# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 16:18:34 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: (1S,2S)-2-[(2S)-2-azanyl-1-hydroxy-1-oxo-3-(9H-xanthen-9-yl)propan-2-yl]cyclopropane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@](CC1c2ccccc2Oc3ccccc13)([C@H]4C[C@@H]4C(O)=O)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
 Z99  Z99  '(1S,2S)-2-[(2S)-2-azanyl-1-hydroxy-1-oxo-3-(9H-xanthen-9-yl)propan-2-yl]cyclopropane-1-carboxylic acid'  ligand  43  26  .  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_Z99
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
 Z99  NAA   N  NH2    0  -0.805  -1.6205   0.4434  -2.0076
 Z99  OAB   O  O      0  -0.624  -4.7563   1.6307   1.9099
 Z99  OAC   O  OC    -1  -0.608  -1.9841  -2.0241  -1.1154
 Z99  OAD   O  OC    -1  -0.635  -5.9829   0.3422   0.5687
 Z99  OAE   O  O      0  -0.598  -1.4672  -1.5267   0.9946
 Z99  CAF   C  CR16   0  -0.255   2.2077  -3.8022   0.1951
 Z99  CAG   C  CR16   0  -0.251   4.4308   2.7706   0.4246
 Z99  CAH   C  CR16   0  -0.235   1.4287  -3.5691  -0.9298
 Z99  CAI   C  CR16   0  -0.231   3.6846   3.1364  -0.6888
 Z99  CAJ   C  CR16   0  -0.329   2.7021  -2.7377   0.9331
 Z99  CAK   C  CR16   0  -0.321   4.1735   1.5737   1.0744
 Z99  CAL   C  CR16   0  -0.279   1.1184  -2.2689  -1.2963
 Z99  CAM   C  CR16   0  -0.309   2.6672   2.3064  -1.1342
 Z99  CAN   C  CH2    0  -0.392  -0.0365   0.7519  -0.1140
 Z99  CAO   C  CH2    0  -0.497  -3.0264   2.2990  -0.3209
 Z99  OAP   O  O2     0  -0.515   2.9331  -0.4195   1.2669
 Z99  CAR   C  C      0   0.479  -1.6329  -1.2487  -0.2045
 Z99  CAS   C  CR6    0   0.325   2.3845  -1.4457   0.5452
 Z99  CAT   C  CR6    0   0.329   3.1533   0.7554   0.6098
 Z99  CAU   C  CR6    0   0.117   1.5662  -1.1888  -0.5485
 Z99  CAV   C  CR6    0   0.093   2.3778   1.1112  -0.4870
 Z99  CAW   C  CH1    0  -0.390   1.2114   0.2381  -0.8630
 Z99  CAX   C  CH1    0  -0.392  -3.8827   1.0614  -0.2089
 Z99  CAY   C  CT     0  -0.026  -1.4117   0.2453  -0.5831
 Z99  CAZ   C  CH1    0  -0.182  -2.4469   1.0376   0.2147
 Z99  HNAA  H  HNH2   0   0.306  -1.0044   1.1491  -2.3856
 Z99  HNAB  H  HNH2   0   0.338  -1.4525  -0.4259  -2.4937
 Z99  HAF   H  HCR6   0   0.236   2.4506  -4.8139   0.4913
 Z99  HAG   H  HCR6   0   0.242   5.2238   3.4122   0.7843
 Z99  HAH   H  HCR6   0   0.229   1.0607  -4.3988  -1.5182
 Z99  HAI   H  HCR6   0   0.234   3.8904   4.0662  -1.2011
 Z99  HAJ   H  HCR6   0   0.241   3.3396  -2.9042   1.7920
 Z99  HAK   H  HCR6   0   0.245   4.7598   1.2706   1.9322
 Z99  HAL   H  HCR6   0   0.229   0.4987  -2.0877  -2.1635
 Z99  HAM   H  HCR6   0   0.220   2.0737   2.5986  -1.9931
 Z99  HAN   H  HCH2   0   0.240   0.0739   0.5462   0.9528
 Z99  HANA  H  HCH2   0   0.213  -0.0375   1.8445  -0.2197
 Z99  HAO   H  HCH2   0   0.207  -2.7395   2.6074  -1.3199
 Z99  HAOA  H  HCH2   0   0.223  -3.2342   3.1063   0.3716
 Z99  HAW   H  HCH1   0   0.229   1.0332   0.3296  -1.9395
 Z99  HAX   H  HCH1   0   0.222  -4.0957   0.5597  -1.1468
 Z99  HAZ   H  HCH1   0   0.233  -2.2963   1.0093   1.2881
 Z99  CAQ   C  C      0   0.440  -4.9633   1.0087   0.8471

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
 Z99  NAA  CAY   single    1.453  0.020  1.453
 Z99  NAA  HNAA  single    0.890  0.020  1.040
 Z99  NAA  HNAB  single    0.890  0.020  1.040
 Z99  OAB  CAQ   deloc     1.249  0.020  1.249
 Z99  CAR  OAC   deloc     1.247  0.020  1.247
 Z99  CAQ  OAD   deloc     1.250  0.020  1.250
 Z99  OAE  CAR   deloc     1.242  0.020  1.242
 Z99  CAH  CAF   aromatic  1.388  0.020  1.388
 Z99  CAF  CAJ   aromatic  1.386  0.020  1.386
 Z99  CAF  HAF   single    0.930  0.020  1.080
 Z99  CAI  CAG   aromatic  1.389  0.020  1.389
 Z99  CAG  CAK   aromatic  1.386  0.020  1.386
 Z99  CAG  HAG   single    0.930  0.020  1.080
 Z99  CAL  CAH   aromatic  1.386  0.020  1.386
 Z99  CAH  HAH   single    0.930  0.020  1.080
 Z99  CAM  CAI   aromatic  1.387  0.020  1.387
 Z99  CAI  HAI   single    0.930  0.020  1.080
 Z99  CAS  CAJ   aromatic  1.386  0.020  1.386
 Z99  CAJ  HAJ   single    0.930  0.020  1.080
 Z99  CAT  CAK   aromatic  1.388  0.020  1.388
 Z99  CAK  HAK   single    0.930  0.020  1.080
 Z99  CAL  CAU   aromatic  1.388  0.020  1.388
 Z99  CAL  HAL   single    0.930  0.020  1.080
 Z99  CAM  CAV   aromatic  1.390  0.020  1.390
 Z99  CAM  HAM   single    0.930  0.020  1.080
 Z99  CAY  CAN   single    1.539  0.020  1.539
 Z99  CAN  CAW   single    1.543  0.020  1.543
 Z99  CAN  HAN   single    0.970  0.020  1.090
 Z99  CAN  HANA  single    0.970  0.020  1.090
 Z99  CAZ  CAO   single    1.488  0.020  1.488
 Z99  CAO  CAX   single    1.509  0.020  1.509
 Z99  CAO  HAO   single    0.970  0.020  1.090
 Z99  CAO  HAOA  single    0.970  0.020  1.090
 Z99  CAS  OAP   single    1.369  0.020  1.369
 Z99  CAT  OAP   single    1.364  0.020  1.364
 Z99  CAQ  CAX   single    1.512  0.020  1.512
 Z99  CAY  CAR   single    1.557  0.020  1.557
 Z99  CAU  CAS   aromatic  1.390  0.020  1.390
 Z99  CAV  CAT   aromatic  1.390  0.020  1.390
 Z99  CAW  CAU   single    1.504  0.020  1.504
 Z99  CAW  CAV   single    1.505  0.020  1.505
 Z99  CAW  HAW   single    0.970  0.020  1.090
 Z99  CAZ  CAX   single    1.497  0.020  1.497
 Z99  CAX  HAX   single    0.970  0.020  1.090
 Z99  CAZ  CAY   single    1.528  0.020  1.528
 Z99  CAZ  HAZ   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
 Z99  HNAB  NAA  HNAA  108.65  3.000
 Z99  HNAB  NAA  CAY   109.30  3.000
 Z99  HNAA  NAA  CAY   111.98  3.000
 Z99  HAF   CAF  CAJ   119.48  3.000
 Z99  HAF   CAF  CAH   120.33  3.000
 Z99  CAJ   CAF  CAH   120.17  3.000
 Z99  HAG   CAG  CAK   119.50  3.000
 Z99  HAG   CAG  CAI   120.27  3.000
 Z99  CAK   CAG  CAI   120.23  3.000
 Z99  HAH   CAH  CAL   119.97  3.000
 Z99  HAH   CAH  CAF   120.20  3.000
 Z99  CAL   CAH  CAF   119.84  3.000
 Z99  HAI   CAI  CAM   120.14  3.000
 Z99  HAI   CAI  CAG   120.26  3.000
 Z99  CAM   CAI  CAG   119.60  3.000
 Z99  HAJ   CAJ  CAS   120.03  3.000
 Z99  HAJ   CAJ  CAF   120.95  3.000
 Z99  CAS   CAJ  CAF   119.01  3.000
 Z99  HAK   CAK  CAT   119.89  3.000
 Z99  HAK   CAK  CAG   120.85  3.000
 Z99  CAT   CAK  CAG   119.25  3.000
 Z99  HAL   CAL  CAU   119.12  3.000
 Z99  HAL   CAL  CAH   119.85  3.000
 Z99  CAU   CAL  CAH   121.01  3.000
 Z99  HAM   CAM  CAV   119.13  3.000
 Z99  HAM   CAM  CAI   119.66  3.000
 Z99  CAV   CAM  CAI   121.20  3.000
 Z99  HANA  CAN  HAN   106.36  3.000
 Z99  HANA  CAN  CAY   107.30  3.000
 Z99  HAN   CAN  CAY   109.03  3.000
 Z99  HANA  CAN  CAW   106.58  3.000
 Z99  HAN   CAN  CAW   109.25  3.000
 Z99  CAY   CAN  CAW   117.71  3.000
 Z99  HAOA  CAO  HAO   115.32  3.000
 Z99  HAOA  CAO  CAZ   118.44  3.000
 Z99  HAO   CAO  CAZ   118.02  3.000
 Z99  HAOA  CAO  CAX   117.05  3.000
 Z99  HAO   CAO  CAX   116.86  3.000
 Z99  CAZ   CAO  CAX    59.94  3.000
 Z99  CAT   OAP  CAS   117.15  3.000
 Z99  CAY   CAR  OAE   115.50  3.000
 Z99  CAY   CAR  OAC   117.33  3.000
 Z99  OAE   CAR  OAC   127.15  3.000
 Z99  CAU   CAS  OAP   120.80  3.000
 Z99  CAU   CAS  CAJ   121.84  3.000
 Z99  OAP   CAS  CAJ   117.35  3.000
 Z99  CAV   CAT  OAP   120.71  3.000
 Z99  CAV   CAT  CAK   121.57  3.000
 Z99  OAP   CAT  CAK   117.72  3.000
 Z99  CAW   CAU  CAS   118.62  3.000
 Z99  CAW   CAU  CAL   123.34  3.000
 Z99  CAS   CAU  CAL   118.04  3.000
 Z99  CAW   CAV  CAT   118.77  3.000
 Z99  CAW   CAV  CAM   122.96  3.000
 Z99  CAT   CAV  CAM   118.14  3.000
 Z99  HAW   CAW  CAV   108.86  3.000
 Z99  HAW   CAW  CAU   108.86  3.000
 Z99  CAV   CAW  CAU   108.39  3.000
 Z99  HAW   CAW  CAN   108.52  3.000
 Z99  CAV   CAW  CAN   108.20  3.000
 Z99  CAU   CAW  CAN   113.91  3.000
 Z99  HAX   CAX  CAZ   115.19  3.000
 Z99  HAX   CAX  CAQ   116.58  3.000
 Z99  CAZ   CAX  CAQ   119.16  3.000
 Z99  HAX   CAX  CAO   115.25  3.000
 Z99  CAZ   CAX  CAO    59.33  3.000
 Z99  CAQ   CAX  CAO   119.08  3.000
 Z99  CAZ   CAY  CAR   105.92  3.000
 Z99  CAZ   CAY  CAN   105.99  3.000
 Z99  CAR   CAY  CAN   111.64  3.000
 Z99  CAZ   CAY  NAA   110.10  3.000
 Z99  CAR   CAY  NAA   110.41  3.000
 Z99  CAN   CAY  NAA   112.48  3.000
 Z99  HAZ   CAZ  CAY   114.15  3.000
 Z99  HAZ   CAZ  CAX   114.44  3.000
 Z99  CAY   CAZ  CAX   120.67  3.000
 Z99  HAZ   CAZ  CAO   115.63  3.000
 Z99  CAY   CAZ  CAO   121.02  3.000
 Z99  CAX   CAZ  CAO    60.74  3.000
 Z99  CAX   CAQ  OAD   116.50  3.000
 Z99  CAX   CAQ  OAB   117.30  3.000
 Z99  OAD   CAQ  OAB   126.20  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
 Z99  CONST_01  CAU  CAL  CAH  CAF     0.00   0.0  0
 Z99  CONST_02  CAU  CAS  CAJ  CAF     0.00   0.0  0
 Z99  CONST_03  CAV  CAM  CAI  CAG     0.00   0.0  0
 Z99  CONST_04  CAV  CAT  CAK  CAG     0.00   0.0  0
 Z99  CONST_05  CAS  CAJ  CAF  CAH     0.00   0.0  0
 Z99  CONST_06  CAS  CAU  CAL  CAH     0.00   0.0  0
 Z99  CONST_07  CAT  CAK  CAG  CAI     0.00   0.0  0
 Z99  CONST_08  CAT  CAV  CAM  CAI     0.00   0.0  0
 Z99  CONST_09  CAL  CAH  CAF  CAJ     0.00   0.0  0
 Z99  CONST_10  CAL  CAU  CAS  CAJ     0.00   0.0  0
 Z99  CONST_11  CAM  CAI  CAG  CAK     0.00   0.0  0
 Z99  CONST_12  CAM  CAV  CAT  CAK     0.00   0.0  0
 Z99  CONST_13  HAL  CAL  CAH  CAF   180.00   0.0  0
 Z99  CONST_14  HAM  CAM  CAI  CAG   180.00   0.0  0
 Z99  CONST_15  HAJ  CAJ  CAF  CAH   180.00   0.0  0
 Z99  CONST_16  HAK  CAK  CAG  CAI   180.00   0.0  0
 Z99  CONST_17  HAH  CAH  CAF  CAJ   180.00   0.0  0
 Z99  CONST_18  HAI  CAI  CAG  CAK   180.00   0.0  0
 Z99  CONST_19  HAF  CAF  CAH  CAL   180.00   0.0  0
 Z99  CONST_20  HAG  CAG  CAI  CAM   180.00   0.0  0
 Z99  Var_01    CAV  CAT  OAP  CAS    27.15  30.0  1
 Z99  Var_02    CAU  CAS  OAP  CAT   -27.66  30.0  1
 Z99  Var_03    CAQ  CAX  CAZ  CAO  -108.43  30.0  1
 Z99  Var_04    CAO  CAX  CAQ  OAB   -31.48  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
 Z99  chir_01  CAW  CAN  CAU  CAV  positiv
 Z99  chir_03  CAY  CAN  CAR  CAZ  negativ
 Z99  chir_04  CAX  CAO  CAQ  CAZ  both
 Z99  chir_05  CAZ  CAO  CAX  CAY  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
 Z99  plan-1  OAC  0.020
 Z99  plan-1  OAE  0.020
 Z99  plan-1  CAR  0.020
 Z99  plan-1  CAY  0.020
 Z99  plan-2  CAF  0.020
 Z99  plan-2  CAH  0.020
 Z99  plan-2  CAJ  0.020
 Z99  plan-2  CAL  0.020
 Z99  plan-2  OAP  0.020
 Z99  plan-2  CAS  0.020
 Z99  plan-2  CAU  0.020
 Z99  plan-2  CAW  0.020
 Z99  plan-2  HAF  0.020
 Z99  plan-2  HAH  0.020
 Z99  plan-2  HAJ  0.020
 Z99  plan-2  HAL  0.020
 Z99  plan-3  CAG  0.020
 Z99  plan-3  CAI  0.020
 Z99  plan-3  CAK  0.020
 Z99  plan-3  CAM  0.020
 Z99  plan-3  OAP  0.020
 Z99  plan-3  CAT  0.020
 Z99  plan-3  CAV  0.020
 Z99  plan-3  CAW  0.020
 Z99  plan-3  HAG  0.020
 Z99  plan-3  HAI  0.020
 Z99  plan-3  HAK  0.020
 Z99  plan-3  HAM  0.020
 Z99  plan-4  OAB  0.020
 Z99  plan-4  OAD  0.020
 Z99  plan-4  CAX  0.020
 Z99  plan-4  CAQ  0.020

