# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 06:46:28 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: N-cyclopropyl-4-methyl-3-(2'-oxo-1',2'-dihydrospiro[cyclopentane-1,3'-indol]-6'-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1c2ccc3c(NC(=O)C34CCCC4)c2)C(=O)NC5CC5
#
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
 I2O  I2O  N-cyclopropyl-4-methyl-3-(2'-oxo-1',2'-dihydrospiro[cyclopentane-1,3'-indol]-6'-yl)benzamide  ligand  51  27  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_I2O
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
 I2O  CAA   C  CR16  0  -0.277   2.7446  -2.8603  -0.2804
 I2O  CAB   C  CR6   0   0.067   1.4074  -2.4763  -0.3496
 I2O  CAC   C  CR6   0   0.069   1.0809  -1.1468  -0.0363
 I2O  CAD   C  CR16  0  -0.316   2.0935  -0.2588   0.3153
 I2O  CAE   C  CR6   0  -0.029   3.4276  -0.6466   0.3597
 I2O  CAF   C  CR16  0  -0.296   3.7454  -1.9700   0.0686
 I2O  CAG   C  CH3   0  -0.748   0.3797  -3.4843  -0.7762
 I2O  CAH   C  C     0   0.533   4.4476   0.3747   0.7478
 I2O  NAI   N  NH1   0  -0.659   5.7019   0.1566   0.3138
 I2O  CAJ   C  CH1   0  -0.078   6.7756   1.0389   0.6323
 I2O  CAK   C  CH2   0  -0.518   7.8562   1.2139  -0.3828
 I2O  CAL   C  CH2   0  -0.482   6.9026   2.3356  -0.1046
 I2O  OAM   O  O     0  -0.485   4.1471   1.3545   1.4154
 I2O  CAN   C  CR6   0   0.025  -0.3122  -0.6440  -0.0857
 I2O  CAO   C  CR16  0  -0.340  -1.3213  -1.2729   0.6514
 I2O  CAP   C  CR56  0   0.383  -2.5982  -0.7552   0.5802
 I2O  CAQ   C  CR56  0   0.126  -2.9079   0.3660  -0.1862
 I2O  CAR   C  CR16  0  -0.325  -1.9118   0.9889  -0.9058
 I2O  CAS   C  CR16  0  -0.309  -0.6146   0.4807  -0.8524
 I2O  NAT   N  NR15  0  -0.750  -3.7513  -1.2066   1.2086
 I2O  CAU   C  CR5   0   0.562  -4.8351  -0.4470   0.8917
 I2O  CAV   C  CR5   0  -0.298  -4.3699   0.6672  -0.0463
 I2O  OAW   O  O     0  -0.452  -5.9678  -0.6312   1.2864
 I2O  CAX   C  CH2   0  -0.431  -5.1545   0.6244  -1.3875
 I2O  CAY   C  CH2   0  -0.441  -6.1741   1.7538  -1.2927
 I2O  CAZ   C  CH2   0  -0.443  -5.4044   2.8391  -0.5521
 I2O  CBA   C  CH2   0  -0.433  -4.6927   2.0659   0.5579
 I2O  HAA   H  HCR6  0   0.257   3.0108  -3.8833  -0.5171
 I2O  HAD   H  HCR6  0   0.254   1.8324   0.7616   0.5658
 I2O  HAF   H  HCR6  0   0.257   4.7646  -2.3321   0.1238
 I2O  HAG   H  HCH3  0   0.253  -0.1249  -3.9334   0.0803
 I2O  HAGA  H  HCH3  0   0.251  -0.3909  -3.0404  -1.4050
 I2O  HAGB  H  HCH3  0   0.256   0.8468  -4.2946  -1.3340
 I2O  HNAI  H  HNH1  0   0.409   5.8993  -0.6364  -0.2739
 I2O  HAJ   H  HCH1  0   0.269   7.0739   1.0339   1.6757
 I2O  HAK   H  HCH2  0   0.261   8.8727   1.2944  -0.0217
 I2O  HAKA  H  HCH2  0   0.259   7.7579   0.6888  -1.3254
 I2O  HAL   H  HCH2  0   0.255   6.1541   2.5554  -0.8548
 I2O  HALA  H  HCH2  0   0.255   7.2587   3.1971   0.4449
 I2O  HAO   H  HCR6  0   0.264  -1.1054  -2.1338   1.2709
 I2O  HAR   H  HCR6  0   0.251  -2.1256   1.8601  -1.5135
 I2O  HAS   H  HCR6  0   0.252   0.1670   0.9585  -1.4292
 I2O  HNAT  H  HNR5  0   0.410  -3.7973  -2.0210   1.8025
 I2O  HAX   H  HCH2  0   0.247  -4.4592   0.8244  -2.2061
 I2O  HAXA  H  HCH2  0   0.255  -5.5974  -0.3529  -1.5838
 I2O  HAY   H  HCH2  0   0.237  -6.5379   2.0676  -2.2720
 I2O  HAYA  H  HCH2  0   0.229  -7.0389   1.4375  -0.7042
 I2O  HAZ   H  HCH2  0   0.226  -4.6785   3.3063  -1.2235
 I2O  HAZA  H  HCH2  0   0.239  -6.0389   3.6341  -0.1582
 I2O  HBA   H  HCH2  0   0.250  -5.3699   1.9517   1.4068
 I2O  HBAA  H  HCH2  0   0.250  -3.7954   2.5629   0.9260

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
 I2O  CAA  CAB   aromatic  1.393  0.020  1.393
 I2O  CAA  CAF   aromatic  1.384  0.020  1.384
 I2O  CAB  CAC   aromatic  1.404  0.020  1.404
 I2O  CAB  CAG   single    1.501  0.020  1.501
 I2O  CAC  CAD   aromatic  1.392  0.020  1.392
 I2O  CAC  CAN   single    1.482  0.020  1.482
 I2O  CAD  CAE   aromatic  1.390  0.020  1.390
 I2O  CAE  CAF   aromatic  1.392  0.020  1.392
 I2O  CAE  CAH   single    1.495  0.020  1.495
 I2O  CAH  NAI   single    1.345  0.020  1.345
 I2O  CAH  OAM   double    1.223  0.020  1.223
 I2O  NAI  CAJ   single    1.426  0.020  1.426
 I2O  CAJ  CAK   single    1.493  0.020  1.493
 I2O  CAJ  CAL   single    1.497  0.020  1.497
 I2O  CAK  CAL   single    1.498  0.020  1.498
 I2O  CAN  CAO   aromatic  1.399  0.020  1.399
 I2O  CAN  CAS   aromatic  1.394  0.020  1.394
 I2O  CAO  CAP   aromatic  1.380  0.020  1.380
 I2O  CAP  CAQ   aromatic  1.393  0.020  1.393
 I2O  CAP  NAT   single    1.389  0.020  1.389
 I2O  CAQ  CAR   aromatic  1.378  0.020  1.378
 I2O  CAQ  CAV   single    1.499  0.020  1.499
 I2O  CAR  CAS   aromatic  1.394  0.020  1.394
 I2O  NAT  CAU   single    1.361  0.020  1.361
 I2O  CAU  CAV   single    1.529  0.020  1.529
 I2O  CAU  OAW   double    1.214  0.020  1.214
 I2O  CAV  CAX   single    1.554  0.020  1.554
 I2O  CAV  CBA   single    1.557  0.020  1.557
 I2O  CAX  CAY   single    1.525  0.020  1.525
 I2O  CAY  CAZ   single    1.523  0.020  1.523
 I2O  CAZ  CBA   single    1.529  0.020  1.529
 I2O  CAA  HAA   single    0.930  0.020  1.080
 I2O  CAD  HAD   single    0.930  0.020  1.080
 I2O  CAF  HAF   single    0.930  0.020  1.080
 I2O  CAG  HAG   single    0.970  0.020  1.090
 I2O  CAG  HAGA  single    0.970  0.020  1.090
 I2O  CAG  HAGB  single    0.970  0.020  1.090
 I2O  NAI  HNAI  single    0.860  0.020  1.020
 I2O  CAJ  HAJ   single    0.970  0.020  1.090
 I2O  CAK  HAK   single    0.970  0.020  1.090
 I2O  CAK  HAKA  single    0.970  0.020  1.090
 I2O  CAL  HAL   single    0.970  0.020  1.090
 I2O  CAL  HALA  single    0.970  0.020  1.090
 I2O  CAO  HAO   single    0.930  0.020  1.080
 I2O  CAR  HAR   single    0.930  0.020  1.080
 I2O  CAS  HAS   single    0.930  0.020  1.080
 I2O  NAT  HNAT  single    0.860  0.020  1.020
 I2O  CAX  HAX   single    0.970  0.020  1.090
 I2O  CAX  HAXA  single    0.970  0.020  1.090
 I2O  CAY  HAY   single    0.970  0.020  1.090
 I2O  CAY  HAYA  single    0.970  0.020  1.090
 I2O  CAZ  HAZ   single    0.970  0.020  1.090
 I2O  CAZ  HAZA  single    0.970  0.020  1.090
 I2O  CBA  HBA   single    0.970  0.020  1.090
 I2O  CBA  HBAA  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
 I2O  HAA   CAA  CAF   119.00  3.000
 I2O  HAA   CAA  CAB   119.04  3.000
 I2O  CAF   CAA  CAB   121.95  3.000
 I2O  CAG   CAB  CAC   122.67  3.000
 I2O  CAG   CAB  CAA   119.09  3.000
 I2O  CAC   CAB  CAA   118.23  3.000
 I2O  CAN   CAC  CAD   118.41  3.000
 I2O  CAN   CAC  CAB   122.16  3.000
 I2O  CAD   CAC  CAB   119.42  3.000
 I2O  HAD   CAD  CAE   119.14  3.000
 I2O  HAD   CAD  CAC   118.97  3.000
 I2O  CAE   CAD  CAC   121.89  3.000
 I2O  CAH   CAE  CAF   123.24  3.000
 I2O  CAH   CAE  CAD   118.21  3.000
 I2O  CAF   CAE  CAD   118.54  3.000
 I2O  HAF   CAF  CAE   121.48  3.000
 I2O  HAF   CAF  CAA   118.56  3.000
 I2O  CAE   CAF  CAA   119.95  3.000
 I2O  HAGB  CAG  HAGA  108.12  3.000
 I2O  HAGB  CAG  HAG   107.11  3.000
 I2O  HAGA  CAG  HAG   107.09  3.000
 I2O  HAGB  CAG  CAB   110.58  3.000
 I2O  HAGA  CAG  CAB   112.01  3.000
 I2O  HAG   CAG  CAB   111.72  3.000
 I2O  OAM   CAH  NAI   122.35  3.000
 I2O  OAM   CAH  CAE   121.43  3.000
 I2O  NAI   CAH  CAE   116.22  3.000
 I2O  HNAI  NAI  CAJ   118.05  3.000
 I2O  HNAI  NAI  CAH   119.93  3.000
 I2O  CAJ   NAI  CAH   122.00  3.000
 I2O  HAJ   CAJ  CAL   117.00  3.000
 I2O  HAJ   CAJ  CAK   117.08  3.000
 I2O  CAL   CAJ  CAK    60.15  3.000
 I2O  HAJ   CAJ  NAI   114.77  3.000
 I2O  CAL   CAJ  NAI   119.34  3.000
 I2O  CAK   CAJ  NAI   117.76  3.000
 I2O  HAKA  CAK  HAK   114.31  3.000
 I2O  HAKA  CAK  CAL   117.82  3.000
 I2O  HAK   CAK  CAL   118.71  3.000
 I2O  HAKA  CAK  CAJ   117.98  3.000
 I2O  HAK   CAK  CAJ   117.51  3.000
 I2O  CAL   CAK  CAJ    60.06  3.000
 I2O  HALA  CAL  HAL   114.70  3.000
 I2O  HALA  CAL  CAK   118.74  3.000
 I2O  HAL   CAL  CAK   117.61  3.000
 I2O  HALA  CAL  CAJ   117.88  3.000
 I2O  HAL   CAL  CAJ   117.29  3.000
 I2O  CAK   CAL  CAJ    59.79  3.000
 I2O  CAS   CAN  CAO   119.73  3.000
 I2O  CAS   CAN  CAC   119.73  3.000
 I2O  CAO   CAN  CAC   120.53  3.000
 I2O  HAO   CAO  CAP   120.84  3.000
 I2O  HAO   CAO  CAN   121.01  3.000
 I2O  CAP   CAO  CAN   118.14  3.000
 I2O  NAT   CAP  CAQ   109.02  3.000
 I2O  NAT   CAP  CAO   128.55  3.000
 I2O  CAQ   CAP  CAO   122.43  3.000
 I2O  CAV   CAQ  CAR   131.52  3.000
 I2O  CAV   CAQ  CAP   109.10  3.000
 I2O  CAR   CAQ  CAP   119.38  3.000
 I2O  HAR   CAR  CAS   119.87  3.000
 I2O  HAR   CAR  CAQ   120.93  3.000
 I2O  CAS   CAR  CAQ   119.20  3.000
 I2O  HAS   CAS  CAR   119.37  3.000
 I2O  HAS   CAS  CAN   119.50  3.000
 I2O  CAR   CAS  CAN   121.12  3.000
 I2O  HNAT  NAT  CAU   123.46  3.000
 I2O  HNAT  NAT  CAP   124.51  3.000
 I2O  CAU   NAT  CAP   111.99  3.000
 I2O  OAW   CAU  CAV   126.45  3.000
 I2O  OAW   CAU  NAT   125.65  3.000
 I2O  CAV   CAU  NAT   107.90  3.000
 I2O  CBA   CAV  CAX   104.76  3.000
 I2O  CBA   CAV  CAU   110.70  3.000
 I2O  CAX   CAV  CAU   110.84  3.000
 I2O  CBA   CAV  CAQ   114.75  3.000
 I2O  CAX   CAV  CAQ   113.96  3.000
 I2O  CAU   CAV  CAQ   101.98  3.000
 I2O  HAXA  CAX  HAX   106.72  3.000
 I2O  HAXA  CAX  CAY   113.79  3.000
 I2O  HAX   CAX  CAY   109.67  3.000
 I2O  HAXA  CAX  CAV   112.63  3.000
 I2O  HAX   CAX  CAV   108.68  3.000
 I2O  CAY   CAX  CAV   105.28  3.000
 I2O  HAYA  CAY  HAY   107.63  3.000
 I2O  HAYA  CAY  CAZ   110.14  3.000
 I2O  HAY   CAY  CAZ   113.59  3.000
 I2O  HAYA  CAY  CAX   110.38  3.000
 I2O  HAY   CAY  CAX   112.36  3.000
 I2O  CAZ   CAY  CAX   102.72  3.000
 I2O  HAZA  CAZ  HAZ   107.25  3.000
 I2O  HAZA  CAZ  CBA   112.17  3.000
 I2O  HAZ   CAZ  CBA   110.66  3.000
 I2O  HAZA  CAZ  CAY   113.65  3.000
 I2O  HAZ   CAZ  CAY   109.96  3.000
 I2O  CBA   CAZ  CAY   103.18  3.000
 I2O  HBAA  CBA  HBA   107.20  3.000
 I2O  HBAA  CBA  CAZ   113.45  3.000
 I2O  HBA   CBA  CAZ   109.19  3.000
 I2O  HBAA  CBA  CAV   111.71  3.000
 I2O  HBA   CBA  CAV   109.64  3.000
 I2O  CAZ   CBA  CAV   105.61  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
 I2O  CONST_01  CAD   CAC  CAB  CAA     0.00   0.0  0
 I2O  CONST_02  CAN   CAC  CAB  CAA   180.00   0.0  0
 I2O  CONST_03  CAD   CAE  CAF  CAA     0.00   0.0  0
 I2O  CONST_04  CAE   CAF  CAA  CAB     0.00   0.0  0
 I2O  CONST_05  CAE   CAD  CAC  CAB     0.00   0.0  0
 I2O  CONST_08  CAF   CAA  CAB  CAC     0.00   0.0  0
 I2O  CONST_09  CAF   CAE  CAD  CAC     0.00   0.0  0
 I2O  CONST_10  CAP   CAO  CAN  CAC   180.00   0.0  0
 I2O  CONST_11  CAR   CAS  CAN  CAC   180.00   0.0  0
 I2O  CONST_14  CAN   CAC  CAD  CAE   180.00   0.0  0
 I2O  CONST_15  CAQ   CAP  CAO  CAN     0.00   0.0  0
 I2O  CONST_16  CAQ   CAR  CAS  CAN     0.00   0.0  0
 I2O  CONST_17  CAR   CAS  CAN  CAO     0.00   0.0  0
 I2O  CONST_18  CAR   CAQ  CAP  CAO     0.00   0.0  0
 I2O  CONST_19  CAS   CAN  CAO  CAP     0.00   0.0  0
 I2O  CONST_20  CAS   CAR  CAQ  CAP     0.00   0.0  0
 I2O  CONST_21  CAV   CAQ  CAP  CAO   180.00   0.0  0
 I2O  CONST_22  CAV   CAQ  CAR  CAS   180.00   0.0  0
 I2O  CONST_23  CAV   CAQ  CAP  NAT     0.00   0.0  0
 I2O  CONST_24  CAV   CAU  NAT  CAP     0.00   0.0  0
 I2O  CONST_25  CAH   CAE  CAF  CAA   180.00   0.0  0
 I2O  CONST_26  CAH   CAE  CAD  CAC   180.00   0.0  0
 I2O  CONST_27  CAG   CAB  CAC  CAD   180.00   0.0  0
 I2O  CONST_28  CAG   CAB  CAA  CAF   180.00   0.0  0
 I2O  CONST_29  CAN   CAC  CAB  CAG     0.00   0.0  0
 I2O  CONST_30  OAW   CAU  NAT  CAP   180.00   0.0  0
 I2O  CONST_31  HAF   CAF  CAA  CAB   180.00   0.0  0
 I2O  CONST_32  HAD   CAD  CAC  CAB   180.00   0.0  0
 I2O  CONST_33  HAA   CAA  CAB  CAC   180.00   0.0  0
 I2O  CONST_34  HAO   CAO  CAN  CAC     0.00   0.0  0
 I2O  CONST_35  HAS   CAS  CAN  CAC     0.00   0.0  0
 I2O  CONST_36  HAR   CAR  CAS  CAN   180.00   0.0  0
 I2O  CONST_37  HNAT  NAT  CAU  CAV   180.00   0.0  0
 I2O  CONST_38  CAJ   NAI  CAH  CAE   180.00   0.0  0
 I2O  CONST_39  OAM   CAH  NAI  CAJ     0.00   0.0  0
 I2O  CONST_40  HNAI  NAI  CAH  CAE     0.00   0.0  0
 I2O  Var_01    CAX   CAV  CAQ  CAP  -120.01  30.0  1
 I2O  Var_02    CAY   CAX  CAV  CAQ  -142.55  30.0  3
 I2O  Var_03    CAZ   CBA  CAV  CAQ   115.41  30.0  3
 I2O  Var_04    CAZ   CAY  CAX  CAV    36.90  30.0  1
 I2O  Var_05    CAY   CAZ  CBA  CAV    33.12  30.0  1
 I2O  Var_06    CBA   CAZ  CAY  CAX   -43.30  30.0  1
 I2O  Var_07    CAL   CAK  CAJ  NAI   109.66  30.0  1
 I2O  Var_08    HAL   CAL  CAK  CAJ  -107.10  30.0  1
 I2O  Var_09    NAI   CAH  CAE  CAD  -155.80  30.0  2
 I2O  Var_10    CAK   CAJ  NAI  CAH  -146.88  30.0  3
 I2O  Var_11    HAG   CAG  CAB  CAA    97.90  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
 I2O  chir_01  CAJ  NAI  CAK  CAL  both

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
 I2O  plan-1  CAA   0.020
 I2O  plan-1  CAB   0.020
 I2O  plan-1  CAC   0.020
 I2O  plan-1  CAD   0.020
 I2O  plan-1  CAE   0.020
 I2O  plan-1  CAF   0.020
 I2O  plan-1  CAG   0.020
 I2O  plan-1  CAH   0.020
 I2O  plan-1  CAN   0.020
 I2O  plan-1  HAA   0.020
 I2O  plan-1  HAD   0.020
 I2O  plan-1  HAF   0.020
 I2O  plan-2  CAE   0.020
 I2O  plan-2  CAH   0.020
 I2O  plan-2  NAI   0.020
 I2O  plan-2  CAJ   0.020
 I2O  plan-2  OAM   0.020
 I2O  plan-2  HNAI  0.020
 I2O  plan-3  CAC   0.020
 I2O  plan-3  CAN   0.020
 I2O  plan-3  CAO   0.020
 I2O  plan-3  CAP   0.020
 I2O  plan-3  CAQ   0.020
 I2O  plan-3  CAR   0.020
 I2O  plan-3  CAS   0.020
 I2O  plan-3  NAT   0.020
 I2O  plan-3  CAU   0.020
 I2O  plan-3  CAV   0.020
 I2O  plan-3  OAW   0.020
 I2O  plan-3  HAO   0.020
 I2O  plan-3  HAR   0.020
 I2O  plan-3  HAS   0.020
 I2O  plan-3  HNAT  0.020

