# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 14:39:55 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  48  25  .  2022-03-18  2022-07-25
;
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  -0.789  -2.6422   0.3709   1.4393
 HV8  CA1   C  CH1    0  -0.115  -2.3122   0.3553   0.0279
 HV8  CB1   C  CH2    0  -0.512  -3.5103   0.0978  -0.9127
 HV8  CG1   C  CR6    0   0.131  -4.1911  -1.2060  -0.6143
 HV8  CD1   C  CR16   0  -0.322  -5.3028  -1.2589   0.2249
 HV8  CD2   C  CR16   0  -0.308  -3.6945  -2.4037  -1.1279
 HV8  CE1   C  CR16   0  -0.241  -5.9062  -2.4707   0.5381
 HV8  CE2   C  CR16   0  -0.240  -4.2924  -3.6173  -0.8178
 HV8  CZ1   C  CR16   0  -0.275  -5.4024  -3.6550   0.0175
 HV8  CM    C  CH1    0   0.069  -1.6204   1.6674  -0.3670
 HV8  OH    O  OH1    0  -0.724  -2.5516   2.7060  -0.1997
 HV8  N2    N  NH1    0  -0.609   0.6551   0.9208   0.1967
 HV8  CA2   C  CH1    0  -0.231  -0.3271   1.9564   0.4337
 HV8  CB2   C  CH2    0  -0.325   1.7088   0.8515   1.1913
 HV8  CG2   C  CR6    0   0.068   2.8793   0.0590   0.6760
 HV8  CD4   C  CR16   0  -0.268   3.4495   0.3886  -0.5560
 HV8  CE3   C  CR16   0  -0.330   4.5320  -0.3082  -1.0539
 HV8  CD3   C  CR16   0  -0.313   3.4324  -0.9957   1.3835
 HV8  CE4   C  CR16   0  -0.371   4.5262  -1.7123   0.8994
 HV8  CZ2   C  CR6    0   0.363   5.0808  -1.3712  -0.3285
 HV8  OE2   O  O2     0  -0.474   6.1323  -1.9995  -0.8954
 HV8  CM2   C  CH3    0  -0.435   6.7176  -3.0850  -0.2075
 HV8  C     C  C      0   0.454   0.2178   3.3533   0.0394
 HV8  O     O  O      0  -0.550   1.3777   3.4750  -0.3644
 HV8  OXT   O  OC    -1  -0.630  -0.6117   4.3010   0.1735
 HV8  HN1   H  HNH2   0   0.335  -3.3477   1.0764   1.6147
 HV8  HN2A  H  HNH2   0   0.348  -3.0502  -0.5141   1.7120
 HV8  HA1   H  HCH1   0   0.227  -1.6134  -0.4730  -0.1356
 HV8  HB11  H  HCH2   0   0.245  -4.2246   0.9181  -0.8210
 HV8  HB12  H  HCH2   0   0.235  -3.1493   0.0987  -1.9455
 HV8  HD1   H  HCR6   0   0.247  -5.7070  -0.3388   0.6309
 HV8  HD2   H  HCR6   0   0.244  -2.8320  -2.3836  -1.7847
 HV8  HE1   H  HCR6   0   0.252  -6.7716  -2.4884   1.1884
 HV8  HE2   H  HCR6   0   0.252  -3.8938  -4.5355  -1.2306
 HV8  HZ1   H  HCR6   0   0.252  -5.8727  -4.6003   0.2561
 HV8  HM    H  HCH1   0   0.180  -1.3258   1.5684  -1.4275
 HV8  HOH   H  HOH1   0   0.437  -1.9951   3.5091  -0.0211
 HV8  HN2   H  HNH1   0   0.342   0.2068   0.0155   0.1600
 HV8  HA2   H  HCH1   0   0.206  -0.6262   2.0141   1.4941
 HV8  HB21  H  HCH2   0   0.237   2.0421   1.8667   1.4080
 HV8  HB22  H  HCH2   0   0.208   1.3685   0.4292   2.1492
 HV8  HD4   H  HCR6   0   0.249   3.0283   1.2114  -1.1202
 HV8  HE3   H  HCR6   0   0.254   4.9643  -0.0404  -2.0106
 HV8  HD3   H  HCR6   0   0.246   3.0092  -1.2792   2.3405
 HV8  HE4   H  HCR6   0   0.271   4.9194  -2.5276   1.4916
 HV8  HM21  H  HCH3   0   0.225   7.1353  -2.7837   0.7573
 HV8  HM22  H  HCH3   0   0.226   6.0048  -3.8975  -0.0415
 HV8  HM23  H  HCH3   0   0.257   7.5255  -3.4520  -0.8361

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    1.450  0.020  1.450
 HV8  N    HN1   single    0.890  0.020  1.040
 HV8  N    HN2A  single    0.890  0.020  1.040
 HV8  CA1  CB1   single    1.545  0.020  1.545
 HV8  CA1  CM    single    1.535  0.020  1.535
 HV8  CA1  HA1   single    0.970  0.020  1.090
 HV8  CB1  CG1   single    1.501  0.020  1.501
 HV8  CB1  HB11  single    0.970  0.020  1.090
 HV8  CB1  HB12  single    0.970  0.020  1.090
 HV8  CG1  CD1   aromatic  1.394  0.020  1.394
 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    1.548  0.020  1.548
 HV8  CM   HM    single    0.970  0.020  1.090
 HV8  OH   HOH   single    0.850  0.020  0.980
 HV8  N2   CA2   single    1.447  0.020  1.447
 HV8  N2   CB2   single    1.451  0.020  1.451
 HV8  N2   HN2   single    0.890  0.020  1.040
 HV8  CA2  C     single    1.550  0.020  1.550
 HV8  CA2  HA2   single    0.970  0.020  1.090
 HV8  CB2  CG2   single    1.504  0.020  1.504
 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  1.385  0.020  1.385
 HV8  CD4  CE3   aromatic  1.380  0.020  1.380
 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  1.394  0.020  1.394
 HV8  CD3  HD3   single    0.930  0.020  1.080
 HV8  CE4  CZ2   aromatic  1.390  0.020  1.390
 HV8  CE4  HE4   single    0.930  0.020  1.080
 HV8  CZ2  OE2   single    1.350  0.020  1.350
 HV8  OE2  CM2   single    1.412  0.020  1.412
 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     deloc     1.231  0.020  1.231
 HV8  C    OXT   deloc     1.267  0.020  1.267

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   106.35  3.000
 HV8  HN2A  N    CA1   110.17  3.000
 HV8  HN1   N    CA1   109.55  3.000
 HV8  HA1   CA1  CM    108.68  3.000
 HV8  HA1   CA1  CB1   106.13  3.000
 HV8  CM    CA1  CB1   109.60  3.000
 HV8  HA1   CA1  N     107.37  3.000
 HV8  CM    CA1  N     110.11  3.000
 HV8  CB1   CA1  N     114.71  3.000
 HV8  HB12  CB1  HB11  107.13  3.000
 HV8  HB12  CB1  CG1   109.76  3.000
 HV8  HB11  CB1  CG1   109.83  3.000
 HV8  HB12  CB1  CA1   108.58  3.000
 HV8  HB11  CB1  CA1   109.34  3.000
 HV8  CG1   CB1  CA1   112.06  3.000
 HV8  CD2   CG1  CD1   118.24  3.000
 HV8  CD2   CG1  CB1   120.75  3.000
 HV8  CD1   CG1  CB1   120.97  3.000
 HV8  HD1   CD1  CE1   119.60  3.000
 HV8  HD1   CD1  CG1   119.39  3.000
 HV8  CE1   CD1  CG1   121.01  3.000
 HV8  HD2   CD2  CE2   119.62  3.000
 HV8  HD2   CD2  CG1   119.37  3.000
 HV8  CE2   CD2  CG1   121.01  3.000
 HV8  HE1   CE1  CZ1   120.09  3.000
 HV8  HE1   CE1  CD1   119.79  3.000
 HV8  CZ1   CE1  CD1   120.12  3.000
 HV8  HE2   CE2  CZ1   120.01  3.000
 HV8  HE2   CE2  CD2   119.85  3.000
 HV8  CZ1   CE2  CD2   120.14  3.000
 HV8  HZ1   CZ1  CE2   120.21  3.000
 HV8  HZ1   CZ1  CE1   120.31  3.000
 HV8  CE2   CZ1  CE1   119.48  3.000
 HV8  HM    CM   CA2   106.88  3.000
 HV8  HM    CM   OH    110.93  3.000
 HV8  CA2   CM   OH    110.74  3.000
 HV8  HM    CM   CA1   106.89  3.000
 HV8  CA2   CM   CA1   113.76  3.000
 HV8  OH    CM   CA1   107.61  3.000
 HV8  HOH   OH   CM    104.35  3.000
 HV8  HN2   N2   CB2   107.71  3.000
 HV8  HN2   N2   CA2   110.24  3.000
 HV8  CB2   N2   CA2   114.52  3.000
 HV8  HA2   CA2  C     107.01  3.000
 HV8  HA2   CA2  N2    112.27  3.000
 HV8  C     CA2  N2    111.39  3.000
 HV8  HA2   CA2  CM    106.28  3.000
 HV8  C     CA2  CM    109.28  3.000
 HV8  N2    CA2  CM    110.41  3.000
 HV8  HB22  CB2  HB21  106.18  3.000
 HV8  HB22  CB2  CG2   109.67  3.000
 HV8  HB21  CB2  CG2   108.71  3.000
 HV8  HB22  CB2  N2    112.98  3.000
 HV8  HB21  CB2  N2    108.29  3.000
 HV8  CG2   CB2  N2    110.82  3.000
 HV8  CD3   CG2  CD4   117.84  3.000
 HV8  CD3   CG2  CB2   122.46  3.000
 HV8  CD4   CG2  CB2   119.69  3.000
 HV8  HD4   CD4  CE3   120.04  3.000
 HV8  HD4   CD4  CG2   118.68  3.000
 HV8  CE3   CD4  CG2   121.27  3.000
 HV8  HE3   CE3  CZ2   119.28  3.000
 HV8  HE3   CE3  CD4   120.44  3.000
 HV8  CZ2   CE3  CD4   120.28  3.000
 HV8  HD3   CD3  CE4   118.58  3.000
 HV8  HD3   CD3  CG2   119.61  3.000
 HV8  CE4   CD3  CG2   121.82  3.000
 HV8  HE4   CE4  CZ2   121.58  3.000
 HV8  HE4   CE4  CD3   118.84  3.000
 HV8  CZ2   CE4  CD3   119.58  3.000
 HV8  OE2   CZ2  CE4   124.59  3.000
 HV8  OE2   CZ2  CE3   116.20  3.000
 HV8  CE4   CZ2  CE3   119.21  3.000
 HV8  CM2   OE2  CZ2   118.43  3.000
 HV8  HM23  CM2  HM22  108.74  3.000
 HV8  HM23  CM2  HM21  108.61  3.000
 HV8  HM22  CM2  HM21  108.65  3.000
 HV8  HM23  CM2  OE2   106.60  3.000
 HV8  HM22  CM2  OE2   112.02  3.000
 HV8  HM21  CM2  OE2   112.10  3.000
 HV8  OXT   C    O     125.20  3.000
 HV8  OXT   C    CA2   114.65  3.000
 HV8  O     C    CA2   120.15  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  Var_01    CD1   CG1  CB1  CA1    94.70  30.0  2
 HV8  Var_02    CD4   CG2  CB2  N2     52.40  30.0  2
 HV8  Var_03    CG2   CB2  N2   CA2  -163.12  30.0  3
 HV8  Var_04    HM21  CM2  OE2  CZ2   -62.17  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

