# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 20:14:23 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: (4R)-4-[(2E)-3-{4-[(E)-phenyldiazenyl]phenyl}prop-2-en-1-yl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[C@@H](C\C=C\c1ccc(cc1)N=Nc2ccccc2)C(O)=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
 11W  11W  '(4R)-4-[(2E)-3-{4-[(E)-phenyldiazenyl]phenyl}prop-2-en-1-yl]-L-glutamic acid'  L-peptide  46  27  .  2016-04-22  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_11W
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
 11W  CAK  C  CR16   0  -0.270   -0.2499  -23.9984  24.7204
 11W  CAI  C  CR16   0  -0.243    0.8763  -23.5747  25.4022
 11W  CAH  C  CR16   0  -0.251    1.9668  -24.4261  25.5646
 11W  CAJ  C  CR16   0  -0.245    1.9265  -25.7098  25.0392
 11W  CAL  C  CR16   0  -0.281    0.7994  -26.1404  24.3544
 11W  CAX  C  CR6    0   0.227   -0.2919  -25.2910  24.1904
 11W  NAS  N  N      0  -0.270   -1.3778  -25.8322  23.4799
 11W  NAT  N  N      0  -0.262   -2.3406  -25.0675  23.3203
 11W  CAY  C  CR6    0   0.205   -3.4279  -25.5954  22.6135
 11W  CAP  C  CR16   0  -0.247   -3.5037  -26.8970  22.1026
 11W  CAN  C  CR16   0  -0.318   -4.6261  -27.3060  21.4170
 11W  CAO  C  CR16   0  -0.268   -4.4988  -24.7287  22.4188
 11W  CAM  C  CR16   0  -0.310   -5.6222  -25.1454  21.7264
 11W  CAW  C  CR6    0   0.151   -5.7135  -26.4407  21.2112
 11W  CAG  C  C1     0  -0.303   -6.9209  -26.8243  20.4829
 11W  CAF  C  C1     0  -0.189   -7.2123  -28.0297  19.9849
 11W  CD1  C  CH2    0  -0.482   -8.4655  -28.3490  19.2422
 11W  CG   C  CH1    0  -0.340   -8.2015  -28.8935  17.8299
 11W  CD2  C  C      0   0.415   -9.5228  -29.3125  17.1503
 11W  OAE  O  O      0  -0.607  -10.4390  -28.4649  17.1475
 11W  OAC  O  OC    -1  -0.610   -9.5694  -30.4540  16.6411
 11W  CB   C  CH2    0  -0.376   -7.4598  -27.8565  16.9798
 11W  CA   C  CH1    0  -0.228   -7.2365  -28.2712  15.5262
 11W  C    C  C      0   0.412   -6.4232  -27.2122  14.7394
 11W  O    O  O     -1  -0.606   -5.5888  -27.6351  13.9126
 11W  OXT  O  OC     0  -0.609   -6.7016  -26.0171  14.9638
 11W  N    N  NH2    0  -0.820   -6.5940  -29.5772  15.4650
 11W  H1   H  HCR6   0   0.266   -1.0943  -23.3341  24.5975
 11W  H2   H  HCR6   0   0.262    0.9083  -22.5738  25.8126
 11W  H3   H  HCR6   0   0.263    2.8434  -24.0856  26.1000
 11W  H4   H  HCR6   0   0.262    2.7706  -26.3757  25.1612
 11W  H5   H  HCR6   0   0.263    0.7523  -27.1386  23.9378
 11W  H6   H  HCR6   0   0.265   -2.6793  -27.5828  22.2431
 11W  H7   H  HCR6   0   0.257   -4.6561  -28.3156  21.0278
 11W  H8   H  HCR6   0   0.262   -4.4392  -23.7228  22.8150
 11W  H9   H  HCR6   0   0.257   -6.4452  -24.4561  21.5815
 11W  H10  H  H      0   0.240   -7.6463  -26.0267  20.3447
 11W  H11  H  H      0   0.244   -6.5116  -28.8526  20.1062
 11W  H12  H  HCH2   0   0.225   -9.1005  -27.4621  19.1865
 11W  H13  H  HCH2   0   0.234   -9.0221  -29.1042  19.8103
 11W  H14  H  HCH1   0   0.193   -7.5651  -29.7793  17.9264
 11W  H16  H  HCH2   0   0.199   -6.4891  -27.6491  17.4433
 11W  H17  H  HCH2   0   0.194   -8.0166  -26.9169  16.9987
 11W  H18  H  HCH1   0   0.187   -8.2264  -28.2833  15.0343
 11W  H20  H  HNH2   0   0.326   -7.2931  -30.2925  15.6217
 11W  H21  H  HNH2   0   0.325   -6.2344  -29.7075  14.5290

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
 11W  O    C    deloc     1.231  0.020  1.231
 11W  C    OXT  deloc     1.247  0.020  1.247
 11W  C    CA   single    1.525  0.021  1.525
 11W  N    CA   single    1.458  0.019  1.458
 11W  CA   CB   single    1.530  0.020  1.530
 11W  CB   CG   single    1.532  0.020  1.532
 11W  OAE  CD2  deloc     1.248  0.020  1.248
 11W  CD2  CG   single    1.544  0.020  1.544
 11W  CD2  OAC  deloc     1.251  0.020  1.251
 11W  CG   CD1  single    1.537  0.020  1.537
 11W  CD1  CAF  single    1.491  0.020  1.491
 11W  CAF  CAG  double    1.336  0.020  1.336
 11W  CAG  CAW  single    1.461  0.020  1.461
 11W  CAW  CAM  aromatic  1.397  0.020  1.397
 11W  CAW  CAN  aromatic  1.405  0.020  1.405
 11W  CAM  CAO  aromatic  1.384  0.020  1.384
 11W  CAN  CAP  aromatic  1.377  0.020  1.377
 11W  CAO  CAY  aromatic  1.391  0.020  1.391
 11W  CAP  CAY  aromatic  1.400  0.020  1.400
 11W  CAY  NAT  single    1.400  0.020  1.400
 11W  NAT  NAS  double    1.240  0.020  1.240
 11W  NAS  CAX  single    1.406  0.020  1.406
 11W  CAK  CAX  aromatic  1.398  0.020  1.398
 11W  CAK  CAI  aromatic  1.383  0.020  1.383
 11W  CAX  CAL  aromatic  1.393  0.020  1.393
 11W  CAI  CAH  aromatic  1.393  0.020  1.393
 11W  CAL  CAJ  aromatic  1.387  0.020  1.387
 11W  CAH  CAJ  aromatic  1.388  0.020  1.388
 11W  CAK  H1   single    0.930  0.020  1.080
 11W  CAI  H2   single    0.930  0.020  1.080
 11W  CAH  H3   single    0.930  0.020  1.080
 11W  CAJ  H4   single    0.930  0.020  1.080
 11W  CAL  H5   single    0.930  0.020  1.080
 11W  CAP  H6   single    0.930  0.020  1.080
 11W  CAN  H7   single    0.930  0.020  1.080
 11W  CAO  H8   single    0.930  0.020  1.080
 11W  CAM  H9   single    0.930  0.020  1.080
 11W  CAG  H10  single    0.930  0.020  1.080
 11W  CAF  H11  single    0.930  0.020  1.080
 11W  CD1  H12  single    0.970  0.020  1.090
 11W  CD1  H13  single    0.970  0.020  1.090
 11W  CG   H14  single    0.970  0.020  1.090
 11W  CB   H16  single    0.970  0.020  1.090
 11W  CB   H17  single    0.970  0.020  1.090
 11W  CA   H18  single    0.970  0.020  1.090
 11W  N    H20  single    0.890  0.020  1.040
 11W  N    H21  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
 11W  H1   CAK  CAX  120.10  3.000
 11W  H1   CAK  CAI  120.25  3.000
 11W  CAX  CAK  CAI  119.65  3.000
 11W  H2   CAI  CAH  119.86  3.000
 11W  H2   CAI  CAK  119.62  3.000
 11W  CAH  CAI  CAK  120.51  3.000
 11W  H3   CAH  CAJ  120.12  3.000
 11W  H3   CAH  CAI  119.97  3.000
 11W  CAJ  CAH  CAI  119.91  3.000
 11W  H4   CAJ  CAL  119.89  3.000
 11W  H4   CAJ  CAH  120.27  3.000
 11W  CAL  CAJ  CAH  119.84  3.000
 11W  H5   CAL  CAX  118.88  3.000
 11W  H5   CAL  CAJ  120.76  3.000
 11W  CAX  CAL  CAJ  120.36  3.000
 11W  NAS  CAX  CAL  115.47  3.000
 11W  CAL  CAX  CAK  119.73  3.000
 11W  NAS  CAX  CAK  124.80  3.000
 11W  NAT  NAS  CAX  115.31  3.000
 11W  CAY  NAT  NAS  115.82  3.000
 11W  CAO  CAY  CAP  119.10  3.000
 11W  CAP  CAY  NAT  125.21  3.000
 11W  CAO  CAY  NAT  115.69  3.000
 11W  H6   CAP  CAN  119.84  3.000
 11W  H6   CAP  CAY  120.05  3.000
 11W  CAN  CAP  CAY  120.11  3.000
 11W  H7   CAN  CAW  120.03  3.000
 11W  H7   CAN  CAP  118.59  3.000
 11W  CAW  CAN  CAP  121.39  3.000
 11W  H8   CAO  CAM  120.51  3.000
 11W  H8   CAO  CAY  119.02  3.000
 11W  CAM  CAO  CAY  120.48  3.000
 11W  H9   CAM  CAW  119.41  3.000
 11W  H9   CAM  CAO  119.47  3.000
 11W  CAW  CAM  CAO  121.12  3.000
 11W  CAG  CAW  CAM  118.76  3.000
 11W  CAM  CAW  CAN  117.81  3.000
 11W  CAG  CAW  CAN  123.43  3.000
 11W  H10  CAG  CAF  117.97  3.000
 11W  H10  CAG  CAW  114.97  3.000
 11W  CAF  CAG  CAW  127.06  3.000
 11W  H11  CAF  CD1  115.79  3.000
 11W  H11  CAF  CAG  120.02  3.000
 11W  CD1  CAF  CAG  124.19  3.000
 11W  H13  CD1  H12  106.89  3.000
 11W  H13  CD1  CG   108.62  3.000
 11W  H12  CD1  CG   109.93  3.000
 11W  H13  CD1  CAF  108.42  3.000
 11W  H12  CD1  CAF  109.88  3.000
 11W  CG   CD1  CAF  112.91  3.000
 11W  H14  CG   CB   108.37  3.000
 11W  H14  CG   CD2  108.46  3.000
 11W  CB   CG   CD2  110.71  3.000
 11W  H14  CG   CD1  107.79  3.000
 11W  CD2  CG   CD1  110.71  3.000
 11W  CB   CG   CD1  110.69  3.000
 11W  OAC  CD2  OAE  126.26  3.000
 11W  OAC  CD2  CG   117.31  3.000
 11W  OAE  CD2  CG   116.42  3.000
 11W  H17  CB   H16  106.35  3.000
 11W  H17  CB   CA   108.93  3.000
 11W  H16  CB   CA   108.93  3.000
 11W  H17  CB   CG   109.01  3.000
 11W  H16  CB   CG   108.80  3.000
 11W  CA   CB   CG   114.51  3.000
 11W  H18  CA   N    111.49  3.000
 11W  H18  CA   C    104.57  3.000
 11W  N    CA   C    111.00  2.800
 11W  H18  CA   CB   107.18  3.000
 11W  N    CA   CB   110.50  1.700
 11W  C    CA   CB   110.10  1.900
 11W  OXT  C    O    126.36  3.000
 11W  OXT  C    CA   116.50  3.000
 11W  O    C    CA   120.80  1.700
 11W  H21  N    H20  107.33  3.000
 11W  H21  N    CA   108.13  3.000
 11W  H20  N    CA   108.80  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
 11W  CONST_01  CAJ  CAL  CAX  CAK     0.00   0.0  0
 11W  CONST_02  CAJ  CAH  CAI  CAK     0.00   0.0  0
 11W  CONST_03  CAL  CAX  CAK  CAI     0.00   0.0  0
 11W  CONST_04  CAL  CAJ  CAH  CAI     0.00   0.0  0
 11W  CONST_05  CAX  CAK  CAI  CAH     0.00   0.0  0
 11W  CONST_06  CAX  CAL  CAJ  CAH     0.00   0.0  0
 11W  CONST_07  CAW  CAM  CAO  CAY     0.00   0.0  0
 11W  CONST_08  CAW  CAN  CAP  CAY     0.00   0.0  0
 11W  CONST_09  CAM  CAW  CAN  CAP     0.00   0.0  0
 11W  CONST_10  CAM  CAO  CAY  CAP     0.00   0.0  0
 11W  CONST_11  CAO  CAM  CAW  CAN     0.00   0.0  0
 11W  CONST_12  CAO  CAY  CAP  CAN     0.00   0.0  0
 11W  CONST_13  NAS  CAX  CAK  CAI   180.00   0.0  0
 11W  CONST_14  NAS  CAX  CAL  CAJ   180.00   0.0  0
 11W  CONST_15  CAM  CAO  CAY  NAT   180.00   0.0  0
 11W  CONST_16  CAN  CAP  CAY  NAT   180.00   0.0  0
 11W  CONST_17  CAG  CAW  CAN  CAP   180.00   0.0  0
 11W  CONST_18  CAG  CAW  CAM  CAO   180.00   0.0  0
 11W  CONST_19  H5   CAL  CAX  CAK   180.00   0.0  0
 11W  CONST_20  H3   CAH  CAI  CAK   180.00   0.0  0
 11W  CONST_21  H4   CAJ  CAH  CAI   180.00   0.0  0
 11W  CONST_22  H1   CAK  CAI  CAH   180.00   0.0  0
 11W  CONST_23  H2   CAI  CAH  CAJ   180.00   0.0  0
 11W  CONST_24  H9   CAM  CAO  CAY   180.00   0.0  0
 11W  CONST_25  H7   CAN  CAP  CAY   180.00   0.0  0
 11W  CONST_26  H8   CAO  CAY  CAP   180.00   0.0  0
 11W  CONST_27  H6   CAP  CAY  CAO   180.00   0.0  0
 11W  CONST_28  NAT  NAS  CAX  CAK     0.00   0.0  0
 11W  CONST_29  NAT  NAS  CAX  CAL   180.00   0.0  0
 11W  CONST_30  CAO  CAY  NAT  NAS   180.00   0.0  0
 11W  CONST_31  CAP  CAY  NAT  NAS     0.00   0.0  0
 11W  Var_01    CAF  CAG  CAW  CAN     4.19  30.0  2
 11W  Var_02    CD1  CAF  CAG  CAW  -179.62   0.0  2
 11W  Var_03    CG   CD1  CAF  CAG   122.20  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
 11W  chir_01  CG  CB  CD2  CD1  positiv
 11W  chir_02  CA  N   C    CB   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
 11W  plan-1  CAK  0.020
 11W  plan-1  CAI  0.020
 11W  plan-1  CAH  0.020
 11W  plan-1  CAJ  0.020
 11W  plan-1  CAL  0.020
 11W  plan-1  CAX  0.020
 11W  plan-1  NAS  0.020
 11W  plan-1  NAT  0.020
 11W  plan-1  CAY  0.020
 11W  plan-1  H1   0.020
 11W  plan-1  H2   0.020
 11W  plan-1  H3   0.020
 11W  plan-1  H4   0.020
 11W  plan-1  H5   0.020
 11W  plan-2  NAS  0.020
 11W  plan-2  NAT  0.020
 11W  plan-2  CAY  0.020
 11W  plan-2  CAP  0.020
 11W  plan-2  CAN  0.020
 11W  plan-2  CAO  0.020
 11W  plan-2  CAM  0.020
 11W  plan-2  CAW  0.020
 11W  plan-2  CAG  0.020
 11W  plan-2  H6   0.020
 11W  plan-2  H7   0.020
 11W  plan-2  H8   0.020
 11W  plan-2  H9   0.020
 11W  plan-3  CG   0.020
 11W  plan-3  CD2  0.020
 11W  plan-3  OAE  0.020
 11W  plan-3  OAC  0.020
 11W  plan-4  CA   0.020
 11W  plan-4  C    0.020
 11W  plan-4  O    0.020
 11W  plan-4  OXT  0.020
 11W  plan-5  CAW  0.020
 11W  plan-5  CAG  0.020
 11W  plan-5  CAF  0.020
 11W  plan-5  CD1  0.020
 11W  plan-5  H10  0.020
 11W  plan-5  H11  0.020

