# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 00:08:30 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  54  26  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  122.1851   95.8281  84.3793
 8IX  C13  C  CH2    0  -0.389  123.4180   96.6872  81.8514
 8IX  C15  C  CH2    0  -0.366  121.9489   97.2208  83.7862
 8IX  C17  C  CH2    0  -0.374  124.3800   97.7357  83.8948
 8IX  C20  C  CR6    0   0.148  127.3383   97.7443  89.9235
 8IX  C21  C  CR16   0  -0.312  128.2729   96.8271  90.4002
 8IX  C22  C  CR16   0  -0.238  129.2406   97.2082  91.3186
 8IX  C24  C  CR16   0  -0.240  128.3584   99.4398  91.3164
 8IX  C02  C  C      0   0.406  127.4384   98.5531  87.0203
 8IX  C03  C  CH1    0  -0.139  126.8457   97.1990  87.4931
 8IX  C05  C  C      0   0.602  125.9242   96.4783  85.3507
 8IX  C06  C  CT     0  -0.249  124.6608   96.3464  84.4996
 8IX  C07  C  CH2    0  -0.396  124.8997   95.3528  83.3552
 8IX  C08  C  CH1    0  -0.251  123.6782   95.3010  82.4393
 8IX  C09  C  CH2    0  -0.389  122.4568   94.8489  83.2358
 8IX  C11  C  CH3    0  -0.641  120.9748   95.3851  85.1896
 8IX  C12  C  CH2    0  -0.401  123.4203   95.8955  85.2850
 8IX  C14  C  CT     0  -0.100  123.1565   97.6972  82.9734
 8IX  C16  C  CH3    0  -0.641  122.8978   99.0829  82.3987
 8IX  C19  C  CH2    0  -0.559  126.3011   97.3267  88.9221
 8IX  C23  C  CR16   0  -0.273  129.2873   98.5182  91.7799
 8IX  C25  C  CR16   0  -0.307  127.3936   99.0525  90.3949
 8IX  N04  N  NH1    0  -0.650  125.7532   96.7534  86.6535
 8IX  O18  O  O      0  -0.502  127.0416   96.3765  84.8569
 8IX  H1   H  HCH2   0   0.218  124.2751   97.0133  81.2519
 8IX  H2   H  HCH2   0   0.218  122.5532   96.6532  81.1798
 8IX  H3   H  HCH2   0   0.215  121.7438   97.9356  84.5926
 8IX  H4   H  HCH2   0   0.217  121.0565   97.2045  83.1486
 8IX  H5   H  HCH2   0   0.229  125.2543   98.0772  83.3303
 8IX  H6   H  HCH2   0   0.225  124.2145   98.4655  84.6952
 8IX  H7   H  HCR6   0   0.243  128.2398   95.8014  90.0497
 8IX  H8   H  HCR6   0   0.249  129.9578   96.4811  91.6781
 8IX  H9   H  HCR6   0   0.249  128.3832  100.4619  91.6728
 8IX  H10  H  HCH1   0   0.224  127.6322   96.4399  87.4875
 8IX  H11  H  HCH2   0   0.225  125.1044   94.3568  83.7625
 8IX  H12  H  HCH2   0   0.229  125.7805   95.6485  82.7820
 8IX  H13  H  HCH1   0   0.222  123.8718   94.5903  81.6303
 8IX  H14  H  HCH2   0   0.218  121.5778   94.7922  82.5841
 8IX  H15  H  HCH2   0   0.218  122.6180   93.8424  83.6382
 8IX  H16  H  HCH3   0   0.219  120.7767   96.0771  86.0113
 8IX  H17  H  HCH3   0   0.221  120.0795   95.3434  84.5651
 8IX  H18  H  HCH3   0   0.220  121.1281   94.3920  85.6181
 8IX  H19  H  HCH2   0   0.223  123.1865   96.5942  86.0958
 8IX  H20  H  HCH2   0   0.234  123.5992   94.9171  85.7439
 8IX  H21  H  HCH3   0   0.219  122.7064   99.8097  83.1917
 8IX  H22  H  HCH3   0   0.220  123.7551   99.4371  81.8217
 8IX  H23  H  HCH3   0   0.220  122.0289   99.0774  81.7366
 8IX  H24  H  HCH2   0   0.245  125.4784   98.0483  88.9233
 8IX  H25  H  HCH2   0   0.254  125.8745   96.3633  89.2169
 8IX  H26  H  HCR6   0   0.249  130.0397   98.8162  92.4988
 8IX  H27  H  HCR6   0   0.242  126.6735   99.7778  90.0340
 8IX  H28  H  HNH1   0   0.393  124.8224   96.9658  86.9723
 8IX  O01  O  OC    -1  -0.605  126.6201   99.3928  86.5986
 8IX  O26  O  O      0  -0.597  128.6684   98.6871  87.1488

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    1.534  0.020  1.534
 8IX  C15  C10  single    1.532  0.020  1.532
 8IX  C17  C06  single    1.541  0.020  1.541
 8IX  C10  C12  single    1.533  0.020  1.533
 8IX  C10  C11  single    1.522  0.020  1.522
 8IX  C06  C12  single    1.536  0.020  1.536
 8IX  C06  C05  single    1.529  0.020  1.529
 8IX  O18  C05  double    1.226  0.020  1.226
 8IX  C05  N04  single    1.343  0.020  1.343
 8IX  N04  C03  single    1.448  0.020  1.448
 8IX  O26  C02  deloc     1.244  0.020  1.244
 8IX  O01  C02  deloc     1.246  0.020  1.246
 8IX  C02  C03  single    1.552  0.020  1.552
 8IX  C03  C19  single    1.535  0.020  1.535
 8IX  C19  C20  single    1.501  0.020  1.501
 8IX  C21  C20  aromatic  1.394  0.020  1.394
 8IX  C21  C22  aromatic  1.388  0.020  1.388
 8IX  C20  C25  aromatic  1.392  0.020  1.392
 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    0.890  0.020  1.040

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  109.81  3.000
 8IX  C11  C10  C09  110.66  3.000
 8IX  C12  C10  C09  109.07  3.000
 8IX  C11  C10  C15  110.36  3.000
 8IX  C12  C10  C15  108.24  3.000
 8IX  C09  C10  C15  108.66  3.000
 8IX  H2   C13  H1   106.94  3.000
 8IX  H2   C13  C14  109.55  3.000
 8IX  H1   C13  C14  109.76  3.000
 8IX  H2   C13  C08  110.01  3.000
 8IX  H1   C13  C08  110.32  3.000
 8IX  C14  C13  C08  110.21  3.000
 8IX  H4   C15  H3   106.55  3.000
 8IX  H4   C15  C14  109.73  3.000
 8IX  H3   C15  C14  109.56  3.000
 8IX  H4   C15  C10  109.69  3.000
 8IX  H3   C15  C10  109.67  3.000
 8IX  C14  C15  C10  111.51  3.000
 8IX  H6   C17  H5   106.82  3.000
 8IX  H6   C17  C14  109.60  3.000
 8IX  H5   C17  C14  109.59  3.000
 8IX  H6   C17  C06  109.95  3.000
 8IX  H5   C17  C06  109.75  3.000
 8IX  C14  C17  C06  111.04  3.000
 8IX  C25  C20  C19  121.00  3.000
 8IX  C25  C20  C21  118.44  3.000
 8IX  C19  C20  C21  120.56  3.000
 8IX  H7   C21  C22  119.67  3.000
 8IX  H7   C21  C20  119.44  3.000
 8IX  C22  C21  C20  120.89  3.000
 8IX  H8   C22  C23  120.04  3.000
 8IX  H8   C22  C21  119.82  3.000
 8IX  C23  C22  C21  120.14  3.000
 8IX  H9   C24  C25  119.83  3.000
 8IX  H9   C24  C23  120.09  3.000
 8IX  C25  C24  C23  120.08  3.000
 8IX  O26  C02  O01  127.72  3.000
 8IX  O01  C02  C03  116.12  3.000
 8IX  O26  C02  C03  116.11  3.000
 8IX  H10  C03  N04  109.04  3.000
 8IX  H10  C03  C19  108.54  3.000
 8IX  N04  C03  C19  107.32  3.000
 8IX  H10  C03  C02  109.25  3.000
 8IX  C19  C03  C02  110.28  3.000
 8IX  N04  C03  C02  112.33  3.000
 8IX  O18  C05  N04  121.60  3.000
 8IX  N04  C05  C06  116.91  3.000
 8IX  O18  C05  C06  121.46  3.000
 8IX  C12  C06  C07  108.48  3.000
 8IX  C12  C06  C05  114.09  3.000
 8IX  C07  C06  C05  110.03  3.000
 8IX  C05  C06  C17  106.93  3.000
 8IX  C12  C06  C17  108.55  3.000
 8IX  C07  C06  C17  108.63  3.000
 8IX  H12  C07  H11  106.90  3.000
 8IX  H12  C07  C08  109.85  3.000
 8IX  H11  C07  C08  109.98  3.000
 8IX  H12  C07  C06  109.98  3.000
 8IX  H11  C07  C06  109.91  3.000
 8IX  C08  C07  C06  110.17  3.000
 8IX  H13  C08  C09  109.57  3.000
 8IX  H13  C08  C07  108.90  3.000
 8IX  C09  C08  C07  109.69  3.000
 8IX  H13  C08  C13  109.57  3.000
 8IX  C07  C08  C13  109.64  3.000
 8IX  C09  C08  C13  109.46  3.000
 8IX  H15  C09  H14  106.79  3.000
 8IX  H15  C09  C08  110.24  3.000
 8IX  H14  C09  C08  110.29  3.000
 8IX  H15  C09  C10  109.85  3.000
 8IX  H14  C09  C10  109.59  3.000
 8IX  C08  C09  C10  110.03  3.000
 8IX  H18  C11  H17  107.73  3.000
 8IX  H18  C11  H16  107.83  3.000
 8IX  H17  C11  H16  107.79  3.000
 8IX  H18  C11  C10  111.20  3.000
 8IX  H17  C11  C10  111.01  3.000
 8IX  H16  C11  C10  111.12  3.000
 8IX  H20  C12  H19  107.12  3.000
 8IX  H20  C12  C06  110.15  3.000
 8IX  H19  C12  C06  111.32  3.000
 8IX  H20  C12  C10  109.86  3.000
 8IX  H19  C12  C10  107.06  3.000
 8IX  C06  C12  C10  111.20  3.000
 8IX  C16  C14  C17  109.87  3.000
 8IX  C17  C14  C15  108.56  3.000
 8IX  C16  C14  C15  110.46  3.000
 8IX  C17  C14  C13  108.70  3.000
 8IX  C15  C14  C13  108.55  3.000
 8IX  C16  C14  C13  110.64  3.000
 8IX  H23  C16  H22  107.81  3.000
 8IX  H23  C16  H21  107.69  3.000
 8IX  H22  C16  H21  107.76  3.000
 8IX  H23  C16  C14  111.07  3.000
 8IX  H22  C16  C14  111.17  3.000
 8IX  H21  C16  C14  111.18  3.000
 8IX  H25  C19  H24  106.69  3.000
 8IX  H25  C19  C03  108.42  3.000
 8IX  H24  C19  C03  108.83  3.000
 8IX  H25  C19  C20  109.55  3.000
 8IX  H24  C19  C20  109.59  3.000
 8IX  C03  C19  C20  113.53  3.000
 8IX  H26  C23  C24  120.28  3.000
 8IX  H26  C23  C22  120.22  3.000
 8IX  C24  C23  C22  119.50  3.000
 8IX  H27  C25  C24  119.71  3.000
 8IX  H27  C25  C20  119.33  3.000
 8IX  C24  C25  C20  120.96  3.000
 8IX  H28  N04  C05  117.93  3.000
 8IX  H28  N04  C03  116.69  3.000
 8IX  C05  N04  C03  121.98  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  Var_01    C03  C19  C20  C21   -77.03  30.0  3
 8IX  Var_02    C25  C20  C19  C03   102.79  30.0  2
 8IX  Var_03    H24  C19  C20  C21   161.07  30.0  3
 8IX  Var_04    H25  C19  C20  C21    44.33  30.0  3
 8IX  Var_05    H24  C19  C20  C25   -19.11  30.0  3
 8IX  Var_06    H25  C19  C20  C25  -135.85  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
 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  O01  0.020
 8IX  plan-3  O26  0.020

