# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 08:10:13 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: 5-methyl-2-[(4-methyl-1~{H}-imidazol-5-yl)methyl]-3,4-dihydropyrido[4,3-b]indol-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c2CCN(Cc3[nH]cnc3C)C(=O)c2c4ccccc14
#
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
 S7Y  S7Y  "alosetron"
  ligand  40  22  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_S7Y
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
 S7Y  N    N  NT    0  -0.492  102.6028  118.3999  92.4668
 S7Y  C    C  CR5   0   0.379  100.0522  119.2585  93.1304
 S7Y  O    O  O     0  -0.507  103.4928  120.1708  93.5906
 S7Y  C1   C  CH2   0  -0.531  100.1693  117.9011  92.5460
 S7Y  C10  C  CR16  0  -0.315   98.4651  122.1064  94.6052
 S7Y  C11  C  CR5   0   0.270  104.0027  116.4101  92.6353
 S7Y  C12  C  CR16  0  -0.263  100.4779  123.3930  95.0284
 S7Y  C13  C  CR16  0  -0.281   99.0850  123.2483  95.0824
 S7Y  C14  C  CR5   0   0.096  103.9072  115.8671  93.8902
 S7Y  C15  C  CH3   0  -0.742  103.6532  116.5771  95.1748
 S7Y  C16  C  CR15  0   0.073  104.2411  114.2322  92.5545
 S7Y  C2   C  CR5   0  -0.196  101.1534  120.0366  93.3897
 S7Y  C3   C  CH2   0  -0.287  101.4621  117.8561  91.7443
 S7Y  C4   C  CR56  0   0.106  100.6838  121.2406  94.0047
 S7Y  C5   C  CR56  0   0.331   99.2802  121.1135  94.0725
 S7Y  C6   C  C     0   0.513  102.5119  119.5701  93.1586
 S7Y  C7   C  CH2   0  -0.405  103.8976  117.8212  92.1617
 S7Y  C8   C  CH3   0  -0.539   97.5726  119.4010  93.4597
 S7Y  C9   C  CR16  0  -0.383  101.2839  122.4027  94.4954
 S7Y  N1   N  NR5   0  -0.585   98.9277  119.8922  93.5378
 S7Y  N2   N  NR15  0  -0.610  104.2127  115.3454  91.8008
 S7Y  N3   N  N     0  -0.460  104.0575  114.5088  93.8213
 S7Y  H3   H  HCH2  0   0.277   99.3400  117.6566  91.8813
 S7Y  H4   H  HCH2  0   0.277  100.1770  117.1522  93.3445
 S7Y  H5   H  HCR6  0   0.268   97.3888  121.9975  94.6506
 S7Y  H6   H  HCR6  0   0.249  100.9292  124.2978  95.4143
 S7Y  H7   H  HCR6  0   0.252   98.4838  124.0425  95.5053
 S7Y  H8   H  HCH3  0   0.240  104.2485  116.1499  95.9822
 S7Y  H9   H  HCH3  0   0.238  103.9005  117.6353  95.1005
 S7Y  H10  H  HCH3  0   0.238  102.6046  116.5093  95.4737
 S7Y  H11  H  HCR5  0   0.274  104.4020  113.2518  92.1334
 S7Y  H12  H  HCH2  0   0.266  101.6846  116.8216  91.4868
 S7Y  H13  H  HCH2  0   0.252  101.3235  118.3997  90.8028
 S7Y  H15  H  HCH2  0   0.282  104.6622  118.4389  92.6292
 S7Y  H16  H  HCH2  0   0.266  104.0798  117.8649  91.0824
 S7Y  H17  H  HCH3  0   0.260   96.9491  120.0865  92.8871
 S7Y  H18  H  HCH3  0   0.270   97.5599  118.4334  92.9675
 S7Y  H19  H  HCH3  0   0.260   97.1471  119.2848  94.4560
 S7Y  H20  H  HCR6  0   0.243  102.3578  122.5245  94.4602
 S7Y  H21  H  HNR5  0   0.414  104.3330  115.3867  90.8007

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
 S7Y  N2   C16  aromatic  1.345  0.020  1.345
 S7Y  N2   C11  aromatic  1.369  0.020  1.369
 S7Y  C16  N3   aromatic  1.310  0.020  1.310
 S7Y  C3   C1   single    1.522  0.020  1.522
 S7Y  C3   N    single    1.456  0.020  1.456
 S7Y  C7   C11  single    1.492  0.020  1.492
 S7Y  C7   N    single    1.451  0.020  1.451
 S7Y  C1   C    single    1.483  0.020  1.483
 S7Y  C11  C14  aromatic  1.371  0.020  1.371
 S7Y  N    C6   single    1.362  0.020  1.362
 S7Y  C6   C2   single    1.455  0.020  1.455
 S7Y  C6   O    double    1.229  0.020  1.229
 S7Y  C    C2   aromatic  1.373  0.020  1.373
 S7Y  C    N1   aromatic  1.354  0.020  1.354
 S7Y  C2   C4   aromatic  1.431  0.020  1.431
 S7Y  N3   C14  aromatic  1.368  0.020  1.368
 S7Y  C8   N1   single    1.444  0.020  1.444
 S7Y  N1   C5   aromatic  1.379  0.020  1.379
 S7Y  C14  C15  single    1.490  0.020  1.490
 S7Y  C4   C5   aromatic  1.411  0.020  1.411
 S7Y  C4   C9   aromatic  1.397  0.020  1.397
 S7Y  C5   C10  aromatic  1.391  0.020  1.391
 S7Y  C9   C12  aromatic  1.384  0.020  1.384
 S7Y  C10  C13  aromatic  1.384  0.020  1.384
 S7Y  C12  C13  aromatic  1.402  0.020  1.402
 S7Y  C1   H3   single    0.970  0.020  1.090
 S7Y  C1   H4   single    0.970  0.020  1.090
 S7Y  C10  H5   single    0.930  0.020  1.080
 S7Y  C12  H6   single    0.930  0.020  1.080
 S7Y  C13  H7   single    0.930  0.020  1.080
 S7Y  C15  H8   single    0.970  0.020  1.090
 S7Y  C15  H9   single    0.970  0.020  1.090
 S7Y  C15  H10  single    0.970  0.020  1.090
 S7Y  C16  H11  single    0.930  0.020  1.080
 S7Y  C3   H12  single    0.970  0.020  1.090
 S7Y  C3   H13  single    0.970  0.020  1.090
 S7Y  C7   H15  single    0.970  0.020  1.090
 S7Y  C7   H16  single    0.970  0.020  1.090
 S7Y  C8   H17  single    0.970  0.020  1.090
 S7Y  C8   H18  single    0.970  0.020  1.090
 S7Y  C8   H19  single    0.970  0.020  1.090
 S7Y  C9   H20  single    0.930  0.020  1.080
 S7Y  N2   H21  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
 S7Y  C7   N    C6   120.60  3.000
 S7Y  C6   N    C3   121.37  3.000
 S7Y  C7   N    C3   116.49  3.000
 S7Y  N1   C    C2   110.13  3.000
 S7Y  N1   C    C1   127.80  3.000
 S7Y  C2   C    C1   122.00  3.000
 S7Y  H4   C1   H3   107.26  3.000
 S7Y  H4   C1   C3   110.98  3.000
 S7Y  H3   C1   C3   108.56  3.000
 S7Y  H4   C1   C    109.84  3.000
 S7Y  H3   C1   C    112.67  3.000
 S7Y  C3   C1   C    107.57  3.000
 S7Y  H5   C10  C5   121.80  3.000
 S7Y  H5   C10  C13  120.91  3.000
 S7Y  C5   C10  C13  117.30  3.000
 S7Y  N2   C11  C7   123.56  3.000
 S7Y  C7   C11  C14  131.33  3.000
 S7Y  N2   C11  C14  105.11  3.000
 S7Y  H6   C12  C9   119.53  3.000
 S7Y  H6   C12  C13  119.14  3.000
 S7Y  C9   C12  C13  121.33  3.000
 S7Y  H7   C13  C12  119.44  3.000
 S7Y  H7   C13  C10  119.43  3.000
 S7Y  C12  C13  C10  121.13  3.000
 S7Y  N3   C14  C15  122.36  3.000
 S7Y  C15  C14  C11  127.78  3.000
 S7Y  N3   C14  C11  109.85  3.000
 S7Y  H10  C15  H9   107.27  3.000
 S7Y  H10  C15  H8   107.29  3.000
 S7Y  H9   C15  H8   107.90  3.000
 S7Y  H10  C15  C14  111.72  3.000
 S7Y  H9   C15  C14  111.44  3.000
 S7Y  H8   C15  C14  111.02  3.000
 S7Y  H11  C16  N3   126.18  3.000
 S7Y  H11  C16  N2   122.45  3.000
 S7Y  N3   C16  N2   111.37  3.000
 S7Y  C6   C2   C4   130.12  3.000
 S7Y  C4   C2   C    107.14  3.000
 S7Y  C6   C2   C    122.49  3.000
 S7Y  H13  C3   H12  107.09  3.000
 S7Y  H13  C3   C1   109.29  3.000
 S7Y  H12  C3   C1   109.03  3.000
 S7Y  H13  C3   N    109.89  3.000
 S7Y  H12  C3   N    108.19  3.000
 S7Y  C1   C3   N    113.15  3.000
 S7Y  C9   C4   C5   119.03  3.000
 S7Y  C9   C4   C2   135.22  3.000
 S7Y  C5   C4   C2   105.74  3.000
 S7Y  N1   C5   C4   108.39  3.000
 S7Y  C4   C5   C10  122.49  3.000
 S7Y  N1   C5   C10  129.12  3.000
 S7Y  C2   C6   O    122.20  3.000
 S7Y  O    C6   N    123.04  3.000
 S7Y  C2   C6   N    114.73  3.000
 S7Y  H16  C7   H15  106.48  3.000
 S7Y  H16  C7   C11  109.80  3.000
 S7Y  H15  C7   C11  110.54  3.000
 S7Y  H16  C7   N    109.86  3.000
 S7Y  H15  C7   N    108.07  3.000
 S7Y  C11  C7   N    111.92  3.000
 S7Y  H19  C8   H18  108.36  3.000
 S7Y  H19  C8   H17  108.92  3.000
 S7Y  H18  C8   H17  108.42  3.000
 S7Y  H19  C8   N1   110.69  3.000
 S7Y  H18  C8   N1   109.80  3.000
 S7Y  H17  C8   N1   110.59  3.000
 S7Y  H20  C9   C4   120.58  3.000
 S7Y  H20  C9   C12  120.69  3.000
 S7Y  C4   C9   C12  118.72  3.000
 S7Y  C8   N1   C5   124.22  3.000
 S7Y  C5   N1   C    108.60  3.000
 S7Y  C8   N1   C    127.18  3.000
 S7Y  H21  N2   C16  125.97  3.000
 S7Y  H21  N2   C11  126.24  3.000
 S7Y  C16  N2   C11  107.78  3.000
 S7Y  C16  N3   C14  105.89  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
 S7Y  CONST_01  C5   C4   C2   C       0.00   0.0  0
 S7Y  CONST_02  C9   C4   C2   C     180.00   0.0  0
 S7Y  CONST_03  C4   C5   N1   C       0.00   0.0  0
 S7Y  CONST_04  C10  C5   N1   C     180.00   0.0  0
 S7Y  CONST_05  C2   C4   C5   C10   180.00   0.0  0
 S7Y  CONST_06  C9   C4   C5   C10     0.00   0.0  0
 S7Y  CONST_07  C9   C12  C13  C10     0.00   0.0  0
 S7Y  CONST_08  N3   C16  N2   C11     0.00   0.0  0
 S7Y  CONST_09  C16  N3   C14  C11     0.00   0.0  0
 S7Y  CONST_10  C2   C4   C9   C12   180.00   0.0  0
 S7Y  CONST_11  C5   C4   C9   C12     0.00   0.0  0
 S7Y  CONST_12  C5   C10  C13  C12     0.00   0.0  0
 S7Y  CONST_13  N1   C5   C10  C13   180.00   0.0  0
 S7Y  CONST_14  C4   C5   C10  C13     0.00   0.0  0
 S7Y  CONST_15  C4   C9   C12  C13     0.00   0.0  0
 S7Y  CONST_16  C16  N2   C11  C14     0.00   0.0  0
 S7Y  CONST_17  N2   C16  N3   C14     0.00   0.0  0
 S7Y  CONST_18  C5   N1   C    C2      0.00   0.0  0
 S7Y  CONST_19  N1   C5   C4   C2      0.00   0.0  0
 S7Y  CONST_20  N1   C    C2   C4      0.00   0.0  0
 S7Y  CONST_21  N1   C5   C4   C9    180.00   0.0  0
 S7Y  CONST_22  N3   C14  C11  N2      0.00   0.0  0
 S7Y  CONST_23  C3   N    C6   C2      0.00   0.0  0
 S7Y  CONST_24  C8   N1   C    C1      0.00   0.0  0
 S7Y  CONST_25  C8   N1   C5   C10     0.00   0.0  0
 S7Y  CONST_26  N2   C11  C14  C15   180.00   0.0  0
 S7Y  CONST_27  C16  N3   C14  C15   180.00   0.0  0
 S7Y  CONST_28  C7   C11  N2   C16   180.00   0.0  0
 S7Y  CONST_29  C8   N1   C    C2    180.00   0.0  0
 S7Y  CONST_30  C8   N1   C5   C4    180.00   0.0  0
 S7Y  CONST_31  N3   C14  C11  C7    180.00   0.0  0
 S7Y  CONST_32  C3   N    C6   O     180.00   0.0  0
 S7Y  CONST_33  C7   N    C6   C2    180.00   0.0  0
 S7Y  CONST_34  H6   C12  C13  C10   180.00   0.0  0
 S7Y  CONST_35  H11  C16  N2   C11   180.00   0.0  0
 S7Y  CONST_36  H5   C10  C13  C12   180.00   0.0  0
 S7Y  CONST_37  H20  C9   C12  C13   180.00   0.0  0
 S7Y  CONST_38  H21  N2   C11  C14   180.00   0.0  0
 S7Y  CONST_39  H11  C16  N3   C14   180.00   0.0  0
 S7Y  CONST_40  H20  C9   C4   C2      0.00   0.0  0
 S7Y  CONST_41  H5   C10  C5   C4    180.00   0.0  0
 S7Y  CONST_42  H6   C12  C9   C4    180.00   0.0  0
 S7Y  CONST_43  H20  C9   C4   C5    180.00   0.0  0
 S7Y  CONST_44  H7   C13  C10  C5    180.00   0.0  0
 S7Y  CONST_45  H7   C13  C12  C9    180.00   0.0  0
 S7Y  CONST_46  H5   C10  C5   N1      0.00   0.0  0
 S7Y  CONST_47  H21  N2   C16  N3    180.00   0.0  0
 S7Y  CONST_48  C7   N    C6   O       0.00   0.0  0
 S7Y  Var_01    C    C1   C3   N      47.30  30.0  1
 S7Y  Var_02    C    C2   C6   N      10.26  30.0  1
 S7Y  Var_03    C4   C2   C6   N    -176.22  30.0  1
 S7Y  Var_04    C6   N    C3   C1    -45.09  30.0  1
 S7Y  Var_05    C3   C1   C    C2    -26.26  30.0  1
 S7Y  Var_06    N1   C    C1   C3    156.95  30.0  1
 S7Y  Var_07    N2   C11  C7   N     118.51  30.0  2
 S7Y  Var_08    C14  C11  C7   N     -60.48  30.0  2
 S7Y  Var_09    O    C6   C2   C    -167.74  30.0  1
 S7Y  Var_10    C4   C2   C6   O       5.78  30.0  1
 S7Y  Var_11    C7   N    C3   C1    149.01  30.0  1
 S7Y  Var_12    C3   N    C7   C11   -68.30  30.0  3
 S7Y  Var_13    C6   N    C7   C11   125.68  30.0  3
 S7Y  Var_14    H3   C1   C3   N     169.49  30.0  1
 S7Y  Var_15    H4   C1   C3   N     -72.88  30.0  1
 S7Y  Var_16    H12  C3   C1   C     167.74  30.0  1
 S7Y  Var_17    H13  C3   C1   C     -75.50  30.0  1
 S7Y  Var_18    H3   C1   C    C2   -145.87  30.0  1
 S7Y  Var_19    H4   C1   C    C2     94.63  30.0  1
 S7Y  Var_20    H12  C3   N    C6   -166.01  30.0  1
 S7Y  Var_21    H13  C3   N    C6     77.38  30.0  1
 S7Y  Var_22    H3   C1   C    N1     37.34  30.0  1
 S7Y  Var_23    H4   C1   C    N1    -82.16  30.0  1
 S7Y  Var_24    H17  C8   N1   C    -122.38  30.0  2
 S7Y  Var_25    H18  C8   N1   C      -2.79  30.0  2
 S7Y  Var_26    H19  C8   N1   C     116.81  30.0  2
 S7Y  Var_27    H8   C15  C14  C11  -141.25  30.0  2
 S7Y  Var_28    H9   C15  C14  C11   -20.95  30.0  2
 S7Y  Var_29    H10  C15  C14  C11    99.03  30.0  2
 S7Y  Var_30    H15  C7   C11  C14    60.04  30.0  1
 S7Y  Var_31    H16  C7   C11  C14   177.23  30.0  1
 S7Y  Var_32    H15  C7   N    C3    169.75  30.0  1
 S7Y  Var_33    H16  C7   N    C3     53.95  30.0  1
 S7Y  Var_34    H17  C8   N1   C5     58.46  30.0  2
 S7Y  Var_35    H18  C8   N1   C5    178.06  30.0  2
 S7Y  Var_36    H19  C8   N1   C5    -62.34  30.0  2
 S7Y  Var_37    H15  C7   N    C6      3.74  30.0  1
 S7Y  Var_38    H16  C7   N    C6   -112.07  30.0  1
 S7Y  Var_39    H12  C3   N    C7     28.09  30.0  1
 S7Y  Var_40    H13  C3   N    C7    -88.53  30.0  1
 S7Y  Var_41    H15  C7   C11  N2   -120.97  30.0  1
 S7Y  Var_42    H16  C7   C11  N2     -3.78  30.0  1
 S7Y  Var_43    H8   C15  C14  N3     40.03  30.0  2
 S7Y  Var_44    H9   C15  C14  N3    160.33  30.0  2
 S7Y  Var_45    H10  C15  C14  N3    -79.69  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
 S7Y  plan-1  C11  0.020
 S7Y  plan-1  C14  0.020
 S7Y  plan-1  C15  0.020
 S7Y  plan-1  C16  0.020
 S7Y  plan-1  C7   0.020
 S7Y  plan-1  N2   0.020
 S7Y  plan-1  N3   0.020
 S7Y  plan-1  H11  0.020
 S7Y  plan-1  H21  0.020
 S7Y  plan-2  C    0.020
 S7Y  plan-2  C1   0.020
 S7Y  plan-2  C10  0.020
 S7Y  plan-2  C12  0.020
 S7Y  plan-2  C13  0.020
 S7Y  plan-2  C2   0.020
 S7Y  plan-2  C4   0.020
 S7Y  plan-2  C5   0.020
 S7Y  plan-2  C6   0.020
 S7Y  plan-2  C8   0.020
 S7Y  plan-2  C9   0.020
 S7Y  plan-2  N1   0.020
 S7Y  plan-2  H5   0.020
 S7Y  plan-2  H6   0.020
 S7Y  plan-2  H7   0.020
 S7Y  plan-2  H20  0.020
 S7Y  plan-3  N    0.020
 S7Y  plan-3  O    0.020
 S7Y  plan-3  C2   0.020
 S7Y  plan-3  C3   0.020
 S7Y  plan-3  C6   0.020
 S7Y  plan-3  C7   0.020

