# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 02:09:18 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 6,7-dimethyl-1'-[(7-methyl-1H-indazol-5-yl)carbonyl]spiro[chromene-2,4'-piperidin]-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2OC3(CCN(CC3)C(=O)c4cc(C)c5[nH]ncc5c4)CC(=O)c2cc1C
#
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
 57J  57J  6,7-dimethyl-1'-[(7-methyl-1H-indazol-5-yl)carbonyl]spiro[chromene-2,4'-piperidin]-4(3H)-one  ligand  55  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_57J
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
 57J  N3   N  NT    0  -0.455  -1.0134   1.3312  -1.0670
 57J  C4   C  CR6   0  -0.076  -3.2705   0.6323  -0.4487
 57J  N2   N  N     0  -0.224  -5.7576  -3.1867  -0.2660
 57J  C7   C  CR56  0   0.399  -5.2308  -1.1107   0.3668
 57J  C6   C  CR56  0  -0.074  -4.3300  -1.4913  -0.6404
 57J  C9   C  C     0   0.521  -2.3128   1.6775  -0.9242
 57J  C13  C  CH2   0  -0.435   0.6153   0.7486   0.6710
 57J  C20  C  CR6   0   0.088   4.7532  -1.7408  -0.9719
 57J  C21  C  CR16  0  -0.408   3.7993  -0.8098  -1.3490
 57J  C8   C  CR15  0  -0.128  -4.7314  -2.8101  -0.9858
 57J  C18  C  CR16  0  -0.332   4.8384  -0.7440   1.2063
 57J  C16  C  C     0   0.392   3.4651   1.2703   1.7563
 57J  C19  C  CR6   0   0.070   5.2840  -1.7169   0.3358
 57J  C2   C  CR6   0   0.091  -5.1947   0.1474   0.9922
 57J  C3   C  CR16  0  -0.352  -4.2093   0.9980   0.5458
 57J  C5   C  CR16  0  -0.349  -3.3277  -0.6058  -1.0517
 57J  N1   N  NR15  0  -0.553  -6.0553  -2.1675   0.5440
 57J  O1   O  O     0  -0.490  -2.7386   2.7893  -1.2134
 57J  C10  C  CH2   0  -0.320  -0.0767   2.2518  -1.6915
 57J  C11  C  CH2   0  -0.438   0.9075   2.8185  -0.6769
 57J  C12  C  CT    0   0.138   1.6395   1.7209   0.0829
 57J  C14  C  CH2   0  -0.310  -0.3667   0.2283  -0.3732
 57J  C15  C  CH2   0  -0.578   2.5514   2.3058   1.1538
 57J  C17  C  CR6   0  -0.133   3.8833   0.2090   0.8344
 57J  C22  C  CR6   0   0.402   3.3561   0.1635  -0.4574
 57J  O3   O  O2    0  -0.486   2.4344   1.0347  -0.8981
 57J  C23  C  CH3   0  -0.738   5.2046  -2.7818  -1.9494
 57J  C24  C  CH3   0  -0.735   6.3046  -2.7283   0.7676
 57J  H13  H  HCH2  0   0.260   1.1018  -0.1041   1.1519
 57J  H12  H  HCH2  0   0.255   0.0589   1.2698   1.4552
 57J  H19  H  HCR6  0   0.261   3.3828  -0.8352  -2.3489
 57J  H7   H  HCR5  0   0.271  -4.3014  -3.4722  -1.7220
 57J  H18  H  HCR6  0   0.256   5.2405  -0.7037   2.2118
 57J  H3   H  HCH3  0   0.251  -6.1461  -0.1772   2.8938
 57J  H4   H  HCH3  0   0.257  -5.9881   1.5181   2.4376
 57J  H2   H  HCH3  0   0.252  -7.2031   0.5011   1.6661
 57J  H5   H  HCR6  0   0.255  -4.1425   1.9875   0.9823
 57J  H6   H  HCR6  0   0.269  -2.6270  -0.8866  -1.8284
 57J  H1   H  HNR5  0   0.420  -6.8287  -2.2527   1.1833
 57J  H9   H  HCH2  0   0.254   0.4582   1.7131  -2.4780
 57J  H8   H  HCH2  0   0.270  -0.6260   3.0580  -2.1684
 57J  H11  H  HCH2  0   0.258   1.6281   3.4637  -1.1849
 57J  H10  H  HCH2  0   0.250   0.3724   3.4410   0.0447
 57J  H14  H  HCH2  0   0.280  -1.1066  -0.3877   0.1281
 57J  H15  H  HCH2  0   0.250   0.1424  -0.4101  -1.0999
 57J  H17  H  HCH2  0   0.282   1.9634   2.7906   1.9339
 57J  H16  H  HCH2  0   0.295   3.1887   3.0785   0.7054
 57J  H21  H  HCH3  0   0.253   4.9443  -3.7846  -1.6044
 57J  H20  H  HCH3  0   0.257   4.7501  -2.6363  -2.9277
 57J  H22  H  HCH3  0   0.250   6.2887  -2.7645  -2.0754
 57J  H23  H  HCH3  0   0.242   7.1843  -2.7203   0.1207
 57J  H25  H  HCH3  0   0.252   6.6405  -2.5360   1.7854
 57J  H24  H  HCH3  0   0.245   5.9018  -3.7429   0.7384
 57J  O2   O  O     0  -0.403   3.8610   1.3432   2.9028
 57J  C1   C  CH3   0  -0.731  -6.1822   0.5185   2.0531

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
 57J  N2   N1   aromatic  1.335  0.020  1.335
 57J  N2   C8   aromatic  1.309  0.020  1.309
 57J  N1   C7   aromatic  1.352  0.020  1.352
 57J  C1   C2   single    1.496  0.020  1.496
 57J  C8   C6   aromatic  1.421  0.020  1.421
 57J  C7   C2   aromatic  1.405  0.020  1.405
 57J  C7   C6   aromatic  1.404  0.020  1.404
 57J  C2   C3   aromatic  1.376  0.020  1.376
 57J  C6   C5   aromatic  1.399  0.020  1.399
 57J  C3   C4   aromatic  1.416  0.020  1.416
 57J  C5   C4   aromatic  1.378  0.020  1.378
 57J  C4   C9   single    1.495  0.020  1.495
 57J  O1   C9   double    1.225  0.020  1.225
 57J  C9   N3   single    1.352  0.020  1.352
 57J  N3   C14  single    1.455  0.020  1.455
 57J  N3   C10  single    1.454  0.020  1.454
 57J  C14  C13  single    1.525  0.020  1.525
 57J  C10  C11  single    1.523  0.020  1.523
 57J  C13  C12  single    1.530  0.020  1.530
 57J  C11  C12  single    1.522  0.020  1.522
 57J  C12  O3   single    1.437  0.020  1.437
 57J  C12  C15  single    1.523  0.020  1.523
 57J  O3   C22  single    1.343  0.020  1.343
 57J  C15  C16  single    1.507  0.020  1.507
 57J  C22  C21  aromatic  1.392  0.020  1.392
 57J  C22  C17  aromatic  1.396  0.020  1.396
 57J  C21  C20  aromatic  1.385  0.020  1.385
 57J  C16  C17  single    1.467  0.020  1.467
 57J  C16  O2   double    1.215  0.020  1.215
 57J  C17  C18  aromatic  1.400  0.020  1.400
 57J  C20  C23  single    1.498  0.020  1.498
 57J  C20  C19  aromatic  1.411  0.020  1.411
 57J  C18  C19  aromatic  1.379  0.020  1.379
 57J  C19  C24  single    1.500  0.020  1.500
 57J  C13  H13  single    0.970  0.020  1.090
 57J  C13  H12  single    0.970  0.020  1.090
 57J  C21  H19  single    0.930  0.020  1.080
 57J  C8   H7   single    0.930  0.020  1.080
 57J  C18  H18  single    0.930  0.020  1.080
 57J  C1   H3   single    0.970  0.020  1.090
 57J  C1   H4   single    0.970  0.020  1.090
 57J  C1   H2   single    0.970  0.020  1.090
 57J  C3   H5   single    0.930  0.020  1.080
 57J  C5   H6   single    0.930  0.020  1.080
 57J  N1   H1   single    0.860  0.020  1.020
 57J  C10  H9   single    0.970  0.020  1.090
 57J  C10  H8   single    0.970  0.020  1.090
 57J  C11  H11  single    0.970  0.020  1.090
 57J  C11  H10  single    0.970  0.020  1.090
 57J  C14  H14  single    0.970  0.020  1.090
 57J  C14  H15  single    0.970  0.020  1.090
 57J  C15  H17  single    0.970  0.020  1.090
 57J  C15  H16  single    0.970  0.020  1.090
 57J  C23  H21  single    0.970  0.020  1.090
 57J  C23  H20  single    0.970  0.020  1.090
 57J  C23  H22  single    0.970  0.020  1.090
 57J  C24  H23  single    0.970  0.020  1.090
 57J  C24  H25  single    0.970  0.020  1.090
 57J  C24  H24  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
 57J  C14  N3   C10  113.48  3.000
 57J  C10  N3   C9   120.14  3.000
 57J  C14  N3   C9   124.82  3.000
 57J  C5   C4   C3   120.78  3.000
 57J  C5   C4   C9   121.02  3.000
 57J  C3   C4   C9   117.88  3.000
 57J  N1   N2   C8   106.78  3.000
 57J  N1   C7   C2   131.07  3.000
 57J  C2   C7   C6   123.05  3.000
 57J  N1   C7   C6   105.87  3.000
 57J  C5   C6   C8   135.90  3.000
 57J  C5   C6   C7   119.93  3.000
 57J  C8   C6   C7   104.16  3.000
 57J  O1   C9   C4   119.13  3.000
 57J  O1   C9   N3   122.78  3.000
 57J  C4   C9   N3   118.04  3.000
 57J  H12  C13  H13  106.43  3.000
 57J  H12  C13  C14  109.02  3.000
 57J  H13  C13  C14  108.76  3.000
 57J  H12  C13  C12  108.26  3.000
 57J  H13  C13  C12  111.53  3.000
 57J  C14  C13  C12  112.63  3.000
 57J  C23  C20  C19  120.21  3.000
 57J  C19  C20  C21  119.99  3.000
 57J  C23  C20  C21  119.80  3.000
 57J  H19  C21  C22  119.01  3.000
 57J  H19  C21  C20  120.01  3.000
 57J  C22  C21  C20  120.97  3.000
 57J  H7   C8   C6   128.49  3.000
 57J  H7   C8   N2   120.73  3.000
 57J  C6   C8   N2   110.78  3.000
 57J  H18  C18  C17  118.33  3.000
 57J  H18  C18  C19  119.47  3.000
 57J  C17  C18  C19  122.20  3.000
 57J  C17  C16  O2   122.93  3.000
 57J  O2   C16  C15  122.25  3.000
 57J  C17  C16  C15  114.77  3.000
 57J  C24  C19  C18  120.90  3.000
 57J  C24  C19  C20  120.73  3.000
 57J  C18  C19  C20  118.37  3.000
 57J  C3   C2   C1   123.32  3.000
 57J  C3   C2   C7   115.30  3.000
 57J  C1   C2   C7   121.37  3.000
 57J  H5   C3   C2   118.55  3.000
 57J  H5   C3   C4   118.55  3.000
 57J  C2   C3   C4   122.89  3.000
 57J  H6   C5   C6   120.67  3.000
 57J  H6   C5   C4   121.31  3.000
 57J  C6   C5   C4   118.01  3.000
 57J  H1   N1   C7   128.15  3.000
 57J  H1   N1   N2   119.45  3.000
 57J  C7   N1   N2   112.40  3.000
 57J  H8   C10  H9   107.30  3.000
 57J  H8   C10  C11  110.07  3.000
 57J  H9   C10  C11  110.27  3.000
 57J  H8   C10  N3   109.44  3.000
 57J  H9   C10  N3   108.19  3.000
 57J  C11  C10  N3   111.45  3.000
 57J  H10  C11  H11  107.07  3.000
 57J  H10  C11  C12  108.45  3.000
 57J  H11  C11  C12  109.92  3.000
 57J  H10  C11  C10  109.60  3.000
 57J  H11  C11  C10  109.65  3.000
 57J  C12  C11  C10  112.02  3.000
 57J  O3   C12  C15  109.40  3.000
 57J  C15  C12  C11  111.21  3.000
 57J  O3   C12  C11  105.63  3.000
 57J  C15  C12  C13  112.00  3.000
 57J  O3   C12  C13  109.23  3.000
 57J  C11  C12  C13  109.16  3.000
 57J  H15  C14  H14  107.04  3.000
 57J  H15  C14  C13  110.77  3.000
 57J  H14  C14  C13  108.44  3.000
 57J  H15  C14  N3   109.44  3.000
 57J  H14  C14  N3   110.34  3.000
 57J  C13  C14  N3   110.74  3.000
 57J  H16  C15  H17  107.00  3.000
 57J  H16  C15  C12  109.31  3.000
 57J  H17  C15  C12  110.54  3.000
 57J  H16  C15  C16  107.17  3.000
 57J  H17  C15  C16  110.27  3.000
 57J  C12  C15  C16  112.35  3.000
 57J  C22  C17  C16  119.83  3.000
 57J  C16  C17  C18  121.35  3.000
 57J  C22  C17  C18  118.78  3.000
 57J  O3   C22  C17  122.81  3.000
 57J  C17  C22  C21  119.68  3.000
 57J  O3   C22  C21  117.51  3.000
 57J  C22  O3   C12  117.74  3.000
 57J  H22  C23  H20  107.99  3.000
 57J  H22  C23  H21  106.72  3.000
 57J  H20  C23  H21  107.89  3.000
 57J  H22  C23  C20  111.33  3.000
 57J  H20  C23  C20  111.59  3.000
 57J  H21  C23  C20  111.11  3.000
 57J  H24  C24  H25  107.63  3.000
 57J  H24  C24  H23  106.75  3.000
 57J  H25  C24  H23  107.69  3.000
 57J  H24  C24  C19  111.57  3.000
 57J  H25  C24  C19  111.09  3.000
 57J  H23  C24  C19  111.87  3.000
 57J  H2   C1   H4   107.85  3.000
 57J  H2   C1   H3   107.08  3.000
 57J  H4   C1   H3   107.90  3.000
 57J  H2   C1   C2   111.21  3.000
 57J  H4   C1   C2   111.14  3.000
 57J  H3   C1   C2   111.48  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
 57J  CONST_01  C7   C2   C3   C4      0.00   0.0  0
 57J  CONST_02  C8   C6   C5   C4    180.00   0.0  0
 57J  CONST_03  C7   C6   C5   C4      0.00   0.0  0
 57J  CONST_04  C2   C7   N1   N2    180.00   0.0  0
 57J  CONST_05  C6   C7   N1   N2      0.00   0.0  0
 57J  CONST_06  C7   C6   C8   N2      0.00   0.0  0
 57J  CONST_07  C5   C6   C8   N2    180.00   0.0  0
 57J  CONST_08  C8   N2   N1   C7      0.00   0.0  0
 57J  CONST_09  N1   N2   C8   C6      0.00   0.0  0
 57J  CONST_10  C3   C2   C7   C6      0.00   0.0  0
 57J  CONST_11  C3   C4   C5   C6      0.00   0.0  0
 57J  CONST_12  C17  C22  C21  C20     0.00   0.0  0
 57J  CONST_13  C17  C18  C19  C20     0.00   0.0  0
 57J  CONST_14  C18  C17  C22  C21     0.00   0.0  0
 57J  CONST_15  C18  C19  C20  C21     0.00   0.0  0
 57J  CONST_16  N1   C7   C6   C8      0.00   0.0  0
 57J  CONST_17  C2   C7   C6   C8    180.00   0.0  0
 57J  CONST_18  C22  C21  C20  C19     0.00   0.0  0
 57J  CONST_19  C22  C17  C18  C19     0.00   0.0  0
 57J  CONST_20  C5   C6   C7   C2      0.00   0.0  0
 57J  CONST_21  C5   C4   C3   C2      0.00   0.0  0
 57J  CONST_22  N1   C7   C2   C3    180.00   0.0  0
 57J  CONST_23  N1   C7   C6   C5    180.00   0.0  0
 57J  CONST_24  C1   C2   C3   C4    180.00   0.0  0
 57J  CONST_25  C1   C2   C7   C6    180.00   0.0  0
 57J  CONST_26  C9   C4   C5   C6    180.00   0.0  0
 57J  CONST_27  C2   C3   C4   C9    180.00   0.0  0
 57J  CONST_28  C24  C19  C20  C21   180.00   0.0  0
 57J  CONST_29  C23  C20  C19  C18   180.00   0.0  0
 57J  CONST_30  N1   C7   C2   C1      0.00   0.0  0
 57J  CONST_31  C24  C19  C18  C17   180.00   0.0  0
 57J  CONST_32  C23  C20  C21  C22   180.00   0.0  0
 57J  CONST_34  C10  N3   C9   C4    180.00   0.0  0
 57J  CONST_35  H5   C3   C2   C7    180.00   0.0  0
 57J  CONST_36  H7   C8   C6   C7    180.00   0.0  0
 57J  CONST_37  H6   C5   C6   C7    180.00   0.0  0
 57J  CONST_38  H1   N1   C7   C6    180.00   0.0  0
 57J  CONST_39  H18  C18  C19  C20   180.00   0.0  0
 57J  CONST_40  H19  C21  C20  C19   180.00   0.0  0
 57J  CONST_42  C10  N3   C9   O1      0.00   0.0  0
 57J  Var_01    C12  C13  C14  N3    -54.29  30.0  1
 57J  Var_02    C12  C11  C10  N3     54.73  30.0  1
 57J  Var_03    C10  N3   C14  C13    56.15  30.0  1
 57J  Var_04    C10  C11  C12  C13   -52.25  30.0  3
 57J  Var_05    C16  C15  C12  C13    67.58  30.0  1
 57J  Var_06    C15  C16  C17  C18   173.29  30.0  1
 57J  Var_07    C14  N3   C10  C11   -56.70  30.0  1
 57J  Var_08    C14  C13  C12  C11    52.43  30.0  3
 57J  Var_09    C17  C22  O3   C12   -21.82  30.0  1
 57J  Var_10    C17  C16  C15  C12    32.50  30.0  1
 57J  Var_11    C3   C4   C9   N3    135.63  30.0  2
 57J  Var_12    H3   C1   C2   C7     58.29  30.0  2
 57J  Var_13    H23  C24  C19  C20    56.86  30.0  2
 57J  Var_14    H21  C23  C20  C21  -116.42  30.0  2

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
 57J  plan-1  C4   0.020
 57J  plan-1  N2   0.020
 57J  plan-1  C7   0.020
 57J  plan-1  C6   0.020
 57J  plan-1  C9   0.020
 57J  plan-1  C8   0.020
 57J  plan-1  C2   0.020
 57J  plan-1  C3   0.020
 57J  plan-1  C5   0.020
 57J  plan-1  N1   0.020
 57J  plan-1  H7   0.020
 57J  plan-1  H5   0.020
 57J  plan-1  H6   0.020
 57J  plan-1  H1   0.020
 57J  plan-1  C1   0.020
 57J  plan-2  C20  0.020
 57J  plan-2  C21  0.020
 57J  plan-2  C18  0.020
 57J  plan-2  C16  0.020
 57J  plan-2  C19  0.020
 57J  plan-2  C17  0.020
 57J  plan-2  C22  0.020
 57J  plan-2  O3   0.020
 57J  plan-2  C23  0.020
 57J  plan-2  C24  0.020
 57J  plan-2  H19  0.020
 57J  plan-2  H18  0.020
 57J  plan-3  N3   0.020
 57J  plan-3  C4   0.020
 57J  plan-3  C9   0.020
 57J  plan-3  O1   0.020
 57J  plan-3  C10  0.020
 57J  plan-3  C14  0.020
 57J  plan-4  C16  0.020
 57J  plan-4  C15  0.020
 57J  plan-4  C17  0.020
 57J  plan-4  O2   0.020

