# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 20:07:57 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 4-amino-N-[(2S,3E)-1-(4'-cyanobiphenyl-4-yl)-3-iminopropan-2-yl]tetrahydro-2H-pyran-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1(CCOCC1)C(=O)N[C@@H](Cc2ccc(cc2)c3ccc(cc3)C#N)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
 U6B  U6B  4-amino-N-[(2S,3E)-1-(4'-cyanobiphenyl-4-yl)-3-iminopropan-2-yl]tetrahydro-2H-pyran-4-carboxamide  ligand  52  28  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U6B
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
 U6B  C9    C  C1    0  -0.032   3.6270  -3.0175  -0.0662
 U6B  C23   C  CR16  0  -0.222  -5.5174   0.6417   1.4948
 U6B  C25   C  CR16  0  -0.222  -5.8767   0.6870  -0.8946
 U6B  C22   C  CR16  0  -0.303  -4.2982   0.0237   1.2923
 U6B  C26   C  CR16  0  -0.304  -4.6565   0.0661  -1.0819
 U6B  C2    C  CR16  0  -0.294  -1.7587  -0.6563  -1.3143
 U6B  C4    C  CR16  0  -0.291  -2.0886  -1.9049   0.7018
 U6B  C1    C  CR16  0  -0.295  -0.5452  -1.2967  -1.5086
 U6B  C5    C  CR16  0  -0.287  -0.8771  -2.5449   0.5005
 U6B  C24   C  CR6   0  -0.012  -6.3120   0.9760   0.3984
 U6B  C21   C  CR6   0   0.110  -3.8471  -0.2773   0.0042
 U6B  C3    C  CR6   0   0.073  -2.5512  -0.9488  -0.2038
 U6B  C6    C  CR6   0   0.152  -0.0859  -2.2524  -0.6075
 U6B  C12   C  C     0   0.586   2.8707   0.1535   0.3239
 U6B  C15   C  CH2   0  -0.449   4.7794   1.3501  -0.7158
 U6B  C19   C  CH2   0  -0.457   2.9793   2.6976   0.3766
 U6B  C16   C  CH2   0  -0.185   5.6166   1.6402   0.5177
 U6B  C18   C  CH2   0  -0.178   3.9621   2.9640   1.5113
 U6B  C14   C  CT    0  -0.064   3.2656   1.4255  -0.4393
 U6B  C7    C  CH2   0  -0.556   1.2432  -2.9234  -0.7936
 U6B  C8    C  CH1   0  -0.117   2.3532  -2.2152   0.0000
 U6B  N28   N  NS    0  -0.253  -8.5913   2.1255   0.7623
 U6B  N10   N  N     0  -0.525   4.7034  -2.5380  -0.5143
 U6B  N20   N  NH2   0  -0.801   2.5828   1.4154  -1.7276
 U6B  N11   N  NH1   0  -0.616   2.5285  -0.8730  -0.4665
 U6B  O13   O  O     0  -0.492   2.8974   0.0823   1.5453
 U6B  O17   O  O2    0  -0.487   5.3038   2.8979   1.0739
 U6B  H9    H  H     0   0.232   3.5282  -4.0404   0.3092
 U6B  H8    H  HCH1  0   0.279   2.0465  -2.1818   1.0496
 U6B  H10   H  H     0   0.347   5.4438  -3.2329  -0.4731
 U6B  H23   H  HCR6  0   0.283  -5.8504   0.8696   2.4981
 U6B  H22   H  HCR6  0   0.271  -3.6837  -0.2119   2.1513
 U6B  H25   H  HCR6  0   0.282  -6.4943   0.9380  -1.7461
 U6B  H26   H  HCR6  0   0.271  -4.3428  -0.1733  -2.0890
 U6B  H2    H  HCR6  0   0.257  -2.0776   0.0920  -2.0291
 U6B  H1    H  HCR6  0   0.249   0.0507  -1.0459  -2.3781
 U6B  H4    H  HCR6  0   0.257  -2.6902  -2.1759   1.5606
 U6B  H5    H  HCR6  0   0.253  -0.5482  -3.2919   1.2136
 U6B  H71C  H  HCH2  0   0.271   1.1869  -3.9620  -0.4607
 U6B  H72C  H  HCH2  0   0.269   1.5145  -2.9455  -1.8523
 U6B  H11   H  HNH1  0   0.396   2.5864  -0.6989  -1.4608
 U6B  H151  H  HCH2  0   0.239   5.0174   2.0911  -1.4864
 U6B  H152  H  HCH2  0   0.250   5.0428   0.3686  -1.1167
 U6B  H161  H  HCH2  0   0.204   5.4910   0.8433   1.2622
 U6B  H162  H  HCH2  0   0.236   6.6739   1.6644   0.2474
 U6B  H191  H  HCH2  0   0.241   1.9604   2.6833   0.7733
 U6B  H192  H  HCH2  0   0.234   3.0296   3.5368  -0.3245
 U6B  H181  H  HCH2  0   0.227   3.8086   3.9745   1.8954
 U6B  H182  H  HCH2  0   0.208   3.7947   2.2687   2.3391
 U6B  H201  H  HNH2  0   0.352   1.5957   1.6141  -1.6058
 U6B  H202  H  HNH2  0   0.357   2.9500   2.1607  -2.3071
 U6B  C27   C  CSP   0   0.054  -7.5723   1.6120   0.5999

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
 U6B  C27  C24   single    1.426  0.020  1.426
 U6B  C27  N28   triple    1.153  0.020  1.153
 U6B  C9   C8    single    1.507  0.020  1.507
 U6B  C9   N10   double    1.261  0.020  1.261
 U6B  C9   H9    single    0.930  0.020  1.080
 U6B  C23  C22   aromatic  1.382  0.020  1.382
 U6B  C23  C24   aromatic  1.395  0.020  1.395
 U6B  C25  C26   aromatic  1.382  0.020  1.382
 U6B  C25  C24   aromatic  1.395  0.020  1.395
 U6B  C22  C21   aromatic  1.398  0.020  1.398
 U6B  C26  C21   aromatic  1.397  0.020  1.397
 U6B  C2   C1    aromatic  1.386  0.020  1.386
 U6B  C2   C3    aromatic  1.395  0.020  1.395
 U6B  C4   C5    aromatic  1.385  0.020  1.385
 U6B  C4   C3    aromatic  1.396  0.020  1.396
 U6B  C1   C6    aromatic  1.392  0.020  1.392
 U6B  C5   C6    aromatic  1.393  0.020  1.393
 U6B  C21  C3    single    1.474  0.020  1.474
 U6B  C6   C7    single    1.501  0.020  1.501
 U6B  C12  C14   single    1.535  0.020  1.535
 U6B  C12  N11   single    1.340  0.020  1.340
 U6B  C12  O13   double    1.224  0.020  1.224
 U6B  C15  C16   single    1.519  0.020  1.519
 U6B  C15  C14   single    1.541  0.020  1.541
 U6B  C19  C18   single    1.525  0.020  1.525
 U6B  C19  C14   single    1.538  0.020  1.538
 U6B  C16  O17   single    1.410  0.020  1.410
 U6B  C18  O17   single    1.413  0.020  1.413
 U6B  C14  N20   single    1.458  0.020  1.458
 U6B  C7   C8    single    1.537  0.020  1.537
 U6B  C8   N11   single    1.432  0.020  1.432
 U6B  C8   H8    single    0.970  0.020  1.090
 U6B  N10  H10   single    0.890  0.020  1.040
 U6B  C23  H23   single    0.930  0.020  1.080
 U6B  C22  H22   single    0.930  0.020  1.080
 U6B  C25  H25   single    0.930  0.020  1.080
 U6B  C26  H26   single    0.930  0.020  1.080
 U6B  C2   H2    single    0.930  0.020  1.080
 U6B  C1   H1    single    0.930  0.020  1.080
 U6B  C4   H4    single    0.930  0.020  1.080
 U6B  C5   H5    single    0.930  0.020  1.080
 U6B  C7   H71C  single    0.970  0.020  1.090
 U6B  C7   H72C  single    0.970  0.020  1.090
 U6B  N11  H11   single    0.860  0.020  1.020
 U6B  C15  H151  single    0.970  0.020  1.090
 U6B  C15  H152  single    0.970  0.020  1.090
 U6B  C16  H161  single    0.970  0.020  1.090
 U6B  C16  H162  single    0.970  0.020  1.090
 U6B  C19  H191  single    0.970  0.020  1.090
 U6B  C19  H192  single    0.970  0.020  1.090
 U6B  C18  H181  single    0.970  0.020  1.090
 U6B  C18  H182  single    0.970  0.020  1.090
 U6B  N20  H201  single    0.890  0.020  1.040
 U6B  N20  H202  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
 U6B  H9    C9   N10   123.69  3.000
 U6B  H9    C9   C8    113.97  3.000
 U6B  N10   C9   C8    122.34  3.000
 U6B  H23   C23  C24   120.23  3.000
 U6B  H23   C23  C22   120.13  3.000
 U6B  C24   C23  C22   119.65  3.000
 U6B  H25   C25  C24   120.24  3.000
 U6B  H25   C25  C26   120.12  3.000
 U6B  C24   C25  C26   119.63  3.000
 U6B  H22   C22  C21   120.10  3.000
 U6B  H22   C22  C23   118.82  3.000
 U6B  C21   C22  C23   121.08  3.000
 U6B  H26   C26  C21   120.08  3.000
 U6B  H26   C26  C25   118.80  3.000
 U6B  C21   C26  C25   121.10  3.000
 U6B  H2    C2   C3    120.20  3.000
 U6B  H2    C2   C1    118.99  3.000
 U6B  C3    C2   C1    120.80  3.000
 U6B  H4    C4   C3    120.12  3.000
 U6B  H4    C4   C5    119.05  3.000
 U6B  C3    C4   C5    120.81  3.000
 U6B  H1    C1   C6    119.81  3.000
 U6B  H1    C1   C2    119.16  3.000
 U6B  C6    C1   C2    121.04  3.000
 U6B  H5    C5   C6    119.72  3.000
 U6B  H5    C5   C4    119.23  3.000
 U6B  C6    C5   C4    121.04  3.000
 U6B  C25   C24  C23   120.09  3.000
 U6B  C25   C24  C27   119.95  3.000
 U6B  C23   C24  C27   119.96  3.000
 U6B  C3    C21  C26   120.76  3.000
 U6B  C3    C21  C22   120.78  3.000
 U6B  C26   C21  C22   118.45  3.000
 U6B  C21   C3   C4    120.78  3.000
 U6B  C21   C3   C2    121.07  3.000
 U6B  C4    C3   C2    118.15  3.000
 U6B  C7    C6   C5    120.53  3.000
 U6B  C7    C6   C1    121.28  3.000
 U6B  C5    C6   C1    118.16  3.000
 U6B  O13   C12  N11   123.34  3.000
 U6B  O13   C12  C14   122.60  3.000
 U6B  N11   C12  C14   114.04  3.000
 U6B  H152  C15  H151  107.29  3.000
 U6B  H152  C15  C14   110.29  3.000
 U6B  H151  C15  C14   107.86  3.000
 U6B  H152  C15  C16   109.68  3.000
 U6B  H151  C15  C16   108.81  3.000
 U6B  C14   C15  C16   112.74  3.000
 U6B  H192  C19  H191  106.57  3.000
 U6B  H192  C19  C14   106.61  3.000
 U6B  H191  C19  C14   110.80  3.000
 U6B  H192  C19  C18   108.25  3.000
 U6B  H191  C19  C18   109.45  3.000
 U6B  C14   C19  C18   114.79  3.000
 U6B  H162  C16  H161  107.16  3.000
 U6B  H162  C16  O17   107.02  3.000
 U6B  H161  C16  O17   110.77  3.000
 U6B  H162  C16  C15   109.70  3.000
 U6B  H161  C16  C15   110.43  3.000
 U6B  O17   C16  C15   111.61  3.000
 U6B  H182  C18  H181  107.48  3.000
 U6B  H182  C18  O17   110.48  3.000
 U6B  H181  C18  O17   106.60  3.000
 U6B  H182  C18  C19   110.70  3.000
 U6B  H181  C18  C19   109.45  3.000
 U6B  O17   C18  C19   111.94  3.000
 U6B  N20   C14  C19   112.78  3.000
 U6B  N20   C14  C15   107.53  3.000
 U6B  C19   C14  C15   108.58  3.000
 U6B  N20   C14  C12   108.24  3.000
 U6B  C19   C14  C12   111.95  3.000
 U6B  C15   C14  C12   107.55  3.000
 U6B  H72C  C7   H71C  106.79  3.000
 U6B  H72C  C7   C8    109.27  3.000
 U6B  H71C  C7   C8    108.54  3.000
 U6B  H72C  C7   C6    110.42  3.000
 U6B  H71C  C7   C6    109.99  3.000
 U6B  C8    C7   C6    111.68  3.000
 U6B  H8    C8   N11   108.56  3.000
 U6B  H8    C8   C7    107.87  3.000
 U6B  N11   C8   C7    110.61  3.000
 U6B  H8    C8   C9    107.19  3.000
 U6B  N11   C8   C9    112.42  3.000
 U6B  C7    C8   C9    110.02  3.000
 U6B  H10   N10  C9    110.34  3.000
 U6B  H202  N20  H201  106.10  3.000
 U6B  H202  N20  C14   109.31  3.000
 U6B  H201  N20  C14   110.38  3.000
 U6B  H11   N11  C8    119.27  3.000
 U6B  H11   N11  C12   115.68  3.000
 U6B  C8    N11  C12   123.87  3.000
 U6B  C18   O17  C16   111.99  3.000
 U6B  N28   C27  C24   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
 U6B  CONST_01  C26   C21  C22  C23     0.00   0.0  0
 U6B  CONST_02  C3    C21  C22  C23   180.00   0.0  0
 U6B  CONST_03  C26   C25  C24  C23     0.00   0.0  0
 U6B  CONST_04  C22   C21  C26  C25     0.00   0.0  0
 U6B  CONST_05  C3    C21  C26  C25   180.00   0.0  0
 U6B  CONST_06  C22   C23  C24  C25     0.00   0.0  0
 U6B  CONST_11  C5    C6   C1   C2      0.00   0.0  0
 U6B  CONST_12  C5    C4   C3   C2      0.00   0.0  0
 U6B  CONST_13  C1    C6   C5   C4      0.00   0.0  0
 U6B  CONST_14  C1    C2   C3   C4      0.00   0.0  0
 U6B  CONST_15  C21   C3   C2   C1    180.00   0.0  0
 U6B  CONST_16  C21   C3   C4   C5    180.00   0.0  0
 U6B  CONST_17  C21   C22  C23  C24     0.00   0.0  0
 U6B  CONST_18  C21   C26  C25  C24     0.00   0.0  0
 U6B  CONST_19  C6    C1   C2   C3      0.00   0.0  0
 U6B  CONST_20  C6    C5   C4   C3      0.00   0.0  0
 U6B  CONST_21  C22   C23  C24  C27   180.00   0.0  0
 U6B  CONST_22  C26   C25  C24  C27   180.00   0.0  0
 U6B  CONST_23  C7    C6   C1   C2    180.00   0.0  0
 U6B  CONST_24  C7    C6   C5   C4    180.00   0.0  0
 U6B  CONST_25  H25   C25  C24  C23   180.00   0.0  0
 U6B  CONST_26  H23   C23  C24  C25   180.00   0.0  0
 U6B  CONST_27  H26   C26  C21  C22   180.00   0.0  0
 U6B  CONST_28  H22   C22  C21  C26   180.00   0.0  0
 U6B  CONST_29  H4    C4   C3   C2    180.00   0.0  0
 U6B  CONST_30  H2    C2   C3   C4    180.00   0.0  0
 U6B  CONST_31  H5    C5   C6   C1    180.00   0.0  0
 U6B  CONST_32  H1    C1   C6   C5    180.00   0.0  0
 U6B  CONST_33  C8    N11  C12  C14   180.00   0.0  0
 U6B  CONST_34  H11   N11  C12  C14     0.00   0.0  0
 U6B  CONST_35  O13   C12  N11  C8      0.00   0.0  0
 U6B  Var_01    O17   C16  C15  C14   -56.38  30.0  1
 U6B  Var_02    O17   C18  C19  C14    50.44  30.0  1
 U6B  Var_03    H181  C18  O17  C16  -178.39  30.0  1
 U6B  Var_04    H161  C16  O17  C18   -61.21  30.0  1
 U6B  Var_05    C8    C7   C6   C1     94.65  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
 U6B  chir_01  C14  C15  C19  N20  negativ
 U6B  chir_02  C8   N11  C7   C9   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
 U6B  plan-1  C23  0.020
 U6B  plan-1  C25  0.020
 U6B  plan-1  C22  0.020
 U6B  plan-1  C26  0.020
 U6B  plan-1  C24  0.020
 U6B  plan-1  C21  0.020
 U6B  plan-1  C3   0.020
 U6B  plan-1  N28  0.020
 U6B  plan-1  H23  0.020
 U6B  plan-1  H22  0.020
 U6B  plan-1  H25  0.020
 U6B  plan-1  H26  0.020
 U6B  plan-1  C27  0.020
 U6B  plan-2  C2   0.020
 U6B  plan-2  C4   0.020
 U6B  plan-2  C1   0.020
 U6B  plan-2  C5   0.020
 U6B  plan-2  C21  0.020
 U6B  plan-2  C3   0.020
 U6B  plan-2  C6   0.020
 U6B  plan-2  C7   0.020
 U6B  plan-2  H2   0.020
 U6B  plan-2  H1   0.020
 U6B  plan-2  H4   0.020
 U6B  plan-2  H5   0.020
 U6B  plan-3  C12  0.020
 U6B  plan-3  C14  0.020
 U6B  plan-3  C8   0.020
 U6B  plan-3  N11  0.020
 U6B  plan-3  O13  0.020
 U6B  plan-3  H11  0.020
 U6B  plan-4  C9   0.020
 U6B  plan-4  C8   0.020
 U6B  plan-4  N10  0.020
 U6B  plan-4  H9   0.020
 U6B  plan-4  H10  0.020

