# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 07:50:52 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 3,5-diamino-N-carbamimidoyl-6-(1-methyl-1H-pyrazol-4-yl)pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)c2nc(c(N)nc2N)C(=O)NC(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
 H55  H55  3,5-diamino-N-carbamimidoyl-6-(1-methyl-1H-pyrazol-4-yl)pyrazine-2-carboxamide  ligand  33  20  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H55
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
 H55  O1   O  O     0  -0.469  -3.6006  -0.8860  -0.1081
 H55  C7   C  C     0   0.558  -2.5316  -0.2956  -0.0609
 H55  N4   N  NH1   0  -0.712  -2.3999   1.0632  -0.0300
 H55  C8   C  C     0   0.554  -3.3960   2.0347  -0.0480
 H55  N6   N  N     0  -0.657  -4.5889   1.7692  -0.4013
 H55  N5   N  NH2   0  -0.841  -2.8849   3.2676   0.2794
 H55  C6   C  CR6   0  -0.058  -1.2360  -0.9982  -0.0190
 H55  N3   N  N     0  -0.417  -0.1334  -0.2516   0.0255
 H55  C9   C  CR6   0   0.475  -1.1170  -2.4091   0.0006
 H55  N7   N  NH2   0  -0.836  -2.1615  -3.2431   0.0124
 H55  N8   N  N     0  -0.467   0.0962  -2.9701   0.0094
 H55  C10  C  CR6   0   0.417   1.1714  -2.2055   0.0268
 H55  N9   N  NH2   0  -0.829   2.3700  -2.8155   0.0249
 H55  C5   C  CR6   0   0.078   1.0620  -0.7778   0.0658
 H55  C4   C  CR5   0  -0.167   2.2150   0.1171   0.1119
 H55  C1   C  CR15  0   0.049   2.2866   1.3715  -0.4653
 H55  C3   C  CR15  0  -0.110   3.4546  -0.0113   0.7737
 H55  N2   N  N     0  -0.277   4.2037   1.0624   0.6078
 H55  N1   N  NR5   0  -0.261   3.4806   1.8867  -0.1420
 H55  C2   C  CH3   0  -0.507   4.0252   3.1586  -0.5545
 H55  H1   H  HNH1  0   0.410  -1.4397   1.3789   0.0280
 H55  H2   H  H     0   0.327  -5.1705   2.5953  -0.3116
 H55  H3   H  HNH2  0   0.392  -2.1402   3.2965   0.9590
 H55  H4   H  HNH2  0   0.394  -3.5643   3.9972   0.4242
 H55  H5   H  HNH2  0   0.412  -3.0989  -2.8857  -0.0511
 H55  H6   H  HNH2  0   0.394  -1.9979  -4.2341  -0.0245
 H55  H7   H  HNH2  0   0.399   2.3886  -3.8071  -0.1491
 H55  H8   H  HNH2  0   0.407   3.1947  -2.3072  -0.2454
 H55  H9   H  HCR5  0   0.291   1.5779   1.9069  -1.0760
 H55  H10  H  HCR5  0   0.265   3.8128  -0.8282   1.3821
 H55  H11  H  HCH3  0   0.262   4.8364   3.0153  -1.2658
 H55  H12  H  HCH3  0   0.260   3.2405   3.7428  -1.0255
 H55  H13  H  HCH3  0   0.264   4.3990   3.7003   0.3111

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
 H55  C2   N1   single    1.444  0.020  1.444
 H55  N2   N1   aromatic  1.328  0.020  1.328
 H55  N2   C3   aromatic  1.320  0.020  1.320
 H55  N1   C1   aromatic  1.340  0.020  1.340
 H55  C3   C4   aromatic  1.411  0.020  1.411
 H55  C1   C4   aromatic  1.383  0.020  1.383
 H55  C4   C5   single    1.460  0.020  1.460
 H55  C5   N3   aromatic  1.307  0.020  1.307
 H55  C5   C10  aromatic  1.432  0.020  1.432
 H55  N6   C8   double    1.272  0.020  1.272
 H55  N3   C6   aromatic  1.332  0.020  1.332
 H55  N9   C10  single    1.345  0.020  1.345
 H55  C10  N8   aromatic  1.319  0.020  1.319
 H55  N4   C8   single    1.392  0.020  1.392
 H55  N4   C7   single    1.366  0.020  1.366
 H55  C8   N5   single    1.374  0.020  1.374
 H55  C6   C7   single    1.475  0.020  1.475
 H55  C6   C9   aromatic  1.416  0.020  1.416
 H55  C7   O1   double    1.222  0.020  1.222
 H55  N8   C9   aromatic  1.337  0.020  1.337
 H55  C9   N7   single    1.337  0.020  1.337
 H55  N4   H1   single    0.860  0.020  1.020
 H55  N6   H2   single    0.890  0.020  1.040
 H55  N5   H3   single    0.890  0.020  1.040
 H55  N5   H4   single    0.890  0.020  1.040
 H55  N7   H5   single    0.860  0.020  1.020
 H55  N7   H6   single    0.860  0.020  1.020
 H55  N9   H7   single    0.890  0.020  1.040
 H55  N9   H8   single    0.890  0.020  1.040
 H55  C1   H9   single    0.930  0.020  1.080
 H55  C3   H10  single    0.930  0.020  1.080
 H55  C2   H11  single    0.970  0.020  1.090
 H55  C2   H12  single    0.970  0.020  1.090
 H55  C2   H13  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
 H55  C6   C7   N4   112.88  3.000
 H55  C6   C7   O1   122.65  3.000
 H55  N4   C7   O1   124.47  3.000
 H55  H1   N4   C8   117.51  3.000
 H55  H1   N4   C7   113.77  3.000
 H55  C8   N4   C7   128.71  3.000
 H55  N5   C8   N6   127.03  3.000
 H55  N5   C8   N4   110.92  3.000
 H55  N6   C8   N4   121.95  3.000
 H55  H2   N6   C8   110.07  3.000
 H55  H4   N5   H3   112.35  3.000
 H55  H4   N5   C8   115.67  3.000
 H55  H3   N5   C8   117.45  3.000
 H55  C9   C6   N3   119.23  3.000
 H55  C9   C6   C7   123.30  3.000
 H55  N3   C6   C7   117.46  3.000
 H55  C5   N3   C6   122.17  3.000
 H55  N8   C9   N7   116.57  3.000
 H55  N7   C9   C6   123.79  3.000
 H55  N8   C9   C6   119.64  3.000
 H55  H6   N7   H5   120.00  3.000
 H55  H6   N7   C9   119.19  3.000
 H55  H5   N7   C9   120.42  3.000
 H55  C10  N8   C9   119.76  3.000
 H55  C5   C10  N9   121.35  3.000
 H55  N9   C10  N8   117.60  3.000
 H55  C5   C10  N8   121.05  3.000
 H55  H8   N9   H7   115.85  3.000
 H55  H8   N9   C10  120.12  3.000
 H55  H7   N9   C10  117.61  3.000
 H55  C4   C5   C10  123.46  3.000
 H55  C10  C5   N3   118.06  3.000
 H55  C4   C5   N3   118.46  3.000
 H55  C3   C4   C1   103.46  3.000
 H55  C1   C4   C5   125.71  3.000
 H55  C3   C4   C5   130.74  3.000
 H55  H9   C1   N1   122.12  3.000
 H55  H9   C1   C4   130.77  3.000
 H55  N1   C1   C4   107.11  3.000
 H55  H10  C3   N2   119.87  3.000
 H55  H10  C3   C4   128.65  3.000
 H55  N2   C3   C4   111.45  3.000
 H55  N1   N2   C3   105.47  3.000
 H55  C2   N1   N2   120.17  3.000
 H55  N2   N1   C1   112.50  3.000
 H55  C2   N1   C1   127.29  3.000
 H55  H13  C2   H12  109.01  3.000
 H55  H13  C2   H11  109.25  3.000
 H55  H12  C2   H11  109.03  3.000
 H55  H13  C2   N1   109.95  3.000
 H55  H12  C2   N1   108.99  3.000
 H55  H11  C2   N1   110.60  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
 H55  CONST_01  C4   C5   N3   C6   180.00   0.0  0
 H55  CONST_02  C10  C5   N3   C6     0.00   0.0  0
 H55  CONST_03  C10  N8   C9   C6     0.00   0.0  0
 H55  CONST_06  N8   C10  C5   N3     0.00   0.0  0
 H55  CONST_07  N8   C9   C6   N3     0.00   0.0  0
 H55  CONST_08  C5   N3   C6   C9     0.00   0.0  0
 H55  CONST_09  C5   C10  N8   C9     0.00   0.0  0
 H55  CONST_10  C4   C5   C10  N8   180.00   0.0  0
 H55  CONST_13  N2   C3   C4   C5   180.00   0.0  0
 H55  CONST_14  N1   C1   C4   C5   180.00   0.0  0
 H55  CONST_15  N1   N2   C3   C4     0.00   0.0  0
 H55  CONST_16  N2   N1   C1   C4     0.00   0.0  0
 H55  CONST_17  C3   N2   N1   C1     0.00   0.0  0
 H55  CONST_18  N2   C3   C4   C1     0.00   0.0  0
 H55  CONST_19  N1   C1   C4   C3     0.00   0.0  0
 H55  CONST_20  C5   N3   C6   C7   180.00   0.0  0
 H55  CONST_21  N8   C9   C6   C7   180.00   0.0  0
 H55  CONST_22  N9   C10  C5   N3   180.00   0.0  0
 H55  CONST_23  N7   C9   C6   N3   180.00   0.0  0
 H55  CONST_24  N9   C10  N8   C9   180.00   0.0  0
 H55  CONST_25  C10  N8   C9   N7   180.00   0.0  0
 H55  CONST_26  C4   C5   C10  N9     0.00   0.0  0
 H55  CONST_27  C2   N1   C1   C4   180.00   0.0  0
 H55  CONST_28  C2   N1   N2   C3   180.00   0.0  0
 H55  CONST_29  H10  C3   C4   C5     0.00   0.0  0
 H55  CONST_30  H9   C1   C4   C5     0.00   0.0  0
 H55  CONST_31  H5   N7   C9   C6     0.00   0.0  0
 H55  CONST_32  H6   N7   C9   C6   180.00   0.0  0
 H55  CONST_33  H7   N9   C10  N8     0.00   0.0  0
 H55  CONST_35  C6   C7   N4   C8   180.00   0.0  0
 H55  CONST_36  H1   N4   C7   C6     0.00   0.0  0
 H55  CONST_37  C8   N4   C7   O1     0.00   0.0  0
 H55  CONST_39  N5   C8   N4   C7   180.00   0.0  0
 H55  CONST_40  H2   N6   C8   N4   180.00   0.0  0
 H55  CONST_42  H4   N5   C8   N4   180.00   0.0  0
 H55  Var_01    N3   C6   C7   O1   179.72  30.0  2
 H55  Var_02    H11  C2   N1   C1  -109.01  30.0  2

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
 H55  plan-1  C5   0.020
 H55  plan-1  C4   0.020
 H55  plan-1  C1   0.020
 H55  plan-1  C3   0.020
 H55  plan-1  N2   0.020
 H55  plan-1  N1   0.020
 H55  plan-1  C2   0.020
 H55  plan-1  H9   0.020
 H55  plan-1  H10  0.020
 H55  plan-2  C7   0.020
 H55  plan-2  C6   0.020
 H55  plan-2  N3   0.020
 H55  plan-2  C9   0.020
 H55  plan-2  N7   0.020
 H55  plan-2  N8   0.020
 H55  plan-2  C10  0.020
 H55  plan-2  N9   0.020
 H55  plan-2  C5   0.020
 H55  plan-2  C4   0.020
 H55  plan-3  O1   0.020
 H55  plan-3  C7   0.020
 H55  plan-3  N4   0.020
 H55  plan-3  C8   0.020
 H55  plan-3  N6   0.020
 H55  plan-3  N5   0.020
 H55  plan-3  C6   0.020
 H55  plan-3  H1   0.020
 H55  plan-3  H2   0.020
 H55  plan-3  H3   0.020
 H55  plan-3  H4   0.020
 H55  plan-4  C9   0.020
 H55  plan-4  N7   0.020
 H55  plan-4  H5   0.020
 H55  plan-4  H6   0.020
 H55  plan-5  C10  0.020
 H55  plan-5  N9   0.020
 H55  plan-5  H7   0.020
 H55  plan-5  H8   0.020

