# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 17:12:49 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 2-amino-6-[2-(1H-indol-6-yl)ethyl]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=CC(=O)N1)CCc2ccc3cc[nH]c3c2
#
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
 C8C  C8C  2-amino-6-[2-(1H-indol-6-yl)ethyl]pyrimidin-4(3H)-one  ligand  33  19  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C8C
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
 C8C  N1    N  NH2   0  -0.830  66.8816  49.2795  5.5721
 C8C  C2    C  CR6   0   0.683  67.7479  49.0251  6.5555
 C8C  C4    C  CR6   0   0.545  68.5319  47.4026  8.1773
 C8C  C5    C  CR16  0  -0.512  69.4482  48.4205  8.5771
 C8C  C6    C  CR6   0   0.319  69.4431  49.6291  7.9405
 C8C  C7    C  CH2   0  -0.488  70.4261  50.6975  8.3077
 C8C  C8    C  CH2   0  -0.516  71.4017  50.9921  7.1574
 C8C  C9    C  CR6   0   0.108  72.2062  49.7821  6.7717
 C8C  C10   C  CR16  0  -0.318  73.3351  49.4219  7.5353
 C8C  C11   C  CR16  0  -0.333  74.0722  48.2888  7.2607
 C8C  C12   C  CR56  0   0.042  73.6864  47.4686  6.1931
 C8C  C13   C  CR15  0  -0.419  74.1835  46.2518  5.6284
 C8C  C14   C  CR15  0  -0.035  73.3615  45.9409  4.5840
 C8C  N15   N  NR15  0  -0.683  72.3873  46.8920  4.4647
 C8C  C16   C  CR56  0   0.365  72.5557  47.8391  5.4331
 C8C  C17   C  CR16  0  -0.349  71.8137  48.9860  5.7106
 C8C  N18   N  N     0  -0.515  68.5977  49.9473  6.9355
 C8C  N3    N  NR16  0  -0.706  67.6978  47.8000  7.1352
 C8C  O5    O  O     0  -0.503  68.4240  46.2742  8.6425
 C8C  H1N1  H  HNH2  0   0.413  66.9267  50.1655  5.1001
 C8C  H1N2  H  HNH2  0   0.417  66.2537  48.5825  5.2120
 C8C  H3    H  HNR6  0   0.419  67.0233  47.1210  6.8062
 C8C  H5    H  HCR6  0   0.254  70.1554  48.2123  9.3668
 C8C  H7C1  H  HCH2  0   0.255  69.8829  51.6145  8.5524
 C8C  H7C2  H  HCH2  0   0.245  70.9804  50.4008  9.1994
 C8C  H8C1  H  HCH2  0   0.244  70.8371  51.3607  6.2996
 C8C  H8C2  H  HCH2  0   0.249  72.0638  51.8019  7.4721
 C8C  H10   H  HCR6  0   0.235  73.6317  50.0589  8.3613
 C8C  H17   H  HCR6  0   0.245  70.9441  49.2472  5.1190
 C8C  H11   H  HCR6  0   0.240  74.9382  48.0400  7.8620
 C8C  H13   H  HCR5  0   0.245  75.0375  45.6806  5.9567
 C8C  H14   H  HCR5  0   0.278  73.3925  45.1029  3.9066
 C8C  H15   H  HNR5  0   0.407  71.6563  46.8851  3.7738

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
 C8C  N1   C2    single    1.335  0.020  1.335
 C8C  C2   N18   double    1.310  0.020  1.310
 C8C  C2   N3    single    1.356  0.020  1.356
 C8C  C4   C5    single    1.427  0.020  1.427
 C8C  C4   N3    single    1.393  0.020  1.393
 C8C  C4   O5    double    1.225  0.020  1.225
 C8C  C5   C6    double    1.366  0.020  1.366
 C8C  C6   C7    single    1.497  0.020  1.497
 C8C  C6   N18   single    1.351  0.020  1.351
 C8C  C7   C8    single    1.537  0.020  1.537
 C8C  C8   C9    single    1.503  0.020  1.503
 C8C  C9   C10   aromatic  1.410  0.020  1.410
 C8C  C9   C17   aromatic  1.383  0.020  1.383
 C8C  C10  C11   aromatic  1.379  0.020  1.379
 C8C  C11  C12   aromatic  1.400  0.020  1.400
 C8C  C12  C13   aromatic  1.431  0.020  1.431
 C8C  C12  C16   aromatic  1.412  0.020  1.412
 C8C  C13  C14   aromatic  1.365  0.020  1.365
 C8C  C14  N15   aromatic  1.367  0.020  1.367
 C8C  N15  C16   aromatic  1.365  0.020  1.365
 C8C  C16  C17   aromatic  1.394  0.020  1.394
 C8C  N1   H1N1  single    0.860  0.020  1.020
 C8C  N1   H1N2  single    0.860  0.020  1.020
 C8C  N3   H3    single    0.860  0.020  1.020
 C8C  C5   H5    single    0.930  0.020  1.080
 C8C  C7   H7C1  single    0.970  0.020  1.090
 C8C  C7   H7C2  single    0.970  0.020  1.090
 C8C  C8   H8C1  single    0.970  0.020  1.090
 C8C  C8   H8C2  single    0.970  0.020  1.090
 C8C  C10  H10   single    0.930  0.020  1.080
 C8C  C17  H17   single    0.930  0.020  1.080
 C8C  C11  H11   single    0.930  0.020  1.080
 C8C  C13  H13   single    0.930  0.020  1.080
 C8C  C14  H14   single    0.930  0.020  1.080
 C8C  N15  H15   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
 C8C  H1N2  N1   H1N1  118.12  3.000
 C8C  H1N2  N1   C2    122.50  3.000
 C8C  H1N1  N1   C2    119.00  3.000
 C8C  N3    C2   N18   122.39  3.000
 C8C  N3    C2   N1    117.58  3.000
 C8C  N18   C2   N1    120.02  3.000
 C8C  O5    C4   N3    119.61  3.000
 C8C  O5    C4   C5    127.39  3.000
 C8C  N3    C4   C5    113.00  3.000
 C8C  H5    C5   C6    120.90  3.000
 C8C  H5    C5   C4    119.19  3.000
 C8C  C6    C5   C4    119.89  3.000
 C8C  N18   C6   C7    115.15  3.000
 C8C  N18   C6   C5    123.87  3.000
 C8C  C7    C6   C5    120.97  3.000
 C8C  H7C2  C7   H7C1  107.30  3.000
 C8C  H7C2  C7   C8    109.96  3.000
 C8C  H7C1  C7   C8    108.79  3.000
 C8C  H7C2  C7   C6    109.87  3.000
 C8C  H7C1  C7   C6    109.09  3.000
 C8C  C8    C7   C6    111.72  3.000
 C8C  H8C2  C8   H8C1  106.84  3.000
 C8C  H8C2  C8   C9    110.26  3.000
 C8C  H8C1  C8   C9    110.31  3.000
 C8C  H8C2  C8   C7    108.14  3.000
 C8C  H8C1  C8   C7    108.95  3.000
 C8C  C9    C8   C7    112.18  3.000
 C8C  C17   C9   C10   119.72  3.000
 C8C  C17   C9   C8    120.54  3.000
 C8C  C10   C9   C8    119.68  3.000
 C8C  H10   C10  C11   119.21  3.000
 C8C  H10   C10  C9    118.79  3.000
 C8C  C11   C10  C9    122.00  3.000
 C8C  H11   C11  C12   120.59  3.000
 C8C  H11   C11  C10   120.35  3.000
 C8C  C12   C11  C10   119.06  3.000
 C8C  C16   C12  C13   106.80  3.000
 C8C  C16   C12  C11   118.51  3.000
 C8C  C13   C12  C11   134.70  3.000
 C8C  H13   C13  C14   126.09  3.000
 C8C  H13   C13  C12   127.26  3.000
 C8C  C14   C13  C12   106.65  3.000
 C8C  H14   C14  N15   120.44  3.000
 C8C  H14   C14  C13   129.83  3.000
 C8C  N15   C14  C13   109.73  3.000
 C8C  H15   N15  C16   125.58  3.000
 C8C  H15   N15  C14   124.97  3.000
 C8C  C16   N15  C14   109.45  3.000
 C8C  C17   C16  N15   130.28  3.000
 C8C  C17   C16  C12   122.34  3.000
 C8C  N15   C16  C12   107.38  3.000
 C8C  H17   C17  C16   121.11  3.000
 C8C  H17   C17  C9    120.51  3.000
 C8C  C16   C17  C9    118.37  3.000
 C8C  C6    N18  C2    117.11  3.000
 C8C  H3    N3   C4    116.81  3.000
 C8C  H3    N3   C2    119.45  3.000
 C8C  C4    N3   C2    123.74  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
 C8C  CONST_01  C12   C11  C10  C9     0.00   0.0  0
 C8C  CONST_02  C12   C16  C17  C9     0.00   0.0  0
 C8C  CONST_03  N15   C16  C17  C9   180.00   0.0  0
 C8C  CONST_04  C16   C17  C9   C10    0.00   0.0  0
 C8C  CONST_05  C13   C12  C11  C10  180.00   0.0  0
 C8C  CONST_06  C16   C12  C11  C10    0.00   0.0  0
 C8C  CONST_07  C17   C9   C10  C11    0.00   0.0  0
 C8C  CONST_08  C14   C13  C12  C11  180.00   0.0  0
 C8C  CONST_09  N15   C16  C12  C11  180.00   0.0  0
 C8C  CONST_10  C17   C16  C12  C11    0.00   0.0  0
 C8C  CONST_11  N15   C14  C13  C12    0.00   0.0  0
 C8C  CONST_12  C14   N15  C16  C12    0.00   0.0  0
 C8C  CONST_13  N15   C16  C12  C13    0.00   0.0  0
 C8C  CONST_14  C17   C16  C12  C13  180.00   0.0  0
 C8C  CONST_15  C16   N15  C14  C13    0.00   0.0  0
 C8C  CONST_16  C16   C12  C13  C14    0.00   0.0  0
 C8C  CONST_17  C17   C16  N15  C14  180.00   0.0  0
 C8C  CONST_18  C5    C4   N3   C2     0.00   0.0  0
 C8C  CONST_19  N18   C2   N3   C4     0.00   0.0  0
 C8C  CONST_20  N3    C2   N18  C6     0.00   0.0  0
 C8C  CONST_21  C11   C10  C9   C8   180.00   0.0  0
 C8C  CONST_22  C16   C17  C9   C8   180.00   0.0  0
 C8C  CONST_23  C6    N18  C2   N1   180.00   0.0  0
 C8C  CONST_24  C4    N3   C2   N1   180.00   0.0  0
 C8C  CONST_25  O5    C4   N3   C2   180.00   0.0  0
 C8C  CONST_26  H11   C11  C10  C9   180.00   0.0  0
 C8C  CONST_27  H17   C17  C9   C10  180.00   0.0  0
 C8C  CONST_28  H13   C13  C12  C11    0.00   0.0  0
 C8C  CONST_29  H10   C10  C11  C12  180.00   0.0  0
 C8C  CONST_30  H14   C14  C13  C12  180.00   0.0  0
 C8C  CONST_31  H15   N15  C16  C12  180.00   0.0  0
 C8C  CONST_32  H3    N3   C4   C5   180.00   0.0  0
 C8C  CONST_33  H1N1  N1   C2   N18    0.00   0.0  0
 C8C  CONST_34  H1N2  N1   C2   N18  180.00   0.0  0
 C8C  Var_01    C8    C7   C6   C5   114.13  30.0  3
 C8C  Var_02    C9    C8   C7   C6   -60.36  30.0  3
 C8C  Var_03    C10   C9   C8   C7   -80.49  30.0  2

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
 C8C  plan-1  N1    0.020
 C8C  plan-1  C2    0.020
 C8C  plan-1  C4    0.020
 C8C  plan-1  C5    0.020
 C8C  plan-1  C6    0.020
 C8C  plan-1  C7    0.020
 C8C  plan-1  N18   0.020
 C8C  plan-1  N3    0.020
 C8C  plan-1  O5    0.020
 C8C  plan-1  H1N1  0.020
 C8C  plan-1  H1N2  0.020
 C8C  plan-1  H3    0.020
 C8C  plan-1  H5    0.020
 C8C  plan-2  C8    0.020
 C8C  plan-2  C9    0.020
 C8C  plan-2  C10   0.020
 C8C  plan-2  C11   0.020
 C8C  plan-2  C12   0.020
 C8C  plan-2  C13   0.020
 C8C  plan-2  C14   0.020
 C8C  plan-2  N15   0.020
 C8C  plan-2  C16   0.020
 C8C  plan-2  C17   0.020
 C8C  plan-2  H10   0.020
 C8C  plan-2  H17   0.020
 C8C  plan-2  H11   0.020
 C8C  plan-2  H13   0.020
 C8C  plan-2  H14   0.020
 C8C  plan-2  H15   0.020

