# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 24 01:24:53 2021
#   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  44  25  .  2021-08-25  2022-11-18
;
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  OH1   0  -0.573  23.7967   -9.0624   9.8368
 ZYM  OAB   O  O     0  -0.488  26.9808   -7.2950   6.6585
 ZYM  OAC   O  O     0  -0.400  22.3687   -7.5051   9.0883
 ZYM  OAD   O  O     0  -0.330  23.9673   -7.2403   6.9086
 ZYM  CAE   C  CH2   0  -0.721  25.5274   -8.8731   7.6992
 ZYM  CAF   C  CR16  0  -0.260  23.9221  -13.4371  11.8777
 ZYM  CAG   C  CR16  0  -0.252  25.0538  -14.2361  11.9630
 ZYM  CAH   C  CR16  0  -0.256  23.7960  -12.5326  10.8302
 ZYM  CAI   C  CR16  0  -0.236  28.5480   -9.9547   9.5692
 ZYM  CAJ   C  CR16  0  -0.314  29.1316   -9.7663   8.3271
 ZYM  CAK   C  CR16  0  -0.320  26.0624  -14.1306  11.0132
 ZYM  CAL   C  CR16  0  -0.296  24.7930  -12.4239   9.8725
 ZYM  CAM   C  CR16  0  -0.350  27.7747  -11.0779   9.8377
 ZYM  CAN   C  CR16  0  -0.411  28.1788  -11.8336   7.5803
 ZYM  CAO   C  CH2   0  -0.449  29.2509   -9.2060   5.2616
 ZYM  CAP   C  CH2   0  -0.299  27.8326   -9.1374   4.7044
 ZYM  CAQ   C  CH2   0  -0.511  29.5970  -10.5195   5.9663
 ZYM  NAR   N  NH1   0  -0.620  26.7927   -9.3270   5.6945
 ZYM  OAS   O  O2    0  -0.516  26.8985  -13.1767   9.0101
 ZYM  CAT   C  C     0   0.486  23.3650   -8.1615   8.9794
 ZYM  CAU   C  C     0   0.579  26.4993   -8.4167   6.6298
 ZYM  CAV   C  C     0   0.319  24.2973   -8.0164   7.7607
 ZYM  CAW   C  CR6   0   0.143  28.9495  -10.7084   7.3143
 ZYM  CAX   C  CR6   0   0.314  25.9220  -13.2267   9.9712
 ZYM  CAY   C  CR6   0   0.372  27.5990  -12.0180   8.8314
 ZYM  HOAA  H  HOH1  0   0.497  23.1975   -9.1351  10.5964
 ZYM  HAE   H  HCH2  0   0.313  25.2007   -9.9098   7.5660
 ZYM  HAEA  H  HCH2  0   0.319  26.0522   -8.8544   8.6581
 ZYM  HAG   H  HCR6  0   0.263  25.1597  -14.9430  12.7753
 ZYM  HAH   H  HCR6  0   0.260  22.9121  -11.9128  10.7525
 ZYM  HAI   H  HCR6  0   0.260  28.6959   -9.2197  10.3502
 ZYM  HAJ   H  HCR6  0   0.247  29.7331   -8.8843   8.1450
 ZYM  HAK   H  HCR6  0   0.270  26.9491  -14.7485  11.0764
 ZYM  HAL   H  HCR6  0   0.274  24.6898  -11.7247   9.0527
 ZYM  HAM   H  HCR6  0   0.274  27.3327  -11.2090  10.8165
 ZYM  HAN   H  HCR6  0   0.261  28.0227  -12.5808   6.8103
 ZYM  HAO   H  HCH2  0   0.244  29.9352   -9.0718   4.4206
 ZYM  HAOA  H  HCH2  0   0.239  29.4246   -8.3632   5.9336
 ZYM  HAP   H  HCH2  0   0.252  27.6848   -8.1794   4.2033
 ZYM  HAPA  H  HCH2  0   0.250  27.6930   -9.9134   3.9513
 ZYM  HAQ   H  HCH2  0   0.243  29.3507  -11.3626   5.3153
 ZYM  HAQA  H  HCH2  0   0.258  30.6818  -10.5538   6.1023
 ZYM  HNAR  H  HNH1  0   0.405  26.3902  -10.2456   5.7726
 ZYM  HAF   H  HCR6  0   0.260  23.1399  -13.5210  12.6203

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   single    1.316  0.020  1.316
 ZYM  OAA  HOAA  single    0.850  0.020  0.980
 ZYM  OAB  CAU   double    1.221  0.020  1.221
 ZYM  OAC  CAT   double    1.198  0.020  1.198
 ZYM  OAD  CAV   double    1.199  0.020  1.199
 ZYM  CAU  CAE   single    1.515  0.020  1.515
 ZYM  CAV  CAE   single    1.500  0.020  1.500
 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  1.387  0.020  1.387
 ZYM  CAH  HAH   single    0.930  0.020  1.080
 ZYM  CAJ  CAI   aromatic  1.385  0.020  1.385
 ZYM  CAI  CAM   aromatic  1.390  0.020  1.390
 ZYM  CAI  HAI   single    0.930  0.020  1.080
 ZYM  CAW  CAJ   aromatic  1.395  0.020  1.395
 ZYM  CAJ  HAJ   single    0.930  0.020  1.080
 ZYM  CAX  CAK   aromatic  1.387  0.020  1.387
 ZYM  CAK  HAK   single    0.930  0.020  1.080
 ZYM  CAX  CAL   aromatic  1.389  0.020  1.389
 ZYM  CAL  HAL   single    0.930  0.020  1.080
 ZYM  CAY  CAM   aromatic  1.388  0.020  1.388
 ZYM  CAM  HAM   single    0.930  0.020  1.080
 ZYM  CAW  CAN   aromatic  1.390  0.020  1.390
 ZYM  CAN  CAY   aromatic  1.391  0.020  1.391
 ZYM  CAN  HAN   single    0.930  0.020  1.080
 ZYM  CAP  CAO   single    1.525  0.020  1.525
 ZYM  CAO  CAQ   single    1.530  0.020  1.530
 ZYM  CAO  HAO   single    0.970  0.020  1.090
 ZYM  CAO  HAOA  single    0.970  0.020  1.090
 ZYM  CAP  NAR   single    1.448  0.020  1.448
 ZYM  CAP  HAP   single    0.970  0.020  1.090
 ZYM  CAP  HAPA  single    0.970  0.020  1.090
 ZYM  CAQ  CAW   single    1.507  0.020  1.507
 ZYM  CAQ  HAQ   single    0.970  0.020  1.090
 ZYM  CAQ  HAQA  single    0.970  0.020  1.090
 ZYM  CAU  NAR   single    1.338  0.020  1.338
 ZYM  NAR  HNAR  single    0.860  0.020  1.020
 ZYM  CAY  OAS   single    1.366  0.020  1.366
 ZYM  OAS  CAX   single    1.371  0.020  1.371
 ZYM  CAV  CAT   single    1.541  0.020  1.541

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  HOAA  OAA  CAT  111.02  3.000
 ZYM  HAEA  CAE  HAE  105.44  3.000
 ZYM  HAEA  CAE  CAV  110.35  3.000
 ZYM  HAE   CAE  CAV  107.52  3.000
 ZYM  HAEA  CAE  CAU  107.81  3.000
 ZYM  HAE   CAE  CAU  112.99  3.000
 ZYM  CAV   CAE  CAU  112.50  3.000
 ZYM  HAF   CAF  CAH  120.15  3.000
 ZYM  HAF   CAF  CAG  120.18  3.000
 ZYM  CAH   CAF  CAG  119.67  3.000
 ZYM  HAG   CAG  CAK  119.46  3.000
 ZYM  HAG   CAG  CAF  120.13  3.000
 ZYM  CAK   CAG  CAF  120.41  3.000
 ZYM  HAH   CAH  CAL  119.52  3.000
 ZYM  HAH   CAH  CAF  120.06  3.000
 ZYM  CAL   CAH  CAF  120.42  3.000
 ZYM  HAI   CAI  CAM  119.04  3.000
 ZYM  HAI   CAI  CAJ  119.80  3.000
 ZYM  CAM   CAI  CAJ  121.17  3.000
 ZYM  HAJ   CAJ  CAW  120.03  3.000
 ZYM  HAJ   CAJ  CAI  119.70  3.000
 ZYM  CAW   CAJ  CAI  120.27  3.000
 ZYM  HAK   CAK  CAX  119.93  3.000
 ZYM  HAK   CAK  CAG  120.75  3.000
 ZYM  CAX   CAK  CAG  119.33  3.000
 ZYM  HAL   CAL  CAX  120.31  3.000
 ZYM  HAL   CAL  CAH  120.34  3.000
 ZYM  CAX   CAL  CAH  119.34  3.000
 ZYM  HAM   CAM  CAY  121.47  3.000
 ZYM  HAM   CAM  CAI  120.00  3.000
 ZYM  CAY   CAM  CAI  118.53  3.000
 ZYM  HAN   CAN  CAY  119.16  3.000
 ZYM  HAN   CAN  CAW  120.13  3.000
 ZYM  CAY   CAN  CAW  120.71  3.000
 ZYM  HAOA  CAO  HAO  106.22  3.000
 ZYM  HAOA  CAO  CAQ  110.07  3.000
 ZYM  HAO   CAO  CAQ  108.56  3.000
 ZYM  HAOA  CAO  CAP  109.76  3.000
 ZYM  HAO   CAO  CAP  107.20  3.000
 ZYM  CAQ   CAO  CAP  114.65  3.000
 ZYM  HAPA  CAP  HAP  106.88  3.000
 ZYM  HAPA  CAP  NAR  106.68  3.000
 ZYM  HAP   CAP  NAR  109.36  3.000
 ZYM  HAPA  CAP  CAO  109.84  3.000
 ZYM  HAP   CAP  CAO  109.46  3.000
 ZYM  NAR   CAP  CAO  114.33  3.000
 ZYM  HAQA  CAQ  HAQ  105.86  3.000
 ZYM  HAQA  CAQ  CAW  108.12  3.000
 ZYM  HAQ   CAQ  CAW  109.82  3.000
 ZYM  HAQA  CAQ  CAO  107.97  3.000
 ZYM  HAQ   CAQ  CAO  109.68  3.000
 ZYM  CAW   CAQ  CAO  114.98  3.000
 ZYM  HNAR  NAR  CAU  118.64  3.000
 ZYM  HNAR  NAR  CAP  117.38  3.000
 ZYM  CAU   NAR  CAP  123.12  3.000
 ZYM  CAY   OAS  CAX  119.21  3.000
 ZYM  CAV   CAT  OAC  121.56  3.000
 ZYM  CAV   CAT  OAA  112.40  3.000
 ZYM  OAC   CAT  OAA  126.05  3.000
 ZYM  NAR   CAU  CAE  115.41  3.000
 ZYM  NAR   CAU  OAB  123.72  3.000
 ZYM  CAE   CAU  OAB  120.86  3.000
 ZYM  CAT   CAV  CAE  118.33  3.000
 ZYM  CAT   CAV  OAD  117.16  3.000
 ZYM  CAE   CAV  OAD  124.49  3.000
 ZYM  CAQ   CAW  CAN  120.73  3.000
 ZYM  CAQ   CAW  CAJ  120.56  3.000
 ZYM  CAN   CAW  CAJ  118.70  3.000
 ZYM  OAS   CAX  CAL  120.53  3.000
 ZYM  OAS   CAX  CAK  118.59  3.000
 ZYM  CAL   CAX  CAK  120.83  3.000
 ZYM  OAS   CAY  CAN  116.35  3.000
 ZYM  OAS   CAY  CAM  122.99  3.000
 ZYM  CAN   CAY  CAM  120.62  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  CONST_31  HOAA  OAA  CAT  OAC    0.00   0.0  0
 ZYM  Var_01    CAO   CAQ  CAW  CAJ  -56.53  30.0  2
 ZYM  Var_02    CAW   CAQ  CAO  CAP  -72.83  30.0  3
 ZYM  Var_03    OAD   CAV  CAT  OAA  178.24  30.0  2
 ZYM  Var_04    CAV   CAE  CAU  OAB   59.83  30.0  3
 ZYM  Var_05    CAU   CAE  CAV  OAD   14.66  30.0  3
 ZYM  Var_06    CAU   NAR  CAP  CAO   71.19  30.0  3
 ZYM  Var_07    NAR   CAP  CAO  CAQ   58.19  30.0  2

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  HAG   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-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
 ZYM  plan-5  HOAA  0.020

