# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 09:18:50 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 5-(aminomethyl)-1-methyl-1H-pyrrole-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c(CN)ccc1C(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
 01Q  01Q  5-(aminomethyl)-1-methyl-1H-pyrrole-2-carboximidamide  ligand  23  11  .  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_01Q
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
 01Q  N     N  N     0  -0.645   3.1264   0.5221  -0.8605
 01Q  C     C  C     0   0.302   2.2417  -0.1165  -0.1908
 01Q  N1    N  NH2   0  -0.801   2.5517  -1.3145   0.3868
 01Q  C1    C  CR5   0   0.223   0.8693   0.3748   0.0167
 01Q  N2    N  NR5   0  -0.496  -0.2655  -0.3956   0.0782
 01Q  C2    C  CH3   0  -0.550  -0.3614  -1.8250  -0.1492
 01Q  C3    C  CR15  0  -0.353   0.5043   1.6867   0.2319
 01Q  C4    C  CR15  0  -0.389  -0.8879   1.7052   0.4375
 01Q  C5    C  CR5   0   0.333  -1.3386   0.4080   0.3324
 01Q  C6    C  CH2   0  -0.397  -2.7404  -0.0955   0.4258
 01Q  N3    N  NH2   0  -0.787  -3.2456  -0.5148  -0.8773
 01Q  H     H  H     0   0.328   2.7101   1.3278  -1.3117
 01Q  H11A  H  HNH2  0   0.384   3.5288  -1.5627   0.3786
 01Q  H12   H  HNH2  0   0.391   2.0744  -1.5712   1.2348
 01Q  H21   H  HCH3  0   0.248  -0.1887  -2.3898   0.7667
 01Q  H22   H  HCH3  0   0.273  -1.3542  -2.0510  -0.5261
 01Q  H23   H  HCH3  0   0.262   0.3652  -2.1380  -0.8927
 01Q  H3    H  HCR5  0   0.253   1.1814   2.5260   0.2711
 01Q  H4    H  HCR5  0   0.245  -1.5063   2.5654   0.6432
 01Q  H61   H  HCH2  0   0.244  -2.7898  -0.9560   1.0983
 01Q  H62   H  HCH2  0   0.234  -3.3368   0.6943   0.8980
 01Q  HN3   H  HNH2  0   0.354  -4.1767  -0.8962  -0.7655
 01Q  H2    H  HNH2  0   0.344  -3.3443   0.2976  -1.4733

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
 01Q  N   C     double    1.280  0.020  1.280
 01Q  N   H     single    0.860  0.020  1.020
 01Q  C   N1    single    1.366  0.020  1.366
 01Q  C   C1    single    1.472  0.020  1.472
 01Q  N1  H11A  single    0.890  0.020  1.040
 01Q  N1  H12   single    0.890  0.020  1.040
 01Q  C1  N2    aromatic  1.373  0.020  1.373
 01Q  C1  C3    aromatic  1.379  0.020  1.379
 01Q  N2  C2    single    1.451  0.020  1.451
 01Q  N2  C5    aromatic  1.364  0.020  1.364
 01Q  C2  H21   single    0.970  0.020  1.090
 01Q  C2  H22   single    0.970  0.020  1.090
 01Q  C2  H23   single    0.970  0.020  1.090
 01Q  C3  C4    aromatic  1.407  0.020  1.407
 01Q  C3  H3    single    0.930  0.020  1.080
 01Q  C4  C5    aromatic  1.377  0.020  1.377
 01Q  C4  H4    single    0.930  0.020  1.080
 01Q  C5  C6    single    1.492  0.020  1.492
 01Q  C6  N3    single    1.459  0.020  1.459
 01Q  C6  H61   single    0.970  0.020  1.090
 01Q  C6  H62   single    0.970  0.020  1.090
 01Q  N3  HN3   single    0.890  0.020  1.040
 01Q  N3  H2    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
 01Q  H     N   C     110.23  3.000
 01Q  C1    C   N1    116.40  3.000
 01Q  C1    C   N     123.46  3.000
 01Q  N1    C   N     120.13  3.000
 01Q  H12   N1  H11A  113.81  3.000
 01Q  H12   N1  C     118.20  3.000
 01Q  H11A  N1  C     115.63  3.000
 01Q  C3    C1  N2    107.95  3.000
 01Q  C3    C1  C     125.90  3.000
 01Q  N2    C1  C     126.12  3.000
 01Q  C5    N2  C2    123.89  3.000
 01Q  C5    N2  C1    109.14  3.000
 01Q  C2    N2  C1    126.91  3.000
 01Q  H23   C2  H22   108.31  3.000
 01Q  H23   C2  H21   108.68  3.000
 01Q  H22   C2  H21   109.19  3.000
 01Q  H23   C2  N2    110.32  3.000
 01Q  H22   C2  N2    108.66  3.000
 01Q  H21   C2  N2    111.62  3.000
 01Q  H3    C3  C4    127.24  3.000
 01Q  H3    C3  C1    125.43  3.000
 01Q  C4    C3  C1    107.29  3.000
 01Q  H4    C4  C5    125.30  3.000
 01Q  H4    C4  C3    127.24  3.000
 01Q  C5    C4  C3    107.47  3.000
 01Q  C6    C5  C4    128.34  3.000
 01Q  C6    C5  N2    123.48  3.000
 01Q  C4    C5  N2    108.16  3.000
 01Q  H62   C6  H61   106.11  3.000
 01Q  H62   C6  N3    113.78  3.000
 01Q  H61   C6  N3    107.91  3.000
 01Q  H62   C6  C5    107.15  3.000
 01Q  H61   C6  C5    110.27  3.000
 01Q  N3    C6  C5    111.48  3.000
 01Q  H2    N3  HN3   106.13  3.000
 01Q  H2    N3  C6    109.20  3.000
 01Q  HN3   N3  C6    109.15  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
 01Q  CONST_01  C4    C5  N2  C1    0.00   0.0  0
 01Q  CONST_02  C5    C4  C3  C1    0.00   0.0  0
 01Q  CONST_03  C4    C3  C1  N2    0.00   0.0  0
 01Q  CONST_04  C3    C4  C5  N2    0.00   0.0  0
 01Q  CONST_05  C5    N2  C1  C3    0.00   0.0  0
 01Q  CONST_06  C5    N2  C1  C   180.00   0.0  0
 01Q  CONST_07  C4    C3  C1  C   180.00   0.0  0
 01Q  CONST_08  C6    C5  N2  C1  180.00   0.0  0
 01Q  CONST_09  C3    C1  N2  C2  180.00   0.0  0
 01Q  CONST_10  C4    C5  N2  C2  180.00   0.0  0
 01Q  CONST_11  C6    C5  C4  C3  180.00   0.0  0
 01Q  CONST_12  H4    C4  C3  C1  180.00   0.0  0
 01Q  CONST_13  H3    C3  C1  N2  180.00   0.0  0
 01Q  CONST_14  H     N   C   C1    0.00   0.0  0
 01Q  CONST_15  H11A  N1  C   C1  180.00   0.0  0
 01Q  Var_01    N2    C1  C   N   144.62  30.0  2
 01Q  Var_02    N3    C6  C5  N2  -70.01  30.0  2
 01Q  Var_03    H21   C2  N2  C1   88.17  30.0  2
 01Q  Var_04    HN3   N3  C6  C5  176.91  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
 01Q  plan-1  C     0.020
 01Q  plan-1  C1    0.020
 01Q  plan-1  N2    0.020
 01Q  plan-1  C2    0.020
 01Q  plan-1  C3    0.020
 01Q  plan-1  C4    0.020
 01Q  plan-1  C5    0.020
 01Q  plan-1  C6    0.020
 01Q  plan-1  H3    0.020
 01Q  plan-1  H4    0.020
 01Q  plan-2  N     0.020
 01Q  plan-2  C     0.020
 01Q  plan-2  N1    0.020
 01Q  plan-2  C1    0.020
 01Q  plan-2  H     0.020
 01Q  plan-2  H11A  0.020
 01Q  plan-2  H12   0.020

