# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 06:38:43 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (1R)-N-methyl-2,3-dihydro-1H-inden-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H]1CCc2ccccc12
#
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
 RM1  RM1  (1R)-N-methyl-2,3-dihydro-1H-inden-1-amine  ligand  24  11  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RM1
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
 RM1  C10   C  CH3   0  -0.525  -2.9009   1.5747  -0.2418
 RM1  N10   N  NH1   0  -0.593  -2.3785   0.4069   0.4392
 RM1  C9    C  CR15  0  -0.122  -1.3465  -0.3234  -0.2618
 RM1  C8    C  CR56  0   0.087   0.0890   0.1620  -0.1466
 RM1  C7    C  CR16  0  -0.330   0.5827   1.4569  -0.0838
 RM1  C6    C  CR16  0  -0.257   1.9550   1.6553   0.0403
 RM1  C5    C  CR16  0  -0.262   2.8218   0.5695   0.0944
 RM1  C4    C  CR16  0  -0.328   2.3265  -0.7294   0.0313
 RM1  C3    C  CR56  0   0.091   0.9594  -0.9243  -0.0857
 RM1  C2    C  CH2   0  -0.498   0.1912  -2.2160  -0.1537
 RM1  C1    C  CH2   0  -0.459  -1.2276  -1.7782   0.2246
 RM1  H101  H  HCH3  0   0.225  -3.3432   1.2755  -1.1938
 RM1  H102  H  HCH3  0   0.232  -3.6954   2.0171   0.3595
 RM1  H103  H  HCH3  0   0.201  -2.1725   2.3664  -0.4557
 RM1  H10   H  HNH1  0   0.342  -2.0581   0.6535   1.3674
 RM1  H9    H  HCR5  0   0.243  -1.6249  -0.3311  -1.3237
 RM1  H7    H  HCR6  0   0.247  -0.0819   2.3105  -0.1223
 RM1  H6    H  HCR6  0   0.250   2.3493   2.6621   0.0977
 RM1  H5    H  HCR6  0   0.250   3.8872   0.7354   0.1927
 RM1  H4    H  HCR6  0   0.245   3.0035  -1.5737   0.0851
 RM1  H2C1  H  HCH2  0   0.248   0.5943  -2.9906   0.5002
 RM1  H2C2  H  HCH2  0   0.245   0.2143  -2.6164  -1.1724
 RM1  H1C1  H  HCH2  0   0.231  -1.3354  -1.7911   1.3134
 RM1  H1C2  H  HCH2  0   0.237  -2.0059  -2.4180  -0.1914

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
 RM1  C10  N10   single    1.449  0.020  1.449
 RM1  C10  H101  single    0.970  0.020  1.090
 RM1  C10  H102  single    0.970  0.020  1.090
 RM1  C10  H103  single    0.970  0.020  1.090
 RM1  N10  C9    single    1.446  0.020  1.446
 RM1  N10  H10   single    0.890  0.020  1.040
 RM1  C9   C8    single    1.520  0.020  1.520
 RM1  C9   C1    single    1.538  0.020  1.538
 RM1  C9   H9    single    0.970  0.020  1.090
 RM1  C8   C7    aromatic  1.387  0.020  1.387
 RM1  C8   C3    aromatic  1.393  0.020  1.393
 RM1  C7   C6    aromatic  1.392  0.020  1.392
 RM1  C7   H7    single    0.930  0.020  1.080
 RM1  C6   C5    aromatic  1.390  0.020  1.390
 RM1  C6   H6    single    0.930  0.020  1.080
 RM1  C5   C4    aromatic  1.392  0.020  1.392
 RM1  C5   H5    single    0.930  0.020  1.080
 RM1  C4   C3    aromatic  1.386  0.020  1.386
 RM1  C4   H4    single    0.930  0.020  1.080
 RM1  C3   C2    single    1.504  0.020  1.504
 RM1  C2   C1    single    1.532  0.020  1.532
 RM1  C2   H2C1  single    0.970  0.020  1.090
 RM1  C2   H2C2  single    0.970  0.020  1.090
 RM1  C1   H1C1  single    0.970  0.020  1.090
 RM1  C1   H1C2  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
 RM1  H103  C10  H102  107.38  3.000
 RM1  H103  C10  H101  107.27  3.000
 RM1  H102  C10  H101  107.28  3.000
 RM1  H103  C10  N10   115.71  3.000
 RM1  H102  C10  N10   109.30  3.000
 RM1  H101  C10  N10   109.57  3.000
 RM1  H10   N10  C9    109.98  3.000
 RM1  H10   N10  C10   110.39  3.000
 RM1  C9    N10  C10   115.88  3.000
 RM1  H9    C9   C1    108.59  3.000
 RM1  H9    C9   C8    108.37  3.000
 RM1  C1    C9   C8    101.84  3.000
 RM1  H9    C9   N10   106.95  3.000
 RM1  C1    C9   N10   112.30  3.000
 RM1  C8    C9   N10   118.44  3.000
 RM1  C3    C8   C7    120.23  3.000
 RM1  C3    C8   C9    110.14  3.000
 RM1  C7    C8   C9    129.63  3.000
 RM1  H7    C7   C6    119.73  3.000
 RM1  H7    C7   C8    121.06  3.000
 RM1  C6    C7   C8    119.21  3.000
 RM1  H6    C6   C5    119.80  3.000
 RM1  H6    C6   C7    119.76  3.000
 RM1  C5    C6   C7    120.44  3.000
 RM1  H5    C5   C4    119.82  3.000
 RM1  H5    C5   C6    119.83  3.000
 RM1  C4    C5   C6    120.35  3.000
 RM1  H4    C4   C3    120.73  3.000
 RM1  H4    C4   C5    120.18  3.000
 RM1  C3    C4   C5    119.09  3.000
 RM1  C2    C3   C4    128.92  3.000
 RM1  C2    C3   C8    110.39  3.000
 RM1  C4    C3   C8    120.68  3.000
 RM1  H2C2  C2   H2C1  106.88  3.000
 RM1  H2C2  C2   C1    110.72  3.000
 RM1  H2C1  C2   C1    113.39  3.000
 RM1  H2C2  C2   C3    110.20  3.000
 RM1  H2C1  C2   C3    113.19  3.000
 RM1  C1    C2   C3    102.49  3.000
 RM1  H1C2  C1   H1C1  107.61  3.000
 RM1  H1C2  C1   C2    113.52  3.000
 RM1  H1C1  C1   C2    109.48  3.000
 RM1  H1C2  C1   C9    112.29  3.000
 RM1  H1C1  C1   C9    108.55  3.000
 RM1  C2    C1   C9    105.29  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
 RM1  CONST_01  C5    C6   C7   C8    0.00   0.0  0
 RM1  CONST_02  C5    C4   C3   C8    0.00   0.0  0
 RM1  CONST_03  C4    C3   C8   C7    0.00   0.0  0
 RM1  CONST_04  C4    C5   C6   C7    0.00   0.0  0
 RM1  CONST_05  C3    C8   C7   C6    0.00   0.0  0
 RM1  CONST_06  C3    C4   C5   C6    0.00   0.0  0
 RM1  CONST_07  H7    C7   C8   C9    0.00   0.0  0
 RM1  CONST_08  H6    C6   C7   C8  180.00   0.0  0
 RM1  CONST_09  H4    C4   C3   C8  180.00   0.0  0
 RM1  CONST_10  H5    C5   C6   C7  180.00   0.0  0
 RM1  Var_01    C3    C2   C1   C9   30.05  30.0  1
 RM1  Var_02    C1    C2   C3   C8  -18.90  30.0  1
 RM1  Var_03    H101  C10  N10  C9   60.43  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
 RM1  chir_01  C9  N10  C8  C1  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
 RM1  plan-1  C9  0.020
 RM1  plan-1  C8  0.020
 RM1  plan-1  C7  0.020
 RM1  plan-1  C6  0.020
 RM1  plan-1  C5  0.020
 RM1  plan-1  C4  0.020
 RM1  plan-1  C3  0.020
 RM1  plan-1  C2  0.020
 RM1  plan-1  H7  0.020
 RM1  plan-1  H6  0.020
 RM1  plan-1  H5  0.020
 RM1  plan-1  H4  0.020

