# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 15:46:05 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: ({[(2R)-2-{[(4-ethyl-2,3-dioxo-3,4-dihydropyrazin-1(2H)-yl)carbonyl]amino}-2-(4-hydroxyphenyl)acetyl]amino}methyl)boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C=CN(C(=O)N[C@@H](C(=O)NCB(O)O)c2ccc(O)cc2)C(=O)C1=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
 CZ7  CZ7  '({[(2R)-2-{[(4-ethyl-2,3-dioxo-3,4-dihydropyrazin-1(2H)-yl)carbonyl]amino}-2-(4-hydroxyphenyl)acetyl]amino}methyl)boronic acid'  ligand  47  28  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CZ7
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
 CZ7  C     C  C     0   0.586   2.1471   1.2181  -0.2981
 CZ7  N     N  NH1   0  -0.629  -0.0500   0.2724  -0.4370
 CZ7  O     O  O     0  -0.496   1.7430   1.8634   0.6639
 CZ7  CA    C  CH1   0  -0.286   1.2950   0.1184  -0.9346
 CZ7  CAA   C  CH3   0  -0.660  -5.9738   1.5511   2.6239
 CZ7  OAC   O  O     0  -0.427  -1.0295  -1.1039  -1.9457
 CZ7  OAG   O  OH1   0  -0.625   4.2124   3.6246   1.9018
 CZ7  OAH   O  OH1   0  -0.623   4.4017   1.2120   1.9284
 CZ7  CAI   C  CR16  0  -0.326   2.5507  -2.9268   0.9636
 CZ7  CAJ   C  CR16  0  -0.374   2.9041  -3.2957  -1.3889
 CZ7  CAK   C  CR16  0  -0.262   1.9982  -1.6910   0.6816
 CZ7  CAL   C  CR16  0  -0.297   2.3423  -2.0551  -1.6558
 CZ7  CAO   C  CR16  0  -0.067  -3.8891   1.7446   0.1012
 CZ7  CAP   C  CR16  0  -0.100  -2.7037   1.3816  -0.3804
 CZ7  NAQ   N  NH1   0  -0.622   3.3474   1.3930  -0.8355
 CZ7  CAT   C  C     0   0.700  -1.0833  -0.3405  -1.0135
 CZ7  CAU   C  CR6   0   0.467  -4.5127  -0.5088   0.6068
 CZ7  CAV   C  CR6   0   0.474  -3.1638  -0.9476   0.0548
 CZ7  CAW   C  CR6   0   0.348   3.0110  -3.7382  -0.0742
 CZ7  CAX   C  CR6   0   0.135   1.8871  -1.2389  -0.6314
 CZ7  BAY   B  B     0   0.518   4.2451   2.4056   1.2916
 CZ7  NBA   N  NR6   0  -0.491  -4.7976   0.8150   0.5752
 CZ7  NBB   N  NR6   0  -0.614  -2.3456   0.0362  -0.4226
 CZ7  HN    H  HNH1  0   0.420  -0.1710   0.8292   0.3985
 CZ7  HA    H  HCH1  0   0.311   1.2926   0.2662  -2.0187
 CZ7  HAA   H  HCH3  0   0.236  -5.2230   2.3091   2.8474
 CZ7  HAAA  H  HCH3  0   0.246  -6.9340   1.9097   2.9930
 CZ7  HAAB  H  HCH3  0   0.239  -5.7201   0.6442   3.1712
 CZ7  HOAF  H  HOH1  0   0.475   3.8363  -5.3964  -0.5392
 CZ7  HOAG  H  HOH1  0   0.482   4.2693   3.6096   2.8622
 CZ7  HOAH  H  HOH1  0   0.478   4.3915   1.2453   2.8896
 CZ7  HAI   H  HCR6  0   0.266   2.6326  -3.2672   1.9881
 CZ7  HAJ   H  HCR6  0   0.273   3.2493  -3.9175  -2.2071
 CZ7  HAK   H  HCR6  0   0.253   1.6487  -1.0765   1.5029
 CZ7  HAL   H  HCR6  0   0.261   2.2572  -1.7255  -2.6844
 CZ7  HAM   H  HCH2  0   0.270  -6.8342   0.5522   0.9105
 CZ7  HAMA  H  HCH2  0   0.267  -6.3317   2.1994   0.5951
 CZ7  HAN   H  HCH2  0   0.254   5.2646   2.1209  -0.6436
 CZ7  HANA  H  HCH2  0   0.243   4.0403   3.3701  -0.7208
 CZ7  HAO   H  HCR6  0   0.317  -4.1919   2.7789   0.1281
 CZ7  HAP   H  HCR6  0   0.328  -2.0033   2.0966  -0.7801
 CZ7  HNAQ  H  HNH1  0   0.403   3.6061   0.8747  -1.6596
 CZ7  OAD   O  O     0  -0.455  -5.2649  -1.3552   1.0464
 CZ7  OAE   O  O     0  -0.431  -2.8593  -2.1176   0.0815
 CZ7  OAF   O  OH1   0  -0.629   3.5425  -4.9318   0.2524
 CZ7  CAM   C  CH2   0  -0.327  -6.0654   1.2895   1.1310
 CZ7  CAN   C  CH2   0  -0.507   4.2617   2.3840  -0.3009

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
 CZ7  O    C     double    1.227  0.020  1.227
 CZ7  C    CA    single    1.530  0.020  1.530
 CZ7  C    NAQ   single    1.327  0.020  1.327
 CZ7  CA   N     single    1.442  0.020  1.442
 CZ7  N    CAT   single    1.333  0.020  1.333
 CZ7  N    HN    single    0.860  0.020  1.020
 CZ7  CAX  CA    single    1.511  0.020  1.511
 CZ7  CA   HA    single    0.970  0.020  1.090
 CZ7  CAM  CAA   single    1.518  0.020  1.518
 CZ7  CAA  HAA   single    0.970  0.020  1.090
 CZ7  CAA  HAAA  single    0.970  0.020  1.090
 CZ7  CAA  HAAB  single    0.970  0.020  1.090
 CZ7  CAT  OAC   double    1.206  0.020  1.206
 CZ7  OAD  CAU   double    1.215  0.020  1.215
 CZ7  OAE  CAV   double    1.209  0.020  1.209
 CZ7  OAF  CAW   single    1.347  0.020  1.347
 CZ7  OAF  HOAF  single    0.850  0.020  0.980
 CZ7  BAY  OAG   single    1.364  0.020  1.364
 CZ7  OAG  HOAG  single    0.850  0.020  0.980
 CZ7  BAY  OAH   single    1.362  0.020  1.362
 CZ7  OAH  HOAH  single    0.850  0.020  0.980
 CZ7  CAW  CAI   aromatic  1.395  0.020  1.395
 CZ7  CAI  CAK   aromatic  1.383  0.020  1.383
 CZ7  CAI  HAI   single    0.930  0.020  1.080
 CZ7  CAJ  CAW   aromatic  1.391  0.020  1.391
 CZ7  CAJ  CAL   aromatic  1.388  0.020  1.388
 CZ7  CAJ  HAJ   single    0.930  0.020  1.080
 CZ7  CAX  CAK   aromatic  1.393  0.020  1.393
 CZ7  CAK  HAK   single    0.930  0.020  1.080
 CZ7  CAL  CAX   aromatic  1.387  0.020  1.387
 CZ7  CAL  HAL   single    0.930  0.020  1.080
 CZ7  NBA  CAM   single    1.463  0.020  1.463
 CZ7  CAM  HAM   single    0.970  0.020  1.090
 CZ7  CAM  HAMA  single    0.970  0.020  1.090
 CZ7  CAN  NAQ   single    1.450  0.020  1.450
 CZ7  CAN  BAY   single    1.593  0.020  1.593
 CZ7  CAN  HAN   single    0.970  0.020  1.090
 CZ7  CAN  HANA  single    0.970  0.020  1.090
 CZ7  NBA  CAO   single    1.384  0.020  1.384
 CZ7  CAP  CAO   double    1.330  0.020  1.330
 CZ7  CAO  HAO   single    0.930  0.020  1.080
 CZ7  NBB  CAP   single    1.393  0.020  1.393
 CZ7  CAP  HAP   single    0.930  0.020  1.080
 CZ7  NAQ  HNAQ  single    0.860  0.020  1.020
 CZ7  CAT  NBB   single    1.444  0.020  1.444
 CZ7  CAV  CAU   single    1.522  0.020  1.522
 CZ7  CAU  NBA   single    1.354  0.020  1.354
 CZ7  CAV  NBB   single    1.366  0.020  1.366

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
 CZ7  NAQ   C    CA    115.48  3.000
 CZ7  NAQ   C    O     123.11  3.000
 CZ7  CA    C    O     121.39  3.000
 CZ7  HN    N    CAT   121.19  3.000
 CZ7  HN    N    CA    117.09  3.000
 CZ7  CAT   N    CA    121.65  3.000
 CZ7  HA    CA   CAX   108.72  3.000
 CZ7  HA    CA   N     108.99  3.000
 CZ7  CAX   CA   N     113.08  3.000
 CZ7  HA    CA   C     108.44  3.000
 CZ7  CAX   CA   C     110.11  3.000
 CZ7  N     CA   C     107.40  3.000
 CZ7  HAAB  CAA  HAAA  108.00  3.000
 CZ7  HAAB  CAA  HAA   108.39  3.000
 CZ7  HAAA  CAA  HAA   107.98  3.000
 CZ7  HAAB  CAA  CAM   111.39  3.000
 CZ7  HAAA  CAA  CAM   109.67  3.000
 CZ7  HAA   CAA  CAM   111.28  3.000
 CZ7  HOAG  OAG  BAY   115.55  3.000
 CZ7  HOAH  OAH  BAY   115.84  3.000
 CZ7  HAI   CAI  CAW   119.73  3.000
 CZ7  HAI   CAI  CAK   120.28  3.000
 CZ7  CAW   CAI  CAK   119.99  3.000
 CZ7  HAJ   CAJ  CAW   120.41  3.000
 CZ7  HAJ   CAJ  CAL   119.77  3.000
 CZ7  CAW   CAJ  CAL   119.82  3.000
 CZ7  HAK   CAK  CAX   120.30  3.000
 CZ7  HAK   CAK  CAI   118.76  3.000
 CZ7  CAX   CAK  CAI   120.94  3.000
 CZ7  HAL   CAL  CAX   119.77  3.000
 CZ7  HAL   CAL  CAJ   119.10  3.000
 CZ7  CAX   CAL  CAJ   121.13  3.000
 CZ7  HAO   CAO  NBA   116.85  3.000
 CZ7  HAO   CAO  CAP   121.41  3.000
 CZ7  NBA   CAO  CAP   121.73  3.000
 CZ7  HAP   CAP  NBB   117.55  3.000
 CZ7  HAP   CAP  CAO   122.17  3.000
 CZ7  NBB   CAP  CAO   120.25  3.000
 CZ7  HNAQ  NAQ  CAN   119.42  3.000
 CZ7  HNAQ  NAQ  C     119.73  3.000
 CZ7  CAN   NAQ  C     120.74  3.000
 CZ7  NBB   CAT  OAC   121.37  3.000
 CZ7  NBB   CAT  N     112.39  3.000
 CZ7  OAC   CAT  N     126.22  3.000
 CZ7  NBA   CAU  CAV   117.37  3.000
 CZ7  NBA   CAU  OAD   124.00  3.000
 CZ7  CAV   CAU  OAD   118.63  3.000
 CZ7  NBB   CAV  CAU   116.74  3.000
 CZ7  NBB   CAV  OAE   123.63  3.000
 CZ7  CAU   CAV  OAE   119.61  3.000
 CZ7  CAJ   CAW  CAI   119.50  3.000
 CZ7  CAJ   CAW  OAF   122.78  3.000
 CZ7  CAI   CAW  OAF   117.73  3.000
 CZ7  CAL   CAX  CAK   118.63  3.000
 CZ7  CAL   CAX  CA    120.59  3.000
 CZ7  CAK   CAX  CA    120.78  3.000
 CZ7  CAN   BAY  OAH   117.03  3.000
 CZ7  CAN   BAY  OAG   117.38  3.000
 CZ7  OAH   BAY  OAG   125.24  3.000
 CZ7  CAU   NBA  CAO   121.77  3.000
 CZ7  CAU   NBA  CAM   119.36  3.000
 CZ7  CAO   NBA  CAM   118.76  3.000
 CZ7  CAV   NBB  CAT   118.61  3.000
 CZ7  CAV   NBB  CAP   122.08  3.000
 CZ7  CAT   NBB  CAP   119.29  3.000
 CZ7  HOAF  OAF  CAW   110.39  3.000
 CZ7  HAMA  CAM  HAM   107.08  3.000
 CZ7  HAMA  CAM  NBA   107.21  3.000
 CZ7  HAM   CAM  NBA   108.39  3.000
 CZ7  HAMA  CAM  CAA   110.77  3.000
 CZ7  HAM   CAM  CAA   111.02  3.000
 CZ7  NBA   CAM  CAA   112.15  3.000
 CZ7  HANA  CAN  HAN   106.41  3.000
 CZ7  HANA  CAN  BAY   111.67  3.000
 CZ7  HAN   CAN  BAY   109.06  3.000
 CZ7  HANA  CAN  NAQ   110.28  3.000
 CZ7  HAN   CAN  NAQ   107.38  3.000
 CZ7  BAY   CAN  NAQ   111.79  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
 CZ7  CONST_01  CAL   CAJ  CAW  CAI     0.00   0.0  0
 CZ7  CONST_02  CAL   CAX  CAK  CAI     0.00   0.0  0
 CZ7  CONST_03  CAK   CAI  CAW  CAJ     0.00   0.0  0
 CZ7  CONST_04  CAK   CAX  CAL  CAJ     0.00   0.0  0
 CZ7  CONST_05  CAX   CAK  CAI  CAW     0.00   0.0  0
 CZ7  CONST_06  CAX   CAL  CAJ  CAW     0.00   0.0  0
 CZ7  CONST_07  CAV   CAU  NBA  CAO     0.00   0.0  0
 CZ7  CONST_08  CAI   CAK  CAX  CA    180.00   0.0  0
 CZ7  CONST_09  CAJ   CAL  CAX  CA    180.00   0.0  0
 CZ7  CONST_10  CAK   CAI  CAW  OAF   180.00   0.0  0
 CZ7  CONST_11  CAL   CAJ  CAW  OAF   180.00   0.0  0
 CZ7  CONST_12  CAO   NBA  CAU  OAD   180.00   0.0  0
 CZ7  CONST_13  CAV   CAU  NBA  CAM   180.00   0.0  0
 CZ7  CONST_14  HAJ   CAJ  CAW  CAI   180.00   0.0  0
 CZ7  CONST_15  HAI   CAI  CAW  CAJ   180.00   0.0  0
 CZ7  CONST_16  HAL   CAL  CAX  CAK   180.00   0.0  0
 CZ7  CONST_17  HAK   CAK  CAX  CAL   180.00   0.0  0
 CZ7  CONST_22  CAM   NBA  CAU  OAD     0.00   0.0  0
 CZ7  CONST_23  NBB   CAT  N    CA    180.00   0.0  0
 CZ7  CONST_24  HN    N    CAT  NBB     0.00   0.0  0
 CZ7  CONST_25  CAN   NAQ  C    O       0.00   0.0  0
 CZ7  CONST_26  CAN   NAQ  C    CA    180.00   0.0  0
 CZ7  CONST_27  OAC   CAT  N    CA      0.00   0.0  0
 CZ7  CONST_28  HNAQ  NAQ  C    O     180.00   0.0  0
 CZ7  Var_01    CAO   NBA  CAM  CAA   -90.00  30.0  3
 CZ7  Var_02    HAA   CAA  CAM  NBA    60.10  30.0  3
 CZ7  Var_03    BAY   CAN  NAQ  C      41.00  30.0  2
 CZ7  Var_04    NAQ   CAN  BAY  OAG  -135.68  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
 CZ7  chir_01  CA  C  N  CAX  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
 CZ7  plan-1  CA    0.020
 CZ7  plan-1  CAI   0.020
 CZ7  plan-1  CAJ   0.020
 CZ7  plan-1  CAK   0.020
 CZ7  plan-1  CAL   0.020
 CZ7  plan-1  CAW   0.020
 CZ7  plan-1  CAX   0.020
 CZ7  plan-1  HAI   0.020
 CZ7  plan-1  HAJ   0.020
 CZ7  plan-1  HAK   0.020
 CZ7  plan-1  HAL   0.020
 CZ7  plan-1  OAF   0.020
 CZ7  plan-2  C     0.020
 CZ7  plan-2  O     0.020
 CZ7  plan-2  CA    0.020
 CZ7  plan-2  NAQ   0.020
 CZ7  plan-2  HNAQ  0.020
 CZ7  plan-2  CAN   0.020
 CZ7  plan-3  N     0.020
 CZ7  plan-3  CA    0.020
 CZ7  plan-3  OAC   0.020
 CZ7  plan-3  CAO   0.020
 CZ7  plan-3  CAP   0.020
 CZ7  plan-3  CAT   0.020
 CZ7  plan-3  CAU   0.020
 CZ7  plan-3  CAV   0.020
 CZ7  plan-3  NBA   0.020
 CZ7  plan-3  NBB   0.020
 CZ7  plan-3  HN    0.020
 CZ7  plan-3  HAO   0.020
 CZ7  plan-3  HAP   0.020
 CZ7  plan-3  OAD   0.020
 CZ7  plan-3  OAE   0.020
 CZ7  plan-3  CAM   0.020

