# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 18:54:42 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: 2-[[(2~{S})-2-azanylpropyl]-methyl-amino]ethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)CN(C)CCO
#
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
 C9N  C9N  2-[[(2~{S})-2-azanylpropyl]-methyl-amino]ethanol  ligand  25  9  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_C9N
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
 C9N  C1   C  CH1   0  -0.128   1.9734  -0.0041   0.0884
 C9N  C2   C  CH2   0  -0.251   0.6297   0.1679  -0.6173
 C9N  C3   C  CH2   0  -0.291  -1.7106   0.7132  -0.4828
 C9N  C4   C  CH2   0  -0.176  -2.2807  -0.6519  -0.8129
 C9N  N2   N  NT    0  -0.394  -0.4354   0.6956   0.2086
 C9N  N    N  NH2   0  -0.779   1.7938  -0.7064   1.3513
 C9N  C1B  C  CH3   0  -0.663   2.9494  -0.6907  -0.8665
 C9N  CN   C  CH3   0  -0.528  -0.1203   2.0067   0.7299
 C9N  O    O  OH1   0  -0.669  -2.4480  -1.3961   0.3724
 C9N  H1   H  HCH1  0   0.220   2.3855   0.9835   0.3219
 C9N  H2   H  HCH2  0   0.187   0.7938   0.7910  -1.5163
 C9N  H3   H  HCH2  0   0.224   0.3276  -0.8174  -0.9851
 C9N  H31  H  HCH2  0   0.187  -1.6677   1.2882  -1.4257
 C9N  H32  H  HCH2  0   0.228  -2.4298   1.2350   0.1557
 C9N  H5   H  HNH2  0   0.330   1.3295  -1.5912   1.1784
 C9N  H6   H  HNH2  0   0.339   2.7022  -0.9428   1.7334
 C9N  HB3  H  HCH3  0   0.218   3.0912  -0.1180  -1.7852
 C9N  HB2  H  HCH3  0   0.229   3.9273  -0.8106  -0.3972
 C9N  HB1  H  HCH3  0   0.215   2.5869  -1.6838  -1.1434
 C9N  HN2  H  HCH3  0   0.184   0.0738   2.7562  -0.0553
 C9N  HN1  H  HCH3  0   0.229  -0.9527   2.3729   1.3329
 C9N  HN3  H  HCH3  0   0.237   0.7543   1.9638   1.3780
 C9N  H    H  HOH1  0   0.451  -2.8677  -2.2287   0.1396
 C9N  H42  H  HCH2  0   0.205  -3.2372  -0.4821  -1.3247
 C9N  H4   H  HCH2  0   0.195  -1.6408  -1.1787  -1.5318

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
 C9N  N    C1   single  1.456  0.020  1.456
 C9N  C1B  C1   single  1.528  0.020  1.528
 C9N  C1   C2   single  1.528  0.020  1.528
 C9N  C2   N2   single  1.447  0.020  1.447
 C9N  CN   N2   single  1.446  0.020  1.446
 C9N  N2   C3   single  1.451  0.020  1.451
 C9N  C3   C4   single  1.516  0.020  1.516
 C9N  C4   O    single  1.409  0.020  1.409
 C9N  C1   H1   single  0.970  0.020  1.090
 C9N  C2   H2   single  0.970  0.020  1.090
 C9N  C2   H3   single  0.970  0.020  1.090
 C9N  C3   H31  single  0.970  0.020  1.090
 C9N  C3   H32  single  0.970  0.020  1.090
 C9N  N    H5   single  0.890  0.020  1.040
 C9N  N    H6   single  0.890  0.020  1.040
 C9N  C1B  HB3  single  0.970  0.020  1.090
 C9N  C1B  HB2  single  0.970  0.020  1.090
 C9N  C1B  HB1  single  0.970  0.020  1.090
 C9N  CN   HN2  single  0.970  0.020  1.090
 C9N  CN   HN1  single  0.970  0.020  1.090
 C9N  CN   HN3  single  0.970  0.020  1.090
 C9N  O    H    single  0.850  0.020  0.980
 C9N  C4   H42  single  0.970  0.020  1.090
 C9N  C4   H4   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
 C9N  H1   C1   C1B  107.34  3.000
 C9N  H1   C1   N    107.24  3.000
 C9N  C1B  C1   N    113.83  3.000
 C9N  H1   C1   C2   109.14  3.000
 C9N  C1B  C1   C2   108.88  3.000
 C9N  N    C1   C2   110.28  3.000
 C9N  H3   C2   H2   105.96  3.000
 C9N  H3   C2   N2   108.48  3.000
 C9N  H2   C2   N2   111.57  3.000
 C9N  H3   C2   C1   107.26  3.000
 C9N  H2   C2   C1   107.97  3.000
 C9N  N2   C2   C1   115.13  3.000
 C9N  H32  C3   H31  105.98  3.000
 C9N  H32  C3   N2   107.78  3.000
 C9N  H31  C3   N2   112.26  3.000
 C9N  H32  C3   C4   108.02  3.000
 C9N  H31  C3   C4   107.29  3.000
 C9N  N2   C3   C4   115.05  3.000
 C9N  H4   C4   H42  106.07  3.000
 C9N  H4   C4   O    111.52  3.000
 C9N  H42  C4   O    111.73  3.000
 C9N  H4   C4   C3   110.84  3.000
 C9N  H42  C4   C3   106.85  3.000
 C9N  O    C4   C3   109.70  3.000
 C9N  CN   N2   C3   110.64  3.000
 C9N  C3   N2   C2   112.29  3.000
 C9N  CN   N2   C2   112.09  3.000
 C9N  H6   N    H5   105.73  3.000
 C9N  H6   N    C1   109.20  3.000
 C9N  H5   N    C1   109.23  3.000
 C9N  HB1  C1B  HB2  107.84  3.000
 C9N  HB1  C1B  HB3  107.85  3.000
 C9N  HB2  C1B  HB3  107.64  3.000
 C9N  HB1  C1B  C1   110.78  3.000
 C9N  HB2  C1B  C1   110.67  3.000
 C9N  HB3  C1B  C1   111.90  3.000
 C9N  HN3  CN   HN1  107.27  3.000
 C9N  HN3  CN   HN2  108.01  3.000
 C9N  HN1  CN   HN2  107.43  3.000
 C9N  HN3  CN   N2   110.72  3.000
 C9N  HN1  CN   N2   109.72  3.000
 C9N  HN2  CN   N2   113.45  3.000
 C9N  H    O    C4   107.79  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
 C9N  Var_01  CN   N2  C2  C1  60.28  30.0  3
 C9N  Var_02  C4   C3  N2  C2  66.33  30.0  3
 C9N  Var_03  O    C4  C3  N2  58.51  30.0  3
 C9N  Var_04  HN2  CN  N2  C2  59.01  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
 C9N  chir_01  C1  N  C1B  C2  negativ

