# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 11:19:53 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: O-(2-bromophenyl)-N-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-ylcarbonyl]-D-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](Cc1ccc(Oc2ccccc2Br)cc1)NC(=O)C34CC5CC(CC(C5)C3)C4
#
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
 PH9  PH9  O-(2-bromophenyl)-N-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-ylcarbonyl]-D-tyrosine  ligand  59  32  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PH9
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
 PH9  CB2   C   CR6    0   0.149  -10.5571  55.8171  47.5166
 PH9  CB3   C   CR16   0  -0.294  -11.2890  55.0261  48.3974
 PH9  CB4   C   CR16   0  -0.285  -12.3679  55.5390  49.0995
 PH9  CB6   C   CR6    0   0.284  -12.7193  56.8675  48.9184
 PH9  CB5   C   CR16   0  -0.298  -12.0304  57.6700  48.0248
 PH9  CB1   C   CR16   0  -0.288  -10.9566  57.1361  47.3284
 PH9  C2    C   CH1    0  -0.202   -8.0420  55.6270  47.6443
 PH9  C1    C   CH2    0  -0.514   -9.3243  55.2793  46.8575
 PH9  N     N   NH1    0  -0.632   -8.1320  55.2288  49.0260
 PH9  C     C   C      0   0.627   -8.4660  56.0363  50.0458
 PH9  CO2   C   C      0   0.419   -6.8398  54.9318  46.9612
 PH9  O     O   O      0  -0.492   -8.8018  57.2029  49.8818
 PH9  OC1   O   OC    -1  -0.606   -6.5359  55.3698  45.8370
 PH9  OC2   O   O      0  -0.594   -6.3095  53.9824  47.5696
 PH9  OAB   O   O2     0  -0.502  -13.7860  57.4003  49.6100
 PH9  CA1   C   CR6    0   0.424  -13.6600  57.5811  50.9448
 PH9  CA2   C   CR6    0  -0.212  -14.8320  57.7315  51.6861
 PH9  CA3   C   CR16   0  -0.229  -14.7863  57.9453  53.0550
 PH9  CA4   C   CR16   0  -0.268  -13.5605  58.0051  53.7018
 PH9  CA5   C   CR16   0  -0.249  -12.3916  57.8592  52.9699
 PH9  CA6   C   CR16   0  -0.351  -12.4331  57.6478  51.5997
 PH9  BRA2  BR  BR     0  -0.030  -16.4946  57.6413  50.8064
 PH9  CC4   C   CH2    0  -0.418   -9.7217  54.8069  54.0127
 PH9  CC3   C   CH1    0  -0.251   -8.5983  55.8396  53.9069
 PH9  CC5   C   CH1    0  -0.245   -9.5125  53.7192  52.9579
 PH9  CC2   C   CH2    0  -0.411   -8.6154  56.4681  52.5133
 PH9  CC6   C   CH2    0  -0.406   -9.5319  54.3438  51.5624
 PH9  CC1   C   CT     0  -0.256   -8.4118  55.3956  51.4356
 PH9  C10   C   CH2    0  -0.419   -8.1618  53.0369  53.1864
 PH9  CC8   C   CH1    0  -0.245   -7.0410  54.0743  53.0880
 PH9  CC9   C   CH2    0  -0.415   -7.2508  55.1580  54.1462
 PH9  CC7   C   CH2    0  -0.420   -7.0568  54.7059  51.6933
 PH9  HB3   H   HCR6   0   0.246  -11.0046  53.9922  48.5500
 PH9  HB4   H   HCR6   0   0.271  -12.9205  54.9122  49.7885
 PH9  HB5   H   HCR6   0   0.265  -12.3227  58.7029  47.8834
 PH9  HB1   H   HCR6   0   0.246  -10.4078  57.7702  46.6418
 PH9  H2    H   HCH1   0   0.242   -7.9002  56.7091  47.6042
 PH9  H11   H   HCH2   0   0.238   -9.4009  54.1919  46.7693
 PH9  H12   H   HCH2   0   0.246   -9.2197  55.6763  45.8467
 PH9  HN    H   HNH1   0   0.379   -7.7604  54.3118  49.2189
 PH9  HA3   H   HCR6   0   0.281  -15.7024  58.0592  53.6190
 PH9  HA4   H   HCR6   0   0.268  -13.5250  58.1652  54.7705
 PH9  HA5   H   HCR6   0   0.265  -11.4325  57.9158  53.4681
 PH9  HA6   H   HCR6   0   0.295  -11.5106  57.5412  51.0408
 PH9  HC3   H   HCH1   0   0.223   -8.7494  56.6254  54.6534
 PH9  HC5   H   HCH1   0   0.226  -10.3149  52.9788  53.0272
 PH9  HC21  H   HCH2   0   0.235   -9.5663  56.9819  52.3539
 PH9  HC22  H   HCH2   0   0.225   -7.8347  57.2311  52.4359
 PH9  HC61  H   HCH2   0   0.224   -9.4012  53.5607  50.8090
 PH9  HC62  H   HCH2   0   0.238  -10.5041  54.8069  51.3642
 PH9  H101  H   HCH2   0   0.224   -8.1438  52.5527  54.1682
 PH9  H102  H   HCH2   0   0.222   -8.0105  52.2485  52.4415
 PH9  HC8   H   HCH1   0   0.226   -6.0735  53.5880  53.2438
 PH9  HC91  H   HCH2   0   0.222   -6.4405  55.8924  54.0979
 PH9  HC92  H   HCH2   0   0.221   -7.2213  54.7188  55.1485
 PH9  HC71  H   HCH2   0   0.224   -6.8617  53.9241  50.9524
 PH9  HC72  H   HCH2   0   0.234   -6.2452  55.4352  51.5961
 PH9  HC41  H   HCH2   0   0.223   -9.7335  54.3616  55.0127
 PH9  HC42  H   HCH2   0   0.219  -10.6938  55.2906  53.8682

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
 PH9  CB2  CB3   aromatic  1.392  0.020  1.392
 PH9  CB2  CB1   aromatic  1.391  0.020  1.391
 PH9  CB2  C1    single    1.498  0.020  1.498
 PH9  CB3  CB4   aromatic  1.386  0.020  1.386
 PH9  CB3  HB3   single    0.930  0.020  1.080
 PH9  CB4  CB6   aromatic  1.386  0.020  1.386
 PH9  CB4  HB4   single    0.930  0.020  1.080
 PH9  CB6  CB5   aromatic  1.385  0.020  1.385
 PH9  CB6  OAB   single    1.378  0.020  1.378
 PH9  CB5  CB1   aromatic  1.387  0.020  1.387
 PH9  CB5  HB5   single    0.930  0.020  1.080
 PH9  CB1  HB1   single    0.930  0.020  1.080
 PH9  C2   C1    single    1.544  0.020  1.544
 PH9  C2   N     single    1.441  0.020  1.441
 PH9  C2   CO2   single    1.548  0.020  1.548
 PH9  C2   H2    single    0.970  0.020  1.090
 PH9  C1   H11   single    0.970  0.020  1.090
 PH9  C1   H12   single    0.970  0.020  1.090
 PH9  N    C     single    1.343  0.020  1.343
 PH9  N    HN    single    0.860  0.020  1.020
 PH9  C    O     double    1.225  0.020  1.225
 PH9  C    CC1   single    1.531  0.020  1.531
 PH9  CO2  OC1   deloc     1.244  0.020  1.244
 PH9  CO2  OC2   deloc     1.246  0.020  1.246
 PH9  OAB  CA1   single    1.353  0.020  1.353
 PH9  CA1  CA2   aromatic  1.395  0.020  1.395
 PH9  CA1  CA6   aromatic  1.392  0.020  1.392
 PH9  CA2  CA3   aromatic  1.386  0.020  1.386
 PH9  CA2  BRA2  single    1.883  0.020  1.883
 PH9  CA3  CA4   aromatic  1.387  0.020  1.387
 PH9  CA3  HA3   single    0.930  0.020  1.080
 PH9  CA4  CA5   aromatic  1.387  0.020  1.387
 PH9  CA4  HA4   single    0.930  0.020  1.080
 PH9  CA5  CA6   aromatic  1.387  0.020  1.387
 PH9  CA5  HA5   single    0.930  0.020  1.080
 PH9  CA6  HA6   single    0.930  0.020  1.080
 PH9  CC4  CC3   single    1.530  0.020  1.530
 PH9  CC4  CC5   single    1.529  0.020  1.529
 PH9  CC4  HC41  single    0.970  0.020  1.090
 PH9  CC4  HC42  single    0.970  0.020  1.090
 PH9  CC3  CC6   single    2.934  0.020  2.934
 PH9  CC3  CC9   single    1.529  0.020  1.529
 PH9  CC3  HC3   single    0.970  0.020  1.090
 PH9  CC5  CC2   single    2.925  0.020  2.925
 PH9  CC5  C10   single    1.530  0.020  1.530
 PH9  CC5  HC5   single    0.970  0.020  1.090
 PH9  CC2  CC1   single    1.534  0.020  1.534
 PH9  CC2  HC21  single    0.970  0.020  1.090
 PH9  CC2  HC22  single    0.970  0.020  1.090
 PH9  CC6  CC1   single    1.542  0.020  1.542
 PH9  CC6  HC61  single    0.970  0.020  1.090
 PH9  CC6  HC62  single    0.970  0.020  1.090
 PH9  CC1  CC7   single    1.542  0.020  1.542
 PH9  C10  CC8   single    1.530  0.020  1.530
 PH9  C10  H101  single    0.970  0.020  1.090
 PH9  C10  H102  single    0.970  0.020  1.090
 PH9  CC8  CC9   single    1.529  0.020  1.529
 PH9  CC8  CC7   single    1.531  0.020  1.531
 PH9  CC8  HC8   single    0.970  0.020  1.090
 PH9  CC9  HC91  single    0.970  0.020  1.090
 PH9  CC9  HC92  single    0.970  0.020  1.090
 PH9  CC7  HC71  single    0.970  0.020  1.090
 PH9  CC7  HC72  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
 PH9  C1    CB2  CB1   121.15  3.000
 PH9  C1    CB2  CB3   120.48  3.000
 PH9  CB1   CB2  CB3   118.27  3.000
 PH9  HB3   CB3  CB4   119.10  3.000
 PH9  HB3   CB3  CB2   119.58  3.000
 PH9  CB4   CB3  CB2   121.31  3.000
 PH9  HB4   CB4  CB6   120.56  3.000
 PH9  HB4   CB4  CB3   120.36  3.000
 PH9  CB6   CB4  CB3   119.08  3.000
 PH9  OAB   CB6  CB5   119.00  3.000
 PH9  OAB   CB6  CB4   120.07  3.000
 PH9  CB5   CB6  CB4   120.91  3.000
 PH9  HB5   CB5  CB1   120.71  3.000
 PH9  HB5   CB5  CB6   120.19  3.000
 PH9  CB1   CB5  CB6   119.10  3.000
 PH9  HB1   CB1  CB5   119.01  3.000
 PH9  HB1   CB1  CB2   119.68  3.000
 PH9  CB5   CB1  CB2   121.29  3.000
 PH9  H2    C2   CO2   109.15  3.000
 PH9  H2    C2   N     108.49  3.000
 PH9  CO2   C2   N     110.35  3.000
 PH9  H2    C2   C1    108.19  3.000
 PH9  CO2   C2   C1    108.60  3.000
 PH9  N     C2   C1    112.00  3.000
 PH9  H12   C1   H11   107.09  3.000
 PH9  H12   C1   C2    108.09  3.000
 PH9  H11   C1   C2    108.85  3.000
 PH9  H12   C1   CB2   110.85  3.000
 PH9  H11   C1   CB2   109.56  3.000
 PH9  C2    C1   CB2   112.23  3.000
 PH9  HN    N    C     119.56  3.000
 PH9  HN    N    C2    114.32  3.000
 PH9  C     N    C2    125.28  3.000
 PH9  CC1   C    O     121.98  3.000
 PH9  CC1   C    N     115.39  3.000
 PH9  O     C    N     122.63  3.000
 PH9  OC2   CO2  OC1   127.26  3.000
 PH9  OC2   CO2  C2    117.21  3.000
 PH9  OC1   CO2  C2    115.50  3.000
 PH9  CA1   OAB  CB6   118.34  3.000
 PH9  CA6   CA1  CA2   119.03  3.000
 PH9  CA6   CA1  OAB   123.54  3.000
 PH9  CA2   CA1  OAB   117.42  3.000
 PH9  BRA2  CA2  CA3   119.85  3.000
 PH9  BRA2  CA2  CA1   119.23  3.000
 PH9  CA3   CA2  CA1   120.91  3.000
 PH9  HA3   CA3  CA4   120.04  3.000
 PH9  HA3   CA3  CA2   120.21  3.000
 PH9  CA4   CA3  CA2   119.75  3.000
 PH9  HA4   CA4  CA5   120.64  3.000
 PH9  HA4   CA4  CA3   119.75  3.000
 PH9  CA5   CA4  CA3   119.61  3.000
 PH9  HA5   CA5  CA6   119.29  3.000
 PH9  HA5   CA5  CA4   119.90  3.000
 PH9  CA6   CA5  CA4   120.81  3.000
 PH9  HA6   CA6  CA5   119.93  3.000
 PH9  HA6   CA6  CA1   120.18  3.000
 PH9  CA5   CA6  CA1   119.89  3.000
 PH9  HC42  CC4  HC41  106.89  3.000
 PH9  HC42  CC4  CC5   110.15  3.000
 PH9  HC41  CC4  CC5   110.01  3.000
 PH9  HC42  CC4  CC3   110.15  3.000
 PH9  HC41  CC4  CC3   110.23  3.000
 PH9  CC5   CC4  CC3   109.39  3.000
 PH9  HC3   CC3  CC9   109.58  3.000
 PH9  HC3   CC3  CC6   150.15  3.000
 PH9  CC9   CC3  CC6   100.27  3.000
 PH9  HC3   CC3  CC4   109.64  3.000
 PH9  CC9   CC3  CC4   109.60  3.000
 PH9  CC6   CC3  CC4    58.48  3.000
 PH9  HC5   CC5  C10   109.64  3.000
 PH9  HC5   CC5  CC2   150.51  3.000
 PH9  C10   CC5  CC2    99.85  3.000
 PH9  HC5   CC5  CC4   109.71  3.000
 PH9  C10   CC5  CC4   109.56  3.000
 PH9  CC2   CC5  CC4    58.57  3.000
 PH9  HC22  CC2  HC21  106.42  3.000
 PH9  HC22  CC2  CC1   110.06  3.000
 PH9  HC21  CC2  CC1   109.98  3.000
 PH9  HC22  CC2  CC5   152.20  3.000
 PH9  HC21  CC2  CC5   101.37  3.000
 PH9  CC1   CC2  CC5    59.37  3.000
 PH9  HC62  CC6  HC61  106.50  3.000
 PH9  HC62  CC6  CC1   109.98  3.000
 PH9  HC61  CC6  CC1   110.17  3.000
 PH9  HC62  CC6  CC3   102.22  3.000
 PH9  HC61  CC6  CC3   151.28  3.000
 PH9  CC1   CC6  CC3    59.11  3.000
 PH9  CC7   CC1  CC6   108.63  3.000
 PH9  CC7   CC1  CC2   108.17  3.000
 PH9  CC6   CC1  CC2   108.83  3.000
 PH9  CC7   CC1  C     111.71  3.000
 PH9  CC6   CC1  C     109.53  3.000
 PH9  CC2   CC1  C     109.90  3.000
 PH9  H102  C10  H101  106.82  3.000
 PH9  H102  C10  CC8   110.07  3.000
 PH9  H101  C10  CC8   110.21  3.000
 PH9  H102  C10  CC5   109.96  3.000
 PH9  H101  C10  CC5   110.21  3.000
 PH9  CC8   C10  CC5   109.54  3.000
 PH9  HC8   CC8  CC7   108.80  3.000
 PH9  HC8   CC8  CC9   109.74  3.000
 PH9  CC7   CC8  CC9   109.67  3.000
 PH9  HC8   CC8  C10   109.71  3.000
 PH9  CC7   CC8  C10   109.31  3.000
 PH9  CC9   CC8  C10   109.60  3.000
 PH9  HC92  CC9  HC91  106.83  3.000
 PH9  HC92  CC9  CC8   110.22  3.000
 PH9  HC91  CC9  CC8   110.08  3.000
 PH9  HC92  CC9  CC3   110.24  3.000
 PH9  HC91  CC9  CC3   110.27  3.000
 PH9  CC8   CC9  CC3   109.18  3.000
 PH9  HC72  CC7  HC71  106.47  3.000
 PH9  HC72  CC7  CC8   110.35  3.000
 PH9  HC71  CC7  CC8   108.67  3.000
 PH9  HC72  CC7  CC1   109.78  3.000
 PH9  HC71  CC7  CC1   111.28  3.000
 PH9  CC8   CC7  CC1   110.23  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
 PH9  CONST_01  CB6   CB4  CB3  CB2     0.00   0.0  0
 PH9  CONST_02  CB6   CB5  CB1  CB2     0.00   0.0  0
 PH9  CONST_03  CB5   CB1  CB2  CB3     0.00   0.0  0
 PH9  CONST_04  CB5   CB6  CB4  CB3     0.00   0.0  0
 PH9  CONST_05  CB1   CB2  CB3  CB4     0.00   0.0  0
 PH9  CONST_06  CB1   CB5  CB6  CB4     0.00   0.0  0
 PH9  CONST_07  CA4   CA3  CA2  CA1     0.00   0.0  0
 PH9  CONST_08  CA4   CA5  CA6  CA1     0.00   0.0  0
 PH9  CONST_09  CA5   CA6  CA1  CA2     0.00   0.0  0
 PH9  CONST_10  CA5   CA4  CA3  CA2     0.00   0.0  0
 PH9  CONST_11  CA6   CA1  CA2  CA3     0.00   0.0  0
 PH9  CONST_12  CA6   CA5  CA4  CA3     0.00   0.0  0
 PH9  CONST_13  OAB   CB6  CB4  CB3   180.00   0.0  0
 PH9  CONST_14  C1    CB2  CB3  CB4   180.00   0.0  0
 PH9  CONST_15  C1    CB2  CB1  CB5   180.00   0.0  0
 PH9  CONST_16  OAB   CB6  CB5  CB1   180.00   0.0  0
 PH9  CONST_17  CA3   CA2  CA1  OAB   180.00   0.0  0
 PH9  CONST_18  CA5   CA6  CA1  OAB   180.00   0.0  0
 PH9  CONST_19  BRA2  CA2  CA3  CA4   180.00   0.0  0
 PH9  CONST_20  BRA2  CA2  CA1  CA6   180.00   0.0  0
 PH9  CONST_21  HB4   CB4  CB3  CB2   180.00   0.0  0
 PH9  CONST_22  HB5   CB5  CB1  CB2   180.00   0.0  0
 PH9  CONST_23  HB1   CB1  CB2  CB3   180.00   0.0  0
 PH9  CONST_24  HB3   CB3  CB4  CB6   180.00   0.0  0
 PH9  CONST_25  HA3   CA3  CA2  CA1   180.00   0.0  0
 PH9  CONST_26  HA5   CA5  CA6  CA1   180.00   0.0  0
 PH9  CONST_27  HA6   CA6  CA1  CA2   180.00   0.0  0
 PH9  CONST_28  HA4   CA4  CA3  CA2   180.00   0.0  0
 PH9  CONST_29  CC1   C    N    C2    180.00   0.0  0
 PH9  CONST_30  HN    N    C    CC1     0.00   0.0  0
 PH9  CONST_31  O     C    N    C2      0.00   0.0  0
 PH9  Var_01    CA2   CA1  OAB  CB6  -161.27  30.0  2
 PH9  Var_02    C2    C1   CB2  CB3   -93.61  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
 PH9  chir_01  C2   C1   N    CO2  negativ
 PH9  chir_02  CC3  CC4  CC6  CC9  positiv
 PH9  chir_03  CC5  C10  CC2  CC4  positiv
 PH9  chir_04  CC1  CC6  CC2  C    positiv
 PH9  chir_05  CC8  C10  CC9  CC7  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
 PH9  plan-1  CB2   0.020
 PH9  plan-1  CB3   0.020
 PH9  plan-1  CB4   0.020
 PH9  plan-1  CB6   0.020
 PH9  plan-1  CB5   0.020
 PH9  plan-1  CB1   0.020
 PH9  plan-1  C1    0.020
 PH9  plan-1  OAB   0.020
 PH9  plan-1  HB3   0.020
 PH9  plan-1  HB4   0.020
 PH9  plan-1  HB5   0.020
 PH9  plan-1  HB1   0.020
 PH9  plan-2  OAB   0.020
 PH9  plan-2  CA1   0.020
 PH9  plan-2  CA2   0.020
 PH9  plan-2  CA3   0.020
 PH9  plan-2  CA4   0.020
 PH9  plan-2  CA5   0.020
 PH9  plan-2  CA6   0.020
 PH9  plan-2  BRA2  0.020
 PH9  plan-2  HA3   0.020
 PH9  plan-2  HA4   0.020
 PH9  plan-2  HA5   0.020
 PH9  plan-2  HA6   0.020
 PH9  plan-3  C2    0.020
 PH9  plan-3  N     0.020
 PH9  plan-3  C     0.020
 PH9  plan-3  O     0.020
 PH9  plan-3  CC1   0.020
 PH9  plan-3  HN    0.020
 PH9  plan-4  C2    0.020
 PH9  plan-4  CO2   0.020
 PH9  plan-4  OC1   0.020
 PH9  plan-4  OC2   0.020

