# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 19:48:32 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (3R,4S)-4-amino-3-hydroxy-N-(4-methoxybenzyl)-5-phenyl-D-norvaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CN[C@H]([C@H](O)[C@@H](N)Cc2ccccc2)C(O)=O)cc1
#
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
 HV8  HV8  (3R,4S)-4-amino-3-hydroxy-N-(4-methoxybenzyl)-5-phenyl-D-norvaline  peptide  49  25  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HV8
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
 HV8  N     N  NH2   0  -0.814  -2.9451   0.7349   1.3791
 HV8  CA1   C  CH1   0  -0.115  -2.3182   0.5094   0.0843
 HV8  CB1   C  CH2   0  -0.547  -3.2995   0.0344  -0.9981
 HV8  CG1   C  CR6   0   0.160  -3.9287  -1.2839  -0.6487
 HV8  CD1   C  CR16  0  -0.332  -5.1899  -1.3519  -0.0616
 HV8  CD2   C  CR16  0  -0.307  -3.2362  -2.4743  -0.8683
 HV8  CE1   C  CR16  0  -0.239  -5.7458  -2.5728   0.3004
 HV8  CE2   C  CR16  0  -0.239  -3.7865  -3.6967  -0.5099
 HV8  CZ1   C  CR16  0  -0.274  -5.0446  -3.7499   0.0781
 HV8  CM    C  CH1   0   0.054  -1.6183   1.8090  -0.3506
 HV8  OH    O  OH1   0  -0.668  -2.5057   2.8940  -0.2549
 HV8  N2    N  NH1   0  -0.600   0.7255   1.1970   0.0378
 HV8  CA2   C  CH1   0  -0.206  -0.3403   2.0706   0.4739
 HV8  CB2   C  CH2   0  -0.330   1.8666   1.1889   0.9384
 HV8  CG2   C  CR6   0   0.064   2.9210   0.2306   0.4615
 HV8  CD4   C  CR16  0  -0.268   3.4494   0.3336  -0.8272
 HV8  CE3   C  CR16  0  -0.329   4.4257  -0.5358  -1.2724
 HV8  CD3   C  CR16  0  -0.303   3.3996  -0.7808   1.2792
 HV8  CE4   C  CR16  0  -0.370   4.3851  -1.6663   0.8506
 HV8  CZ2   C  CR6   0   0.368   4.9052  -1.5468  -0.4335
 HV8  OE2   O  O2    0  -0.472   5.8581  -2.3486  -0.9488
 HV8  CM2   C  CH3   0  -0.436   6.3807  -3.3798  -0.1360
 HV8  C     C  C     0   0.536   0.0630   3.5146   0.2294
 HV8  O     O  O     0  -0.440   0.6180   3.9039  -0.7659
 HV8  OXT   O  OH1   0  -0.587  -0.2806   4.3109   1.2337
 HV8  HN1   H  HNH2  0   0.355  -3.9420   0.8793   1.2830
 HV8  HN2A  H  HNH2  0   0.366  -2.8328  -0.0654   1.9839
 HV8  HA1   H  HCH1  0   0.243  -1.5620  -0.2732   0.2034
 HV8  HB11  H  HCH2  0   0.252  -4.0720   0.7964  -1.1370
 HV8  HB12  H  HCH2  0   0.253  -2.7634  -0.0483  -1.9472
 HV8  HD1   H  HCR6  0   0.245  -5.7521  -0.4399   0.1040
 HV8  HD2   H  HCR6  0   0.245  -2.2556  -2.4438  -1.3305
 HV8  HE1   H  HCR6  0   0.253  -6.7284  -2.6031   0.7541
 HV8  HE2   H  HCR6  0   0.253  -3.2352  -4.6102  -0.6933
 HV8  HZ1   H  HCR6  0   0.254  -5.4768  -4.7029   0.3542
 HV8  HM    H  HCH1  0   0.245  -1.3167   1.7354  -1.4003
 HV8  HOH   H  HOH1  0   0.443  -2.8593   2.8826   0.6454
 HV8  HN2   H  HNH1  0   0.355   0.3750   0.2502  -0.0400
 HV8  HA2   H  HCH1  0   0.240  -0.5837   1.9475   1.5414
 HV8  HB21  H  HCH2  0   0.240   2.2864   2.1998   0.9725
 HV8  HB22  H  HCH2  0   0.221   1.5876   0.9401   1.9728
 HV8  HD4   H  HCR6  0   0.249   3.0871   1.1081  -1.4920
 HV8  HE3   H  HCR6  0   0.259   4.8262  -0.4408  -2.2742
 HV8  HD3   H  HCR6  0   0.252   3.0033  -0.8924   2.2817
 HV8  HE4   H  HCR6  0   0.276   4.7265  -2.4353   1.5301
 HV8  HM21  H  HCH3  0   0.227   6.8633  -2.9880   0.7638
 HV8  HM22  H  HCH3  0   0.227   5.6106  -4.0965   0.1619
 HV8  HM23  H  HCH3  0   0.259   7.1264  -3.8976  -0.7340
 HV8  HXT   H  HOH1  0   0.479  -0.0565   5.2289   1.0176

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
 HV8  N    CA1   single    1.456  0.020  1.456
 HV8  N    HN1   single    0.890  0.020  1.040
 HV8  N    HN2A  single    0.890  0.020  1.040
 HV8  CA1  CB1   single    1.536  0.020  1.536
 HV8  CA1  CM    single    1.539  0.020  1.539
 HV8  CA1  HA1   single    0.970  0.020  1.090
 HV8  CB1  CG1   single    1.502  0.020  1.502
 HV8  CB1  HB11  single    0.970  0.020  1.090
 HV8  CB1  HB12  single    0.970  0.020  1.090
 HV8  CG1  CD1   aromatic  1.393  0.020  1.393
 HV8  CG1  CD2   aromatic  1.395  0.020  1.395
 HV8  CD1  CE1   aromatic  1.389  0.020  1.389
 HV8  CD1  HD1   single    0.930  0.020  1.080
 HV8  CD2  CE2   aromatic  1.388  0.020  1.388
 HV8  CD2  HD2   single    0.930  0.020  1.080
 HV8  CE1  CZ1   aromatic  1.388  0.020  1.388
 HV8  CE1  HE1   single    0.930  0.020  1.080
 HV8  CE2  CZ1   aromatic  1.390  0.020  1.390
 HV8  CE2  HE2   single    0.930  0.020  1.080
 HV8  CZ1  HZ1   single    0.930  0.020  1.080
 HV8  CM   OH    single    1.405  0.020  1.405
 HV8  CM   CA2   single    1.543  0.020  1.543
 HV8  CM   HM    single    0.970  0.020  1.090
 HV8  OH   HOH   single    0.850  0.020  0.980
 HV8  N2   CA2   single    1.445  0.020  1.445
 HV8  N2   CB2   single    1.454  0.020  1.454
 HV8  N2   HN2   single    0.890  0.020  1.040
 HV8  CA2  C     single    1.519  0.020  1.519
 HV8  CA2  HA2   single    0.970  0.020  1.090
 HV8  CB2  CG2   single    1.502  0.020  1.502
 HV8  CB2  HB21  single    0.970  0.020  1.090
 HV8  CB2  HB22  single    0.970  0.020  1.090
 HV8  CG2  CD4   aromatic  1.397  0.020  1.397
 HV8  CG2  CD3   aromatic  1.386  0.020  1.386
 HV8  CD4  CE3   aromatic  1.381  0.020  1.381
 HV8  CD4  HD4   single    0.930  0.020  1.080
 HV8  CE3  CZ2   aromatic  1.399  0.020  1.399
 HV8  CE3  HE3   single    0.930  0.020  1.080
 HV8  CD3  CE4   aromatic  1.393  0.020  1.393
 HV8  CD3  HD3   single    0.930  0.020  1.080
 HV8  CE4  CZ2   aromatic  1.391  0.020  1.391
 HV8  CE4  HE4   single    0.930  0.020  1.080
 HV8  CZ2  OE2   single    1.348  0.020  1.348
 HV8  OE2  CM2   single    1.413  0.020  1.413
 HV8  CM2  HM21  single    0.970  0.020  1.090
 HV8  CM2  HM22  single    0.970  0.020  1.090
 HV8  CM2  HM23  single    0.970  0.020  1.090
 HV8  C    O     double    1.231  0.020  1.231
 HV8  C    OXT   single    1.327  0.020  1.327
 HV8  OXT  HXT   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
 HV8  HN2A  N    HN1   106.23  3.000
 HV8  HN2A  N    CA1   111.24  3.000
 HV8  HN1   N    CA1   111.21  3.000
 HV8  HA1   CA1  CM    108.69  3.000
 HV8  HA1   CA1  CB1   107.26  3.000
 HV8  CM    CA1  CB1   110.65  3.000
 HV8  HA1   CA1  N     108.14  3.000
 HV8  CM    CA1  N     108.44  3.000
 HV8  CB1   CA1  N     113.54  3.000
 HV8  HB12  CB1  HB11  106.79  3.000
 HV8  HB12  CB1  CG1   109.94  3.000
 HV8  HB11  CB1  CG1   110.19  3.000
 HV8  HB12  CB1  CA1   108.77  3.000
 HV8  HB11  CB1  CA1   108.97  3.000
 HV8  CG1   CB1  CA1   112.03  3.000
 HV8  CD2   CG1  CD1   118.32  3.000
 HV8  CD2   CG1  CB1   120.31  3.000
 HV8  CD1   CG1  CB1   121.35  3.000
 HV8  HD1   CD1  CE1   119.46  3.000
 HV8  HD1   CD1  CG1   119.54  3.000
 HV8  CE1   CD1  CG1   121.00  3.000
 HV8  HD2   CD2  CE2   119.57  3.000
 HV8  HD2   CD2  CG1   119.48  3.000
 HV8  CE2   CD2  CG1   120.96  3.000
 HV8  HE1   CE1  CZ1   120.12  3.000
 HV8  HE1   CE1  CD1   119.79  3.000
 HV8  CZ1   CE1  CD1   120.09  3.000
 HV8  HE2   CE2  CZ1   120.02  3.000
 HV8  HE2   CE2  CD2   119.84  3.000
 HV8  CZ1   CE2  CD2   120.13  3.000
 HV8  HZ1   CZ1  CE2   120.21  3.000
 HV8  HZ1   CZ1  CE1   120.28  3.000
 HV8  CE2   CZ1  CE1   119.51  3.000
 HV8  HM    CM   CA2   107.19  3.000
 HV8  HM    CM   OH    106.93  3.000
 HV8  CA2   CM   OH    110.84  3.000
 HV8  HM    CM   CA1   109.85  3.000
 HV8  CA2   CM   CA1   111.65  3.000
 HV8  OH    CM   CA1   110.23  3.000
 HV8  HOH   OH   CM    106.57  3.000
 HV8  HN2   N2   CB2   108.30  3.000
 HV8  HN2   N2   CA2   109.46  3.000
 HV8  CB2   N2   CA2   113.28  3.000
 HV8  HA2   CA2  C     108.71  3.000
 HV8  HA2   CA2  N2    112.81  3.000
 HV8  C     CA2  N2    109.28  3.000
 HV8  HA2   CA2  CM    108.40  3.000
 HV8  C     CA2  CM    107.16  3.000
 HV8  N2    CA2  CM    110.30  3.000
 HV8  HB22  CB2  HB21  106.07  3.000
 HV8  HB22  CB2  CG2   109.40  3.000
 HV8  HB21  CB2  CG2   109.24  3.000
 HV8  HB22  CB2  N2    112.63  3.000
 HV8  HB21  CB2  N2    108.36  3.000
 HV8  CG2   CB2  N2    110.97  3.000
 HV8  CD3   CG2  CD4   117.88  3.000
 HV8  CD3   CG2  CB2   121.37  3.000
 HV8  CD4   CG2  CB2   120.76  3.000
 HV8  HD4   CD4  CE3   119.26  3.000
 HV8  HD4   CD4  CG2   119.50  3.000
 HV8  CE3   CD4  CG2   121.23  3.000
 HV8  HE3   CE3  CZ2   119.43  3.000
 HV8  HE3   CE3  CD4   120.29  3.000
 HV8  CZ2   CE3  CD4   120.28  3.000
 HV8  HD3   CD3  CE4   118.55  3.000
 HV8  HD3   CD3  CG2   119.65  3.000
 HV8  CE4   CD3  CG2   121.80  3.000
 HV8  HE4   CE4  CZ2   121.55  3.000
 HV8  HE4   CE4  CD3   118.83  3.000
 HV8  CZ2   CE4  CD3   119.62  3.000
 HV8  OE2   CZ2  CE4   124.50  3.000
 HV8  OE2   CZ2  CE3   116.31  3.000
 HV8  CE4   CZ2  CE3   119.20  3.000
 HV8  CM2   OE2  CZ2   118.41  3.000
 HV8  HM23  CM2  HM22  108.71  3.000
 HV8  HM23  CM2  HM21  108.70  3.000
 HV8  HM22  CM2  HM21  108.74  3.000
 HV8  HM23  CM2  OE2   106.55  3.000
 HV8  HM22  CM2  OE2   112.00  3.000
 HV8  HM21  CM2  OE2   112.02  3.000
 HV8  OXT   C    O     123.43  3.000
 HV8  OXT   C    CA2   112.33  3.000
 HV8  O     C    CA2   124.24  3.000
 HV8  HXT   OXT  C     109.86  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
 HV8  CONST_01  CZ1   CE1  CD1  CG1    0.00   0.0  0
 HV8  CONST_02  CZ1   CE2  CD2  CG1    0.00   0.0  0
 HV8  CONST_03  CE2   CD2  CG1  CD1    0.00   0.0  0
 HV8  CONST_04  CE2   CZ1  CE1  CD1    0.00   0.0  0
 HV8  CONST_05  CE1   CD1  CG1  CD2    0.00   0.0  0
 HV8  CONST_06  CE1   CZ1  CE2  CD2    0.00   0.0  0
 HV8  CONST_07  CZ2   CE3  CD4  CG2    0.00   0.0  0
 HV8  CONST_08  CZ2   CE4  CD3  CG2    0.00   0.0  0
 HV8  CONST_09  CE4   CD3  CG2  CD4    0.00   0.0  0
 HV8  CONST_10  CE4   CZ2  CE3  CD4    0.00   0.0  0
 HV8  CONST_11  CD3   CG2  CD4  CE3    0.00   0.0  0
 HV8  CONST_12  CD3   CE4  CZ2  CE3    0.00   0.0  0
 HV8  CONST_13  CE1   CD1  CG1  CB1  180.00   0.0  0
 HV8  CONST_14  CE2   CD2  CG1  CB1  180.00   0.0  0
 HV8  CONST_15  CE3   CD4  CG2  CB2  180.00   0.0  0
 HV8  CONST_16  CE4   CD3  CG2  CB2  180.00   0.0  0
 HV8  CONST_17  OE2   CZ2  CE3  CD4  180.00   0.0  0
 HV8  CONST_18  OE2   CZ2  CE4  CD3  180.00   0.0  0
 HV8  CONST_19  HE1   CE1  CD1  CG1  180.00   0.0  0
 HV8  CONST_20  HE2   CE2  CD2  CG1  180.00   0.0  0
 HV8  CONST_21  HD2   CD2  CG1  CD1  180.00   0.0  0
 HV8  CONST_22  HZ1   CZ1  CE1  CD1  180.00   0.0  0
 HV8  CONST_23  HD1   CD1  CG1  CD2  180.00   0.0  0
 HV8  CONST_24  HE3   CE3  CD4  CG2  180.00   0.0  0
 HV8  CONST_25  HE4   CE4  CD3  CG2  180.00   0.0  0
 HV8  CONST_26  HD3   CD3  CG2  CD4  180.00   0.0  0
 HV8  CONST_27  HD4   CD4  CG2  CD3  180.00   0.0  0
 HV8  CONST_28  HXT   OXT  C    CA2  180.00   0.0  0
 HV8  Var_01    CD1   CG1  CB1  CA1   97.36  30.0  2
 HV8  Var_02    CD4   CG2  CB2  N2    55.20  30.0  2
 HV8  Var_03    CG2   CB2  N2   CA2  178.05  30.0  3
 HV8  Var_04    HM21  CM2  OE2  CZ2  -61.09  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
 HV8  chir_01  CA1  N   CB1  CM   negativ
 HV8  chir_02  CM   OH  CA1  CA2  positiv
 HV8  chir_03  CA2  N2  CM   C    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
 HV8  plan-1  CB1  0.020
 HV8  plan-1  CG1  0.020
 HV8  plan-1  CD1  0.020
 HV8  plan-1  CD2  0.020
 HV8  plan-1  CE1  0.020
 HV8  plan-1  CE2  0.020
 HV8  plan-1  CZ1  0.020
 HV8  plan-1  HD1  0.020
 HV8  plan-1  HD2  0.020
 HV8  plan-1  HE1  0.020
 HV8  plan-1  HE2  0.020
 HV8  plan-1  HZ1  0.020
 HV8  plan-2  CB2  0.020
 HV8  plan-2  CG2  0.020
 HV8  plan-2  CD4  0.020
 HV8  plan-2  CE3  0.020
 HV8  plan-2  CD3  0.020
 HV8  plan-2  CE4  0.020
 HV8  plan-2  CZ2  0.020
 HV8  plan-2  OE2  0.020
 HV8  plan-2  HD4  0.020
 HV8  plan-2  HE3  0.020
 HV8  plan-2  HD3  0.020
 HV8  plan-2  HE4  0.020
 HV8  plan-3  CA2  0.020
 HV8  plan-3  C    0.020
 HV8  plan-3  O    0.020
 HV8  plan-3  OXT  0.020
 HV8  plan-3  HXT  0.020

