# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 21:28:52 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: (2S)-1-[(8aR)-hexahydropyrrolo[1,2-a]pyrimidin-1(2H)-yl]-4-methylpentan-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)CN1CCCN2CCC[C@@H]12
#
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
 TLX  TLX  (2S)-1-[(8aR)-hexahydropyrrolo[1,2-a]pyrimidin-1(2H)-yl]-4-methylpentan-2-amine  ligand  43  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TLX
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
 TLX  N1    N  NT    0  -0.446  102.9381   99.2477  76.5573
 TLX  C2    C  CH2   0  -0.284  103.9740   99.1556  77.5746
 TLX  C3    C  CH2   0  -0.492  104.4109   97.7181  77.8286
 TLX  C4    C  CH2   0  -0.255  103.2090   96.8593  78.2389
 TLX  N5    N  NR5   0  -0.470  101.9840   97.4670  77.7655
 TLX  C6    C  CH2   0  -0.254  100.8246   96.5966  77.7637
 TLX  C7    C  CH2   0  -0.488   99.8731   97.1892  76.7065
 TLX  C8    C  CH2   0  -0.451  100.6299   98.3929  76.1351
 TLX  C9    C  CR15  0   0.168  102.0872   98.0774  76.4558
 TLX  C1'   C  CH2   0  -0.300  103.2929   99.9123  75.3268
 TLX  C2'   C  CH1   0  -0.105  104.4619   99.3765  74.4797
 TLX  C3'   C  CH2   0  -0.401  104.7192  100.3549  73.3184
 TLX  C4'   C  CH1   0  -0.230  106.1613  100.4484  72.8118
 TLX  C5'   C  CH3   0  -0.673  106.7313   99.1222  72.3173
 TLX  CM'   C  CH3   0  -0.650  106.2528  101.5017  71.7115
 TLX  N'    N  NH2   0  -0.785  104.2027   98.0005  74.0705
 TLX  H21   H  HCH2  0   0.228  104.8359   99.7493  77.2634
 TLX  H22   H  HCH2  0   0.209  103.6312   99.5983  78.5185
 TLX  H31   H  HCH2  0   0.227  104.8671   97.3216  76.9193
 TLX  H32   H  HCH2  0   0.235  105.1800   97.6882  78.6026
 TLX  H41   H  HCH2  0   0.191  103.3323   95.8347  77.8495
 TLX  H42   H  HCH2  0   0.219  103.1556   96.7700  79.3282
 TLX  H61   H  HCH2  0   0.192  101.0951   95.5647  77.4920
 TLX  H62   H  HCH2  0   0.221  100.3763   96.5493  78.7599
 TLX  H71   H  HCH2  0   0.232   99.6703   96.4516  75.9301
 TLX  H72   H  HCH2  0   0.239   98.9110   97.4778  77.1287
 TLX  H81   H  HCH2  0   0.229  100.4500   98.5379  75.0698
 TLX  H82   H  HCH2  0   0.217  100.3531   99.3138  76.6526
 TLX  H9    H  HCR5  0   0.180  102.4710   97.3567  75.7093
 TLX  H1'1  H  HCH2  0   0.224  102.4000   99.9539  74.6919
 TLX  H1'2  H  HCH2  0   0.225  103.5267  100.9556  75.5650
 TLX  H2'   H  HCH1  0   0.213  105.3587   99.3600  75.1120
 TLX  H3'1  H  HCH2  0   0.207  104.0555  100.0900  72.4856
 TLX  H3'2  H  HCH2  0   0.213  104.4228  101.3642  73.6255
 TLX  H4'   H  HCH1  0   0.212  106.7815  100.7849  73.6516
 TLX  H5'1  H  HCH3  0   0.230  107.7161   99.2683  71.8694
 TLX  H5'2  H  HCH3  0   0.224  106.8613   98.3976  73.1228
 TLX  H5'3  H  HCH3  0   0.214  106.0882   98.6740  71.5560
 TLX  HM'1  H  HCH3  0   0.223  107.2822  101.6381  71.3753
 TLX  HM'2  H  HCH3  0   0.212  105.6577  101.2088  70.8430
 TLX  HM'3  H  HCH3  0   0.221  105.8835  102.4699  72.0541
 TLX  HN'1  H  HNH2  0   0.352  104.9651   97.6538  73.5036
 TLX  HN'2  H  HNH2  0   0.331  103.3847   97.9804  73.4713

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
 TLX  N1   C2    single  1.455  0.020  1.455
 TLX  N1   C9    single  1.451  0.020  1.451
 TLX  N1   C1'   single  1.443  0.020  1.443
 TLX  C2   C3    single  1.524  0.020  1.524
 TLX  C2   H21   single  0.970  0.020  1.090
 TLX  C2   H22   single  0.970  0.020  1.090
 TLX  C3   C4    single  1.533  0.020  1.533
 TLX  C3   H31   single  0.970  0.020  1.090
 TLX  C3   H32   single  0.970  0.020  1.090
 TLX  C4   N5    single  1.447  0.020  1.447
 TLX  C4   H41   single  0.970  0.020  1.090
 TLX  C4   H42   single  0.970  0.020  1.090
 TLX  N5   C6    single  1.450  0.020  1.450
 TLX  N5   C9    single  1.449  0.020  1.449
 TLX  C6   C7    single  1.541  0.020  1.541
 TLX  C6   H61   single  0.970  0.020  1.090
 TLX  C6   H62   single  0.970  0.020  1.090
 TLX  C7   C8    single  1.532  0.020  1.532
 TLX  C7   H71   single  0.970  0.020  1.090
 TLX  C7   H72   single  0.970  0.020  1.090
 TLX  C8   C9    single  1.525  0.020  1.525
 TLX  C8   H81   single  0.970  0.020  1.090
 TLX  C8   H82   single  0.970  0.020  1.090
 TLX  C9   H9    single  0.970  0.020  1.090
 TLX  C1'  C2'   single  1.540  0.020  1.540
 TLX  C1'  H1'1  single  0.970  0.020  1.090
 TLX  C1'  H1'2  single  0.970  0.020  1.090
 TLX  C2'  C3'   single  1.540  0.020  1.540
 TLX  C2'  N'    single  1.459  0.020  1.459
 TLX  C2'  H2'   single  0.970  0.020  1.090
 TLX  C3'  C4'   single  1.531  0.020  1.531
 TLX  C3'  H3'1  single  0.970  0.020  1.090
 TLX  C3'  H3'2  single  0.970  0.020  1.090
 TLX  C4'  C5'   single  1.526  0.020  1.526
 TLX  C4'  CM'   single  1.526  0.020  1.526
 TLX  C4'  H4'   single  0.970  0.020  1.090
 TLX  C5'  H5'1  single  0.970  0.020  1.090
 TLX  C5'  H5'2  single  0.970  0.020  1.090
 TLX  C5'  H5'3  single  0.970  0.020  1.090
 TLX  CM'  HM'1  single  0.970  0.020  1.090
 TLX  CM'  HM'2  single  0.970  0.020  1.090
 TLX  CM'  HM'3  single  0.970  0.020  1.090
 TLX  N'   HN'1  single  0.890  0.020  1.040
 TLX  N'   HN'2  single  0.890  0.020  1.040

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
 TLX  C1'   N1   C9    117.15  3.000
 TLX  C1'   N1   C2    116.77  3.000
 TLX  C9    N1   C2    114.55  3.000
 TLX  H22   C2   H21   105.80  3.000
 TLX  H22   C2   C3    109.07  3.000
 TLX  H21   C2   C3    109.52  3.000
 TLX  H22   C2   N1    110.70  3.000
 TLX  H21   C2   N1    109.17  3.000
 TLX  C3    C2   N1    112.37  3.000
 TLX  H32   C3   H31   106.63  3.000
 TLX  H32   C3   C4    110.32  3.000
 TLX  H31   C3   C4    110.31  3.000
 TLX  H32   C3   C2    110.25  3.000
 TLX  H31   C3   C2    108.88  3.000
 TLX  C4    C3   C2    110.38  3.000
 TLX  H42   C4   H41   106.33  3.000
 TLX  H42   C4   N5    108.58  3.000
 TLX  H41   C4   N5    111.67  3.000
 TLX  H42   C4   C3    110.51  3.000
 TLX  H41   C4   C3    109.76  3.000
 TLX  N5    C4   C3    109.93  3.000
 TLX  C9    N5   C6    107.99  3.000
 TLX  C9    N5   C4    114.36  3.000
 TLX  C6    N5   C4    115.17  3.000
 TLX  H62   C6   H61   106.56  3.000
 TLX  H62   C6   C7    112.86  3.000
 TLX  H61   C6   C7    110.05  3.000
 TLX  H62   C6   N5    110.65  3.000
 TLX  H61   C6   N5    111.50  3.000
 TLX  C7    C6   N5    105.30  3.000
 TLX  H72   C7   H71   106.92  3.000
 TLX  H72   C7   C8    111.87  3.000
 TLX  H71   C7   C8    110.97  3.000
 TLX  H72   C7   C6    112.42  3.000
 TLX  H71   C7   C6    110.08  3.000
 TLX  C8    C7   C6    104.65  3.000
 TLX  H82   C8   H81   108.01  3.000
 TLX  H82   C8   C9    108.48  3.000
 TLX  H81   C8   C9    112.99  3.000
 TLX  H82   C8   C7    111.13  3.000
 TLX  H81   C8   C7    112.79  3.000
 TLX  C9    C8   C7    103.35  3.000
 TLX  H9    C9   C8    108.93  3.000
 TLX  H9    C9   N5    111.12  3.000
 TLX  C8    C9   N5    102.08  3.000
 TLX  H9    C9   N1    111.67  3.000
 TLX  C8    C9   N1    114.10  3.000
 TLX  N5    C9   N1    108.57  3.000
 TLX  H1'2  C1'  H1'1  105.29  3.000
 TLX  H1'2  C1'  C2'   106.80  3.000
 TLX  H1'1  C1'  C2'   108.23  3.000
 TLX  H1'2  C1'  N1    107.80  3.000
 TLX  H1'1  C1'  N1    108.12  3.000
 TLX  C2'   C1'  N1    119.71  3.000
 TLX  H2'   C2'  N'    107.02  3.000
 TLX  H2'   C2'  C3'   107.91  3.000
 TLX  N'    C2'  C3'   114.67  3.000
 TLX  H2'   C2'  C1'   107.98  3.000
 TLX  N'    C2'  C1'   110.34  3.000
 TLX  C3'   C2'  C1'   108.70  3.000
 TLX  H3'2  C3'  H3'1  105.75  3.000
 TLX  H3'2  C3'  C4'   106.93  3.000
 TLX  H3'1  C3'  C4'   109.47  3.000
 TLX  H3'2  C3'  C2'   109.19  3.000
 TLX  H3'1  C3'  C2'   108.53  3.000
 TLX  C4'   C3'  C2'   116.46  3.000
 TLX  H4'   C4'  CM'   107.84  3.000
 TLX  H4'   C4'  C5'   107.67  3.000
 TLX  CM'   C4'  C5'   110.11  3.000
 TLX  H4'   C4'  C3'   107.34  3.000
 TLX  CM'   C4'  C3'   109.71  3.000
 TLX  C5'   C4'  C3'   113.95  3.000
 TLX  H5'3  C5'  H5'2  108.18  3.000
 TLX  H5'3  C5'  H5'1  107.46  3.000
 TLX  H5'2  C5'  H5'1  106.52  3.000
 TLX  H5'3  C5'  C4'   111.25  3.000
 TLX  H5'2  C5'  C4'   112.48  3.000
 TLX  H5'1  C5'  C4'   110.71  3.000
 TLX  HM'3  CM'  HM'2  107.63  3.000
 TLX  HM'3  CM'  HM'1  107.76  3.000
 TLX  HM'2  CM'  HM'1  107.60  3.000
 TLX  HM'3  CM'  C4'   111.45  3.000
 TLX  HM'2  CM'  C4'   110.82  3.000
 TLX  HM'1  CM'  C4'   111.41  3.000
 TLX  HN'2  N'   HN'1  105.66  3.000
 TLX  HN'2  N'   C2'   109.14  3.000
 TLX  HN'1  N'   C2'   110.28  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
 TLX  Var_01  C4    C3   C2   N1    -57.32  30.0  1
 TLX  Var_02  N5    C4   C3   C2     22.84  30.0  1
 TLX  Var_03  C9    N1   C2   C3     28.48  30.0  1
 TLX  Var_04  C6    N5   C4   C3    164.01  30.0  1
 TLX  Var_05  C7    C6   N5   C4   -155.84  30.0  1
 TLX  Var_06  C8    C7   C6   N5      1.61  30.0  1
 TLX  Var_07  C9    C8   C7   C6     22.07  30.0  1
 TLX  Var_08  C2'   C1'  N1   C2     58.85  30.0  3
 TLX  Var_09  C5'   C4'  C3'  C2'    58.60  30.0  3
 TLX  Var_10  H5'1  C5'  C4'  C3'   173.80  30.0  3
 TLX  Var_11  HM'1  CM'  C4'  C3'   176.26  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
 TLX  chir_01  C9   N1  N5   C8   negativ
 TLX  chir_02  C2'  N'  C1'  C3'  positiv

