# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 01:17:21 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: ~{N}-[[4-(diethylaminomethyl)phenyl]methyl]-4-pyrimidin-2-yl-piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC)Cc1ccc(CNC(=O)N2CCN(CC2)c3ncccn3)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
 M7N  M7N  ~{N}-[[4-(diethylaminomethyl)phenyl]methyl]-4-pyrimidin-2-yl-piperazine-1-carboxamide  ligand  58  28  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M7N
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
 M7N  C7   C  CR16  0  -0.283  -2.7389  -0.5541  -0.9132
 M7N  C6   C  CR16  0  -0.266  -3.8462   0.2246  -0.6132
 M7N  C5   C  CR6   0   0.082  -4.4219   0.1842   0.6544
 M7N  C4   C  CH2   0  -0.333  -5.6053   1.0569   0.9856
 M7N  C3   C  CH3   0  -0.668  -8.0037  -0.5367  -1.3951
 M7N  C2   C  CH2   0  -0.276  -7.3035  -0.2643  -0.0741
 M7N  C1   C  CH2   0  -0.283  -7.5459   2.1435   0.0690
 M7N  C8   C  CR6   0   0.034  -2.1844  -1.4039   0.0405
 M7N  C9   C  CH2   0  -0.303  -0.9726  -2.2380  -0.2701
 M7N  C10  C  C     0   0.744   1.4232  -2.2008   0.1810
 M7N  C11  C  CH2   0  -0.326   3.8091  -2.1132   0.6230
 M7N  N1   N  NH1   0  -0.681   0.2131  -1.5926   0.2658
 M7N  C12  C  CH2   0  -0.295   4.5304  -1.3126  -0.4518
 M7N  C13  C  CH2   0  -0.347   2.5028  -0.2082   1.2304
 M7N  C14  C  CH2   0  -0.286   3.1726   0.6316   0.1526
 M7N  N2   N  NT    0  -0.495   2.4675  -1.6083   0.8474
 M7N  C15  C  CR6   0   0.646   5.5517   0.9181  -0.3713
 M7N  C16  C  CR16  0  -0.009   6.4303   3.0100  -0.3868
 M7N  N3   N  NT    0  -0.506   4.4913   0.1052  -0.1418
 M7N  C17  C  CR16  0  -0.399   7.6681   2.5234  -0.7750
 M7N  C18  C  CR16  0  -0.010   7.7334   1.1504  -0.9487
 M7N  C19  C  CR16  0  -0.269  -2.7629  -1.4487   1.3047
 M7N  C20  C  CR16  0  -0.302  -3.8676  -0.6637   1.6070
 M7N  N4   N  N     0  -0.474   5.3803   2.2338  -0.1864
 M7N  O    O  O     0  -0.545   1.5621  -3.2453  -0.4486
 M7N  N5   N  N     0  -0.473   6.7012   0.3486  -0.7569
 M7N  N    N  NT    0  -0.406  -6.6243   1.0226  -0.0436
 M7N  C    C  CH3   0  -0.665  -6.9600   3.4451  -0.4539
 M7N  H1   H  HCR6  0   0.248  -2.3045  -0.5076  -1.9050
 M7N  H2   H  HCR6  0   0.243  -4.2806   0.8646  -1.3709
 M7N  H3   H  HCH2  0   0.213  -6.0013   0.7751   1.9762
 M7N  H4   H  HCH2  0   0.252  -5.2505   2.0856   1.0899
 M7N  H5   H  HCH3  0   0.223  -8.8103   0.1691  -1.5953
 M7N  H6   H  HCH3  0   0.222  -7.2949  -0.4823  -2.2217
 M7N  H7   H  HCH3  0   0.226  -8.4426  -1.5349  -1.3885
 M7N  H8   H  HCH2  0   0.193  -8.0199  -0.3634   0.7588
 M7N  H9   H  HCH2  0   0.231  -6.5534  -1.0437   0.0767
 M7N  H10  H  HCH2  0   0.231  -8.4368   1.9136  -0.5168
 M7N  H11  H  HCH2  0   0.194  -7.8950   2.2760   1.1065
 M7N  H12  H  HCH2  0   0.242  -1.0955  -3.2401   0.1517
 M7N  H13  H  HCH2  0   0.247  -0.8718  -2.3576  -1.3504
 M7N  H14  H  HCH2  0   0.269   3.7751  -3.1614   0.3405
 M7N  H15  H  HCH2  0   0.248   4.3617  -2.0415   1.5640
 M7N  H16  H  HNH1  0   0.399   0.0572  -0.8646   0.9411
 M7N  H17  H  HCH2  0   0.272   5.5638  -1.6393  -0.5200
 M7N  H18  H  HCH2  0   0.234   4.0595  -1.4977  -1.4253
 M7N  H19  H  HCH2  0   0.258   3.0688  -0.1261   2.1616
 M7N  H20  H  HCH2  0   0.264   1.5149   0.1948   1.4400
 M7N  H21  H  HCH2  0   0.235   2.5514   0.6227  -0.7518
 M7N  H22  H  HCH2  0   0.275   3.2562   1.6614   0.4867
 M7N  H23  H  HCR6  0   0.268   6.2763   4.0731  -0.2331
 M7N  H24  H  HCR6  0   0.270   8.5172   3.1687  -0.9397
 M7N  H25  H  HCR6  0   0.268   8.6581   0.6753  -1.2593
 M7N  H26  H  HCR6  0   0.251  -2.3557  -2.1117   2.0595
 M7N  H27  H  HCR6  0   0.248  -4.3089  -0.7210   2.5953
 M7N  H29  H  HCH3  0   0.226  -7.6970   4.2458  -0.3867
 M7N  H30  H  HCH3  0   0.223  -6.0827   3.7658   0.1091
 M7N  H31  H  HCH3  0   0.222  -6.6661   3.3395  -1.4984

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
 M7N  C3   C2   single    1.520  0.020  1.520
 M7N  C    C1   single    1.520  0.020  1.520
 M7N  C2   N    single    1.455  0.020  1.455
 M7N  C1   N    single    1.456  0.020  1.456
 M7N  N    C4   single    1.449  0.020  1.449
 M7N  C20  C19  aromatic  1.388  0.020  1.388
 M7N  C20  C5   aromatic  1.391  0.020  1.391
 M7N  C4   C5   single    1.507  0.020  1.507
 M7N  C19  C8   aromatic  1.391  0.020  1.391
 M7N  C5   C6   aromatic  1.393  0.020  1.393
 M7N  C8   C9   single    1.504  0.020  1.504
 M7N  C8   C7   aromatic  1.392  0.020  1.392
 M7N  C6   C7   aromatic  1.387  0.020  1.387
 M7N  C9   N1   single    1.452  0.020  1.452
 M7N  O    C10  double    1.228  0.020  1.228
 M7N  N1   C10  single    1.357  0.020  1.357
 M7N  C10  N2   single    1.373  0.020  1.373
 M7N  N2   C11  single    1.451  0.020  1.451
 M7N  N2   C13  single    1.452  0.020  1.452
 M7N  C11  C12  single    1.522  0.020  1.522
 M7N  C13  C14  single    1.522  0.020  1.522
 M7N  C12  N3   single    1.452  0.020  1.452
 M7N  C14  N3   single    1.450  0.020  1.450
 M7N  N3   C15  single    1.356  0.020  1.356
 M7N  C15  N4   aromatic  1.340  0.020  1.340
 M7N  C15  N5   aromatic  1.340  0.020  1.340
 M7N  N4   C16  aromatic  1.321  0.020  1.321
 M7N  N5   C18  aromatic  1.321  0.020  1.321
 M7N  C16  C17  aromatic  1.385  0.020  1.385
 M7N  C18  C17  aromatic  1.385  0.020  1.385
 M7N  C7   H1   single    0.930  0.020  1.080
 M7N  C6   H2   single    0.930  0.020  1.080
 M7N  C4   H3   single    0.970  0.020  1.090
 M7N  C4   H4   single    0.970  0.020  1.090
 M7N  C3   H5   single    0.970  0.020  1.090
 M7N  C3   H6   single    0.970  0.020  1.090
 M7N  C3   H7   single    0.970  0.020  1.090
 M7N  C2   H8   single    0.970  0.020  1.090
 M7N  C2   H9   single    0.970  0.020  1.090
 M7N  C1   H10  single    0.970  0.020  1.090
 M7N  C1   H11  single    0.970  0.020  1.090
 M7N  C9   H12  single    0.970  0.020  1.090
 M7N  C9   H13  single    0.970  0.020  1.090
 M7N  C11  H14  single    0.970  0.020  1.090
 M7N  C11  H15  single    0.970  0.020  1.090
 M7N  N1   H16  single    0.890  0.020  1.040
 M7N  C12  H17  single    0.970  0.020  1.090
 M7N  C12  H18  single    0.970  0.020  1.090
 M7N  C13  H19  single    0.970  0.020  1.090
 M7N  C13  H20  single    0.970  0.020  1.090
 M7N  C14  H21  single    0.970  0.020  1.090
 M7N  C14  H22  single    0.970  0.020  1.090
 M7N  C16  H23  single    0.930  0.020  1.080
 M7N  C17  H24  single    0.930  0.020  1.080
 M7N  C18  H25  single    0.930  0.020  1.080
 M7N  C19  H26  single    0.930  0.020  1.080
 M7N  C20  H27  single    0.930  0.020  1.080
 M7N  C    H29  single    0.970  0.020  1.090
 M7N  C    H30  single    0.970  0.020  1.090
 M7N  C    H31  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
 M7N  H1   C7   C8   119.55  3.000
 M7N  H1   C7   C6   119.61  3.000
 M7N  C8   C7   C6   120.84  3.000
 M7N  H2   C6   C5   119.22  3.000
 M7N  H2   C6   C7   120.06  3.000
 M7N  C5   C6   C7   120.71  3.000
 M7N  C20  C5   C4   121.04  3.000
 M7N  C4   C5   C6   120.51  3.000
 M7N  C20  C5   C6   118.44  3.000
 M7N  H4   C4   H3   105.74  3.000
 M7N  H4   C4   N    108.56  3.000
 M7N  H3   C4   N    112.29  3.000
 M7N  H4   C4   C5   108.12  3.000
 M7N  H3   C4   C5   109.34  3.000
 M7N  N    C4   C5   112.49  3.000
 M7N  H7   C3   H6   108.17  3.000
 M7N  H7   C3   H5   107.21  3.000
 M7N  H6   C3   H5   108.03  3.000
 M7N  H7   C3   C2   110.14  3.000
 M7N  H6   C3   C2   110.52  3.000
 M7N  H5   C3   C2   112.61  3.000
 M7N  H9   C2   H8   106.12  3.000
 M7N  H9   C2   N    107.91  3.000
 M7N  H8   C2   N    111.51  3.000
 M7N  H9   C2   C3   107.97  3.000
 M7N  H8   C2   C3   109.94  3.000
 M7N  N    C2   C3   113.06  3.000
 M7N  H11  C1   H10  105.79  3.000
 M7N  H11  C1   C    110.05  3.000
 M7N  H10  C1   C    108.09  3.000
 M7N  H11  C1   N    111.46  3.000
 M7N  H10  C1   N    108.25  3.000
 M7N  C    C1   N    112.88  3.000
 M7N  C19  C8   C9   120.33  3.000
 M7N  C9   C8   C7   121.20  3.000
 M7N  C19  C8   C7   118.45  3.000
 M7N  H13  C9   H12  106.95  3.000
 M7N  H13  C9   N1   109.78  3.000
 M7N  H12  C9   N1   110.89  3.000
 M7N  H13  C9   C8   109.85  3.000
 M7N  H12  C9   C8   109.75  3.000
 M7N  N1   C9   C8   109.58  3.000
 M7N  O    C10  N2   122.00  3.000
 M7N  N2   C10  N1   117.03  3.000
 M7N  O    C10  N1   120.96  3.000
 M7N  H15  C11  H14  107.63  3.000
 M7N  H15  C11  N2   108.14  3.000
 M7N  H14  C11  N2   110.31  3.000
 M7N  H15  C11  C12  109.50  3.000
 M7N  H14  C11  C12  109.81  3.000
 M7N  N2   C11  C12  111.37  3.000
 M7N  H16  N1   C10  120.32  3.000
 M7N  H16  N1   C9   116.30  3.000
 M7N  C10  N1   C9   120.38  3.000
 M7N  H18  C12  H17  107.57  3.000
 M7N  H18  C12  N3   110.04  3.000
 M7N  H17  C12  N3   109.44  3.000
 M7N  H18  C12  C11  109.54  3.000
 M7N  H17  C12  C11  109.70  3.000
 M7N  N3   C12  C11  110.50  3.000
 M7N  H20  C13  H19  106.17  3.000
 M7N  H20  C13  N2   112.72  3.000
 M7N  H19  C13  N2   108.04  3.000
 M7N  H20  C13  C14  109.38  3.000
 M7N  H19  C13  C14  109.52  3.000
 M7N  N2   C13  C14  110.86  3.000
 M7N  H22  C14  H21  107.75  3.000
 M7N  H22  C14  N3   109.68  3.000
 M7N  H21  C14  N3   110.16  3.000
 M7N  H22  C14  C13  109.84  3.000
 M7N  H21  C14  C13  109.27  3.000
 M7N  N3   C14  C13  110.10  3.000
 M7N  C13  N2   C11  110.72  3.000
 M7N  C13  N2   C10  124.23  3.000
 M7N  C11  N2   C10  118.56  3.000
 M7N  N5   C15  N4   124.55  3.000
 M7N  N5   C15  N3   117.71  3.000
 M7N  N4   C15  N3   117.74  3.000
 M7N  H23  C16  N4   116.19  3.000
 M7N  H23  C16  C17  120.70  3.000
 M7N  N4   C16  C17  123.11  3.000
 M7N  C15  N3   C14  121.87  3.000
 M7N  C15  N3   C12  121.90  3.000
 M7N  C14  N3   C12  114.99  3.000
 M7N  H24  C17  C18  122.43  3.000
 M7N  H24  C17  C16  122.39  3.000
 M7N  C18  C17  C16  115.17  3.000
 M7N  H25  C18  N5   116.21  3.000
 M7N  H25  C18  C17  120.67  3.000
 M7N  N5   C18  C17  123.12  3.000
 M7N  H26  C19  C20  119.55  3.000
 M7N  H26  C19  C8   119.75  3.000
 M7N  C20  C19  C8   120.70  3.000
 M7N  H27  C20  C19  119.51  3.000
 M7N  H27  C20  C5   119.64  3.000
 M7N  C19  C20  C5   120.85  3.000
 M7N  C16  N4   C15  117.03  3.000
 M7N  C18  N5   C15  117.01  3.000
 M7N  C1   N    C2   112.77  3.000
 M7N  C1   N    C4   111.85  3.000
 M7N  C2   N    C4   111.35  3.000
 M7N  H31  C    H30  107.83  3.000
 M7N  H31  C    H29  108.20  3.000
 M7N  H30  C    H29  107.21  3.000
 M7N  H31  C    C1   110.53  3.000
 M7N  H30  C    C1   112.60  3.000
 M7N  H29  C    C1   110.31  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
 M7N  CONST_01  C20  C19  C8   C7      0.00   0.0  0
 M7N  CONST_02  C20  C5   C6   C7      0.00   0.0  0
 M7N  CONST_03  C19  C20  C5   C6      0.00   0.0  0
 M7N  CONST_04  C19  C8   C7   C6      0.00   0.0  0
 M7N  CONST_05  C8   C19  C20  C5      0.00   0.0  0
 M7N  CONST_06  C8   C7   C6   C5      0.00   0.0  0
 M7N  CONST_07  C17  C16  N4   C15     0.00   0.0  0
 M7N  CONST_08  C17  C18  N5   C15     0.00   0.0  0
 M7N  CONST_09  N5   C15  N4   C16     0.00   0.0  0
 M7N  CONST_10  N5   C18  C17  C16     0.00   0.0  0
 M7N  CONST_11  N4   C15  N5   C18     0.00   0.0  0
 M7N  CONST_12  N4   C16  C17  C18     0.00   0.0  0
 M7N  CONST_13  N3   C15  N4   C16   180.00   0.0  0
 M7N  CONST_14  C18  N5   C15  N3    180.00   0.0  0
 M7N  CONST_15  C4   C5   C6   C7    180.00   0.0  0
 M7N  CONST_16  C9   C8   C7   C6    180.00   0.0  0
 M7N  CONST_17  C19  C20  C5   C4    180.00   0.0  0
 M7N  CONST_18  C20  C19  C8   C9    180.00   0.0  0
 M7N  CONST_19  H26  C19  C8   C7    180.00   0.0  0
 M7N  CONST_20  H27  C20  C5   C6    180.00   0.0  0
 M7N  CONST_21  H1   C7   C6   C5    180.00   0.0  0
 M7N  CONST_22  H2   C6   C7   C8    180.00   0.0  0
 M7N  CONST_23  H23  C16  N4   C15   180.00   0.0  0
 M7N  CONST_24  H25  C18  N5   C15   180.00   0.0  0
 M7N  CONST_25  H24  C17  C16  N4    180.00   0.0  0
 M7N  CONST_26  O    C10  N2   C11     0.00   0.0  0
 M7N  CONST_28  N1   C10  N2   C11   180.00   0.0  0
 M7N  CONST_30  N2   C10  N1   C9    180.00   0.0  0
 M7N  CONST_31  H16  N1   C10  N2      0.00   0.0  0
 M7N  CONST_32  O    C10  N1   C9      0.00   0.0  0
 M7N  Var_01    C14  C13  N2   C11    58.97  30.0  1
 M7N  Var_02    C14  N3   C12  C11   -51.26  30.0  1
 M7N  Var_03    C13  N2   C11  C12   -58.00  30.0  1
 M7N  Var_04    C13  C14  N3   C12    52.25  30.0  1
 M7N  Var_05    N4   C15  N3   C12   173.17  30.0  2
 M7N  Var_06    N3   C12  C11  N2     52.97  30.0  1
 M7N  Var_07    N3   C14  C13  N2    -54.95  30.0  1
 M7N  Var_08    N1   C9   C8   C7     99.49  30.0  2
 M7N  Var_09    N    C4   C5   C6     46.37  30.0  2
 M7N  Var_10    C2   N    C4   C5     70.35  30.0  2
 M7N  Var_11    C10  N1   C9   C8    175.95  30.0  3
 M7N  Var_12    C3   C2   N    C4   -159.61  30.0  2
 M7N  Var_13    C    C1   N    C4     77.05  30.0  3
 M7N  Var_14    H5   C3   C2   N     -63.89  30.0  3
 M7N  Var_15    H29  C    C1   N     177.74  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
 M7N  plan-1  C15  0.020
 M7N  plan-1  C16  0.020
 M7N  plan-1  N3   0.020
 M7N  plan-1  C17  0.020
 M7N  plan-1  C18  0.020
 M7N  plan-1  N4   0.020
 M7N  plan-1  N5   0.020
 M7N  plan-1  H23  0.020
 M7N  plan-1  H24  0.020
 M7N  plan-1  H25  0.020
 M7N  plan-2  C7   0.020
 M7N  plan-2  C6   0.020
 M7N  plan-2  C5   0.020
 M7N  plan-2  C4   0.020
 M7N  plan-2  C8   0.020
 M7N  plan-2  C9   0.020
 M7N  plan-2  C19  0.020
 M7N  plan-2  C20  0.020
 M7N  plan-2  H1   0.020
 M7N  plan-2  H2   0.020
 M7N  plan-2  H26  0.020
 M7N  plan-2  H27  0.020
 M7N  plan-3  C9   0.020
 M7N  plan-3  C10  0.020
 M7N  plan-3  C11  0.020
 M7N  plan-3  N1   0.020
 M7N  plan-3  C13  0.020
 M7N  plan-3  N2   0.020
 M7N  plan-3  O    0.020
 M7N  plan-3  H16  0.020

