# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 14:24:12 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 2,4-dioxo-4-{[3-(3-phenoxyphenyl)propyl]amino}butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(=O)CC(=O)NCCCc1cccc(Oc2ccccc2)c1
#
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
 ZYM  ZYM  '2,4-dioxo-4-{[3-(3-phenoxyphenyl)propyl]amino}butanoic acid'  ligand  43  25  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZYM
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
 ZYM  OAA   O  OC    -1  -0.576  -7.8665  -1.3117   1.3626
 ZYM  OAB   O  O      0  -0.504  -4.2147   1.1081  -1.8974
 ZYM  OAC   O  O      0  -0.574  -7.3587   0.7973   1.9226
 ZYM  OAD   O  O      0  -0.381  -5.7851  -1.2472  -0.3890
 ZYM  CAE   C  CH2    0  -0.697  -5.0939   0.9186   0.3224
 ZYM  CAF   C  CR16   0  -0.272   7.3148   2.0912  -0.6958
 ZYM  CAG   C  CR16   0  -0.246   6.7317   1.0057  -1.3341
 ZYM  CAH   C  CR16   0  -0.247   7.0034   2.3438   0.6347
 ZYM  CAI   C  CR16   0  -0.236   2.8848  -3.3171   0.4025
 ZYM  CAJ   C  CR16   0  -0.316   1.8624  -2.7612  -0.3515
 ZYM  CAK   C  CR16   0  -0.333   5.8449   0.1743  -0.6616
 ZYM  CAL   C  CR16   0  -0.331   6.1154   1.5275   1.3184
 ZYM  CAM   C  CR16   0  -0.340   3.8587  -2.5095   0.9765
 ZYM  CAN   C  CR16   0  -0.364   2.7584  -0.5724   0.0451
 ZYM  CAO   C  CH2    0  -0.471  -0.5714  -0.5501  -0.4062
 ZYM  CAP   C  CH2    0  -0.237  -1.7004   0.1336  -1.1588
 ZYM  CAQ   C  CH2    0  -0.511   0.6498  -0.7656  -1.2997
 ZYM  NAR   N  NH1    0  -0.630  -2.8403   0.3362  -0.2907
 ZYM  OAS   O  O2     0  -0.514   4.7118  -0.3446   1.4159
 ZYM  CAT   C  C      0   0.354  -7.2020  -0.2698   1.3071
 ZYM  CAU   C  C      0   0.545  -4.0152   0.8079  -0.7275
 ZYM  CAV   C  C      0   0.248  -5.9940  -0.2978   0.3255
 ZYM  CAW   C  CR6    0   0.142   1.7893  -1.3813  -0.5379
 ZYM  CAX   C  CR6    0   0.356   5.5385   0.4413   0.6682
 ZYM  CAY   C  CR6    0   0.335   3.7824  -1.1385   0.7933
 ZYM  HAE   H  HCH2   0   0.289  -4.6841   1.0436   1.3289
 ZYM  HAEA  H  HCH2   0   0.296  -5.7004   1.8068   0.1367
 ZYM  HAH   H  HCR6   0   0.260   7.4490   3.1866   1.1471
 ZYM  HAI   H  HCR6   0   0.261   2.9331  -4.3894   0.5409
 ZYM  HAJ   H  HCR6   0   0.250   1.1121  -3.4022  -0.7990
 ZYM  HAK   H  HCR6   0   0.277   5.4092  -0.6718  -1.1768
 ZYM  HAL   H  HCR6   0   0.268   5.8697   1.7257   2.3542
 ZYM  HAM   H  HCR6   0   0.268   4.6637  -2.9377   1.5599
 ZYM  HAN   H  HCR6   0   0.268   2.7116   0.5036  -0.0832
 ZYM  HAO   H  HCH2   0   0.242  -0.2835   0.0559   0.4584
 ZYM  HAOA  H  HCH2   0   0.243  -0.9145  -1.5137  -0.0187
 ZYM  HAP   H  HCH2   0   0.232  -1.3509   1.0925  -1.5546
 ZYM  HAPA  H  HCH2   0   0.235  -1.9965  -0.4734  -2.0184
 ZYM  HAQ   H  HCH2   0   0.249   0.3733  -1.4059  -2.1415
 ZYM  HAQA  H  HCH2   0   0.247   0.9637   0.1922  -1.7222
 ZYM  HNAR  H  HNH1   0   0.402  -2.7289   0.1418   0.6912
 ZYM  HAF   H  HCR6   0   0.255   8.0051   2.7317  -1.2283
 ZYM  HAG   H  HCR6   0   0.262   6.9687   0.7932  -2.3685

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
 ZYM  CAT  OAA   deloc     1.237  0.020  1.237
 ZYM  OAB  CAU   double    1.224  0.020  1.224
 ZYM  OAC  CAT   deloc     1.242  0.020  1.242
 ZYM  OAD  CAV   double    1.206  0.020  1.206
 ZYM  CAU  CAE   single    1.509  0.020  1.509
 ZYM  CAV  CAE   single    1.513  0.020  1.513
 ZYM  CAE  HAE   single    0.970  0.020  1.090
 ZYM  CAE  HAEA  single    0.970  0.020  1.090
 ZYM  CAH  CAF   aromatic  1.390  0.020  1.390
 ZYM  CAG  CAF   aromatic  1.388  0.020  1.388
 ZYM  CAF  HAF   single    0.930  0.020  1.080
 ZYM  CAK  CAG   aromatic  1.389  0.020  1.389
 ZYM  CAG  HAG   single    0.930  0.020  1.080
 ZYM  CAL  CAH   aromatic  1.386  0.020  1.386
 ZYM  CAH  HAH   single    0.930  0.020  1.080
 ZYM  CAJ  CAI   aromatic  1.387  0.020  1.387
 ZYM  CAI  CAM   aromatic  1.389  0.020  1.389
 ZYM  CAI  HAI   single    0.930  0.020  1.080
 ZYM  CAW  CAJ   aromatic  1.394  0.020  1.394
 ZYM  CAJ  HAJ   single    0.930  0.020  1.080
 ZYM  CAX  CAK   aromatic  1.391  0.020  1.391
 ZYM  CAK  HAK   single    0.930  0.020  1.080
 ZYM  CAX  CAL   aromatic  1.391  0.020  1.391
 ZYM  CAL  HAL   single    0.930  0.020  1.080
 ZYM  CAY  CAM   aromatic  1.385  0.020  1.385
 ZYM  CAM  HAM   single    0.930  0.020  1.080
 ZYM  CAW  CAN   aromatic  1.390  0.020  1.390
 ZYM  CAN  CAY   aromatic  1.389  0.020  1.389
 ZYM  CAN  HAN   single    0.930  0.020  1.080
 ZYM  CAP  CAO   single    1.519  0.020  1.519
 ZYM  CAO  CAQ   single    1.528  0.020  1.528
 ZYM  CAO  HAO   single    0.970  0.020  1.090
 ZYM  CAO  HAOA  single    0.970  0.020  1.090
 ZYM  CAP  NAR   single    1.447  0.020  1.447
 ZYM  CAP  HAP   single    0.970  0.020  1.090
 ZYM  CAP  HAPA  single    0.970  0.020  1.090
 ZYM  CAQ  CAW   single    1.503  0.020  1.503
 ZYM  CAQ  HAQ   single    0.970  0.020  1.090
 ZYM  CAQ  HAQA  single    0.970  0.020  1.090
 ZYM  CAU  NAR   single    1.339  0.020  1.339
 ZYM  NAR  HNAR  single    0.860  0.020  1.020
 ZYM  CAY  OAS   single    1.372  0.020  1.372
 ZYM  OAS  CAX   single    1.364  0.020  1.364
 ZYM  CAV  CAT   single    1.557  0.020  1.557

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
 ZYM  HAEA  CAE  HAE  105.77  3.000
 ZYM  HAEA  CAE  CAV  108.90  3.000
 ZYM  HAE   CAE  CAV  108.23  3.000
 ZYM  HAEA  CAE  CAU  109.79  3.000
 ZYM  HAE   CAE  CAU  112.38  3.000
 ZYM  CAV   CAE  CAU  111.57  3.000
 ZYM  HAF   CAF  CAH  120.44  3.000
 ZYM  HAF   CAF  CAG  120.33  3.000
 ZYM  CAH   CAF  CAG  119.23  3.000
 ZYM  HAG   CAG  CAK  119.01  3.000
 ZYM  HAG   CAG  CAF  120.08  3.000
 ZYM  CAK   CAG  CAF  120.91  3.000
 ZYM  HAH   CAH  CAL  119.25  3.000
 ZYM  HAH   CAH  CAF  120.17  3.000
 ZYM  CAL   CAH  CAF  120.58  3.000
 ZYM  HAI   CAI  CAM  119.46  3.000
 ZYM  HAI   CAI  CAJ  119.97  3.000
 ZYM  CAM   CAI  CAJ  120.56  3.000
 ZYM  HAJ   CAJ  CAW  119.59  3.000
 ZYM  HAJ   CAJ  CAI  119.87  3.000
 ZYM  CAW   CAJ  CAI  120.54  3.000
 ZYM  HAK   CAK  CAX  121.11  3.000
 ZYM  HAK   CAK  CAG  119.63  3.000
 ZYM  CAX   CAK  CAG  119.26  3.000
 ZYM  HAL   CAL  CAX  119.73  3.000
 ZYM  HAL   CAL  CAH  120.62  3.000
 ZYM  CAX   CAL  CAH  119.66  3.000
 ZYM  HAM   CAM  CAY  120.25  3.000
 ZYM  HAM   CAM  CAI  120.93  3.000
 ZYM  CAY   CAM  CAI  118.82  3.000
 ZYM  HAN   CAN  CAY  120.00  3.000
 ZYM  HAN   CAN  CAW  119.83  3.000
 ZYM  CAY   CAN  CAW  120.17  3.000
 ZYM  HAOA  CAO  HAO  106.88  3.000
 ZYM  HAOA  CAO  CAQ  109.48  3.000
 ZYM  HAO   CAO  CAQ  109.25  3.000
 ZYM  HAOA  CAO  CAP  109.80  3.000
 ZYM  HAO   CAO  CAP  109.74  3.000
 ZYM  CAQ   CAO  CAP  111.57  3.000
 ZYM  HAPA  CAP  HAP  106.77  3.000
 ZYM  HAPA  CAP  NAR  109.64  3.000
 ZYM  HAP   CAP  NAR  110.23  3.000
 ZYM  HAPA  CAP  CAO  109.93  3.000
 ZYM  HAP   CAP  CAO  109.63  3.000
 ZYM  NAR   CAP  CAO  110.56  3.000
 ZYM  HAQA  CAQ  HAQ  106.76  3.000
 ZYM  HAQA  CAQ  CAW  109.71  3.000
 ZYM  HAQ   CAQ  CAW  110.01  3.000
 ZYM  HAQA  CAQ  CAO  109.38  3.000
 ZYM  HAQ   CAQ  CAO  109.31  3.000
 ZYM  CAW   CAQ  CAO  111.55  3.000
 ZYM  HNAR  NAR  CAU  118.88  3.000
 ZYM  HNAR  NAR  CAP  118.08  3.000
 ZYM  CAU   NAR  CAP  123.00  3.000
 ZYM  CAY   OAS  CAX  119.70  3.000
 ZYM  CAV   CAT  OAC  115.21  3.000
 ZYM  CAV   CAT  OAA  115.46  3.000
 ZYM  OAC   CAT  OAA  129.33  3.000
 ZYM  NAR   CAU  CAE  115.21  3.000
 ZYM  NAR   CAU  OAB  122.76  3.000
 ZYM  CAE   CAU  OAB  122.02  3.000
 ZYM  CAT   CAV  CAE  116.64  3.000
 ZYM  CAT   CAV  OAD  121.46  3.000
 ZYM  CAE   CAV  OAD  121.90  3.000
 ZYM  CAQ   CAW  CAN  120.18  3.000
 ZYM  CAQ   CAW  CAJ  120.87  3.000
 ZYM  CAN   CAW  CAJ  118.89  3.000
 ZYM  OAS   CAX  CAL  116.43  3.000
 ZYM  OAS   CAX  CAK  123.17  3.000
 ZYM  CAL   CAX  CAK  120.37  3.000
 ZYM  OAS   CAY  CAN  120.54  3.000
 ZYM  OAS   CAY  CAM  118.39  3.000
 ZYM  CAN   CAY  CAM  121.01  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
 ZYM  CONST_01  CAX   CAL  CAH  CAF     0.00   0.0  0
 ZYM  CONST_02  CAX   CAK  CAG  CAF     0.00   0.0  0
 ZYM  CONST_03  CAL   CAH  CAF  CAG     0.00   0.0  0
 ZYM  CONST_04  CAL   CAX  CAK  CAG     0.00   0.0  0
 ZYM  CONST_05  CAK   CAG  CAF  CAH     0.00   0.0  0
 ZYM  CONST_06  CAK   CAX  CAL  CAH     0.00   0.0  0
 ZYM  CONST_07  CAN   CAW  CAJ  CAI     0.00   0.0  0
 ZYM  CONST_08  CAN   CAY  CAM  CAI     0.00   0.0  0
 ZYM  CONST_09  CAY   CAM  CAI  CAJ     0.00   0.0  0
 ZYM  CONST_10  CAY   CAN  CAW  CAJ     0.00   0.0  0
 ZYM  CONST_11  CAW   CAJ  CAI  CAM     0.00   0.0  0
 ZYM  CONST_12  CAW   CAN  CAY  CAM     0.00   0.0  0
 ZYM  CONST_13  OAS   CAX  CAK  CAG   180.00   0.0  0
 ZYM  CONST_14  OAS   CAX  CAL  CAH   180.00   0.0  0
 ZYM  CONST_15  CAQ   CAW  CAJ  CAI   180.00   0.0  0
 ZYM  CONST_16  OAS   CAY  CAM  CAI   180.00   0.0  0
 ZYM  CONST_17  CAY   CAN  CAW  CAQ   180.00   0.0  0
 ZYM  CONST_18  CAW   CAN  CAY  OAS   180.00   0.0  0
 ZYM  CONST_19  HAL   CAL  CAH  CAF   180.00   0.0  0
 ZYM  CONST_20  HAK   CAK  CAG  CAF   180.00   0.0  0
 ZYM  CONST_21  HAH   CAH  CAF  CAG   180.00   0.0  0
 ZYM  CONST_22  HAG   CAG  CAF  CAH   180.00   0.0  0
 ZYM  CONST_23  HAM   CAM  CAI  CAJ   180.00   0.0  0
 ZYM  CONST_24  HAN   CAN  CAW  CAJ   180.00   0.0  0
 ZYM  CONST_25  HAF   CAF  CAG  CAK   180.00   0.0  0
 ZYM  CONST_26  HAJ   CAJ  CAI  CAM   180.00   0.0  0
 ZYM  CONST_27  HAI   CAI  CAJ  CAW   180.00   0.0  0
 ZYM  CONST_28  CAP   NAR  CAU  OAB     0.00   0.0  0
 ZYM  CONST_29  CAP   NAR  CAU  CAE   180.00   0.0  0
 ZYM  CONST_30  HNAR  NAR  CAU  OAB   180.00   0.0  0
 ZYM  Var_01    CAO   CAQ  CAW  CAJ    83.88  30.0  2
 ZYM  Var_02    CAW   CAQ  CAO  CAP   177.26  30.0  3
 ZYM  Var_03    OAD   CAV  CAT  OAA     4.58  30.0  2
 ZYM  Var_04    CAV   CAE  CAU  OAB    83.24  30.0  3
 ZYM  Var_05    CAU   CAE  CAV  OAD     4.02  30.0  3
 ZYM  Var_06    CAU   NAR  CAP  CAO  -173.79  30.0  3
 ZYM  Var_07    NAR   CAP  CAO  CAQ  -179.55  30.0  1

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
 ZYM  plan-1  CAF   0.020
 ZYM  plan-1  CAG   0.020
 ZYM  plan-1  CAH   0.020
 ZYM  plan-1  CAK   0.020
 ZYM  plan-1  CAL   0.020
 ZYM  plan-1  OAS   0.020
 ZYM  plan-1  CAX   0.020
 ZYM  plan-1  HAH   0.020
 ZYM  plan-1  HAK   0.020
 ZYM  plan-1  HAL   0.020
 ZYM  plan-1  HAF   0.020
 ZYM  plan-1  HAG   0.020
 ZYM  plan-2  CAI   0.020
 ZYM  plan-2  CAJ   0.020
 ZYM  plan-2  CAM   0.020
 ZYM  plan-2  CAN   0.020
 ZYM  plan-2  CAQ   0.020
 ZYM  plan-2  OAS   0.020
 ZYM  plan-2  CAW   0.020
 ZYM  plan-2  CAY   0.020
 ZYM  plan-2  HAI   0.020
 ZYM  plan-2  HAJ   0.020
 ZYM  plan-2  HAM   0.020
 ZYM  plan-2  HAN   0.020
 ZYM  plan-3  OAB   0.020
 ZYM  plan-3  CAE   0.020
 ZYM  plan-3  CAP   0.020
 ZYM  plan-3  NAR   0.020
 ZYM  plan-3  CAU   0.020
 ZYM  plan-3  HNAR  0.020
 ZYM  plan-4  OAD   0.020
 ZYM  plan-4  CAE   0.020
 ZYM  plan-4  CAT   0.020
 ZYM  plan-4  CAV   0.020
 ZYM  plan-5  OAA   0.020
 ZYM  plan-5  OAC   0.020
 ZYM  plan-5  CAT   0.020
 ZYM  plan-5  CAV   0.020

