# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 16:49:26 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 2-methyl-3-{[4-(pyridin-2-yl)piperazin-1-yl]methyl}-1H-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]c2ccccc2c1CN3CCN(CC3)c4ccccn4
#
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
 RM8  RM8  2-methyl-3-{[4-(pyridin-2-yl)piperazin-1-yl]methyl}-1H-indole  ligand  45  23  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RM8
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
 RM8  C1    C  CH3   0  -0.740  -2.4346   2.6180   1.4323
 RM8  N1    N  NR15  0  -0.727  -4.0299   0.7086   1.3167
 RM8  C2    C  CR5   0   0.301  -2.9646   1.3886   0.7883
 RM8  N2    N  NT    0  -0.405  -0.1098   1.0333  -0.5513
 RM8  C3    C  CR5   0  -0.053  -2.5412   0.7506  -0.3491
 RM8  N3    N  NT    0  -0.505   2.5878   0.2139  -0.1560
 RM8  C4    C  CR56  0   0.067  -3.3907  -0.3884  -0.5218
 RM8  N4    N  N     0  -0.475   4.8335   0.6435  -0.4588
 RM8  C5    C  CR16  0  -0.383  -3.4568  -1.4183  -1.4677
 RM8  C6    C  CR16  0  -0.269  -4.4262  -2.3943  -1.3309
 RM8  C7    C  CR16  0  -0.290  -5.3381  -2.3649  -0.2638
 RM8  C8    C  CR16  0  -0.311  -5.2967  -1.3605   0.6865
 RM8  C9    C  CR56  0   0.329  -4.3172  -0.3803   0.5449
 RM8  C10   C  CH2   0  -0.384  -1.3963   1.1586  -1.2183
 RM8  C11   C  CH2   0  -0.289   0.9603   1.6042  -1.3394
 RM8  C12   C  CH2   0  -0.296   2.2677   1.5681  -0.5753
 RM8  C13   C  CH2   0  -0.301   1.5049  -0.4496   0.5408
 RM8  C14   C  CH2   0  -0.272   0.2060  -0.3411  -0.2356
 RM8  C15   C  CR6   0   0.536   3.8935  -0.1200   0.1020
 RM8  C16   C  CR16  0  -0.415   4.2491  -1.2271   0.9009
 RM8  C17   C  CR16  0  -0.150   5.5851  -1.5284   1.0625
 RM8  C18   C  CR16  0  -0.367   6.5582  -0.7400   0.4563
 RM8  C19   C  CR16  0  -0.063   6.1122   0.3374  -0.2856
 RM8  H1    H  HCH3  0   0.251  -2.1907   2.4453   2.4822
 RM8  H1A   H  HCH3  0   0.258  -1.5257   2.9388   0.9302
 RM8  H1B   H  HCH3  0   0.250  -3.1582   3.4347   1.3964
 RM8  HN1   H  HNR5  0   0.403  -4.5190   0.9737   2.1558
 RM8  H5    H  HCR6  0   0.239  -2.7587  -1.4541  -2.2961
 RM8  H6    H  HCR6  0   0.243  -4.4859  -3.1958  -2.0560
 RM8  H7    H  HCR6  0   0.246  -6.0866  -3.1423  -0.1823
 RM8  H8    H  HCR6  0   0.255  -5.9989  -1.3396   1.5103
 RM8  H10   H  HCH2  0   0.242  -1.5063   2.2033  -1.5236
 RM8  H10A  H  HCH2  0   0.212  -1.4227   0.5687  -2.1503
 RM8  H11   H  HCH2  0   0.192   1.0889   1.0815  -2.3040
 RM8  H11A  H  HCH2  0   0.240   0.7232   2.6461  -1.5679
 RM8  H12   H  HCH2  0   0.216   2.1954   2.2293   0.2993
 RM8  H12A  H  HCH2  0   0.261   3.0654   1.9482  -1.2066
 RM8  H13   H  HCH2  0   0.253   1.7240  -1.5099   0.6522
 RM8  H13A  H  HCH2  0   0.222   1.3691  -0.0317   1.5478
 RM8  H14   H  HCH2  0   0.249  -0.5899  -0.7687   0.3769
 RM8  H14A  H  HCH2  0   0.189   0.2755  -0.9582  -1.1496
 RM8  H16   H  HCR6  0   0.268   3.5088  -1.8352   1.3986
 RM8  H17   H  HCR6  0   0.266   5.8666  -2.3781   1.6717
 RM8  H18   H  HCR6  0   0.257   7.6133  -0.9462   0.5650
 RM8  H19   H  HCR6  0   0.253   6.8244   0.9978  -0.7700

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
 RM8  C1   C2    single    1.486  0.020  1.486
 RM8  N1   C2    aromatic  1.370  0.020  1.370
 RM8  N1   C9    aromatic  1.365  0.020  1.365
 RM8  C2   C3    aromatic  1.371  0.020  1.371
 RM8  N2   C10   single    1.455  0.020  1.455
 RM8  N2   C11   single    1.446  0.020  1.446
 RM8  N2   C14   single    1.445  0.020  1.445
 RM8  C3   C4    aromatic  1.431  0.020  1.431
 RM8  C3   C10   single    1.494  0.020  1.494
 RM8  N3   C12   single    1.453  0.020  1.453
 RM8  N3   C13   single    1.449  0.020  1.449
 RM8  N3   C15   single    1.372  0.020  1.372
 RM8  C4   C5    aromatic  1.400  0.020  1.400
 RM8  C4   C9    aromatic  1.413  0.020  1.413
 RM8  N4   C15   aromatic  1.335  0.020  1.335
 RM8  N4   C19   aromatic  1.326  0.020  1.326
 RM8  C5   C6    aromatic  1.382  0.020  1.382
 RM8  C6   C7    aromatic  1.404  0.020  1.404
 RM8  C7   C8    aromatic  1.383  0.020  1.383
 RM8  C8   C9    aromatic  1.393  0.020  1.393
 RM8  C11  C12   single    1.515  0.020  1.515
 RM8  C13  C14   single    1.517  0.020  1.517
 RM8  C15  C16   aromatic  1.411  0.020  1.411
 RM8  C16  C17   aromatic  1.379  0.020  1.379
 RM8  C17  C18   aromatic  1.391  0.020  1.391
 RM8  C18  C19   aromatic  1.382  0.020  1.382
 RM8  C1   H1    single    0.970  0.020  1.090
 RM8  C1   H1A   single    0.970  0.020  1.090
 RM8  C1   H1B   single    0.970  0.020  1.090
 RM8  N1   HN1   single    0.860  0.020  1.020
 RM8  C5   H5    single    0.930  0.020  1.080
 RM8  C6   H6    single    0.930  0.020  1.080
 RM8  C7   H7    single    0.930  0.020  1.080
 RM8  C8   H8    single    0.930  0.020  1.080
 RM8  C10  H10   single    0.970  0.020  1.090
 RM8  C10  H10A  single    0.970  0.020  1.090
 RM8  C11  H11   single    0.970  0.020  1.090
 RM8  C11  H11A  single    0.970  0.020  1.090
 RM8  C12  H12   single    0.970  0.020  1.090
 RM8  C12  H12A  single    0.970  0.020  1.090
 RM8  C13  H13   single    0.970  0.020  1.090
 RM8  C13  H13A  single    0.970  0.020  1.090
 RM8  C14  H14   single    0.970  0.020  1.090
 RM8  C14  H14A  single    0.970  0.020  1.090
 RM8  C16  H16   single    0.930  0.020  1.080
 RM8  C17  H17   single    0.930  0.020  1.080
 RM8  C18  H18   single    0.930  0.020  1.080
 RM8  C19  H19   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
 RM8  H1B   C1   H1A  108.56  3.000
 RM8  H1B   C1   H1   107.34  3.000
 RM8  H1A   C1   H1   107.72  3.000
 RM8  H1B   C1   C2   111.62  3.000
 RM8  H1A   C1   C2   110.02  3.000
 RM8  H1    C1   C2   111.45  3.000
 RM8  HN1   N1   C9   125.38  3.000
 RM8  HN1   N1   C2   124.65  3.000
 RM8  C9    N1   C2   109.97  3.000
 RM8  C3    C2   N1   109.22  3.000
 RM8  C3    C2   C1   129.39  3.000
 RM8  N1    C2   C1   121.40  3.000
 RM8  C14   N2   C11  109.44  3.000
 RM8  C14   N2   C10  112.05  3.000
 RM8  C11   N2   C10  111.74  3.000
 RM8  C10   C3   C4   127.00  3.000
 RM8  C10   C3   C2   126.30  3.000
 RM8  C4    C3   C2   106.68  3.000
 RM8  C15   N3   C13  120.62  3.000
 RM8  C15   N3   C12  119.38  3.000
 RM8  C13   N3   C12  113.63  3.000
 RM8  C9    C4   C5   118.91  3.000
 RM8  C9    C4   C3   107.07  3.000
 RM8  C5    C4   C3   134.03  3.000
 RM8  C19   N4   C15  119.49  3.000
 RM8  H5    C5   C6   120.27  3.000
 RM8  H5    C5   C4   120.68  3.000
 RM8  C6    C5   C4   119.05  3.000
 RM8  H6    C6   C7   119.26  3.000
 RM8  H6    C6   C5   119.68  3.000
 RM8  C7    C6   C5   121.06  3.000
 RM8  H7    C7   C8   119.38  3.000
 RM8  H7    C7   C6   119.44  3.000
 RM8  C8    C7   C6   121.19  3.000
 RM8  H8    C8   C9   121.32  3.000
 RM8  H8    C8   C7   121.15  3.000
 RM8  C9    C8   C7   117.53  3.000
 RM8  C8    C9   C4   122.26  3.000
 RM8  C8    C9   N1   130.67  3.000
 RM8  C4    C9   N1   107.06  3.000
 RM8  H10A  C10  H10  105.81  3.000
 RM8  H10A  C10  C3   109.09  3.000
 RM8  H10   C10  C3   110.25  3.000
 RM8  H10A  C10  N2   111.25  3.000
 RM8  H10   C10  N2   107.41  3.000
 RM8  C3    C10  N2   112.79  3.000
 RM8  H11A  C11  H11  107.09  3.000
 RM8  H11A  C11  C12  108.39  3.000
 RM8  H11   C11  C12  109.19  3.000
 RM8  H11A  C11  N2   109.25  3.000
 RM8  H11   C11  N2   112.03  3.000
 RM8  C12   C11  N2   110.75  3.000
 RM8  H12A  C12  H12  107.48  3.000
 RM8  H12A  C12  C11  109.42  3.000
 RM8  H12   C12  C11  109.30  3.000
 RM8  H12A  C12  N3   109.39  3.000
 RM8  H12   C12  N3   110.21  3.000
 RM8  C11   C12  N3   110.97  3.000
 RM8  H13A  C13  H13  107.56  3.000
 RM8  H13A  C13  C14  109.63  3.000
 RM8  H13   C13  C14  107.12  3.000
 RM8  H13A  C13  N3   111.04  3.000
 RM8  H13   C13  N3   110.18  3.000
 RM8  C14   C13  N3   111.17  3.000
 RM8  H14A  C14  H14  106.93  3.000
 RM8  H14A  C14  C13  109.24  3.000
 RM8  H14   C14  C13  108.00  3.000
 RM8  H14A  C14  N2   111.36  3.000
 RM8  H14   C14  N2   109.62  3.000
 RM8  C13   C14  N2   111.52  3.000
 RM8  C16   C15  N4   120.62  3.000
 RM8  C16   C15  N3   122.50  3.000
 RM8  N4    C15  N3   116.87  3.000
 RM8  H16   C16  C17  119.16  3.000
 RM8  H16   C16  C15  122.02  3.000
 RM8  C17   C16  C15  118.81  3.000
 RM8  H17   C17  C18  120.53  3.000
 RM8  H17   C17  C16  119.29  3.000
 RM8  C18   C17  C16  120.18  3.000
 RM8  H18   C18  C19  121.19  3.000
 RM8  H18   C18  C17  122.07  3.000
 RM8  C19   C18  C17  116.74  3.000
 RM8  H19   C19  C18  120.15  3.000
 RM8  H19   C19  N4   115.72  3.000
 RM8  C18   C19  N4   124.13  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
 RM8  CONST_01  C4   C3   C2   N1      0.00   0.0  0
 RM8  CONST_02  C3   C4   C9   N1      0.00   0.0  0
 RM8  CONST_03  C5   C4   C9   N1    180.00   0.0  0
 RM8  CONST_04  C7   C8   C9   N1    180.00   0.0  0
 RM8  CONST_05  C4   C9   N1   C2      0.00   0.0  0
 RM8  CONST_06  C8   C9   N1   C2    180.00   0.0  0
 RM8  CONST_07  C5   C4   C3   C2    180.00   0.0  0
 RM8  CONST_08  C9   C4   C3   C2      0.00   0.0  0
 RM8  CONST_09  C9   N1   C2   C3      0.00   0.0  0
 RM8  CONST_10  C6   C5   C4   C3    180.00   0.0  0
 RM8  CONST_11  C8   C9   C4   C3    180.00   0.0  0
 RM8  CONST_12  C7   C6   C5   C4      0.00   0.0  0
 RM8  CONST_13  C7   C8   C9   C4      0.00   0.0  0
 RM8  CONST_14  C17  C16  C15  N4      0.00   0.0  0
 RM8  CONST_15  C17  C18  C19  N4      0.00   0.0  0
 RM8  CONST_16  C8   C9   C4   C5      0.00   0.0  0
 RM8  CONST_17  C8   C7   C6   C5      0.00   0.0  0
 RM8  CONST_18  C9   C4   C5   C6      0.00   0.0  0
 RM8  CONST_19  C9   C8   C7   C6      0.00   0.0  0
 RM8  CONST_20  C18  C19  N4   C15     0.00   0.0  0
 RM8  CONST_21  C18  C17  C16  C15     0.00   0.0  0
 RM8  CONST_22  C19  N4   C15  C16     0.00   0.0  0
 RM8  CONST_23  C19  C18  C17  C16     0.00   0.0  0
 RM8  CONST_24  C19  N4   C15  N3    180.00   0.0  0
 RM8  CONST_25  C17  C16  C15  N3    180.00   0.0  0
 RM8  CONST_26  C9   N1   C2   C1    180.00   0.0  0
 RM8  CONST_27  C4   C3   C2   C1    180.00   0.0  0
 RM8  CONST_28  C10  C3   C2   N1    180.00   0.0  0
 RM8  CONST_29  C10  C3   C4   C5      0.00   0.0  0
 RM8  CONST_30  C10  C3   C4   C9    180.00   0.0  0
 RM8  CONST_31  H8   C8   C9   N1      0.00   0.0  0
 RM8  CONST_32  HN1  N1   C2   C3    180.00   0.0  0
 RM8  CONST_33  H5   C5   C4   C3      0.00   0.0  0
 RM8  CONST_34  H16  C16  C15  N3      0.00   0.0  0
 RM8  CONST_35  H6   C6   C5   C4    180.00   0.0  0
 RM8  CONST_36  H18  C18  C19  N4    180.00   0.0  0
 RM8  CONST_37  H7   C7   C6   C5    180.00   0.0  0
 RM8  CONST_38  H19  C19  N4   C15   180.00   0.0  0
 RM8  CONST_39  H17  C17  C16  C15   180.00   0.0  0
 RM8  Var_01    N3   C12  C11  N2     55.96  30.0  1
 RM8  Var_02    N3   C13  C14  N2    -54.01  30.0  1
 RM8  Var_03    C12  N3   C15  N4    -21.95  30.0  2
 RM8  Var_04    C13  C14  N2   C11    59.26  30.0  1
 RM8  Var_05    C14  C13  N3   C12    50.13  30.0  1
 RM8  Var_06    C14  N2   C11  C12   -60.12  30.0  1
 RM8  Var_07    N2   C10  C3   C2     66.47  30.0  2
 RM8  Var_08    C11  N2   C10  C3   -172.04  30.0  1
 RM8  Var_09    H1   C1   C2   N1     54.06  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
 RM8  plan-1  N3   0.020
 RM8  plan-1  N4   0.020
 RM8  plan-1  C15  0.020
 RM8  plan-1  C16  0.020
 RM8  plan-1  C17  0.020
 RM8  plan-1  C18  0.020
 RM8  plan-1  C19  0.020
 RM8  plan-1  H16  0.020
 RM8  plan-1  H17  0.020
 RM8  plan-1  H18  0.020
 RM8  plan-1  H19  0.020
 RM8  plan-2  C1   0.020
 RM8  plan-2  N1   0.020
 RM8  plan-2  C2   0.020
 RM8  plan-2  C3   0.020
 RM8  plan-2  C4   0.020
 RM8  plan-2  C5   0.020
 RM8  plan-2  C6   0.020
 RM8  plan-2  C7   0.020
 RM8  plan-2  C8   0.020
 RM8  plan-2  C9   0.020
 RM8  plan-2  C10  0.020
 RM8  plan-2  HN1  0.020
 RM8  plan-2  H5   0.020
 RM8  plan-2  H6   0.020
 RM8  plan-2  H7   0.020
 RM8  plan-2  H8   0.020

