# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:37:17 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: 3-pyridin-3-yl-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cccnc1)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
 1MH  1MH  '3-pyridin-3-yl-L-alanine '  L-peptide  21  12  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_1MH
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
 1MH  N    N  NH2    0  -0.807  60.4148  80.8447  155.8419
 1MH  CA   C  CH1    0  -0.155  60.6558  79.4151  155.6666
 1MH  C    C  C      0   0.397  59.3140  78.6376  155.6841
 1MH  O    O  O      0  -0.603  59.0530  77.9574  154.6729
 1MH  CB   C  CH2    0  -0.511  61.5676  78.9445  156.8054
 1MH  C6   C  CR6    0   0.027  61.9250  77.4927  156.7018
 1MH  C7   C  CR16   0  -0.109  63.0427  77.0791  155.9813
 1MH  N8   N  N      0  -0.400  63.4068  75.8127  155.8217
 1MH  C9   C  CR16   0  -0.078  62.6550  74.8766  156.3897
 1MH  C10  C  CR16   0  -0.320  61.5214  75.1675  157.1335
 1MH  C11  C  CR16   0  -0.184  61.1532  76.4949  157.2881
 1MH  O1   O  OC    -1  -0.605  58.6156  78.7553  156.7108
 1MH  H1   H  HNH2   0   0.335  61.2888  81.3421  155.7159
 1MH  H2   H  HNH2   0   0.338  59.8088  81.1800  155.1027
 1MH  H4   H  HCH1   0   0.179  61.1630  79.1881  154.7173
 1MH  H5   H  HCH2   0   0.236  62.4839  79.5435  156.7934
 1MH  H6   H  HCH2   0   0.235  61.0694  79.1450  157.7558
 1MH  H7   H  HCR6   0   0.249  63.6792  77.8249  155.5126
 1MH  H8   H  HCR6   0   0.256  62.9698  73.8480  156.2495
 1MH  H9   H  HCR6   0   0.264  60.9431  74.3703  157.5808
 1MH  H10  H  HCR6   0   0.258  60.2696  76.7590  157.8556

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
 1MH  O    C    deloc     1.231  0.020  1.231
 1MH  C    CA   single    1.525  0.021  1.525
 1MH  CA   N    single    1.458  0.019  1.458
 1MH  CA   CB   single    1.521  0.033  1.521
 1MH  N8   C7   aromatic  1.327  0.020  1.327
 1MH  N8   C9   aromatic  1.328  0.020  1.328
 1MH  C7   C6   aromatic  1.393  0.020  1.393
 1MH  C9   C10  aromatic  1.387  0.020  1.387
 1MH  C6   CB   single    1.499  0.020  1.499
 1MH  C6   C11  aromatic  1.391  0.020  1.391
 1MH  C10  C11  aromatic  1.386  0.020  1.386
 1MH  C    O1   deloc     1.247  0.020  1.247
 1MH  N    H1   single    0.890  0.020  1.040
 1MH  N    H2   single    0.890  0.020  1.040
 1MH  CA   H4   single    0.970  0.020  1.090
 1MH  CB   H5   single    0.970  0.020  1.090
 1MH  CB   H6   single    0.970  0.020  1.090
 1MH  C7   H7   single    0.930  0.020  1.080
 1MH  C9   H8   single    0.930  0.020  1.080
 1MH  C10  H9   single    0.930  0.020  1.080
 1MH  C11  H10  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
 1MH  H2   N    H1   105.24  3.000
 1MH  H2   N    CA   109.58  3.000
 1MH  H1   N    CA   108.86  3.000
 1MH  H4   CA   CB   107.67  3.000
 1MH  H4   CA   C    107.77  3.000
 1MH  CB   CA   C    110.50  1.500
 1MH  H4   CA   N    112.44  3.000
 1MH  CB   CA   N    110.40  1.500
 1MH  C    CA   N    111.00  2.800
 1MH  O1   C    O    127.02  3.000
 1MH  O1   C    CA   116.51  3.000
 1MH  O    C    CA   120.80  1.700
 1MH  H6   CB   H5   106.92  3.000
 1MH  H6   CB   C6   110.30  3.000
 1MH  H5   CB   C6   109.25  3.000
 1MH  H6   CB   CA   108.60  3.000
 1MH  H5   CB   CA   108.77  3.000
 1MH  C6   CB   CA   112.82  3.000
 1MH  C11  C6   C7   116.77  3.000
 1MH  C11  C6   CB   122.23  3.000
 1MH  C7   C6   CB   120.99  3.000
 1MH  H7   C7   N8   116.25  3.000
 1MH  H7   C7   C6   119.30  3.000
 1MH  N8   C7   C6   124.45  3.000
 1MH  C9   N8   C7   117.76  3.000
 1MH  H8   C9   C10  120.36  3.000
 1MH  H8   C9   N8   116.66  3.000
 1MH  C10  C9   N8   122.97  3.000
 1MH  H9   C10  C11  121.17  3.000
 1MH  H9   C10  C9   120.28  3.000
 1MH  C11  C10  C9   118.55  3.000
 1MH  H10  C11  C10  120.58  3.000
 1MH  H10  C11  C6   119.91  3.000
 1MH  C10  C11  C6   119.50  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
 1MH  CONST_01  C9   N8   C7   C6    0.00   0.0  0
 1MH  CONST_02  C9   C10  C11  C6    0.00   0.0  0
 1MH  CONST_03  C10  C9   N8   C7    0.00   0.0  0
 1MH  CONST_04  C10  C11  C6   C7    0.00   0.0  0
 1MH  CONST_05  C11  C6   C7   N8    0.00   0.0  0
 1MH  CONST_06  C11  C10  C9   N8    0.00   0.0  0
 1MH  CONST_07  N8   C7   C6   CB  180.00   0.0  0
 1MH  CONST_08  C10  C11  C6   CB  180.00   0.0  0
 1MH  CONST_09  H9   C10  C11  C6  180.00   0.0  0
 1MH  CONST_10  H8   C9   N8   C7  180.00   0.0  0
 1MH  CONST_11  H10  C11  C6   C7  180.00   0.0  0
 1MH  CONST_12  H7   C7   N8   C9  180.00   0.0  0
 1MH  Var_01    C7   C6   CB   CA   88.88  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
 1MH  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
 1MH  plan-1  CB   0.020
 1MH  plan-1  C6   0.020
 1MH  plan-1  C7   0.020
 1MH  plan-1  N8   0.020
 1MH  plan-1  C9   0.020
 1MH  plan-1  C10  0.020
 1MH  plan-1  C11  0.020
 1MH  plan-1  H7   0.020
 1MH  plan-1  H8   0.020
 1MH  plan-1  H9   0.020
 1MH  plan-1  H10  0.020
 1MH  plan-2  CA   0.020
 1MH  plan-2  C    0.020
 1MH  plan-2  O    0.020
 1MH  plan-2  O1   0.020

