# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 10:13:04 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: methyl 5-{3-[(4S)-6-amino-5-cyano-3-methyl-4-(propan-2-yl)-2,4-dihydropyrano[2,3-c]pyrazol-4-yl]-5-cyanophenyl}thiophene-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1sc(cc1)c2cc(cc(c2)[C@@]3(C(C)C)C(=C(N)Oc4n[nH]c(C)c34)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
 99S  99S  'methyl 5-{3-[(4S)-6-amino-5-cyano-3-methyl-4-(propan-2-yl)-2,4-dihydropyrano[2,3-c]pyrazol-4-yl]-5-cyanophenyl}thiophene-2-carboxylate'  ligand  54  33  .  2022-07-24  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_99S
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
 99S  O31  O  O     0  -0.439   6.8325   0.1943   0.2847
 99S  C30  C  C     0   0.581   5.6900   0.5183   0.0706
 99S  O32  O  O2    0  -0.463   5.2997   1.7439  -0.2431
 99S  C33  C  CH3   0  -0.422   6.3007   2.7605  -0.3186
 99S  C28  C  CR5   0  -0.332   4.5561  -0.4043   0.1305
 99S  C27  C  CR15  0  -0.148   4.6094  -1.7352   0.4417
 99S  C26  C  CR15  0  -0.224   3.3402  -2.3459   0.4233
 99S  S29  S  S2    0   0.290   2.9478   0.1055  -0.1930
 99S  C25  C  CR5   0  -0.210   2.3314  -1.4725   0.1002
 99S  C21  C  CR6   0   0.196   0.9014  -1.7578  -0.0029
 99S  C20  C  CR16  0  -0.345   0.4711  -3.0538  -0.2781
 99S  C19  C  CR6   0   0.064  -0.8897  -3.3090  -0.3621
 99S  C23  C  CSP   0   0.051  -1.3370  -4.6345  -0.6503
 99S  N24  N  NS    0  -0.244  -1.7000  -5.7030  -0.8812
 99S  C18  C  CR16  0  -0.355  -1.8344  -2.2973  -0.1821
 99S  C22  C  CR16  0  -0.333  -0.0513  -0.7583   0.1795
 99S  C17  C  CR6   0   0.211  -1.4188  -1.0038   0.0950
 99S  C4   C  CR6   0  -0.173  -2.3900   0.1753   0.2342
 99S  C14  C  CH1   0  -0.221  -3.8656  -0.2738   0.4463
 99S  C16  C  CH3   0  -0.679  -4.0914  -1.0561   1.7394
 99S  C15  C  CH3   0  -0.660  -4.8373   0.8997   0.3963
 99S  C3   C  CR6   0  -0.227  -1.9238   1.0951   1.3599
 99S  C8   C  CSP   0   0.030  -1.5819   0.5297   2.6007
 99S  N9   N  NS    0  -0.283  -1.2695   0.0740   3.6189
 99S  C2   C  CR6   0   0.614  -1.8009   2.4601   1.2589
 99S  N7   N  NH2   0  -0.834  -1.5512   3.2985   2.2702
 99S  C5   C  CR56  0  -0.149  -2.2792   0.9907  -1.0193
 99S  C10  C  CR5   0   0.372  -2.3695   0.6922  -2.3678
 99S  C13  C  CH3   0  -0.753  -2.5676  -0.5911  -3.0895
 99S  N11  N  NR15  0  -0.491  -2.2282   1.8674  -3.0058
 99S  N12  N  N     0  -0.292  -2.0513   2.9146  -2.1952
 99S  C6   C  CR56  0   0.463  -2.0865   2.3672  -1.0096
 99S  O1   O  O     0  -0.451  -1.9488   3.1258   0.1037
 99S  H1   H  HCH3  0   0.257   5.7722   3.6805  -0.5480
 99S  H2   H  HCH3  0   0.244   6.8252   2.8701   0.6298
 99S  H3   H  HCH3  0   0.244   7.0206   2.5486  -1.1085
 99S  H4   H  HCR5  0   0.282   5.5267  -2.2522   0.6836
 99S  H5   H  HCR5  0   0.278   3.1742  -3.3863   0.6632
 99S  H6   H  HCR6  0   0.285   1.1822  -3.8522  -0.4406
 99S  H7   H  HCR6  0   0.295  -2.8817  -2.5472  -0.2713
 99S  H8   H  HCR6  0   0.256   0.2768   0.2496   0.4070
 99S  H9   H  HCH1  0   0.235  -4.1166  -0.9253  -0.3979
 99S  H10  H  HCH3  0   0.234  -4.0832  -0.3979   2.6090
 99S  H11  H  HCH3  0   0.245  -5.0712  -1.5346   1.7114
 99S  H12  H  HCH3  0   0.238  -3.3510  -1.8370   1.9093
 99S  H13  H  HCH3  0   0.239  -4.8003   1.4374  -0.5508
 99S  H14  H  HCH3  0   0.240  -5.8568   0.5328   0.5213
 99S  H15  H  HCH3  0   0.225  -4.6481   1.6096   1.2040
 99S  H16  H  HNH2  0   0.422  -1.3657   2.9375   3.1910
 99S  H17  H  HNH2  0   0.418  -1.1831   4.2150   2.0724
 99S  H18  H  HCH3  0   0.261  -3.4645  -1.1035  -2.7428
 99S  H19  H  HCH3  0   0.271  -2.6717  -0.4279  -4.1613
 99S  H20  H  HCH3  0   0.264  -1.7231  -1.2630  -2.9342
 99S  H21  H  HNR5  0   0.423  -2.2442   2.0138  -4.0029

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
 99S  C33  O32  single    1.429  0.020  1.429
 99S  O32  C30  single    1.324  0.020  1.324
 99S  C27  C28  aromatic  1.368  0.020  1.368
 99S  C27  C26  aromatic  1.409  0.020  1.409
 99S  C30  C28  single    1.463  0.020  1.463
 99S  C30  O31  double    1.207  0.020  1.207
 99S  C28  S29  aromatic  1.718  0.020  1.718
 99S  N11  N12  aromatic  1.336  0.020  1.336
 99S  N11  C10  aromatic  1.345  0.020  1.345
 99S  C26  C25  aromatic  1.373  0.020  1.373
 99S  C13  C10  single    1.486  0.020  1.486
 99S  N12  C6   aromatic  1.306  0.020  1.306
 99S  C10  C5   aromatic  1.384  0.020  1.384
 99S  C25  S29  aromatic  1.719  0.020  1.719
 99S  C25  C21  single    1.462  0.020  1.462
 99S  C6   C5   aromatic  1.390  0.020  1.390
 99S  C6   O1   single    1.354  0.020  1.354
 99S  C5   C4   single    1.499  0.020  1.499
 99S  C22  C21  aromatic  1.393  0.020  1.393
 99S  C22  C17  aromatic  1.392  0.020  1.392
 99S  C21  C20  aromatic  1.393  0.020  1.393
 99S  O1   C2   single    1.341  0.020  1.341
 99S  C16  C14  single    1.528  0.020  1.528
 99S  C4   C17  single    1.534  0.020  1.534
 99S  C4   C14  single    1.557  0.020  1.557
 99S  C4   C3   single    1.527  0.020  1.527
 99S  C17  C18  aromatic  1.387  0.020  1.387
 99S  C20  C19  aromatic  1.387  0.020  1.387
 99S  C14  C15  single    1.524  0.020  1.524
 99S  C2   C3   double    1.374  0.020  1.374
 99S  C2   N7   single    1.337  0.020  1.337
 99S  C3   C8   single    1.406  0.020  1.406
 99S  C18  C19  aromatic  1.396  0.020  1.396
 99S  C19  C23  single    1.428  0.020  1.428
 99S  C8   N9   triple    1.158  0.020  1.158
 99S  C23  N24  triple    1.152  0.020  1.152
 99S  C33  H1   single    0.970  0.020  1.090
 99S  C33  H2   single    0.970  0.020  1.090
 99S  C33  H3   single    0.970  0.020  1.090
 99S  C27  H4   single    0.930  0.020  1.080
 99S  C26  H5   single    0.930  0.020  1.080
 99S  C20  H6   single    0.930  0.020  1.080
 99S  C18  H7   single    0.930  0.020  1.080
 99S  C22  H8   single    0.930  0.020  1.080
 99S  C14  H9   single    0.970  0.020  1.090
 99S  C16  H10  single    0.970  0.020  1.090
 99S  C16  H11  single    0.970  0.020  1.090
 99S  C16  H12  single    0.970  0.020  1.090
 99S  C15  H13  single    0.970  0.020  1.090
 99S  C15  H14  single    0.970  0.020  1.090
 99S  C15  H15  single    0.970  0.020  1.090
 99S  N7   H16  single    0.890  0.020  1.040
 99S  N7   H17  single    0.890  0.020  1.040
 99S  C13  H18  single    0.970  0.020  1.090
 99S  C13  H19  single    0.970  0.020  1.090
 99S  C13  H20  single    0.970  0.020  1.090
 99S  N11  H21  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
 99S  C28  C30  O32  111.40  3.000
 99S  C28  C30  O31  123.87  3.000
 99S  O32  C30  O31  124.73  3.000
 99S  C33  O32  C30  117.69  3.000
 99S  H3   C33  H2   109.43  3.000
 99S  H3   C33  H1   109.47  3.000
 99S  H2   C33  H1   109.46  3.000
 99S  H3   C33  O32  111.27  3.000
 99S  H2   C33  O32  111.28  3.000
 99S  H1   C33  O32  105.85  3.000
 99S  S29  C28  C27  111.60  3.000
 99S  S29  C28  C30  122.06  3.000
 99S  C27  C28  C30  126.35  3.000
 99S  H4   C27  C26  124.09  3.000
 99S  H4   C27  C28  123.34  3.000
 99S  C26  C27  C28  112.57  3.000
 99S  H5   C26  C25  123.50  3.000
 99S  H5   C26  C27  123.57  3.000
 99S  C25  C26  C27  112.91  3.000
 99S  C25  S29  C28   91.79  3.000
 99S  C21  C25  S29  121.19  3.000
 99S  C21  C25  C26  127.68  3.000
 99S  S29  C25  C26  111.13  3.000
 99S  C22  C21  C20  118.83  3.000
 99S  C20  C21  C25  119.85  3.000
 99S  C22  C21  C25  121.32  3.000
 99S  H6   C20  C19  120.01  3.000
 99S  H6   C20  C21  120.90  3.000
 99S  C19  C20  C21  119.09  3.000
 99S  C18  C19  C23  119.12  3.000
 99S  C23  C19  C20  119.35  3.000
 99S  C18  C19  C20  121.52  3.000
 99S  N24  C23  C19  180.00  3.000
 99S  H7   C18  C17  121.52  3.000
 99S  H7   C18  C19  118.54  3.000
 99S  C17  C18  C19  119.94  3.000
 99S  H8   C22  C17  118.29  3.000
 99S  H8   C22  C21  119.19  3.000
 99S  C17  C22  C21  122.51  3.000
 99S  C4   C17  C22  118.75  3.000
 99S  C4   C17  C18  123.06  3.000
 99S  C22  C17  C18  118.10  3.000
 99S  C5   C4   C3   105.44  3.000
 99S  C3   C4   C14  111.27  3.000
 99S  C5   C4   C14  109.93  3.000
 99S  C3   C4   C17  109.67  3.000
 99S  C14  C4   C17  112.99  3.000
 99S  C5   C4   C17  107.18  3.000
 99S  H9   C14  C15  106.65  3.000
 99S  H9   C14  C16  108.29  3.000
 99S  C15  C14  C16  109.12  3.000
 99S  H9   C14  C4   106.48  3.000
 99S  C15  C14  C4   112.18  3.000
 99S  C16  C14  C4   113.77  3.000
 99S  H12  C16  H11  107.46  3.000
 99S  H12  C16  H10  107.64  3.000
 99S  H11  C16  H10  106.98  3.000
 99S  H12  C16  C14  113.48  3.000
 99S  H11  C16  C14  109.61  3.000
 99S  H10  C16  C14  111.39  3.000
 99S  H15  C15  H14  107.21  3.000
 99S  H15  C15  H13  108.43  3.000
 99S  H14  C15  H13  107.29  3.000
 99S  H15  C15  C14  111.46  3.000
 99S  H14  C15  C14  109.46  3.000
 99S  H13  C15  C14  112.75  3.000
 99S  C2   C3   C8   116.27  3.000
 99S  C8   C3   C4   118.87  3.000
 99S  C2   C3   C4   124.86  3.000
 99S  N9   C8   C3   180.00  3.000
 99S  O1   C2   N7   111.15  3.000
 99S  N7   C2   C3   125.72  3.000
 99S  O1   C2   C3   123.11  3.000
 99S  H17  N7   H16  116.03  3.000
 99S  H17  N7   C2   119.35  3.000
 99S  H16  N7   C2   120.11  3.000
 99S  C6   C5   C10  103.27  3.000
 99S  C6   C5   C4   122.88  3.000
 99S  C10  C5   C4   133.82  3.000
 99S  N11  C10  C13  122.58  3.000
 99S  C13  C10  C5   131.94  3.000
 99S  N11  C10  C5   105.48  3.000
 99S  H20  C13  H19  107.85  3.000
 99S  H20  C13  H18  107.61  3.000
 99S  H19  C13  H18  107.75  3.000
 99S  H20  C13  C10  111.10  3.000
 99S  H19  C13  C10  111.18  3.000
 99S  H18  C13  C10  111.19  3.000
 99S  H21  N11  N12  119.24  3.000
 99S  H21  N11  C10  126.49  3.000
 99S  N12  N11  C10  114.27  3.000
 99S  C6   N12  N11  102.63  3.000
 99S  O1   C6   N12  120.58  3.000
 99S  O1   C6   C5   125.07  3.000
 99S  N12  C6   C5   114.35  3.000
 99S  C6   O1   C2   116.18  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
 99S  CONST_01  C25  C26  C27  C28     0.00   0.0  0
 99S  CONST_02  C26  C25  S29  C28     0.00   0.0  0
 99S  CONST_03  C21  C25  S29  C28   180.00   0.0  0
 99S  CONST_04  C25  S29  C28  C27     0.00   0.0  0
 99S  CONST_05  S29  C25  C26  C27     0.00   0.0  0
 99S  CONST_06  C21  C25  C26  C27   180.00   0.0  0
 99S  CONST_07  S29  C28  C27  C26     0.00   0.0  0
 99S  CONST_12  C17  C22  C21  C25   180.00   0.0  0
 99S  CONST_13  C19  C20  C21  C25   180.00   0.0  0
 99S  CONST_14  C18  C17  C22  C21     0.00   0.0  0
 99S  CONST_15  C18  C19  C20  C21     0.00   0.0  0
 99S  CONST_16  C17  C22  C21  C20     0.00   0.0  0
 99S  CONST_17  C17  C18  C19  C20     0.00   0.0  0
 99S  CONST_18  C22  C21  C20  C19     0.00   0.0  0
 99S  CONST_19  C22  C17  C18  C19     0.00   0.0  0
 99S  CONST_20  N12  N11  C10  C5      0.00   0.0  0
 99S  CONST_21  N11  N12  C6   C5      0.00   0.0  0
 99S  CONST_22  C6   N12  N11  C10     0.00   0.0  0
 99S  CONST_23  N12  C6   C5   C10     0.00   0.0  0
 99S  CONST_24  C6   C5   C10  N11     0.00   0.0  0
 99S  CONST_25  C4   C17  C22  C21   180.00   0.0  0
 99S  CONST_26  C4   C17  C18  C19   180.00   0.0  0
 99S  CONST_27  C26  C27  C28  C30   180.00   0.0  0
 99S  CONST_28  C25  S29  C28  C30   180.00   0.0  0
 99S  CONST_29  C23  C19  C20  C21   180.00   0.0  0
 99S  CONST_30  C17  C18  C19  C23   180.00   0.0  0
 99S  CONST_31  C13  C10  C5   C4      0.00   0.0  0
 99S  CONST_32  N12  N11  C10  C13   180.00   0.0  0
 99S  CONST_33  C6   C5   C10  C13   180.00   0.0  0
 99S  CONST_34  H5   C26  C27  C28   180.00   0.0  0
 99S  CONST_35  H4   C27  C28  S29   180.00   0.0  0
 99S  CONST_36  H8   C22  C21  C25     0.00   0.0  0
 99S  CONST_37  H6   C20  C21  C25     0.00   0.0  0
 99S  CONST_38  H7   C18  C19  C20   180.00   0.0  0
 99S  CONST_39  H21  N11  C10  C5    180.00   0.0  0
 99S  Var_01    O1   C2   C3   C4     -7.12  30.0  1
 99S  Var_02    N12  C6   O1   C2   -170.53  30.0  1
 99S  Var_03    C27  C28  C30  O31     0.67  30.0  2
 99S  Var_04    C2   C3   C8   N9    -63.52  30.0  2
 99S  Var_05    H16  N7   C2   C3      4.72  30.0  2
 99S  Var_06    H18  C13  C10  C5     55.15  30.0  2
 99S  Var_07    C28  C30  O32  C33   179.07  30.0  3
 99S  Var_08    H10  C16  C14  C4     75.07  30.0  3
 99S  Var_09    H13  C15  C14  C4     59.07  30.0  3
 99S  Var_10    H1   C33  O32  C30  -177.93  30.0  3

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
 99S  chir_01  C4  C17  C5  C3  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
 99S  plan-1  C30  0.020
 99S  plan-1  C28  0.020
 99S  plan-1  C27  0.020
 99S  plan-1  C26  0.020
 99S  plan-1  S29  0.020
 99S  plan-1  C25  0.020
 99S  plan-1  C21  0.020
 99S  plan-1  H4   0.020
 99S  plan-1  H5   0.020
 99S  plan-2  C25  0.020
 99S  plan-2  C21  0.020
 99S  plan-2  C20  0.020
 99S  plan-2  C19  0.020
 99S  plan-2  C23  0.020
 99S  plan-2  N24  0.020
 99S  plan-2  C18  0.020
 99S  plan-2  C22  0.020
 99S  plan-2  C17  0.020
 99S  plan-2  C4   0.020
 99S  plan-2  H6   0.020
 99S  plan-2  H7   0.020
 99S  plan-2  H8   0.020
 99S  plan-3  C4   0.020
 99S  plan-3  C5   0.020
 99S  plan-3  C10  0.020
 99S  plan-3  C13  0.020
 99S  plan-3  N11  0.020
 99S  plan-3  N12  0.020
 99S  plan-3  C6   0.020
 99S  plan-3  O1   0.020
 99S  plan-3  H21  0.020
 99S  plan-4  O31  0.020
 99S  plan-4  C30  0.020
 99S  plan-4  O32  0.020
 99S  plan-4  C28  0.020

