# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 15:58:05 2022
#   Inital geometry file: a 73 line input string
#   Ligand name: (2~{S},3~{R})-2-azanyl-3-(1~{H}-indol-3-yl)-3-oxidanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@H](O)c1c[nH]c2ccccc12)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
 UX8  UX8  '(2~{S},3~{R})-2-azanyl-3-(1~{H}-indol-3-yl)-3-oxidanyl-propanoic acid'  L-peptide  27  16  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UX8
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
 UX8  C    C  C      0   0.406  184.3119  174.4098  172.9289
 UX8  CA   C  CH1    0  -0.229  184.4065  175.1881  171.5978
 UX8  CG   C  CR5    0  -0.000  185.5219  173.3426  170.2544
 UX8  CE2  C  CR56   0   0.352  185.6552  171.0680  170.0294
 UX8  CB   C  CH1    0  -0.012  185.6322  174.7390  170.7703
 UX8  CD1  C  CR15   0  -0.085  185.0139  172.9613  169.0444
 UX8  CD2  C  CR56   0   0.023  185.9418  172.1381  170.9070
 UX8  CE3  C  CR16   0  -0.361  186.5418  171.8572  172.1408
 UX8  CZ3  C  CR16   0  -0.270  186.8420  170.5472  172.4582
 UX8  CH2  C  CR16   0  -0.283  186.5474  169.4989  171.5701
 UX8  CZ2  C  CR16   0  -0.306  185.9503  169.7429  170.3487
 UX8  N    N  NH2    0  -0.817  184.5372  176.6351  171.7701
 UX8  NE1  N  NR15   0  -0.688  185.0859  171.6022  168.9120
 UX8  O    O  O      0  -0.610  185.1424  174.7467  173.8020
 UX8  O9   O  OH1    0  -0.689  185.7899  175.6236  169.6854
 UX8  OXT  O  OC    -1  -0.597  183.4394  173.5283  173.0191
 UX8  HA   H  HCH1   0   0.211  183.5148  175.0024  170.9918
 UX8  HB2  H  HCH1   0   0.182  186.5083  174.7946  171.4386
 UX8  HD1  H  HCR5   0   0.274  184.6068  173.5629  168.2474
 UX8  HE3  H  HCR6   0   0.231  186.7522  172.6546  172.8425
 UX8  HZ3  H  HCR6   0   0.239  187.3064  170.3190  173.4094
 UX8  HH2  H  HCR6   0   0.243  186.7905  168.4816  171.8491
 UX8  HZ2  H  HCR6   0   0.253  185.7221  168.9355  169.6640
 UX8  H    H  HNH2   0   0.355  183.6359  177.0462  171.9754
 UX8  H2   H  HNH2   0   0.340  185.1212  176.8055  172.5821
 UX8  HE1  H  HNR5   0   0.404  184.8015  171.0863  168.0963
 UX8  H4   H  HOH1   0   0.432  185.4672  176.4694  170.0480

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
 UX8  CD1  NE1  aromatic  1.368  0.020  1.368
 UX8  CD1  CG   aromatic  1.367  0.020  1.367
 UX8  NE1  CE2  aromatic  1.363  0.020  1.363
 UX8  O9   CB   single    1.409  0.020  1.409
 UX8  CG   CB   single    1.493  0.020  1.493
 UX8  CG   CD2  aromatic  1.433  0.020  1.433
 UX8  CE2  CZ2  aromatic  1.395  0.020  1.395
 UX8  CE2  CD2  aromatic  1.413  0.020  1.413
 UX8  CZ2  CH2  aromatic  1.381  0.020  1.381
 UX8  CB   CA   single    1.530  0.020  1.530
 UX8  CD2  CE3  aromatic  1.400  0.020  1.400
 UX8  CA   N    single    1.458  0.019  1.458
 UX8  CA   C    single    1.525  0.021  1.525
 UX8  CH2  CZ3  aromatic  1.405  0.020  1.405
 UX8  CE3  CZ3  aromatic  1.381  0.020  1.381
 UX8  C    O    deloc     1.231  0.020  1.231
 UX8  C    OXT  deloc     1.244  0.020  1.244
 UX8  CA   HA   single    0.970  0.020  0.970
 UX8  CB   HB2  single    0.970  0.020  1.090
 UX8  CD1  HD1  single    0.930  0.020  1.080
 UX8  CE3  HE3  single    0.930  0.020  1.080
 UX8  CZ3  HZ3  single    0.930  0.020  1.080
 UX8  CH2  HH2  single    0.930  0.020  1.080
 UX8  CZ2  HZ2  single    0.930  0.020  1.080
 UX8  N    H    single    0.860  0.020  0.860
 UX8  N    H2   single    0.890  0.020  1.040
 UX8  NE1  HE1  single    0.860  0.020  1.020
 UX8  O9   H4   single    0.850  0.020  0.980

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
 UX8  OXT  C    O    127.30  3.000
 UX8  OXT  C    CA   117.55  3.000
 UX8  O    C    CA   120.80  1.700
 UX8  HA   CA   N    110.00  3.000
 UX8  HA   CA   CB   109.00  3.000
 UX8  N    CA   CB   110.50  1.700
 UX8  HA   CA   C    109.00  3.000
 UX8  N    CA   C    111.00  2.800
 UX8  CB   CA   C    110.10  1.900
 UX8  CD2  CG   CD1  106.12  3.000
 UX8  CD2  CG   CB   127.40  3.000
 UX8  CD1  CG   CB   126.47  3.000
 UX8  NE1  CE2  CZ2  130.42  3.000
 UX8  CZ2  CE2  CD2  122.30  3.000
 UX8  NE1  CE2  CD2  107.28  3.000
 UX8  HB2  CB   O9   110.24  3.000
 UX8  HB2  CB   CG   108.37  3.000
 UX8  O9   CB   CG   109.24  3.000
 UX8  HB2  CB   CA   106.90  3.000
 UX8  CG   CB   CA   113.47  3.000
 UX8  O9   CB   CA   108.58  3.000
 UX8  HD1  CD1  NE1  120.19  3.000
 UX8  HD1  CD1  CG   129.73  3.000
 UX8  NE1  CD1  CG   110.08  3.000
 UX8  CE3  CD2  CE2  118.82  3.000
 UX8  CE3  CD2  CG   134.07  3.000
 UX8  CE2  CD2  CG   107.11  3.000
 UX8  HE3  CE3  CZ3  120.49  3.000
 UX8  HE3  CE3  CD2  120.42  3.000
 UX8  CZ3  CE3  CD2  119.08  3.000
 UX8  HZ3  CZ3  CH2  119.20  3.000
 UX8  HZ3  CZ3  CE3  119.68  3.000
 UX8  CH2  CZ3  CE3  121.12  3.000
 UX8  HH2  CH2  CZ2  119.40  3.000
 UX8  HH2  CH2  CZ3  119.42  3.000
 UX8  CZ2  CH2  CZ3  121.18  3.000
 UX8  HZ2  CZ2  CH2  121.22  3.000
 UX8  HZ2  CZ2  CE2  121.27  3.000
 UX8  CH2  CZ2  CE2  117.50  3.000
 UX8  H2   N    H    106.39  3.000
 UX8  H2   N    CA   108.17  3.000
 UX8  H    N    CA   114.00  3.000
 UX8  HE1  NE1  CD1  124.97  3.000
 UX8  HE1  NE1  CE2  125.57  3.000
 UX8  CD1  NE1  CE2  109.40  3.000
 UX8  H4   O9   CB   102.79  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
 UX8  CONST_01  CE2  NE1  CD1  CG     0.00  0.0  0
 UX8  CONST_02  NE1  CE2  CD2  CG     0.00  0.0  0
 UX8  CONST_03  CZ2  CE2  CD2  CG   180.00  0.0  0
 UX8  CONST_04  CZ3  CE3  CD2  CG   180.00  0.0  0
 UX8  CONST_05  CZ3  CH2  CZ2  CE2    0.00  0.0  0
 UX8  CONST_06  CD1  CG   CD2  CE2    0.00  0.0  0
 UX8  CONST_07  CZ3  CE3  CD2  CE2    0.00  0.0  0
 UX8  CONST_08  CZ2  CE2  NE1  CD1  180.00  0.0  0
 UX8  CONST_09  CD2  CE2  NE1  CD1    0.00  0.0  0
 UX8  CONST_10  CE3  CD2  CG   CD1  180.00  0.0  0
 UX8  CONST_11  NE1  CD1  CG   CD2    0.00  0.0  0
 UX8  CONST_12  CH2  CZ2  CE2  CD2    0.00  0.0  0
 UX8  CONST_13  CH2  CZ3  CE3  CD2    0.00  0.0  0
 UX8  CONST_14  NE1  CE2  CD2  CE3  180.00  0.0  0
 UX8  CONST_15  CZ2  CE2  CD2  CE3    0.00  0.0  0
 UX8  CONST_16  CZ2  CH2  CZ3  CE3    0.00  0.0  0
 UX8  CONST_17  NE1  CE2  CZ2  CH2  180.00  0.0  0
 UX8  CONST_18  CB   CG   CD2  CE2  180.00  0.0  0
 UX8  CONST_19  NE1  CD1  CG   CB   180.00  0.0  0
 UX8  CONST_20  CE3  CD2  CG   CB     0.00  0.0  0
 UX8  CONST_21  HE1  NE1  CD1  CG   180.00  0.0  0
 UX8  CONST_22  HE3  CE3  CD2  CG     0.00  0.0  0
 UX8  CONST_23  HD1  CD1  NE1  CE2  180.00  0.0  0
 UX8  CONST_24  HH2  CH2  CZ2  CE2  180.00  0.0  0
 UX8  CONST_25  HZ2  CZ2  CE2  CD2  180.00  0.0  0
 UX8  CONST_26  HZ3  CZ3  CE3  CD2  180.00  0.0  0

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
 UX8  chir_01  CA  CB  N   C   positiv
 UX8  chir_02  CB  O9  CA  CG  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
 UX8  plan-1  CG   0.020
 UX8  plan-1  CE2  0.020
 UX8  plan-1  CB   0.020
 UX8  plan-1  CD1  0.020
 UX8  plan-1  CD2  0.020
 UX8  plan-1  CE3  0.020
 UX8  plan-1  CZ3  0.020
 UX8  plan-1  CH2  0.020
 UX8  plan-1  CZ2  0.020
 UX8  plan-1  NE1  0.020
 UX8  plan-1  HD1  0.020
 UX8  plan-1  HE3  0.020
 UX8  plan-1  HZ3  0.020
 UX8  plan-1  HH2  0.020
 UX8  plan-1  HZ2  0.020
 UX8  plan-1  HE1  0.020
 UX8  plan-2  C    0.020
 UX8  plan-2  CA   0.020
 UX8  plan-2  O    0.020
 UX8  plan-2  OXT  0.020

