# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 07:57:42 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: [(1S)-1-methyl-6-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,3-dihydro-1H-inden-1-yl]cyanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(CCc2ccc(cc12)c3ncnc4[nH]ccc34)NC#N
#
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
 G54  G54  '[(1S)-1-methyl-6-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,3-dihydro-1H-inden-1-yl]cyanamide'  ligand  37  22  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G54
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
 G54  N3   N  NR15  0  -0.658   5.0632  -0.3662   0.4282
 G54  C4   C  CR56  0   0.084  -2.1220  -1.7871  -0.3444
 G54  N2   N  N     0  -0.422   4.0070   1.6704  -0.2398
 G54  C7   C  CH2   0  -0.505  -3.5490  -2.2515  -0.2973
 G54  C6   C  CR16  0  -0.365  -0.8202   0.2159   0.0051
 G54  C9   C  CR5   0   0.017  -3.4124   0.1224   0.2745
 G54  C13  C  CR56  0   0.496   3.9967   0.3830   0.0714
 G54  C8   C  CH2   0  -0.457  -4.3386  -0.9378  -0.3556
 G54  N5   N  NS    0  -0.344  -3.1241   3.5708   0.7536
 G54  C16  C  CR15  0  -0.474   3.2935  -1.7355   0.5358
 G54  C1   C  CR6   0   0.062   0.3475  -0.5011  -0.2712
 G54  C2   C  CR16  0  -0.316   0.2547  -1.8558  -0.6007
 G54  C3   C  CR16  0  -0.307  -0.9730  -2.5029  -0.6390
 G54  C5   C  CR56  0   0.186  -2.0368  -0.4355  -0.0316
 G54  C11  C  CR6   0   0.211   1.6493   0.1874  -0.2317
 G54  N1   N  N     0  -0.446   1.6562   1.4871  -0.5238
 G54  C12  C  CR16  0   0.027   2.8080   2.1515  -0.5130
 G54  C14  C  CR56  0  -0.001   2.8496  -0.4446   0.1102
 G54  C15  C  CR15  0   0.009   4.6413  -1.6386   0.7126
 G54  N4   N  NH1   0  -0.625  -3.6658   1.4237  -0.3533
 G54  C17  C  CSP   0   0.277  -3.3541   2.5604   0.2343
 G54  H1   H  HNR5  0   0.419   6.0130  -0.0362   0.4953
 G54  H2   H  HCH2  0   0.264  -3.8033  -2.9327  -1.1101
 G54  H3   H  HCH2  0   0.259  -3.7414  -2.7888   0.6361
 G54  H4   H  HCR6  0   0.251  -0.7521   1.2695   0.2483
 G54  H5   H  HCH2  0   0.258  -4.5237  -0.6763  -1.4006
 G54  H6   H  HCH2  0   0.258  -5.3046  -0.9868   0.1467
 G54  H7   H  HCR5  0   0.263   2.7064  -2.6226   0.7036
 G54  H8   H  HCR6  0   0.258   1.1455  -2.4086  -0.8669
 G54  H9   H  HCR6  0   0.255  -1.0231  -3.5505  -0.9089
 G54  H10  H  HCH3  0   0.253  -4.6287   0.5810   2.0106
 G54  H11  H  HCH3  0   0.259  -3.4961  -0.7537   2.2382
 G54  H12  H  HCH3  0   0.248  -2.9001   0.8973   2.2483
 G54  H13  H  HCR6  0   0.252   2.7536   3.2055  -0.7618
 G54  H14  H  HCR5  0   0.296   5.3474  -2.3888   1.0291
 G54  H15  H  HNH1  0   0.426  -3.6461   1.4434  -1.3644
 G54  C10  C  CH3   0  -0.669  -3.6228   0.2269   1.7806

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
 G54  C10  C9   single    1.524  0.020  1.524
 G54  C8   C9   single    1.542  0.020  1.542
 G54  C8   C7   single    1.534  0.020  1.534
 G54  C9   N4   single    1.467  0.020  1.467
 G54  C9   C5   single    1.516  0.020  1.516
 G54  N4   C17  single    1.317  0.020  1.317
 G54  C17  N5   triple    1.159  0.020  1.159
 G54  C7   C4   single    1.501  0.020  1.501
 G54  C5   C6   aromatic  1.381  0.020  1.381
 G54  C5   C4   aromatic  1.390  0.020  1.390
 G54  C6   C1   aromatic  1.398  0.020  1.398
 G54  C4   C3   aromatic  1.385  0.020  1.385
 G54  C3   C2   aromatic  1.388  0.020  1.388
 G54  C1   C2   aromatic  1.397  0.020  1.397
 G54  C1   C11  single    1.473  0.020  1.473
 G54  C16  C15  aromatic  1.363  0.020  1.363
 G54  C16  C14  aromatic  1.430  0.020  1.430
 G54  C15  N3   aromatic  1.370  0.020  1.370
 G54  C14  C11  aromatic  1.399  0.020  1.399
 G54  C14  C13  aromatic  1.415  0.020  1.415
 G54  C11  N1   aromatic  1.332  0.020  1.332
 G54  N3   C13  aromatic  1.351  0.020  1.351
 G54  N1   C12  aromatic  1.330  0.020  1.330
 G54  C13  N2   aromatic  1.325  0.020  1.325
 G54  C12  N2   aromatic  1.321  0.020  1.321
 G54  N3   H1   single    0.860  0.020  1.020
 G54  C7   H2   single    0.970  0.020  1.090
 G54  C7   H3   single    0.970  0.020  1.090
 G54  C6   H4   single    0.930  0.020  1.080
 G54  C8   H5   single    0.970  0.020  1.090
 G54  C8   H6   single    0.970  0.020  1.090
 G54  C16  H7   single    0.930  0.020  1.080
 G54  C2   H8   single    0.930  0.020  1.080
 G54  C3   H9   single    0.930  0.020  1.080
 G54  C10  H10  single    0.970  0.020  1.090
 G54  C10  H11  single    0.970  0.020  1.090
 G54  C10  H12  single    0.970  0.020  1.090
 G54  C12  H13  single    0.930  0.020  1.080
 G54  C15  H14  single    0.930  0.020  1.080
 G54  N4   H15  single    0.890  0.020  1.040

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
 G54  H1   N3   C15  125.48  3.000
 G54  H1   N3   C13  125.44  3.000
 G54  C15  N3   C13  109.06  3.000
 G54  C5   C4   C3   119.96  3.000
 G54  C3   C4   C7   129.43  3.000
 G54  C5   C4   C7   110.61  3.000
 G54  C12  N2   C13  113.31  3.000
 G54  H3   C7   H2   106.74  3.000
 G54  H3   C7   C8   111.26  3.000
 G54  H2   C7   C8   112.75  3.000
 G54  H3   C7   C4   110.22  3.000
 G54  H2   C7   C4   113.05  3.000
 G54  C8   C7   C4   102.90  3.000
 G54  H4   C6   C5   121.35  3.000
 G54  H4   C6   C1   119.38  3.000
 G54  C5   C6   C1   119.26  3.000
 G54  N4   C9   C10  109.77  3.000
 G54  N4   C9   C5   113.39  3.000
 G54  C10  C9   C5   110.49  3.000
 G54  C5   C9   C8   102.09  3.000
 G54  N4   C9   C8   109.34  3.000
 G54  C10  C9   C8   111.58  3.000
 G54  C14  C13  N2   125.54  3.000
 G54  N2   C13  N3   126.50  3.000
 G54  C14  C13  N3   107.96  3.000
 G54  H6   C8   H5   107.54  3.000
 G54  H6   C8   C9   112.02  3.000
 G54  H5   C8   C9   109.14  3.000
 G54  H6   C8   C7   113.59  3.000
 G54  H5   C8   C7   109.17  3.000
 G54  C9   C8   C7   105.31  3.000
 G54  H7   C16  C15  125.28  3.000
 G54  H7   C16  C14  128.37  3.000
 G54  C15  C16  C14  106.35  3.000
 G54  C11  C1   C2   121.20  3.000
 G54  C11  C1   C6   119.55  3.000
 G54  C2   C1   C6   119.24  3.000
 G54  H8   C2   C3   118.90  3.000
 G54  H8   C2   C1   119.92  3.000
 G54  C3   C2   C1   121.14  3.000
 G54  H9   C3   C2   119.92  3.000
 G54  H9   C3   C4   120.96  3.000
 G54  C2   C3   C4   119.12  3.000
 G54  C9   C5   C6   128.37  3.000
 G54  C6   C5   C4   121.26  3.000
 G54  C9   C5   C4   110.35  3.000
 G54  C14  C11  N1   119.34  3.000
 G54  N1   C11  C1   117.04  3.000
 G54  C14  C11  C1   123.62  3.000
 G54  C12  N1   C11  119.35  3.000
 G54  H13  C12  N1   116.13  3.000
 G54  H13  C12  N2   116.56  3.000
 G54  N1   C12  N2   127.31  3.000
 G54  C11  C14  C16  138.33  3.000
 G54  C11  C14  C13  115.13  3.000
 G54  C16  C14  C13  106.53  3.000
 G54  H14  C15  C16  129.53  3.000
 G54  H14  C15  N3   120.37  3.000
 G54  C16  C15  N3   110.10  3.000
 G54  H15  N4   C17  115.13  3.000
 G54  H15  N4   C9   116.21  3.000
 G54  C17  N4   C9   122.26  3.000
 G54  N4   C17  N5   180.00  3.000
 G54  H12  C10  H11  107.21  3.000
 G54  H12  C10  H10  108.72  3.000
 G54  H11  C10  H10  108.11  3.000
 G54  H12  C10  C9   111.98  3.000
 G54  H11  C10  C9   109.71  3.000
 G54  H10  C10  C9   110.96  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
 G54  CONST_01  C14  C16  C15  N3     0.00   0.0  0
 G54  CONST_02  C16  C14  C13  N3     0.00   0.0  0
 G54  CONST_03  C11  C14  C13  N3   180.00   0.0  0
 G54  CONST_04  C12  N2   C13  N3   180.00   0.0  0
 G54  CONST_05  C1   C6   C5   C4     0.00   0.0  0
 G54  CONST_06  C1   C2   C3   C4     0.00   0.0  0
 G54  CONST_07  C16  C14  C13  N2   180.00   0.0  0
 G54  CONST_08  C11  C14  C13  N2     0.00   0.0  0
 G54  CONST_09  C15  N3   C13  N2   180.00   0.0  0
 G54  CONST_10  C11  N1   C12  N2     0.00   0.0  0
 G54  CONST_11  C3   C4   C5   C6     0.00   0.0  0
 G54  CONST_12  C3   C2   C1   C6     0.00   0.0  0
 G54  CONST_15  C15  C16  C14  C13    0.00   0.0  0
 G54  CONST_16  C1   C11  C14  C13  180.00   0.0  0
 G54  CONST_17  N1   C11  C14  C13    0.00   0.0  0
 G54  CONST_18  C16  C15  N3   C13    0.00   0.0  0
 G54  CONST_19  N1   C12  N2   C13    0.00   0.0  0
 G54  CONST_20  C1   C11  C14  C16    0.00   0.0  0
 G54  CONST_21  N1   C11  C14  C16  180.00   0.0  0
 G54  CONST_22  C12  N1   C11  C1   180.00   0.0  0
 G54  CONST_23  C5   C4   C3   C2     0.00   0.0  0
 G54  CONST_24  C5   C6   C1   C2     0.00   0.0  0
 G54  CONST_27  C11  C1   C2   C3   180.00   0.0  0
 G54  CONST_28  C11  C1   C6   C5   180.00   0.0  0
 G54  CONST_29  C15  C16  C14  C11  180.00   0.0  0
 G54  CONST_30  C14  C11  N1   C12    0.00   0.0  0
 G54  CONST_31  C14  C13  N2   C12    0.00   0.0  0
 G54  CONST_32  C15  N3   C13  C14    0.00   0.0  0
 G54  CONST_33  H7   C16  C15  N3   180.00   0.0  0
 G54  CONST_34  H4   C6   C5   C4   180.00   0.0  0
 G54  CONST_35  H8   C2   C3   C4   180.00   0.0  0
 G54  CONST_36  H1   N3   C13  N2     0.00   0.0  0
 G54  CONST_37  H9   C3   C4   C7     0.00   0.0  0
 G54  CONST_38  H14  C15  N3   C13  180.00   0.0  0
 G54  CONST_39  H13  C12  N2   C13  180.00   0.0  0
 G54  Var_01    C9   C8   C7   C4   -28.08  30.0  1
 G54  Var_02    C5   C4   C7   C8    17.26  30.0  1
 G54  Var_03    H15  N4   C17  N5    94.42  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
 G54  chir_01  C9  C8  N4  C5  positiv

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
 G54  plan-1  N3   0.020
 G54  plan-1  N2   0.020
 G54  plan-1  C13  0.020
 G54  plan-1  C16  0.020
 G54  plan-1  C1   0.020
 G54  plan-1  C11  0.020
 G54  plan-1  N1   0.020
 G54  plan-1  C12  0.020
 G54  plan-1  C14  0.020
 G54  plan-1  C15  0.020
 G54  plan-1  H1   0.020
 G54  plan-1  H7   0.020
 G54  plan-1  H13  0.020
 G54  plan-1  H14  0.020
 G54  plan-2  C4   0.020
 G54  plan-2  C7   0.020
 G54  plan-2  C6   0.020
 G54  plan-2  C9   0.020
 G54  plan-2  C1   0.020
 G54  plan-2  C2   0.020
 G54  plan-2  C3   0.020
 G54  plan-2  C5   0.020
 G54  plan-2  C11  0.020
 G54  plan-2  H4   0.020
 G54  plan-2  H8   0.020
 G54  plan-2  H9   0.020

