# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 23:28:48 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: (2S)-2-cyano-N-(1-hydroxy-2-methylpropan-2-yl)-3-[3-(3,4,5-trimethoxyphenyl)-1H-indazol-5-yl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(OC)c1OC)c2n[nH]c3ccc(C[C@@H](C#N)C(=O)NC(C)(C)CO)cc23
#
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
 1LE  1LE  (2S)-2-cyano-N-(1-hydroxy-2-methylpropan-2-yl)-3-[3-(3,4,5-trimethoxyphenyl)-1H-indazol-5-yl]propanamide  ligand  61  33  .  2021-08-03  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1LE
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
 1LE  O01   O  O     0  -0.462   4.5953   0.2499   2.0188
 1LE  C02   C  C     0   0.609   4.2668   0.1816   0.8506
 1LE  N03   N  NH1   0  -0.660   4.8740  -0.5428  -0.0955
 1LE  C04   C  CT    0   0.081   6.0347  -1.4243   0.0839
 1LE  C05   C  CH3   0  -0.654   7.2189  -0.6614   0.6736
 1LE  C06   C  CH3   0  -0.643   5.6604  -2.6204   0.9590
 1LE  C07   C  CH2   0  -0.161   6.3735  -1.8831  -1.3418
 1LE  O08   O  OH1   0  -0.662   7.4420  -2.7894  -1.2966
 1LE  C09   C  CH1   0  -0.500   3.0542   0.9822   0.3232
 1LE  C10   C  CSP   0   0.158   3.5434   2.0758  -0.5058
 1LE  N11   N  NS    0  -0.257   3.9414   2.9442  -1.1468
 1LE  C12   C  CH2   0  -0.512   2.1578   1.5004   1.4588
 1LE  C13   C  CR6   0   0.112   0.9272   2.1879   0.9342
 1LE  C14   C  CR16  0  -0.302   0.9299   3.5877   0.7339
 1LE  C15   C  CR16  0  -0.285  -0.1629   4.2632   0.2447
 1LE  C16   C  CR56  0   0.408  -1.2928   3.4991  -0.0617
 1LE  N17   N  NR15  0  -0.540  -2.5160   3.8450  -0.5226
 1LE  N18   N  N     0  -0.250  -3.3215   2.7965  -0.6579
 1LE  C19   C  CR5   0   0.199  -2.6466   1.7301  -0.2896
 1LE  C20   C  CR6   0   0.117  -3.2722   0.4055  -0.2976
 1LE  C21   C  CR16  0  -0.509  -2.4998  -0.7325  -0.5123
 1LE  C22   C  CR6   0   0.362  -3.1003  -1.9894  -0.5083
 1LE  O23   O  O2    0  -0.464  -2.4401  -3.1436  -0.6999
 1LE  C24   C  CH3   0  -0.442  -1.0365  -3.0992  -0.8613
 1LE  C25   C  CR6   0   0.170  -4.4779  -2.1068  -0.3117
 1LE  O26   O  O2    0  -0.480  -5.0686  -3.3293  -0.3397
 1LE  C27   C  CH3   0  -0.409  -5.1402  -3.9736   0.9261
 1LE  C28   C  CR6   0   0.355  -5.2488  -0.9585  -0.1035
 1LE  O29   O  O2    0  -0.463  -6.5619  -1.1691   0.0843
 1LE  C30   C  CH3   0  -0.440  -7.4032  -0.0476   0.2710
 1LE  C31   C  CR16  0  -0.474  -4.6460   0.2953  -0.0972
 1LE  C32   C  CR56  0  -0.076  -1.3256   2.1050   0.1125
 1LE  C33   C  CR16  0  -0.408  -0.1990   1.4524   0.6294
 1LE  H031  H  HNH1  0   0.407   4.4266  -0.5708  -1.0000
 1LE  H052  H  HCH3  0   0.244   7.0205  -0.3329   1.6910
 1LE  H053  H  HCH3  0   0.238   8.0984  -1.3034   0.6992
 1LE  H051  H  HCH3  0   0.229   7.4579   0.2161   0.0702
 1LE  H063  H  HCH3  0   0.228   4.8153  -3.1643   0.5336
 1LE  H061  H  HCH3  0   0.237   6.4982  -3.3109   1.0485
 1LE  H062  H  HCH3  0   0.240   5.3887  -2.2984   1.9630
 1LE  H071  H  HCH2  0   0.207   5.4790  -2.3425  -1.7884
 1LE  H072  H  HCH2  0   0.219   6.6176  -0.9969  -1.9431
 1LE  H081  H  HOH1  0   0.461   7.7573  -2.9278  -2.1938
 1LE  H091  H  HCH1  0   0.353   2.4610   0.3314  -0.3283
 1LE  H121  H  HCH2  0   0.284   1.8736   0.6386   2.0633
 1LE  H122  H  HCH2  0   0.278   2.7315   2.1697   2.1000
 1LE  H141  H  HCR6  0   0.258   1.8199   4.1495   0.9901
 1LE  H151  H  HCR6  0   0.273  -0.1492   5.3369   0.1140
 1LE  H171  H  HNR5  0   0.419  -2.8504   4.7641  -0.7618
 1LE  H211  H  HCR6  0   0.269  -1.4437  -0.6318  -0.7169
 1LE  H242  H  HCH3  0   0.227  -0.5387  -2.6627   0.0092
 1LE  H243  H  HCH3  0   0.264  -0.7070  -4.1294  -0.9700
 1LE  H241  H  HCH3  0   0.232  -0.7427  -2.5420  -1.7547
 1LE  H272  H  HCH3  0   0.222  -5.7267  -3.3943   1.6431
 1LE  H273  H  HCH3  0   0.237  -5.6291  -4.9335   0.7699
 1LE  H271  H  HCH3  0   0.221  -4.1474  -4.1516   1.3465
 1LE  H302  H  HCH3  0   0.262  -8.4125  -0.4361   0.3801
 1LE  H303  H  HCH3  0   0.230  -7.1432   0.5140   1.1717
 1LE  H301  H  HCH3  0   0.230  -7.3760   0.6285  -0.5871
 1LE  H311  H  HCR6  0   0.275  -5.2249   1.1917   0.0739
 1LE  H331  H  HCR6  0   0.243  -0.2071   0.3845   0.8112

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
 1LE  N11  C10   triple    1.150  0.020  1.150
 1LE  O08  C07   single    1.402  0.020  1.402
 1LE  C10  C09   single    1.457  0.020  1.457
 1LE  C07  C04   single    1.536  0.020  1.536
 1LE  C15  C14   aromatic  1.375  0.020  1.375
 1LE  C15  C16   aromatic  1.398  0.020  1.398
 1LE  C14  C13   aromatic  1.414  0.020  1.414
 1LE  C05  C04   single    1.527  0.020  1.527
 1LE  N03  C04   single    1.468  0.020  1.468
 1LE  N03  C02   single    1.337  0.020  1.337
 1LE  C04  C06   single    1.529  0.020  1.529
 1LE  C09  C02   single    1.546  0.020  1.546
 1LE  C09  C12   single    1.537  0.020  1.537
 1LE  C16  N17   aromatic  1.352  0.020  1.352
 1LE  C16  C32   aromatic  1.405  0.020  1.405
 1LE  C02  O01   double    1.216  0.020  1.216
 1LE  C13  C12   single    1.504  0.020  1.504
 1LE  C13  C33   aromatic  1.379  0.020  1.379
 1LE  N17  N18   aromatic  1.329  0.020  1.329
 1LE  C32  C33   aromatic  1.401  0.020  1.401
 1LE  C32  C19   aromatic  1.431  0.020  1.431
 1LE  N18  C19   aromatic  1.315  0.020  1.315
 1LE  C19  C20   single    1.465  0.020  1.465
 1LE  C20  C31   aromatic  1.393  0.020  1.393
 1LE  C20  C21   aromatic  1.392  0.020  1.392
 1LE  C31  C28   aromatic  1.391  0.020  1.391
 1LE  C21  C22   aromatic  1.393  0.020  1.393
 1LE  C28  O29   single    1.343  0.020  1.343
 1LE  C28  C25   aromatic  1.399  0.020  1.399
 1LE  C22  C25   aromatic  1.397  0.020  1.397
 1LE  C22  O23   single    1.343  0.020  1.343
 1LE  O29  C30   single    1.414  0.020  1.414
 1LE  C25  O26   single    1.358  0.020  1.358
 1LE  O23  C24   single    1.414  0.020  1.414
 1LE  O26  C27   single    1.422  0.020  1.422
 1LE  N03  H031  single    0.860  0.020  1.020
 1LE  C05  H052  single    0.970  0.020  1.090
 1LE  C05  H053  single    0.970  0.020  1.090
 1LE  C05  H051  single    0.970  0.020  1.090
 1LE  C06  H063  single    0.970  0.020  1.090
 1LE  C06  H061  single    0.970  0.020  1.090
 1LE  C06  H062  single    0.970  0.020  1.090
 1LE  C07  H071  single    0.970  0.020  1.090
 1LE  C07  H072  single    0.970  0.020  1.090
 1LE  O08  H081  single    0.850  0.020  0.980
 1LE  C09  H091  single    0.970  0.020  1.090
 1LE  C12  H121  single    0.970  0.020  1.090
 1LE  C12  H122  single    0.970  0.020  1.090
 1LE  C14  H141  single    0.930  0.020  1.080
 1LE  C15  H151  single    0.930  0.020  1.080
 1LE  N17  H171  single    0.860  0.020  1.020
 1LE  C21  H211  single    0.930  0.020  1.080
 1LE  C24  H242  single    0.970  0.020  1.090
 1LE  C24  H243  single    0.970  0.020  1.090
 1LE  C24  H241  single    0.970  0.020  1.090
 1LE  C27  H272  single    0.970  0.020  1.090
 1LE  C27  H273  single    0.970  0.020  1.090
 1LE  C27  H271  single    0.970  0.020  1.090
 1LE  C30  H302  single    0.970  0.020  1.090
 1LE  C30  H303  single    0.970  0.020  1.090
 1LE  C30  H301  single    0.970  0.020  1.090
 1LE  C31  H311  single    0.930  0.020  1.080
 1LE  C33  H331  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
 1LE  C09   C02  N03   113.29  3.000
 1LE  C09   C02  O01   120.72  3.000
 1LE  N03   C02  O01   125.99  3.000
 1LE  H031  N03  C04   116.31  3.000
 1LE  H031  N03  C02   116.59  3.000
 1LE  C04   N03  C02   126.70  3.000
 1LE  C07   C04  C06   110.60  3.000
 1LE  C06   C04  C05   111.08  3.000
 1LE  C07   C04  C05   109.68  3.000
 1LE  C06   C04  N03   110.25  3.000
 1LE  C05   C04  N03   111.11  3.000
 1LE  C07   C04  N03   103.90  3.000
 1LE  H051  C05  H053  108.06  3.000
 1LE  H051  C05  H052  108.32  3.000
 1LE  H053  C05  H052  107.67  3.000
 1LE  H051  C05  C04   110.97  3.000
 1LE  H053  C05  C04   109.93  3.000
 1LE  H052  C05  C04   111.76  3.000
 1LE  H062  C06  H061  107.67  3.000
 1LE  H062  C06  H063  108.27  3.000
 1LE  H061  C06  H063  108.16  3.000
 1LE  H062  C06  C04   110.95  3.000
 1LE  H061  C06  C04   110.78  3.000
 1LE  H063  C06  C04   110.88  3.000
 1LE  H072  C07  H071  107.18  3.000
 1LE  H072  C07  O08   111.70  3.000
 1LE  H071  C07  O08   111.27  3.000
 1LE  H072  C07  C04   108.44  3.000
 1LE  H071  C07  C04   108.80  3.000
 1LE  O08   C07  C04   109.35  3.000
 1LE  H081  O08  C07   108.25  3.000
 1LE  H091  C09  C12   108.90  3.000
 1LE  H091  C09  C10   106.82  3.000
 1LE  C12   C09  C10   111.30  3.000
 1LE  H091  C09  C02   108.66  3.000
 1LE  C12   C09  C02   112.34  3.000
 1LE  C10   C09  C02   108.63  3.000
 1LE  N11   C10  C09   180.00  3.000
 1LE  H122  C12  H121  107.24  3.000
 1LE  H122  C12  C13   110.80  3.000
 1LE  H121  C12  C13   109.97  3.000
 1LE  H122  C12  C09   109.55  3.000
 1LE  H121  C12  C09   107.17  3.000
 1LE  C13   C12  C09   111.94  3.000
 1LE  C33   C13  C14   119.88  3.000
 1LE  C33   C13  C12   120.09  3.000
 1LE  C14   C13  C12   120.02  3.000
 1LE  H141  C14  C15   118.84  3.000
 1LE  H141  C14  C13   118.78  3.000
 1LE  C15   C14  C13   122.37  3.000
 1LE  H151  C15  C16   121.76  3.000
 1LE  H151  C15  C14   121.38  3.000
 1LE  C16   C15  C14   116.86  3.000
 1LE  C32   C16  N17   105.96  3.000
 1LE  C32   C16  C15   122.27  3.000
 1LE  N17   C16  C15   131.76  3.000
 1LE  H171  N17  N18   119.65  3.000
 1LE  H171  N17  C16   127.94  3.000
 1LE  N18   N17  C16   112.40  3.000
 1LE  C19   N18  N17   107.47  3.000
 1LE  C32   C19  C20   129.25  3.000
 1LE  C20   C19  N18   120.84  3.000
 1LE  C32   C19  N18   109.89  3.000
 1LE  C31   C20  C21   120.32  3.000
 1LE  C21   C20  C19   120.20  3.000
 1LE  C31   C20  C19   119.48  3.000
 1LE  H211  C21  C22   120.40  3.000
 1LE  H211  C21  C20   119.70  3.000
 1LE  C22   C21  C20   119.87  3.000
 1LE  C25   C22  O23   115.63  3.000
 1LE  O23   C22  C21   124.26  3.000
 1LE  C25   C22  C21   120.10  3.000
 1LE  C24   O23  C22   118.50  3.000
 1LE  H241  C24  H243  108.66  3.000
 1LE  H241  C24  H242  108.95  3.000
 1LE  H243  C24  H242  108.65  3.000
 1LE  H241  C24  O23   112.10  3.000
 1LE  H243  C24  O23   106.42  3.000
 1LE  H242  C24  O23   111.94  3.000
 1LE  C28   C25  O26   120.16  3.000
 1LE  O26   C25  C22   120.12  3.000
 1LE  C28   C25  C22   119.72  3.000
 1LE  C27   O26  C25   114.29  3.000
 1LE  H271  C27  H273  108.64  3.000
 1LE  H271  C27  H272  108.76  3.000
 1LE  H273  C27  H272  108.70  3.000
 1LE  H271  C27  O26   111.75  3.000
 1LE  H273  C27  O26   107.12  3.000
 1LE  H272  C27  O26   111.77  3.000
 1LE  C31   C28  O29   124.35  3.000
 1LE  O29   C28  C25   115.53  3.000
 1LE  C31   C28  C25   120.12  3.000
 1LE  C30   O29  C28   118.40  3.000
 1LE  H301  C30  H303  108.86  3.000
 1LE  H301  C30  H302  108.85  3.000
 1LE  H303  C30  H302  108.77  3.000
 1LE  H301  C30  O29   111.85  3.000
 1LE  H303  C30  O29   112.01  3.000
 1LE  H302  C30  O29   106.39  3.000
 1LE  H311  C31  C28   121.08  3.000
 1LE  H311  C31  C20   119.04  3.000
 1LE  C28   C31  C20   119.87  3.000
 1LE  C33   C32  C19   136.40  3.000
 1LE  C19   C32  C16   104.28  3.000
 1LE  C33   C32  C16   119.28  3.000
 1LE  H331  C33  C32   121.01  3.000
 1LE  H331  C33  C13   119.65  3.000
 1LE  C32   C33  C13   119.33  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
 1LE  CONST_01  C16   C15  C14  C13     0.00   0.0  0
 1LE  CONST_02  C16   C32  C33  C13     0.00   0.0  0
 1LE  CONST_03  C19   C32  C33  C13   180.00   0.0  0
 1LE  CONST_04  N17   C16  C15  C14   180.00   0.0  0
 1LE  CONST_05  C32   C16  C15  C14     0.00   0.0  0
 1LE  CONST_06  C32   C33  C13  C14     0.00   0.0  0
 1LE  CONST_07  C33   C13  C14  C15     0.00   0.0  0
 1LE  CONST_08  N18   N17  C16  C15   180.00   0.0  0
 1LE  CONST_09  C33   C32  C16  C15     0.00   0.0  0
 1LE  CONST_10  C19   C32  C16  C15   180.00   0.0  0
 1LE  CONST_11  C19   N18  N17  C16     0.00   0.0  0
 1LE  CONST_12  N18   C19  C32  C16     0.00   0.0  0
 1LE  CONST_13  C20   C19  C32  C16   180.00   0.0  0
 1LE  CONST_14  C33   C32  C16  N17   180.00   0.0  0
 1LE  CONST_15  C19   C32  C16  N17     0.00   0.0  0
 1LE  CONST_16  C32   C19  N18  N17     0.00   0.0  0
 1LE  CONST_17  C20   C19  N18  N17   180.00   0.0  0
 1LE  CONST_18  C32   C16  N17  N18     0.00   0.0  0
 1LE  CONST_19  C33   C32  C19  N18   180.00   0.0  0
 1LE  CONST_22  C28   C31  C20  C19   180.00   0.0  0
 1LE  CONST_23  C22   C21  C20  C19   180.00   0.0  0
 1LE  CONST_24  C33   C32  C19  C20     0.00   0.0  0
 1LE  CONST_25  C25   C28  C31  C20     0.00   0.0  0
 1LE  CONST_26  C25   C22  C21  C20     0.00   0.0  0
 1LE  CONST_28  C28   C31  C20  C21     0.00   0.0  0
 1LE  CONST_29  C28   C25  C22  C21     0.00   0.0  0
 1LE  CONST_30  C31   C20  C21  C22     0.00   0.0  0
 1LE  CONST_31  C31   C28  C25  C22     0.00   0.0  0
 1LE  CONST_33  C15   C14  C13  C12   180.00   0.0  0
 1LE  CONST_34  C32   C33  C13  C12   180.00   0.0  0
 1LE  CONST_35  O29   C28  C31  C20   180.00   0.0  0
 1LE  CONST_36  O23   C22  C21  C20   180.00   0.0  0
 1LE  CONST_37  O26   C25  C22  C21   180.00   0.0  0
 1LE  CONST_38  O29   C28  C25  C22   180.00   0.0  0
 1LE  CONST_39  C28   C25  C22  O23   180.00   0.0  0
 1LE  CONST_40  C31   C28  C25  O26   180.00   0.0  0
 1LE  CONST_41  H151  C15  C14  C13   180.00   0.0  0
 1LE  CONST_42  H331  C33  C13  C14   180.00   0.0  0
 1LE  CONST_43  H171  N17  C16  C15     0.00   0.0  0
 1LE  CONST_44  H141  C14  C15  C16   180.00   0.0  0
 1LE  CONST_45  H311  C31  C20  C19     0.00   0.0  0
 1LE  CONST_46  H211  C21  C20  C19     0.00   0.0  0
 1LE  CONST_47  C04   N03  C02  O01     0.00   0.0  0
 1LE  CONST_48  C09   C02  N03  C04   180.00   0.0  0
 1LE  CONST_49  H031  N03  C02  O01   180.00   0.0  0
 1LE  Var_01    C14   C13  C12  C09   -92.93  30.0  1
 1LE  Var_02    C25   C22  O23  C24  -177.96  30.0  3
 1LE  Var_03    C28   C25  O26  C27   -90.37  30.0  2
 1LE  Var_04    C31   C28  O29  C30     1.55  30.0  2
 1LE  Var_05    H242  C24  O23  C22    59.71  30.0  3
 1LE  Var_06    H272  C27  O26  C25    61.04  30.0  3
 1LE  Var_07    H302  C30  O29  C28   178.73  30.0  3
 1LE  Var_08    C07   C04  N03  C02  -174.91  30.0  3
 1LE  Var_09    O08   C07  C04  N03  -177.34  30.0  3
 1LE  Var_10    H052  C05  C04  N03    66.55  30.0  3
 1LE  Var_11    H063  C06  C04  N03    56.49  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
 1LE  chir_01  C09  C10  C02  C12  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
 1LE  plan-1  C19   0.020
 1LE  plan-1  C20   0.020
 1LE  plan-1  C21   0.020
 1LE  plan-1  C22   0.020
 1LE  plan-1  O23   0.020
 1LE  plan-1  C25   0.020
 1LE  plan-1  O26   0.020
 1LE  plan-1  C28   0.020
 1LE  plan-1  O29   0.020
 1LE  plan-1  C31   0.020
 1LE  plan-1  H211  0.020
 1LE  plan-1  H311  0.020
 1LE  plan-2  C12   0.020
 1LE  plan-2  C13   0.020
 1LE  plan-2  C14   0.020
 1LE  plan-2  C15   0.020
 1LE  plan-2  C16   0.020
 1LE  plan-2  N17   0.020
 1LE  plan-2  N18   0.020
 1LE  plan-2  C19   0.020
 1LE  plan-2  C20   0.020
 1LE  plan-2  C32   0.020
 1LE  plan-2  C33   0.020
 1LE  plan-2  H141  0.020
 1LE  plan-2  H151  0.020
 1LE  plan-2  H171  0.020
 1LE  plan-2  H331  0.020
 1LE  plan-3  O01   0.020
 1LE  plan-3  C02   0.020
 1LE  plan-3  N03   0.020
 1LE  plan-3  C04   0.020
 1LE  plan-3  C09   0.020
 1LE  plan-3  H031  0.020

