# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 16:16:05 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: 4-[(4R,5R)-6,7-dihydro-5H-pyrrolo[1,2-c]imidazol-5-yl]-3-fluorobenzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cc(ccc1[C@H]2CCc3cncn23)C#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
 YSY  YSY  4-[(4R,5R)-6,7-dihydro-5H-pyrrolo[1,2-c]imidazol-5-yl]-3-fluorobenzonitrile  ligand  27  17  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_YSY
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
 YSY  C10   C  CR15  0  -0.140  25.7780  -28.4630  -13.7991
 YSY  C13   C  CR55  0   0.314  25.5318  -28.8224  -16.1180
 YSY  C03   C  CR6   0   0.009  29.7667  -28.9013  -12.2418
 YSY  C04   C  CR16  0  -0.230  29.4406  -29.5054  -13.4521
 YSY  C05   C  CR16  0  -0.284  28.1560  -29.3772  -13.9548
 YSY  C06   C  CR6   0  -0.071  27.1828  -28.6525  -13.2760
 YSY  C07   C  CR6   0   0.571  27.5531  -28.0595  -12.0751
 YSY  C09   C  CR16  0  -0.393  28.8151  -28.1661  -11.5377
 YSY  C11   C  CH2   0  -0.464  25.5861  -27.1014  -14.5153
 YSY  C12   C  CH2   0  -0.534  25.8758  -27.3762  -16.0049
 YSY  C14   C  CR15  0  -0.280  25.2588  -29.8439  -16.9822
 YSY  C16   C  CR15  0   0.082  25.1792  -30.6890  -15.0100
 YSY  F08   F  F     0  -0.301  26.6387  -27.3461  -11.4063
 YSY  N01   N  NS    0  -0.240  32.1483  -29.1394  -11.2805
 YSY  N15   N  N     0  -0.446  25.0387  -30.9992  -16.2751
 YSY  N17   N  N     0  -0.443  25.4705  -29.3786  -14.8752
 YSY  H101  H  HCR5  0   0.305  25.0598  -28.5873  -12.9879
 YSY  H041  H  HCR6  0   0.287  30.1819  -30.0742  -13.9957
 YSY  H051  H  HCR6  0   0.286  27.9164  -29.8585  -14.8935
 YSY  H091  H  HCR6  0   0.303  29.0522  -27.6909  -10.5950
 YSY  H111  H  HCH2  0   0.271  26.2177  -26.3203  -14.0966
 YSY  H112  H  HCH2  0   0.272  24.5484  -26.7895  -14.3934
 YSY  H121  H  HCH2  0   0.263  26.9272  -27.2010  -16.2465
 YSY  H122  H  HCH2  0   0.274  25.2819  -26.7389  -16.6586
 YSY  H141  H  HCR5  0   0.247  25.2013  -29.8175  -18.0594
 YSY  H161  H  HCR5  0   0.279  25.0752  -31.3603  -14.1714
 YSY  C02   C  CSP   0   0.061  31.0847  -29.0330  -11.7095

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
 YSY  C14  N15   aromatic  1.372  0.020  1.372
 YSY  C14  C13   aromatic  1.366  0.020  1.366
 YSY  N15  C16   aromatic  1.310  0.020  1.310
 YSY  C13  C12   single    1.491  0.020  1.491
 YSY  C13  N17   aromatic  1.363  0.020  1.363
 YSY  C12  C11   single    1.542  0.020  1.542
 YSY  C16  N17   aromatic  1.349  0.020  1.349
 YSY  N17  C10   single    1.446  0.020  1.446
 YSY  C11  C10   single    1.550  0.020  1.550
 YSY  C10  C06   single    1.511  0.020  1.511
 YSY  C05  C04   aromatic  1.385  0.020  1.385
 YSY  C05  C06   aromatic  1.390  0.020  1.390
 YSY  C04  C03   aromatic  1.391  0.020  1.391
 YSY  C06  C07   aromatic  1.390  0.020  1.390
 YSY  C07  F08   single    1.339  0.020  1.339
 YSY  C07  C09   aromatic  1.376  0.020  1.376
 YSY  C03  C09   aromatic  1.393  0.020  1.393
 YSY  C03  C02   single    1.428  0.020  1.428
 YSY  C02  N01   triple    1.152  0.020  1.152
 YSY  C10  H101  single    0.970  0.020  1.090
 YSY  C04  H041  single    0.930  0.020  1.080
 YSY  C05  H051  single    0.930  0.020  1.080
 YSY  C09  H091  single    0.930  0.020  1.080
 YSY  C11  H111  single    0.970  0.020  1.090
 YSY  C11  H112  single    0.970  0.020  1.090
 YSY  C12  H121  single    0.970  0.020  1.090
 YSY  C12  H122  single    0.970  0.020  1.090
 YSY  C14  H141  single    0.930  0.020  1.080
 YSY  C16  H161  single    0.930  0.020  1.080

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
 YSY  H101  C10  N17   109.96  3.000
 YSY  H101  C10  C11   111.23  3.000
 YSY  N17   C10  C11   100.72  3.000
 YSY  H101  C10  C06   109.91  3.000
 YSY  C11   C10  C06   112.65  3.000
 YSY  N17   C10  C06   112.09  3.000
 YSY  N17   C13  C14   105.24  3.000
 YSY  N17   C13  C12   109.69  3.000
 YSY  C14   C13  C12   145.06  3.000
 YSY  C09   C03  C04   120.56  3.000
 YSY  C09   C03  C02   119.39  3.000
 YSY  C04   C03  C02   120.04  3.000
 YSY  H041  C04  C05   120.14  3.000
 YSY  H041  C04  C03   120.34  3.000
 YSY  C05   C04  C03   119.52  3.000
 YSY  H051  C05  C06   120.04  3.000
 YSY  H051  C05  C04   118.62  3.000
 YSY  C06   C05  C04   121.34  3.000
 YSY  C07   C06  C05   117.24  3.000
 YSY  C07   C06  C10   119.57  3.000
 YSY  C05   C06  C10   123.17  3.000
 YSY  F08   C07  C09   118.21  3.000
 YSY  C09   C07  C06   123.29  3.000
 YSY  F08   C07  C06   118.50  3.000
 YSY  H091  C09  C07   120.48  3.000
 YSY  H091  C09  C03   121.49  3.000
 YSY  C07   C09  C03   118.03  3.000
 YSY  H112  C11  H111  107.70  3.000
 YSY  H112  C11  C12   109.73  3.000
 YSY  H111  C11  C12   112.99  3.000
 YSY  H112  C11  C10   108.51  3.000
 YSY  H111  C11  C10   112.38  3.000
 YSY  C12   C11  C10   105.46  3.000
 YSY  H122  C12  H121  107.34  3.000
 YSY  H122  C12  C11   111.91  3.000
 YSY  H121  C12  C11   111.45  3.000
 YSY  H122  C12  C13   113.34  3.000
 YSY  H121  C12  C13   111.14  3.000
 YSY  C11   C12  C13   101.70  3.000
 YSY  H141  C14  N15   121.76  3.000
 YSY  H141  C14  C13   128.62  3.000
 YSY  N15   C14  C13   109.62  3.000
 YSY  H161  C16  N17   123.19  3.000
 YSY  H161  C16  N15   126.35  3.000
 YSY  N17   C16  N15   110.46  3.000
 YSY  C16   N15  C14   106.32  3.000
 YSY  C16   N17  C13   108.36  3.000
 YSY  C16   N17  C10   137.33  3.000
 YSY  C13   N17  C10   114.25  3.000
 YSY  N01   C02  C03   180.00  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
 YSY  CONST_01  C16   N15  C14  C13    0.00   0.0  0
 YSY  CONST_02  N15   C16  N17  C13    0.00   0.0  0
 YSY  CONST_03  C06   C05  C04  C03    0.00   0.0  0
 YSY  CONST_04  C06   C07  C09  C03    0.00   0.0  0
 YSY  CONST_05  C07   C06  C05  C04    0.00   0.0  0
 YSY  CONST_06  C07   C09  C03  C04    0.00   0.0  0
 YSY  CONST_07  C09   C03  C04  C05    0.00   0.0  0
 YSY  CONST_08  C09   C07  C06  C05    0.00   0.0  0
 YSY  CONST_09  N17   C16  N15  C14    0.00   0.0  0
 YSY  CONST_10  C16   N17  C13  C14    0.00   0.0  0
 YSY  CONST_11  N17   C13  C14  N15    0.00   0.0  0
 YSY  CONST_12  C04   C05  C06  C10  180.00   0.0  0
 YSY  CONST_13  C09   C07  C06  C10  180.00   0.0  0
 YSY  CONST_14  F08   C07  C06  C10    0.00   0.0  0
 YSY  CONST_15  C05   C04  C03  C02  180.00   0.0  0
 YSY  CONST_16  C07   C09  C03  C02  180.00   0.0  0
 YSY  CONST_17  F08   C07  C09  C03  180.00   0.0  0
 YSY  CONST_18  F08   C07  C06  C05  180.00   0.0  0
 YSY  CONST_19  H161  C16  N17  C10    0.00   0.0  0
 YSY  CONST_20  H051  C05  C06  C10    0.00   0.0  0
 YSY  CONST_21  H091  C09  C03  C04  180.00   0.0  0
 YSY  CONST_22  H041  C04  C05  C06  180.00   0.0  0
 YSY  CONST_23  H141  C14  C13  C12    0.00   0.0  0
 YSY  Var_01    C13   C12  C11  C10   26.81  30.0  1
 YSY  Var_02    C14   C13  C12  C11  164.64  30.0  1

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
 YSY  chir_01  C10  N17  C11  C06  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
 YSY  plan-1  C10   0.020
 YSY  plan-1  C03   0.020
 YSY  plan-1  C04   0.020
 YSY  plan-1  C05   0.020
 YSY  plan-1  C06   0.020
 YSY  plan-1  C07   0.020
 YSY  plan-1  C09   0.020
 YSY  plan-1  F08   0.020
 YSY  plan-1  N01   0.020
 YSY  plan-1  H041  0.020
 YSY  plan-1  H051  0.020
 YSY  plan-1  H091  0.020
 YSY  plan-1  C02   0.020
 YSY  plan-2  C10   0.020
 YSY  plan-2  C13   0.020
 YSY  plan-2  C12   0.020
 YSY  plan-2  C14   0.020
 YSY  plan-2  C16   0.020
 YSY  plan-2  N15   0.020
 YSY  plan-2  N17   0.020
 YSY  plan-2  H141  0.020
 YSY  plan-2  H161  0.020

