# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 15:40:23 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: methyl 4-[(4-methylpiperazin-1-yl)methyl]benzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1ccc(CN2CCN(C)CC2)cc1
#
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
 54V  54V  'methyl 4-[(4-methylpiperazin-1-yl)methyl]benzoate'  ligand  38  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_54V
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
 54V  N1   N  NT    0  -0.420  -2.2980  -0.5553   0.2772
 54V  C4   C  CH2   0  -0.281  -3.4724   1.4538  -0.4579
 54V  C5   C  CH2   0  -0.314  -1.2687  -1.1308   1.1112
 54V  C6   C  CR6   0   0.085   0.1203  -0.7152   0.7017
 54V  C7   C  CR16  0  -0.297   1.1064  -0.5166   1.6629
 54V  C8   C  CR16  0  -0.251   2.4019  -0.1830   1.3007
 54V  C10  C  CR16  0  -0.243   1.7476  -0.2258  -1.0106
 54V  C13  C  CH3   0  -0.422   6.2865   0.8605   0.1979
 54V  O    O  O     0  -0.450   4.4159   0.4588  -1.6518
 54V  O1   O  O2    0  -0.457   4.9423   0.5000   0.5148
 54V  C9   C  CR6   0  -0.098   2.7346  -0.0339  -0.0441
 54V  C11  C  CR16  0  -0.270   0.4577  -0.5622  -0.6417
 54V  C2   C  CH2   0  -0.284  -3.5766  -1.2161   0.4565
 54V  C1   C  CH2   0  -0.282  -4.6099  -0.6333  -0.4881
 54V  C3   C  CH2   0  -0.284  -2.4352   0.8742   0.4842
 54V  N    N  NT    0  -0.412  -4.7495   0.7934  -0.2811
 54V  C    C  CH3   0  -0.516  -5.7712   1.3595  -1.1300
 54V  H2   H  HCH2  0   0.234  -3.5890   2.5195  -0.2459
 54V  H3   H  HCH2  0   0.188  -3.1070   1.3676  -1.4966
 54V  H4   H  HCH2  0   0.217  -1.4158  -0.9010   2.1799
 54V  H5   H  HCH2  0   0.261  -1.3336  -2.2208   1.0262
 54V  H6   H  HCR6  0   0.257   0.8598  -0.6198   2.7127
 54V  H7   H  HCR6  0   0.262   3.1416  -0.0352   2.0752
 54V  H8   H  HCR6  0   0.259   1.9889  -0.1092  -2.0589
 54V  H9   H  HCH3  0   0.240   6.7772   0.0861  -0.3911
 54V  H10  H  HCH3  0   0.240   6.3272   1.8048  -0.3442
 54V  H11  H  HCH3  0   0.253   6.7979   0.9685   1.1497
 54V  H12  H  HCR6  0   0.252  -0.3027  -0.6961  -1.4000
 54V  H13  H  HCH2  0   0.237  -3.4610  -2.2813   0.2431
 54V  H14  H  HCH2  0   0.192  -3.9410  -1.1294   1.4944
 54V  H15  H  HCH2  0   0.188  -4.3186  -0.8673  -1.5271
 54V  H16  H  HCH2  0   0.235  -5.5724  -1.1180  -0.3061
 54V  H17  H  HCH2  0   0.196  -2.7213   1.1017   1.5254
 54V  H18  H  HCH2  0   0.240  -1.4772   1.3638   0.2974
 54V  H20  H  HCH3  0   0.190  -5.5604   1.2423  -2.2049
 54V  H21  H  HCH3  0   0.232  -6.7319   0.8835  -0.9267
 54V  H22  H  HCH3  0   0.232  -5.8777   2.4264  -0.9268
 54V  C12  C  C     0   0.592   4.1005   0.3298  -0.4926

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
 54V  C13  O1   single    1.427  0.020  1.427
 54V  O1   C12  single    1.324  0.020  1.324
 54V  C10  C11  aromatic  1.383  0.020  1.383
 54V  C10  C9   aromatic  1.395  0.020  1.395
 54V  C11  C6   aromatic  1.394  0.020  1.394
 54V  C12  C9   single    1.483  0.020  1.483
 54V  C12  O    double    1.208  0.020  1.208
 54V  C9   C8   aromatic  1.393  0.020  1.393
 54V  C6   C5   single    1.507  0.020  1.507
 54V  C6   C7   aromatic  1.391  0.020  1.391
 54V  C5   N1   single    1.444  0.020  1.444
 54V  C8   C7   aromatic  1.386  0.020  1.386
 54V  N1   C2   single    1.450  0.020  1.450
 54V  N1   C3   single    1.451  0.020  1.451
 54V  C2   C1   single    1.516  0.020  1.516
 54V  C3   C4   single    1.516  0.020  1.516
 54V  C1   N    single    1.448  0.020  1.448
 54V  C4   N    single    1.449  0.020  1.449
 54V  N    C    single    1.444  0.020  1.444
 54V  C4   H2   single    0.970  0.020  1.090
 54V  C4   H3   single    0.970  0.020  1.090
 54V  C5   H4   single    0.970  0.020  1.090
 54V  C5   H5   single    0.970  0.020  1.090
 54V  C7   H6   single    0.930  0.020  1.080
 54V  C8   H7   single    0.930  0.020  1.080
 54V  C10  H8   single    0.930  0.020  1.080
 54V  C13  H9   single    0.970  0.020  1.090
 54V  C13  H10  single    0.970  0.020  1.090
 54V  C13  H11  single    0.970  0.020  1.090
 54V  C11  H12  single    0.930  0.020  1.080
 54V  C2   H13  single    0.970  0.020  1.090
 54V  C2   H14  single    0.970  0.020  1.090
 54V  C1   H15  single    0.970  0.020  1.090
 54V  C1   H16  single    0.970  0.020  1.090
 54V  C3   H17  single    0.970  0.020  1.090
 54V  C3   H18  single    0.970  0.020  1.090
 54V  C    H20  single    0.970  0.020  1.090
 54V  C    H21  single    0.970  0.020  1.090
 54V  C    H22  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
 54V  C3   N1   C2   110.35  3.000
 54V  C3   N1   C5   112.19  3.000
 54V  C2   N1   C5   112.04  3.000
 54V  H3   C4   H2   107.09  3.000
 54V  H3   C4   N    111.77  3.000
 54V  H2   C4   N    109.08  3.000
 54V  H3   C4   C3   109.16  3.000
 54V  H2   C4   C3   108.98  3.000
 54V  N    C4   C3   110.67  3.000
 54V  H5   C5   H4   105.94  3.000
 54V  H5   C5   C6   107.94  3.000
 54V  H4   C5   C6   109.20  3.000
 54V  H5   C5   N1   108.03  3.000
 54V  H4   C5   N1   112.42  3.000
 54V  C6   C5   N1   112.96  3.000
 54V  C11  C6   C7   118.60  3.000
 54V  C7   C6   C5   120.34  3.000
 54V  C11  C6   C5   121.04  3.000
 54V  H6   C7   C8   119.27  3.000
 54V  H6   C7   C6   119.64  3.000
 54V  C8   C7   C6   121.09  3.000
 54V  H7   C8   C9   120.90  3.000
 54V  H7   C8   C7   119.03  3.000
 54V  C9   C8   C7   120.07  3.000
 54V  H8   C10  C11  119.51  3.000
 54V  H8   C10  C9   119.92  3.000
 54V  C11  C10  C9   120.57  3.000
 54V  H11  C13  H10  109.41  3.000
 54V  H11  C13  H9   109.41  3.000
 54V  H10  C13  H9   109.27  3.000
 54V  H11  C13  O1   105.91  3.000
 54V  H10  C13  O1   111.38  3.000
 54V  H9   C13  O1   111.39  3.000
 54V  C12  O1   C13  117.54  3.000
 54V  C12  C9   C10  118.42  3.000
 54V  C12  C9   C8   122.55  3.000
 54V  C10  C9   C8   119.03  3.000
 54V  H12  C11  C10  119.90  3.000
 54V  H12  C11  C6   119.46  3.000
 54V  C10  C11  C6   120.64  3.000
 54V  H14  C2   H13  107.17  3.000
 54V  H14  C2   C1   109.31  3.000
 54V  H13  C2   C1   108.97  3.000
 54V  H14  C2   N1   111.82  3.000
 54V  H13  C2   N1   109.07  3.000
 54V  C1   C2   N1   110.40  3.000
 54V  H16  C1   H15  107.16  3.000
 54V  H16  C1   N    109.16  3.000
 54V  H15  C1   N    111.63  3.000
 54V  H16  C1   C2   109.02  3.000
 54V  H15  C1   C2   108.96  3.000
 54V  N    C1   C2   110.80  3.000
 54V  H18  C3   H17  107.24  3.000
 54V  H18  C3   C4   108.81  3.000
 54V  H17  C3   C4   109.28  3.000
 54V  H18  C3   N1   109.53  3.000
 54V  H17  C3   N1   111.24  3.000
 54V  C4   C3   N1   110.65  3.000
 54V  C    N    C1   111.74  3.000
 54V  C    N    C4   111.92  3.000
 54V  C1   N    C4   110.28  3.000
 54V  H22  C    H21  107.81  3.000
 54V  H22  C    H20  107.72  3.000
 54V  H21  C    H20  107.69  3.000
 54V  H22  C    N    110.05  3.000
 54V  H21  C    N    110.02  3.000
 54V  H20  C    N    113.36  3.000
 54V  C9   C12  O1   112.78  3.000
 54V  C9   C12  O    123.83  3.000
 54V  O1   C12  O    123.39  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
 54V  CONST_01  C9   C10  C11  C6      0.00   0.0  0
 54V  CONST_02  C9   C8   C7   C6      0.00   0.0  0
 54V  CONST_03  C10  C11  C6   C7      0.00   0.0  0
 54V  CONST_04  C10  C9   C8   C7      0.00   0.0  0
 54V  CONST_05  C11  C10  C9   C8      0.00   0.0  0
 54V  CONST_06  C11  C6   C7   C8      0.00   0.0  0
 54V  CONST_07  C10  C11  C6   C5    180.00   0.0  0
 54V  CONST_08  C8   C7   C6   C5    180.00   0.0  0
 54V  CONST_09  C12  C9   C8   C7    180.00   0.0  0
 54V  CONST_10  C11  C10  C9   C12   180.00   0.0  0
 54V  CONST_11  H8   C10  C11  C6    180.00   0.0  0
 54V  CONST_12  H7   C8   C7   C6    180.00   0.0  0
 54V  CONST_13  H12  C11  C6   C7    180.00   0.0  0
 54V  CONST_14  H6   C7   C8   C9    180.00   0.0  0
 54V  Var_01    N    C1   C2   N1    -57.56  30.0  1
 54V  Var_02    N    C4   C3   N1     57.31  30.0  1
 54V  Var_03    C2   N1   C3   C4    -57.24  30.0  1
 54V  Var_04    C2   C1   N    C4     57.38  30.0  1
 54V  Var_05    C3   N1   C2   C1     57.24  30.0  1
 54V  Var_06    C3   C4   N    C1    -57.16  30.0  1
 54V  Var_07    C11  C6   C5   N1    -37.13  30.0  2
 54V  Var_08    O1   C12  C9   C8     -0.41  30.0  2
 54V  Var_09    H20  C    N    C4     62.95  30.0  3
 54V  Var_10    C9   C12  O1   C13  -179.66  30.0  3
 54V  Var_11    H9   C13  O1   C12   -62.21  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
 54V  plan-1  C5   0.020
 54V  plan-1  C6   0.020
 54V  plan-1  C7   0.020
 54V  plan-1  C8   0.020
 54V  plan-1  C10  0.020
 54V  plan-1  C9   0.020
 54V  plan-1  C11  0.020
 54V  plan-1  H6   0.020
 54V  plan-1  H7   0.020
 54V  plan-1  H8   0.020
 54V  plan-1  H12  0.020
 54V  plan-1  C12  0.020
 54V  plan-2  O    0.020
 54V  plan-2  O1   0.020
 54V  plan-2  C9   0.020
 54V  plan-2  C12  0.020

