# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 13:14:15 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: (1~{S})-~{N}'-(4-azanylbutyl)-~{N}"-(2-methoxyethyl)methanetriamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCN[C@@H](N)NCCCCN
#
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
 M3B  M3B  "(1~{S})-~{N}'-(4-azanylbutyl)-~{N}"-(2-methoxyethyl)methanetriamine"
  ligand  35  13  .  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_M3B
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
 M3B  C01  C  CH2   0  -0.242  -1.7605  -0.5760   0.0050
 M3B  C02  C  CH2   0  -0.440  -2.8514   0.4822   0.0718
 M3B  C03  C  CH2   0  -0.429  -4.2490  -0.1190   0.0021
 M3B  C04  C  CH2   0  -0.271  -5.3445   0.9352   0.0130
 M3B  C07  C  CH1   0   0.190   0.6527  -0.8471  -0.2433
 M3B  C12  C  CH2   0  -0.148   4.2355   0.1928  -0.7583
 M3B  C14  C  CH3   0  -0.393   5.6432   1.4829   0.5974
 M3B  N05  N  NH2   0  -0.801  -6.6638   0.3212  -0.0455
 M3B  N06  N  NH1   0  -0.616  -0.4437   0.0280   0.0955
 M3B  N08  N  NH2   0  -0.797   0.6354  -2.0794   0.5342
 M3B  N10  N  NH1   0  -0.610   1.8720  -0.0612  -0.1915
 M3B  O13  O  O2    0  -0.488   4.6021   0.5427   0.5550
 M3B  H01  H  HCH2  0   0.192  -1.9409  -1.3386   0.7739
 M3B  H02  H  HCH2  0   0.209  -1.8267  -1.0968  -0.9556
 M3B  H04  H  HCH2  0   0.212  -2.7493   1.0563   1.0001
 M3B  H03  H  HCH2  0   0.212  -2.7110   1.1945  -0.7472
 M3B  H06  H  HCH2  0   0.212  -4.3481  -0.7273  -0.9028
 M3B  H05  H  HCH2  0   0.211  -4.3931  -0.8009   0.8479
 M3B  H08  H  HCH2  0   0.186  -5.2037   1.5874   0.8878
 M3B  H07  H  HCH2  0   0.211  -5.2280   1.5772  -0.8646
 M3B  H1   H  HCH1  0   0.221   0.5200  -1.1493  -1.2887
 M3B  H12  H  HCH2  0   0.231   2.8363  -1.0583  -1.7344
 M3B  H11  H  HCH2  0   0.197   3.3245  -1.6447  -0.1530
 M3B  H13  H  HCH2  0   0.203   5.0673  -0.3053  -1.2757
 M3B  H14  H  HCH2  0   0.196   3.9775   1.0871  -1.3431
 M3B  H17  H  HCH3  0   0.203   5.3672   2.4244   0.1076
 M3B  H15  H  HCH3  0   0.233   5.8683   1.6923   1.6427
 M3B  H16  H  HCH3  0   0.202   6.5559   1.1110   0.1166
 M3B  H18  H  HNH2  0   0.336  -6.8415  -0.1681   0.8234
 M3B  H19  H  HNH2  0   0.345  -7.3706   1.0437  -0.0974
 M3B  H2   H  HNH1  0   0.334  -0.3087   0.4062   1.0278
 M3B  H3   H  HNH2  0   0.348   1.3450  -2.7205   0.2000
 M3B  H2C  H  HNH2  0   0.333   0.8583  -1.8850   1.5051
 M3B  H4   H  HNH1  0   0.334   2.0492   0.2280   0.7653
 M3B  C11  C  CH2   0  -0.315   3.0442  -0.7375  -0.7096

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
 M3B  C11  C12  single  1.512  0.020  1.512
 M3B  C11  N10  single  1.449  0.020  1.449
 M3B  C12  O13  single  1.408  0.020  1.408
 M3B  O13  C14  single  1.403  0.020  1.403
 M3B  N08  C07  single  1.457  0.020  1.457
 M3B  N10  C07  single  1.452  0.020  1.452
 M3B  C07  N06  single  1.443  0.020  1.443
 M3B  C04  N05  single  1.456  0.020  1.456
 M3B  C04  C03  single  1.520  0.020  1.520
 M3B  C02  C03  single  1.523  0.020  1.523
 M3B  C02  C01  single  1.521  0.020  1.521
 M3B  N06  C01  single  1.452  0.020  1.452
 M3B  C01  H01  single  0.970  0.020  1.090
 M3B  C01  H02  single  0.970  0.020  1.090
 M3B  C02  H04  single  0.970  0.020  1.090
 M3B  C02  H03  single  0.970  0.020  1.090
 M3B  C03  H06  single  0.970  0.020  1.090
 M3B  C03  H05  single  0.970  0.020  1.090
 M3B  C04  H08  single  0.970  0.020  1.090
 M3B  C04  H07  single  0.970  0.020  1.090
 M3B  C07  H1   single  0.970  0.020  1.090
 M3B  C11  H12  single  0.970  0.020  1.090
 M3B  C11  H11  single  0.970  0.020  1.090
 M3B  C12  H13  single  0.970  0.020  1.090
 M3B  C12  H14  single  0.970  0.020  1.090
 M3B  C14  H17  single  0.970  0.020  1.090
 M3B  C14  H15  single  0.970  0.020  1.090
 M3B  C14  H16  single  0.970  0.020  1.090
 M3B  N05  H18  single  0.890  0.020  1.040
 M3B  N05  H19  single  0.890  0.020  1.040
 M3B  N06  H2   single  0.890  0.020  1.040
 M3B  N08  H3   single  0.890  0.020  1.040
 M3B  N08  H2C  single  0.890  0.020  1.040
 M3B  N10  H4   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
 M3B  H02  C01  H01  105.91  3.000
 M3B  H02  C01  N06  107.91  3.000
 M3B  H01  C01  N06  113.23  3.000
 M3B  H02  C01  C02  109.03  3.000
 M3B  H01  C01  C02  109.55  3.000
 M3B  N06  C01  C02  111.00  3.000
 M3B  H03  C02  H04  106.32  3.000
 M3B  H03  C02  C03  109.89  3.000
 M3B  H04  C02  C03  109.33  3.000
 M3B  H03  C02  C01  109.14  3.000
 M3B  H04  C02  C01  109.55  3.000
 M3B  C03  C02  C01  112.42  3.000
 M3B  H05  C03  H06  106.27  3.000
 M3B  H05  C03  C04  109.34  3.000
 M3B  H06  C03  C04  109.02  3.000
 M3B  H05  C03  C02  109.33  3.000
 M3B  H06  C03  C02  109.89  3.000
 M3B  C04  C03  C02  112.78  3.000
 M3B  H07  C04  H08  106.05  3.000
 M3B  H07  C04  N05  108.17  3.000
 M3B  H08  C04  N05  113.44  3.000
 M3B  H07  C04  C03  108.94  3.000
 M3B  H08  C04  C03  108.93  3.000
 M3B  N05  C04  C03  111.11  3.000
 M3B  H1   C07  N10  106.56  3.000
 M3B  H1   C07  N08  105.92  3.000
 M3B  N10  C07  N08  116.67  3.000
 M3B  H1   C07  N06  107.40  3.000
 M3B  N10  C07  N06  107.55  3.000
 M3B  N08  C07  N06  112.24  3.000
 M3B  H14  C12  H13  107.21  3.000
 M3B  H14  C12  O13  110.81  3.000
 M3B  H13  C12  O13  110.78  3.000
 M3B  H14  C12  C11  109.43  3.000
 M3B  H13  C12  C11  109.43  3.000
 M3B  O13  C12  C11  109.15  3.000
 M3B  H16  C14  H15  108.29  3.000
 M3B  H16  C14  H17  107.75  3.000
 M3B  H15  C14  H17  108.39  3.000
 M3B  H16  C14  O13  112.15  3.000
 M3B  H15  C14  O13  108.12  3.000
 M3B  H17  C14  O13  112.03  3.000
 M3B  H19  N05  H18  105.45  3.000
 M3B  H19  N05  C04  109.50  3.000
 M3B  H18  N05  C04  109.15  3.000
 M3B  H2   N06  C07  109.91  3.000
 M3B  H2   N06  C01  109.44  3.000
 M3B  C07  N06  C01  114.98  3.000
 M3B  H2C  N08  H3   106.43  3.000
 M3B  H2C  N08  C07  110.24  3.000
 M3B  H3   N08  C07  110.54  3.000
 M3B  H4   N10  C11  109.19  3.000
 M3B  H4   N10  C07  109.55  3.000
 M3B  C11  N10  C07  114.46  3.000
 M3B  C14  O13  C12  112.82  3.000
 M3B  H11  C11  H12  106.29  3.000
 M3B  H11  C11  N10  114.20  3.000
 M3B  H12  C11  N10  108.55  3.000
 M3B  H11  C11  C12  108.83  3.000
 M3B  H12  C11  C12  107.45  3.000
 M3B  N10  C11  C12  111.20  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
 M3B  Var_01  C04  C03  C02  C01  -177.73  30.0  3
 M3B  Var_02  N05  C04  C03  C02  -179.61  30.0  1
 M3B  Var_03  C07  N06  C01  C02  -167.31  30.0  1
 M3B  Var_04  N06  C01  C02  C03  -179.08  30.0  3
 M3B  Var_05  C12  C11  N10  C07   173.92  30.0  1
 M3B  Var_06  O13  C12  C11  N10    66.05  30.0  3
 M3B  Var_07  H18  N05  C04  C03    68.66  30.0  3
 M3B  Var_08  H17  C14  O13  C12    61.00  30.0  3
 M3B  Var_09  H13  C12  O13  C14    63.74  30.0  1

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
 M3B  chir_01  C07  N08  N10  N06  positiv

