# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 17:07:03 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: (1S)-1-(7-amino-6-methyl-1H-pyrazolo[4,3-d]pyrimidin-6-ium-3-yl)-1,4-anhydro-D-ribitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[n+]1cnc2c([nH]nc2[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)c1N
#
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
 FM2  FM2  (1S)-1-(7-amino-6-methyl-1H-pyrazolo[4,3-d]pyrimidin-6-ium-3-yl)-1,4-anhydro-D-ribitol  ligand  36  20  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_FM2
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
 FM2  N1    N  NR6   1  -0.508   3.8867   0.4234   0.2829
 FM2  C2    C  CR16  0   0.144   3.1194   1.4268   0.8330
 FM2  N3    N  N     0  -0.412   1.8449   1.4011   0.9636
 FM2  C4    C  CR56  0   0.088   1.2461   0.2742   0.5110
 FM2  C5    C  CR56  0   0.305   1.9372  -0.7861  -0.0548
 FM2  C6    C  CR6   0   0.726   3.3411  -0.7230  -0.1840
 FM2  N6    N  NH2   0  -0.809   4.0815  -1.6722  -0.7055
 FM2  N7    N  NR15  0  -0.516   1.0181  -1.7144  -0.3789
 FM2  N8    N  N     0  -0.200  -0.2028  -1.3184  -0.0568
 FM2  C9    C  CR5   0   0.179  -0.1093  -0.1223   0.4829
 FM2  C1'   C  CH1   0  -0.079  -1.2933   0.6654   0.9545
 FM2  C2'   C  CH1   0  -0.004  -1.7978   1.6252  -0.1220
 FM2  O2'   O  OH1   0  -0.666  -2.4655   2.6789   0.5201
 FM2  C3'   C  CH1   0  -0.035  -2.7663   0.7175  -0.8746
 FM2  O3'   O  OH1   0  -0.664  -3.6715   1.4838  -1.6180
 FM2  C4'   C  CH1   0   0.011  -3.3912  -0.0887   0.2708
 FM2  O4'   O  O2    0  -0.490  -2.3781  -0.1827   1.2652
 FM2  C5'   C  CH2   0  -0.156  -3.8447  -1.4610  -0.1629
 FM2  O5'   O  OH1   0  -0.670  -4.4770  -2.1049   0.9168
 FM2  C11   C  CH3   0  -0.574   5.3344   0.6085   0.2009
 FM2  H2    H  HCR6  0   0.321   3.6824   2.2866   1.1693
 FM2  HN61  H  HNH2  0   0.450   3.6642  -2.5189  -1.0571
 FM2  HN62  H  HNH2  0   0.462   5.0851  -1.6120  -0.7806
 FM2  H7    H  HNR5  0   0.442   1.1481  -2.6207  -0.8026
 FM2  H1'   H  HCH1  0   0.278  -0.9954   1.2258   1.8476
 FM2  H2'   H  HCH1  0   0.254  -0.9859   1.9902  -0.7636
 FM2  HO2'  H  HOH1  0   0.454  -3.0150   3.1343  -0.1273
 FM2  H3'   H  HCH1  0   0.235  -2.1895   0.0441  -1.5248
 FM2  HO3'  H  HOH1  0   0.464  -4.1791   0.9066  -2.1961
 FM2  H4'   H  HCH1  0   0.228  -4.2490   0.4668   0.6734
 FM2  H5'1  H  HCH2  0   0.194  -4.5285  -1.3339  -1.0145
 FM2  H5'2  H  HCH2  0   0.202  -2.9757  -2.0239  -0.5277
 FM2  HO5'  H  HOH1  0   0.457  -4.7671  -2.9724   0.6211
 FM2  H111  H  HCH3  0   0.294   5.8455  -0.1633   0.7731
 FM2  H112  H  HCH3  0   0.295   5.6581   0.5841  -0.8379
 FM2  H113  H  HCH3  0   0.302   5.5890   1.5748   0.6203

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
 FM2  N1   C2    aromatic  1.378  0.020  1.378
 FM2  N1   C6    aromatic  1.353  0.020  1.353
 FM2  N1   C11   single    1.462  0.020  1.462
 FM2  C2   N3    aromatic  1.282  0.020  1.282
 FM2  C2   H2    single    0.930  0.020  1.080
 FM2  N3   C4    aromatic  1.354  0.020  1.354
 FM2  C4   C5    aromatic  1.386  0.020  1.386
 FM2  C4   C9    aromatic  1.412  0.020  1.412
 FM2  C5   C6    aromatic  1.411  0.020  1.411
 FM2  C5   N7    aromatic  1.346  0.020  1.346
 FM2  C6   N6    single    1.312  0.020  1.312
 FM2  N6   HN61  single    0.860  0.020  1.020
 FM2  N6   HN62  single    0.860  0.020  1.020
 FM2  N7   N8    aromatic  1.323  0.020  1.323
 FM2  N7   H7    single    0.860  0.020  1.020
 FM2  N8   C9    aromatic  1.316  0.020  1.316
 FM2  C9   C1'   single    1.498  0.020  1.498
 FM2  C1'  C2'   single    1.528  0.020  1.528
 FM2  C1'  O4'   single    1.412  0.020  1.412
 FM2  C1'  H1'   single    0.970  0.020  1.090
 FM2  C2'  O2'   single    1.403  0.020  1.403
 FM2  C2'  C3'   single    1.526  0.020  1.526
 FM2  C2'  H2'   single    0.970  0.020  1.090
 FM2  O2'  HO2'  single    0.850  0.020  0.980
 FM2  C3'  O3'   single    1.400  0.020  1.400
 FM2  C3'  C4'   single    1.534  0.020  1.534
 FM2  C3'  H3'   single    0.970  0.020  1.090
 FM2  O3'  HO3'  single    0.850  0.020  0.980
 FM2  C4'  O4'   single    1.423  0.020  1.423
 FM2  C4'  C5'   single    1.509  0.020  1.509
 FM2  C4'  H4'   single    0.970  0.020  1.090
 FM2  C5'  O5'   single    1.407  0.020  1.407
 FM2  C5'  H5'1  single    0.970  0.020  1.090
 FM2  C5'  H5'2  single    0.970  0.020  1.090
 FM2  O5'  HO5'  single    0.850  0.020  0.980
 FM2  C11  H111  single    0.970  0.020  1.090
 FM2  C11  H112  single    0.970  0.020  1.090
 FM2  C11  H113  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
 FM2  C11   N1   C6    119.17  3.000
 FM2  C11   N1   C2    118.80  3.000
 FM2  C6    N1   C2    122.03  3.000
 FM2  H2    C2   N3    120.13  3.000
 FM2  H2    C2   N1    114.41  3.000
 FM2  N3    C2   N1    125.45  3.000
 FM2  C4    N3   C2    114.99  3.000
 FM2  C9    C4   C5    104.81  3.000
 FM2  C9    C4   N3    131.65  3.000
 FM2  C5    C4   N3    123.54  3.000
 FM2  N7    C5   C6    133.48  3.000
 FM2  N7    C5   C4    106.58  3.000
 FM2  C6    C5   C4    119.94  3.000
 FM2  N6    C6   C5    124.44  3.000
 FM2  N6    C6   N1    121.51  3.000
 FM2  C5    C6   N1    114.05  3.000
 FM2  HN62  N6   HN61  115.89  3.000
 FM2  HN62  N6   C6    123.24  3.000
 FM2  HN61  N6   C6    120.87  3.000
 FM2  H7    N7   N8    119.33  3.000
 FM2  H7    N7   C5    129.26  3.000
 FM2  N8    N7   C5    111.41  3.000
 FM2  C9    N8   N7    107.84  3.000
 FM2  C1'   C9   N8    123.44  3.000
 FM2  C1'   C9   C4    127.19  3.000
 FM2  N8    C9   C4    109.36  3.000
 FM2  H1'   C1'  O4'   109.68  3.000
 FM2  H1'   C1'  C2'   110.05  3.000
 FM2  O4'   C1'  C2'   106.19  3.000
 FM2  H1'   C1'  C9    108.10  3.000
 FM2  O4'   C1'  C9    111.14  3.000
 FM2  C2'   C1'  C9    111.68  3.000
 FM2  H2'   C2'  C3'   112.28  3.000
 FM2  H2'   C2'  O2'   111.71  3.000
 FM2  C3'   C2'  O2'   111.74  3.000
 FM2  H2'   C2'  C1'   112.13  3.000
 FM2  C3'   C2'  C1'   100.57  3.000
 FM2  O2'   C2'  C1'   107.85  3.000
 FM2  HO2'  O2'  C2'   108.60  3.000
 FM2  H3'   C3'  C4'   109.48  3.000
 FM2  H3'   C3'  O3'   111.14  3.000
 FM2  C4'   C3'  O3'   114.89  3.000
 FM2  H3'   C3'  C2'   108.85  3.000
 FM2  C4'   C3'  C2'   101.71  3.000
 FM2  O3'   C3'  C2'   110.29  3.000
 FM2  HO3'  O3'  C3'   109.38  3.000
 FM2  H4'   C4'  C5'   109.30  3.000
 FM2  H4'   C4'  O4'   109.48  3.000
 FM2  C5'   C4'  O4'   110.78  3.000
 FM2  H4'   C4'  C3'   109.03  3.000
 FM2  C5'   C4'  C3'   112.69  3.000
 FM2  O4'   C4'  C3'   105.46  3.000
 FM2  C4'   O4'  C1'   110.71  3.000
 FM2  H5'2  C5'  H5'1  107.11  3.000
 FM2  H5'2  C5'  O5'   112.09  3.000
 FM2  H5'1  C5'  O5'   111.58  3.000
 FM2  H5'2  C5'  C4'   108.90  3.000
 FM2  H5'1  C5'  C4'   107.72  3.000
 FM2  O5'   C5'  C4'   109.31  3.000
 FM2  HO5'  O5'  C5'   108.21  3.000
 FM2  H113  C11  H112  108.63  3.000
 FM2  H113  C11  H111  108.57  3.000
 FM2  H112  C11  H111  110.25  3.000
 FM2  H113  C11  N1    108.90  3.000
 FM2  H112  C11  N1    110.20  3.000
 FM2  H111  C11  N1    110.23  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
 FM2  CONST_01  C4    N3   C2  N1    0.00   0.0  0
 FM2  CONST_02  C4    C5   C6  N1    0.00   0.0  0
 FM2  CONST_03  N7    C5   C6  N1  180.00   0.0  0
 FM2  CONST_04  C5    C6   N1  C2    0.00   0.0  0
 FM2  CONST_05  C5    C4   N3  C2    0.00   0.0  0
 FM2  CONST_06  C9    C4   N3  C2  180.00   0.0  0
 FM2  CONST_07  C6    N1   C2  N3    0.00   0.0  0
 FM2  CONST_08  C6    C5   C4  N3    0.00   0.0  0
 FM2  CONST_09  N7    C5   C4  N3  180.00   0.0  0
 FM2  CONST_10  N8    C9   C4  N3  180.00   0.0  0
 FM2  CONST_11  N8    N7   C5  C4    0.00   0.0  0
 FM2  CONST_12  N7    N8   C9  C4    0.00   0.0  0
 FM2  CONST_13  N8    C9   C4  C5    0.00   0.0  0
 FM2  CONST_14  C9    N8   N7  C5    0.00   0.0  0
 FM2  CONST_15  C9    C4   C5  C6  180.00   0.0  0
 FM2  CONST_16  N8    N7   C5  C6  180.00   0.0  0
 FM2  CONST_17  C9    C4   C5  N7    0.00   0.0  0
 FM2  CONST_18  C1'   C9   C4  N3    0.00   0.0  0
 FM2  CONST_19  C1'   C9   C4  C5  180.00   0.0  0
 FM2  CONST_20  C1'   C9   N8  N7  180.00   0.0  0
 FM2  CONST_21  N6    C6   N1  C2  180.00   0.0  0
 FM2  CONST_22  C11   N1   C2  N3  180.00   0.0  0
 FM2  CONST_23  N6    C6   C5  C4  180.00   0.0  0
 FM2  CONST_24  C11   N1   C6  C5  180.00   0.0  0
 FM2  CONST_25  N7    C5   C6  N6    0.00   0.0  0
 FM2  CONST_26  H2    C2   N3  C4  180.00   0.0  0
 FM2  CONST_27  H7    N7   C5  C4  180.00   0.0  0
 FM2  CONST_28  HN61  N6   C6  N1  180.00   0.0  0
 FM2  CONST_29  HN62  N6   C6  N1    0.00   0.0  0
 FM2  Var_01    H111  C11  N1  C2  119.23  30.0  2

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
 FM2  chir_01  C1'  C9   C2'  O4'  negativ
 FM2  chir_02  C2'  O2'  C3'  C1'  positiv
 FM2  chir_03  C3'  O3'  C4'  C2'  positiv
 FM2  chir_04  C4'  O4'  C3'  C5'  negativ

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
 FM2  plan-1  N1    0.020
 FM2  plan-1  C2    0.020
 FM2  plan-1  N3    0.020
 FM2  plan-1  C4    0.020
 FM2  plan-1  C5    0.020
 FM2  plan-1  C6    0.020
 FM2  plan-1  N6    0.020
 FM2  plan-1  N7    0.020
 FM2  plan-1  N8    0.020
 FM2  plan-1  C9    0.020
 FM2  plan-1  C1'   0.020
 FM2  plan-1  C11   0.020
 FM2  plan-1  H2    0.020
 FM2  plan-1  H7    0.020
 FM2  plan-2  C6    0.020
 FM2  plan-2  N6    0.020
 FM2  plan-2  HN61  0.020
 FM2  plan-2  HN62  0.020

