# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 09:36:47 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: (2S)-1-(1,3-benzodioxol-5-yl)-N-methylpropan-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H](C)Cc1ccc2OCOc2c1
#
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
 B41  B41  (2S)-1-(1,3-benzodioxol-5-yl)-N-methylpropan-2-amine  ligand  29  14  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B41
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
 B41  O1   O  O     0  -0.490  -2.5687  -1.3178  -0.6831
 B41  O2   O  O     0  -0.489  -3.5048   0.3374   0.5817
 B41  N    N  NH1   0  -0.572   2.5529  -1.2012   0.1698
 B41  CA   C  CH1   0  -0.072   2.8294   0.2225   0.1265
 B41  C    C  CH3   0  -0.674   4.2788   0.5746  -0.2146
 B41  CB   C  CH2   0  -0.516   1.8792   0.9038  -0.8673
 B41  CG   C  CR6   0   0.145   0.4321   0.8055  -0.4777
 B41  CD1  C  CR16  0  -0.386  -0.3330  -0.3081  -0.8619
 B41  CD2  C  CR16  0  -0.332  -0.1513   1.8068   0.2897
 B41  CE1  C  CR56  0   0.304  -1.6433  -0.3486  -0.4574
 B41  CE2  C  CR16  0  -0.331  -1.4890   1.7527   0.7028
 B41  CZ   C  CR56  0   0.278  -2.2115   0.6545   0.3105
 B41  CT   C  CH2   0   0.068  -3.8066  -0.7879  -0.2308
 B41  HN   H  HNH1  0   0.335   2.8219  -1.6244  -0.7109
 B41  HA   H  HCH1  0   0.221   2.6046   0.6182   1.1243
 B41  H    H  HCH3  0   0.215   4.5296   0.2369  -1.2231
 B41  HB   H  HCH3  0   0.224   4.4414   1.6528  -0.1751
 B41  HC   H  HCH3  0   0.232   4.9831   0.1129   0.4784
 B41  HBA  H  HCH2  0   0.242   2.1623   1.9560  -0.9489
 B41  HBB  H  HCH2  0   0.236   2.0376   0.4677  -1.8595
 B41  HD1  H  HCR6  0   0.255   0.0977  -1.1016  -1.4576
 B41  HD2  H  HCR6  0   0.246   0.4440   2.6648   0.5784
 B41  HE2  H  HCR6  0   0.267  -1.9259   2.5422   1.2993
 B41  HM   H  HCH3  0   0.219   2.8030  -1.5274   2.2143
 B41  HMA  H  HCH3  0   0.230   2.9162  -2.9666   1.2124
 B41  HMB  H  HCH3  0   0.193   4.2763  -1.8494   1.3001
 B41  HT   H  HCH2  0   0.228  -4.4129  -0.4745  -1.0885
 B41  HTA  H  HCH2  0   0.244  -4.3371  -1.5370   0.3565
 B41  CM   C  CH3   0  -0.518   3.1806  -1.9102   1.2640

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
 B41  O1   CT   single    1.420  0.020  1.420
 B41  O1   CE1  single    1.359  0.020  1.359
 B41  CT   O2   single    1.420  0.020  1.420
 B41  O2   CZ   single    1.359  0.020  1.359
 B41  CM   N    single    1.447  0.020  1.447
 B41  N    CA   single    1.451  0.020  1.451
 B41  N    HN   single    0.890  0.020  1.040
 B41  C    CA   single    1.530  0.020  1.530
 B41  CA   CB   single    1.534  0.020  1.534
 B41  CA   HA   single    0.970  0.020  1.090
 B41  C    H    single    0.970  0.020  1.090
 B41  C    HB   single    0.970  0.020  1.090
 B41  C    HC   single    0.970  0.020  1.090
 B41  CB   CG   single    1.502  0.020  1.502
 B41  CB   HBA  single    0.970  0.020  1.090
 B41  CB   HBB  single    0.970  0.020  1.090
 B41  CD1  CG   aromatic  1.405  0.020  1.405
 B41  CG   CD2  aromatic  1.390  0.020  1.390
 B41  CD1  CE1  aromatic  1.372  0.020  1.372
 B41  CD1  HD1  single    0.930  0.020  1.080
 B41  CD2  CE2  aromatic  1.401  0.020  1.401
 B41  CD2  HD2  single    0.930  0.020  1.080
 B41  CE1  CZ   aromatic  1.385  0.020  1.385
 B41  CZ   CE2  aromatic  1.372  0.020  1.372
 B41  CE2  HE2  single    0.930  0.020  1.080
 B41  CM   HM   single    0.970  0.020  1.090
 B41  CM   HMA  single    0.970  0.020  1.090
 B41  CM   HMB  single    0.970  0.020  1.090
 B41  CT   HT   single    0.970  0.020  1.090
 B41  CT   HTA  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
 B41  CT   O1   CE1  105.93  3.000
 B41  CT   O2   CZ   105.84  3.000
 B41  HN   N    CM   109.72  3.000
 B41  HN   N    CA   109.46  3.000
 B41  CM   N    CA   114.88  3.000
 B41  HA   CA   CB   107.59  3.000
 B41  HA   CA   C    108.30  3.000
 B41  CB   CA   C    109.88  3.000
 B41  HA   CA   N    106.72  3.000
 B41  CB   CA   N    109.70  3.000
 B41  C    CA   N    114.39  3.000
 B41  HC   C    HB   107.40  3.000
 B41  HC   C    H    107.91  3.000
 B41  HB   C    H    107.73  3.000
 B41  HC   C    CA   111.88  3.000
 B41  HB   C    CA   111.13  3.000
 B41  H    C    CA   110.61  3.000
 B41  HBB  CB   HBA  106.16  3.000
 B41  HBB  CB   CG   110.38  3.000
 B41  HBA  CB   CG   109.39  3.000
 B41  HBB  CB   CA   108.68  3.000
 B41  HBA  CB   CA   108.39  3.000
 B41  CG   CB   CA   113.55  3.000
 B41  CD2  CG   CD1  119.57  3.000
 B41  CD2  CG   CB   120.03  3.000
 B41  CD1  CG   CB   120.38  3.000
 B41  HD1  CD1  CE1  121.40  3.000
 B41  HD1  CD1  CG   121.02  3.000
 B41  CE1  CD1  CG   117.58  3.000
 B41  HD2  CD2  CE2  118.46  3.000
 B41  HD2  CD2  CG   119.14  3.000
 B41  CE2  CD2  CG   122.39  3.000
 B41  CZ   CE1  CD1  122.27  3.000
 B41  CZ   CE1  O1   109.22  3.000
 B41  CD1  CE1  O1   128.50  3.000
 B41  HE2  CE2  CZ   121.95  3.000
 B41  HE2  CE2  CD2  121.34  3.000
 B41  CZ   CE2  CD2  116.71  3.000
 B41  CE2  CZ   CE1  121.48  3.000
 B41  CE2  CZ   O2   129.12  3.000
 B41  CE1  CZ   O2   109.39  3.000
 B41  HTA  CT   HT   110.42  3.000
 B41  HTA  CT   O2   109.87  3.000
 B41  HT   CT   O2   109.79  3.000
 B41  HTA  CT   O1   109.84  3.000
 B41  HT   CT   O1   109.85  3.000
 B41  O2   CT   O1   107.01  3.000
 B41  HMB  CM   HMA  107.29  3.000
 B41  HMB  CM   HM   107.28  3.000
 B41  HMA  CM   HM   107.28  3.000
 B41  HMB  CM   N    115.50  3.000
 B41  HMA  CM   N    109.50  3.000
 B41  HM   CM   N    109.65  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
 B41  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 B41  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 B41  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 B41  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 B41  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 B41  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 B41  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 B41  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 B41  CONST_09  HD1  CD1  CE1  O1     0.00   0.0  0
 B41  CONST_10  HE2  CE2  CZ   O2     0.00   0.0  0
 B41  CONST_11  HD2  CD2  CG   CD1  180.00   0.0  0
 B41  Var_01    HT   CT   O1   CE1  103.39  30.0  1
 B41  Var_02    CD1  CG   CB   CA   -87.12  30.0  2
 B41  Var_03    HM   CM   N    CA    62.57  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
 B41  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
 B41  plan-1  O1   0.020
 B41  plan-1  O2   0.020
 B41  plan-1  CB   0.020
 B41  plan-1  CG   0.020
 B41  plan-1  CD1  0.020
 B41  plan-1  CD2  0.020
 B41  plan-1  CE1  0.020
 B41  plan-1  CE2  0.020
 B41  plan-1  CZ   0.020
 B41  plan-1  HD1  0.020
 B41  plan-1  HD2  0.020
 B41  plan-1  HE2  0.020

