19  aromatic  1.388  0.020  1.388
 8KD  C12  C15  single    1.510  0.020  1.510
 8KD  C13  C18  aromatic  1.389  0.020  1.389
 8KD  C19  C18  aromatic  1.389  0.020  1.389
 8KD  C15  O17  double    1.228  0.020  1.228
 8KD  C15  N16  single    1.337  0.020  1.337
 8KD  N16  C22  single    1.451  0.020  1.451
 8KD  N16  C24  single    1.455  0.020  1.455
 8KD  C22  C23  single    1.540  0.020  1.540
 8KD  C24  C23  single    1.549  0.020  1.549
 8KD  C23  O25  single    1.394  0.020  1.394
 8KD  C13  H44  single    0.930  0.020  1.080
 8KD  C18  H45  single    0.930  0.020  1.080
 8KD  C19  H46  single    0.930  0.020  1.080
 8KD  C20  H47  single    0.930  0.020  1.080
 8KD  C21  H48  single    0.930  0.020  1.080
 8KD  C22  H50  single    0.970  0.020  1.090
 8KD  C22  H49  single    0.970  0.020  1.090
 8KD  C23  H51  single    0.970  0.020  1.090
 8KD  C24  H52  single    0.970  0.020  1.090
 8KD  C24  H53  single    0.970  0.020  1.090
 8KD  C11  H40  single    0.970  0.020  1.090
 8KD  C11  H41  single    0.970  0.020  1.090
 8KD  C12  H42  single    0.970  0.020  1.090
 8KD  C12  H43  single    0.970  0.020  1.090
 8KD  C1   H27  single    0.970  0.020  1.090
 8KD  C3   H28  single    0.970  0.020  1.090
 8KD  C4   H29  single    0.970  0.020  1.090
 8KD  C4   H30  single    0.970  0.020  1.090
 8KD  C5   H31  single    0.970  0.020  1.090
 8KD  C6   H33  single    0.970  0.020  1.090
 8KD  C6   H32  single    0.970  0.020  1.090
 8KD  C7   H34  single    0.970  0.020  1.090
 8KD  C7   H35  single    0.970  0.020  1.090
 8KD  C8   H36  single    0.970  0.020  1.090
 8KD  C9   H37  single    0.970  0.020  1.090
 8KD  C10  H39  single    0.970  0.020  1.090
 8KD  C10  H38  single    0.970  0.020  1.090
 8KD  O25  H54  single    0.850  0.020  0.980
 8KD  O26  H55  single    0.850  0.020  0.980

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
 8KD  H44  C13  C14  120.10  3.000
 8KD  H44  C13  C18  118.77  3.000
 8KD  C14  C13  C18  121.12  3.000
 8KD  H45  C18  C19  119.96  3.000
 8KD  H45  C18  C13  119.69  3.000
 8KD  C19  C18  C13  120.35  3.000
 8KD  O17  C15  N16  120.68  3.000
 8KD  N16  C15  C12  115.31  3.000
 8KD  O17  C15  C12  123.94  3.000
 8KD  H46  C19  C20  120.40  3.000
 8KD  H46  C19  C18  120.33  3.000
 8KD  C20  C19  C18  119.27  3.000
 8KD  H47  C20  C21  119.76  3.000
 8KD  H47  C20  C19  120.15  3.000
 8KD  C21  C20  C19  120.09  3.000
 8KD  H48  C21  C14  119.13  3.000
 8KD  H48  C21  C20  119.42  3.000
 8KD  C14  C21  C20  121.45  3.000
 8KD  H49  C22  H50  109.01  3.000
 8KD  H49  C22  N16  113.90  3.000
 8KD  H50  C22  N16  114.40  3.000
 8KD  H49  C22  C23  113.96  3.000
 8KD  H50  C22  C23  116.06  3.000
 8KD  N16  C22  C23   88.46  3.000
 8KD  H51  C23  O25  112.10  3.000
 8KD  H51  C23  C24  111.52  3.000
 8KD  O25  C23  C24  117.60  3.000
 8KD  H51  C23  C22  112.40  3.000
 8KD  O25  C23  C22  113.08  3.000
 8KD  C24  C23  C22   88.06  3.000
 8KD  H53  C24  H52  109.55  3.000
 8KD  H53  C24  N16  114.58  3.000
 8KD  H52  C24  N16  113.72  3.000
 8KD  H53  C24  C23  115.89  3.000
 8KD  H52  C24  C23  113.86  3.000
 8KD  N16  C24  C23   87.98  3.000
 8KD  H41  C11  H40  105.30  3.000
 8KD  H41  C11  C14  108.05  3.000
 8KD  H40  C11  C14  108.02  3.000
 8KD  H41  C11  C2   109.51  3.000
 8KD  H40  C11  C2   107.56  3.000
 8KD  C14  C11  C2   117.71  3.000
 8KD  H43  C12  H42  104.87  3.000
 8KD  H43  C12  C2   108.43  3.000
 8KD  H42  C12  C2   110.43  3.000
 8KD  H43  C12  C15  109.91  3.000
 8KD  H42  C12  C15  105.47  3.000
 8KD  C2   C12  C15  117.05  3.000
 8KD  H27  C1   C7   108.19  3.000
 8KD  H27  C1   C6   109.38  3.000
 8KD  C7   C1   C6   106.93  3.000
 8KD  H27  C1   C2   109.56  3.000
 8KD  C7   C1   C2   111.12  3.000
 8KD  C6   C1   C2   111.56  3.000
 8KD  C3   C2   C1   106.08  3.000
 8KD  C1   C2   C12  107.86  3.000
 8KD  C3   C2   C12  112.86  3.000
 8KD  C12  C2   C11  109.13  3.000
 8KD  C1   C2   C11  112.46  3.000
 8KD  C3   C2   C11  108.50  3.000
 8KD  H28  C3   C10  109.35  3.000
 8KD  H28  C3   C4   109.09  3.000
 8KD  C10  C3   C4   107.28  3.000
 8KD  H28  C3   C2   108.81  3.000
 8KD  C10  C3   C2   111.67  3.000
 8KD  C4   C3   C2   110.59  3.000
 8KD  H30  C4   H29  105.70  3.000
 8KD  H30  C4   C5   110.24  3.000
 8KD  H29  C4   C5   109.90  3.000
 8KD  H30  C4   C3   109.09  3.000
 8KD  H29  C4   C3   111.64  3.000
 8KD  C5   C4   C3   110.19  3.000
 8KD  H31  C5   C8   109.15  3.000
 8KD  H31  C5   C6   109.47  3.000
 8KD  C8   C5   C6   108.06  3.000
 8KD  H31  C5   C4   110.16  3.000
 8KD  C6   C5   C4   109.71  3.000
 8KD  C8   C5   C4   110.25  3.000
 8KD  H32  C6   H33  105.57  3.000
 8KD  H32  C6   C5   110.45  3.000
 8KD  H33  C6   C5   110.07  3.000
 8KD  H32  C6   C1   111.96  3.000
 8KD  H33  C6   C1   108.67  3.000
 8KD  C5   C6   C1   110.01  3.000
 8KD  H35  C7   H34  105.75  3.000
 8KD  H35  C7   C9   110.00  3.000
 8KD  H34  C7   C9   110.36  3.000
 8KD  H35  C7   C1   108.77  3.000
 8KD  H34  C7   C1   111.86  3.000
 8KD  C9   C7   C1   109.99  3.000
 8KD  H36  C8   O26  109.66  3.000
 8KD  H36  C8   C9   108.29  3.000
 8KD  O26  C8   C9   112.78  3.000
 8KD  H36  C8   C5   108.51  3.000
 8KD  C9   C8   C5   108.76  3.000
 8KD  O26  C8   C5   108.75  3.000
 8KD  H37  C9   C10  109.90  3.000
 8KD  H37  C9   C8   109.15  3.000
 8KD  C10  C9   C8   110.23  3.000
 8KD  H37  C9   C7   109.43  3.000
 8KD  C10  C9   C7   109.46  3.000
 8KD  C8   C9   C7   108.65  3.000
 8KD  H38  C10  H39  105.51  3.000
 8KD  H38  C10  C9   110.02  3.000
 8KD  H39  C10  C9   110.60  3.000
 8KD  H38  C10  C3   111.56  3.000
 8KD  H39  C10  C3   109.19  3.000
 8KD  C9   C10  C3   109.89  3.000
 8KD  C11  C14  C21  119.93  3.000
 8KD  C21  C14  C13  117.71  3.000
 8KD  C11  C14  C13  122.31  3.000
 8KD  C24  N16  C22   95.25  3.000
 8KD  C24  N16  C15  134.64  3.000
 8KD  C22  N16  C15  128.80  3.000
 8KD  H55  O26  C8   108.08  3.000
 8KD  H54  O25  C23  108.56  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
 8KD  CONST_01  C20  C21  C14  C13    0.00   0.0  0
 8KD  CONST_02  C20  C19  C18  C13    0.00   0.0  0
 8KD  CONST_03  C21  C14  C13  C18    0.00   0.0  0
 8KD  CONST_04  C21  C20  C19  C18    0.00   0.0  0
 8KD  CONST_05  C14  C21  C20  C19    0.00   0.0  0
 8KD  CONST_06  C14  C13  C18  C19    0.00   0.0  0
 8KD  CONST_07  C11  C14  C13  C18  180.00   0.0  0
 8KD  CONST_08  C11  C14  C21  C20  180.00   0.0  0
 8KD  CONST_09  H48  C21  C14  C13  180.00   0.0  0
 8KD  CONST_10  H46  C19  C18  C13  180.00   0.0  0
 8KD  CONST_11  H47  C20  C19  C18  180.00   0.0  0
 8KD  CONST_12  H44  C13  C18  C19  180.00   0.0  0
 8KD  CONST_13  H45  C18  C19  C20  180.00   0.0  0
 8KD  CONST_14  C12  C15  N16  C22  180.00   0.0  0
 8KD  CONST_15  O17  C15  N16  C22    0.00   0.0  0
 8KD  CONST_16  C12  C15  N16  C24    0.00   0.0  0
 8KD  CONST_17  O17  C15  N16  C24  180.00   0.0  0
 8KD  Var_01    C23  C24  N16  C22    3.92  30.0  1
 8KD  Var_02    C2   C11  C14  C13  -69.28  30.0  2
 8KD  Var_03    N16  C15  C12  C2   140.30  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
 8KD  chir_01  C23  C22  C24  O25  negativ
 8KD  chir_02  C1   C6   C7   C2   negativ
 8KD  chir_03  C2   C11  C1   C3   negativ
 8KD  chir_04  C3   C4   C10  C2   positiv
 8KD  chir_05  C5   C6   C4   C8   negativ
 8KD  chir_06  C8   O26  C5   C9   positiv
 8KD  chir_07  C9   C7   C10  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
 8KD  plan-1  C13  0.020
 8KD  plan-1  C18  0.020
 8KD  plan-1  C19  0.020
 8KD  plan-1  C20  0.020
 8KD  plan-1  C21  0.020
 8KD  plan-1  C11  0.020
 8KD  plan-1  C14  0.020
 8KD  plan-1  H44  0.020
 8KD  plan-1  H45  0.020
 8KD  plan-1  H46  0.020
 8KD  plan-1  H47  0.020
 8KD  plan-1  H48  0.020
 8KD  plan-2  C15  0.020
 8KD  plan-2  C22  0.020
 8KD  plan-2  C24  0.020
 8KD  plan-2  C12  0.020
 8KD  plan-2  N16  0.020
 8KD  plan-2  O17  0.020

