# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Sep 19 17:16:46 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: N-[(1r,3R,5S,7R)-3,5-dimethyltricyclo[3.3.1.1~3,7~]decane-1-carbonyl]-D-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]12CC3C[C@@](C)(C1)CC(C3)(C2)C(=O)N[C@H](Cc4ccccc4)C(O)=O
#
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
 8IX  8IX  "N-[(1r,3R,5S,7R)-3,5-dimethyltricyclo[3.3.1.1~3,7~]decane-1-carbonyl]-D-phenylalanine"  ligand  55  26  .  2022-09-16  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_8IX
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
 8IX  C10  C  CT    0  -0.096  122.1869   95.7864  84.3719
 8IX  C13  C  CH2   0  -0.390  123.4165   96.6965  81.8601
 8IX  C15  C  CH2   0  -0.366  121.9188   97.1774  83.7880
 8IX  C17  C  CH2   0  -0.375  124.3353   97.7556  83.9163
 8IX  C20  C  CR6   0   0.121  127.3418   97.7982  89.9305
 8IX  C21  C  CR16  0  -0.303  128.2384   96.8525  90.4240
 8IX  C22  C  CR16  0  -0.237  129.2314   97.2190  91.3205
 8IX  C24  C  CR16  0  -0.238  128.4513   99.4887  91.2550
 8IX  C02  C  C     0   0.534  127.5873   98.3320  87.0292
 8IX  C03  C  CH1   0  -0.130  126.8162   97.1236  87.5379
 8IX  C05  C  C     0   0.620  125.8924   96.5291  85.3731
 8IX  C06  C  CT    0  -0.250  124.6449   96.3681  84.5133
 8IX  C07  C  CH2   0  -0.396  124.9223   95.3892  83.3643
 8IX  C08  C  CH1   0  -0.252  123.7089   95.3131  82.4396
 8IX  C09  C  CH2   0  -0.390  122.4940   94.8229  83.2243
 8IX  C11  C  CH3   0  -0.641  120.9831   95.3040  85.1691
 8IX  C12  C  CH2   0  -0.406  123.4127   95.8790  85.2879
 8IX  C14  C  CT    0  -0.101  123.1189   97.6911  82.9870
 8IX  C16  C  CH3   0  -0.641  122.8293   99.0740  82.4207
 8IX  C19  C  CH2   0  -0.569  126.2753   97.4012  88.9509
 8IX  C23  C  CR16  0  -0.267  129.3412   98.5399  91.7384
 8IX  C25  C  CR16  0  -0.304  127.4602   99.1180  90.3548
 8IX  N04  N  NH1   0  -0.669  125.7096   96.7854  86.6819
 8IX  O18  O  O     0  -0.488  127.0212   96.4938  84.9006
 8IX  O26  O  O     0  -0.427  128.7832   98.4424  87.1032
 8IX  H1   H  HCH2  0   0.220  124.2696   97.0507  81.2712
 8IX  H2   H  HCH2  0   0.220  122.5592   96.6436  81.1803
 8IX  H3   H  HCH2  0   0.216  121.6888   97.8794  84.5989
 8IX  H4   H  HCH2  0   0.219  121.0318   97.1432  83.1438
 8IX  H5   H  HCH2  0   0.233  125.2041   98.1194  83.3575
 8IX  H6   H  HCH2  0   0.230  124.1473   98.4766  84.7198
 8IX  H7   H  HCR6  0   0.250  128.1551   95.8191  90.1066
 8IX  H8   H  HCR6  0   0.254  129.9190   96.4722  91.6964
 8IX  H9   H  HCR6  0   0.254  128.5263  100.5189  91.5787
 8IX  H10  H  HCH1  0   0.285  127.5278   96.2955  87.5895
 8IX  H11  H  HCH2  0   0.229  125.1489   94.3965  83.7674
 8IX  H12  H  HCH2  0   0.232  125.7996   95.7135  82.8011
 8IX  H13  H  HCH1  0   0.224  123.9275   94.6141  81.6269
 8IX  H14  H  HCH2  0   0.220  121.6226   94.7472  82.5644
 8IX  H15  H  HCH2  0   0.220  122.6793   93.8184  83.6210
 8IX  H16  H  HCH3  0   0.220  120.7603   95.9807  85.9974
 8IX  H17  H  HCH3  0   0.222  120.0938   95.2462  84.5375
 8IX  H18  H  HCH3  0   0.221  121.1594   94.3104  85.5876
 8IX  H19  H  HCH2  0   0.225  123.1544   96.5658  86.1018
 8IX  H20  H  HCH2  0   0.239  123.6146   94.9020  85.7402
 8IX  H21  H  HCH3  0   0.220  122.6256   99.7925  83.2182
 8IX  H22  H  HCH3  0   0.221  123.6771   99.4483  81.8425
 8IX  H23  H  HCH3  0   0.221  121.9583   99.0535  81.7617
 8IX  H24  H  HCH2  0   0.272  125.5109   98.1801  88.8931
 8IX  H25  H  HCH2  0   0.283  125.7767   96.4894  89.2893
 8IX  H26  H  HCR6  0   0.254  130.1140   98.8256  92.4403
 8IX  H27  H  HCR6  0   0.251  126.7675   99.8633  89.9811
 8IX  H28  H  HNH1  0   0.413  124.7785   96.8822  87.0521
 8IX  H29  H  HOH1  0   0.481  127.3041  100.0455  86.2801
 8IX  O01  O  OH1   0  -0.587  126.7836   99.2772  86.5604

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
 8IX  C13  C08  single    1.528  0.020  1.528
 8IX  C13  C14  single    1.532  0.020  1.532
 8IX  C16  C14  single    1.522  0.020  1.522
 8IX  C08  C09  single    1.527  0.020  1.527
 8IX  C08  C07  single    1.528  0.020  1.528
 8IX  C14  C15  single    1.532  0.020  1.532
 8IX  C14  C17  single    1.532  0.020  1.532
 8IX  C09  C10  single    1.530  0.020  1.530
 8IX  C07  C06  single    1.535  0.020  1.535
 8IX  C15  C10  single    1.532  0.020  1.532
 8IX  C17  C06  single    1.542  0.020  1.542
 8IX  C10  C12  single    1.533  0.020  1.533
 8IX  C10  C11  single    1.522  0.020  1.522
 8IX  C06  C12  single    1.535  0.020  1.535
 8IX  C06  C05  single    1.524  0.020  1.524
 8IX  O18  C05  double    1.224  0.020  1.224
 8IX  C05  N04  single    1.346  0.020  1.346
 8IX  N04  C03  single    1.439  0.020  1.439
 8IX  O26  C02  double    1.203  0.020  1.203
 8IX  O01  C02  single    1.326  0.020  1.326
 8IX  C02  C03  single    1.521  0.020  1.521
 8IX  C03  C19  single    1.538  0.020  1.538
 8IX  C19  C20  single    1.502  0.020  1.502
 8IX  C21  C20  aromatic  1.393  0.020  1.393
 8IX  C21  C22  aromatic  1.387  0.020  1.387
 8IX  C20  C25  aromatic  1.391  0.020  1.391
 8IX  C22  C23  aromatic  1.390  0.020  1.390
 8IX  C25  C24  aromatic  1.389  0.020  1.389
 8IX  C23  C24  aromatic  1.388  0.020  1.388
 8IX  C13  H1   single    0.970  0.020  1.090
 8IX  C13  H2   single    0.970  0.020  1.090
 8IX  C15  H3   single    0.970  0.020  1.090
 8IX  C15  H4   single    0.970  0.020  1.090
 8IX  C17  H5   single    0.970  0.020  1.090
 8IX  C17  H6   single    0.970  0.020  1.090
 8IX  C21  H7   single    0.930  0.020  1.080
 8IX  C22  H8   single    0.930  0.020  1.080
 8IX  C24  H9   single    0.930  0.020  1.080
 8IX  C03  H10  single    0.970  0.020  1.090
 8IX  C07  H11  single    0.970  0.020  1.090
 8IX  C07  H12  single    0.970  0.020  1.090
 8IX  C08  H13  single    0.970  0.020  1.090
 8IX  C09  H14  single    0.970  0.020  1.090
 8IX  C09  H15  single    0.970  0.020  1.090
 8IX  C11  H16  single    0.970  0.020  1.090
 8IX  C11  H17  single    0.970  0.020  1.090
 8IX  C11  H18  single    0.970  0.020  1.090
 8IX  C12  H19  single    0.970  0.020  1.090
 8IX  C12  H20  single    0.970  0.020  1.090
 8IX  C16  H21  single    0.970  0.020  1.090
 8IX  C16  H22  single    0.970  0.020  1.090
 8IX  C16  H23  single    0.970  0.020  1.090
 8IX  C19  H24  single    0.970  0.020  1.090
 8IX  C19  H25  single    0.970  0.020  1.090
 8IX  C23  H26  single    0.930  0.020  1.080
 8IX  C25  H27  single    0.930  0.020  1.080
 8IX  N04  H28  single    0.860  0.020  1.020
 8IX  O01  H29  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
 8IX  C12  C10  C11  109.79  3.000
 8IX  C11  C10  C09  110.61  3.000
 8IX  C12  C10  C09  109.02  3.000
 8IX  C11  C10  C15  110.42  3.000
 8IX  C12  C10  C15  108.23  3.000
 8IX  C09  C10  C15  108.73  3.000
 8IX  H2   C13  H1   106.94  3.000
 8IX  H2   C13  C14  109.62  3.000
 8IX  H1   C13  C14  109.68  3.000
 8IX  H2   C13  C08  109.96  3.000
 8IX  H1   C13  C08  110.34  3.000
 8IX  C14  C13  C08  110.24  3.000
 8IX  H4   C15  H3   106.54  3.000
 8IX  H4   C15  C14  109.69  3.000
 8IX  H3   C15  C14  109.65  3.000
 8IX  H4   C15  C10  109.70  3.000
 8IX  H3   C15  C10  109.63  3.000
 8IX  C14  C15  C10  111.51  3.000
 8IX  H6   C17  H5   106.96  3.000
 8IX  H6   C17  C14  109.64  3.000
 8IX  H5   C17  C14  109.54  3.000
 8IX  H6   C17  C06  110.04  3.000
 8IX  H5   C17  C06  109.71  3.000
 8IX  C14  C17  C06  110.88  3.000
 8IX  C25  C20  C19  120.67  3.000
 8IX  C25  C20  C21  118.75  3.000
 8IX  C19  C20  C21  120.57  3.000
 8IX  H7   C21  C22  119.74  3.000
 8IX  H7   C21  C20  119.58  3.000
 8IX  C22  C21  C20  120.68  3.000
 8IX  H8   C22  C23  120.07  3.000
 8IX  H8   C22  C21  119.79  3.000
 8IX  C23  C22  C21  120.13  3.000
 8IX  H9   C24  C25  119.81  3.000
 8IX  H9   C24  C23  120.14  3.000
 8IX  C25  C24  C23  120.05  3.000
 8IX  O26  C02  O01  123.96  3.000
 8IX  O01  C02  C03  112.16  3.000
 8IX  O26  C02  C03  123.79  3.000
 8IX  H10  C03  N04  110.52  3.000
 8IX  H10  C03  C19  108.80  3.000
 8IX  N04  C03  C19  108.56  3.000
 8IX  H10  C03  C02  106.71  3.000
 8IX  C19  C03  C02  110.01  3.000
 8IX  N04  C03  C02  112.18  3.000
 8IX  O18  C05  N04  120.39  3.000
 8IX  N04  C05  C06  117.23  3.000
 8IX  O18  C05  C06  122.29  3.000
 8IX  C12  C06  C07  108.64  3.000
 8IX  C12  C06  C05  113.96  3.000
 8IX  C07  C06  C05  109.99  3.000
 8IX  C05  C06  C17  106.73  3.000
 8IX  C12  C06  C17  108.72  3.000
 8IX  C07  C06  C17  108.69  3.000
 8IX  H12  C07  H11  107.03  3.000
 8IX  H12  C07  C08  109.93  3.000
 8IX  H11  C07  C08  110.00  3.000
 8IX  H12  C07  C06  110.00  3.000
 8IX  H11  C07  C06  109.88  3.000
 8IX  C08  C07  C06  109.96  3.000
 8IX  H13  C08  C09  109.61  3.000
 8IX  H13  C08  C07  108.83  3.000
 8IX  C09  C08  C07  109.69  3.000
 8IX  H13  C08  C13  109.57  3.000
 8IX  C07  C08  C13  109.66  3.000
 8IX  C09  C08  C13  109.47  3.000
 8IX  H15  C09  H14  106.81  3.000
 8IX  H15  C09  C08  110.23  3.000
 8IX  H14  C09  C08  110.21  3.000
 8IX  H15  C09  C10  109.86  3.000
 8IX  H14  C09  C10  109.62  3.000
 8IX  C08  C09  C10  110.06  3.000
 8IX  H18  C11  H17  107.74  3.000
 8IX  H18  C11  H16  107.81  3.000
 8IX  H17  C11  H16  107.77  3.000
 8IX  H18  C11  C10  111.18  3.000
 8IX  H17  C11  C10  110.96  3.000
 8IX  H16  C11  C10  111.22  3.000
 8IX  H20  C12  H19  107.20  3.000
 8IX  H20  C12  C06  110.15  3.000
 8IX  H19  C12  C06  111.36  3.000
 8IX  H20  C12  C10  109.90  3.000
 8IX  H19  C12  C10  107.05  3.000
 8IX  C06  C12  C10  111.06  3.000
 8IX  C16  C14  C17  109.78  3.000
 8IX  C17  C14  C15  108.61  3.000
 8IX  C16  C14  C15  110.50  3.000
 8IX  C17  C14  C13  108.61  3.000
 8IX  C15  C14  C13  108.61  3.000
 8IX  C16  C14  C13  110.67  3.000
 8IX  H23  C16  H22  107.81  3.000
 8IX  H23  C16  H21  107.70  3.000
 8IX  H22  C16  H21  107.80  3.000
 8IX  H23  C16  C14  111.04  3.000
 8IX  H22  C16  C14  111.14  3.000
 8IX  H21  C16  C14  111.19  3.000
 8IX  H25  C19  H24  106.97  3.000
 8IX  H25  C19  C03  107.12  3.000
 8IX  H24  C19  C03  109.03  3.000
 8IX  H25  C19  C20  110.03  3.000
 8IX  H24  C19  C20  110.05  3.000
 8IX  C03  C19  C20  113.40  3.000
 8IX  H26  C23  C24  120.22  3.000
 8IX  H26  C23  C22  120.15  3.000
 8IX  C24  C23  C22  119.63  3.000
 8IX  H27  C25  C24  119.73  3.000
 8IX  H27  C25  C20  119.52  3.000
 8IX  C24  C25  C20  120.75  3.000
 8IX  H28  N04  C05  120.10  3.000
 8IX  H28  N04  C03  118.02  3.000
 8IX  C05  N04  C03  121.24  3.000
 8IX  H29  O01  C02  109.98  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
 8IX  CONST_01  C23  C22  C21  C20     0.00   0.0  0
 8IX  CONST_02  C23  C24  C25  C20     0.00   0.0  0
 8IX  CONST_03  C24  C25  C20  C21     0.00   0.0  0
 8IX  CONST_04  C24  C23  C22  C21     0.00   0.0  0
 8IX  CONST_05  C25  C20  C21  C22     0.00   0.0  0
 8IX  CONST_06  C25  C24  C23  C22     0.00   0.0  0
 8IX  CONST_07  C19  C20  C21  C22   180.00   0.0  0
 8IX  CONST_08  C19  C20  C25  C24   180.00   0.0  0
 8IX  CONST_09  H8   C22  C21  C20   180.00   0.0  0
 8IX  CONST_10  H9   C24  C25  C20   180.00   0.0  0
 8IX  CONST_11  H27  C25  C20  C21   180.00   0.0  0
 8IX  CONST_12  H26  C23  C22  C21   180.00   0.0  0
 8IX  CONST_13  H9   C24  C23  C22   180.00   0.0  0
 8IX  CONST_14  H8   C22  C23  C24   180.00   0.0  0
 8IX  CONST_15  H7   C21  C22  C23   180.00   0.0  0
 8IX  CONST_16  H27  C25  C24  C23   180.00   0.0  0
 8IX  CONST_17  H7   C21  C20  C25   180.00   0.0  0
 8IX  CONST_18  H26  C23  C24  C25   180.00   0.0  0
 8IX  CONST_19  C06  C05  N04  C03   180.00   0.0  0
 8IX  CONST_20  H28  N04  C05  C06     0.00   0.0  0
 8IX  CONST_21  O18  C05  N04  C03     0.00   0.0  0
 8IX  CONST_22  H28  N04  C05  O18   180.00   0.0  0
 8IX  CONST_23  H29  O01  C02  C03   180.00   0.0  0
 8IX  CONST_24  H29  O01  C02  O26     0.00   0.0  0
 8IX  Var_01    C03  C19  C20  C21   -73.42  30.0  2
 8IX  Var_02    C25  C20  C19  C03   106.09  30.0  2
 8IX  Var_03    H24  C19  C20  C21   164.16  30.0  2
 8IX  Var_04    H25  C19  C20  C21    46.53  30.0  2
 8IX  Var_05    H24  C19  C20  C25   -16.33  30.0  2
 8IX  Var_06    H25  C19  C20  C25  -133.97  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
 8IX  chir_01  C10  C15  C09  C11  positiv
 8IX  chir_02  C03  N04  C02  C19  negativ
 8IX  chir_03  C06  C17  C12  C05  positiv
 8IX  chir_04  C08  C13  C09  C07  positiv
 8IX  chir_05  C14  C13  C15  C17  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
 8IX  plan-1  C20  0.020
 8IX  plan-1  C21  0.020
 8IX  plan-1  C22  0.020
 8IX  plan-1  C24  0.020
 8IX  plan-1  C19  0.020
 8IX  plan-1  C23  0.020
 8IX  plan-1  C25  0.020
 8IX  plan-1  H7   0.020
 8IX  plan-1  H8   0.020
 8IX  plan-1  H9   0.020
 8IX  plan-1  H26  0.020
 8IX  plan-1  H27  0.020
 8IX  plan-2  C03  0.020
 8IX  plan-2  C05  0.020
 8IX  plan-2  C06  0.020
 8IX  plan-2  N04  0.020
 8IX  plan-2  O18  0.020
 8IX  plan-2  H28  0.020
 8IX  plan-3  C02  0.020
 8IX  plan-3  C03  0.020
 8IX  plan-3  O26  0.020
 8IX  plan-3  H29  0.020
 8IX  plan-3  O01  0.020

