FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: N81KQ

Calculation Name: 3A58-B-Xray547

Preferred Name:

Target Type:

Ligand Name: phosphoaminophosphonic acid-guanylate ester | phosphate ion | magnesium ion

Ligand 3-letter code: GNP | PO4 | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3A58

Chain ID: B

ChEMBL ID:

UniProt ID: P06780

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 178
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1866144.31608
FMO2-HF: Nuclear repulsion 1796347.551188
FMO2-HF: Total energy -69796.764892
FMO2-MP2: Total energy -69998.625185


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:8:SER)


Summations of interaction energy for fragment #1(A:8:SER)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-166.838-157.9848.375-7.734-9.494-0.063
Interaction energy analysis for fragmet #1(A:8:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.838 / q_NPA : 0.912
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A10ARG10.8910.9423.69540.58542.0670.003-0.571-0.914-0.001
43A50ASP-1-0.907-0.9503.328-58.701-57.7360.006-0.608-0.363-0.005
50A57ARG10.8900.9502.26246.55147.5622.609-1.483-2.136-0.005
51A58VAL0-0.042-0.0272.486-24.701-21.0433.393-3.554-3.497-0.040
52A59GLU-1-0.823-0.8961.964-50.190-48.5872.357-1.448-2.512-0.011
53A60LEU0-0.012-0.0103.7223.9394.0740.007-0.070-0.072-0.001
4A11ARG10.8260.9195.50834.58034.5800.0000.0000.0000.000
5A12LYS10.8290.9387.91517.83617.8360.0000.0000.0000.000
6A13LEU00.0280.02411.3200.7510.7510.0000.0000.0000.000
7A14VAL0-0.0040.00013.4880.0970.0970.0000.0000.0000.000
8A15ILE0-0.0250.00417.1260.1910.1910.0000.0000.0000.000
9A16VAL0-0.0040.00619.5660.3360.3360.0000.0000.0000.000
10A17GLY00.1020.04823.301-0.109-0.1090.0000.0000.0000.000
11A18ASP-1-0.742-0.84726.593-9.830-9.8300.0000.0000.0000.000
12A19GLY0-0.019-0.00528.454-0.405-0.4050.0000.0000.0000.000
13A20ALA0-0.026-0.01729.7350.1450.1450.0000.0000.0000.000
14A21CYS0-0.0060.00127.093-0.077-0.0770.0000.0000.0000.000
15A22GLY00.0490.00725.9570.0280.0280.0000.0000.0000.000
16A23LYS10.8220.92021.91211.69711.6970.0000.0000.0000.000
17A24THR00.020-0.01120.994-0.408-0.4080.0000.0000.0000.000
18A25CYS0-0.025-0.01121.099-0.430-0.4300.0000.0000.0000.000
19A26LEU00.0160.00819.144-0.265-0.2650.0000.0000.0000.000
20A27LEU00.0240.01415.542-0.707-0.7070.0000.0000.0000.000
21A28ILE00.0060.01516.863-0.954-0.9540.0000.0000.0000.000
22A29VAL0-0.052-0.03018.543-0.417-0.4170.0000.0000.0000.000
23A30ASN00.0010.00512.8900.1870.1870.0000.0000.0000.000
24A31SER0-0.057-0.03113.804-1.322-1.3220.0000.0000.0000.000
25A32LYS10.8420.91213.50818.93718.9370.0000.0000.0000.000
26A33GLY00.0380.03017.3800.2800.2800.0000.0000.0000.000
27A34GLN0-0.057-0.03520.967-0.195-0.1950.0000.0000.0000.000
28A35PHE00.0580.02624.092-0.149-0.1490.0000.0000.0000.000
29A36PRO0-0.015-0.01024.3590.3580.3580.0000.0000.0000.000
30A37GLU-1-0.893-0.94927.411-9.736-9.7360.0000.0000.0000.000
31A38VAL0-0.030-0.00830.2420.2500.2500.0000.0000.0000.000
32A39TYR00.0150.00728.753-0.240-0.2400.0000.0000.0000.000
33A40VAL00.0230.00927.5780.3080.3080.0000.0000.0000.000
34A41PRO0-0.062-0.03627.673-0.368-0.3680.0000.0000.0000.000
35A42THR00.0060.01922.5130.1850.1850.0000.0000.0000.000
36A43VAL0-0.026-0.00825.6710.2910.2910.0000.0000.0000.000
37A44PHE0-0.018-0.04021.0810.1120.1120.0000.0000.0000.000
38A45GLU-1-0.913-0.94818.646-14.171-14.1710.0000.0000.0000.000
39A46ASN0-0.034-0.00814.911-0.142-0.1420.0000.0000.0000.000
40A47TYR00.0190.01213.581-0.072-0.0720.0000.0000.0000.000
41A48VAL0-0.020-0.0207.062-0.926-0.9260.0000.0000.0000.000
42A49ALA0-0.014-0.0018.4931.4001.4000.0000.0000.0000.000
44A51VAL0-0.024-0.0125.4664.9144.9140.0000.0000.0000.000
45A52GLU-1-0.837-0.9155.762-46.760-46.7600.0000.0000.0000.000
46A53VAL00.0280.0137.8603.4713.4710.0000.0000.0000.000
47A54ASP-1-0.834-0.9119.142-24.092-24.0920.0000.0000.0000.000
48A55GLY0-0.031-0.0089.3060.1960.1960.0000.0000.0000.000
49A56ARG10.8740.9385.52526.98026.9800.0000.0000.0000.000
54A61ALA00.0140.0037.2121.9841.9840.0000.0000.0000.000
55A62LEU0-0.019-0.01310.0870.8750.8750.0000.0000.0000.000
56A63TRP00.0380.01413.1011.1991.1990.0000.0000.0000.000
57A64ASP-1-0.733-0.86616.530-13.358-13.3580.0000.0000.0000.000
58A65THR0-0.038-0.04619.6350.4610.4610.0000.0000.0000.000
59A66ALA00.0100.01623.0970.2150.2150.0000.0000.0000.000
60A67GLY0-0.005-0.00226.787-0.080-0.0800.0000.0000.0000.000
61A68GLN0-0.026-0.02728.7160.4140.4140.0000.0000.0000.000
62A69GLU-1-0.766-0.88031.811-9.111-9.1110.0000.0000.0000.000
63A70ASP-1-0.935-0.95334.117-8.412-8.4120.0000.0000.0000.000
64A71TYR0-0.123-0.08329.2700.0380.0380.0000.0000.0000.000
65A72ASP-1-0.755-0.86229.730-10.004-10.0040.0000.0000.0000.000
66A73ARG10.9050.94129.2889.1809.1800.0000.0000.0000.000
67A74LEU0-0.011-0.00525.726-0.033-0.0330.0000.0000.0000.000
68A75ARG10.7440.83224.59310.33810.3380.0000.0000.0000.000
69A76PRO00.000-0.00623.930-0.574-0.5740.0000.0000.0000.000
70A77LEU0-0.019-0.00623.198-0.283-0.2830.0000.0000.0000.000
71A78SER0-0.013-0.01019.913-0.772-0.7720.0000.0000.0000.000
72A79TYR0-0.010-0.04018.909-1.087-1.0870.0000.0000.0000.000
73A80PRO0-0.0220.00319.080-0.744-0.7440.0000.0000.0000.000
74A81ASP-1-0.905-0.93315.505-17.344-17.3440.0000.0000.0000.000
75A82SER0-0.039-0.05314.462-1.838-1.8380.0000.0000.0000.000
76A83ASN0-0.059-0.03810.906-2.038-2.0380.0000.0000.0000.000
77A84VAL00.0100.01412.9550.1790.1790.0000.0000.0000.000
78A85VAL00.0160.00515.417-0.259-0.2590.0000.0000.0000.000
79A86LEU0-0.020-0.00616.5820.3060.3060.0000.0000.0000.000
80A87ILE00.0400.01619.7000.2200.2200.0000.0000.0000.000
81A88CYS0-0.070-0.03322.350-0.115-0.1150.0000.0000.0000.000
82A89PHE00.0540.02424.9760.2320.2320.0000.0000.0000.000
83A90SER0-0.032-0.06028.213-0.387-0.3870.0000.0000.0000.000
84A91ILE0-0.029-0.00130.0020.2590.2590.0000.0000.0000.000
85A92ASP-1-0.821-0.87632.553-8.923-8.9230.0000.0000.0000.000
86A93LEU00.0280.01333.9760.2100.2100.0000.0000.0000.000
87A94PRO00.0580.04134.805-0.294-0.2940.0000.0000.0000.000
88A95ASP-1-0.800-0.88035.994-8.034-8.0340.0000.0000.0000.000
89A96SER0-0.037-0.03031.602-0.265-0.2650.0000.0000.0000.000
90A97LEU0-0.058-0.03930.912-0.375-0.3750.0000.0000.0000.000
91A98GLU-1-0.865-0.91133.009-8.254-8.2540.0000.0000.0000.000
92A99ASN00.012-0.01332.5920.0260.0260.0000.0000.0000.000
93A100VAL0-0.082-0.04328.328-0.323-0.3230.0000.0000.0000.000
94A101GLN0-0.036-0.03830.622-0.361-0.3610.0000.0000.0000.000
95A102GLU-1-0.935-0.96433.181-7.935-7.9350.0000.0000.0000.000
96A103LYS10.8040.90230.9039.6179.6170.0000.0000.0000.000
97A104TRP0-0.033-0.03826.724-0.387-0.3870.0000.0000.0000.000
98A105ILE00.0350.01727.512-0.406-0.4060.0000.0000.0000.000
99A106ALA0-0.0170.00628.565-0.171-0.1710.0000.0000.0000.000
100A107GLU-1-0.767-0.82427.268-11.118-11.1180.0000.0000.0000.000
101A108VAL00.017-0.00322.706-0.308-0.3080.0000.0000.0000.000
102A109LEU00.006-0.00324.641-0.382-0.3820.0000.0000.0000.000
103A110HIS0-0.082-0.02126.9000.3120.3120.0000.0000.0000.000
104A111PHE0-0.051-0.04324.192-0.024-0.0240.0000.0000.0000.000
105A112CYS0-0.048-0.01020.486-0.670-0.6700.0000.0000.0000.000
106A113GLN00.0420.02622.295-0.318-0.3180.0000.0000.0000.000
107A114GLY0-0.020-0.01522.586-0.397-0.3970.0000.0000.0000.000
108A115VAL0-0.045-0.00416.992-0.673-0.6730.0000.0000.0000.000
109A116PRO00.0030.00516.4570.7070.7070.0000.0000.0000.000
110A117ILE00.0450.02818.595-0.480-0.4800.0000.0000.0000.000
111A118ILE0-0.026-0.00516.9900.0490.0490.0000.0000.0000.000
112A119LEU00.0110.02320.904-0.019-0.0190.0000.0000.0000.000
113A120VAL0-0.008-0.03520.580-0.231-0.2310.0000.0000.0000.000
114A121GLY00.0750.04623.8690.3180.3180.0000.0000.0000.000
115A122CYS0-0.059-0.03824.942-0.461-0.4610.0000.0000.0000.000
116A123LYS10.8570.93526.96410.06110.0610.0000.0000.0000.000
117A124VAL00.0400.01527.7680.3550.3550.0000.0000.0000.000
118A125ASP-1-0.895-0.93129.916-9.835-9.8350.0000.0000.0000.000
119A126LEU00.003-0.00532.2070.2600.2600.0000.0000.0000.000
120A127ARG10.7670.85131.1719.7019.7010.0000.0000.0000.000
121A128ASN0-0.003-0.01935.7550.2590.2590.0000.0000.0000.000
122A129ASP-1-0.807-0.86637.712-7.679-7.6790.0000.0000.0000.000
123A130PRO0-0.010-0.01039.3160.0680.0680.0000.0000.0000.000
124A131GLN0-0.050-0.03041.6490.2820.2820.0000.0000.0000.000
125A132THR00.013-0.01637.2870.0280.0280.0000.0000.0000.000
126A133ILE0-0.035-0.01640.4480.0750.0750.0000.0000.0000.000
127A134GLU-1-0.961-0.98842.587-6.344-6.3440.0000.0000.0000.000
128A135GLN0-0.050-0.02740.4690.0900.0900.0000.0000.0000.000
129A136LEU00.0160.00938.7720.1020.1020.0000.0000.0000.000
130A137ARG10.9450.98843.3566.4116.4110.0000.0000.0000.000
131A138GLN0-0.105-0.05646.8280.0900.0900.0000.0000.0000.000
132A139GLU-1-0.880-0.92642.087-7.366-7.3660.0000.0000.0000.000
133A140GLY0-0.056-0.01446.1100.0110.0110.0000.0000.0000.000
134A141GLN0-0.082-0.06440.525-0.056-0.0560.0000.0000.0000.000
135A142GLN0-0.044-0.03240.8240.2570.2570.0000.0000.0000.000
136A143PRO0-0.004-0.01036.472-0.105-0.1050.0000.0000.0000.000
137A144VAL00.0030.03133.0360.0750.0750.0000.0000.0000.000
138A145THR0-0.043-0.04834.417-0.232-0.2320.0000.0000.0000.000
139A146SER0-0.009-0.02331.498-0.059-0.0590.0000.0000.0000.000
140A147GLN0-0.026-0.01732.169-0.245-0.2450.0000.0000.0000.000
141A148GLU-1-0.790-0.86534.509-8.305-8.3050.0000.0000.0000.000
142A149GLY00.0410.02130.740-0.095-0.0950.0000.0000.0000.000
143A150GLN0-0.053-0.05128.203-0.543-0.5430.0000.0000.0000.000
144A151SER0-0.024-0.00230.859-0.038-0.0380.0000.0000.0000.000
145A152VAL00.0290.00630.180-0.073-0.0730.0000.0000.0000.000
146A153ALA0-0.003-0.00126.889-0.238-0.2380.0000.0000.0000.000
147A154ASP-1-0.902-0.95028.202-10.471-10.4710.0000.0000.0000.000
148A155GLN0-0.074-0.02930.4070.0790.0790.0000.0000.0000.000
149A156ILE0-0.057-0.02626.3600.0480.0480.0000.0000.0000.000
150A157GLY0-0.0280.00027.561-0.279-0.2790.0000.0000.0000.000
151A158ALA0-0.027-0.00123.732-0.492-0.4920.0000.0000.0000.000
152A159THR0-0.048-0.03819.5420.0350.0350.0000.0000.0000.000
153A160GLY0-0.022-0.02021.026-0.579-0.5790.0000.0000.0000.000
154A161TYR0-0.030-0.03122.5960.0330.0330.0000.0000.0000.000
155A162TYR0-0.028-0.01320.119-0.276-0.2760.0000.0000.0000.000
156A163GLU-1-0.739-0.80723.713-9.916-9.9160.0000.0000.0000.000
157A164CYS0-0.058-0.02322.663-0.339-0.3390.0000.0000.0000.000
158A165SER0-0.027-0.04624.6670.3840.3840.0000.0000.0000.000
159A166ALA00.0360.00823.447-0.178-0.1780.0000.0000.0000.000
160A167LYS10.9390.98224.4329.2219.2210.0000.0000.0000.000
161A168THR0-0.018-0.02827.0040.1150.1150.0000.0000.0000.000
162A169GLY00.0120.01722.924-0.060-0.0600.0000.0000.0000.000
163A170TYR0-0.008-0.00422.531-0.521-0.5210.0000.0000.0000.000
164A171GLY00.0680.02622.1620.0970.0970.0000.0000.0000.000
165A172VAL0-0.037-0.00218.204-0.482-0.4820.0000.0000.0000.000
166A173ARG10.8600.91214.88216.07116.0710.0000.0000.0000.000
167A174GLU-1-0.825-0.91715.722-16.072-16.0720.0000.0000.0000.000
168A175VAL00.0270.02117.254-0.440-0.4400.0000.0000.0000.000
169A176PHE00.0360.01312.708-0.573-0.5730.0000.0000.0000.000
170A177GLU-1-0.843-0.89512.327-21.084-21.0840.0000.0000.0000.000
171A178ALA0-0.0240.00013.206-0.909-0.9090.0000.0000.0000.000
172A179ALA00.0360.00913.559-0.262-0.2620.0000.0000.0000.000
173A180THR0-0.023-0.0268.019-1.615-1.6150.0000.0000.0000.000
174A181ARG10.8240.88810.60718.89718.8970.0000.0000.0000.000
175A182ALA00.0380.02612.749-0.053-0.0530.0000.0000.0000.000
176A183SER0-0.069-0.0409.750-0.934-0.9340.0000.0000.0000.000
177A184LEU0-0.077-0.0727.346-2.792-2.7920.0000.0000.0000.000
178A185MET-1-0.985-0.95211.211-19.532-19.5320.0000.0000.0000.000