# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:41:30 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: (betaS)-beta-methyl-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]([C@H](N)C(O)=O)c1ccccc1
#
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
 41H  41H  (betaS)-beta-methyl-L-phenylalanine  L-peptide  25  13  .  2019-03-22  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_41H
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
 41H  N    N  NH2    0  -0.789  46.6992  -7.1693  68.2246
 41H  C    C  C      0   0.386  44.6977  -8.3463  69.1837
 41H  O    O  O      0  -0.607  43.5734  -7.9699  69.5703
 41H  CA   C  CH1    0  -0.162  45.3265  -7.6035  67.9798
 41H  CB   C  CH1    0  -0.340  45.3003  -8.5111  66.7367
 41H  CG   C  CR6    0   0.214  45.8810  -7.8111  65.5330
 41H  CD1  C  CR16   0  -0.317  45.2393  -6.7145  64.9566
 41H  CD2  C  CR16   0  -0.341  47.0708  -8.2483  64.9588
 41H  CE1  C  CR16   0  -0.239  45.7718  -6.0756  63.8458
 41H  CE2  C  CR16   0  -0.239  47.6090  -7.6153  63.8448
 41H  CZ   C  CR16   0  -0.278  46.9612  -6.5239  63.2835
 41H  CW   C  CH3    0  -0.657  43.8980  -9.0422  66.4356
 41H  H1   H  HNH2   0   0.335  46.6977  -6.4940  68.9803
 41H  H2   H  HNH2   0   0.322  47.2102  -7.9666  68.5892
 41H  H4   H  HCH1   0   0.198  44.7290  -6.7119  67.7605
 41H  H5   H  HCH1   0   0.226  45.9404  -9.3722  66.9601
 41H  H6   H  HCR6   0   0.241  44.3113  -6.3500  65.3824
 41H  H7   H  HCR6   0   0.240  47.5863  -9.1001  65.3880
 41H  H8   H  HCR6   0   0.246  45.2563  -5.2250  63.4175
 41H  H9   H  HCR6   0   0.246  48.5359  -7.9751  63.4160
 41H  H10  H  HCR6   0   0.246  47.3760  -6.0269  62.4158
 41H  H11  H  HCH3   0   0.233  43.5319  -9.6831  67.2371
 41H  H12  H  HCH3   0   0.217  43.1785  -8.2319  66.3055
 41H  H13  H  HCH3   0   0.227  43.8982  -9.6340  65.5197
 41H  O1   O  OC    -1  -0.610  45.3818  -9.2767  69.6629

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
 41H  CZ   CE1  aromatic  1.390  0.020  1.390
 41H  CZ   CE2  aromatic  1.388  0.020  1.388
 41H  CE1  CD1  aromatic  1.388  0.020  1.388
 41H  CE2  CD2  aromatic  1.390  0.020  1.390
 41H  CD1  CG   aromatic  1.395  0.020  1.395
 41H  CD2  CG   aromatic  1.392  0.020  1.392
 41H  CG   CB   single    1.509  0.020  1.509
 41H  CW   CB   single    1.529  0.020  1.529
 41H  CB   CA   single    1.530  0.020  1.530
 41H  CA   N    single    1.458  0.019  1.458
 41H  CA   C    single    1.525  0.021  1.525
 41H  O    C    deloc     1.231  0.020  1.231
 41H  C    O1   deloc     1.250  0.020  1.250
 41H  N    H1   single    0.890  0.020  1.040
 41H  N    H2   single    0.890  0.020  1.040
 41H  CA   H4   single    0.970  0.020  1.090
 41H  CB   H5   single    0.970  0.020  1.090
 41H  CD1  H6   single    0.930  0.020  1.080
 41H  CD2  H7   single    0.930  0.020  1.080
 41H  CE1  H8   single    0.930  0.020  1.080
 41H  CE2  H9   single    0.930  0.020  1.080
 41H  CZ   H10  single    0.930  0.020  1.080
 41H  CW   H11  single    0.970  0.020  1.090
 41H  CW   H12  single    0.970  0.020  1.090
 41H  CW   H13  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
 41H  H2   N    H1   104.86  3.000
 41H  H2   N    CA   107.45  3.000
 41H  H1   N    CA   108.76  3.000
 41H  O1   C    CA   115.65  3.000
 41H  O1   C    O    126.80  3.000
 41H  CA   C    O    120.80  1.700
 41H  H4   CA   CB   108.00  3.000
 41H  H4   CA   C    108.95  3.000
 41H  CB   CA   C    110.10  1.900
 41H  H4   CA   N    107.71  3.000
 41H  C    CA   N    111.00  2.800
 41H  CB   CA   N    110.50  1.700
 41H  H5   CB   CW   107.62  3.000
 41H  H5   CB   CG   107.60  3.000
 41H  CW   CB   CG   110.92  3.000
 41H  H5   CB   CA   106.78  3.000
 41H  CW   CB   CA   112.29  3.000
 41H  CG   CB   CA   111.36  3.000
 41H  CD2  CG   CD1  118.02  3.000
 41H  CD2  CG   CB   120.83  3.000
 41H  CD1  CG   CB   121.15  3.000
 41H  H6   CD1  CE1  119.21  3.000
 41H  H6   CD1  CG   119.72  3.000
 41H  CE1  CD1  CG   121.07  3.000
 41H  H7   CD2  CE2  119.41  3.000
 41H  H7   CD2  CG   119.34  3.000
 41H  CE2  CD2  CG   121.25  3.000
 41H  H8   CE1  CZ   120.05  3.000
 41H  H8   CE1  CD1  119.71  3.000
 41H  CZ   CE1  CD1  120.24  3.000
 41H  H9   CE2  CZ   120.05  3.000
 41H  H9   CE2  CD2  119.84  3.000
 41H  CZ   CE2  CD2  120.11  3.000
 41H  H10  CZ   CE2  120.42  3.000
 41H  H10  CZ   CE1  120.27  3.000
 41H  CE2  CZ   CE1  119.31  3.000
 41H  H13  CW   H12  107.63  3.000
 41H  H13  CW   H11  107.38  3.000
 41H  H12  CW   H11  107.63  3.000
 41H  H13  CW   CB   110.71  3.000
 41H  H12  CW   CB   111.72  3.000
 41H  H11  CW   CB   111.57  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
 41H  CONST_01  CZ   CE1  CD1  CG     0.00  0.0  0
 41H  CONST_02  CZ   CE2  CD2  CG     0.00  0.0  0
 41H  CONST_03  CE2  CZ   CE1  CD1    0.00  0.0  0
 41H  CONST_04  CE2  CD2  CG   CD1    0.00  0.0  0
 41H  CONST_05  CE1  CZ   CE2  CD2    0.00  0.0  0
 41H  CONST_06  CE1  CD1  CG   CD2    0.00  0.0  0
 41H  CONST_07  CE1  CD1  CG   CB   180.00  0.0  0
 41H  CONST_08  CE2  CD2  CG   CB   180.00  0.0  0
 41H  CONST_09  H8   CE1  CD1  CG   180.00  0.0  0
 41H  CONST_10  H9   CE2  CD2  CG   180.00  0.0  0
 41H  CONST_11  H10  CZ   CE1  CD1  180.00  0.0  0
 41H  CONST_12  H7   CD2  CG   CD1  180.00  0.0  0
 41H  CONST_13  H6   CD1  CG   CD2  180.00  0.0  0

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
 41H  chir_01  CA  CB  N   C   positiv
 41H  chir_02  CB  CA  CW  CG  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
 41H  plan-1  CB   0.020
 41H  plan-1  CG   0.020
 41H  plan-1  CD1  0.020
 41H  plan-1  CD2  0.020
 41H  plan-1  CE1  0.020
 41H  plan-1  CE2  0.020
 41H  plan-1  CZ   0.020
 41H  plan-1  H6   0.020
 41H  plan-1  H7   0.020
 41H  plan-1  H8   0.020
 41H  plan-1  H9   0.020
 41H  plan-1  H10  0.020
 41H  plan-2  C    0.020
 41H  plan-2  O    0.020
 41H  plan-2  CA   0.020
 41H  plan-2  O1   0.020

