# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 11:51:11 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: 1-[5-[4-fluoranyl-2-[2-(1,3,5-trimethylpyrazol-4-yl)ethoxy]phenyl]-2~{H}-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)Cc1[nH]nc2ccc(cc12)c3ccc(F)cc3OCCc4c(C)nn(C)c4C
#
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
 9M2  9M2  1-[5-[4-fluoranyl-2-[2-(1,3,5-trimethylpyrazol-4-yl)ethoxy]phenyl]-2~{H}-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine  ligand  59  31  .  2023-02-02  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9M2
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
 9M2  C12  C  CR16  0  -0.436   1.0514   4.0605   0.5891
 9M2  C8   C  CR16  0  -0.379   2.7909   0.0651   0.0319
 9M2  C9   C  CR56  0  -0.120   3.4561  -1.1632   0.2267
 9M2  C10  C  CR6   0  -0.060   0.9693   1.6269   0.6254
 9M2  C11  C  CR16  0  -0.273   1.6680   2.8226   0.7288
 9M2  C7   C  CR6   0   0.065   1.6692   0.3320   0.7753
 9M2  C6   C  CR16  0  -0.277   1.2065  -0.6229   1.7368
 9M2  N1   N  NR15  0  -0.475   4.6854  -2.9442   0.2938
 9M2  C5   C  CR16  0  -0.292   1.8372  -1.8131   1.9526
 9M2  C4   C  CR56  0   0.227   2.9865  -2.1055   1.1813
 9M2  C13  C  CR6   0   0.545  -0.3028   4.0700   0.3417
 9M2  C14  C  CR16  0  -0.545  -1.0520   2.9133   0.2206
 9M2  C15  C  CR6   0   0.381  -0.4106   1.6853   0.3542
 9M2  N2   N  N     0  -0.317   3.7553  -3.1967   1.2075
 9M2  C3   C  CR5   0   0.404   4.5801  -1.7700  -0.3352
 9M2  C2   C  CH2   0  -0.357   5.5081  -1.3261  -1.4126
 9M2  N    N  NT    0  -0.397   5.9136   0.0508  -1.2256
 9M2  C1   C  CH3   0  -0.520   6.7425   0.2166  -0.0513
 9M2  C    C  CH3   0  -0.522   6.5642   0.5695  -2.4089
 9M2  O    O  O2    0  -0.462  -1.0387   0.5099   0.2143
 9M2  C16  C  CH2   0  -0.167  -2.4440   0.4765   0.0248
 9M2  C17  C  CH2   0  -0.565  -2.8661  -0.9818  -0.0370
 9M2  C18  C  CR5   0  -0.218  -4.3450  -1.1098  -0.1880
 9M2  C22  C  CR5   0   0.248  -5.3108  -1.1303   0.8399
 9M2  C23  C  CH3   0  -0.746  -5.0695  -1.0457   2.3081
 9M2  N4   N  N     0  -0.318  -6.5274  -1.2478   0.3410
 9M2  N3   N  NR5   0  -0.323  -6.3698  -1.3045  -0.9834
 9M2  C21  C  CH3   0  -0.520  -7.5229  -1.3732  -1.8457
 9M2  C19  C  CR5   0   0.405  -5.0762  -1.2160  -1.3554
 9M2  C20  C  CH3   0  -0.749  -4.6358  -1.2405  -2.7748
 9M2  H1   H  HCR6  0   0.275   1.6115   4.9807   0.6839
 9M2  H2   H  HCR6  0   0.246   3.1653   0.7752  -0.6944
 9M2  H3   H  HCR6  0   0.263   2.7287   2.7883   0.9422
 9M2  H4   H  HCR6  0   0.246   0.3330  -0.3817   2.3278
 9M2  H5   H  HNR5  0   0.423   5.4007  -3.6368   0.1241
 9M2  H6   H  HCR6  0   0.254   1.4716  -2.5111   2.6946
 9M2  H7   H  HCR6  0   0.300  -2.1107   2.9893   0.0116
 9M2  H8   H  HCH2  0   0.224   6.3650  -2.0205  -1.4650
 9M2  H9   H  HCH2  0   0.265   4.9932  -1.4017  -2.3750
 9M2  H11  H  HCH3  0   0.195   7.6939  -0.3348  -0.1148
 9M2  H12  H  HCH3  0   0.237   6.9752   1.2720   0.0920
 9M2  H13  H  HCH3  0   0.239   6.2160  -0.1275   0.8395
 9M2  H14  H  HCH3  0   0.236   5.8928   0.5046  -3.2662
 9M2  H15  H  HCH3  0   0.237   6.8146   1.6207  -2.2620
 9M2  H16  H  HCH3  0   0.195   7.4935   0.0384  -2.6664
 9M2  H17  H  HCH2  0   0.230  -2.9538   0.9866   0.8504
 9M2  H18  H  HCH2  0   0.229  -2.7209   0.9876  -0.9038
 9M2  H19  H  HCH2  0   0.254  -2.3522  -1.4714  -0.8681
 9M2  H20  H  HCH2  0   0.251  -2.5376  -1.4872   0.8755
 9M2  H21  H  HCH3  0   0.243  -4.3134  -1.7652   2.6271
 9M2  H22  H  HCH3  0   0.243  -4.7094  -0.0569   2.5989
 9M2  H23  H  HCH3  0   0.249  -5.9821  -1.2456   2.8675
 9M2  H24  H  HCH3  0   0.251  -7.8812  -0.3789  -2.1144
 9M2  H25  H  HCH3  0   0.256  -7.2730  -1.9115  -2.7570
 9M2  H26  H  HCH3  0   0.264  -8.3170  -1.9094  -1.3336
 9M2  H27  H  HCH3  0   0.258  -4.9650  -2.1453  -3.2888
 9M2  H28  H  HCH3  0   0.258  -5.0223  -0.3870  -3.3345
 9M2  H29  H  HCH3  0   0.261  -3.5492  -1.2056  -2.8326
 9M2  F    F  F     0  -0.317  -0.9372   5.2459   0.2089

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
 9M2  F    C13  single    1.343  0.020  1.343
 9M2  C13  C14  aromatic  1.383  0.020  1.383
 9M2  C13  C12  aromatic  1.377  0.020  1.377
 9M2  C14  C15  aromatic  1.392  0.020  1.392
 9M2  C23  C22  single    1.490  0.020  1.490
 9M2  C12  C11  aromatic  1.390  0.020  1.390
 9M2  C16  C17  single    1.519  0.020  1.519
 9M2  C16  O    single    1.418  0.020  1.418
 9M2  C15  O    single    1.340  0.020  1.340
 9M2  C15  C10  aromatic  1.407  0.020  1.407
 9M2  C11  C10  aromatic  1.389  0.020  1.389
 9M2  C22  N4   aromatic  1.320  0.020  1.320
 9M2  C22  C18  aromatic  1.411  0.020  1.411
 9M2  C17  C18  single    1.492  0.020  1.492
 9M2  C10  C7   single    1.480  0.020  1.480
 9M2  N4   N3   aromatic  1.335  0.020  1.335
 9M2  C18  C19  aromatic  1.382  0.020  1.382
 9M2  N3   C19  aromatic  1.349  0.020  1.349
 9M2  N3   C21  single    1.441  0.020  1.441
 9M2  C7   C8   aromatic  1.372  0.020  1.372
 9M2  C7   C6   aromatic  1.432  0.020  1.432
 9M2  C19  C20  single    1.486  0.020  1.486
 9M2  C8   C9   aromatic  1.410  0.020  1.410
 9M2  C6   C5   aromatic  1.364  0.020  1.364
 9M2  C    N    single    1.447  0.020  1.447
 9M2  C9   C3   aromatic  1.395  0.020  1.395
 9M2  C9   C4   aromatic  1.421  0.020  1.421
 9M2  N    C2   single    1.448  0.020  1.448
 9M2  N    C1   single    1.447  0.020  1.447
 9M2  C5   C4   aromatic  1.415  0.020  1.415
 9M2  C2   C3   single    1.490  0.020  1.490
 9M2  C3   N1   aromatic  1.336  0.020  1.336
 9M2  C4   N2   aromatic  1.335  0.020  1.335
 9M2  N1   N2   aromatic  1.328  0.020  1.328
 9M2  C12  H1   single    0.930  0.020  1.080
 9M2  C8   H2   single    0.930  0.020  1.080
 9M2  C11  H3   single    0.930  0.020  1.080
 9M2  C6   H4   single    0.930  0.020  1.080
 9M2  N1   H5   single    0.860  0.020  1.020
 9M2  C5   H6   single    0.930  0.020  1.080
 9M2  C14  H7   single    0.930  0.020  1.080
 9M2  C2   H8   single    0.970  0.020  1.090
 9M2  C2   H9   single    0.970  0.020  1.090
 9M2  C1   H11  single    0.970  0.020  1.090
 9M2  C1   H12  single    0.970  0.020  1.090
 9M2  C1   H13  single    0.970  0.020  1.090
 9M2  C    H14  single    0.970  0.020  1.090
 9M2  C    H15  single    0.970  0.020  1.090
 9M2  C    H16  single    0.970  0.020  1.090
 9M2  C16  H17  single    0.970  0.020  1.090
 9M2  C16  H18  single    0.970  0.020  1.090
 9M2  C17  H19  single    0.970  0.020  1.090
 9M2  C17  H20  single    0.970  0.020  1.090
 9M2  C23  H21  single    0.970  0.020  1.090
 9M2  C23  H22  single    0.970  0.020  1.090
 9M2  C23  H23  single    0.970  0.020  1.090
 9M2  C21  H24  single    0.970  0.020  1.090
 9M2  C21  H25  single    0.970  0.020  1.090
 9M2  C21  H26  single    0.970  0.020  1.090
 9M2  C20  H27  single    0.970  0.020  1.090
 9M2  C20  H28  single    0.970  0.020  1.090
 9M2  C20  H29  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
 9M2  H1   C12  C13  121.29  3.000
 9M2  H1   C12  C11  121.28  3.000
 9M2  C13  C12  C11  117.42  3.000
 9M2  H2   C8   C7   121.25  3.000
 9M2  H2   C8   C9   120.05  3.000
 9M2  C7   C8   C9   118.70  3.000
 9M2  C3   C9   C4   104.38  3.000
 9M2  C4   C9   C8   120.95  3.000
 9M2  C3   C9   C8   134.67  3.000
 9M2  C15  C10  C7   121.31  3.000
 9M2  C7   C10  C11  120.53  3.000
 9M2  C15  C10  C11  118.16  3.000
 9M2  H3   C11  C10  118.71  3.000
 9M2  H3   C11  C12  118.86  3.000
 9M2  C10  C11  C12  122.42  3.000
 9M2  C6   C7   C10  119.92  3.000
 9M2  C6   C7   C8   119.89  3.000
 9M2  C10  C7   C8   120.14  3.000
 9M2  H4   C6   C5   118.77  3.000
 9M2  H4   C6   C7   118.63  3.000
 9M2  C5   C6   C7   122.59  3.000
 9M2  H5   N1   C3   125.40  3.000
 9M2  H5   N1   N2   118.76  3.000
 9M2  C3   N1   N2   115.83  3.000
 9M2  H6   C5   C4   120.99  3.000
 9M2  H6   C5   C6   120.99  3.000
 9M2  C4   C5   C6   118.02  3.000
 9M2  N2   C4   C5   128.76  3.000
 9M2  N2   C4   C9   111.40  3.000
 9M2  C5   C4   C9   119.84  3.000
 9M2  C14  C13  F    117.88  3.000
 9M2  C14  C13  C12  122.87  3.000
 9M2  F    C13  C12  119.25  3.000
 9M2  H7   C14  C15  122.11  3.000
 9M2  H7   C14  C13  119.23  3.000
 9M2  C15  C14  C13  118.66  3.000
 9M2  O    C15  C14  123.22  3.000
 9M2  O    C15  C10  116.31  3.000
 9M2  C14  C15  C10  120.46  3.000
 9M2  C4   N2   N1   103.55  3.000
 9M2  C2   C3   N1   123.59  3.000
 9M2  N1   C3   C9   104.84  3.000
 9M2  C2   C3   C9   131.56  3.000
 9M2  H9   C2   H8   106.26  3.000
 9M2  H9   C2   N    108.13  3.000
 9M2  H8   C2   N    112.76  3.000
 9M2  H9   C2   C3   108.81  3.000
 9M2  H8   C2   C3   109.29  3.000
 9M2  N    C2   C3   111.38  3.000
 9M2  C    N    C1   111.42  3.000
 9M2  C1   N    C2   111.98  3.000
 9M2  C    N    C2   111.19  3.000
 9M2  H13  C1   H12  107.52  3.000
 9M2  H13  C1   H11  107.82  3.000
 9M2  H12  C1   H11  107.93  3.000
 9M2  H13  C1   N    110.51  3.000
 9M2  H12  C1   N    109.87  3.000
 9M2  H11  C1   N    113.00  3.000
 9M2  H16  C    H15  107.62  3.000
 9M2  H16  C    H14  107.88  3.000
 9M2  H15  C    H14  107.73  3.000
 9M2  H16  C    N    113.45  3.000
 9M2  H15  C    N    109.80  3.000
 9M2  H14  C    N    110.16  3.000
 9M2  C16  O    C15  119.94  3.000
 9M2  H18  C16  H17  107.68  3.000
 9M2  H18  C16  C17  110.06  3.000
 9M2  H17  C16  C17  110.37  3.000
 9M2  H18  C16  O    110.65  3.000
 9M2  H17  C16  O    110.44  3.000
 9M2  C17  C16  O    107.66  3.000
 9M2  H20  C17  H19  106.63  3.000
 9M2  H20  C17  C18  110.03  3.000
 9M2  H19  C17  C18  110.52  3.000
 9M2  H20  C17  C16  109.04  3.000
 9M2  H19  C17  C16  109.28  3.000
 9M2  C18  C17  C16  111.21  3.000
 9M2  C19  C18  C22  104.61  3.000
 9M2  C19  C18  C17  128.08  3.000
 9M2  C22  C18  C17  127.31  3.000
 9M2  N4   C22  C23  121.77  3.000
 9M2  N4   C22  C18  110.91  3.000
 9M2  C23  C22  C18  127.32  3.000
 9M2  H23  C23  H22  107.81  3.000
 9M2  H23  C23  H21  108.03  3.000
 9M2  H22  C23  H21  106.90  3.000
 9M2  H23  C23  C22  111.10  3.000
 9M2  H22  C23  C22  111.54  3.000
 9M2  H21  C23  C22  111.27  3.000
 9M2  N3   N4   C22  105.66  3.000
 9M2  C19  N3   C21  127.25  3.000
 9M2  C21  N3   N4   120.07  3.000
 9M2  C19  N3   N4   112.58  3.000
 9M2  H26  C21  H25  108.58  3.000
 9M2  H26  C21  H24  109.02  3.000
 9M2  H25  C21  H24  108.69  3.000
 9M2  H26  C21  N3   109.04  3.000
 9M2  H25  C21  N3   109.94  3.000
 9M2  H24  C21  N3   111.51  3.000
 9M2  C20  C19  N3   123.12  3.000
 9M2  C20  C19  C18  130.64  3.000
 9M2  N3   C19  C18  106.24  3.000
 9M2  H29  C20  H28  107.53  3.000
 9M2  H29  C20  H27  107.62  3.000
 9M2  H28  C20  H27  107.46  3.000
 9M2  H29  C20  C19  110.23  3.000
 9M2  H28  C20  C19  111.83  3.000
 9M2  H27  C20  C19  111.96  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
 9M2  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 9M2  CONST_02  C15  C10  C11  C12     0.00   0.0  0
 9M2  CONST_03  C7   C10  C11  C12   180.00   0.0  0
 9M2  CONST_06  C5   C6   C7   C8      0.00   0.0  0
 9M2  CONST_07  N1   C3   C9   C8    180.00   0.0  0
 9M2  CONST_08  C5   C4   C9   C8      0.00   0.0  0
 9M2  CONST_09  N2   C4   C9   C8    180.00   0.0  0
 9M2  CONST_10  C10  C7   C8   C9    180.00   0.0  0
 9M2  CONST_11  C6   C7   C8   C9      0.00   0.0  0
 9M2  CONST_12  N2   N1   C3   C9      0.00   0.0  0
 9M2  CONST_13  C6   C5   C4   C9      0.00   0.0  0
 9M2  CONST_14  N1   N2   C4   C9      0.00   0.0  0
 9M2  CONST_15  C13  C14  C15  C10     0.00   0.0  0
 9M2  CONST_16  C13  C12  C11  C10     0.00   0.0  0
 9M2  CONST_17  C5   C6   C7   C10   180.00   0.0  0
 9M2  CONST_18  C14  C13  C12  C11     0.00   0.0  0
 9M2  CONST_19  C14  C15  C10  C11     0.00   0.0  0
 9M2  CONST_21  C14  C15  C10  C7    180.00   0.0  0
 9M2  CONST_22  C3   C9   C8   C7    180.00   0.0  0
 9M2  CONST_23  C4   C9   C8   C7      0.00   0.0  0
 9M2  CONST_24  C4   C5   C6   C7      0.00   0.0  0
 9M2  CONST_26  N2   C4   C5   C6    180.00   0.0  0
 9M2  CONST_27  C4   C9   C3   N1      0.00   0.0  0
 9M2  CONST_28  C5   C4   N2   N1    180.00   0.0  0
 9M2  CONST_29  C3   C9   C4   C5    180.00   0.0  0
 9M2  CONST_30  C3   N1   N2   C4      0.00   0.0  0
 9M2  CONST_31  C3   C9   C4   N2      0.00   0.0  0
 9M2  CONST_32  N3   N4   C22  C18     0.00   0.0  0
 9M2  CONST_33  N4   N3   C19  C18     0.00   0.0  0
 9M2  CONST_34  C19  N3   N4   C22     0.00   0.0  0
 9M2  CONST_35  N3   C19  C18  C22     0.00   0.0  0
 9M2  CONST_36  C19  C18  C22  N4      0.00   0.0  0
 9M2  CONST_37  C2   C3   C9   C8      0.00   0.0  0
 9M2  CONST_38  F    C13  C12  C11   180.00   0.0  0
 9M2  CONST_39  O    C15  C10  C11   180.00   0.0  0
 9M2  CONST_40  O    C15  C10  C7      0.00   0.0  0
 9M2  CONST_41  C2   C3   C9   C4    180.00   0.0  0
 9M2  CONST_42  C15  C14  C13  F     180.00   0.0  0
 9M2  CONST_43  O    C15  C14  C13   180.00   0.0  0
 9M2  CONST_44  C2   C3   N1   N2    180.00   0.0  0
 9M2  CONST_45  N4   C22  C18  C17   180.00   0.0  0
 9M2  CONST_46  N3   C19  C18  C17   180.00   0.0  0
 9M2  CONST_47  C21  N3   C19  C18   180.00   0.0  0
 9M2  CONST_48  C21  N3   N4   C22   180.00   0.0  0
 9M2  CONST_49  C20  C19  C18  C22   180.00   0.0  0
 9M2  CONST_50  N3   N4   C22  C23   180.00   0.0  0
 9M2  CONST_51  C19  C18  C22  C23   180.00   0.0  0
 9M2  CONST_52  C20  C19  N3   N4    180.00   0.0  0
 9M2  CONST_53  H7   C14  C13  C12   180.00   0.0  0
 9M2  CONST_54  H4   C6   C7   C8    180.00   0.0  0
 9M2  CONST_55  H5   N1   C3   C9    180.00   0.0  0
 9M2  CONST_56  H6   C5   C4   C9    180.00   0.0  0
 9M2  CONST_57  H1   C12  C11  C10   180.00   0.0  0
 9M2  CONST_58  H2   C8   C7   C10     0.00   0.0  0
 9M2  CONST_59  H3   C11  C10  C7      0.00   0.0  0
 9M2  Var_01    N    C2   C3   C9     46.25  30.0  2
 9M2  Var_02    C22  C18  C17  C16   -86.54  30.0  2
 9M2  Var_03    H21  C23  C22  C18   -50.48  30.0  2
 9M2  Var_04    H27  C20  C19  C18   122.46  30.0  2
 9M2  Var_05    H24  C21  N3   N4     88.80  30.0  2
 9M2  Var_06    C17  C16  O    C15  -177.49  30.0  1
 9M2  Var_07    C    N    C2   C3   -167.28  30.0  1
 9M2  Var_08    C18  C17  C16  O     178.01  30.0  3
 9M2  Var_09    H14  C    N    C2     58.66  30.0  3
 9M2  Var_10    H11  C1   N    C2     62.97  30.0  3

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
 9M2  plan-1  C17  0.020
 9M2  plan-1  C18  0.020
 9M2  plan-1  C22  0.020
 9M2  plan-1  C23  0.020
 9M2  plan-1  N4   0.020
 9M2  plan-1  N3   0.020
 9M2  plan-1  C21  0.020
 9M2  plan-1  C19  0.020
 9M2  plan-1  C20  0.020
 9M2  plan-2  C12  0.020
 9M2  plan-2  C10  0.020
 9M2  plan-2  C11  0.020
 9M2  plan-2  C7   0.020
 9M2  plan-2  C13  0.020
 9M2  plan-2  C14  0.020
 9M2  plan-2  C15  0.020
 9M2  plan-2  O    0.020
 9M2  plan-2  H1   0.020
 9M2  plan-2  H3   0.020
 9M2  plan-2  H7   0.020
 9M2  plan-2  F    0.020
 9M2  plan-3  C8   0.020
 9M2  plan-3  C9   0.020
 9M2  plan-3  C10  0.020
 9M2  plan-3  C7   0.020
 9M2  plan-3  C6   0.020
 9M2  plan-3  N1   0.020
 9M2  plan-3  C5   0.020
 9M2  plan-3  C4   0.020
 9M2  plan-3  N2   0.020
 9M2  plan-3  C3   0.020
 9M2  plan-3  C2   0.020
 9M2  plan-3  H2   0.020
 9M2  plan-3  H4   0.020
 9M2  plan-3  H5   0.020
 9M2  plan-3  H6   0.020

