# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 01:52:57 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: 5-phenyl-L-norvaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCc1ccccc1)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
 PH8  PH8  '5-phenyl-L-norvaline     '  L-peptide  28  14  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PH8
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
 PH8  C    C  C      0   0.409  -4.3924   3.9088   2.6169
 PH8  N    N  NH2    0  -0.812  -5.9319   5.5731   3.4714
 PH8  O    O  O      0  -0.617  -4.8063   2.7862   2.9770
 PH8  CA   C  CH1    0  -0.191  -5.4884   4.9304   2.2259
 PH8  CB   C  CH2    0  -0.406  -5.0226   6.0117   1.2643
 PH8  CG   C  CR6    0   0.135  -5.9018   3.4548  -0.7469
 PH8  CI   C  CH2    0  -0.441  -4.5444   5.5482  -0.1083
 PH8  CJ   C  CH2    0  -0.506  -5.6100   4.9090  -1.0095
 PH8  CZ   C  CR16   0  -0.274  -6.4300   0.7348  -0.2971
 PH8  CD1  C  CR16   0  -0.312  -7.1754   3.0217  -0.3860
 PH8  CD2  C  CR16   0  -0.301  -4.8986   2.4961  -0.8885
 PH8  CE1  C  CR16   0  -0.244  -7.4401   1.6770  -0.1595
 PH8  CE2  C  CR16   0  -0.241  -5.1565   1.1511  -0.6653
 PH8  HN   H  HNH2   0   0.332  -6.7257   6.1698   3.2669
 PH8  HA   H  HCH1   0   0.191  -6.3082   4.3702   1.7575
 PH8  HZ   H  HCR6   0   0.248  -6.6332  -0.3141  -0.1227
 PH8  HB   H  HCH2   0   0.205  -4.2165   6.5739   1.7426
 PH8  HBA  H  HCH2   0   0.197  -5.8439   6.7245   1.1154
 PH8  HD1  H  HCR6   0   0.244  -7.9711   3.7493  -0.2731
 PH8  HD2  H  HCR6   0   0.242  -3.9011   2.8055  -1.1798
 PH8  HE1  H  HCR6   0   0.247  -8.4376   1.3664   0.1251
 PH8  HE2  H  HCR6   0   0.248  -4.3616   0.4251  -0.7817
 PH8  HI   H  HCH2   0   0.222  -3.6959   4.8698   0.0021
 PH8  HIA  H  HCH2   0   0.221  -4.1555   6.4245  -0.6335
 PH8  HJ   H  HCH2   0   0.242  -5.2746   5.0024  -2.0469
 PH8  HJA  H  HCH2   0   0.233  -6.5367   5.4866  -0.9435
 PH8  OXT  O  OC    -1  -0.602  -3.2053   4.2897   2.5927
 PH8  HNA  H  HNH2   0   0.331  -6.2901   4.8613   4.0970

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
 PH8  CA   C    single    1.525  0.021  1.525
 PH8  O    C    deloc     1.231  0.020  1.231
 PH8  C    OXT  deloc     1.247  0.020  1.247
 PH8  CA   N    single    1.458  0.019  1.458
 PH8  N    HN   single    0.890  0.020  1.040
 PH8  N    HNA  single    0.890  0.020  1.040
 PH8  CB   CA   single    1.521  0.033  1.521
 PH8  HA   CA   single    0.970  0.020  0.970
 PH8  CI   CB   single    1.526  0.020  1.526
 PH8  HBA  CB   single    0.970  0.020  1.090
 PH8  CB   HB   single    0.970  0.020  1.090
 PH8  CD2  CG   aromatic  1.395  0.020  1.395
 PH8  CJ   CG   single    1.506  0.020  1.506
 PH8  CG   CD1  aromatic  1.393  0.020  1.393
 PH8  CJ   CI   single    1.535  0.020  1.535
 PH8  HIA  CI   single    0.970  0.020  1.090
 PH8  CI   HI   single    0.970  0.020  1.090
 PH8  HJ   CJ   single    0.970  0.020  1.090
 PH8  CJ   HJA  single    0.970  0.020  1.090
 PH8  CE2  CZ   aromatic  1.390  0.020  1.390
 PH8  CZ   HZ   single    0.930  0.020  1.080
 PH8  CZ   CE1  aromatic  1.388  0.020  1.388
 PH8  CD1  CE1  aromatic  1.389  0.020  1.389
 PH8  CD1  HD1  single    0.930  0.020  1.080
 PH8  HD2  CD2  single    0.930  0.020  1.080
 PH8  CD2  CE2  aromatic  1.388  0.020  1.388
 PH8  CE1  HE1  single    0.930  0.020  1.080
 PH8  HE2  CE2  single    0.930  0.020  1.080

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
 PH8  OXT  C    CA   120.80  1.700
 PH8  OXT  C    O    126.55  3.000
 PH8  CA   C    O    120.80  1.700
 PH8  HNA  N    HN   105.14  3.000
 PH8  HNA  N    CA   108.83  3.000
 PH8  HN   N    CA   108.83  3.000
 PH8  HA   CA   CB   109.00  3.000
 PH8  HA   CA   N    110.00  3.000
 PH8  CB   CA   N    110.40  1.500
 PH8  HA   CA   C    110.00  3.000
 PH8  CB   CA   C    110.50  1.500
 PH8  N    CA   C    111.00  2.800
 PH8  HBA  CB   HB   106.09  3.000
 PH8  HB   CB   CI   108.59  3.000
 PH8  HBA  CB   CI   108.05  3.000
 PH8  HB   CB   CA   108.36  3.000
 PH8  HBA  CB   CA   108.57  3.000
 PH8  CI   CB   CA   116.68  3.000
 PH8  CD2  CG   CD1  118.06  3.000
 PH8  CD1  CG   CJ   121.50  3.000
 PH8  CD2  CG   CJ   120.43  3.000
 PH8  HIA  CI   HI   105.68  3.000
 PH8  HI   CI   CJ   109.88  3.000
 PH8  HIA  CI   CJ   107.38  3.000
 PH8  HI   CI   CB   109.96  3.000
 PH8  HIA  CI   CB   107.47  3.000
 PH8  CJ   CI   CB   115.92  3.000
 PH8  HJA  CJ   HJ   105.77  3.000
 PH8  HJA  CJ   CI   109.44  3.000
 PH8  HJ   CJ   CI   107.95  3.000
 PH8  HJA  CJ   CG   109.58  3.000
 PH8  HJ   CJ   CG   107.89  3.000
 PH8  CI   CJ   CG   115.73  3.000
 PH8  HZ   CZ   CE2  120.33  3.000
 PH8  HZ   CZ   CE1  120.34  3.000
 PH8  CE2  CZ   CE1  119.33  3.000
 PH8  HD1  CD1  CE1  119.53  3.000
 PH8  HD1  CD1  CG   119.30  3.000
 PH8  CE1  CD1  CG   121.16  3.000
 PH8  HD2  CD2  CE2  119.40  3.000
 PH8  CE2  CD2  CG   121.08  3.000
 PH8  HD2  CD2  CG   119.53  3.000
 PH8  HE1  CE1  CD1  119.74  3.000
 PH8  HE1  CE1  CZ   120.11  3.000
 PH8  CD1  CE1  CZ   120.15  3.000
 PH8  HE2  CE2  CD2  119.75  3.000
 PH8  HE2  CE2  CZ   120.03  3.000
 PH8  CD2  CE2  CZ   120.22  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
 PH8  CONST_01  CZ   CE2  CD2  CG     0.00   0.0  0
 PH8  CONST_02  CZ   CE1  CD1  CG     0.00   0.0  0
 PH8  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 PH8  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 PH8  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 PH8  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 PH8  CONST_07  CE2  CD2  CG   CJ   180.00   0.0  0
 PH8  CONST_08  CE1  CD1  CG   CJ   180.00   0.0  0
 PH8  CONST_09  HE2  CE2  CD2  CG   180.00   0.0  0
 PH8  CONST_10  HE1  CE1  CD1  CG   180.00   0.0  0
 PH8  CONST_11  HD2  CD2  CE2  CZ   180.00   0.0  0
 PH8  CONST_12  HD1  CD1  CE1  CZ   180.00   0.0  0
 PH8  CONST_13  HZ   CZ   CE1  CD1  180.00   0.0  0
 PH8  Var_01    CD2  CG   CJ   CI   -61.27  30.0  2
 PH8  Var_02    CG   CJ   CI   CB   -81.91  30.0  2
 PH8  Var_03    CJ   CI   CB   CA    65.46  30.0  1

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
 PH8  chir_01  CA  C  N  CB  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
 PH8  plan-1  CG   0.020
 PH8  plan-1  CJ   0.020
 PH8  plan-1  CZ   0.020
 PH8  plan-1  CD1  0.020
 PH8  plan-1  CD2  0.020
 PH8  plan-1  CE1  0.020
 PH8  plan-1  CE2  0.020
 PH8  plan-1  HZ   0.020
 PH8  plan-1  HD1  0.020
 PH8  plan-1  HD2  0.020
 PH8  plan-1  HE1  0.020
 PH8  plan-1  HE2  0.020
 PH8  plan-2  C    0.020
 PH8  plan-2  O    0.020
 PH8  plan-2  CA   0.020
 PH8  plan-2  OXT  0.020

