# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:11:45 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: (2R)-amino(2,3-dihydro-1H-inden-2-yl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](C1Cc2ccccc2C1)C(O)=O
#
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
 IGL  IGL  '(2R)-amino(2,3-dihydro-1H-inden-2-yl)ethanoic acid'  L-peptide  26  14  .  2012-08-28  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_IGL
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
 IGL  N     N  NH2    0  -0.790   1.2225   3.5716   0.2200
 IGL  CA    C  CH1    0  -0.171   1.1964   4.6868   1.1628
 IGL  C     C  C      0   0.389   1.3660   4.2356   2.6342
 IGL  O     O  O      0  -0.609   2.3558   3.5082   2.8668
 IGL  OXT   O  OC    -1  -0.609   0.5234   4.6346   3.4642
 IGL  CB    C  CR15   0  -0.276   2.3053   5.6842   0.7934
 IGL  CG1   C  CH2    0  -0.480   2.1244   6.2342  -0.6361
 IGL  CG2   C  CH2    0  -0.491   2.2693   6.9433   1.6863
 IGL  CD1   C  CR5    0   0.099   1.3586   7.5097  -0.4337
 IGL  CE1   C  C1     0  -0.328   0.6546   8.2670  -1.3568
 IGL  CH1   C  C1     0  -0.261   0.0213   9.4333  -0.9362
 IGL  CH2   C  C1     0  -0.261   0.0928   9.8318   0.3942
 IGL  CE2   C  C1     0  -0.328   0.8022   9.0712   1.3195
 IGL  CD2   C  CR5    0   0.097   1.4334   7.9114   0.8977
 IGL  H     H  HNH2   0   0.323   2.0135   2.9833   0.4589
 IGL  H2    H  HNH2   0   0.336   0.4059   2.9904   0.3693
 IGL  HA    H  HCH1   0   0.196   0.2280   5.1883   1.0532
 IGL  HB    H  HCR5   0   0.220   3.2627   5.1663   0.8925
 IGL  HG12  H  HCH2   0   0.244   1.6181   5.5200  -1.2865
 IGL  HG13  H  HCH2   0   0.241   3.0951   6.4475  -1.0968
 IGL  HG22  H  HCH2   0   0.244   3.2772   7.3488   1.8228
 IGL  HG23  H  HCH2   0   0.245   1.8720   6.7564   2.6850
 IGL  HE1   H  H      0   0.239   0.5918   7.9573  -2.3935
 IGL  HH1   H  H      0   0.245  -0.5348  10.0303  -1.6476
 IGL  HH2   H  H      0   0.245  -0.4090  10.7371   0.7121
 IGL  HE2   H  H      0   0.240   0.8530   9.3838   2.3559

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
 IGL  N    CA    single    1.451  0.016  1.451
 IGL  N    H     single    0.860  0.020  0.860
 IGL  N    H2    single    0.890  0.020  1.040
 IGL  CA   C     single    1.516  0.018  1.516
 IGL  CA   CB    single    1.536  0.020  1.536
 IGL  CA   HA    single    0.970  0.020  1.090
 IGL  C    O     deloc     1.231  0.020  1.231
 IGL  C    OXT   deloc     1.248  0.020  1.248
 IGL  CB   CG1   single    1.542  0.020  1.542
 IGL  CB   CG2   single    1.544  0.020  1.544
 IGL  CB   HB    single    0.970  0.020  1.090
 IGL  CG1  CD1   single    1.501  0.020  1.501
 IGL  CG1  HG12  single    0.970  0.020  1.090
 IGL  CG1  HG13  single    0.970  0.020  1.090
 IGL  CG2  CD2   single    1.503  0.020  1.503
 IGL  CG2  HG22  single    0.970  0.020  1.090
 IGL  CG2  HG23  single    0.970  0.020  1.090
 IGL  CD1  CE1   aromatic  1.386  0.020  1.386
 IGL  CD1  CD2   aromatic  1.393  0.020  1.393
 IGL  CE1  CH1   aromatic  1.392  0.020  1.392
 IGL  CE1  HE1   single    0.930  0.020  1.080
 IGL  CH1  CH2   aromatic  1.391  0.020  1.391
 IGL  CH1  HH1   single    0.930  0.020  1.080
 IGL  CH2  CE2   aromatic  1.392  0.020  1.392
 IGL  CH2  HH2   single    0.930  0.020  1.080
 IGL  CE2  CD2   aromatic  1.386  0.020  1.386
 IGL  CE2  HE2   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
 IGL  H2    N    H     105.14  3.000
 IGL  H2    N    CA    109.18  3.000
 IGL  H     N    CA    114.00  3.000
 IGL  HA    CA   CB    108.46  3.000
 IGL  HA    CA   C     108.98  3.000
 IGL  CB    CA   C     109.79  3.000
 IGL  HA    CA   N     107.49  3.000
 IGL  CB    CA   N     109.12  3.000
 IGL  C     CA   N     113.30  2.900
 IGL  OXT   C    O     126.63  3.000
 IGL  OXT   C    CA    117.70  3.000
 IGL  O     C    CA    120.80  2.100
 IGL  HB    CB   CG2   110.76  3.000
 IGL  HB    CB   CG1   110.84  3.000
 IGL  CG2   CB   CG1   104.03  3.000
 IGL  HB    CB   CA    107.63  3.000
 IGL  CG2   CB   CA    111.93  3.000
 IGL  CG1   CB   CA    111.70  3.000
 IGL  HG13  CG1  HG12  106.74  3.000
 IGL  HG13  CG1  CD1   110.07  3.000
 IGL  HG12  CG1  CD1   113.58  3.000
 IGL  HG13  CG1  CB    110.82  3.000
 IGL  HG12  CG1  CB    111.94  3.000
 IGL  CD1   CG1  CB    103.76  3.000
 IGL  HG23  CG2  HG22  106.53  3.000
 IGL  HG23  CG2  CD2   112.85  3.000
 IGL  HG22  CG2  CD2   109.81  3.000
 IGL  HG23  CG2  CB    113.46  3.000
 IGL  HG22  CG2  CB    110.65  3.000
 IGL  CD2   CG2  CB    103.59  3.000
 IGL  CD2   CD1  CE1   120.42  3.000
 IGL  CD2   CD1  CG1   110.27  3.000
 IGL  CE1   CD1  CG1   129.31  3.000
 IGL  HE1   CE1  CH1   120.13  3.000
 IGL  HE1   CE1  CD1   120.68  3.000
 IGL  CH1   CE1  CD1   119.18  3.000
 IGL  HH1   CH1  CH2   119.80  3.000
 IGL  HH1   CH1  CE1   119.81  3.000
 IGL  CH2   CH1  CE1   120.38  3.000
 IGL  HH2   CH2  CE2   119.86  3.000
 IGL  HH2   CH2  CH1   119.78  3.000
 IGL  CE2   CH2  CH1   120.36  3.000
 IGL  HE2   CE2  CD2   120.73  3.000
 IGL  HE2   CE2  CH2   120.13  3.000
 IGL  CD2   CE2  CH2   119.14  3.000
 IGL  CE2   CD2  CD1   120.52  3.000
 IGL  CE2   CD2  CG2   129.25  3.000
 IGL  CD1   CD2  CG2   110.23  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
 IGL  CONST_01  CH2  CH1  CE1  CD1     0.00   0.0  0
 IGL  CONST_02  CH2  CE2  CD2  CD1     0.00   0.0  0
 IGL  CONST_03  CE2  CD2  CD1  CE1     0.00   0.0  0
 IGL  CONST_04  CE2  CH2  CH1  CE1     0.00   0.0  0
 IGL  CONST_05  CD2  CD1  CE1  CH1     0.00   0.0  0
 IGL  CONST_06  CD2  CE2  CH2  CH1     0.00   0.0  0
 IGL  CONST_07  HE1  CE1  CD1  CG1     0.00   0.0  0
 IGL  CONST_08  HE2  CE2  CD2  CG2     0.00   0.0  0
 IGL  CONST_09  HH1  CH1  CE1  CD1   180.00   0.0  0
 IGL  CONST_10  HH2  CH2  CH1  CE1   180.00   0.0  0
 IGL  Var_01    CE1  CD1  CG1  CB   -163.60  30.0  1
 IGL  Var_02    CD1  CD2  CG2  CB    -17.88  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
 IGL  chir_01  CA  N   C    CB   negativ
 IGL  chir_02  CB  CA  CG1  CG2  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
 IGL  plan-1  CA   0.020
 IGL  plan-1  C    0.020
 IGL  plan-1  O    0.020
 IGL  plan-1  OXT  0.020
 IGL  plan-2  CG1  0.020
 IGL  plan-2  CG2  0.020
 IGL  plan-2  CD1  0.020
 IGL  plan-2  CE1  0.020
 IGL  plan-2  CH1  0.020
 IGL  plan-2  CH2  0.020
 IGL  plan-2  CE2  0.020
 IGL  plan-2  CD2  0.020
 IGL  plan-2  HE1  0.020
 IGL  plan-2  HH1  0.020
 IGL  plan-2  HH2  0.020
 IGL  plan-2  HE2  0.020

