# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 12:02:34 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 2-[2-[(1~{R},2~{R})-1-azanyl-2-oxidanyl-propyl]-4-(1~{H}-indol-3-ylmethyl)-5-oxidanyl-imidazol-1-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H](N)c1nc(Cc2c[nH]c3ccccc23)c(O)n1CC(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
 B2H  B2H  '2-[2-[(1~{R},2~{R})-1-azanyl-2-oxidanyl-propyl]-4-(1~{H}-indol-3-ylmethyl)-5-oxidanyl-imidazol-1-yl]ethanoic acid'  L-peptide  44  25  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_B2H
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
 B2H  N1   N  NH2    0  -0.792  -2.0714   2.5747   1.5286
 B2H  CA1  C  CH1    0  -0.234  -2.5215   1.2603   1.1153
 B2H  CB1  C  CH1    0   0.020  -3.8610   1.2360   0.3348
 B2H  CG1  C  CH3    0  -0.697  -5.0251   1.7314   1.1803
 B2H  OG1  O  OH1    0  -0.659  -3.7571   1.9370  -0.8843
 B2H  C1   C  CR5    0   0.475  -1.4412   0.6220   0.2965
 B2H  N2   N  N      0  -0.477  -0.4913   1.2607  -0.3260
 B2H  N3   N  NR5    0  -0.502  -1.3901  -0.7148   0.0292
 B2H  C2   C  CR5    0   0.416  -0.3372  -0.9042  -0.8374
 B2H  O2   O  OH1    0  -0.685  -0.0134  -2.1131  -1.2902
 B2H  CA2  C  CR5    0   0.071   0.2134   0.3271  -1.0479
 B2H  CA3  C  CH2    0  -0.480  -2.1967  -1.7743   0.6035
 B2H  C3   C  C      0   0.477  -3.0094  -2.5619  -0.4422
 B2H  O3   O  O      0  -0.613  -2.3751  -2.9344  -1.4708
 B2H  CB2  C  CH2    0  -0.631   1.4044   0.6793  -1.8782
 B2H  CG2  C  CR5    0   0.034   2.6148   1.0189  -1.0651
 B2H  CD1  C  CR15   0  -0.100   3.2059   2.2428  -0.9388
 B2H  CD2  C  CR56   0   0.024   3.3743   0.1258  -0.2404
 B2H  CE2  C  CR56   0   0.350   4.4105   0.8839   0.3513
 B2H  NE1  N  NR15   0  -0.689   4.2795   2.1665  -0.0919
 B2H  CE3  C  CR16   0  -0.370   3.2810  -1.2408   0.0490
 B2H  CZ2  C  CR16   0  -0.309   5.3459   0.3147   1.2149
 B2H  CZ3  C  CR16   0  -0.272   4.2056  -1.8078   0.9049
 B2H  CH2  C  CR16   0  -0.284   5.2282  -1.0361   1.4821
 B2H  H1   H  HNH2   0   0.343  -1.7877   3.1277   0.7302
 B2H  H2   H  HNH2   0   0.353  -2.8076   3.0748   2.0074
 B2H  H4   H  HCH1   0   0.246  -2.6816   0.6694   2.0255
 B2H  H5   H  HCH1   0   0.227  -4.0701   0.1985   0.0548
 B2H  H6   H  HCH3   0   0.219  -4.9034   2.7751   1.4798
 B2H  H7   H  HCH3   0   0.246  -5.9599   1.6588   0.6241
 B2H  H8   H  HCH3   0   0.232  -5.1303   1.1347   2.0872
 B2H  H9   H  HOH1   0   0.436  -3.6223   2.8699  -0.6860
 B2H  H10  H  HCH2   0   0.285  -1.5404  -2.4733   1.1326
 B2H  H11  H  HCH2   0   0.267  -2.8565  -1.3400   1.3497
 B2H  H13  H  HCH2   0   0.244   1.6267  -0.1572  -2.5473
 B2H  H14  H  HCR5   0   0.276   2.9360   3.1818  -1.3970
 B2H  H15  H  HNR5   0   0.405   4.8759   2.9378   0.1546
 B2H  H16  H  HCR6   0   0.246   2.4973  -1.8457  -0.3906
 B2H  H17  H  HCR6   0   0.255   6.1355   0.9070   1.6600
 B2H  H18  H  HCR6   0   0.242   4.1444  -2.8632   1.1384
 B2H  H19  H  HCR6   0   0.246   5.9382  -1.5095   2.1482
 B2H  OXT  O  OC    -1  -0.553  -4.1903  -2.8021  -0.1920
 B2H  H3   H  HOH1   0   0.466  -0.9050  -2.5900  -1.4411
 B2H  H12  H  HCH2   0   0.244   1.1667   1.5281  -2.5259

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
 B2H  CG1  CB1  single    1.522  0.020  1.522
 B2H  OG1  CB1  single    1.410  0.020  1.410
 B2H  CB1  CA1  single    1.551  0.020  1.551
 B2H  NE1  CD1  aromatic  1.370  0.020  1.370
 B2H  NE1  CE2  aromatic  1.363  0.020  1.363
 B2H  N1   CA1  single    1.449  0.020  1.449
 B2H  CA1  C1   single    1.498  0.020  1.498
 B2H  CD1  CG2  aromatic  1.365  0.020  1.365
 B2H  CZ2  CE2  aromatic  1.395  0.020  1.395
 B2H  CZ2  CH2  aromatic  1.382  0.020  1.382
 B2H  CE2  CD2  aromatic  1.414  0.020  1.414
 B2H  N2   C1   aromatic  1.303  0.020  1.303
 B2H  N2   CA2  aromatic  1.375  0.020  1.375
 B2H  C1   N3   aromatic  1.364  0.020  1.364
 B2H  CH2  CZ3  aromatic  1.405  0.020  1.405
 B2H  CG2  CD2  aromatic  1.433  0.020  1.433
 B2H  CG2  CB2  single    1.497  0.020  1.497
 B2H  CD2  CE3  aromatic  1.400  0.020  1.400
 B2H  CA2  CB2  single    1.494  0.020  1.494
 B2H  CA2  C2   aromatic  1.365  0.020  1.365
 B2H  N3   CA3  single    1.450  0.020  1.450
 B2H  N3   C2   aromatic  1.377  0.020  1.377
 B2H  CZ3  CE3  aromatic  1.382  0.020  1.382
 B2H  CA3  C3   single    1.541  0.020  1.541
 B2H  C2   O2   single    1.331  0.020  1.331
 B2H  C3   O3   deloc     1.265  0.020  1.265
 B2H  N1   H1   single    0.890  0.020  1.040
 B2H  N1   H2   single    0.890  0.020  1.040
 B2H  CA1  H4   single    0.970  0.020  1.090
 B2H  CB1  H5   single    0.970  0.020  1.090
 B2H  CG1  H6   single    0.970  0.020  1.090
 B2H  CG1  H7   single    0.970  0.020  1.090
 B2H  CG1  H8   single    0.970  0.020  1.090
 B2H  OG1  H9   single    0.850  0.020  0.980
 B2H  CA3  H10  single    0.970  0.020  1.090
 B2H  CA3  H11  single    0.970  0.020  1.090
 B2H  CB2  H13  single    0.970  0.020  1.090
 B2H  CD1  H14  single    0.930  0.020  1.080
 B2H  NE1  H15  single    0.860  0.020  1.020
 B2H  CE3  H16  single    0.930  0.020  1.080
 B2H  CZ2  H17  single    0.930  0.020  1.080
 B2H  CZ3  H18  single    0.930  0.020  1.080
 B2H  CH2  H19  single    0.930  0.020  1.080
 B2H  C3   OXT  deloc     1.231  0.020  1.231
 B2H  O2   H3   single    0.850  0.020  0.980
 B2H  CB2  H12  single    0.970  0.020  1.090

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
 B2H  H2   N1   H1   107.91  3.000
 B2H  H2   N1   CA1  110.95  3.000
 B2H  H1   N1   CA1  110.97  3.000
 B2H  H4   CA1  C1   109.23  3.000
 B2H  H4   CA1  CB1  106.45  3.000
 B2H  C1   CA1  CB1  109.94  3.000
 B2H  H4   CA1  N1   107.29  3.000
 B2H  C1   CA1  N1   108.56  3.000
 B2H  CB1  CA1  N1   115.21  3.000
 B2H  H5   CB1  OG1  105.32  3.000
 B2H  H5   CB1  CG1  107.73  3.000
 B2H  OG1  CB1  CG1  112.02  3.000
 B2H  H5   CB1  CA1  107.97  3.000
 B2H  OG1  CB1  CA1  111.34  3.000
 B2H  CG1  CB1  CA1  112.09  3.000
 B2H  H8   CG1  H7   107.77  3.000
 B2H  H8   CG1  H6   107.79  3.000
 B2H  H7   CG1  H6   107.39  3.000
 B2H  H8   CG1  CB1  110.96  3.000
 B2H  H7   CG1  CB1  110.53  3.000
 B2H  H6   CG1  CB1  112.21  3.000
 B2H  H9   OG1  CB1  108.29  3.000
 B2H  N3   C1   N2   111.06  3.000
 B2H  N3   C1   CA1  123.47  3.000
 B2H  N2   C1   CA1  125.30  3.000
 B2H  CA2  N2   C1   106.96  3.000
 B2H  CA3  N3   C2   125.04  3.000
 B2H  C2   N3   C1   106.67  3.000
 B2H  CA3  N3   C1   128.13  3.000
 B2H  CA2  C2   O2   131.96  3.000
 B2H  O2   C2   N3   121.68  3.000
 B2H  CA2  C2   N3   106.35  3.000
 B2H  H3   O2   C2   105.18  3.000
 B2H  CB2  CA2  C2   128.31  3.000
 B2H  C2   CA2  N2   108.95  3.000
 B2H  CB2  CA2  N2   122.72  3.000
 B2H  H11  CA3  H10  106.69  3.000
 B2H  H11  CA3  C3   110.49  3.000
 B2H  H10  CA3  C3   108.53  3.000
 B2H  H11  CA3  N3   108.52  3.000
 B2H  H10  CA3  N3   108.92  3.000
 B2H  C3   CA3  N3   113.46  3.000
 B2H  OXT  C3   O3   126.10  3.000
 B2H  OXT  C3   CA3  117.89  3.000
 B2H  O3   C3   CA3  115.98  3.000
 B2H  H12  CB2  H13  105.98  3.000
 B2H  H12  CB2  CG2  108.74  3.000
 B2H  H13  CB2  CG2  109.95  3.000
 B2H  H12  CB2  CA2  109.80  3.000
 B2H  H13  CB2  CA2  108.77  3.000
 B2H  CG2  CB2  CA2  113.34  3.000
 B2H  CD2  CG2  CD1  106.02  3.000
 B2H  CD2  CG2  CB2  126.84  3.000
 B2H  CD1  CG2  CB2  127.13  3.000
 B2H  H14  CD1  NE1  120.47  3.000
 B2H  H14  CD1  CG2  129.25  3.000
 B2H  NE1  CD1  CG2  110.28  3.000
 B2H  CE3  CD2  CE2  119.06  3.000
 B2H  CE3  CD2  CG2  133.77  3.000
 B2H  CE2  CD2  CG2  107.16  3.000
 B2H  CZ2  CE2  NE1  130.53  3.000
 B2H  CZ2  CE2  CD2  122.14  3.000
 B2H  NE1  CE2  CD2  107.34  3.000
 B2H  H15  NE1  CE2  125.79  3.000
 B2H  H15  NE1  CD1  125.01  3.000
 B2H  CE2  NE1  CD1  109.20  3.000
 B2H  H16  CE3  CZ3  120.42  3.000
 B2H  H16  CE3  CD2  120.63  3.000
 B2H  CZ3  CE3  CD2  118.95  3.000
 B2H  H17  CZ2  CH2  121.15  3.000
 B2H  H17  CZ2  CE2  121.36  3.000
 B2H  CH2  CZ2  CE2  117.49  3.000
 B2H  H18  CZ3  CH2  119.21  3.000
 B2H  H18  CZ3  CE3  119.73  3.000
 B2H  CH2  CZ3  CE3  121.07  3.000
 B2H  H19  CH2  CZ3  119.33  3.000
 B2H  H19  CH2  CZ2  119.37  3.000
 B2H  CZ3  CH2  CZ2  121.29  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
 B2H  CONST_01  C2   CA2  N2   C1      0.00   0.0  0
 B2H  CONST_02  CA2  C2   N3   C1      0.00   0.0  0
 B2H  CONST_03  C2   N3   C1   N2      0.00   0.0  0
 B2H  CONST_04  N3   C2   CA2  N2      0.00   0.0  0
 B2H  CONST_05  CA2  N2   C1   N3      0.00   0.0  0
 B2H  CONST_06  CE2  NE1  CD1  CG2     0.00   0.0  0
 B2H  CONST_07  NE1  CE2  CD2  CG2     0.00   0.0  0
 B2H  CONST_08  CZ2  CE2  CD2  CG2   180.00   0.0  0
 B2H  CONST_09  CZ3  CE3  CD2  CG2   180.00   0.0  0
 B2H  CONST_10  CZ2  CE2  NE1  CD1   180.00   0.0  0
 B2H  CONST_11  CD2  CE2  NE1  CD1     0.00   0.0  0
 B2H  CONST_12  CE2  CD2  CG2  CD1     0.00   0.0  0
 B2H  CONST_13  CE3  CD2  CG2  CD1   180.00   0.0  0
 B2H  CONST_14  CH2  CZ2  CE2  CD2     0.00   0.0  0
 B2H  CONST_15  NE1  CD1  CG2  CD2     0.00   0.0  0
 B2H  CONST_16  CH2  CZ3  CE3  CD2     0.00   0.0  0
 B2H  CONST_17  CZ3  CH2  CZ2  CE2     0.00   0.0  0
 B2H  CONST_18  CZ3  CE3  CD2  CE2     0.00   0.0  0
 B2H  CONST_19  CH2  CZ2  CE2  NE1   180.00   0.0  0
 B2H  CONST_20  CE3  CD2  CE2  NE1   180.00   0.0  0
 B2H  CONST_21  CZ2  CE2  CD2  CE3     0.00   0.0  0
 B2H  CONST_22  CZ2  CH2  CZ3  CE3     0.00   0.0  0
 B2H  CONST_23  CA2  N2   C1   CA1   180.00   0.0  0
 B2H  CONST_24  C2   N3   C1   CA1   180.00   0.0  0
 B2H  CONST_25  CB2  CA2  N2   C1    180.00   0.0  0
 B2H  CONST_26  O2   C2   N3   C1    180.00   0.0  0
 B2H  CONST_27  CA3  N3   C1   N2    180.00   0.0  0
 B2H  CONST_28  O2   C2   CA2  N2    180.00   0.0  0
 B2H  CONST_29  CB2  CA2  C2   N3    180.00   0.0  0
 B2H  CONST_30  CA3  N3   C2   CA2   180.00   0.0  0
 B2H  CONST_31  NE1  CD1  CG2  CB2   180.00   0.0  0
 B2H  CONST_32  CE2  CD2  CG2  CB2   180.00   0.0  0
 B2H  CONST_33  CE3  CD2  CG2  CB2     0.00   0.0  0
 B2H  CONST_34  H15  NE1  CD1  CG2   180.00   0.0  0
 B2H  CONST_35  H16  CE3  CD2  CG2     0.00   0.0  0
 B2H  CONST_36  H17  CZ2  CE2  CD2   180.00   0.0  0
 B2H  CONST_37  H14  CD1  CG2  CD2   180.00   0.0  0
 B2H  CONST_38  H18  CZ3  CE3  CD2   180.00   0.0  0
 B2H  CONST_39  H19  CH2  CZ2  CE2   180.00   0.0  0
 B2H  Var_01    CG2  CB2  CA2  N2     71.98  30.0  2
 B2H  Var_02    CD1  CG2  CB2  CA2  -111.31  30.0  3
 B2H  Var_03    C3   CA3  N3   C1    120.69  30.0  2
 B2H  Var_04    O3   C3   CA3  N3     47.20  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
 B2H  chir_01  CA1  CB1  N1   C1   positiv
 B2H  chir_02  CB1  OG1  CA1  CG1  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
 B2H  plan-1  CA1  0.020
 B2H  plan-1  C1   0.020
 B2H  plan-1  N2   0.020
 B2H  plan-1  N3   0.020
 B2H  plan-1  C2   0.020
 B2H  plan-1  O2   0.020
 B2H  plan-1  CA2  0.020
 B2H  plan-1  CA3  0.020
 B2H  plan-1  CB2  0.020
 B2H  plan-2  CB2  0.020
 B2H  plan-2  CG2  0.020
 B2H  plan-2  CD1  0.020
 B2H  plan-2  CD2  0.020
 B2H  plan-2  CE2  0.020
 B2H  plan-2  NE1  0.020
 B2H  plan-2  CE3  0.020
 B2H  plan-2  CZ2  0.020
 B2H  plan-2  CZ3  0.020
 B2H  plan-2  CH2  0.020
 B2H  plan-2  H14  0.020
 B2H  plan-2  H15  0.020
 B2H  plan-2  H16  0.020
 B2H  plan-2  H17  0.020
 B2H  plan-2  H18  0.020
 B2H  plan-2  H19  0.020
 B2H  plan-3  CA3  0.020
 B2H  plan-3  C3   0.020
 B2H  plan-3  O3   0.020
 B2H  plan-3  OXT  0.020

