# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 21:46:39 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 1-(1,3-benzodioxol-5-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc2OCOc2c1
#
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
 MR1  MR1  1-(1,3-benzodioxol-5-yl)methanamine  ligand  20  11  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MR1
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
 MR1  C36   C  CR16  0  -0.388  -1.3090   0.4143   1.5629
 MR1  C35   C  CR56  0   0.310  -1.4814   1.0529   2.7633
 MR1  O39   O  O     0  -0.487  -2.5982   1.1282   3.5296
 MR1  C38   C  CH2   0   0.069  -2.1993   1.7382   4.7495
 MR1  O37   O  O     0  -0.487  -0.9200   2.3139   4.5262
 MR1  C34   C  CR56  0   0.285  -0.4613   1.7715   3.3702
 MR1  C33   C  CR16  0  -0.332   0.7809   1.8762   2.7997
 MR1  C32   C  CR16  0  -0.320   0.9684   1.2243   1.5725
 MR1  C31   C  CR6   0   0.088  -0.0440   0.5043   0.9542
 MR1  C30   C  CH2   0  -0.381   0.1823  -0.1394  -0.3938
 MR1  N     N  NH2   0  -0.781  -0.4888   0.5098  -1.5128
 MR1  H36   H  HCR6  0   0.266  -2.1152  -0.1447   1.1034
 MR1  H381  H  HCH2  0   0.231  -2.1345   0.9817   5.5391
 MR1  H382  H  HCH2  0   0.245  -2.9121   2.5157   5.0241
 MR1  H33   H  HCR6  0   0.270   1.5794   2.4365   3.2669
 MR1  H32   H  HCR6  0   0.252   1.9405   1.2823   1.0983
 MR1  H301  H  HCH2  0   0.236   1.2548  -0.1589  -0.5996
 MR1  H302  H  HCH2  0   0.238  -0.1433  -1.1819  -0.3670
 MR1  HN1   H  HNH2  0   0.341  -0.2753   1.4997  -1.5039
 MR1  HN2   H  HNH2  0   0.345  -1.4924   0.4408  -1.3989

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
 MR1  C36  C35   aromatic  1.371  0.020  1.371
 MR1  C36  C31   aromatic  1.407  0.020  1.407
 MR1  C36  H36   single    0.930  0.020  1.080
 MR1  C35  O39   single    1.356  0.020  1.356
 MR1  C35  C34   aromatic  1.388  0.020  1.388
 MR1  O39  C38   single    1.421  0.020  1.421
 MR1  C38  O37   single    1.421  0.020  1.421
 MR1  C38  H381  single    0.970  0.020  1.090
 MR1  C38  H382  single    0.970  0.020  1.090
 MR1  O37  C34   single    1.357  0.020  1.357
 MR1  C34  C33   aromatic  1.371  0.020  1.371
 MR1  C33  C32   aromatic  1.402  0.020  1.402
 MR1  C33  H33   single    0.930  0.020  1.080
 MR1  C32  C31   aromatic  1.388  0.020  1.388
 MR1  C32  H32   single    0.930  0.020  1.080
 MR1  C31  C30   single    1.511  0.020  1.511
 MR1  C30  N     single    1.457  0.020  1.457
 MR1  C30  H301  single    0.970  0.020  1.090
 MR1  C30  H302  single    0.970  0.020  1.090
 MR1  N    HN1   single    0.890  0.020  1.040
 MR1  N    HN2   single    0.890  0.020  1.040

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
 MR1  H36   C36  C31   121.25  3.000
 MR1  H36   C36  C35   121.22  3.000
 MR1  C31   C36  C35   117.53  3.000
 MR1  C34   C35  O39   109.24  3.000
 MR1  C34   C35  C36   122.13  3.000
 MR1  O39   C35  C36   128.62  3.000
 MR1  C38   O39  C35   106.12  3.000
 MR1  H382  C38  H381  110.47  3.000
 MR1  H382  C38  O37   109.84  3.000
 MR1  H381  C38  O37   109.87  3.000
 MR1  H382  C38  O39   109.82  3.000
 MR1  H381  C38  O39   109.82  3.000
 MR1  O37   C38  O39   106.97  3.000
 MR1  C34   O37  C38   106.04  3.000
 MR1  C33   C34  O37   129.08  3.000
 MR1  C33   C34  C35   121.58  3.000
 MR1  O37   C34  C35   109.33  3.000
 MR1  H33   C33  C32   121.34  3.000
 MR1  H33   C33  C34   121.92  3.000
 MR1  C32   C33  C34   116.73  3.000
 MR1  H32   C32  C31   119.17  3.000
 MR1  H32   C32  C33   118.57  3.000
 MR1  C31   C32  C33   122.25  3.000
 MR1  C30   C31  C32   120.62  3.000
 MR1  C30   C31  C36   119.57  3.000
 MR1  C32   C31  C36   119.77  3.000
 MR1  H302  C30  H301  106.27  3.000
 MR1  H302  C30  N     107.86  3.000
 MR1  H301  C30  N     108.38  3.000
 MR1  H302  C30  C31   109.88  3.000
 MR1  H301  C30  C31   108.83  3.000
 MR1  N     C30  C31   115.23  3.000
 MR1  HN2   N    HN1   105.94  3.000
 MR1  HN2   N    C30   109.86  3.000
 MR1  HN1   N    C30   109.37  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
 MR1  CONST_01  C33  C34  C35  C36     0.00   0.0  0
 MR1  CONST_02  C33  C32  C31  C36     0.00   0.0  0
 MR1  CONST_03  C32  C31  C36  C35     0.00   0.0  0
 MR1  CONST_04  C32  C33  C34  C35     0.00   0.0  0
 MR1  CONST_05  C31  C36  C35  C34     0.00   0.0  0
 MR1  CONST_06  C31  C32  C33  C34     0.00   0.0  0
 MR1  CONST_07  C30  C31  C36  C35   180.00   0.0  0
 MR1  CONST_08  C30  C31  C32  C33   180.00   0.0  0
 MR1  CONST_09  H32  C32  C31  C36   180.00   0.0  0
 MR1  CONST_10  H33  C33  C34  C35   180.00   0.0  0
 MR1  CONST_11  H36  C36  C35  O39     0.00   0.0  0
 MR1  Var_01    O37  C38  O39  C35    14.70  30.0  1
 MR1  Var_02    C34  C35  O39  C38    -9.10  30.0  1
 MR1  Var_03    C33  C34  O37  C38  -171.64  30.0  1
 MR1  Var_04    N    C30  C31  C36    70.42  30.0  2
 MR1  Var_05    HN1  N    C30  C31    51.25  30.0  3

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
 MR1  plan-1  C36  0.020
 MR1  plan-1  C35  0.020
 MR1  plan-1  O39  0.020
 MR1  plan-1  O37  0.020
 MR1  plan-1  C34  0.020
 MR1  plan-1  C33  0.020
 MR1  plan-1  C32  0.020
 MR1  plan-1  C31  0.020
 MR1  plan-1  C30  0.020
 MR1  plan-1  H36  0.020
 MR1  plan-1  H33  0.020
 MR1  plan-1  H32  0.020

