# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 08:15:29 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 4-(piperazin-1-yl)-1H-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN(CCN1)c2cccc3[nH]ccc23
#
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
 XF5  XF5  4-(piperazin-1-yl)-1H-indole  ligand  30  15  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XF5
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
 XF5  C11   C  CH2   0  -0.313  -2.1643   0.7848  -0.9804
 XF5  C12   C  CH2   0  -0.319  -3.4139  -0.0704  -1.1576
 XF5  N13   N  NH1   0  -0.579  -3.9623  -0.5749   0.0896
 XF5  C14   C  CH2   0  -0.321  -2.9281  -1.2349   0.8696
 XF5  C15   C  CH2   0  -0.315  -1.6800  -0.3852   1.0585
 XF5  N10   N  NT    0  -0.505  -1.1631   0.0413  -0.2389
 XF5  C3    C  CR6   0   0.269   0.1435   0.5432  -0.2421
 XF5  C4    C  CR56  0   0.007   1.2109  -0.3062   0.1274
 XF5  C5    C  CR15  0  -0.420   1.2923  -1.6838   0.5068
 XF5  C6    C  CR15  0  -0.031   2.6129  -1.9573   0.7172
 XF5  N7    N  NR15  0  -0.681   3.3539  -0.8345   0.4877
 XF5  C8    C  CR56  0   0.347   2.5312   0.1887   0.1158
 XF5  C9    C  CR16  0  -0.331   2.8473   1.4932  -0.2724
 XF5  C1    C  CR16  0  -0.272   1.7937   2.2954  -0.6517
 XF5  C2    C  CR16  0  -0.385   0.4648   1.8372  -0.6314
 XF5  H111  H  HCH2  0   0.245  -1.7649   1.0505  -1.9611
 XF5  H112  H  HCH2  0   0.202  -2.4393   1.7245  -0.4737
 XF5  H121  H  HCH2  0   0.239  -4.1780   0.5106  -1.6775
 XF5  H122  H  HCH2  0   0.221  -3.1699  -0.9238  -1.7979
 XF5  H13   H  HNH1  0   0.341  -4.3257   0.2049   0.6266
 XF5  H141  H  HCH2  0   0.238  -3.3337  -1.5084   1.8454
 XF5  H142  H  HCH2  0   0.221  -2.6505  -2.1644   0.3625
 XF5  H151  H  HCH2  0   0.210  -1.9254   0.4898   1.6826
 XF5  H152  H  HCH2  0   0.251  -0.9241  -0.9559   1.5961
 XF5  H2    H  HCR6  0   0.254  -0.3158   2.5271  -0.9245
 XF5  H5    H  HCR5  0   0.246   0.4837  -2.3900   0.6009
 XF5  H6    H  HCR5  0   0.279   3.0884  -2.8781   1.0140
 XF5  H7    H  HNR5  0   0.408   4.3561  -0.7812   0.5570
 XF5  H9    H  HCR6  0   0.252   3.8692   1.8493  -0.2904
 XF5  H1    H  HCR6  0   0.246   1.9871   3.3131  -0.9663

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
 XF5  C11  C12   single    1.525  0.020  1.525
 XF5  C11  N10   single    1.451  0.020  1.451
 XF5  C12  N13   single    1.453  0.020  1.453
 XF5  N13  C14   single    1.454  0.020  1.454
 XF5  C14  C15   single    1.522  0.020  1.522
 XF5  C15  N10   single    1.460  0.020  1.460
 XF5  N10  C3    single    1.400  0.020  1.400
 XF5  C3   C4    aromatic  1.413  0.020  1.413
 XF5  C3   C2    aromatic  1.389  0.020  1.389
 XF5  C4   C5    aromatic  1.431  0.020  1.431
 XF5  C4   C8    aromatic  1.410  0.020  1.410
 XF5  C5   C6    aromatic  1.365  0.020  1.365
 XF5  C6   N7    aromatic  1.365  0.020  1.365
 XF5  N7   C8    aromatic  1.365  0.020  1.365
 XF5  C8   C9    aromatic  1.397  0.020  1.397
 XF5  C9   C1    aromatic  1.377  0.020  1.377
 XF5  C1   C2    aromatic  1.406  0.020  1.406
 XF5  C11  H111  single    0.970  0.020  1.090
 XF5  C11  H112  single    0.970  0.020  1.090
 XF5  C12  H121  single    0.970  0.020  1.090
 XF5  C12  H122  single    0.970  0.020  1.090
 XF5  N13  H13   single    0.890  0.020  1.040
 XF5  C14  H141  single    0.970  0.020  1.090
 XF5  C14  H142  single    0.970  0.020  1.090
 XF5  C15  H151  single    0.970  0.020  1.090
 XF5  C15  H152  single    0.970  0.020  1.090
 XF5  C2   H2    single    0.930  0.020  1.080
 XF5  C5   H5    single    0.930  0.020  1.080
 XF5  C6   H6    single    0.930  0.020  1.080
 XF5  N7   H7    single    0.860  0.020  1.020
 XF5  C9   H9    single    0.930  0.020  1.080
 XF5  C1   H1    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
 XF5  H112  C11  H111  107.26  3.000
 XF5  H112  C11  N10   111.96  3.000
 XF5  H111  C11  N10   109.35  3.000
 XF5  H112  C11  C12   109.10  3.000
 XF5  H111  C11  C12   109.39  3.000
 XF5  N10   C11  C12   109.73  3.000
 XF5  H122  C12  H121  107.01  3.000
 XF5  H122  C12  N13   108.40  3.000
 XF5  H121  C12  N13   109.24  3.000
 XF5  H122  C12  C11   108.82  3.000
 XF5  H121  C12  C11   109.30  3.000
 XF5  N13   C12  C11   113.85  3.000
 XF5  H13   N13  C14   108.65  3.000
 XF5  H13   N13  C12   108.83  3.000
 XF5  C14   N13  C12   110.47  3.000
 XF5  H142  C14  H141  107.20  3.000
 XF5  H142  C14  C15   108.88  3.000
 XF5  H141  C14  C15   109.49  3.000
 XF5  H142  C14  N13   108.50  3.000
 XF5  H141  C14  N13   109.21  3.000
 XF5  C15   C14  N13   113.36  3.000
 XF5  H152  C15  H151  106.92  3.000
 XF5  H152  C15  N10   110.24  3.000
 XF5  H151  C15  N10   110.48  3.000
 XF5  H152  C15  C14   109.75  3.000
 XF5  H151  C15  C14   109.32  3.000
 XF5  N10   C15  C14   110.07  3.000
 XF5  C3    N10  C15   115.93  3.000
 XF5  C3    N10  C11   117.34  3.000
 XF5  C15   N10  C11   111.07  3.000
 XF5  C2    C3   C4    117.29  3.000
 XF5  C2    C3   N10   123.41  3.000
 XF5  C4    C3   N10   119.27  3.000
 XF5  C8    C4   C5    106.66  3.000
 XF5  C8    C4   C3    119.61  3.000
 XF5  C5    C4   C3    133.69  3.000
 XF5  H5    C5   C6    125.53  3.000
 XF5  H5    C5   C4    127.68  3.000
 XF5  C6    C5   C4    106.78  3.000
 XF5  H6    C6   N7    120.63  3.000
 XF5  H6    C6   C5    129.83  3.000
 XF5  N7    C6   C5    109.54  3.000
 XF5  H7    N7   C8    125.43  3.000
 XF5  H7    N7   C6    124.95  3.000
 XF5  C8    N7   C6    109.60  3.000
 XF5  C9    C8   N7    129.74  3.000
 XF5  C9    C8   C4    122.80  3.000
 XF5  N7    C8   C4    107.41  3.000
 XF5  H9    C9   C1    121.74  3.000
 XF5  H9    C9   C8    121.70  3.000
 XF5  C1    C9   C8    116.56  3.000
 XF5  H1    C1   C2    118.65  3.000
 XF5  H1    C1   C9    119.39  3.000
 XF5  C2    C1   C9    121.96  3.000
 XF5  H2    C2   C1    118.05  3.000
 XF5  H2    C2   C3    120.19  3.000
 XF5  C1    C2   C3    121.76  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
 XF5  CONST_01  C6   C5   C4   C3    180.00   0.0  0
 XF5  CONST_02  N7   C8   C4   C3    180.00   0.0  0
 XF5  CONST_03  C9   C8   C4   C3      0.00   0.0  0
 XF5  CONST_04  C9   C1   C2   C3      0.00   0.0  0
 XF5  CONST_05  C1   C2   C3   C4      0.00   0.0  0
 XF5  CONST_06  N7   C6   C5   C4      0.00   0.0  0
 XF5  CONST_07  C6   N7   C8   C4      0.00   0.0  0
 XF5  CONST_08  C1   C9   C8   C4      0.00   0.0  0
 XF5  CONST_09  C2   C3   C4   C5    180.00   0.0  0
 XF5  CONST_10  N7   C8   C4   C5      0.00   0.0  0
 XF5  CONST_11  C9   C8   C4   C5    180.00   0.0  0
 XF5  CONST_12  C8   N7   C6   C5      0.00   0.0  0
 XF5  CONST_13  C8   C4   C5   C6      0.00   0.0  0
 XF5  CONST_14  C9   C8   N7   C6    180.00   0.0  0
 XF5  CONST_15  C1   C9   C8   N7    180.00   0.0  0
 XF5  CONST_16  C2   C3   C4   C8      0.00   0.0  0
 XF5  CONST_17  C2   C1   C9   C8      0.00   0.0  0
 XF5  CONST_18  C5   C4   C3   N10     0.00   0.0  0
 XF5  CONST_19  C8   C4   C3   N10   180.00   0.0  0
 XF5  CONST_20  C1   C2   C3   N10   180.00   0.0  0
 XF5  CONST_21  H2   C2   C3   N10     0.00   0.0  0
 XF5  CONST_22  H5   C5   C4   C3      0.00   0.0  0
 XF5  CONST_23  H1   C1   C2   C3    180.00   0.0  0
 XF5  CONST_24  H6   C6   C5   C4    180.00   0.0  0
 XF5  CONST_25  H7   N7   C8   C4    180.00   0.0  0
 XF5  CONST_26  H9   C9   C8   C4    180.00   0.0  0
 XF5  Var_01    C14  N13  C12  C11   -51.60  30.0  1
 XF5  Var_02    C14  C15  N10  C11    57.83  30.0  1
 XF5  Var_03    C4   C3   N10  C11  -162.31  30.0  2
 XF5  Var_04    C15  N10  C11  C12   -57.49  30.0  1
 XF5  Var_05    C15  C14  N13  C12    51.48  30.0  1
 XF5  Var_06    N10  C11  C12  N13    55.09  30.0  1
 XF5  Var_07    N10  C15  C14  N13   -55.08  30.0  1

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
 XF5  plan-1  N10  0.020
 XF5  plan-1  C3   0.020
 XF5  plan-1  C4   0.020
 XF5  plan-1  C5   0.020
 XF5  plan-1  C6   0.020
 XF5  plan-1  N7   0.020
 XF5  plan-1  C8   0.020
 XF5  plan-1  C9   0.020
 XF5  plan-1  C1   0.020
 XF5  plan-1  C2   0.020
 XF5  plan-1  H2   0.020
 XF5  plan-1  H5   0.020
 XF5  plan-1  H6   0.020
 XF5  plan-1  H7   0.020
 XF5  plan-1  H9   0.020
 XF5  plan-1  H1   0.020

