# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 17:33:55 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: 1-cyano-2-(2-methyl-1-benzofuran-5-yl)-3-[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]guanidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1oc2ccc(cc2c1)N=C(NC#N)N[C@H]3CCCCN(CC(=O)N4CCCC4)C3=O
#
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
 YET  YET  1-cyano-2-(2-methyl-1-benzofuran-5-yl)-3-[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]guanidine  ligand  60  32  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_YET
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
 YET  O31   O  O     0  -0.496   3.0671   1.0245  -1.5195
 YET  C11   C  C     0   0.558   3.6691   0.7774  -0.4835
 YET  N27   N  NT    0  -0.472   4.3181   1.7153   0.2159
 YET  C20   C  CH2   0  -0.259   4.3443   3.1102  -0.2139
 YET  C16   C  CH2   0  -0.484   4.9315   3.8375   0.9900
 YET  C19   C  CH2   0  -0.282   5.0698   1.4981   1.4503
 YET  C15   C  CH2   0  -0.473   5.8538   2.7949   1.6135
 YET  C23   C  CH2   0  -0.442   3.7557  -0.6413   0.0748
 YET  N26   N  NT    0  -0.448   2.7793  -1.5191  -0.5201
 YET  C10   C  C     0   0.586   1.4950  -1.2702  -0.2110
 YET  O30   O  O     0  -0.481   1.1806  -0.4194   0.6081
 YET  C18   C  CH2   0  -0.339   3.1978  -2.4797  -1.5362
 YET  C14   C  CH2   0  -0.427   2.8258  -2.0971  -2.9634
 YET  C13   C  CH2   0  -0.446   1.3646  -2.3504  -3.3097
 YET  C17   C  CH2   0  -0.476   0.3465  -1.6535  -2.4161
 YET  C21   C  CH1   0  -0.195   0.4291  -2.0880  -0.9443
 YET  N29   N  NH1   0  -0.645  -0.8754  -1.9123  -0.3327
 YET  C12   C  C     0   0.618  -1.1095  -1.9559   1.0053
 YET  N25   N  NH1   0  -0.667  -0.3557  -2.9021   1.7187
 YET  C1    C  CSP   0   0.287  -0.0434  -4.0949   1.2374
 YET  N24   N  NS    0  -0.303   0.2652  -5.1319   0.8309
 YET  N28   N  N     0  -0.489  -1.9678  -1.3015   1.6771
 YET  C7    C  CR6   0   0.181  -2.6724  -0.2373   1.0996
 YET  C2    C  CR16  0  -0.325  -2.0089   0.9100   0.6195
 YET  C4    C  CR16  0  -0.406  -4.0623  -0.2995   1.0766
 YET  C6    C  CR56  0   0.087  -4.7767   0.7811   0.5637
 YET  C8    C  CR56  0   0.336  -4.0857   1.8997   0.0960
 YET  C3    C  CR16  0  -0.339  -2.7076   1.9948   0.1131
 YET  O32   O  O     0  -0.459  -4.9591   2.8343  -0.3490
 YET  C9    C  CR5   0   0.371  -6.2116   2.3269  -0.1730
 YET  C22   C  CH3   0  -0.753  -7.3410   3.1853  -0.5924
 YET  C5    C  CR15  0  -0.432  -6.1665   1.0911   0.3735
 YET  H20   H  HCH2  0   0.236   4.9786   3.2245  -1.0977
 YET  H20A  H  HCH2  0   0.248   3.3451   3.4599  -0.4730
 YET  H16   H  HCH2  0   0.253   5.4472   4.7535   0.7051
 YET  H16A  H  HCH2  0   0.239   4.1367   4.1056   1.6893
 YET  H19   H  HCH2  0   0.245   4.3915   1.3414   2.2949
 YET  H19A  H  HCH2  0   0.258   5.7222   0.6275   1.3766
 YET  H15   H  HCH2  0   0.241   6.7917   2.7375   1.0572
 YET  H15A  H  HCH2  0   0.254   6.0949   2.9982   2.6559
 YET  H23   H  HCH2  0   0.298   4.7530  -1.0338  -0.1327
 YET  H23A  H  HCH2  0   0.283   3.6477  -0.6377   1.1609
 YET  H18   H  HCH2  0   0.272   4.2793  -2.5670  -1.4537
 YET  H18A  H  HCH2  0   0.250   2.8043  -3.4710  -1.2926
 YET  H14   H  HCH2  0   0.241   3.0887  -1.0511  -3.1299
 YET  H14A  H  HCH2  0   0.239   3.4455  -2.6913  -3.6391
 YET  H13   H  HCH2  0   0.247   1.1835  -2.0422  -4.3412
 YET  H13A  H  HCH2  0   0.228   1.1731  -3.4279  -3.2747
 YET  H17   H  HCH2  0   0.252   0.4435  -0.5664  -2.4872
 YET  H17A  H  HCH2  0   0.264  -0.6510  -1.9084  -2.7819
 YET  H21   H  HCH1  0   0.274   0.6983  -3.1481  -0.9297
 YET  HN29  H  HNH1  0   0.409  -1.4679  -1.2488  -0.8117
 YET  HN25  H  HNH1  0   0.446  -0.4125  -2.8236   2.7264
 YET  H2    H  HCR6  0   0.280  -0.9283   0.9467   0.6579
 YET  H4    H  HCR6  0   0.249  -4.5692  -1.1774   1.4571
 YET  H3    H  HCR6  0   0.268  -2.1892   2.8733  -0.2483
 YET  H22   H  HCH3  0   0.259  -7.3468   4.1308  -0.0470
 YET  H22A  H  HCH3  0   0.259  -7.2909   3.4199  -1.6572
 YET  H22B  H  HCH3  0   0.260  -8.2830   2.6766  -0.4003
 YET  H5    H  HCR5  0   0.261  -7.0191   0.4755   0.6122

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
 YET  O31  C11   double    1.223  0.020  1.223
 YET  C11  N27   single    1.338  0.020  1.338
 YET  C11  C23   single    1.527  0.020  1.527
 YET  C19  N27   single    1.462  0.020  1.462
 YET  N27  C20   single    1.460  0.020  1.460
 YET  C20  C16   single    1.524  0.020  1.524
 YET  C20  H20   single    0.970  0.020  1.090
 YET  C20  H20A  single    0.970  0.020  1.090
 YET  C15  C16   single    1.525  0.020  1.525
 YET  C16  H16   single    0.970  0.020  1.090
 YET  C16  H16A  single    0.970  0.020  1.090
 YET  C19  C15   single    1.524  0.020  1.524
 YET  C19  H19   single    0.970  0.020  1.090
 YET  C19  H19A  single    0.970  0.020  1.090
 YET  C15  H15   single    0.970  0.020  1.090
 YET  C15  H15A  single    0.970  0.020  1.090
 YET  N26  C23   single    1.441  0.020  1.441
 YET  C23  H23   single    0.970  0.020  1.090
 YET  C23  H23A  single    0.970  0.020  1.090
 YET  C10  N26   single    1.344  0.020  1.344
 YET  N26  C18   single    1.460  0.020  1.460
 YET  C21  C10   single    1.531  0.020  1.531
 YET  O30  C10   double    1.222  0.020  1.222
 YET  C18  C14   single    1.524  0.020  1.524
 YET  C18  H18   single    0.970  0.020  1.090
 YET  C18  H18A  single    0.970  0.020  1.090
 YET  C13  C14   single    1.523  0.020  1.523
 YET  C14  H14   single    0.970  0.020  1.090
 YET  C14  H14A  single    0.970  0.020  1.090
 YET  C17  C13   single    1.523  0.020  1.523
 YET  C13  H13   single    0.970  0.020  1.090
 YET  C13  H13A  single    0.970  0.020  1.090
 YET  C21  C17   single    1.537  0.020  1.537
 YET  C17  H17   single    0.970  0.020  1.090
 YET  C17  H17A  single    0.970  0.020  1.090
 YET  N29  C21   single    1.451  0.020  1.451
 YET  C21  H21   single    0.970  0.020  1.090
 YET  C12  N29   single    1.359  0.020  1.359
 YET  N29  HN29  single    0.890  0.020  1.040
 YET  N28  C12   double    1.271  0.020  1.271
 YET  N25  C12   single    1.404  0.020  1.404
 YET  C1   N25   single    1.324  0.020  1.324
 YET  N25  HN25  single    0.890  0.020  1.040
 YET  N24  C1    triple    1.156  0.020  1.156
 YET  N28  C7    single    1.401  0.020  1.401
 YET  C4   C7    aromatic  1.391  0.020  1.391
 YET  C7   C2    aromatic  1.410  0.020  1.410
 YET  C2   C3    aromatic  1.386  0.020  1.386
 YET  C2   H2    single    0.930  0.020  1.080
 YET  C4   C6    aromatic  1.393  0.020  1.393
 YET  C4   H4    single    0.930  0.020  1.080
 YET  C5   C6    aromatic  1.437  0.020  1.437
 YET  C6   C8    aromatic  1.395  0.020  1.395
 YET  C8   O32   aromatic  1.354  0.020  1.354
 YET  C8   C3    aromatic  1.381  0.020  1.381
 YET  C3   H3    single    0.930  0.020  1.080
 YET  C9   O32   aromatic  1.363  0.020  1.363
 YET  C5   C9    aromatic  1.352  0.020  1.352
 YET  C22  C9    single    1.479  0.020  1.479
 YET  C22  H22   single    0.970  0.020  1.090
 YET  C22  H22A  single    0.970  0.020  1.090
 YET  C22  H22B  single    0.970  0.020  1.090
 YET  C5   H5    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
 YET  C23   C11  N27   115.64  3.000
 YET  C23   C11  O31   121.67  3.000
 YET  N27   C11  O31   122.67  3.000
 YET  C19   N27  C20   112.42  3.000
 YET  C20   N27  C11   121.64  3.000
 YET  C19   N27  C11   125.94  3.000
 YET  H20A  C20  H20   107.82  3.000
 YET  H20A  C20  C16   112.82  3.000
 YET  H20   C20  C16   111.41  3.000
 YET  H20A  C20  N27   111.10  3.000
 YET  H20   C20  N27   110.37  3.000
 YET  C16   C20  N27   103.32  3.000
 YET  H16A  C16  H16   107.80  3.000
 YET  H16A  C16  C15   110.25  3.000
 YET  H16   C16  C15   113.29  3.000
 YET  H16A  C16  C20   110.04  3.000
 YET  H16   C16  C20   112.16  3.000
 YET  C15   C16  C20   103.28  3.000
 YET  H19A  C19  H19   107.98  3.000
 YET  H19A  C19  C15   112.26  3.000
 YET  H19   C19  C15   110.98  3.000
 YET  H19A  C19  N27   111.67  3.000
 YET  H19   C19  N27   110.74  3.000
 YET  C15   C19  N27   103.21  3.000
 YET  H15A  C15  H15   107.90  3.000
 YET  H15A  C15  C19   112.04  3.000
 YET  H15   C15  C19   110.03  3.000
 YET  H15A  C15  C16   113.43  3.000
 YET  H15   C15  C16   110.31  3.000
 YET  C19   C15  C16   103.11  3.000
 YET  H23A  C23  H23   106.30  3.000
 YET  H23A  C23  N26   110.22  3.000
 YET  H23   C23  N26   108.75  3.000
 YET  H23A  C23  C11   110.80  3.000
 YET  H23   C23  C11   108.44  3.000
 YET  N26   C23  C11   112.12  3.000
 YET  C18   N26  C10   123.77  3.000
 YET  C18   N26  C23   119.60  3.000
 YET  C10   N26  C23   116.07  3.000
 YET  C21   C10  O30   120.93  3.000
 YET  O30   C10  N26   121.92  3.000
 YET  C21   C10  N26   117.14  3.000
 YET  H18A  C18  H18   105.54  3.000
 YET  H18A  C18  C14   110.39  3.000
 YET  H18   C18  C14   109.50  3.000
 YET  H18A  C18  N26   109.77  3.000
 YET  H18   C18  N26   106.56  3.000
 YET  C14   C18  N26   114.64  3.000
 YET  H14A  C14  H14   106.88  3.000
 YET  H14A  C14  C13   108.25  3.000
 YET  H14   C14  C13   110.84  3.000
 YET  H14A  C14  C18   107.71  3.000
 YET  H14   C14  C18   108.95  3.000
 YET  C13   C14  C18   113.92  3.000
 YET  H13A  C13  H13   106.20  3.000
 YET  H13A  C13  C17   108.33  3.000
 YET  H13   C13  C17   108.32  3.000
 YET  H13A  C13  C14   108.91  3.000
 YET  H13   C13  C14   109.09  3.000
 YET  C17   C13  C14   115.58  3.000
 YET  H17A  C17  H17   106.93  3.000
 YET  H17A  C17  C21   107.68  3.000
 YET  H17   C17  C21   109.78  3.000
 YET  H17A  C17  C13   107.88  3.000
 YET  H17   C17  C13   110.93  3.000
 YET  C21   C17  C13   113.36  3.000
 YET  H21   C21  N29   109.44  3.000
 YET  H21   C21  C17   107.46  3.000
 YET  N29   C21  C17   108.72  3.000
 YET  H21   C21  C10   109.88  3.000
 YET  N29   C21  C10   111.06  3.000
 YET  C17   C21  C10   110.20  3.000
 YET  HN29  N29  C12   112.75  3.000
 YET  HN29  N29  C21   114.01  3.000
 YET  C12   N29  C21   124.46  3.000
 YET  N28   C12  N25   116.16  3.000
 YET  N25   C12  N29   115.42  3.000
 YET  N28   C12  N29   128.31  3.000
 YET  HN25  N25  C1    116.43  3.000
 YET  HN25  N25  C12   115.04  3.000
 YET  C1    N25  C12   123.30  3.000
 YET  N24   C1   N25   180.00  3.000
 YET  C7    N28  C12   120.85  3.000
 YET  C4    C7   C2    120.07  3.000
 YET  C2    C7   N28   121.46  3.000
 YET  C4    C7   N28   118.38  3.000
 YET  H2    C2   C3    119.33  3.000
 YET  H2    C2   C7    119.06  3.000
 YET  C3    C2   C7    121.60  3.000
 YET  H4    C4   C6    121.21  3.000
 YET  H4    C4   C7    119.88  3.000
 YET  C6    C4   C7    118.92  3.000
 YET  C5    C6   C8    105.17  3.000
 YET  C8    C6   C4    119.42  3.000
 YET  C5    C6   C4    135.41  3.000
 YET  O32   C8   C3    126.86  3.000
 YET  C3    C8   C6    123.03  3.000
 YET  O32   C8   C6    110.12  3.000
 YET  H3    C3   C8    121.98  3.000
 YET  H3    C3   C2    121.05  3.000
 YET  C8    C3   C2    116.97  3.000
 YET  C9    O32  C8    107.05  3.000
 YET  C5    C9   C22   132.10  3.000
 YET  C22   C9   O32   116.68  3.000
 YET  C5    C9   O32   111.21  3.000
 YET  H22B  C22  H22A  108.22  3.000
 YET  H22B  C22  H22   108.19  3.000
 YET  H22A  C22  H22   107.55  3.000
 YET  H22B  C22  C9    109.86  3.000
 YET  H22A  C22  C9    111.48  3.000
 YET  H22   C22  C9    111.41  3.000
 YET  H5    C5   C9    125.80  3.000
 YET  H5    C5   C6    127.76  3.000
 YET  C9    C5   C6    106.44  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
 YET  CONST_01  C5    C6   C4   C7   180.00   0.0  0
 YET  CONST_02  C8    C6   C4   C7     0.00   0.0  0
 YET  CONST_03  C8    C3   C2   C7     0.00   0.0  0
 YET  CONST_04  C6    C4   C7   C2     0.00   0.0  0
 YET  CONST_05  C6    C8   C3   C2     0.00   0.0  0
 YET  CONST_06  O32   C8   C3   C2   180.00   0.0  0
 YET  CONST_07  C3    C2   C7   C4     0.00   0.0  0
 YET  CONST_08  C9    C5   C6   C4   180.00   0.0  0
 YET  CONST_09  O32   C8   C6   C4   180.00   0.0  0
 YET  CONST_10  C3    C8   C6   C4     0.00   0.0  0
 YET  CONST_11  O32   C9   C5   C6     0.00   0.0  0
 YET  CONST_12  C9    O32  C8   C6     0.00   0.0  0
 YET  CONST_13  C9    C5   C6   C8     0.00   0.0  0
 YET  CONST_14  C5    C9   O32  C8     0.00   0.0  0
 YET  CONST_15  C5    C6   C8   C3   180.00   0.0  0
 YET  CONST_16  C9    O32  C8   C3   180.00   0.0  0
 YET  CONST_17  C5    C6   C8   O32    0.00   0.0  0
 YET  CONST_18  C6    C4   C7   N28  180.00   0.0  0
 YET  CONST_19  C3    C2   C7   N28  180.00   0.0  0
 YET  CONST_20  C22   C9   C5   C6   180.00   0.0  0
 YET  CONST_21  C22   C9   O32  C8   180.00   0.0  0
 YET  CONST_22  H3    C3   C2   C7   180.00   0.0  0
 YET  CONST_23  H4    C4   C7   C2   180.00   0.0  0
 YET  CONST_24  H2    C2   C7   C4   180.00   0.0  0
 YET  CONST_25  H5    C5   C6   C4     0.00   0.0  0
 YET  CONST_26  C19   N27  C11  O31  180.00   0.0  0
 YET  CONST_27  C20   N27  C11  O31    0.00   0.0  0
 YET  CONST_28  C23   C11  N27  C20  180.00   0.0  0
 YET  CONST_29  C23   C11  N27  C19    0.00   0.0  0
 YET  CONST_32  C7    N28  C12  N29    0.00   0.0  0
 YET  CONST_33  C7    N28  C12  N25  180.00   0.0  0
 YET  CONST_36  HN25  N25  C12  N29  180.00   0.0  0
 YET  CONST_37  HN29  N29  C12  N25  180.00   0.0  0
 YET  Var_01    C16   C15  C19  N27   31.35  30.0  1
 YET  Var_02    C15   C16  C20  N27   30.56  30.0  1
 YET  Var_03    C15   C19  N27  C20  -12.71  30.0  1
 YET  Var_04    C19   C15  C16  C20  -38.60  30.0  1
 YET  Var_05    C19   N27  C20  C16  -11.27  30.0  1
 YET  Var_06    N26   C23  C11  N27  165.42  30.0  3
 YET  Var_07    C4    C7   N28  C12  121.87  30.0  2
 YET  Var_08    H22   C22  C9   O32  -59.91  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
 YET  chir_01  C21  C10  C17  N29  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
 YET  plan-1  O31   0.020
 YET  plan-1  C11   0.020
 YET  plan-1  N27   0.020
 YET  plan-1  C20   0.020
 YET  plan-1  C19   0.020
 YET  plan-1  C23   0.020
 YET  plan-2  N28   0.020
 YET  plan-2  C7    0.020
 YET  plan-2  C2    0.020
 YET  plan-2  C4    0.020
 YET  plan-2  C6    0.020
 YET  plan-2  C8    0.020
 YET  plan-2  C3    0.020
 YET  plan-2  O32   0.020
 YET  plan-2  C9    0.020
 YET  plan-2  C22   0.020
 YET  plan-2  C5    0.020
 YET  plan-2  H2    0.020
 YET  plan-2  H4    0.020
 YET  plan-2  H3    0.020
 YET  plan-2  H5    0.020
 YET  plan-3  C21   0.020
 YET  plan-3  N29   0.020
 YET  plan-3  C12   0.020
 YET  plan-3  N25   0.020
 YET  plan-3  C1    0.020
 YET  plan-3  N28   0.020
 YET  plan-3  C7    0.020
 YET  plan-3  HN29  0.020
 YET  plan-3  HN25  0.020
 YET  plan-4  C23   0.020
 YET  plan-4  N26   0.020
 YET  plan-4  C10   0.020
 YET  plan-4  O30   0.020
 YET  plan-4  C18   0.020
 YET  plan-4  C21   0.020

