# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:05:23 2022
#   Inital geometry file: a 65 line input string
#   Ligand name: (2S)-N-methyl-1-phenylpropan-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H](C)Cc1ccccc1
#
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
 B40  B40  (2S)-N-methyl-1-phenylpropan-2-amine  ligand  26  11  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B40
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
 B40  N    N  NH1   0  -0.573  -1.8627  -1.0206   0.0580
 B40  CA   C  CH1   0  -0.073  -1.8104   0.4102  -0.1779
 B40  C    C  CH3   0  -0.673  -3.1389   1.1372   0.0377
 B40  CB   C  CH2   0  -0.518  -0.7208   1.0336   0.7051
 B40  CG   C  CR6   0   0.166   0.6568   0.5274   0.3909
 B40  CD1  C  CR16  0  -0.316   1.4274   1.1428  -0.5938
 B40  CD2  C  CR16  0  -0.307   1.1874  -0.5812   1.0473
 B40  CE1  C  CR16  0  -0.242   2.6921   0.6666  -0.9155
 B40  CE2  C  CR16  0  -0.246   2.4531  -1.0587   0.7348
 B40  CZ   C  CR16  0  -0.276   3.2099  -0.4374  -0.2512
 B40  CM   C  CH3   0  -0.516  -2.6522  -1.7704  -0.8953
 B40  HN   H  HNH1  0   0.335  -2.2038  -1.1944   0.9961
 B40  HA   H  HCH1  0   0.222  -1.5117   0.5486  -1.2239
 B40  H    H  HCH3  0   0.225  -3.0555   2.1943  -0.2189
 B40  HB   H  HCH3  0   0.232  -3.9366   0.7151  -0.5748
 B40  HC   H  HCH3  0   0.215  -3.4516   1.0712   1.0830
 B40  HBA  H  HCH2  0   0.242  -0.7524   2.1189   0.5788
 B40  HBB  H  HCH2  0   0.236  -0.9638   0.8364   1.7547
 B40  HD1  H  HCR6  0   0.242   1.0351   2.0094  -1.1144
 B40  HD2  H  HCR6  0   0.238   0.6037  -1.0712   1.8167
 B40  HE1  H  HCR6  0   0.250   3.2757   1.1613  -1.6816
 B40  HE2  H  HCR6  0   0.249   2.8492  -1.9185   1.2606
 B40  HZ   H  HCR6  0   0.251   4.1975  -0.8075  -0.4953
 B40  HM   H  HCH3  0   0.192  -3.7050  -1.4701  -0.9762
 B40  HMA  H  HCH3  0   0.218  -2.2116  -1.6806  -1.8906
 B40  HMB  H  HCH3  0   0.230  -2.6357  -2.8275  -0.6284

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
 B40  N    CM   single    1.447  0.020  1.447
 B40  N    CA   single    1.451  0.020  1.451
 B40  N    HN   single    0.890  0.020  1.040
 B40  C    CA   single    1.530  0.020  1.530
 B40  CA   CB   single    1.535  0.020  1.535
 B40  CA   HA   single    0.970  0.020  1.090
 B40  C    H    single    0.970  0.020  1.090
 B40  C    HB   single    0.970  0.020  1.090
 B40  C    HC   single    0.970  0.020  1.090
 B40  CB   CG   single    1.501  0.020  1.501
 B40  CB   HBA  single    0.970  0.020  1.090
 B40  CB   HBB  single    0.970  0.020  1.090
 B40  CD2  CG   aromatic  1.393  0.020  1.393
 B40  CG   CD1  aromatic  1.394  0.020  1.394
 B40  CD1  CE1  aromatic  1.389  0.020  1.389
 B40  CD1  HD1  single    0.930  0.020  1.080
 B40  CD2  CE2  aromatic  1.388  0.020  1.388
 B40  CD2  HD2  single    0.930  0.020  1.080
 B40  CZ   CE1  aromatic  1.389  0.020  1.389
 B40  CE1  HE1  single    0.930  0.020  1.080
 B40  CE2  CZ   aromatic  1.390  0.020  1.390
 B40  CE2  HE2  single    0.930  0.020  1.080
 B40  CZ   HZ   single    0.930  0.020  1.080
 B40  CM   HM   single    0.970  0.020  1.090
 B40  CM   HMA  single    0.970  0.020  1.090
 B40  CM   HMB  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
 B40  HN   N    CM   109.72  3.000
 B40  HN   N    CA   109.38  3.000
 B40  CM   N    CA   115.05  3.000
 B40  HA   CA   CB   107.70  3.000
 B40  HA   CA   C    108.12  3.000
 B40  CB   CA   C    110.02  3.000
 B40  HA   CA   N    106.82  3.000
 B40  CB   CA   N    109.42  3.000
 B40  C    CA   N    114.49  3.000
 B40  HC   C    HB   107.72  3.000
 B40  HC   C    H    107.78  3.000
 B40  HB   C    H    107.39  3.000
 B40  HC   C    CA   110.77  3.000
 B40  HB   C    CA   111.84  3.000
 B40  H    C    CA   111.16  3.000
 B40  HBB  CB   HBA  106.44  3.000
 B40  HBB  CB   CG   110.09  3.000
 B40  HBA  CB   CG   109.70  3.000
 B40  HBB  CB   CA   108.71  3.000
 B40  HBA  CB   CA   108.44  3.000
 B40  CG   CB   CA   113.22  3.000
 B40  CD2  CG   CD1  118.27  3.000
 B40  CD1  CG   CB   120.43  3.000
 B40  CD2  CG   CB   121.28  3.000
 B40  HD1  CD1  CE1  119.48  3.000
 B40  HD1  CD1  CG   119.48  3.000
 B40  CE1  CD1  CG   121.05  3.000
 B40  HD2  CD2  CE2  119.72  3.000
 B40  HD2  CD2  CG   119.30  3.000
 B40  CE2  CD2  CG   120.98  3.000
 B40  HE1  CE1  CZ   120.05  3.000
 B40  HE1  CE1  CD1  119.87  3.000
 B40  CZ   CE1  CD1  120.08  3.000
 B40  HE2  CE2  CZ   120.02  3.000
 B40  HE2  CE2  CD2  119.82  3.000
 B40  CZ   CE2  CD2  120.17  3.000
 B40  HZ   CZ   CE2  120.27  3.000
 B40  HZ   CZ   CE1  120.27  3.000
 B40  CE2  CZ   CE1  119.46  3.000
 B40  HMB  CM   HMA  107.25  3.000
 B40  HMB  CM   HM   107.32  3.000
 B40  HMA  CM   HM   107.29  3.000
 B40  HMB  CM   N    109.44  3.000
 B40  HMA  CM   N    109.74  3.000
 B40  HM   CM   N    115.47  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
 B40  CONST_01  CZ   CE2  CD2  CG     0.00   0.0  0
 B40  CONST_02  CZ   CE1  CD1  CG     0.00   0.0  0
 B40  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 B40  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 B40  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 B40  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 B40  CONST_07  CE2  CD2  CG   CB   180.00   0.0  0
 B40  CONST_08  CE1  CD1  CG   CB   180.00   0.0  0
 B40  CONST_09  HE2  CE2  CD2  CG   180.00   0.0  0
 B40  CONST_10  HE1  CE1  CD1  CG   180.00   0.0  0
 B40  CONST_11  HD2  CD2  CG   CD1  180.00   0.0  0
 B40  CONST_12  HZ   CZ   CE1  CD1  180.00   0.0  0
 B40  CONST_13  HD1  CD1  CG   CD2  180.00   0.0  0
 B40  Var_01    CD2  CG   CB   CA   -90.99  30.0  2
 B40  Var_02    HM   CM   N    CA   -58.35  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
 B40  chir_01  CA  N  C  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
 B40  plan-1  CB   0.020
 B40  plan-1  CG   0.020
 B40  plan-1  CD1  0.020
 B40  plan-1  CD2  0.020
 B40  plan-1  CE1  0.020
 B40  plan-1  CE2  0.020
 B40  plan-1  CZ   0.020
 B40  plan-1  HD1  0.020
 B40  plan-1  HD2  0.020
 B40  plan-1  HE1  0.020
 B40  plan-1  HE2  0.020
 B40  plan-1  HZ   0.020

