# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 18:59:51 2022
#   Inital geometry file: a 73 line input string
#   Ligand name: (1R)-N-(prop-2-en-1-yl)-2,3-dihydro-1H-inden-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C=CCN[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
 RAS  RAS  (1R)-N-(prop-2-en-1-yl)-2,3-dihydro-1H-inden-1-amine  ligand  28  13  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RAS
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
 RAS  N10   N  NH1   0  -0.590  -1.5737   0.7264  -0.2520
 RAS  C11   C  CH2   0  -0.315  -2.5036  -0.0527   0.5441
 RAS  C12   C  C1    0  -0.159  -3.8669   0.0015  -0.0698
 RAS  C13   C  C2    0  -0.501  -4.5681  -1.0629  -0.4381
 RAS  C9    C  CR15  0  -0.120  -0.2711   0.9825   0.3220
 RAS  C1    C  CH2   0  -0.445   0.4153   2.1924  -0.3368
 RAS  C2    C  CH2   0  -0.482   1.9176   1.9803  -0.1238
 RAS  C3    C  CR56  0   0.095   2.0339   0.4823  -0.0633
 RAS  C8    C  CR56  0   0.091   0.7930  -0.0932   0.1981
 RAS  C7    C  CR16  0  -0.308   0.6719  -1.4710   0.3038
 RAS  C4    C  CR16  0  -0.308   3.1602  -0.3089  -0.2253
 RAS  C5    C  CR16  0  -0.242   3.0366  -1.6904  -0.1263
 RAS  C6    C  CR16  0  -0.234   1.7996  -2.2670   0.1362
 RAS  H10   H  HNH1  0   0.328  -1.4765   0.3175  -1.1735
 RAS  H111  H  HCH2  0   0.203  -2.2139  -1.1016   0.6947
 RAS  H112  H  HCH2  0   0.228  -2.5443   0.3988   1.5409
 RAS  H13   H  H     0   0.220  -4.1862  -2.0691  -0.3126
 RAS  H9    H  HCR5  0   0.237  -0.4275   1.2008   1.3863
 RAS  H11   H  HCH2  0   0.224   0.1958   2.1779  -1.4081
 RAS  H12   H  HCH2  0   0.233   0.0494   3.1391   0.0586
 RAS  H21   H  HCH2  0   0.239   2.5282   2.4271  -0.9095
 RAS  H22   H  HCH2  0   0.239   2.2452   2.4227   0.8220
 RAS  H7    H  HCR6  0   0.225  -0.2818  -1.9378   0.5135
 RAS  H4    H  HCR6  0   0.225   4.1244   0.1368  -0.4374
 RAS  H5    H  HCR6  0   0.232   3.9059  -2.3209  -0.2597
 RAS  H6    H  HCR6  0   0.229   1.7124  -3.3430   0.2097
 RAS  H24   H  H     0   0.230  -4.2764   0.9956  -0.2211
 RAS  H23   H  H     0   0.227  -5.5522  -0.9712  -0.8779

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
 RAS  N10  C11   single    1.451  0.020  1.451
 RAS  N10  C9    single    1.446  0.020  1.446
 RAS  N10  H10   single    0.890  0.020  1.040
 RAS  C11  C12   single    1.496  0.020  1.496
 RAS  C11  H111  single    0.970  0.020  1.090
 RAS  C11  H112  single    0.970  0.020  1.090
 RAS  C12  C13   double    1.327  0.020  1.327
 RAS  C13  H13   single    0.930  0.020  1.080
 RAS  C9   C1    single    1.539  0.020  1.539
 RAS  C9   C8    single    1.518  0.020  1.518
 RAS  C9   H9    single    0.970  0.020  1.090
 RAS  C1   C2    single    1.532  0.020  1.532
 RAS  C1   H11   single    0.970  0.020  1.090
 RAS  C1   H12   single    0.970  0.020  1.090
 RAS  C2   C3    single    1.504  0.020  1.504
 RAS  C2   H21   single    0.970  0.020  1.090
 RAS  C2   H22   single    0.970  0.020  1.090
 RAS  C3   C8    aromatic  1.393  0.020  1.393
 RAS  C3   C4    aromatic  1.386  0.020  1.386
 RAS  C8   C7    aromatic  1.387  0.020  1.387
 RAS  C7   C6    aromatic  1.390  0.020  1.390
 RAS  C7   H7    single    0.930  0.020  1.080
 RAS  C4   C5    aromatic  1.391  0.020  1.391
 RAS  C4   H4    single    0.930  0.020  1.080
 RAS  C5   C6    aromatic  1.390  0.020  1.390
 RAS  C5   H5    single    0.930  0.020  1.080
 RAS  C6   H6    single    0.930  0.020  1.080
 RAS  C12  H24   single    0.930  0.020  1.080
 RAS  C13  H23   single    0.930  0.020  1.080

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
 RAS  H10   N10  C9    110.25  3.000
 RAS  H10   N10  C11   110.12  3.000
 RAS  C9    N10  C11   117.03  3.000
 RAS  H112  C11  H111  106.18  3.000
 RAS  H112  C11  C12   108.95  3.000
 RAS  H111  C11  C12   109.33  3.000
 RAS  H112  C11  N10   107.57  3.000
 RAS  H111  C11  N10   114.77  3.000
 RAS  C12   C11  N10   109.84  3.000
 RAS  H24   C12  C13   119.77  3.000
 RAS  H24   C12  C11   115.72  3.000
 RAS  C13   C12  C11   124.50  3.000
 RAS  H23   C13  H13   116.52  3.000
 RAS  H23   C13  C12   121.71  3.000
 RAS  H13   C13  C12   121.77  3.000
 RAS  H9    C9   C8    108.66  3.000
 RAS  H9    C9   C1    108.80  3.000
 RAS  C8    C9   C1    102.09  3.000
 RAS  H9    C9   N10   106.96  3.000
 RAS  C8    C9   N10   118.25  3.000
 RAS  C1    C9   N10   111.77  3.000
 RAS  H12   C1   H11   107.44  3.000
 RAS  H12   C1   C2    113.53  3.000
 RAS  H11   C1   C2    109.34  3.000
 RAS  H12   C1   C9    112.21  3.000
 RAS  H11   C1   C9    108.62  3.000
 RAS  C2    C1   C9    105.60  3.000
 RAS  H22   C2   H21   106.83  3.000
 RAS  H22   C2   C3    110.17  3.000
 RAS  H21   C2   C3    113.19  3.000
 RAS  H22   C2   C1    110.96  3.000
 RAS  H21   C2   C1    113.08  3.000
 RAS  C3    C2   C1    102.67  3.000
 RAS  C4    C3   C8    120.67  3.000
 RAS  C4    C3   C2    128.82  3.000
 RAS  C8    C3   C2    110.51  3.000
 RAS  C7    C8   C3    120.17  3.000
 RAS  C7    C8   C9    129.53  3.000
 RAS  C3    C8   C9    110.31  3.000
 RAS  H7    C7   C6    119.42  3.000
 RAS  H7    C7   C8    121.33  3.000
 RAS  C6    C7   C8    119.25  3.000
 RAS  H4    C4   C5    120.12  3.000
 RAS  H4    C4   C3    120.76  3.000
 RAS  C5    C4   C3    119.12  3.000
 RAS  H5    C5   C6    119.77  3.000
 RAS  H5    C5   C4    119.92  3.000
 RAS  C6    C5   C4    120.31  3.000
 RAS  H6    C6   C5    119.81  3.000
 RAS  H6    C6   C7    119.71  3.000
 RAS  C5    C6   C7    120.47  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
 RAS  CONST_01  C6   C7   C8   C3     0.00   0.0  0
 RAS  CONST_02  C6   C5   C4   C3     0.00   0.0  0
 RAS  CONST_03  C5   C4   C3   C8     0.00   0.0  0
 RAS  CONST_04  C5   C6   C7   C8     0.00   0.0  0
 RAS  CONST_05  C4   C3   C8   C7     0.00   0.0  0
 RAS  CONST_06  C4   C5   C6   C7     0.00   0.0  0
 RAS  CONST_07  H7   C7   C8   C9     0.00   0.0  0
 RAS  CONST_08  H4   C4   C3   C2     0.00   0.0  0
 RAS  CONST_09  H5   C5   C4   C3   180.00   0.0  0
 RAS  CONST_10  H6   C6   C7   C8   180.00   0.0  0
 RAS  Var_01    C3   C2   C1   C9    28.63  30.0  1
 RAS  Var_02    C8   C3   C2   C1   -18.37  30.0  1
 RAS  Var_03    C9   N10  C11  C12  169.13  30.0  1
 RAS  Var_04    C13  C12  C11  N10  123.24  30.0  3
 RAS  Var_05    H13  C13  C12  C11    0.07   0.0  2

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
 RAS  chir_01  C9  N10  C1  C8  positiv

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
 RAS  plan-1  C11  0.020
 RAS  plan-1  C12  0.020
 RAS  plan-1  C13  0.020
 RAS  plan-1  H13  0.020
 RAS  plan-1  H24  0.020
 RAS  plan-1  H23  0.020
 RAS  plan-2  C9   0.020
 RAS  plan-2  C2   0.020
 RAS  plan-2  C3   0.020
 RAS  plan-2  C8   0.020
 RAS  plan-2  C7   0.020
 RAS  plan-2  C4   0.020
 RAS  plan-2  C5   0.020
 RAS  plan-2  C6   0.020
 RAS  plan-2  H7   0.020
 RAS  plan-2  H4   0.020
 RAS  plan-2  H5   0.020
 RAS  plan-2  H6   0.020

