# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 09:14:04 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 5-(aminomethyl)thiophene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1sc(cc1)C(N)=N
#
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
 02D  02D  5-(aminomethyl)thiophene-2-carboximidamide  ligand  19  10  .  2021-07-27  2021-07-27  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_02D
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
 02D  C1    C  CR5   0  -0.216  -0.9510  -0.3313   0.0909
 02D  C2    C  CR15  0  -0.191  -0.4097  -1.5799  -0.0124
 02D  C3    C  CR15  0  -0.205   1.0019  -1.5798   0.1051
 02D  C4    C  CR5   0  -0.155   1.5265  -0.3362   0.3077
 02D  S5    S  S2    0   0.230   0.2791   0.8482   0.3537
 02D  C6    C  C     0   0.333  -2.3771   0.0296   0.0271
 02D  N7    N  N     0  -0.644  -3.2413  -0.8631   0.3209
 02D  N8    N  NH2   0  -0.826  -2.6244   1.3370  -0.2962
 02D  C9    C  CH2   0  -0.359   2.9639   0.0608   0.4302
 02D  N10   N  NH2   0  -0.786   3.4835   0.5426  -0.8449
 02D  H2    H  HCR5  0   0.265  -1.0070  -2.4650  -0.1776
 02D  H3    H  HCR5  0   0.266   1.6138  -2.4693   0.0414
 02D  HN7   H  H     0   0.327  -4.1863  -0.5133   0.1874
 02D  HN81  H  HNH2  0   0.394  -1.9955   1.7901  -0.9409
 02D  HN82  H  HNH2  0   0.393  -3.5881   1.5901  -0.4500
 02D  H91   H  HCH2  0   0.225   3.0757   0.7774   1.2537
 02D  H92   H  HCH2  0   0.251   3.5284  -0.8277   0.7178
 02D  HN10  H  HNH2  0   0.342   3.0395   1.4226  -1.0784
 02D  H1    H  HNH2  0   0.355   4.4664   0.7590  -0.7316

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
 02D  C1   C2    aromatic  1.365  0.020  1.365
 02D  C1   S5    aromatic  1.724  0.020  1.724
 02D  C1   C6    single    1.472  0.020  1.472
 02D  C2   C3    aromatic  1.416  0.020  1.416
 02D  C2   H2    single    0.930  0.020  1.080
 02D  C3   C4    aromatic  1.365  0.020  1.365
 02D  C3   H3    single    0.930  0.020  1.080
 02D  C4   S5    aromatic  1.721  0.020  1.721
 02D  C4   C9    single    1.496  0.020  1.496
 02D  C6   N7    double    1.277  0.020  1.277
 02D  C6   N8    single    1.369  0.020  1.369
 02D  N7   HN7   single    0.890  0.020  1.040
 02D  N8   HN81  single    0.890  0.020  1.040
 02D  N8   HN82  single    0.890  0.020  1.040
 02D  C9   N10   single    1.459  0.020  1.459
 02D  C9   H91   single    0.970  0.020  1.090
 02D  C9   H92   single    0.970  0.020  1.090
 02D  N10  HN10  single    0.890  0.020  1.040
 02D  N10  H1    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
 02D  C6    C1   S5    121.99  3.000
 02D  C6    C1   C2    127.24  3.000
 02D  S5    C1   C2    110.76  3.000
 02D  H2    C2   C3    124.31  3.000
 02D  H2    C2   C1    122.80  3.000
 02D  C3    C2   C1    112.89  3.000
 02D  H3    C3   C4    122.73  3.000
 02D  H3    C3   C2    123.98  3.000
 02D  C4    C3   C2    113.29  3.000
 02D  C9    C4   S5    120.77  3.000
 02D  C9    C4   C3    128.55  3.000
 02D  S5    C4   C3    110.64  3.000
 02D  C4    S5   C1     92.42  3.000
 02D  N8    C6   N7    126.85  3.000
 02D  N8    C6   C1    114.78  3.000
 02D  N7    C6   C1    118.31  3.000
 02D  HN7   N7   C6    111.01  3.000
 02D  HN82  N8   HN81  112.71  3.000
 02D  HN82  N8   C6    116.63  3.000
 02D  HN81  N8   C6    117.86  3.000
 02D  H92   C9   H91   106.33  3.000
 02D  H92   C9   N10   108.36  3.000
 02D  H91   C9   N10   113.83  3.000
 02D  H92   C9   C4    107.60  3.000
 02D  H91   C9   C4    109.42  3.000
 02D  N10   C9   C4    110.99  3.000
 02D  H1    N10  HN10  105.40  3.000
 02D  H1    N10  C9    108.57  3.000
 02D  HN10  N10  C9    109.41  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
 02D  CONST_01  C4    C3   C2  C1    0.00   0.0  0
 02D  CONST_02  C3    C4   S5  C1    0.00   0.0  0
 02D  CONST_03  C4    S5   C1  C2    0.00   0.0  0
 02D  CONST_04  S5    C4   C3  C2    0.00   0.0  0
 02D  CONST_05  S5    C1   C2  C3    0.00   0.0  0
 02D  CONST_06  C9    C4   S5  C1  180.00   0.0  0
 02D  CONST_07  C9    C4   C3  C2  180.00   0.0  0
 02D  CONST_08  C6    C1   C2  C3  180.00   0.0  0
 02D  CONST_09  C6    C1   S5  C4  180.00   0.0  0
 02D  CONST_10  H3    C3   C2  C1  180.00   0.0  0
 02D  CONST_11  H2    C2   C3  C4  180.00   0.0  0
 02D  CONST_12  HN7   N7   C6  C1  180.00   0.0  0
 02D  CONST_14  HN82  N8   C6  C1  180.00   0.0  0
 02D  Var_01    N7    C6   C1  C2   23.92  30.0  2
 02D  Var_02    N10   C9   C4  C3   96.67  30.0  2
 02D  Var_03    HN10  N10  C9  C4   68.10  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
 02D  plan-1  C1    0.020
 02D  plan-1  C2    0.020
 02D  plan-1  C3    0.020
 02D  plan-1  C4    0.020
 02D  plan-1  S5    0.020
 02D  plan-1  C6    0.020
 02D  plan-1  C9    0.020
 02D  plan-1  H2    0.020
 02D  plan-1  H3    0.020
 02D  plan-2  C1    0.020
 02D  plan-2  C6    0.020
 02D  plan-2  N7    0.020
 02D  plan-2  N8    0.020
 02D  plan-2  HN7   0.020
 02D  plan-2  HN81  0.020
 02D  plan-2  HN82  0.020

