# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 19:18:40 2022
#   Inital geometry file: a 94 line input string
#   Ligand name: N-(2-aminoethyl)-N-(1H-indol-3-ylacetyl)glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCN(CC(O)=O)C(=O)Cc1c[nH]c2ccccc12
#
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
 GIC  GIC  N-(2-aminoethyl)-N-(1H-indol-3-ylacetyl)glycine  peptide  36  20  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GIC
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
 GIC  C    C  C      0   0.405  -31.0724  0.9617  41.8936
 GIC  N    N  NT     0  -0.420  -31.6971  3.4056  41.8892
 GIC  O    O  O      0  -0.618  -30.2593  0.1081  41.4862
 GIC  C1   C  CH2    0  -0.343  -31.4822  4.0152  43.1891
 GIC  N1   N  NH2    0  -0.788  -29.4049  5.1994  42.5867
 GIC  O1   O  O      0  -0.498  -33.0415  2.9164  40.1510
 GIC  C2   C  CH2    0  -0.276  -30.7375  5.3435  43.1478
 GIC  N2   N  NR15   0  -0.689  -36.7346  5.3273  39.5223
 GIC  C3   C  C      0   0.553  -32.8345  3.5448  41.1812
 GIC  C4   C  CH2    0  -0.746  -33.8693  4.5369  41.7057
 GIC  C5   C  CR5    0   0.074  -34.8384  4.9664  40.6610
 GIC  C6   C  CR15   0  -0.096  -36.1832  4.7386  40.6280
 GIC  C7   C  CR56   0   0.351  -35.7541  5.9555  38.8115
 GIC  C8   C  CR16   0  -0.305  -35.8172  6.6842  37.6243
 GIC  C9   C  CR16   0  -0.282  -34.6363  7.2100  37.1353
 GIC  CA   C  CH2    0  -0.457  -30.7402  2.4088  41.4617
 GIC  C10  C  CR16   0  -0.268  -33.4176  7.0193  37.8081
 GIC  C11  C  CR16   0  -0.374  -33.3597  6.2943  38.9824
 GIC  C12  C  CR56   0   0.045  -34.5396  5.7513  39.5017
 GIC  OXT  O  OC    -1  -0.595  -32.0804  0.7790  42.5971
 GIC  H1   H  HCH2   0   0.257  -32.4298  4.1540  43.7096
 GIC  H1A  H  HCH2   0   0.254  -30.9203  3.3043  43.7997
 GIC  HN1  H  HNH2   0   0.349  -28.9730  6.1102  42.5001
 GIC  H2   H  HCH2   0   0.221  -31.2930  6.0505  42.5264
 GIC  H4   H  HCH2   0   0.288  -34.4029  4.0652  42.5378
 GIC  H4A  H  HCH2   0   0.270  -33.3780  5.4149  42.1307
 GIC  H6   H  HCR5   0   0.278  -36.8009  4.1929  41.3245
 GIC  H8   H  HCR6   0   0.254  -36.7551  6.8323  37.1038
 GIC  H9   H  HCR6   0   0.245  -34.6507  7.7806  36.2155
 GIC  HA   H  HCH2   0   0.246  -29.7658  2.6837  41.8665
 GIC  HAA  H  HCH2   0   0.240  -30.6327  2.4413  40.3766
 GIC  H10  H  HCR6   0   0.242  -32.5129  7.4456  37.3939
 GIC  H11  H  HCR6   0   0.238  -32.4149  6.1519  39.4941
 GIC  HN2  H  HNR5   0   0.405  -37.7112  5.3046  39.2818
 GIC  H15  H  HNH2   0   0.340  -28.8225  4.6770  43.2299
 GIC  H16  H  HCH2   0   0.198  -30.7483  5.7550  44.1671

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
 GIC  C    CA   single    1.525  0.021  1.525
 GIC  C    OXT  deloc     1.243  0.020  1.243
 GIC  N    C1   single    1.452  0.020  1.452
 GIC  O    C    deloc     1.231  0.020  1.231
 GIC  C1   C2   single    1.523  0.020  1.523
 GIC  C1   H1   single    0.970  0.020  1.090
 GIC  C1   H1A  single    0.970  0.020  1.090
 GIC  N1   C2   single    1.453  0.020  1.453
 GIC  N1   HN1  single    0.890  0.020  1.040
 GIC  O1   C3   double    1.224  0.020  1.224
 GIC  C2   H2   single    0.970  0.020  1.090
 GIC  N2   C6   aromatic  1.369  0.020  1.369
 GIC  N2   HN2  single    0.860  0.020  1.020
 GIC  C3   N    single    1.347  0.020  1.347
 GIC  C3   C4   single    1.526  0.020  1.526
 GIC  C4   H4   single    0.970  0.020  1.090
 GIC  C4   H4A  single    0.970  0.020  1.090
 GIC  C5   C4   single    1.488  0.020  1.488
 GIC  C5   C6   aromatic  1.364  0.020  1.364
 GIC  C6   H6   single    0.930  0.020  1.080
 GIC  C7   N2   aromatic  1.364  0.020  1.364
 GIC  C7   C12  aromatic  1.412  0.020  1.412
 GIC  C8   C7   aromatic  1.394  0.020  1.394
 GIC  C8   H8   single    0.930  0.020  1.080
 GIC  C9   C8   aromatic  1.382  0.020  1.382
 GIC  C9   C10  aromatic  1.405  0.020  1.405
 GIC  C9   H9   single    0.930  0.020  1.080
 GIC  CA   N    single    1.458  0.019  1.458
 GIC  CA   HA   single    0.970  0.020  0.970
 GIC  CA   HAA  single    0.970  0.020  1.090
 GIC  C10  C11  aromatic  1.381  0.020  1.381
 GIC  C10  H10  single    0.930  0.020  1.080
 GIC  C11  C12  aromatic  1.399  0.020  1.399
 GIC  C11  H11  single    0.930  0.020  1.080
 GIC  C12  C5   aromatic  1.431  0.020  1.431
 GIC  N1   H15  single    0.890  0.020  1.040
 GIC  C2   H16  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
 GIC  OXT  C    CA   120.80  1.700
 GIC  OXT  C    O    127.81  3.000
 GIC  CA   C    O    120.80  1.700
 GIC  CA   N    C3   118.32  3.000
 GIC  CA   N    C1   117.14  3.000
 GIC  C3   N    C1   123.52  3.000
 GIC  H1A  C1   H1   105.26  3.000
 GIC  H1A  C1   C2   109.33  3.000
 GIC  H1   C1   C2   109.08  3.000
 GIC  H1A  C1   N    107.65  3.000
 GIC  H1   C1   N    110.63  3.000
 GIC  C2   C1   N    114.47  3.000
 GIC  H15  N1   HN1  105.86  3.000
 GIC  H15  N1   C2   109.47  3.000
 GIC  HN1  N1   C2   109.59  3.000
 GIC  H16  C2   H2   106.26  3.000
 GIC  H16  C2   N1   113.84  3.000
 GIC  H2   C2   N1   108.11  3.000
 GIC  H16  C2   C1   107.24  3.000
 GIC  H2   C2   C1   109.33  3.000
 GIC  N1   C2   C1   111.86  3.000
 GIC  HN2  N2   C7   125.70  3.000
 GIC  C7   N2   C6   109.24  3.000
 GIC  HN2  N2   C6   125.06  3.000
 GIC  C4   C3   O1   120.54  3.000
 GIC  C4   C3   N    117.32  3.000
 GIC  O1   C3   N    122.14  3.000
 GIC  H4A  C4   H4   105.65  3.000
 GIC  H4A  C4   C5   109.51  3.000
 GIC  H4   C4   C5   109.89  3.000
 GIC  C5   C4   C3   112.81  3.000
 GIC  H4A  C4   C3   110.56  3.000
 GIC  H4   C4   C3   108.15  3.000
 GIC  C12  C5   C6   106.13  3.000
 GIC  C12  C5   C4   126.21  3.000
 GIC  C6   C5   C4   127.63  3.000
 GIC  H6   C6   C5   129.28  3.000
 GIC  H6   C6   N2   120.55  3.000
 GIC  C5   C6   N2   110.17  3.000
 GIC  C12  C7   C8   122.06  3.000
 GIC  C8   C7   N2   130.67  3.000
 GIC  C12  C7   N2   107.27  3.000
 GIC  H8   C8   C9   121.19  3.000
 GIC  C9   C8   C7   117.48  3.000
 GIC  H8   C8   C7   121.33  3.000
 GIC  H9   C9   C10  119.34  3.000
 GIC  H9   C9   C8   119.32  3.000
 GIC  C10  C9   C8   121.33  3.000
 GIC  HAA  CA   HA   105.88  3.000
 GIC  HAA  CA   N    109.80  3.000
 GIC  HA   CA   N    110.00  3.000
 GIC  HAA  CA   C    109.09  3.000
 GIC  HA   CA   C    110.00  3.000
 GIC  N    CA   C    111.00  2.800
 GIC  H10  C10  C11  119.80  3.000
 GIC  H10  C10  C9   119.22  3.000
 GIC  C11  C10  C9   120.98  3.000
 GIC  H11  C11  C12  120.60  3.000
 GIC  H11  C11  C10  120.46  3.000
 GIC  C12  C11  C10  118.95  3.000
 GIC  C11  C12  C7   119.21  3.000
 GIC  C11  C12  C5   133.60  3.000
 GIC  C7   C12  C5   107.19  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
 GIC  CONST_01  C12  C5   C6   N2    0.00   0.0  0
 GIC  CONST_02  C11  C12  C7   N2  180.00   0.0  0
 GIC  CONST_03  C5   C12  C7   N2    0.00   0.0  0
 GIC  CONST_04  C9   C8   C7   N2  180.00   0.0  0
 GIC  CONST_05  C7   N2   C6   C5    0.00   0.0  0
 GIC  CONST_06  C8   C7   C12  C5  180.00   0.0  0
 GIC  CONST_07  C10  C11  C12  C5  180.00   0.0  0
 GIC  CONST_08  C12  C7   N2   C6    0.00   0.0  0
 GIC  CONST_09  C8   C7   N2   C6  180.00   0.0  0
 GIC  CONST_10  C7   C12  C5   C6    0.00   0.0  0
 GIC  CONST_11  C11  C12  C5   C6  180.00   0.0  0
 GIC  CONST_12  C10  C11  C12  C7    0.00   0.0  0
 GIC  CONST_13  C10  C9   C8   C7    0.00   0.0  0
 GIC  CONST_14  C11  C12  C7   C8    0.00   0.0  0
 GIC  CONST_15  C11  C10  C9   C8    0.00   0.0  0
 GIC  CONST_16  C12  C7   C8   C9    0.00   0.0  0
 GIC  CONST_17  C12  C11  C10  C9    0.00   0.0  0
 GIC  CONST_18  C4   C5   C6   N2  180.00   0.0  0
 GIC  CONST_19  C7   C12  C5   C4  180.00   0.0  0
 GIC  CONST_20  C11  C12  C5   C4    0.00   0.0  0
 GIC  CONST_21  H8   C8   C7   N2    0.00   0.0  0
 GIC  CONST_22  HN2  N2   C6   C5  180.00   0.0  0
 GIC  CONST_23  H11  C11  C12  C5    0.00   0.0  0
 GIC  CONST_24  H6   C6   N2   C7  180.00   0.0  0
 GIC  CONST_25  H9   C9   C8   C7  180.00   0.0  0
 GIC  CONST_26  H10  C10  C9   C8  180.00   0.0  0
 GIC  CONST_27  O1   C3   N    C1  180.00   0.0  0
 GIC  CONST_28  C4   C3   N    C1    0.00   0.0  0
 GIC  CONST_29  CA   N    C3   O1    0.00   0.0  0
 GIC  CONST_30  CA   N    C3   C4  180.00   0.0  0
 GIC  Var_01    C6   C5   C4   C3  115.53  30.0  2
 GIC  Var_02    C5   C4   C3   N   160.23  30.0  3
 GIC  Var_03    C1   N    CA   C    88.79  30.0  3
 GIC  Var_04    N1   C2   C1   N   -61.28  30.0  3
 GIC  Var_05    OXT  C    CA   N    -2.57  30.0  2
 GIC  Var_06    HN1  N1   C2   C1  175.06  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
 GIC  plan-1  N2   0.020
 GIC  plan-1  C4   0.020
 GIC  plan-1  C5   0.020
 GIC  plan-1  C6   0.020
 GIC  plan-1  C7   0.020
 GIC  plan-1  C8   0.020
 GIC  plan-1  C9   0.020
 GIC  plan-1  C10  0.020
 GIC  plan-1  C11  0.020
 GIC  plan-1  C12  0.020
 GIC  plan-1  H6   0.020
 GIC  plan-1  H8   0.020
 GIC  plan-1  H9   0.020
 GIC  plan-1  H10  0.020
 GIC  plan-1  H11  0.020
 GIC  plan-1  HN2  0.020
 GIC  plan-2  N    0.020
 GIC  plan-2  C1   0.020
 GIC  plan-2  O1   0.020
 GIC  plan-2  C3   0.020
 GIC  plan-2  C4   0.020
 GIC  plan-2  CA   0.020
 GIC  plan-3  C    0.020
 GIC  plan-3  O    0.020
 GIC  plan-3  CA   0.020
 GIC  plan-3  OXT  0.020

