# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 09:14:50 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: (2~{S},4~{R})-4-azanyl-2-methyl-5-phenyl-pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](C[C@@H](N)Cc1ccccc1)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
 OH5  OH5  '(2~{S},4~{R})-4-azanyl-2-methyl-5-phenyl-pentanoic acid'  ligand  31  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_OH5
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
 OH5  NBI  N  NH2    0  -0.820  -3.8896  22.6632  13.6259
 OH5  CBJ  C  CH1    0  -0.057  -4.1341  21.2407  13.4125
 OH5  CBL  C  CH2    0  -0.432  -3.0235  20.6408  12.5381
 OH5  CBT  C  CH1    0  -0.368  -1.8850  19.9433  13.2994
 OH5  CBX  C  CH3    0  -0.647  -2.3450  18.6086  13.8731
 OH5  CBU  C  C      0   0.421  -1.2278  20.8783  14.3436
 OH5  OXT  O  OC     0  -0.586  -1.1458  20.4777  15.5196
 OH5  O    O  O     -1  -0.622  -0.8181  21.9811  13.9101
 OH5  CBM  C  CH2    0  -0.503  -5.5020  21.0570  12.7405
 OH5  CBN  C  C      0   0.131  -6.6283  21.6603  13.5296
 OH5  CBO  C  C1     0  -0.307  -7.1344  21.0084  14.6545
 OH5  CBP  C  C1     0  -0.238  -8.1498  21.5741  15.4126
 OH5  CBQ  C  C1     0  -0.273  -8.6819  22.8078  15.0560
 OH5  CBR  C  C1     0  -0.240  -8.1879  23.4673  13.9388
 OH5  CBS  C  C1     0  -0.311  -7.1676  22.8981  13.1868
 OH5  H1   H  HNH2   0   0.335  -4.4462  22.9968  14.4029
 OH5  H2   H  HNH2   0   0.348  -2.9193  22.7979  13.8837
 OH5  H4   H  HCH1   0   0.199  -4.1670  20.6820  14.3615
 OH5  H5   H  HCH2   0   0.217  -3.4622  19.9091  11.8526
 OH5  H6   H  HCH2   0   0.218  -2.6204  21.4365  11.9066
 OH5  H7   H  HCH1   0   0.217  -1.1101  19.7290  12.5518
 OH5  H8   H  HCH3   0   0.215  -1.5273  18.0753  14.3572
 OH5  H9   H  HCH3   0   0.208  -3.1343  18.7341  14.6161
 OH5  H10  H  HCH3   0   0.202  -2.7362  17.9637  13.0831
 OH5  H12  H  HCH2   0   0.231  -5.4610  21.5057  11.7439
 OH5  H13  H  HCH2   0   0.234  -5.6776  19.9862  12.6035
 OH5  H14  H  H      0   0.242  -6.7280  20.0435  14.9369
 OH5  H15  H  H      0   0.248  -8.5287  21.0505  16.2813
 OH5  H16  H  H      0   0.249  -9.4770  23.2489  15.6434
 OH5  H17  H  H      0   0.248  -8.5971  24.4277  13.6513
 OH5  H18  H  H      0   0.241  -6.7882  23.4203  12.3164

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
 OH5  CBL  CBJ  single    1.536  0.020  1.536
 OH5  CBL  CBT  single    1.537  0.020  1.537
 OH5  CBM  CBJ  single    1.535  0.020  1.535
 OH5  CBM  CBN  single    1.502  0.020  1.502
 OH5  NBI  CBJ  single    1.459  0.020  1.459
 OH5  CBT  CBX  single    1.524  0.020  1.524
 OH5  CBT  CBU  single    1.548  0.020  1.548
 OH5  CBS  CBN  aromatic  1.393  0.020  1.393
 OH5  CBS  CBR  aromatic  1.389  0.020  1.389
 OH5  CBN  CBO  aromatic  1.395  0.020  1.395
 OH5  CBR  CBQ  aromatic  1.388  0.020  1.388
 OH5  O    CBU  deloc     1.254  0.020  1.254
 OH5  CBU  OXT  deloc     1.245  0.020  1.245
 OH5  CBO  CBP  aromatic  1.388  0.020  1.388
 OH5  CBQ  CBP  aromatic  1.390  0.020  1.390
 OH5  NBI  H1   single    0.890  0.020  1.040
 OH5  NBI  H2   single    0.890  0.020  1.040
 OH5  CBJ  H4   single    0.970  0.020  1.090
 OH5  CBL  H5   single    0.970  0.020  1.090
 OH5  CBL  H6   single    0.970  0.020  1.090
 OH5  CBT  H7   single    0.970  0.020  1.090
 OH5  CBX  H8   single    0.970  0.020  1.090
 OH5  CBX  H9   single    0.970  0.020  1.090
 OH5  CBX  H10  single    0.970  0.020  1.090
 OH5  CBM  H12  single    0.970  0.020  1.090
 OH5  CBM  H13  single    0.970  0.020  1.090
 OH5  CBO  H14  single    0.930  0.020  1.080
 OH5  CBP  H15  single    0.930  0.020  1.080
 OH5  CBQ  H16  single    0.930  0.020  1.080
 OH5  CBR  H17  single    0.930  0.020  1.080
 OH5  CBS  H18  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
 OH5  H2   NBI  H1   106.71  3.000
 OH5  H2   NBI  CBJ  109.11  3.000
 OH5  H1   NBI  CBJ  109.97  3.000
 OH5  H4   CBJ  CBM  106.85  3.000
 OH5  H4   CBJ  CBL  108.30  3.000
 OH5  CBM  CBJ  CBL  110.39  3.000
 OH5  H4   CBJ  NBI  111.93  3.000
 OH5  CBM  CBJ  NBI  109.27  3.000
 OH5  CBL  CBJ  NBI  110.06  3.000
 OH5  H6   CBL  H5   105.83  3.000
 OH5  H6   CBL  CBT  110.08  3.000
 OH5  H5   CBL  CBT  107.68  3.000
 OH5  H6   CBL  CBJ  108.14  3.000
 OH5  H5   CBL  CBJ  109.14  3.000
 OH5  CBT  CBL  CBJ  115.53  3.000
 OH5  H7   CBT  CBU  106.12  3.000
 OH5  H7   CBT  CBX  107.36  3.000
 OH5  CBU  CBT  CBX  113.78  3.000
 OH5  H7   CBT  CBL  105.91  3.000
 OH5  CBU  CBT  CBL  111.99  3.000
 OH5  CBX  CBT  CBL  111.12  3.000
 OH5  H10  CBX  H9   107.54  3.000
 OH5  H10  CBX  H8   107.52  3.000
 OH5  H9   CBX  H8   107.25  3.000
 OH5  H10  CBX  CBT  110.67  3.000
 OH5  H9   CBX  CBT  111.96  3.000
 OH5  H8   CBX  CBT  111.67  3.000
 OH5  O    CBU  OXT  126.02  3.000
 OH5  OXT  CBU  CBT  118.08  3.000
 OH5  O    CBU  CBT  115.90  3.000
 OH5  H13  CBM  H12  107.07  3.000
 OH5  H13  CBM  CBN  109.80  3.000
 OH5  H12  CBM  CBN  110.00  3.000
 OH5  H13  CBM  CBJ  108.37  3.000
 OH5  H12  CBM  CBJ  108.44  3.000
 OH5  CBN  CBM  CBJ  112.97  3.000
 OH5  CBS  CBN  CBO  118.24  3.000
 OH5  CBO  CBN  CBM  120.53  3.000
 OH5  CBS  CBN  CBM  121.20  3.000
 OH5  H14  CBO  CBP  119.65  3.000
 OH5  H14  CBO  CBN  119.33  3.000
 OH5  CBP  CBO  CBN  121.02  3.000
 OH5  H15  CBP  CBQ  120.07  3.000
 OH5  H15  CBP  CBO  119.81  3.000
 OH5  CBQ  CBP  CBO  120.12  3.000
 OH5  H16  CBQ  CBR  120.29  3.000
 OH5  H16  CBQ  CBP  120.24  3.000
 OH5  CBR  CBQ  CBP  119.47  3.000
 OH5  H17  CBR  CBS  119.82  3.000
 OH5  H17  CBR  CBQ  120.03  3.000
 OH5  CBS  CBR  CBQ  120.15  3.000
 OH5  H18  CBS  CBR  119.63  3.000
 OH5  H18  CBS  CBN  119.36  3.000
 OH5  CBR  CBS  CBN  121.01  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
 OH5  CONST_01  CBQ  CBR  CBS  CBN    0.00   0.0  0
 OH5  CONST_02  CBQ  CBP  CBO  CBN    0.00   0.0  0
 OH5  CONST_03  CBR  CBS  CBN  CBO    0.00   0.0  0
 OH5  CONST_04  CBR  CBQ  CBP  CBO    0.00   0.0  0
 OH5  CONST_05  CBS  CBN  CBO  CBP    0.00   0.0  0
 OH5  CONST_06  CBS  CBR  CBQ  CBP    0.00   0.0  0
 OH5  CONST_07  CBR  CBS  CBN  CBM  180.00   0.0  0
 OH5  CONST_08  CBP  CBO  CBN  CBM  180.00   0.0  0
 OH5  CONST_09  H17  CBR  CBS  CBN  180.00   0.0  0
 OH5  CONST_10  H15  CBP  CBO  CBN  180.00   0.0  0
 OH5  CONST_11  H18  CBS  CBN  CBO  180.00   0.0  0
 OH5  CONST_12  H16  CBQ  CBP  CBO  180.00   0.0  0
 OH5  CONST_13  H14  CBO  CBP  CBQ  180.00   0.0  0
 OH5  Var_01    CBS  CBN  CBM  CBJ  100.55  30.0  2

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
 OH5  chir_01  CBJ  CBL  CBM  NBI  positiv
 OH5  chir_02  CBT  CBU  CBX  CBL  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
 OH5  plan-1  CBM  0.020
 OH5  plan-1  CBN  0.020
 OH5  plan-1  CBO  0.020
 OH5  plan-1  CBP  0.020
 OH5  plan-1  CBQ  0.020
 OH5  plan-1  CBR  0.020
 OH5  plan-1  CBS  0.020
 OH5  plan-1  H14  0.020
 OH5  plan-1  H15  0.020
 OH5  plan-1  H16  0.020
 OH5  plan-1  H17  0.020
 OH5  plan-1  H18  0.020
 OH5  plan-2  CBT  0.020
 OH5  plan-2  CBU  0.020
 OH5  plan-2  OXT  0.020
 OH5  plan-2  O    0.020

