# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 10:13:34 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: 2,3-dihydro-1H-inden-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1Cc2ccccc2C1
#
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
 XM0  XM0  2,3-dihydro-1H-inden-2-amine  ligand  21  10  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XM0
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
 XM0  C1    C  CR16  0  -0.261  -2.6413   0.7099   0.0442
 XM0  C2    C  CR16  0  -0.261  -2.6369  -0.6805   0.0507
 XM0  C3    C  CR16  0  -0.327  -1.4349  -1.3816   0.0092
 XM0  C4    C  CR56  0   0.088  -0.2431  -0.6758  -0.0382
 XM0  C5    C  CR56  0   0.091  -0.2475   0.7198  -0.0434
 XM0  C6    C  CR16  0  -0.327  -1.4437   1.4182  -0.0036
 XM0  C7    C  CH2   0  -0.496   1.1588   1.2421  -0.1029
 XM0  C8    C  CR15  0  -0.088   1.9916   0.0381   0.3679
 XM0  C9    C  CH2   0  -0.505   1.1684  -1.1845  -0.0976
 XM0  N10   N  NH2   0  -0.798   3.3745   0.1197  -0.0496
 XM0  H1    H  HCR6  0   0.250  -3.5816   1.2452   0.0831
 XM0  H2    H  HCR6  0   0.249  -3.5738  -1.2215   0.0946
 XM0  H6    H  HCR6  0   0.244  -1.4530   2.5018  -0.0021
 XM0  H3    H  HCR6  0   0.244  -1.4367  -2.4651   0.0195
 XM0  H91C  H  HCH2  0   0.246   1.3440  -2.0720   0.5133
 XM0  H92C  H  HCH2  0   0.240   1.4349  -1.4433  -1.1298
 XM0  H71C  H  HCH2  0   0.241   1.4227   1.5005  -1.1360
 XM0  H72C  H  HCH2  0   0.249   1.3245   2.1335   0.5040
 XM0  H8    H  HCR5  0   0.239   1.9803   0.0393   1.4628
 XM0  H101  H  HNH2  0   0.346   3.8949  -0.6604   0.3320
 XM0  H102  H  HNH2  0   0.336   3.4329   0.0228  -1.0572

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
 XM0  C1   C2    aromatic  1.390  0.020  1.390
 XM0  C1   C6    aromatic  1.392  0.020  1.392
 XM0  C2   C3    aromatic  1.392  0.020  1.392
 XM0  C3   C4    aromatic  1.386  0.020  1.386
 XM0  C4   C5    aromatic  1.396  0.020  1.396
 XM0  C4   C9    single    1.501  0.020  1.501
 XM0  C5   C6    aromatic  1.386  0.020  1.386
 XM0  C5   C7    single    1.501  0.020  1.501
 XM0  C7   C8    single    1.538  0.020  1.538
 XM0  C8   C9    single    1.546  0.020  1.546
 XM0  C8   N10   single    1.447  0.020  1.447
 XM0  C1   H1    single    0.930  0.020  1.080
 XM0  C2   H2    single    0.930  0.020  1.080
 XM0  C6   H6    single    0.930  0.020  1.080
 XM0  C3   H3    single    0.930  0.020  1.080
 XM0  C9   H91C  single    0.970  0.020  1.090
 XM0  C9   H92C  single    0.970  0.020  1.090
 XM0  C7   H71C  single    0.970  0.020  1.090
 XM0  C7   H72C  single    0.970  0.020  1.090
 XM0  C8   H8    single    0.970  0.020  1.090
 XM0  N10  H101  single    0.890  0.020  1.040
 XM0  N10  H102  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
 XM0  H1    C1   C6    119.78  3.000
 XM0  H1    C1   C2    119.80  3.000
 XM0  C6    C1   C2    120.41  3.000
 XM0  H2    C2   C3    119.78  3.000
 XM0  H2    C2   C1    119.81  3.000
 XM0  C3    C2   C1    120.41  3.000
 XM0  H3    C3   C4    120.73  3.000
 XM0  H3    C3   C2    120.12  3.000
 XM0  C4    C3   C2    119.15  3.000
 XM0  C9    C4   C5    109.97  3.000
 XM0  C9    C4   C3    129.58  3.000
 XM0  C5    C4   C3    120.44  3.000
 XM0  C7    C5   C6    129.37  3.000
 XM0  C7    C5   C4    110.19  3.000
 XM0  C6    C5   C4    120.44  3.000
 XM0  H6    C6   C5    120.76  3.000
 XM0  H6    C6   C1    120.09  3.000
 XM0  C5    C6   C1    119.15  3.000
 XM0  H72C  C7   H71C  107.15  3.000
 XM0  H72C  C7   C8    112.78  3.000
 XM0  H71C  C7   C8    110.02  3.000
 XM0  H72C  C7   C5    113.85  3.000
 XM0  H71C  C7   C5    110.16  3.000
 XM0  C8    C7   C5    102.87  3.000
 XM0  H8    C8   N10   107.36  3.000
 XM0  H8    C8   C9    107.25  3.000
 XM0  N10   C8   C9    117.83  3.000
 XM0  H8    C8   C7    107.43  3.000
 XM0  N10   C8   C7    112.65  3.000
 XM0  C9    C8   C7    103.81  3.000
 XM0  H92C  C9   H91C  107.19  3.000
 XM0  H92C  C9   C8    109.91  3.000
 XM0  H91C  C9   C8    112.88  3.000
 XM0  H92C  C9   C4    110.22  3.000
 XM0  H91C  C9   C4    113.86  3.000
 XM0  C8    C9   C4    102.76  3.000
 XM0  H102  N10  H101  105.74  3.000
 XM0  H102  N10  C8    109.66  3.000
 XM0  H101  N10  C8    109.82  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
 XM0  CONST_01  C4  C3  C2  C1     0.00   0.0  0
 XM0  CONST_02  C4  C5  C6  C1     0.00   0.0  0
 XM0  CONST_03  C5  C6  C1  C2     0.00   0.0  0
 XM0  CONST_04  C5  C4  C3  C2     0.00   0.0  0
 XM0  CONST_05  C6  C1  C2  C3     0.00   0.0  0
 XM0  CONST_06  C6  C5  C4  C3     0.00   0.0  0
 XM0  CONST_07  H3  C3  C2  C1   180.00   0.0  0
 XM0  CONST_08  H6  C6  C1  C2   180.00   0.0  0
 XM0  CONST_09  H1  C1  C2  C3   180.00   0.0  0
 XM0  CONST_10  H2  C2  C3  C4   180.00   0.0  0
 XM0  Var_01    C8  C9  C4  C3  -160.79  30.0  1
 XM0  Var_02    C8  C7  C5  C4   -19.47  30.0  1

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
 XM0  chir_01  C8  C7  C9  N10  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
 XM0  plan-1  C1  0.020
 XM0  plan-1  C2  0.020
 XM0  plan-1  C3  0.020
 XM0  plan-1  C4  0.020
 XM0  plan-1  C5  0.020
 XM0  plan-1  C6  0.020
 XM0  plan-1  C7  0.020
 XM0  plan-1  C9  0.020
 XM0  plan-1  H1  0.020
 XM0  plan-1  H2  0.020
 XM0  plan-1  H6  0.020
 XM0  plan-1  H3  0.020

