# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 02:25:48 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 3-cyclopentyl-1-[3-[4-(methylaminomethyl)phenyl]-1,3-diazinan-1-yl]propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCc1ccc(cc1)N2CCCN(C2)C(=O)CCC3CCCC3
#
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
 5TB  5TB  3-cyclopentyl-1-[3-[4-(methylaminomethyl)phenyl]-1,3-diazinan-1-yl]propan-1-one  ligand  55  24  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5TB
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
 5TB  C1   C  CH1   0  -0.222  -5.4606  -0.6545  -0.7426
 5TB  C2   C  CH2   0  -0.439  -6.2720   0.1039   0.3168
 5TB  C3   C  CH2   0  -0.443  -7.7218  -0.1950  -0.0478
 5TB  O    O  O     0  -0.497  -1.3692  -1.3186   0.3561
 5TB  C7   C  C     0   0.581  -1.7831  -0.1703   0.4373
 5TB  C5   C  CH2   0  -0.411  -4.0505  -1.0337  -0.3072
 5TB  C4   C  CH2   0  -0.444  -7.6861  -1.6821  -0.3977
 5TB  C    C  CH2   0  -0.437  -6.3320  -1.8848  -1.1019
 5TB  N    N  NT    0  -0.476  -1.0024   0.8373   0.9029
 5TB  C11  C  CH2   0  -0.157   0.3800   0.5969   1.2419
 5TB  N1   N  NT    0  -0.514   1.2461   1.2288   0.2686
 5TB  C10  C  CH2   0  -0.315   1.0210   2.6710   0.2004
 5TB  C9   C  CH2   0  -0.431  -0.4392   2.9708  -0.0968
 5TB  C8   C  CH2   0  -0.330  -1.3441   2.2485   0.8900
 5TB  C12  C  CR6   0   0.343   2.5735   0.7923   0.2060
 5TB  C17  C  CR16  0  -0.345   3.1281  -0.0918   1.1398
 5TB  C16  C  CR16  0  -0.275   4.4338  -0.5424   1.0076
 5TB  C15  C  CR6   0   0.067   5.2507  -0.1149  -0.0326
 5TB  C14  C  CR16  0  -0.303   4.7030   0.7742  -0.9525
 5TB  C13  C  CR16  0  -0.312   3.3956   1.2177  -0.8444
 5TB  C18  C  CH2   0  -0.344   6.6608  -0.6176  -0.1702
 5TB  N2   N  NH1   0  -0.579   6.6892  -2.0574  -0.3485
 5TB  C19  C  CH3   0  -0.518   8.0322  -2.5684  -0.5278
 5TB  H1   H  HCH1  0   0.220  -5.3868  -0.0164  -1.6318
 5TB  H2   H  HCH2  0   0.211  -6.0517  -0.2976   1.3129
 5TB  H3   H  HCH2  0   0.229  -6.0466   1.1717   0.3430
 5TB  H4   H  HCH2  0   0.226  -8.4277   0.0407   0.7508
 5TB  H5   H  HCH2  0   0.214  -8.0140   0.3935  -0.9230
 5TB  H6   H  HCH2  0   0.268  -3.6750   0.7328   0.8681
 5TB  H7   H  HCH2  0   0.265  -3.1873   0.8744  -0.7992
 5TB  H8   H  HCH2  0   0.217  -4.1142  -1.7084   0.5525
 5TB  H9   H  HCH2  0   0.229  -3.5673  -1.5986  -1.1082
 5TB  H10  H  HCH2  0   0.218  -7.7211  -2.2710   0.5222
 5TB  H11  H  HCH2  0   0.227  -8.5329  -1.9982  -1.0088
 5TB  H12  H  HCH2  0   0.225  -6.4574  -1.9590  -2.1833
 5TB  H13  H  HCH2  0   0.223  -5.8568  -2.8151  -0.7822
 5TB  H14  H  HCH2  0   0.232   0.5554   0.9873   2.2568
 5TB  H15  H  HCH2  0   0.271   0.5551  -0.4745   1.2573
 5TB  H16  H  HCH2  0   0.218   1.3083   3.1466   1.1511
 5TB  H17  H  HCH2  0   0.261   1.6464   3.1059  -0.5759
 5TB  H18  H  HCH2  0   0.247  -0.6071   4.0474  -0.0367
 5TB  H19  H  HCH2  0   0.235  -0.6817   2.6521  -1.1136
 5TB  H20  H  HCH2  0   0.276  -2.3891   2.3979   0.6382
 5TB  H21  H  HCH2  0   0.246  -1.1963   2.6490   1.8983
 5TB  H22  H  HCR6  0   0.263   2.5552  -0.4363   1.9902
 5TB  H23  H  HCR6  0   0.244   4.8252  -1.2312   1.7472
 5TB  H24  H  HCR6  0   0.245   5.3058   1.1248  -1.7828
 5TB  H25  H  HCR6  0   0.262   3.0060   1.8833  -1.6041
 5TB  H26  H  HCH2  0   0.225   7.1597  -0.0737  -0.9882
 5TB  H27  H  HCH2  0   0.242   7.2290  -0.3829   0.7365
 5TB  H28  H  HNH1  0   0.331   6.1314  -2.2976  -1.1586
 5TB  H30  H  HCH3  0   0.226   7.9958  -3.6400  -0.7239
 5TB  H31  H  HCH3  0   0.198   8.5897  -2.0950  -1.3488
 5TB  H32  H  HCH3  0   0.221   8.6122  -2.4213   0.3858
 5TB  C6   C  CH2   0  -0.614  -3.2063   0.1804   0.0488

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
 5TB  C3   C2   single    1.525  0.020  1.525
 5TB  C3   C4   single    1.528  0.020  1.528
 5TB  C2   C1   single    1.535  0.020  1.535
 5TB  C4   C    single    1.540  0.020  1.540
 5TB  C9   C8   single    1.521  0.020  1.521
 5TB  C9   C10  single    1.520  0.020  1.520
 5TB  C8   N    single    1.452  0.020  1.452
 5TB  C6   C5   single    1.521  0.020  1.521
 5TB  C6   C7   single    1.516  0.020  1.516
 5TB  C1   C    single    1.550  0.020  1.550
 5TB  C1   C5   single    1.524  0.020  1.524
 5TB  C10  N1   single    1.461  0.020  1.461
 5TB  N    C7   single    1.357  0.020  1.357
 5TB  N    C11  single    1.444  0.020  1.444
 5TB  C7   O    double    1.223  0.020  1.223
 5TB  N1   C11  single    1.448  0.020  1.448
 5TB  N1   C12  single    1.399  0.020  1.399
 5TB  C17  C12  aromatic  1.400  0.020  1.400
 5TB  C17  C16  aromatic  1.388  0.020  1.388
 5TB  C12  C13  aromatic  1.400  0.020  1.400
 5TB  C16  C15  aromatic  1.390  0.020  1.390
 5TB  C13  C14  aromatic  1.385  0.020  1.385
 5TB  C15  C14  aromatic  1.392  0.020  1.392
 5TB  C15  C18  single    1.503  0.020  1.503
 5TB  C19  N2   single    1.448  0.020  1.448
 5TB  C18  N2   single    1.451  0.020  1.451
 5TB  C1   H1   single    0.970  0.020  1.090
 5TB  C2   H2   single    0.970  0.020  1.090
 5TB  C2   H3   single    0.970  0.020  1.090
 5TB  C3   H4   single    0.970  0.020  1.090
 5TB  C3   H5   single    0.970  0.020  1.090
 5TB  C6   H6   single    0.970  0.020  1.090
 5TB  C6   H7   single    0.970  0.020  1.090
 5TB  C5   H8   single    0.970  0.020  1.090
 5TB  C5   H9   single    0.970  0.020  1.090
 5TB  C4   H10  single    0.970  0.020  1.090
 5TB  C4   H11  single    0.970  0.020  1.090
 5TB  C    H12  single    0.970  0.020  1.090
 5TB  C    H13  single    0.970  0.020  1.090
 5TB  C11  H14  single    0.970  0.020  1.090
 5TB  C11  H15  single    0.970  0.020  1.090
 5TB  C10  H16  single    0.970  0.020  1.090
 5TB  C10  H17  single    0.970  0.020  1.090
 5TB  C9   H18  single    0.970  0.020  1.090
 5TB  C9   H19  single    0.970  0.020  1.090
 5TB  C8   H20  single    0.970  0.020  1.090
 5TB  C8   H21  single    0.970  0.020  1.090
 5TB  C17  H22  single    0.930  0.020  1.080
 5TB  C16  H23  single    0.930  0.020  1.080
 5TB  C14  H24  single    0.930  0.020  1.080
 5TB  C13  H25  single    0.930  0.020  1.080
 5TB  C18  H26  single    0.970  0.020  1.090
 5TB  C18  H27  single    0.970  0.020  1.090
 5TB  N2   H28  single    0.890  0.020  1.040
 5TB  C19  H30  single    0.970  0.020  1.090
 5TB  C19  H31  single    0.970  0.020  1.090
 5TB  C19  H32  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
 5TB  H1   C1   C    108.17  3.000
 5TB  H1   C1   C5   108.31  3.000
 5TB  C    C1   C5   112.89  3.000
 5TB  H1   C1   C2   107.92  3.000
 5TB  C5   C1   C2   114.51  3.000
 5TB  C    C1   C2   104.77  3.000
 5TB  H3   C2   H2   107.16  3.000
 5TB  H3   C2   C3   113.19  3.000
 5TB  H2   C2   C3   109.67  3.000
 5TB  H3   C2   C1   113.00  3.000
 5TB  H2   C2   C1   109.87  3.000
 5TB  C3   C2   C1   103.93  3.000
 5TB  H5   C3   H4   107.24  3.000
 5TB  H5   C3   C4   110.27  3.000
 5TB  H4   C3   C4   113.13  3.000
 5TB  H5   C3   C2   109.86  3.000
 5TB  H4   C3   C2   113.43  3.000
 5TB  C4   C3   C2   102.90  3.000
 5TB  N    C7   C6   117.13  3.000
 5TB  N    C7   O    121.68  3.000
 5TB  C6   C7   O    121.18  3.000
 5TB  H9   C5   H8   106.43  3.000
 5TB  H9   C5   C6   109.80  3.000
 5TB  H8   C5   C6   109.90  3.000
 5TB  H9   C5   C1   109.17  3.000
 5TB  H8   C5   C1   108.90  3.000
 5TB  C6   C5   C1   112.45  3.000
 5TB  H11  C4   H10  106.89  3.000
 5TB  H11  C4   C    112.85  3.000
 5TB  H10  C4   C    110.01  3.000
 5TB  H11  C4   C3   113.09  3.000
 5TB  H10  C4   C3   109.33  3.000
 5TB  C    C4   C3   104.68  3.000
 5TB  H13  C    H12  106.38  3.000
 5TB  H13  C    C4   111.16  3.000
 5TB  H12  C    C4   111.17  3.000
 5TB  H13  C    C1   111.32  3.000
 5TB  H12  C    C1   110.38  3.000
 5TB  C4   C    C1   106.50  3.000
 5TB  C8   N    C11  112.91  3.000
 5TB  C11  N    C7   120.52  3.000
 5TB  C8   N    C7   125.68  3.000
 5TB  H15  C11  H14  108.12  3.000
 5TB  H15  C11  N1   110.10  3.000
 5TB  H14  C11  N1   111.68  3.000
 5TB  H15  C11  N    108.79  3.000
 5TB  H14  C11  N    108.05  3.000
 5TB  N1   C11  N    110.02  3.000
 5TB  C12  N1   C10  116.88  3.000
 5TB  C12  N1   C11  117.49  3.000
 5TB  C10  N1   C11  111.71  3.000
 5TB  H17  C10  H16  107.07  3.000
 5TB  H17  C10  C9   109.51  3.000
 5TB  H16  C10  C9   109.53  3.000
 5TB  H17  C10  N1   109.84  3.000
 5TB  H16  C10  N1   110.23  3.000
 5TB  C9   C10  N1   110.59  3.000
 5TB  H19  C9   H18  107.75  3.000
 5TB  H19  C9   C8   109.46  3.000
 5TB  H18  C9   C8   109.95  3.000
 5TB  H19  C9   C10  109.73  3.000
 5TB  H18  C9   C10  109.36  3.000
 5TB  C8   C9   C10  110.54  3.000
 5TB  H21  C8   H20  107.06  3.000
 5TB  H21  C8   C9   110.08  3.000
 5TB  H20  C8   C9   110.91  3.000
 5TB  H21  C8   N    108.39  3.000
 5TB  H20  C8   N    111.26  3.000
 5TB  C9   C8   N    109.10  3.000
 5TB  C13  C12  C17  117.36  3.000
 5TB  C13  C12  N1   119.74  3.000
 5TB  C17  C12  N1   122.89  3.000
 5TB  H22  C17  C16  118.02  3.000
 5TB  H22  C17  C12  121.04  3.000
 5TB  C16  C17  C12  120.94  3.000
 5TB  H23  C16  C15  119.60  3.000
 5TB  H23  C16  C17  118.76  3.000
 5TB  C15  C16  C17  121.63  3.000
 5TB  C18  C15  C14  121.49  3.000
 5TB  C18  C15  C16  121.12  3.000
 5TB  C14  C15  C16  117.38  3.000
 5TB  H24  C14  C13  118.76  3.000
 5TB  H24  C14  C15  119.60  3.000
 5TB  C13  C14  C15  121.64  3.000
 5TB  H25  C13  C14  118.81  3.000
 5TB  H25  C13  C12  120.13  3.000
 5TB  C14  C13  C12  121.04  3.000
 5TB  H27  C18  H26  105.90  3.000
 5TB  H27  C18  N2   107.70  3.000
 5TB  H26  C18  N2   112.94  3.000
 5TB  H27  C18  C15  109.83  3.000
 5TB  H26  C18  C15  109.13  3.000
 5TB  N2   C18  C15  111.18  3.000
 5TB  H28  N2   C19  109.15  3.000
 5TB  H28  N2   C18  108.84  3.000
 5TB  C19  N2   C18  112.55  3.000
 5TB  H32  C19  H31  107.30  3.000
 5TB  H32  C19  H30  107.50  3.000
 5TB  H31  C19  H30  107.81  3.000
 5TB  H32  C19  N2   109.96  3.000
 5TB  H31  C19  N2   114.25  3.000
 5TB  H30  C19  N2   109.77  3.000
 5TB  H7   C6   H6   105.50  3.000
 5TB  H7   C6   C5   109.51  3.000
 5TB  H6   C6   C5   109.92  3.000
 5TB  H7   C6   C7   109.18  3.000
 5TB  H6   C6   C7   109.09  3.000
 5TB  C5   C6   C7   113.34  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
 5TB  CONST_01  C15  C16  C17  C12     0.00   0.0  0
 5TB  CONST_02  C15  C14  C13  C12     0.00   0.0  0
 5TB  CONST_03  C14  C13  C12  C17     0.00   0.0  0
 5TB  CONST_04  C14  C15  C16  C17     0.00   0.0  0
 5TB  CONST_05  C13  C12  C17  C16     0.00   0.0  0
 5TB  CONST_06  C13  C14  C15  C16     0.00   0.0  0
 5TB  CONST_07  C16  C17  C12  N1    180.00   0.0  0
 5TB  CONST_08  C14  C13  C12  N1    180.00   0.0  0
 5TB  CONST_09  C18  C15  C16  C17   180.00   0.0  0
 5TB  CONST_10  C18  C15  C14  C13   180.00   0.0  0
 5TB  CONST_11  H22  C17  C12  N1      0.00   0.0  0
 5TB  CONST_12  H25  C13  C12  N1      0.00   0.0  0
 5TB  CONST_13  H23  C16  C17  C12   180.00   0.0  0
 5TB  CONST_14  H24  C14  C13  C12   180.00   0.0  0
 5TB  CONST_15  C8   N    C7   O     180.00   0.0  0
 5TB  CONST_16  C11  N    C7   O       0.00   0.0  0
 5TB  CONST_17  C8   N    C7   C6      0.00   0.0  0
 5TB  CONST_18  C11  N    C7   C6    180.00   0.0  0
 5TB  Var_01    C4   C3   C2   C1     41.83  30.0  1
 5TB  Var_02    C3   C4   C    C1     17.54  30.0  1
 5TB  Var_03    C    C4   C3   C2    -36.52  30.0  1
 5TB  Var_04    C10  C9   C8   N     -52.85  30.0  1
 5TB  Var_05    C10  N1   C11  N      59.01  30.0  1
 5TB  Var_06    C9   C8   N    C11    57.66  30.0  1
 5TB  Var_07    C9   C10  N1   C11   -55.93  30.0  1
 5TB  Var_08    C17  C12  N1   C11    -8.15  30.0  2
 5TB  Var_09    C8   C9   C10  N1     52.74  30.0  1
 5TB  Var_10    C8   N    C11  N1    -60.77  30.0  1
 5TB  Var_11    N2   C18  C15  C16    60.88  30.0  2
 5TB  Var_12    C7   C6   C5   C1   -177.93  30.0  2
 5TB  Var_13    N    C7   C6   C5   -173.34  30.0  3
 5TB  Var_14    C19  N2   C18  C15   178.11  30.0  3
 5TB  Var_15    H30  C19  N2   C18  -176.22  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 5TB  chir_01  C1  C2  C  C5  positiv

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
 5TB  plan-1  O    0.020
 5TB  plan-1  C7   0.020
 5TB  plan-1  N    0.020
 5TB  plan-1  C11  0.020
 5TB  plan-1  C8   0.020
 5TB  plan-1  C6   0.020
 5TB  plan-2  N1   0.020
 5TB  plan-2  C12  0.020
 5TB  plan-2  C17  0.020
 5TB  plan-2  C16  0.020
 5TB  plan-2  C15  0.020
 5TB  plan-2  C14  0.020
 5TB  plan-2  C13  0.020
 5TB  plan-2  C18  0.020
 5TB  plan-2  H22  0.020
 5TB  plan-2  H23  0.020
 5TB  plan-2  H24  0.020
 5TB  plan-2  H25  0.020

