# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 19 13:45:36 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: 3-[1-[3-[(4~{S})-6-azanyl-5-cyano-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazol-4-yl]-5-fluoranyl-phenyl]piperidin-4-yl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@]1(c2cc(F)cc(c2)N3CCC(CC3)CCC(O)=O)C(=C(N)Oc4n[nH]c(C)c14)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
 N05  N05  '3-[1-[3-[(4~{S})-6-azanyl-5-cyano-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazol-4-yl]-5-fluoranyl-phenyl]piperidin-4-yl]propanoic acid'  ligand  64  34  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_N05
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
 N05  O33  O  OH1   0  -0.599   -9.2828  -0.2539   0.0882
 N05  C31  C  C     0   0.556   -8.1717  -0.9727   0.2276
 N05  O32  O  O     0  -0.446   -8.1802  -2.1280   0.5739
 N05  C30  C  CH2   0  -0.592   -6.9425  -0.1704  -0.0976
 N05  C29  C  CH2   0  -0.407   -5.6534  -0.9692   0.0062
 N05  C26  C  CH1   0  -0.244   -4.4206  -0.1925  -0.4480
 N05  C25  C  CH2   0  -0.427   -4.1227   1.0314   0.4110
 N05  C24  C  CH2   0  -0.307   -2.8558   1.7453  -0.0414
 N05  C27  C  CH2   0  -0.421   -3.1895  -1.0924  -0.4543
 N05  C28  C  CH2   0  -0.301   -1.9466  -0.3356  -0.8851
 N05  N23  N  NT    0  -0.512   -1.7210   0.8410  -0.0495
 N05  C19  C  CR6   0   0.398   -0.4479   1.4049  -0.1279
 N05  C34  C  CR16  0  -0.553   -0.2459   2.7568  -0.4282
 N05  C18  C  CR6   0   0.600    1.0476   3.2300  -0.4875
 N05  F21  F  F     0  -0.324    1.2311   4.5297  -0.7877
 N05  C17  C  CR16  0  -0.558    2.1632   2.4467  -0.2763
 N05  C20  C  CR16  0  -0.363    0.6757   0.6075   0.1145
 N05  C16  C  CR6   0   0.209    1.9690   1.1045   0.0400
 N05  C4   C  CR6   0  -0.162    3.1278   0.1201   0.2538
 N05  C14  C  CH1   0  -0.216    4.5241   0.8089   0.3247
 N05  C22  C  CH3   0  -0.679    4.7153   1.6966   1.5533
 N05  C15  C  CH3   0  -0.662    5.6660  -0.2021   0.2709
 N05  C3   C  CR6   0  -0.219    2.8642  -0.7131   1.5081
 N05  C8   C  CSP   0   0.034    2.4549  -0.0626   2.6842
 N05  N9   N  NS    0  -0.293    2.0991   0.4533   3.6588
 N05  C2   C  CR6   0   0.614    2.9664  -2.0817   1.5788
 N05  N7   N  NH2   0  -0.840    2.8287  -2.8153   2.6863
 N05  C5   C  CR56  0  -0.152    3.1006  -0.8585  -0.8817
 N05  C10  C  CR5   0   0.368    3.0622  -0.7261  -2.2577
 N05  C13  C  CH3   0  -0.747    2.9968   0.4693  -3.1357
 N05  N11  N  NR15  0  -0.493    3.0918  -1.9808  -2.7426
 N05  N12  N  N     0  -0.296    3.1411  -2.9302  -1.8034
 N05  C6   C  CR56  0   0.459    3.1467  -2.2346  -0.6966
 N05  O1   O  O     0  -0.456    3.1968  -2.8560   0.5064
 N05  H1   H  HOH1  0   0.478  -10.0556  -0.7989   0.2987
 N05  H2   H  HCH2  0   0.275   -7.0616   0.2385  -1.1063
 N05  H3   H  HCH2  0   0.281   -6.9297   0.6974   0.5686
 N05  H4   H  HCH2  0   0.224   -5.5068  -1.3094   1.0358
 N05  H5   H  HCH2  0   0.233   -5.7363  -1.8698  -0.6082
 N05  H6   H  HCH1  0   0.215   -4.5910   0.1497  -1.4785
 N05  H7   H  HCH2  0   0.241   -4.9438   1.7506   0.3742
 N05  H8   H  HCH2  0   0.219   -4.0122   0.7247   1.4566
 N05  H9   H  HCH2  0   0.207   -3.0276   2.1909  -1.0349
 N05  H10  H  HCH2  0   0.251   -2.6495   2.5661   0.6474
 N05  H11  H  HCH2  0   0.219   -3.0322  -1.5099   0.5460
 N05  H12  H  HCH2  0   0.235   -3.3376  -1.9350  -1.1344
 N05  H13  H  HCH2  0   0.252   -1.0835  -0.9953  -0.8289
 N05  H14  H  HCH2  0   0.211   -2.0490  -0.0358  -1.9400
 N05  H15  H  HCR6  0   0.284   -1.0649   3.4315  -0.6358
 N05  H16  H  HCR6  0   0.271    3.1434   2.8926  -0.3623
 N05  H17  H  HCR6  0   0.252    0.5371  -0.4332   0.3791
 N05  H18  H  HCH1  0   0.233    4.6108   1.4351  -0.5703
 N05  H19  H  HCH3  0   0.229    4.8287   1.0992   2.4587
 N05  H20  H  HCH3  0   0.240    5.6283   2.2837   1.4419
 N05  H21  H  HCH3  0   0.237    3.8973   2.3970   1.7196
 N05  H22  H  HCH3  0   0.238    5.6740  -0.7763  -0.6547
 N05  H23  H  HCH3  0   0.237    6.6220   0.3188   0.3400
 N05  H24  H  HCH3  0   0.222    5.6158  -0.9019   1.1075
 N05  H25  H  HNH2  0   0.422    2.8375  -2.3898   3.5971
 N05  H26  H  HNH2  0   0.419    2.9063  -3.8176   2.6462
 N05  H27  H  HCH3  0   0.260    3.8511   1.1262  -2.9739
 N05  H28  H  HCH3  0   0.264    2.9895   0.1866  -4.1876
 N05  H29  H  HCH3  0   0.263    2.0969   1.0508  -2.9364
 N05  H30  H  HNR5  0   0.420    3.0737  -2.2488  -3.7139

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
 N05  N9   C8   triple    1.159  0.020  1.159
 N05  F21  C18  single    1.346  0.020  1.346
 N05  C8   C3   single    1.405  0.020  1.405
 N05  C18  C17  aromatic  1.379  0.020  1.379
 N05  C18  C34  aromatic  1.379  0.020  1.379
 N05  C17  C16  aromatic  1.393  0.020  1.393
 N05  N7   C2   single    1.336  0.020  1.336
 N05  C3   C2   double    1.374  0.020  1.374
 N05  C3   C4   single    1.529  0.020  1.529
 N05  C14  C22  single    1.528  0.020  1.528
 N05  C14  C4   single    1.559  0.020  1.559
 N05  C14  C15  single    1.526  0.020  1.526
 N05  C2   O1   single    1.343  0.020  1.343
 N05  C34  C19  aromatic  1.399  0.020  1.399
 N05  C16  C4   single    1.535  0.020  1.535
 N05  C16  C20  aromatic  1.387  0.020  1.387
 N05  C4   C5   single    1.499  0.020  1.499
 N05  C19  C20  aromatic  1.399  0.020  1.399
 N05  C19  N23  single    1.395  0.020  1.395
 N05  O1   C6   single    1.355  0.020  1.355
 N05  C24  N23  single    1.451  0.020  1.451
 N05  C24  C25  single    1.523  0.020  1.523
 N05  C5   C6   aromatic  1.389  0.020  1.389
 N05  C5   C10  aromatic  1.383  0.020  1.383
 N05  N23  C28  single    1.461  0.020  1.461
 N05  C6   N12  aromatic  1.307  0.020  1.307
 N05  C25  C26  single    1.525  0.020  1.525
 N05  C10  C13  single    1.485  0.020  1.485
 N05  C10  N11  aromatic  1.345  0.020  1.345
 N05  C28  C27  single    1.518  0.020  1.518
 N05  N12  N11  aromatic  1.336  0.020  1.336
 N05  C26  C27  single    1.525  0.020  1.525
 N05  C26  C29  single    1.526  0.020  1.526
 N05  C29  C30  single    1.520  0.020  1.520
 N05  C30  C31  single    1.503  0.020  1.503
 N05  O32  C31  double    1.206  0.020  1.206
 N05  C31  O33  single    1.331  0.020  1.331
 N05  O33  H1   single    0.850  0.020  0.980
 N05  C30  H2   single    0.970  0.020  1.090
 N05  C30  H3   single    0.970  0.020  1.090
 N05  C29  H4   single    0.970  0.020  1.090
 N05  C29  H5   single    0.970  0.020  1.090
 N05  C26  H6   single    0.970  0.020  1.090
 N05  C25  H7   single    0.970  0.020  1.090
 N05  C25  H8   single    0.970  0.020  1.090
 N05  C24  H9   single    0.970  0.020  1.090
 N05  C24  H10  single    0.970  0.020  1.090
 N05  C27  H11  single    0.970  0.020  1.090
 N05  C27  H12  single    0.970  0.020  1.090
 N05  C28  H13  single    0.970  0.020  1.090
 N05  C28  H14  single    0.970  0.020  1.090
 N05  C34  H15  single    0.930  0.020  1.080
 N05  C17  H16  single    0.930  0.020  1.080
 N05  C20  H17  single    0.930  0.020  1.080
 N05  C14  H18  single    0.970  0.020  1.090
 N05  C22  H19  single    0.970  0.020  1.090
 N05  C22  H20  single    0.970  0.020  1.090
 N05  C22  H21  single    0.970  0.020  1.090
 N05  C15  H22  single    0.970  0.020  1.090
 N05  C15  H23  single    0.970  0.020  1.090
 N05  C15  H24  single    0.970  0.020  1.090
 N05  N7   H25  single    0.860  0.020  1.020
 N05  N7   H26  single    0.860  0.020  1.020
 N05  C13  H27  single    0.970  0.020  1.090
 N05  C13  H28  single    0.970  0.020  1.090
 N05  C13  H29  single    0.970  0.020  1.090
 N05  N11  H30  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
 N05  H1   O33  C31  109.84  3.000
 N05  C30  C31  O32  125.38  3.000
 N05  O32  C31  O33  122.79  3.000
 N05  C30  C31  O33  111.82  3.000
 N05  H3   C30  H2   105.43  3.000
 N05  H3   C30  C29  111.43  3.000
 N05  H2   C30  C29  110.58  3.000
 N05  H3   C30  C31  107.52  3.000
 N05  H2   C30  C31  108.03  3.000
 N05  C29  C30  C31  113.46  3.000
 N05  H5   C29  H4   106.43  3.000
 N05  H5   C29  C26  108.25  3.000
 N05  H4   C29  C26  109.27  3.000
 N05  H5   C29  C30  109.28  3.000
 N05  H4   C29  C30  109.95  3.000
 N05  C26  C29  C30  113.40  3.000
 N05  H6   C26  C27  107.76  3.000
 N05  H6   C26  C25  107.98  3.000
 N05  C27  C26  C25  108.56  3.000
 N05  H6   C26  C29  108.19  3.000
 N05  C27  C26  C29  110.67  3.000
 N05  C25  C26  C29  113.50  3.000
 N05  H8   C25  H7   107.00  3.000
 N05  H8   C25  C24  109.32  3.000
 N05  H7   C25  C24  107.87  3.000
 N05  H8   C25  C26  109.44  3.000
 N05  H7   C25  C26  111.27  3.000
 N05  C24  C25  C26  111.81  3.000
 N05  H10  C24  H9   107.11  3.000
 N05  H10  C24  N23  108.93  3.000
 N05  H9   C24  N23  111.64  3.000
 N05  H10  C24  C25  108.81  3.000
 N05  H9   C24  C25  109.12  3.000
 N05  N23  C24  C25  111.11  3.000
 N05  H12  C27  H11  107.09  3.000
 N05  H12  C27  C28  108.59  3.000
 N05  H11  C27  C28  109.38  3.000
 N05  H12  C27  C26  110.37  3.000
 N05  H11  C27  C26  109.70  3.000
 N05  C28  C27  C26  111.59  3.000
 N05  H14  C28  H13  106.76  3.000
 N05  H14  C28  N23  110.06  3.000
 N05  H13  C28  N23  109.66  3.000
 N05  H14  C28  C27  109.36  3.000
 N05  H13  C28  C27  109.43  3.000
 N05  N23  C28  C27  111.46  3.000
 N05  C19  N23  C28  115.76  3.000
 N05  C28  N23  C24  112.61  3.000
 N05  C19  N23  C24  117.53  3.000
 N05  C20  C19  C34  118.16  3.000
 N05  C20  C19  N23  119.54  3.000
 N05  C34  C19  N23  122.30  3.000
 N05  H15  C34  C18  119.22  3.000
 N05  H15  C34  C19  122.32  3.000
 N05  C18  C34  C19  118.44  3.000
 N05  C17  C18  F21  118.17  3.000
 N05  C17  C18  C34  123.87  3.000
 N05  F21  C18  C34  117.96  3.000
 N05  H16  C17  C16  122.85  3.000
 N05  H16  C17  C18  119.16  3.000
 N05  C16  C17  C18  117.99  3.000
 N05  H17  C20  C16  118.47  3.000
 N05  H17  C20  C19  119.17  3.000
 N05  C16  C20  C19  122.36  3.000
 N05  C4   C16  C20  117.80  3.000
 N05  C20  C16  C17  119.17  3.000
 N05  C4   C16  C17  122.97  3.000
 N05  C5   C4   C3   105.22  3.000
 N05  C5   C4   C14  109.83  3.000
 N05  C3   C4   C14  110.98  3.000
 N05  C5   C4   C16  107.42  3.000
 N05  C14  C4   C16  113.52  3.000
 N05  C3   C4   C16  109.48  3.000
 N05  H18  C14  C15  106.89  3.000
 N05  H18  C14  C22  108.36  3.000
 N05  C15  C14  C22  108.64  3.000
 N05  H18  C14  C4   106.64  3.000
 N05  C15  C14  C4   112.08  3.000
 N05  C22  C14  C4   113.92  3.000
 N05  H21  C22  H20  107.33  3.000
 N05  H21  C22  H19  107.66  3.000
 N05  H20  C22  H19  107.01  3.000
 N05  H21  C22  C14  113.72  3.000
 N05  H20  C22  C14  109.59  3.000
 N05  H19  C22  C14  111.24  3.000
 N05  H24  C15  H23  107.33  3.000
 N05  H24  C15  H22  108.28  3.000
 N05  H23  C15  H22  107.41  3.000
 N05  H24  C15  C14  111.29  3.000
 N05  H23  C15  C14  109.70  3.000
 N05  H22  C15  C14  112.62  3.000
 N05  C2   C3   C8   116.09  3.000
 N05  C2   C3   C4   124.90  3.000
 N05  C8   C3   C4   118.99  3.000
 N05  N9   C8   C3   180.00  3.000
 N05  O1   C2   N7   111.30  3.000
 N05  O1   C2   C3   123.10  3.000
 N05  N7   C2   C3   125.59  3.000
 N05  H26  N7   H25  117.20  3.000
 N05  H26  N7   C2   120.41  3.000
 N05  H25  N7   C2   121.19  3.000
 N05  C6   C5   C10  103.20  3.000
 N05  C10  C5   C4   133.76  3.000
 N05  C6   C5   C4   123.03  3.000
 N05  N11  C10  C13  122.60  3.000
 N05  N11  C10  C5   105.59  3.000
 N05  C13  C10  C5   131.82  3.000
 N05  H29  C13  H28  108.04  3.000
 N05  H29  C13  H27  107.38  3.000
 N05  H28  C13  H27  107.76  3.000
 N05  H29  C13  C10  110.97  3.000
 N05  H28  C13  C10  111.24  3.000
 N05  H27  C13  C10  111.29  3.000
 N05  H30  N11  N12  119.28  3.000
 N05  H30  N11  C10  126.51  3.000
 N05  N12  N11  C10  114.21  3.000
 N05  C6   N12  N11  102.54  3.000
 N05  O1   C6   N12  120.52  3.000
 N05  N12  C6   C5   114.46  3.000
 N05  O1   C6   C5   125.01  3.000
 N05  C6   O1   C2   116.00  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
 N05  CONST_01  C17  C18  C34  C19     0.00   0.0  0
 N05  CONST_02  C17  C16  C20  C19     0.00   0.0  0
 N05  CONST_03  C16  C17  C18  C34     0.00   0.0  0
 N05  CONST_04  C16  C20  C19  C34     0.00   0.0  0
 N05  CONST_05  C20  C16  C17  C18     0.00   0.0  0
 N05  CONST_06  C20  C19  C34  C18     0.00   0.0  0
 N05  CONST_07  N11  N12  C6   C5      0.00   0.0  0
 N05  CONST_08  N12  N11  C10  C5      0.00   0.0  0
 N05  CONST_09  N12  C6   C5   C10     0.00   0.0  0
 N05  CONST_10  C6   N12  N11  C10     0.00   0.0  0
 N05  CONST_11  C6   C5   C10  N11     0.00   0.0  0
 N05  CONST_12  C18  C34  C19  N23   180.00   0.0  0
 N05  CONST_13  C16  C20  C19  N23   180.00   0.0  0
 N05  CONST_14  C4   C16  C20  C19   180.00   0.0  0
 N05  CONST_15  C4   C16  C17  C18   180.00   0.0  0
 N05  CONST_16  F21  C18  C34  C19   180.00   0.0  0
 N05  CONST_17  C16  C17  C18  F21   180.00   0.0  0
 N05  CONST_18  C13  C10  C5   C4      0.00   0.0  0
 N05  CONST_19  C6   C5   C10  C13   180.00   0.0  0
 N05  CONST_20  N12  N11  C10  C13   180.00   0.0  0
 N05  CONST_21  H15  C34  C19  N23     0.00   0.0  0
 N05  CONST_22  H17  C20  C19  N23     0.00   0.0  0
 N05  CONST_23  H16  C17  C18  C34   180.00   0.0  0
 N05  CONST_24  H30  N11  C10  C5    180.00   0.0  0
 N05  CONST_25  H1   O33  C31  O32     0.00   0.0  0
 N05  Var_01    N23  C24  C25  C26   -55.99  30.0  1
 N05  Var_02    N23  C28  C27  C26    55.70  30.0  1
 N05  Var_03    C19  N23  C24  C25  -165.03  30.0  1
 N05  Var_04    C34  C19  N23  C24   -11.31  30.0  1
 N05  Var_05    C27  C28  N23  C24   -56.69  30.0  1
 N05  Var_06    O1   C2   C3   C4     -6.21  30.0  1
 N05  Var_07    C5   C6   O1   C2     11.23  30.0  1
 N05  Var_08    C2   C3   C8   N9    -39.74  30.0  3
 N05  Var_09    H25  N7   C2   C3    -13.74  30.0  2
 N05  Var_10    H27  C13  C10  C5     59.38  30.0  2
 N05  Var_11    C26  C29  C30  C31   174.66  30.0  2
 N05  Var_12    H19  C22  C14  C4     72.36  30.0  3
 N05  Var_13    H22  C15  C14  C4     61.38  30.0  3
 N05  Var_14    C29  C30  C31  O33  -178.14  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
 N05  chir_01  C26  C25  C27  C29  negativ
 N05  chir_02  C4   C3   C16  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
 N05  plan-1  N23  0.020
 N05  plan-1  C19  0.020
 N05  plan-1  C34  0.020
 N05  plan-1  C18  0.020
 N05  plan-1  F21  0.020
 N05  plan-1  C17  0.020
 N05  plan-1  C20  0.020
 N05  plan-1  C16  0.020
 N05  plan-1  C4   0.020
 N05  plan-1  H15  0.020
 N05  plan-1  H16  0.020
 N05  plan-1  H17  0.020
 N05  plan-2  C4   0.020
 N05  plan-2  C5   0.020
 N05  plan-2  C10  0.020
 N05  plan-2  C13  0.020
 N05  plan-2  N11  0.020
 N05  plan-2  N12  0.020
 N05  plan-2  C6   0.020
 N05  plan-2  O1   0.020
 N05  plan-2  H30  0.020
 N05  plan-3  O33  0.020
 N05  plan-3  C31  0.020
 N05  plan-3  O32  0.020
 N05  plan-3  C30  0.020
 N05  plan-3  H1   0.020

