# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 21:51:55 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: N-(carboxycarbonyl)-S-(3-nitrobenzyl)-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](CSCc1cccc(c1)[N+]([O-])=O)NC(=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
 MD5  MD5  N-(carboxycarbonyl)-S-(3-nitrobenzyl)-L-cysteine  L-peptide  32  22  .  2012-08-28  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MD5
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
 MD5  C     C  C      0   0.422  -4.0357   1.3596  -0.7085
 MD5  N     N  NH1    0  -0.587  -2.7379   0.5533   1.2340
 MD5  OXT   O  OC    -1  -0.586  -3.5282   0.3936  -1.3049
 MD5  CA    C  CH1    0  -0.204  -3.5442   1.6331   0.7427
 MD5  CB    C  CH2    0  -0.567  -2.7840   2.9658   0.7312
 MD5  CAA   C  C      0   0.331  -1.8518  -1.2011   2.6543
 MD5  CAB   C  C      0   0.357  -2.8217   0.0080   2.4500
 MD5  OAH   O  O      0  -0.507  -3.5809   0.3935   3.3339
 MD5  OAI   O  OC    -1  -0.575  -1.8545  -1.6998   3.7863
 MD5  OAJ   O  O      0  -0.586  -1.1803  -1.5298   1.6582
 MD5  SAL   S  S2     0  -0.013  -1.9968   3.4399   2.2919
 MD5  CAM   C  CH2    0  -0.623  -3.4458   3.7669   3.3443
 MD5  CAN   C  CR6    0   0.107  -2.9417   4.0644   4.7230
 MD5  CAO   C  CR16   0  -0.262  -2.6095   3.0247   5.5900
 MD5  CAP   C  CR16   0  -0.234  -2.1079   3.2887   6.8554
 MD5  CAQ   C  CR16   0  -0.277  -1.9216   4.5949   7.2788
 MD5  CAR   C  CR6    0   0.265  -2.2497   5.6215   6.4066
 MD5  CAS   C  CR16   0  -0.311  -2.7523   5.3755   5.1367
 MD5  NAT   N  N      1   0.326  -2.0606   7.0012   6.8336
 MD5  OAU   O  O      0  -0.375  -1.6178   7.1977   7.9409
 MD5  OAV   O  O     -1  -0.375  -2.3556   7.8810   6.0595
 MD5  O     O  O      0  -0.598  -4.8759   2.1694  -1.1397
 MD5  H2    H  HNH1   0   0.373  -2.1525   0.0687   0.5703
 MD5  HA    H  HCH1   0   0.243  -4.4190   1.7299   1.3896
 MD5  HB2   H  HCH2   0   0.272  -1.9570   2.9152   0.0175
 MD5  HB3   H  HCH2   0   0.269  -3.4471   3.7664   0.4034
 MD5  HAM   H  HCH2   0   0.281  -4.0140   4.6060   2.9416
 MD5  HAMA  H  HCH2   0   0.294  -4.0772   2.8798   3.3532
 MD5  HAO   H  HCR6   0   0.276  -2.7523   2.0006   5.2676
 MD5  HAP   H  HCR6   0   0.275  -1.8596   2.4731   7.5206
 MD5  HAQ   H  HCR6   0   0.296  -1.5322   4.7978   8.2655
 MD5  HAS   H  HCR6   0   0.292  -3.0013   6.1886   4.4688

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
 MD5  C    CA    single    1.525  0.021  1.525
 MD5  N    CAB   single    1.335  0.020  1.335
 MD5  N    H2    single    0.860  0.020  1.020
 MD5  OXT  C     deloc     1.243  0.020  1.243
 MD5  CA   N     single    1.458  0.019  1.458
 MD5  CA   CB    single    1.530  0.020  1.530
 MD5  CA   HA    single    0.970  0.020  0.970
 MD5  CB   SAL   single    1.811  0.020  1.811
 MD5  CB   HB2   single    0.970  0.020  1.090
 MD5  CB   HB3   single    0.970  0.020  1.090
 MD5  CAA  OAI   deloc     1.237  0.020  1.237
 MD5  CAB  CAA   single    1.563  0.020  1.563
 MD5  CAB  OAH   double    1.227  0.020  1.227
 MD5  OAJ  CAA   deloc     1.246  0.020  1.246
 MD5  SAL  CAM   single    1.820  0.020  1.820
 MD5  CAM  CAN   single    1.498  0.020  1.498
 MD5  CAM  HAM   single    0.970  0.020  1.090
 MD5  CAM  HAMA  single    0.970  0.020  1.090
 MD5  CAN  CAO   aromatic  1.394  0.020  1.394
 MD5  CAN  CAS   aromatic  1.388  0.020  1.388
 MD5  CAO  CAP   aromatic  1.387  0.020  1.387
 MD5  CAO  HAO   single    0.930  0.020  1.080
 MD5  CAP  CAQ   aromatic  1.386  0.020  1.386
 MD5  CAP  HAP   single    0.930  0.020  1.080
 MD5  CAQ  HAQ   single    0.930  0.020  1.080
 MD5  CAR  CAQ   aromatic  1.386  0.020  1.386
 MD5  CAR  NAT   single    1.457  0.020  1.457
 MD5  CAS  CAR   aromatic  1.388  0.020  1.388
 MD5  CAS  HAS   single    0.930  0.020  1.080
 MD5  NAT  OAU   double    1.209  0.020  1.209
 MD5  OAV  NAT   single    1.208  0.020  1.208
 MD5  O    C     deloc     1.231  0.020  1.231

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
 MD5  O     C    CA   120.80  1.700
 MD5  O     C    OXT  127.96  3.000
 MD5  CA    C    OXT  117.06  3.000
 MD5  H2    N    CAB  116.05  3.000
 MD5  H2    N    CA   117.55  3.000
 MD5  CAB   N    CA   125.74  3.000
 MD5  HA    CA   CB   109.00  3.000
 MD5  HA    CA   N    110.00  3.000
 MD5  CB    CA   N    110.50  1.700
 MD5  HA    CA   C    109.00  3.000
 MD5  CB    CA   C    110.10  1.900
 MD5  N     CA   C    111.00  2.800
 MD5  HB3   CB   HB2  107.33  3.000
 MD5  HB3   CB   SAL  109.35  3.000
 MD5  HB2   CB   SAL  104.23  3.000
 MD5  HB3   CB   CA   109.80  3.000
 MD5  HB2   CB   CA   109.84  3.000
 MD5  SAL   CB   CA   115.87  3.000
 MD5  OAJ   CAA  OAI  128.80  3.000
 MD5  OAJ   CAA  CAB  115.73  3.000
 MD5  OAI   CAA  CAB  115.47  3.000
 MD5  OAH   CAB  CAA  122.18  3.000
 MD5  OAH   CAB  N    124.50  3.000
 MD5  CAA   CAB  N    113.32  3.000
 MD5  CAM   SAL  CB   101.49  3.000
 MD5  HAMA  CAM  HAM  109.13  3.000
 MD5  HAMA  CAM  CAN  110.45  3.000
 MD5  HAM   CAM  CAN  111.25  3.000
 MD5  HAMA  CAM  SAL  108.66  3.000
 MD5  HAM   CAM  SAL  109.84  3.000
 MD5  CAN   CAM  SAL  107.45  3.000
 MD5  CAS   CAN  CAO  119.12  3.000
 MD5  CAS   CAN  CAM  120.53  3.000
 MD5  CAO   CAN  CAM  120.31  3.000
 MD5  HAO   CAO  CAP  119.96  3.000
 MD5  HAO   CAO  CAN  119.25  3.000
 MD5  CAP   CAO  CAN  120.79  3.000
 MD5  HAP   CAP  CAQ  119.48  3.000
 MD5  HAP   CAP  CAO  120.05  3.000
 MD5  CAQ   CAP  CAO  120.46  3.000
 MD5  HAQ   CAQ  CAR  121.39  3.000
 MD5  CAR   CAQ  CAP  118.29  3.000
 MD5  HAQ   CAQ  CAP  120.31  3.000
 MD5  NAT   CAR  CAS  118.89  3.000
 MD5  CAS   CAR  CAQ  122.02  3.000
 MD5  NAT   CAR  CAQ  119.09  3.000
 MD5  HAS   CAS  CAR  121.02  3.000
 MD5  HAS   CAS  CAN  119.66  3.000
 MD5  CAR   CAS  CAN  119.32  3.000
 MD5  OAV   NAT  OAU  123.91  3.000
 MD5  OAV   NAT  CAR  118.04  3.000
 MD5  OAU   NAT  CAR  118.05  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
 MD5  CONST_01  CAQ  CAP  CAO  CAN    0.00   0.0  0
 MD5  CONST_02  CAQ  CAR  CAS  CAN    0.00   0.0  0
 MD5  CONST_03  CAR  CAS  CAN  CAO    0.00   0.0  0
 MD5  CONST_04  CAR  CAQ  CAP  CAO    0.00   0.0  0
 MD5  CONST_05  CAS  CAN  CAO  CAP    0.00   0.0  0
 MD5  CONST_06  CAS  CAR  CAQ  CAP    0.00   0.0  0
 MD5  CONST_07  CAP  CAO  CAN  CAM  180.00   0.0  0
 MD5  CONST_08  CAR  CAS  CAN  CAM  180.00   0.0  0
 MD5  CONST_09  NAT  CAR  CAS  CAN  180.00   0.0  0
 MD5  CONST_10  NAT  CAR  CAQ  CAP  180.00   0.0  0
 MD5  CONST_11  HAP  CAP  CAO  CAN  180.00   0.0  0
 MD5  CONST_12  HAS  CAS  CAN  CAO  180.00   0.0  0
 MD5  CONST_13  HAQ  CAQ  CAP  CAO  180.00   0.0  0
 MD5  CONST_14  HAO  CAO  CAP  CAQ  180.00   0.0  0
 MD5  CONST_15  OAU  NAT  CAR  CAQ    0.00   0.0  0
 MD5  CONST_16  OAV  NAT  CAR  CAQ  180.00   0.0  0
 MD5  CONST_17  OAU  NAT  CAR  CAS  180.00   0.0  0
 MD5  CONST_18  OAV  NAT  CAR  CAS    0.00   0.0  0
 MD5  CONST_19  CAA  CAB  N    CA   180.00   0.0  0
 MD5  CONST_20  OAH  CAB  N    CA     0.00   0.0  0
 MD5  CONST_21  H2   N    CAB  CAA    0.00   0.0  0
 MD5  Var_01    CAO  CAN  CAM  SAL  -81.94  30.0  2
 MD5  Var_02    CAN  CAM  SAL  CB   175.31  30.0  3
 MD5  Var_03    OAI  CAA  CAB  N    176.97  30.0  2
 MD5  Var_04    HB2  CB   SAL  CAM  171.15  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
 MD5  chir_01  CA  C  N  CB  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
 MD5  plan-1  CAM  0.020
 MD5  plan-1  CAN  0.020
 MD5  plan-1  CAO  0.020
 MD5  plan-1  CAP  0.020
 MD5  plan-1  CAQ  0.020
 MD5  plan-1  CAR  0.020
 MD5  plan-1  CAS  0.020
 MD5  plan-1  NAT  0.020
 MD5  plan-1  HAO  0.020
 MD5  plan-1  HAP  0.020
 MD5  plan-1  HAQ  0.020
 MD5  plan-1  HAS  0.020
 MD5  plan-2  N    0.020
 MD5  plan-2  CA   0.020
 MD5  plan-2  CAA  0.020
 MD5  plan-2  CAB  0.020
 MD5  plan-2  OAH  0.020
 MD5  plan-2  H2   0.020
 MD5  plan-3  CAR  0.020
 MD5  plan-3  NAT  0.020
 MD5  plan-3  OAU  0.020
 MD5  plan-3  OAV  0.020
 MD5  plan-4  C    0.020
 MD5  plan-4  OXT  0.020
 MD5  plan-4  CA   0.020
 MD5  plan-4  O    0.020
 MD5  plan-5  CAA  0.020
 MD5  plan-5  CAB  0.020
 MD5  plan-5  OAI  0.020
 MD5  plan-5  OAJ  0.020

