# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 07:17:05 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 4-[[(5~{S},7~{R})-3-azanyl-1-adamantyl]carbonylamino]-1~{H}-indole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1[nH]c2cccc(NC(=O)C34C[C@@H]5C[C@@H](CC(N)(C5)C3)C4)c2c1
#
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
 E7H  E7H  4-[[(5~{S},7~{R})-3-azanyl-1-adamantyl]carbonylamino]-1~{H}-indole-2-carboxamide  ligand  50  26  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_E7H
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
 E7H  C1   C  CH1   0  -0.251   3.0328   1.9662  -0.6224
 E7H  C2   C  CH2   0  -0.383   3.5344  -0.9109  -0.6340
 E7H  C3   C  CT    0  -0.298   2.2570  -0.3451  -0.0037
 E7H  C11  C  C     0   0.608   1.1226  -1.3579  -0.1377
 E7H  C15  C  CR16  0  -0.331  -1.4982  -2.9398   0.2868
 E7H  C16  C  CR16  0  -0.275  -2.7914  -3.4876   0.2066
 E7H  C17  C  CR16  0  -0.316  -3.9233  -2.7071   0.1256
 E7H  C18  C  CR6   0   0.299  -1.3112  -1.5703   0.2812
 E7H  C19  C  CR56  0  -0.008  -2.4478  -0.7418   0.1929
 E7H  C20  C  CR56  0   0.353  -3.7287  -1.3245   0.1172
 E7H  C22  C  CR5   0   0.224  -3.9768   0.8921   0.0425
 E7H  C23  C  CR15  0  -0.392  -2.6303   0.6682   0.1459
 E7H  C24  C  C     0   0.475  -4.6239   2.2151  -0.0742
 E7H  C4   C  CH2   0  -0.409   2.5355  -0.0279   1.4785
 E7H  C5   C  CH1   0  -0.252   3.6734   0.9895   1.5832
 E7H  C6   C  CH2   0  -0.416   4.9359   0.4103   0.9462
 E7H  C7   C  CT    0   0.079   4.6900   0.0897  -0.5345
 E7H  C8   C  CH2   0  -0.413   1.8874   0.9610  -0.7376
 E7H  C9   C  CH2   0  -0.420   3.2847   2.2762   0.8535
 E7H  C10  C  CH2   0  -0.411   4.2939   1.3810  -1.2538
 E7H  N12  N  NH1   0  -0.751  -0.0662  -0.9414   0.3817
 E7H  O13  O  O     0  -0.454   1.2571  -2.4408  -0.6755
 E7H  N14  N  NH2   0  -0.801   5.8515  -0.4902  -1.1972
 E7H  N21  N  NR15  0  -0.746  -4.6338  -0.3126   0.0200
 E7H  N25  N  NH2   0  -0.817  -5.9076   2.2266  -0.4662
 E7H  O26  O  O     0  -0.476  -3.9907   3.2308   0.1792
 E7H  H1   H  HCH1  0   0.235   2.7511   2.8824  -1.1490
 E7H  H2   H  HCH2  0   0.229   3.8199  -1.8403  -0.1300
 E7H  H3   H  HCH2  0   0.232   3.3647  -1.1564  -1.6856
 E7H  H5   H  HCR6  0   0.258  -2.8923  -4.5649   0.2152
 E7H  H6   H  HCR6  0   0.264  -4.9117  -3.1427   0.0637
 E7H  H7   H  HCR5  0   0.257  -1.8759   1.4387   0.1541
 E7H  H8   H  HCH2  0   0.234   1.6435   0.3702   1.9731
 E7H  H9   H  HCH2  0   0.242   2.8047  -0.9477   2.0073
 E7H  H10  H  HCH1  0   0.233   3.8578   1.2043   2.6394
 E7H  H11  H  HCH2  0   0.223   5.7640   1.1230   1.0341
 E7H  H12  H  HCH2  0   0.221   5.2433  -0.5013   1.4716
 E7H  H13  H  HCH2  0   0.225   0.9816   1.4128  -0.3205
 E7H  H14  H  HCH2  0   0.245   1.6716   0.7465  -1.7887
 E7H  H15  H  HCH2  0   0.229   4.0822   3.0194   0.9533
 E7H  H16  H  HCH2  0   0.227   2.3891   2.7142   1.3056
 E7H  H17  H  HCH2  0   0.226   4.1309   1.1753  -2.3166
 E7H  H18  H  HCH2  0   0.225   5.1151   2.1040  -1.1912
 E7H  H19  H  HNH1  0   0.407  -0.0890  -0.0108   0.7677
 E7H  H20  H  HNH2  0   0.336   6.6293   0.1581  -1.1325
 E7H  H21  H  HNH2  0   0.335   6.1468  -1.3147  -0.6842
 E7H  H23  H  HNR5  0   0.414  -5.6311  -0.4486   0.0472
 E7H  H24  H  HNH2  0   0.407  -6.3851   1.4153  -0.8186
 E7H  H25  H  HNH2  0   0.411  -6.3750   3.1096  -0.5950
 E7H  H4   H  HCR6  0   0.265  -0.6560  -3.6087   0.3649

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
 E7H  N14  C7   single    1.458  0.020  1.458
 E7H  C6   C7   single    1.535  0.020  1.535
 E7H  C6   C5   single    1.528  0.020  1.528
 E7H  C7   C2   single    1.532  0.020  1.532
 E7H  C7   C10  single    1.530  0.020  1.530
 E7H  C2   C3   single    1.533  0.020  1.533
 E7H  C5   C4   single    1.530  0.020  1.530
 E7H  C5   C9   single    1.529  0.020  1.529
 E7H  N25  C24  single    1.342  0.020  1.342
 E7H  C4   C3   single    1.541  0.020  1.541
 E7H  C10  C1   single    1.527  0.020  1.527
 E7H  C24  C22  single    1.477  0.020  1.477
 E7H  C24  O26  double    1.223  0.020  1.223
 E7H  C23  C22  aromatic  1.369  0.020  1.369
 E7H  C23  C19  aromatic  1.423  0.020  1.423
 E7H  N12  C18  single    1.398  0.020  1.398
 E7H  N12  C11  single    1.363  0.020  1.363
 E7H  C3   C11  single    1.527  0.020  1.527
 E7H  C3   C8   single    1.543  0.020  1.543
 E7H  C22  N21  aromatic  1.372  0.020  1.372
 E7H  C19  C18  aromatic  1.409  0.020  1.409
 E7H  C19  C20  aromatic  1.409  0.020  1.409
 E7H  C18  C15  aromatic  1.382  0.020  1.382
 E7H  C9   C1   single    1.529  0.020  1.529
 E7H  C11  O13  double    1.217  0.020  1.217
 E7H  N21  C20  aromatic  1.361  0.020  1.361
 E7H  C20  C17  aromatic  1.396  0.020  1.396
 E7H  C15  C16  aromatic  1.407  0.020  1.407
 E7H  C1   C8   single    1.528  0.020  1.528
 E7H  C16  C17  aromatic  1.377  0.020  1.377
 E7H  C1   H1   single    0.970  0.020  1.090
 E7H  C2   H2   single    0.970  0.020  1.090
 E7H  C2   H3   single    0.970  0.020  1.090
 E7H  C15  H4   single    0.930  0.020  1.080
 E7H  C16  H5   single    0.930  0.020  1.080
 E7H  C17  H6   single    0.930  0.020  1.080
 E7H  C23  H7   single    0.930  0.020  1.080
 E7H  C4   H8   single    0.970  0.020  1.090
 E7H  C4   H9   single    0.970  0.020  1.090
 E7H  C5   H10  single    0.970  0.020  1.090
 E7H  C6   H11  single    0.970  0.020  1.090
 E7H  C6   H12  single    0.970  0.020  1.090
 E7H  C8   H13  single    0.970  0.020  1.090
 E7H  C8   H14  single    0.970  0.020  1.090
 E7H  C9   H15  single    0.970  0.020  1.090
 E7H  C9   H16  single    0.970  0.020  1.090
 E7H  C10  H17  single    0.970  0.020  1.090
 E7H  C10  H18  single    0.970  0.020  1.090
 E7H  N12  H19  single    0.860  0.020  1.020
 E7H  N14  H20  single    0.890  0.020  1.040
 E7H  N14  H21  single    0.890  0.020  1.040
 E7H  N21  H23  single    0.860  0.020  1.020
 E7H  N25  H24  single    0.860  0.020  1.020
 E7H  N25  H25  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
 E7H  H1   C1   C10  109.55  3.000
 E7H  H1   C1   C9   109.72  3.000
 E7H  C10  C1   C9   109.92  3.000
 E7H  H1   C1   C8   108.77  3.000
 E7H  C9   C1   C8   109.24  3.000
 E7H  C10  C1   C8   109.62  3.000
 E7H  H3   C2   H2   107.02  3.000
 E7H  H3   C2   C7   109.04  3.000
 E7H  H2   C2   C7   109.13  3.000
 E7H  H3   C2   C3   110.44  3.000
 E7H  H2   C2   C3   109.96  3.000
 E7H  C7   C2   C3   111.15  3.000
 E7H  C8   C3   C4   109.06  3.000
 E7H  C8   C3   C11  109.99  3.000
 E7H  C4   C3   C11  110.81  3.000
 E7H  C8   C3   C2   108.45  3.000
 E7H  C11  C3   C2   109.77  3.000
 E7H  C4   C3   C2   108.72  3.000
 E7H  O13  C11  N12  122.49  3.000
 E7H  O13  C11  C3   123.17  3.000
 E7H  N12  C11  C3   114.33  3.000
 E7H  H4   C15  C18  120.61  3.000
 E7H  H4   C15  C16  118.72  3.000
 E7H  C18  C15  C16  120.66  3.000
 E7H  H5   C16  C17  119.21  3.000
 E7H  H5   C16  C15  118.23  3.000
 E7H  C17  C16  C15  122.56  3.000
 E7H  H6   C17  C20  121.71  3.000
 E7H  H6   C17  C16  121.74  3.000
 E7H  C20  C17  C16  116.55  3.000
 E7H  N12  C18  C19  117.27  3.000
 E7H  C19  C18  C15  118.27  3.000
 E7H  N12  C18  C15  124.45  3.000
 E7H  C23  C19  C20  106.95  3.000
 E7H  C20  C19  C18  119.56  3.000
 E7H  C23  C19  C18  133.49  3.000
 E7H  N21  C20  C19  107.51  3.000
 E7H  N21  C20  C17  130.09  3.000
 E7H  C19  C20  C17  122.40  3.000
 E7H  N21  C22  C24  125.11  3.000
 E7H  N21  C22  C23  109.18  3.000
 E7H  C24  C22  C23  125.68  3.000
 E7H  H7   C23  C22  124.88  3.000
 E7H  H7   C23  C19  128.19  3.000
 E7H  C22  C23  C19  106.90  3.000
 E7H  O26  C24  N25  123.25  3.000
 E7H  O26  C24  C22  120.03  3.000
 E7H  N25  C24  C22  116.72  3.000
 E7H  H9   C4   H8   106.72  3.000
 E7H  H9   C4   C5   110.05  3.000
 E7H  H8   C4   C5   109.46  3.000
 E7H  H9   C4   C3   109.64  3.000
 E7H  H8   C4   C3   111.23  3.000
 E7H  C5   C4   C3   109.70  3.000
 E7H  H10  C5   C9   109.78  3.000
 E7H  H10  C5   C6   109.74  3.000
 E7H  C9   C5   C6   109.27  3.000
 E7H  H10  C5   C4   108.80  3.000
 E7H  C9   C5   C4   109.74  3.000
 E7H  C6   C5   C4   109.50  3.000
 E7H  H12  C6   H11  106.89  3.000
 E7H  H12  C6   C7   109.49  3.000
 E7H  H11  C6   C7   109.53  3.000
 E7H  H12  C6   C5   110.31  3.000
 E7H  H11  C6   C5   110.14  3.000
 E7H  C7   C6   C5   110.42  3.000
 E7H  N14  C7   C10  109.16  3.000
 E7H  C10  C7   C6   108.59  3.000
 E7H  N14  C7   C6   113.21  3.000
 E7H  C10  C7   C2   108.99  3.000
 E7H  C6   C7   C2   108.66  3.000
 E7H  N14  C7   C2   108.17  3.000
 E7H  H14  C8   H13  106.47  3.000
 E7H  H14  C8   C3   109.77  3.000
 E7H  H13  C8   C3   111.49  3.000
 E7H  H14  C8   C1   110.43  3.000
 E7H  H13  C8   C1   108.66  3.000
 E7H  C3   C8   C1   109.96  3.000
 E7H  H16  C9   H15  106.66  3.000
 E7H  H16  C9   C5   110.33  3.000
 E7H  H15  C9   C5   110.04  3.000
 E7H  H16  C9   C1   110.18  3.000
 E7H  H15  C9   C1   110.22  3.000
 E7H  C5   C9   C1   109.38  3.000
 E7H  H18  C10  H17  106.92  3.000
 E7H  H18  C10  C7   109.62  3.000
 E7H  H17  C10  C7   109.65  3.000
 E7H  H18  C10  C1   110.03  3.000
 E7H  H17  C10  C1   110.52  3.000
 E7H  C7   C10  C1   110.05  3.000
 E7H  H19  N12  C18  115.00  3.000
 E7H  H19  N12  C11  116.62  3.000
 E7H  C18  N12  C11  127.73  3.000
 E7H  H21  N14  H20  105.30  3.000
 E7H  H21  N14  C7   108.98  3.000
 E7H  H20  N14  C7   109.13  3.000
 E7H  H23  N21  C22  126.32  3.000
 E7H  H23  N21  C20  123.80  3.000
 E7H  C22  N21  C20  109.46  3.000
 E7H  H25  N25  H24  116.25  3.000
 E7H  H25  N25  C24  119.25  3.000
 E7H  H24  N25  C24  123.35  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
 E7H  CONST_01  C23  C19  C18  C15  180.00   0.0  0
 E7H  CONST_02  C20  C19  C18  C15    0.00   0.0  0
 E7H  CONST_03  C20  C17  C16  C15    0.00   0.0  0
 E7H  CONST_04  C19  C18  C15  C16    0.00   0.0  0
 E7H  CONST_05  C19  C20  C17  C16    0.00   0.0  0
 E7H  CONST_06  N21  C20  C17  C16  180.00   0.0  0
 E7H  CONST_07  C23  C19  C20  C17  180.00   0.0  0
 E7H  CONST_08  C18  C19  C20  C17    0.00   0.0  0
 E7H  CONST_09  C22  N21  C20  C17  180.00   0.0  0
 E7H  CONST_10  C18  C15  C16  C17    0.00   0.0  0
 E7H  CONST_11  C22  C23  C19  C18  180.00   0.0  0
 E7H  CONST_12  N21  C20  C19  C18  180.00   0.0  0
 E7H  CONST_13  N21  C22  C23  C19    0.00   0.0  0
 E7H  CONST_14  C22  N21  C20  C19    0.00   0.0  0
 E7H  CONST_15  C22  C23  C19  C20    0.00   0.0  0
 E7H  CONST_16  C23  C22  N21  C20    0.00   0.0  0
 E7H  CONST_17  N21  C20  C19  C23    0.00   0.0  0
 E7H  CONST_18  N12  C18  C15  C16  180.00   0.0  0
 E7H  CONST_19  C24  C22  C23  C19  180.00   0.0  0
 E7H  CONST_20  N12  C18  C19  C20  180.00   0.0  0
 E7H  CONST_21  C24  C22  N21  C20  180.00   0.0  0
 E7H  CONST_22  N12  C18  C19  C23    0.00   0.0  0
 E7H  CONST_23  H6   C17  C16  C15  180.00   0.0  0
 E7H  CONST_24  H23  N21  C20  C17    0.00   0.0  0
 E7H  CONST_25  H4   C15  C16  C17  180.00   0.0  0
 E7H  CONST_26  H7   C23  C19  C18    0.00   0.0  0
 E7H  CONST_27  H5   C16  C15  C18  180.00   0.0  0
 E7H  CONST_28  C18  N12  C11  C3   180.00   0.0  0
 E7H  CONST_32  O13  C11  N12  C18    0.00   0.0  0
 E7H  CONST_33  H24  N25  C24  C22    0.00   0.0  0
 E7H  CONST_34  H25  N25  C24  C22  180.00   0.0  0
 E7H  Var_01    N25  C24  C22  C23  165.34  30.0  2

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
 E7H  chir_01  C1  C10  C9  C8   positiv
 E7H  chir_02  C3  C8   C4  C2   positiv
 E7H  chir_03  C5  C9   C4  C6   negativ
 E7H  chir_04  C7  C6   C2  C10  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
 E7H  plan-1  C15  0.020
 E7H  plan-1  C16  0.020
 E7H  plan-1  C17  0.020
 E7H  plan-1  C18  0.020
 E7H  plan-1  C19  0.020
 E7H  plan-1  C20  0.020
 E7H  plan-1  C22  0.020
 E7H  plan-1  C23  0.020
 E7H  plan-1  C24  0.020
 E7H  plan-1  N12  0.020
 E7H  plan-1  N21  0.020
 E7H  plan-1  H5   0.020
 E7H  plan-1  H6   0.020
 E7H  plan-1  H7   0.020
 E7H  plan-1  H23  0.020
 E7H  plan-1  H4   0.020
 E7H  plan-2  C3   0.020
 E7H  plan-2  C11  0.020
 E7H  plan-2  C18  0.020
 E7H  plan-2  N12  0.020
 E7H  plan-2  O13  0.020
 E7H  plan-2  H19  0.020
 E7H  plan-3  C22  0.020
 E7H  plan-3  C24  0.020
 E7H  plan-3  N25  0.020
 E7H  plan-3  O26  0.020
 E7H  plan-3  H24  0.020
 E7H  plan-3  H25  0.020

