# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 13:27:13 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: S-(3-oxo-3-{[4-(phenylamino)quinazolin-6-yl]amino}propyl)-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSCCC(=O)Nc1ccc2ncnc(Nc3ccccc3)c2c1)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
 CY0  CY0  S-(3-oxo-3-{[4-(phenylamino)quinazolin-6-yl]amino}propyl)-L-cysteine  L-peptide  49  29  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_CY0
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
 CY0  CAI   C  CR16   0  -0.299  -52.7146   0.7095  -26.3681
 CY0  CAF   C  CR16   0  -0.246  -52.6583   0.7588  -27.7551
 CY0  CAE   C  CR16   0  -0.270  -52.3481  -0.3647  -28.5063
 CY0  CAG   C  CR16   0  -0.241  -52.0851  -1.5598  -27.8490
 CY0  CAJ   C  CR16   0  -0.357  -52.1412  -1.6256  -26.4682
 CY0  CAX   C  CR6    0   0.369  -52.4590  -0.4944  -25.7093
 CY0  NAT   N  NH1    0  -0.777  -52.4541  -0.6619  -24.3203
 CY0  C6    C  CR6    0   0.532  -53.0060   0.0900  -23.3419
 CY0  C5    C  CR66   0  -0.008  -52.8551  -0.3145  -21.9646
 CY0  CAM   C  CR16   0  -0.368  -52.1395  -1.4474  -21.5370
 CY0  N1    N  N      0  -0.477  -53.6779   1.1759  -23.6524
 CY0  C2    C  CR16   0   0.044  -54.2259   1.8864  -22.6553
 CY0  N3    N  N      0  -0.451  -54.1821   1.6335  -21.3817
 CY0  C4    C  CR66   0   0.222  -53.4896   0.5191  -21.0219
 CY0  CAL   C  CR16   0  -0.304  -53.3953   0.1851  -19.6575
 CY0  CAK   C  CR16   0  -0.312  -52.6883  -0.9141  -19.2567
 CY0  CAY   C  CR6    0   0.363  -52.0457  -1.7503  -20.1955
 CY0  NAS   N  NH1    0  -0.774  -51.3567  -2.8644  -19.6989
 CY0  CAW   C  C      0   0.511  -50.1697  -3.3069  -20.1763
 CY0  OAC   O  O      0  -0.484  -49.6075  -2.8087  -21.1393
 CY0  CAO   C  CH2    0  -0.542  -49.4834  -4.4259  -19.4149
 CY0  CAN   C  CH2    0  -0.581  -50.2769  -5.2383  -18.4094
 CY0  SAU   S  S2     0  -0.042  -51.5855  -6.1983  -19.2342
 CY0  CB    C  CH2    0  -0.570  -52.8355  -6.3305  -17.9227
 CY0  CA    C  CH1    0  -0.182  -53.8214  -5.1692  -17.8622
 CY0  C     C  C      0   0.391  -54.9323  -5.5068  -16.8242
 CY0  O     O  O      0  -0.591  -55.0525  -4.7435  -15.8488
 CY0  N     N  NH2    0  -0.793  -53.1279  -3.9093  -17.6265
 CY0  OXT   O  OC    -1  -0.607  -55.5985  -6.5308  -17.0731
 CY0  HAI   H  HCR6   0   0.278  -52.9577   1.5987  -25.8111
 CY0  HAF   H  HCR6   0   0.255  -52.8600   1.7003  -28.2500
 CY0  HAE   H  HCR6   0   0.253  -52.3092  -0.3110  -29.5861
 CY0  HAG   H  HCR6   0   0.258  -51.8380  -2.4506  -28.4119
 CY0  HAJ   H  HCR6   0   0.269  -51.9386  -2.5666  -25.9695
 CY0  HAT   H  HNH1   0   0.432  -52.0427  -1.5333  -24.0281
 CY0  HAM   H  HCR6   0   0.264  -51.6591  -2.1024  -22.2474
 CY0  H2    H  HCR6   0   0.248  -54.7691   2.7736  -22.9654
 CY0  HAL   H  HCR6   0   0.264  -53.8791   0.8257  -18.9319
 CY0  HAK   H  HCR6   0   0.274  -52.6025  -1.1412  -18.2018
 CY0  HAS   H  HNH1   0   0.461  -51.8237  -3.3323  -18.9011
 CY0  HAO1  H  HCH2   0   0.285  -48.6436  -3.9602  -18.8888
 CY0  HAO2  H  HCH2   0   0.268  -49.0308  -5.0844  -20.1592
 CY0  HAN1  H  HCH2   0   0.272  -50.7257  -4.6041  -17.6474
 CY0  HAN2  H  HCH2   0   0.284  -49.5977  -5.9210  -17.8981
 CY0  HBC1  H  HCH2   0   0.264  -52.3190  -6.4592  -16.9673
 CY0  HBC2  H  HCH2   0   0.277  -53.3806  -7.2525  -18.1166
 CY0  HA    H  HCH1   0   0.231  -54.2999  -5.0958  -18.8443
 CY0  HN1   H  HNH2   0   0.346  -52.7874  -3.9021  -16.6704
 CY0  HN2   H  HNH2   0   0.359  -53.8132  -3.1629  -17.6493

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
 CY0  CAI  CAF   aromatic  1.389  0.020  1.389
 CY0  CAI  CAX   aromatic  1.396  0.020  1.396
 CY0  CAI  HAI   single    0.930  0.020  1.080
 CY0  CAF  CAE   aromatic  1.387  0.020  1.387
 CY0  CAF  HAF   single    0.930  0.020  1.080
 CY0  CAE  CAG   aromatic  1.389  0.020  1.389
 CY0  CAE  HAE   single    0.930  0.020  1.080
 CY0  CAG  CAJ   aromatic  1.384  0.020  1.384
 CY0  CAG  HAG   single    0.930  0.020  1.080
 CY0  CAJ  CAX   aromatic  1.399  0.020  1.399
 CY0  CAJ  HAJ   single    0.930  0.020  1.080
 CY0  CAX  NAT   single    1.399  0.020  1.399
 CY0  NAT  C6    single    1.352  0.020  1.352
 CY0  NAT  HAT   single    0.860  0.020  1.020
 CY0  C6   C5    aromatic  1.443  0.020  1.443
 CY0  C6   N1    aromatic  1.314  0.020  1.314
 CY0  C5   CAM   aromatic  1.407  0.020  1.407
 CY0  C5   C4    aromatic  1.409  0.020  1.409
 CY0  CAM  CAY   aromatic  1.378  0.020  1.378
 CY0  CAM  HAM   single    0.930  0.020  1.080
 CY0  N1   C2    aromatic  1.341  0.020  1.341
 CY0  C2   N3    aromatic  1.299  0.020  1.299
 CY0  C2   H2    single    0.930  0.020  1.080
 CY0  N3   C4    aromatic  1.360  0.020  1.360
 CY0  C4   CAL   aromatic  1.408  0.020  1.408
 CY0  CAL  CAK   aromatic  1.367  0.020  1.367
 CY0  CAL  HAL   single    0.930  0.020  1.080
 CY0  CAK  CAY   aromatic  1.412  0.020  1.412
 CY0  CAK  HAK   single    0.930  0.020  1.080
 CY0  CAY  NAS   single    1.401  0.020  1.401
 CY0  NAS  CAW   single    1.354  0.020  1.354
 CY0  NAS  HAS   single    0.860  0.020  1.020
 CY0  CAW  OAC   double    1.221  0.020  1.221
 CY0  CAW  CAO   single    1.518  0.020  1.518
 CY0  CAO  CAN   single    1.517  0.020  1.517
 CY0  CAO  HAO1  single    0.970  0.020  1.090
 CY0  CAO  HAO2  single    0.970  0.020  1.090
 CY0  CAN  SAU   single    1.821  0.020  1.821
 CY0  CAN  HAN1  single    0.970  0.020  1.090
 CY0  CAN  HAN2  single    0.970  0.020  1.090
 CY0  SAU  CB    single    1.817  0.020  1.817
 CY0  CB   CA    single    1.530  0.020  1.530
 CY0  CB   HBC1  single    0.970  0.020  1.090
 CY0  CB   HBC2  single    0.970  0.020  1.090
 CY0  CA   C     single    1.525  0.021  1.525
 CY0  CA   N     single    1.458  0.019  1.458
 CY0  CA   HA    single    0.970  0.020  0.970
 CY0  C    O     deloc     1.231  0.020  1.231
 CY0  C    OXT   deloc     1.247  0.020  1.247
 CY0  N    HN1   single    0.890  0.020  1.040
 CY0  N    HN2   single    0.890  0.020  1.040

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
 CY0  HAI   CAI  CAX   120.61  3.000
 CY0  HAI   CAI  CAF   119.75  3.000
 CY0  CAX   CAI  CAF   119.64  3.000
 CY0  HAF   CAF  CAE   119.91  3.000
 CY0  HAF   CAF  CAI   118.67  3.000
 CY0  CAE   CAF  CAI   121.41  3.000
 CY0  HAE   CAE  CAG   120.55  3.000
 CY0  HAE   CAE  CAF   120.57  3.000
 CY0  CAG   CAE  CAF   118.89  3.000
 CY0  HAG   CAG  CAJ   119.28  3.000
 CY0  HAG   CAG  CAE   120.35  3.000
 CY0  CAJ   CAG  CAE   120.37  3.000
 CY0  HAJ   CAJ  CAX   119.66  3.000
 CY0  HAJ   CAJ  CAG   119.53  3.000
 CY0  CAX   CAJ  CAG   120.81  3.000
 CY0  NAT   CAX  CAJ   116.17  3.000
 CY0  NAT   CAX  CAI   124.92  3.000
 CY0  CAJ   CAX  CAI   118.88  3.000
 CY0  HAT   NAT  C6    115.98  3.000
 CY0  HAT   NAT  CAX   113.15  3.000
 CY0  C6    NAT  CAX   130.58  3.000
 CY0  N1    C6   C5    120.70  3.000
 CY0  N1    C6   NAT   119.82  3.000
 CY0  C5    C6   NAT   119.48  3.000
 CY0  C4    C5   CAM   120.14  3.000
 CY0  C4    C5   C6    115.18  3.000
 CY0  CAM   C5   C6    124.68  3.000
 CY0  HAM   CAM  CAY   118.49  3.000
 CY0  HAM   CAM  C5    121.02  3.000
 CY0  CAY   CAM  C5    120.49  3.000
 CY0  C2    N1   C6    118.09  3.000
 CY0  H2    C2   N3    117.13  3.000
 CY0  H2    C2   N1    115.15  3.000
 CY0  N3    C2   N1    127.72  3.000
 CY0  C4    N3   C2    115.84  3.000
 CY0  CAL   C4   N3    118.99  3.000
 CY0  CAL   C4   C5    118.54  3.000
 CY0  N3    C4   C5    122.47  3.000
 CY0  HAL   CAL  CAK   120.71  3.000
 CY0  HAL   CAL  C4    118.65  3.000
 CY0  CAK   CAL  C4    120.63  3.000
 CY0  HAK   CAK  CAY   119.19  3.000
 CY0  HAK   CAK  CAL   119.69  3.000
 CY0  CAY   CAK  CAL   121.11  3.000
 CY0  NAS   CAY  CAK   117.33  3.000
 CY0  NAS   CAY  CAM   123.59  3.000
 CY0  CAK   CAY  CAM   119.08  3.000
 CY0  HAS   NAS  CAW   121.27  3.000
 CY0  HAS   NAS  CAY   114.23  3.000
 CY0  CAW   NAS  CAY   124.49  3.000
 CY0  CAO   CAW  OAC   119.23  3.000
 CY0  CAO   CAW  NAS   117.43  3.000
 CY0  OAC   CAW  NAS   123.25  3.000
 CY0  HAO2  CAO  HAO1  105.43  3.000
 CY0  HAO2  CAO  CAN   110.23  3.000
 CY0  HAO1  CAO  CAN   108.09  3.000
 CY0  HAO2  CAO  CAW   106.86  3.000
 CY0  HAO1  CAO  CAW   105.92  3.000
 CY0  CAN   CAO  CAW   119.40  3.000
 CY0  HAN2  CAN  HAN1  107.07  3.000
 CY0  HAN2  CAN  SAU   109.27  3.000
 CY0  HAN1  CAN  SAU   109.15  3.000
 CY0  HAN2  CAN  CAO   108.68  3.000
 CY0  HAN1  CAN  CAO   111.58  3.000
 CY0  SAU   CAN  CAO   110.98  3.000
 CY0  CB    SAU  CAN   101.88  3.000
 CY0  HBC2  CB   HBC1  107.01  3.000
 CY0  HBC2  CB   CA    109.17  3.000
 CY0  HBC1  CB   CA    111.12  3.000
 CY0  HBC2  CB   SAU   106.12  3.000
 CY0  HBC1  CB   SAU   108.32  3.000
 CY0  CA    CB   SAU   114.72  3.000
 CY0  HA    CA   N     110.00  3.000
 CY0  HA    CA   C     109.00  3.000
 CY0  N     CA   C     111.00  2.800
 CY0  HA    CA   CB    109.00  3.000
 CY0  N     CA   CB    110.50  1.700
 CY0  C     CA   CB    110.10  1.900
 CY0  OXT   C    O     127.50  3.000
 CY0  OXT   C    CA    115.22  3.000
 CY0  O     C    CA    120.80  1.700
 CY0  HN2   N    HN1   104.05  3.000
 CY0  HN2   N    CA    108.14  3.000
 CY0  HN1   N    CA    108.55  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
 CY0  CONST_01  CAG  CAE  CAF  CAI    0.00   0.0  0
 CY0  CONST_02  CAG  CAJ  CAX  CAI    0.00   0.0  0
 CY0  CONST_03  CAJ  CAX  CAI  CAF    0.00   0.0  0
 CY0  CONST_04  CAJ  CAG  CAE  CAF    0.00   0.0  0
 CY0  CONST_05  CAX  CAI  CAF  CAE    0.00   0.0  0
 CY0  CONST_06  CAX  CAJ  CAG  CAE    0.00   0.0  0
 CY0  CONST_07  CAY  CAM  C5   C6   180.00   0.0  0
 CY0  CONST_08  N3   C4   C5   C6     0.00   0.0  0
 CY0  CONST_09  CAL  C4   C5   C6   180.00   0.0  0
 CY0  CONST_10  N3   C2   N1   C6     0.00   0.0  0
 CY0  CONST_11  C2   N1   C6   C5     0.00   0.0  0
 CY0  CONST_12  CAK  CAY  CAM  C5     0.00   0.0  0
 CY0  CONST_13  C2   N3   C4   C5     0.00   0.0  0
 CY0  CONST_14  CAK  CAL  C4   C5     0.00   0.0  0
 CY0  CONST_15  N1   C6   C5   CAM  180.00   0.0  0
 CY0  CONST_16  N3   C4   C5   CAM  180.00   0.0  0
 CY0  CONST_17  CAL  C4   C5   CAM    0.00   0.0  0
 CY0  CONST_18  CAL  CAK  CAY  CAM    0.00   0.0  0
 CY0  CONST_19  C4   C5   C6   N1     0.00   0.0  0
 CY0  CONST_20  C4   N3   C2   N1     0.00   0.0  0
 CY0  CONST_21  CAL  C4   N3   C2   180.00   0.0  0
 CY0  CONST_22  CAK  CAL  C4   N3   180.00   0.0  0
 CY0  CONST_23  CAY  CAM  C5   C4     0.00   0.0  0
 CY0  CONST_24  CAY  CAK  CAL  C4     0.00   0.0  0
 CY0  CONST_25  NAT  CAX  CAI  CAF  180.00   0.0  0
 CY0  CONST_26  NAT  CAX  CAJ  CAG  180.00   0.0  0
 CY0  CONST_27  CAM  C5   C6   NAT    0.00   0.0  0
 CY0  CONST_28  C4   C5   C6   NAT  180.00   0.0  0
 CY0  CONST_29  C2   N1   C6   NAT  180.00   0.0  0
 CY0  CONST_30  NAS  CAY  CAM  C5   180.00   0.0  0
 CY0  CONST_31  NAS  CAY  CAK  CAL  180.00   0.0  0
 CY0  CONST_32  HAE  CAE  CAF  CAI  180.00   0.0  0
 CY0  CONST_33  HAJ  CAJ  CAX  CAI  180.00   0.0  0
 CY0  CONST_34  HAG  CAG  CAE  CAF  180.00   0.0  0
 CY0  CONST_35  HAI  CAI  CAF  CAE  180.00   0.0  0
 CY0  CONST_36  HAF  CAF  CAE  CAG  180.00   0.0  0
 CY0  CONST_37  HAM  CAM  C5   C6     0.00   0.0  0
 CY0  CONST_38  H2   C2   N1   C6   180.00   0.0  0
 CY0  CONST_39  HAL  CAL  C4   C5   180.00   0.0  0
 CY0  CONST_40  HAK  CAK  CAY  CAM  180.00   0.0  0
 CY0  CONST_44  OAC  CAW  NAS  CAY    0.00   0.0  0
 CY0  CONST_45  CAO  CAW  NAS  CAY  180.00   0.0  0
 CY0  Var_01    C6   NAT  CAX  CAI   19.98  30.0  2
 CY0  Var_02    C5   C6   NAT  CAX  179.76  30.0  2
 CY0  Var_03    CAN  CAO  CAW  NAS   15.93  30.0  3
 CY0  Var_04    SAU  CAN  CAO  CAW   65.34  30.0  3
 CY0  Var_05    CA   CB   SAU  CAN   87.36  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
 CY0  chir_01  CA  CB  C  N  negativ

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
 CY0  plan-1  CAI  0.020
 CY0  plan-1  CAF  0.020
 CY0  plan-1  CAE  0.020
 CY0  plan-1  CAG  0.020
 CY0  plan-1  CAJ  0.020
 CY0  plan-1  CAX  0.020
 CY0  plan-1  NAT  0.020
 CY0  plan-1  HAI  0.020
 CY0  plan-1  HAF  0.020
 CY0  plan-1  HAE  0.020
 CY0  plan-1  HAG  0.020
 CY0  plan-1  HAJ  0.020
 CY0  plan-2  NAT  0.020
 CY0  plan-2  C6   0.020
 CY0  plan-2  C5   0.020
 CY0  plan-2  CAM  0.020
 CY0  plan-2  N1   0.020
 CY0  plan-2  C2   0.020
 CY0  plan-2  N3   0.020
 CY0  plan-2  C4   0.020
 CY0  plan-2  CAL  0.020
 CY0  plan-2  CAK  0.020
 CY0  plan-2  CAY  0.020
 CY0  plan-2  NAS  0.020
 CY0  plan-2  HAM  0.020
 CY0  plan-2  H2   0.020
 CY0  plan-2  HAL  0.020
 CY0  plan-2  HAK  0.020
 CY0  plan-3  CAY  0.020
 CY0  plan-3  NAS  0.020
 CY0  plan-3  CAW  0.020
 CY0  plan-3  OAC  0.020
 CY0  plan-3  CAO  0.020
 CY0  plan-3  HAS  0.020
 CY0  plan-4  CA   0.020
 CY0  plan-4  C    0.020
 CY0  plan-4  O    0.020
 CY0  plan-4  OXT  0.020

