# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 01:26:36 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: [6-hydroxy-3-(3-methylbenzyl)-1H-indazol-5-yl][(3S)-3-hydroxypyrrolidin-1-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(Cc2n[nH]c3cc(O)c(cc23)C(=O)N4CC[C@H](O)C4)c1
#
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
 62M  62M  '[6-hydroxy-3-(3-methylbenzyl)-1H-indazol-5-yl][(3S)-3-hydroxypyrrolidin-1-yl]methanone'  ligand  47  26  .  2022-07-23  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_62M
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
 62M  C2   C  CH1   0   0.041   3.9103  -2.1592   0.3704
 62M  C4   C  CH2   0  -0.511   2.7934  -2.5541  -0.5808
 62M  C5   C  CH2   0  -0.295   1.8074  -1.3877  -0.5185
 62M  C7   C  CH2   0  -0.311   3.1494  -1.4248   1.4732
 62M  O9   O  O     0  -0.550   2.3705   1.1097   2.0539
 62M  C11  C  CR16  0  -0.330  -0.1777   0.8307  -0.4402
 62M  C12  C  CR56  0  -0.107  -1.0556   1.6499  -1.1435
 62M  C15  C  CR6   0   0.355   1.0114   2.8163   0.3156
 62M  C19  C  CR5   0   0.241  -2.2146   1.4547  -1.9586
 62M  C21  C  CR6   0   0.106  -2.7862  -0.8935  -1.3207
 62M  C23  C  CR16  0  -0.229  -1.9920  -3.0152  -0.5000
 62M  C24  C  CR16  0  -0.311  -2.6196  -2.7888   0.7151
 62M  C27  C  CR16  0  -0.327  -3.4204  -0.6858  -0.0986
 62M  O1   O  OH1   0  -0.663   4.6147  -3.2878   0.8098
 62M  N6   N  NT    0  -0.481   2.1406  -0.6823   0.7277
 62M  C10  C  CR6   0  -0.195   0.8763   1.3845   0.2638
 62M  C13  C  CR56  0   0.446  -0.8708   3.0429  -1.1133
 62M  C14  C  CR16  0  -0.411   0.1569   3.6439  -0.3874
 62M  N17  N  NR15  0  -0.562  -1.8650   3.5587  -1.8611
 62M  N18  N  N     0  -0.260  -2.6752   2.6084  -2.3625
 62M  C20  C  CH2   0  -0.585  -2.8361   0.1651  -2.3922
 62M  C22  C  CR16  0  -0.337  -2.0750  -2.0718  -1.5171
 62M  C25  C  CR6   0   0.114  -3.3471  -1.6182   0.9310
 62M  C26  C  CH3   0  -0.723  -4.0072  -1.3558   2.2537
 62M  H1   H  HCH1  0   0.221   4.5766  -1.4419  -0.1268
 62M  H2   H  HCH2  0   0.268   3.1358  -2.7419  -1.5976
 62M  H3   H  HCH2  0   0.249   2.3199  -3.4666  -0.2109
 62M  H4   H  HCH2  0   0.268   1.9078  -0.7136  -1.3697
 62M  H5   H  HCH2  0   0.256   0.7860  -1.7673  -0.5083
 62M  H6   H  HCH2  0   0.247   2.6774  -2.1451   2.1496
 62M  H7   H  HCH2  0   0.269   3.7768  -0.7593   2.0600
 62M  H8   H  HCR6  0   0.259  -0.3544  -0.2322  -0.4263
 62M  H9   H  HCR6  0   0.254  -1.4344  -3.9298  -0.6587
 62M  H10  H  HCR6  0   0.247  -2.5469  -3.5289   1.5032
 62M  H11  H  HCR6  0   0.240  -3.9812   0.2308   0.0561
 62M  H12  H  HOH1  0   0.456   5.4000  -2.9945   1.2815
 62M  H13  H  HCR6  0   0.274   0.2761   4.7185  -0.3384
 62M  H14  H  HOH1  0   0.474   2.3367   2.6850   1.6331
 62M  H15  H  HNR5  0   0.415  -2.0660   4.5282  -2.0412
 62M  H16  H  HCH2  0   0.272  -3.8674   0.3582  -2.6974
 62M  H17  H  HCH2  0   0.273  -2.3156  -0.2001  -3.2821
 62M  H18  H  HCR6  0   0.253  -1.5760  -2.2493  -2.4626
 62M  H19  H  HCH3  0   0.249  -3.3140  -0.8705   2.9440
 62M  H20  H  HCH3  0   0.243  -4.8709  -0.7000   2.1488
 62M  H21  H  HCH3  0   0.244  -4.3399  -2.2791   2.7271
 62M  C8   C  C     0   0.595   1.8348   0.5785   1.0640
 62M  O16  O  OH1   0  -0.642   1.9715   3.3906   1.0442

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
 62M  O16  C15  single    1.335  0.020  1.335
 62M  C15  C14  aromatic  1.382  0.020  1.382
 62M  C15  C10  aromatic  1.439  0.020  1.439
 62M  C14  C13  aromatic  1.394  0.020  1.394
 62M  O9   C8   double    1.245  0.020  1.245
 62M  O1   C2   single    1.401  0.020  1.401
 62M  C8   C10  single    1.486  0.020  1.486
 62M  C8   N6   single    1.340  0.020  1.340
 62M  C10  C11  aromatic  1.383  0.020  1.383
 62M  C5   N6   single    1.470  0.020  1.470
 62M  C5   C4   single    1.529  0.020  1.529
 62M  C13  N17  aromatic  1.347  0.020  1.347
 62M  C13  C12  aromatic  1.406  0.020  1.406
 62M  N6   C7   single    1.458  0.020  1.458
 62M  N17  N18  aromatic  1.346  0.020  1.346
 62M  C2   C4   single    1.519  0.020  1.519
 62M  C2   C7   single    1.528  0.020  1.528
 62M  C11  C12  aromatic  1.392  0.020  1.392
 62M  C12  C19  aromatic  1.430  0.020  1.430
 62M  N18  C19  aromatic  1.306  0.020  1.306
 62M  C19  C20  single    1.496  0.020  1.496
 62M  C22  C23  aromatic  1.390  0.020  1.390
 62M  C22  C21  aromatic  1.390  0.020  1.390
 62M  C20  C21  single    1.507  0.020  1.507
 62M  C23  C24  aromatic  1.386  0.020  1.386
 62M  C21  C27  aromatic  1.392  0.020  1.392
 62M  C24  C25  aromatic  1.395  0.020  1.395
 62M  C27  C25  aromatic  1.391  0.020  1.391
 62M  C25  C26  single    1.501  0.020  1.501
 62M  C2   H1   single    0.970  0.020  1.090
 62M  C4   H2   single    0.970  0.020  1.090
 62M  C4   H3   single    0.970  0.020  1.090
 62M  C5   H4   single    0.970  0.020  1.090
 62M  C5   H5   single    0.970  0.020  1.090
 62M  C7   H6   single    0.970  0.020  1.090
 62M  C7   H7   single    0.970  0.020  1.090
 62M  C11  H8   single    0.930  0.020  1.080
 62M  C23  H9   single    0.930  0.020  1.080
 62M  C24  H10  single    0.930  0.020  1.080
 62M  C27  H11  single    0.930  0.020  1.080
 62M  O1   H12  single    0.850  0.020  0.980
 62M  C14  H13  single    0.930  0.020  1.080
 62M  O16  H14  single    0.850  0.020  0.980
 62M  N17  H15  single    0.860  0.020  1.020
 62M  C20  H16  single    0.970  0.020  1.090
 62M  C20  H17  single    0.970  0.020  1.090
 62M  C22  H18  single    0.930  0.020  1.080
 62M  C26  H19  single    0.970  0.020  1.090
 62M  C26  H20  single    0.970  0.020  1.090
 62M  C26  H21  single    0.970  0.020  1.090

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
 62M  H1   C2   O1   111.29  3.000
 62M  H1   C2   C7   108.37  3.000
 62M  O1   C2   C7   114.28  3.000
 62M  H1   C2   C4   109.41  3.000
 62M  C7   C2   C4   102.17  3.000
 62M  O1   C2   C4   110.89  3.000
 62M  H3   C4   H2   107.95  3.000
 62M  H3   C4   C5   110.12  3.000
 62M  H2   C4   C5   111.87  3.000
 62M  H3   C4   C2   108.89  3.000
 62M  H2   C4   C2   113.47  3.000
 62M  C5   C4   C2   104.50  3.000
 62M  H5   C5   H4   108.00  3.000
 62M  H5   C5   N6   111.81  3.000
 62M  H4   C5   N6   110.13  3.000
 62M  H5   C5   C4   109.83  3.000
 62M  H4   C5   C4   112.37  3.000
 62M  N6   C5   C4   104.74  3.000
 62M  H7   C7   H6   108.55  3.000
 62M  H7   C7   N6   111.33  3.000
 62M  H6   C7   N6   110.65  3.000
 62M  H7   C7   C2   113.37  3.000
 62M  H6   C7   C2   110.14  3.000
 62M  N6   C7   C2   102.73  3.000
 62M  H8   C11  C10  120.88  3.000
 62M  H8   C11  C12  118.93  3.000
 62M  C10  C11  C12  120.15  3.000
 62M  C13  C12  C19  104.71  3.000
 62M  C19  C12  C11  135.96  3.000
 62M  C13  C12  C11  119.32  3.000
 62M  O16  C15  C14  117.69  3.000
 62M  C14  C15  C10  121.30  3.000
 62M  O16  C15  C10  121.01  3.000
 62M  C20  C19  N18  121.69  3.000
 62M  C20  C19  C12  128.28  3.000
 62M  N18  C19  C12  109.96  3.000
 62M  C22  C21  C20  120.79  3.000
 62M  C20  C21  C27  120.27  3.000
 62M  C22  C21  C27  118.91  3.000
 62M  H9   C23  C22  119.79  3.000
 62M  H9   C23  C24  119.97  3.000
 62M  C22  C23  C24  120.24  3.000
 62M  H10  C24  C25  119.70  3.000
 62M  H10  C24  C23  119.71  3.000
 62M  C25  C24  C23  120.59  3.000
 62M  H11  C27  C25  119.19  3.000
 62M  H11  C27  C21  119.10  3.000
 62M  C25  C27  C21  121.71  3.000
 62M  H12  O1   C2   108.57  3.000
 62M  C8   N6   C7   120.58  3.000
 62M  C7   N6   C5   110.24  3.000
 62M  C8   N6   C5   127.76  3.000
 62M  C15  C10  C11  119.22  3.000
 62M  C11  C10  C8   123.25  3.000
 62M  C15  C10  C8   117.37  3.000
 62M  N17  C13  C14  131.92  3.000
 62M  N17  C13  C12  105.70  3.000
 62M  C14  C13  C12  122.36  3.000
 62M  H13  C14  C13  122.19  3.000
 62M  H13  C14  C15  120.24  3.000
 62M  C13  C14  C15  117.55  3.000
 62M  H15  N17  N18  119.56  3.000
 62M  H15  N17  C13  128.01  3.000
 62M  N18  N17  C13  112.39  3.000
 62M  N17  N18  C19  107.23  3.000
 62M  H17  C20  H16  106.31  3.000
 62M  H17  C20  C21  109.16  3.000
 62M  H16  C20  C21  110.73  3.000
 62M  H17  C20  C19  109.03  3.000
 62M  H16  C20  C19  108.71  3.000
 62M  C21  C20  C19  112.69  3.000
 62M  H18  C22  C23  119.99  3.000
 62M  H18  C22  C21  119.84  3.000
 62M  C23  C22  C21  120.17  3.000
 62M  C26  C25  C27  120.79  3.000
 62M  C26  C25  C24  120.82  3.000
 62M  C27  C25  C24  118.38  3.000
 62M  H21  C26  H20  108.04  3.000
 62M  H21  C26  H19  107.20  3.000
 62M  H20  C26  H19  107.25  3.000
 62M  H21  C26  C25  111.65  3.000
 62M  H20  C26  C25  111.65  3.000
 62M  H19  C26  C25  110.83  3.000
 62M  C10  C8   N6   121.48  3.000
 62M  N6   C8   O9   120.19  3.000
 62M  C10  C8   O9   118.32  3.000
 62M  H14  O16  C15  106.48  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
 62M  CONST_01  C14  C15  C10  C11     0.00   0.0  0
 62M  CONST_02  C14  C13  C12  C11     0.00   0.0  0
 62M  CONST_03  N17  C13  C12  C11   180.00   0.0  0
 62M  CONST_04  N18  C19  C12  C11   180.00   0.0  0
 62M  CONST_05  C15  C14  C13  C12     0.00   0.0  0
 62M  CONST_06  N18  N17  C13  C12     0.00   0.0  0
 62M  CONST_07  C15  C10  C11  C12     0.00   0.0  0
 62M  CONST_08  N17  N18  C19  C12     0.00   0.0  0
 62M  CONST_09  N17  C13  C14  C15   180.00   0.0  0
 62M  CONST_10  C14  C13  C12  C19   180.00   0.0  0
 62M  CONST_11  N17  C13  C12  C19     0.00   0.0  0
 62M  CONST_12  C10  C11  C12  C19   180.00   0.0  0
 62M  CONST_13  C13  N17  N18  C19     0.00   0.0  0
 62M  CONST_14  C24  C23  C22  C21     0.00   0.0  0
 62M  CONST_15  C24  C25  C27  C21     0.00   0.0  0
 62M  CONST_16  C27  C21  C22  C23     0.00   0.0  0
 62M  CONST_17  C27  C25  C24  C23     0.00   0.0  0
 62M  CONST_18  C13  C14  C15  C10     0.00   0.0  0
 62M  CONST_19  C13  C12  C11  C10     0.00   0.0  0
 62M  CONST_20  N18  C19  C12  C13     0.00   0.0  0
 62M  CONST_21  N18  N17  C13  C14   180.00   0.0  0
 62M  CONST_22  C25  C24  C23  C22     0.00   0.0  0
 62M  CONST_23  C25  C27  C21  C22     0.00   0.0  0
 62M  CONST_24  C14  C15  C10  C8    180.00   0.0  0
 62M  CONST_25  C12  C11  C10  C8    180.00   0.0  0
 62M  CONST_26  O16  C15  C10  C11   180.00   0.0  0
 62M  CONST_27  C20  C19  C12  C11     0.00   0.0  0
 62M  CONST_28  C26  C25  C27  C21   180.00   0.0  0
 62M  CONST_29  C20  C21  C22  C23   180.00   0.0  0
 62M  CONST_30  C26  C25  C24  C23   180.00   0.0  0
 62M  CONST_31  O16  C15  C14  C13   180.00   0.0  0
 62M  CONST_32  C20  C19  C12  C13   180.00   0.0  0
 62M  CONST_33  C20  C19  N18  N17   180.00   0.0  0
 62M  CONST_34  C25  C27  C21  C20   180.00   0.0  0
 62M  CONST_35  C10  C8   N6   C5      0.00   0.0  0
 62M  CONST_36  C10  C8   N6   C7    180.00   0.0  0
 62M  CONST_37  H13  C14  C13  C12   180.00   0.0  0
 62M  CONST_38  H15  N17  C13  C12   180.00   0.0  0
 62M  CONST_39  H8   C11  C10  C15   180.00   0.0  0
 62M  CONST_40  H9   C23  C22  C21   180.00   0.0  0
 62M  CONST_41  H18  C22  C23  C24   180.00   0.0  0
 62M  CONST_42  H11  C27  C25  C24   180.00   0.0  0
 62M  CONST_43  H10  C24  C25  C27   180.00   0.0  0
 62M  CONST_44  O9   C8   N6   C5    180.00   0.0  0
 62M  CONST_45  O9   C8   N6   C7      0.00   0.0  0
 62M  Var_01    N6   C5   C4   C2    -18.92  30.0  1
 62M  Var_02    C5   N6   C7   C2     28.30  30.0  1
 62M  Var_03    C7   N6   C5   C4     -6.06  30.0  1
 62M  Var_04    N6   C8   C10  C11    30.12  30.0  2
 62M  Var_05    C21  C20  C19  C12    37.42  30.0  2
 62M  Var_06    C22  C21  C20  C19  -117.15  30.0  2
 62M  Var_07    H19  C26  C25  C24    86.97  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
 62M  chir_01  C2  O1  C4  C7  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
 62M  plan-1  C21  0.020
 62M  plan-1  C23  0.020
 62M  plan-1  C24  0.020
 62M  plan-1  C27  0.020
 62M  plan-1  C20  0.020
 62M  plan-1  C22  0.020
 62M  plan-1  C25  0.020
 62M  plan-1  C26  0.020
 62M  plan-1  H9   0.020
 62M  plan-1  H10  0.020
 62M  plan-1  H11  0.020
 62M  plan-1  H18  0.020
 62M  plan-2  C11  0.020
 62M  plan-2  C12  0.020
 62M  plan-2  C15  0.020
 62M  plan-2  C19  0.020
 62M  plan-2  C10  0.020
 62M  plan-2  C13  0.020
 62M  plan-2  C14  0.020
 62M  plan-2  N17  0.020
 62M  plan-2  N18  0.020
 62M  plan-2  C20  0.020
 62M  plan-2  H8   0.020
 62M  plan-2  H13  0.020
 62M  plan-2  H15  0.020
 62M  plan-2  C8   0.020
 62M  plan-2  O16  0.020
 62M  plan-3  C5   0.020
 62M  plan-3  C7   0.020
 62M  plan-3  O9   0.020
 62M  plan-3  N6   0.020
 62M  plan-3  C10  0.020
 62M  plan-3  C8   0.020

