# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 05:29:45 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: N,N-dimethyl-4-[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)c1ccc(cc1)n2nc(c3CCCCc23)C(F)(F)F
#
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
 1NE  1NE  N,N-dimethyl-4-[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]benzamide  ligand  42  24  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1NE
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
 1NE  C1    C  CH3   0  -0.524   7.0678  -0.7572  -0.4144
 1NE  N2    N  NT    0  -0.439   5.6531  -0.4824  -0.5599
 1NE  C3    C  CH3   0  -0.529   5.2250  -0.2158  -1.9189
 1NE  C4    C  C     0   0.514   4.9074  -0.2583   0.5379
 1NE  O5    O  O     0  -0.489   5.3846  -0.1858   1.6642
 1NE  C6    C  CR6   0  -0.068   3.4250  -0.1409   0.3670
 1NE  C7    C  CR16  0  -0.270   2.7535   0.8992   0.9993
 1NE  C8    C  CR16  0  -0.275   1.3724   0.9876   0.9376
 1NE  C9    C  CR6   0   0.331   0.6528   0.0181   0.2512
 1NE  C10   C  CR16  0  -0.270   1.3091  -1.0423  -0.3619
 1NE  C11   C  CR16  0  -0.251   2.6899  -1.1158  -0.3023
 1NE  N12   N  NR5   0  -0.470  -0.7546   0.0917   0.1842
 1NE  N13   N  N     0  -0.286  -1.4703  -1.0214   0.3168
 1NE  C14   C  CR5   0  -0.043  -2.7206  -0.6396   0.1766
 1NE  C15   C  CR5   0  -0.172  -2.8340   0.7424  -0.0526
 1NE  C16   C  CH2   0  -0.508  -4.0068   1.6337  -0.2994
 1NE  C17   C  CH2   0  -0.452  -3.5693   3.0972  -0.2114
 1NE  C18   C  CH2   0  -0.448  -2.2594   3.3406  -0.9575
 1NE  C19   C  CH2   0  -0.518  -1.0953   2.5809  -0.3153
 1NE  C20   C  CR5   0   0.436  -1.5332   1.1830  -0.0482
 1NE  C21   C  CT    0   1.068  -3.8273  -1.6215   0.2922
 1NE  F22   F  F     0  -0.305  -3.3865  -2.8780   0.3393
 1NE  F23   F  F     0  -0.316  -4.5608  -1.4127   1.3966
 1NE  F24   F  F     0  -0.315  -4.6719  -1.5257  -0.7447
 1NE  H11C  H  HCH3  0   0.241   7.6645   0.1557  -0.4819
 1NE  H12C  H  HCH3  0   0.255   7.2730  -1.2374   0.5377
 1NE  H13C  H  HCH3  0   0.246   7.3811  -1.4276  -1.2139
 1NE  H31C  H  HCH3  0   0.253   5.8966   0.5151  -2.3733
 1NE  H32C  H  HCH3  0   0.247   5.2498  -1.1229  -2.5245
 1NE  H33C  H  HCH3  0   0.265   4.2215   0.1954  -1.9491
 1NE  H7    H  HCR6  0   0.271   3.3063   1.6504   1.5475
 1NE  H11   H  HCR6  0   0.276   3.1922  -1.9457  -0.7828
 1NE  H8    H  HCR6  0   0.281   0.8652   1.7939   1.4491
 1NE  H10   H  HCR6  0   0.280   0.7469  -1.8040  -0.8841
 1NE  H161  H  HCH2  0   0.247  -4.4245   1.4317  -1.2901
 1NE  H162  H  HCH2  0   0.250  -4.8063   1.4354   0.4179
 1NE  H171  H  HCH2  0   0.244  -4.3562   3.7358  -0.6157
 1NE  H172  H  HCH2  0   0.230  -3.4433   3.3791   0.8383
 1NE  H181  H  HCH2  0   0.234  -2.3678   3.0264  -1.9997
 1NE  H182  H  HCH2  0   0.247  -2.0241   4.4055  -0.9712
 1NE  H191  H  HCH2  0   0.271  -0.2175   2.5992  -0.9654
 1NE  H192  H  HCH2  0   0.262  -0.8062   3.0747   0.6170

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
 1NE  C1   N2    single    1.448  0.020  1.448
 1NE  N2   C3    single    1.450  0.020  1.450
 1NE  N2   C4    single    1.346  0.020  1.346
 1NE  C4   O5    double    1.225  0.020  1.225
 1NE  C4   C6    single    1.497  0.020  1.497
 1NE  C6   C7    aromatic  1.390  0.020  1.390
 1NE  C6   C11   aromatic  1.392  0.020  1.392
 1NE  C7   C8    aromatic  1.385  0.020  1.385
 1NE  C8   C9    aromatic  1.389  0.020  1.389
 1NE  C9   C10   aromatic  1.390  0.020  1.390
 1NE  C9   N12   single    1.411  0.020  1.411
 1NE  C10  C11   aromatic  1.384  0.020  1.384
 1NE  N12  N13   aromatic  1.330  0.020  1.330
 1NE  N12  C20   aromatic  1.361  0.020  1.361
 1NE  N13  C14   aromatic  1.315  0.020  1.315
 1NE  C14  C15   aromatic  1.405  0.020  1.405
 1NE  C14  C21   single    1.484  0.020  1.484
 1NE  C15  C16   single    1.494  0.020  1.494
 1NE  C15  C20   aromatic  1.373  0.020  1.373
 1NE  C16  C17   single    1.530  0.020  1.530
 1NE  C17  C18   single    1.527  0.020  1.527
 1NE  C18  C19   single    1.531  0.020  1.531
 1NE  C19  C20   single    1.489  0.020  1.489
 1NE  C21  F22   single    1.332  0.020  1.332
 1NE  C21  F23   single    1.342  0.020  1.342
 1NE  C21  F24   single    1.341  0.020  1.341
 1NE  C1   H11C  single    0.970  0.020  1.090
 1NE  C1   H12C  single    0.970  0.020  1.090
 1NE  C1   H13C  single    0.970  0.020  1.090
 1NE  C3   H31C  single    0.970  0.020  1.090
 1NE  C3   H32C  single    0.970  0.020  1.090
 1NE  C3   H33C  single    0.970  0.020  1.090
 1NE  C7   H7    single    0.930  0.020  1.080
 1NE  C11  H11   single    0.930  0.020  1.080
 1NE  C8   H8    single    0.930  0.020  1.080
 1NE  C10  H10   single    0.930  0.020  1.080
 1NE  C16  H161  single    0.970  0.020  1.090
 1NE  C16  H162  single    0.970  0.020  1.090
 1NE  C17  H171  single    0.970  0.020  1.090
 1NE  C17  H172  single    0.970  0.020  1.090
 1NE  C18  H181  single    0.970  0.020  1.090
 1NE  C18  H182  single    0.970  0.020  1.090
 1NE  C19  H191  single    0.970  0.020  1.090
 1NE  C19  H192  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
 1NE  H13C  C1   H12C  108.48  3.000
 1NE  H13C  C1   H11C  108.16  3.000
 1NE  H12C  C1   H11C  108.69  3.000
 1NE  H13C  C1   N2    108.90  3.000
 1NE  H12C  C1   N2    110.89  3.000
 1NE  H11C  C1   N2    111.63  3.000
 1NE  C4    N2   C3    124.78  3.000
 1NE  C4    N2   C1    119.39  3.000
 1NE  C3    N2   C1    114.68  3.000
 1NE  H33C  C3   H32C  108.71  3.000
 1NE  H33C  C3   H31C  107.68  3.000
 1NE  H32C  C3   H31C  108.16  3.000
 1NE  H33C  C3   N2    111.65  3.000
 1NE  H32C  C3   N2    111.15  3.000
 1NE  H31C  C3   N2    109.37  3.000
 1NE  C6    C4   O5    119.08  3.000
 1NE  C6    C4   N2    117.94  3.000
 1NE  O5    C4   N2    122.94  3.000
 1NE  C11   C6   C7    119.18  3.000
 1NE  C11   C6   C4    121.52  3.000
 1NE  C7    C6   C4    119.02  3.000
 1NE  H7    C7   C8    119.19  3.000
 1NE  H7    C7   C6    120.21  3.000
 1NE  C8    C7   C6    120.60  3.000
 1NE  H8    C8   C9    120.75  3.000
 1NE  H8    C8   C7    119.62  3.000
 1NE  C9    C8   C7    119.61  3.000
 1NE  N12   C9   C10   119.33  3.000
 1NE  N12   C9   C8    120.26  3.000
 1NE  C10   C9   C8    120.40  3.000
 1NE  H10   C10  C11   120.14  3.000
 1NE  H10   C10  C9    120.34  3.000
 1NE  C11   C10  C9    119.52  3.000
 1NE  H11   C11  C10   118.98  3.000
 1NE  H11   C11  C6    120.34  3.000
 1NE  C10   C11  C6    120.68  3.000
 1NE  C20   N12  N13   112.36  3.000
 1NE  C20   N12  C9    128.37  3.000
 1NE  N13   N12  C9    119.24  3.000
 1NE  C14   N13  N12   104.96  3.000
 1NE  C21   C14  C15   127.10  3.000
 1NE  C21   C14  N13   120.58  3.000
 1NE  C15   C14  N13   112.31  3.000
 1NE  C20   C15  C16   123.56  3.000
 1NE  C20   C15  C14   103.80  3.000
 1NE  C16   C15  C14   132.62  3.000
 1NE  H162  C16  H161  106.37  3.000
 1NE  H162  C16  C17   110.19  3.000
 1NE  H161  C16  C17   109.75  3.000
 1NE  H162  C16  C15   110.97  3.000
 1NE  H161  C16  C15   109.83  3.000
 1NE  C17   C16  C15   109.68  3.000
 1NE  H172  C17  H171  106.72  3.000
 1NE  H172  C17  C18   109.20  3.000
 1NE  H171  C17  C18   110.14  3.000
 1NE  H172  C17  C16   109.54  3.000
 1NE  H171  C17  C16   109.41  3.000
 1NE  C18   C17  C16   111.70  3.000
 1NE  H182  C18  H181  106.85  3.000
 1NE  H182  C18  C19   109.00  3.000
 1NE  H181  C18  C19   109.41  3.000
 1NE  H182  C18  C17   110.30  3.000
 1NE  H181  C18  C17   109.56  3.000
 1NE  C19   C18  C17   111.60  3.000
 1NE  H192  C19  H191  106.69  3.000
 1NE  H192  C19  C20   110.41  3.000
 1NE  H191  C19  C20   111.02  3.000
 1NE  H192  C19  C18   109.54  3.000
 1NE  H191  C19  C18   110.67  3.000
 1NE  C20   C19  C18   108.51  3.000
 1NE  C19   C20  C15   125.39  3.000
 1NE  C19   C20  N12   127.98  3.000
 1NE  C15   C20  N12   106.57  3.000
 1NE  F24   C21  F23   106.32  3.000
 1NE  F24   C21  F22   107.65  3.000
 1NE  F23   C21  F22   107.36  3.000
 1NE  F24   C21  C14   111.24  3.000
 1NE  F23   C21  C14   111.64  3.000
 1NE  F22   C21  C14   112.33  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
 1NE  CONST_01  C9    C8   C7   C6      0.00   0.0  0
 1NE  CONST_02  C9    C10  C11  C6      0.00   0.0  0
 1NE  CONST_03  C10   C11  C6   C7      0.00   0.0  0
 1NE  CONST_04  C10   C9   C8   C7      0.00   0.0  0
 1NE  CONST_05  N12   C9   C8   C7    180.00   0.0  0
 1NE  CONST_06  C11   C6   C7   C8      0.00   0.0  0
 1NE  CONST_07  C11   C10  C9   C8      0.00   0.0  0
 1NE  CONST_10  C14   N13  N12  C9    180.00   0.0  0
 1NE  CONST_11  C15   C20  N12  C9    180.00   0.0  0
 1NE  CONST_14  N12   C9   C10  C11   180.00   0.0  0
 1NE  CONST_15  C15   C14  N13  N12     0.00   0.0  0
 1NE  CONST_16  C14   C15  C20  N12     0.00   0.0  0
 1NE  CONST_17  C15   C20  N12  N13     0.00   0.0  0
 1NE  CONST_18  C20   C15  C14  N13     0.00   0.0  0
 1NE  CONST_19  C20   N12  N13  C14     0.00   0.0  0
 1NE  CONST_20  C19   C20  N12  C9      0.00   0.0  0
 1NE  CONST_21  C8    C7   C6   C4    180.00   0.0  0
 1NE  CONST_22  C10   C11  C6   C4    180.00   0.0  0
 1NE  CONST_23  C21   C14  N13  N12   180.00   0.0  0
 1NE  CONST_24  C21   C14  C15  C16     0.00   0.0  0
 1NE  CONST_25  C21   C14  C15  C20   180.00   0.0  0
 1NE  CONST_26  H8    C8   C7   C6    180.00   0.0  0
 1NE  CONST_27  H10   C10  C11  C6    180.00   0.0  0
 1NE  CONST_28  H11   C11  C6   C7    180.00   0.0  0
 1NE  CONST_29  H7    C7   C8   C9    180.00   0.0  0
 1NE  CONST_30  C6    C4   N2   C1    180.00   0.0  0
 1NE  CONST_32  O5    C4   N2   C1      0.00   0.0  0
 1NE  Var_01    C18   C19  C20  N12   161.60  30.0  1
 1NE  Var_02    C17   C16  C15  C14   168.95  30.0  1
 1NE  Var_03    C18   C17  C16  C15    44.67  30.0  1
 1NE  Var_04    C19   C18  C17  C16   -64.71  30.0  1
 1NE  Var_05    C20   C19  C18  C17    46.55  30.0  1
 1NE  Var_06    C7    C6   C4   N2   -133.92  30.0  2
 1NE  Var_07    F22   C21  C14  N13    -9.45  30.0  2
 1NE  Var_08    H31C  C3   N2   C1    -48.28  30.0  3
 1NE  Var_09    H11C  C1   N2   C3     76.01  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
 1NE  plan-1  C4   0.020
 1NE  plan-1  C6   0.020
 1NE  plan-1  C7   0.020
 1NE  plan-1  C8   0.020
 1NE  plan-1  C9   0.020
 1NE  plan-1  C10  0.020
 1NE  plan-1  C11  0.020
 1NE  plan-1  N12  0.020
 1NE  plan-1  H7   0.020
 1NE  plan-1  H11  0.020
 1NE  plan-1  H8   0.020
 1NE  plan-1  H10  0.020
 1NE  plan-2  C9   0.020
 1NE  plan-2  N12  0.020
 1NE  plan-2  N13  0.020
 1NE  plan-2  C14  0.020
 1NE  plan-2  C15  0.020
 1NE  plan-2  C16  0.020
 1NE  plan-2  C19  0.020
 1NE  plan-2  C20  0.020
 1NE  plan-2  C21  0.020
 1NE  plan-3  C1   0.020
 1NE  plan-3  N2   0.020
 1NE  plan-3  C3   0.020
 1NE  plan-3  C4   0.020
 1NE  plan-3  O5   0.020
 1NE  plan-3  C6   0.020

