# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 02:57:10 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 2-(1H-indol-4-yl)ethan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCc1cccc2[nH]ccc12
#
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
 KDY  KDY  2-(1H-indol-4-yl)ethan-1-amine  ligand  24  12  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KDY
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
 KDY  C1   C  CH2   0  -0.275  -2.6777   0.2823  -0.5765
 KDY  C10  C  CR56  0   0.034   0.4717   0.3296   0.1878
 KDY  C2   C  CH2   0  -0.527  -1.9480  -0.2309   0.6650
 KDY  C3   C  CR6   0   0.068  -0.5338  -0.6371   0.3676
 KDY  C4   C  CR16  0  -0.352  -0.1729  -1.9658   0.2272
 KDY  C5   C  CR16  0  -0.270   1.1417  -2.3525  -0.0837
 KDY  C6   C  CR16  0  -0.327   2.1415  -1.4187  -0.2654
 KDY  C7   C  CR56  0   0.351   1.7881  -0.0765  -0.1249
 KDY  C8   C  CR15  0  -0.027   1.7692   2.1498  -0.0134
 KDY  C9   C  CR15  0  -0.443   0.4888   1.7591   0.2541
 KDY  N1   N  NH2   0  -0.800  -4.0380   0.6772  -0.2426
 KDY  N2   N  NR15  0  -0.679   2.5473   1.0515  -0.2416
 KDY  H1   H  HCH2  0   0.201  -2.0851   1.0858  -1.0348
 KDY  H2   H  HCH2  0   0.220  -2.7247  -0.5225  -1.3144
 KDY  H3   H  HCH2  0   0.231  -1.9562   0.5517   1.4314
 KDY  H4   H  HCH2  0   0.241  -2.5043  -1.0768   1.0754
 KDY  H5   H  HCR6  0   0.236  -0.9258  -2.7342   0.3592
 KDY  H6   H  HCR6  0   0.246   1.3731  -3.4054  -0.1809
 KDY  H7   H  HCR6  0   0.256   3.1545  -1.7153  -0.5059
 KDY  H8   H  HCR5  0   0.279   2.1922   3.1404  -0.0630
 KDY  H9   H  HCR5  0   0.242  -0.3391   2.4165   0.4682
 KDY  H10  H  HNH2  0   0.339  -4.0126   1.5115   0.3318
 KDY  H11  H  HNH2  0   0.348  -4.5262   0.9466  -1.0872
 KDY  H13  H  HNR5  0   0.408   3.5312   1.0766  -0.4500

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
 KDY  N1   C1   single    1.455  0.020  1.455
 KDY  C5   C4   aromatic  1.405  0.020  1.405
 KDY  C5   C6   aromatic  1.380  0.020  1.380
 KDY  C4   C3   aromatic  1.384  0.020  1.384
 KDY  C6   C7   aromatic  1.395  0.020  1.395
 KDY  C1   C2   single    1.529  0.020  1.529
 KDY  C3   C2   single    1.501  0.020  1.501
 KDY  C3   C10  aromatic  1.406  0.020  1.406
 KDY  C7   C10  aromatic  1.413  0.020  1.413
 KDY  C7   N2   aromatic  1.365  0.020  1.365
 KDY  C10  C9   aromatic  1.431  0.020  1.431
 KDY  N2   C8   aromatic  1.365  0.020  1.365
 KDY  C9   C8   aromatic  1.365  0.020  1.365
 KDY  C1   H1   single    0.970  0.020  1.090
 KDY  C1   H2   single    0.970  0.020  1.090
 KDY  C2   H3   single    0.970  0.020  1.090
 KDY  C2   H4   single    0.970  0.020  1.090
 KDY  C4   H5   single    0.930  0.020  1.080
 KDY  C5   H6   single    0.930  0.020  1.080
 KDY  C6   H7   single    0.930  0.020  1.080
 KDY  C8   H8   single    0.930  0.020  1.080
 KDY  C9   H9   single    0.930  0.020  1.080
 KDY  N1   H10  single    0.890  0.020  1.040
 KDY  N1   H11  single    0.890  0.020  1.040
 KDY  N2   H13  single    0.860  0.020  1.020

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
 KDY  H2   C1   H1   106.27  3.000
 KDY  H2   C1   N1   108.34  3.000
 KDY  H1   C1   N1   113.67  3.000
 KDY  H2   C1   C2   108.76  3.000
 KDY  H1   C1   C2   109.07  3.000
 KDY  N1   C1   C2   110.54  3.000
 KDY  C9   C10  C7   106.64  3.000
 KDY  C9   C10  C3   133.57  3.000
 KDY  C7   C10  C3   119.80  3.000
 KDY  H4   C2   H3   106.65  3.000
 KDY  H4   C2   C3   110.16  3.000
 KDY  H3   C2   C3   109.81  3.000
 KDY  H4   C2   C1   108.78  3.000
 KDY  H3   C2   C1   108.96  3.000
 KDY  C3   C2   C1   112.31  3.000
 KDY  C4   C3   C2   121.70  3.000
 KDY  C2   C3   C10  120.86  3.000
 KDY  C4   C3   C10  117.42  3.000
 KDY  H5   C4   C5   118.79  3.000
 KDY  H5   C4   C3   119.16  3.000
 KDY  C5   C4   C3   122.05  3.000
 KDY  H6   C5   C6   119.44  3.000
 KDY  H6   C5   C4   119.18  3.000
 KDY  C6   C5   C4   121.38  3.000
 KDY  H7   C6   C7   121.54  3.000
 KDY  H7   C6   C5   121.45  3.000
 KDY  C7   C6   C5   117.01  3.000
 KDY  N2   C7   C6   130.22  3.000
 KDY  N2   C7   C10  107.44  3.000
 KDY  C6   C7   C10  122.34  3.000
 KDY  H8   C8   N2   120.52  3.000
 KDY  H8   C8   C9   129.78  3.000
 KDY  N2   C8   C9   109.70  3.000
 KDY  H9   C9   C8   125.76  3.000
 KDY  H9   C9   C10  127.50  3.000
 KDY  C8   C9   C10  106.74  3.000
 KDY  H11  N1   H10  105.43  3.000
 KDY  H11  N1   C1   109.37  3.000
 KDY  H10  N1   C1   109.28  3.000
 KDY  H13  N2   C8   124.89  3.000
 KDY  H13  N2   C7   125.62  3.000
 KDY  C8   N2   C7   109.49  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
 KDY  CONST_01  C5   C4   C3   C10     0.00   0.0  0
 KDY  CONST_02  C5   C6   C7   C10     0.00   0.0  0
 KDY  CONST_03  C8   N2   C7   C10     0.00   0.0  0
 KDY  CONST_04  N2   C8   C9   C10     0.00   0.0  0
 KDY  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 KDY  CONST_06  C6   C7   C10  C3      0.00   0.0  0
 KDY  CONST_07  N2   C7   C10  C3    180.00   0.0  0
 KDY  CONST_08  C8   C9   C10  C3    180.00   0.0  0
 KDY  CONST_09  C7   C6   C5   C4      0.00   0.0  0
 KDY  CONST_10  C7   C10  C3   C4      0.00   0.0  0
 KDY  CONST_11  C9   C10  C3   C4    180.00   0.0  0
 KDY  CONST_12  N2   C7   C6   C5    180.00   0.0  0
 KDY  CONST_13  C9   C10  C7   C6    180.00   0.0  0
 KDY  CONST_14  C8   N2   C7   C6    180.00   0.0  0
 KDY  CONST_15  C8   C9   C10  C7      0.00   0.0  0
 KDY  CONST_16  C9   C8   N2   C7      0.00   0.0  0
 KDY  CONST_17  N2   C7   C10  C9      0.00   0.0  0
 KDY  CONST_18  C5   C4   C3   C2    180.00   0.0  0
 KDY  CONST_19  C7   C10  C3   C2    180.00   0.0  0
 KDY  CONST_20  C9   C10  C3   C2      0.00   0.0  0
 KDY  CONST_21  H5   C4   C3   C10   180.00   0.0  0
 KDY  CONST_22  H7   C6   C7   C10   180.00   0.0  0
 KDY  CONST_23  H13  N2   C7   C10   180.00   0.0  0
 KDY  CONST_24  H8   C8   C9   C10   180.00   0.0  0
 KDY  CONST_25  H6   C5   C4   C3    180.00   0.0  0
 KDY  CONST_26  H9   C9   C10  C3      0.00   0.0  0
 KDY  Var_01    C4   C3   C2   C1   -102.09  30.0  2
 KDY  Var_02    N1   C1   C2   C3   -179.43  30.0  1
 KDY  Var_03    H10  N1   C1   C2     69.34  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
 KDY  plan-1  C10  0.020
 KDY  plan-1  C2   0.020
 KDY  plan-1  C3   0.020
 KDY  plan-1  C4   0.020
 KDY  plan-1  C5   0.020
 KDY  plan-1  C6   0.020
 KDY  plan-1  C7   0.020
 KDY  plan-1  C8   0.020
 KDY  plan-1  C9   0.020
 KDY  plan-1  N2   0.020
 KDY  plan-1  H5   0.020
 KDY  plan-1  H6   0.020
 KDY  plan-1  H7   0.020
 KDY  plan-1  H8   0.020
 KDY  plan-1  H9   0.020
 KDY  plan-1  H13  0.020

