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: RQRY8

Calculation Name: 2C95-A-Xray547

Preferred Name: Adenylate kinase 1

Target Type: SINGLE PROTEIN

Ligand Name: bis(adenosine)-5'-tetraphosphate | malonate ion

Ligand 3-letter code: B4P | MLI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2C95

Chain ID: A

ChEMBL ID: CHEMBL4925

UniProt ID: P00568

Base Structure: X-ray

Registration Date: 2025-10-03

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 195
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2181073.386563
FMO2-HF: Nuclear repulsion 2104647.202469
FMO2-HF: Total energy -76426.184094
FMO2-MP2: Total energy -76648.065456


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:0:SER)


Summations of interaction energy for fragment #1(A:0: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.
37.10540.4647.134-3.996-6.4960.002
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.892 / q_NPA : 0.938
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].
3A2GLU-1-0.745-0.8732.517-36.326-34.0170.599-1.133-1.774-0.002
4A3GLU-1-0.875-0.9272.001-55.068-54.8306.521-2.587-4.1730.004
5A4LYS10.8560.9283.43066.46467.2760.014-0.276-0.5490.000
6A5LEU00.0530.0226.0735.2445.2440.0000.0000.0000.000
7A6LYS10.8720.9285.10242.78242.7820.0000.0000.0000.000
8A7LYS10.8510.9356.32139.72839.7280.0000.0000.0000.000
9A8THR0-0.042-0.01110.3861.6801.6800.0000.0000.0000.000
10A9ASN00.0570.04212.547-0.812-0.8120.0000.0000.0000.000
11A10ILE0-0.015-0.00211.003-0.154-0.1540.0000.0000.0000.000
12A11ILE00.0390.02115.5450.5890.5890.0000.0000.0000.000
13A12PHE00.0000.00515.840-0.096-0.0960.0000.0000.0000.000
14A13VAL00.0090.00020.5040.6110.6110.0000.0000.0000.000
15A14VAL00.002-0.00123.6020.0750.0750.0000.0000.0000.000
16A15GLY00.0780.02926.1020.2920.2920.0000.0000.0000.000
17A16GLY00.0490.02729.610-0.201-0.2010.0000.0000.0000.000
18A17PRO0-0.0240.00432.137-0.212-0.2120.0000.0000.0000.000
19A18GLY00.0740.02133.2130.2410.2410.0000.0000.0000.000
20A19SER0-0.018-0.03031.7130.1020.1020.0000.0000.0000.000
21A20GLY00.0040.00433.4020.0790.0790.0000.0000.0000.000
22A21LYS10.8850.93926.43511.39811.3980.0000.0000.0000.000
23A22GLY00.0600.03727.703-0.296-0.2960.0000.0000.0000.000
24A23THR0-0.023-0.02128.770-0.200-0.2000.0000.0000.0000.000
25A24GLN00.0320.00629.622-0.113-0.1130.0000.0000.0000.000
26A25CYS0-0.046-0.01725.125-0.342-0.3420.0000.0000.0000.000
27A26GLU-1-0.838-0.90026.496-12.105-12.1050.0000.0000.0000.000
28A27LYS10.8480.93328.5619.1339.1330.0000.0000.0000.000
29A28ILE00.0190.00724.4730.0150.0150.0000.0000.0000.000
30A29VAL0-0.032-0.01323.771-0.277-0.2770.0000.0000.0000.000
31A30GLN0-0.049-0.03425.7970.0660.0660.0000.0000.0000.000
32A31LYS10.8810.96428.74010.35610.3560.0000.0000.0000.000
33A32TYR0-0.028-0.06224.0800.0980.0980.0000.0000.0000.000
34A33GLY0-0.0040.01223.100-0.534-0.5340.0000.0000.0000.000
35A34TYR0-0.017-0.00719.319-1.005-1.0050.0000.0000.0000.000
36A35THR0-0.026-0.02416.7470.6670.6670.0000.0000.0000.000
37A36HIS10.7790.85419.04512.35612.3560.0000.0000.0000.000
38A37LEU0-0.017-0.00515.566-0.050-0.0500.0000.0000.0000.000
39A38SER0-0.030-0.02120.0900.0560.0560.0000.0000.0000.000
40A39THR00.0580.02019.1720.1960.1960.0000.0000.0000.000
41A40GLY00.002-0.00221.6510.2110.2110.0000.0000.0000.000
42A41ASP-1-0.776-0.85924.560-11.197-11.1970.0000.0000.0000.000
43A42LEU0-0.0200.01918.3870.1610.1610.0000.0000.0000.000
44A43LEU00.0380.00622.6070.2170.2170.0000.0000.0000.000
45A44ARG10.8860.92524.76911.35011.3500.0000.0000.0000.000
46A45SER0-0.024-0.00424.2320.3970.3970.0000.0000.0000.000
47A46GLU-1-0.769-0.85623.641-12.590-12.5900.0000.0000.0000.000
48A47VAL0-0.035-0.00425.9150.2790.2790.0000.0000.0000.000
49A48SER0-0.034-0.03529.2740.4090.4090.0000.0000.0000.000
50A49SER0-0.074-0.04527.0140.2050.2050.0000.0000.0000.000
51A50GLY00.0240.01929.1600.1500.1500.0000.0000.0000.000
52A51SER0-0.031-0.01626.5670.2980.2980.0000.0000.0000.000
53A52ALA00.0450.00729.6670.1200.1200.0000.0000.0000.000
54A53ARG10.8050.89519.90913.95013.9500.0000.0000.0000.000
55A54GLY00.0720.02727.5240.0430.0430.0000.0000.0000.000
56A55LYS00.0360.02528.7900.1660.1660.0000.0000.0000.000
57A56LYS10.9660.96928.81110.42610.4260.0000.0000.0000.000
58A57LEU0-0.043-0.01524.612-0.107-0.1070.0000.0000.0000.000
59A58SER0-0.004-0.00828.906-0.004-0.0040.0000.0000.0000.000
60A59GLU-1-0.945-0.95932.322-8.827-8.8270.0000.0000.0000.000
61A60ILE00.003-0.00427.9910.1110.1110.0000.0000.0000.000
62A61MET0-0.052-0.02628.695-0.028-0.0280.0000.0000.0000.000
63A62GLU-1-0.902-0.96531.868-8.474-8.4740.0000.0000.0000.000
64A63LYS0-0.028-0.01034.8460.3730.3730.0000.0000.0000.000
65A64GLY0-0.025-0.01933.6450.0950.0950.0000.0000.0000.000
66A65GLN0-0.046-0.01831.176-0.160-0.1600.0000.0000.0000.000
67A66LEU0-0.018-0.01625.670-0.271-0.2710.0000.0000.0000.000
68A67VAL00.0040.00523.2560.1730.1730.0000.0000.0000.000
69A68PRO00.019-0.00123.457-0.369-0.3690.0000.0000.0000.000
70A69LEU00.0410.02317.256-0.447-0.4470.0000.0000.0000.000
71A70GLU-1-0.798-0.88615.775-17.792-17.7920.0000.0000.0000.000
72A71THR0-0.023-0.00517.191-0.479-0.4790.0000.0000.0000.000
73A72VAL0-0.012-0.01119.025-0.265-0.2650.0000.0000.0000.000
74A73LEU0-0.0090.00212.923-0.578-0.5780.0000.0000.0000.000
75A74ASP-1-0.858-0.93713.027-21.952-21.9520.0000.0000.0000.000
76A75MET0-0.060-0.02314.303-0.503-0.5030.0000.0000.0000.000
77A76LEU0-0.005-0.00114.541-0.290-0.2900.0000.0000.0000.000
78A77ARG10.8750.9315.97230.41830.4180.0000.0000.0000.000
79A78ASP-1-0.876-0.93811.259-24.131-24.1310.0000.0000.0000.000
80A79ALA0-0.034-0.01712.975-0.332-0.3320.0000.0000.0000.000
81A80MET0-0.020-0.00711.1730.1100.1100.0000.0000.0000.000
82A81VAL0-0.024-0.0187.615-1.798-1.7980.0000.0000.0000.000
83A82ALA0-0.011-0.00210.033-0.676-0.6760.0000.0000.0000.000
84A83LYS10.9400.96412.69419.29619.2960.0000.0000.0000.000
85A84VAL00.0040.0087.557-0.061-0.0610.0000.0000.0000.000
86A85ASN0-0.032-0.0217.949-3.841-3.8410.0000.0000.0000.000
87A86THR0-0.072-0.03910.4381.7801.7800.0000.0000.0000.000
88A87SER0-0.0100.01113.3381.9151.9150.0000.0000.0000.000
89A88LYS10.9800.98414.42717.31017.3100.0000.0000.0000.000
90A89GLY00.0410.03015.7610.2870.2870.0000.0000.0000.000
91A90PHE0-0.044-0.02912.1090.1880.1880.0000.0000.0000.000
92A91LEU00.0060.01217.0320.3760.3760.0000.0000.0000.000
93A92ILE00.0280.00515.3910.0420.0420.0000.0000.0000.000
94A93ASP-1-0.756-0.86119.439-11.498-11.4980.0000.0000.0000.000
95A94GLY0-0.045-0.03623.0700.1660.1660.0000.0000.0000.000
96A95TYR0-0.018-0.00716.7310.2780.2780.0000.0000.0000.000
97A96PRO00.0210.01919.058-0.270-0.2700.0000.0000.0000.000
98A97ARG10.8980.91621.02412.08112.0810.0000.0000.0000.000
99A98GLU-1-0.806-0.87722.969-11.918-11.9180.0000.0000.0000.000
100A99VAL00.0390.01722.497-0.547-0.5470.0000.0000.0000.000
101A100GLN00.0600.02220.835-0.631-0.6310.0000.0000.0000.000
102A101GLN0-0.019-0.01218.723-0.902-0.9020.0000.0000.0000.000
103A102GLY00.0260.02117.318-0.997-0.9970.0000.0000.0000.000
104A103GLU-1-0.912-0.96116.004-15.038-15.0380.0000.0000.0000.000
105A104GLU-1-0.801-0.87615.067-18.907-18.9070.0000.0000.0000.000
106A105PHE0-0.008-0.01312.807-1.658-1.6580.0000.0000.0000.000
107A106GLU-1-0.733-0.82811.353-19.450-19.4500.0000.0000.0000.000
108A107ARG10.8210.90810.95817.89317.8930.0000.0000.0000.000
109A108ARG10.7820.8738.63218.81818.8180.0000.0000.0000.000
110A109ILE0-0.079-0.0267.371-3.325-3.3250.0000.0000.0000.000
111A110GLY00.0770.0367.248-3.822-3.8220.0000.0000.0000.000
112A111GLN0-0.073-0.0558.7491.7171.7170.0000.0000.0000.000
113A112PRO0-0.055-0.00812.651-0.397-0.3970.0000.0000.0000.000
114A113THR0-0.009-0.01815.965-0.021-0.0210.0000.0000.0000.000
115A114LEU0-0.018-0.01017.6800.8360.8360.0000.0000.0000.000
116A115LEU0-0.0120.00520.368-0.538-0.5380.0000.0000.0000.000
117A116LEU00.0120.01022.8850.4960.4960.0000.0000.0000.000
118A117TYR00.006-0.02525.657-0.056-0.0560.0000.0000.0000.000
119A118VAL0-0.053-0.03428.4460.3220.3220.0000.0000.0000.000
120A119ASP-1-0.829-0.90430.977-8.814-8.8140.0000.0000.0000.000
121A120ALA00.001-0.00334.0720.1420.1420.0000.0000.0000.000
122A121GLY00.0710.04937.208-0.071-0.0710.0000.0000.0000.000
123A122PRO00.0120.00039.442-0.107-0.1070.0000.0000.0000.000
124A123GLU-1-0.862-0.92340.416-7.262-7.2620.0000.0000.0000.000
125A124THR0-0.036-0.05139.6230.0850.0850.0000.0000.0000.000
126A125MET0-0.085-0.02135.612-0.213-0.2130.0000.0000.0000.000
127A126THR00.019-0.01038.892-0.079-0.0790.0000.0000.0000.000
128A127GLN00.0130.01341.3410.0450.0450.0000.0000.0000.000
129A128ARG10.7880.88437.1488.3328.3320.0000.0000.0000.000
130A129LEU0-0.077-0.03235.299-0.120-0.1200.0000.0000.0000.000
131A130LEU00.0330.00939.2640.0090.0090.0000.0000.0000.000
132A131LYS10.7860.88742.3946.8916.8910.0000.0000.0000.000
133A132ARG10.8110.87433.8108.9058.9050.0000.0000.0000.000
134A133GLY00.0330.02140.545-0.023-0.0230.0000.0000.0000.000
135A134GLU-1-0.841-0.89242.108-6.657-6.6570.0000.0000.0000.000
136A135THR0-0.094-0.04341.1860.0480.0480.0000.0000.0000.000
137A136SER00.0180.00441.338-0.113-0.1130.0000.0000.0000.000
138A137GLY00.0270.00937.384-0.111-0.1110.0000.0000.0000.000
139A138ARG10.7480.83531.3709.2979.2970.0000.0000.0000.000
140A139VAL00.0960.05136.2800.1390.1390.0000.0000.0000.000
141A140ASP-1-0.752-0.83533.148-9.313-9.3130.0000.0000.0000.000
142A141ASP-1-0.773-0.85836.237-8.771-8.7710.0000.0000.0000.000
143A142ASN00.0510.03038.6080.2230.2230.0000.0000.0000.000
144A143GLU-1-0.827-0.92640.801-7.016-7.0160.0000.0000.0000.000
145A144GLU-1-0.849-0.90342.467-7.263-7.2630.0000.0000.0000.000
146A145THR0-0.059-0.03636.405-0.037-0.0370.0000.0000.0000.000
147A146ILE0-0.038-0.02837.417-0.269-0.2690.0000.0000.0000.000
148A147LYS10.8400.91838.0886.9166.9160.0000.0000.0000.000
149A148LYS11.0171.02436.5927.6447.6440.0000.0000.0000.000
150A149ARG10.7460.88433.2478.6828.6820.0000.0000.0000.000
151A150LEU0-0.047-0.01833.666-0.307-0.3070.0000.0000.0000.000
152A151GLU-1-0.910-0.95935.323-8.061-8.0610.0000.0000.0000.000
153A152THR0-0.036-0.03430.186-0.179-0.1790.0000.0000.0000.000
154A153TYR0-0.047-0.01729.950-0.462-0.4620.0000.0000.0000.000
155A154TYR00.0390.00431.515-0.178-0.1780.0000.0000.0000.000
156A155LYS10.9150.97632.8189.1209.1200.0000.0000.0000.000
157A156ALA0-0.043-0.02027.964-0.087-0.0870.0000.0000.0000.000
158A157THR0-0.035-0.04226.543-0.334-0.3340.0000.0000.0000.000
159A158GLU-1-0.868-0.93827.871-9.268-9.2680.0000.0000.0000.000
160A159PRO00.003-0.01028.346-0.119-0.1190.0000.0000.0000.000
161A160VAL0-0.019-0.00422.893-0.246-0.2460.0000.0000.0000.000
162A161ILE00.0040.00824.998-0.380-0.3800.0000.0000.0000.000
163A162ALA00.0400.01826.951-0.134-0.1340.0000.0000.0000.000
164A163PHE0-0.071-0.02619.8730.0850.0850.0000.0000.0000.000
165A164TYR0-0.033-0.06417.760-0.197-0.1970.0000.0000.0000.000
166A165GLU-1-0.923-0.95823.647-10.437-10.4370.0000.0000.0000.000
167A166LYS10.9270.97024.70311.64911.6490.0000.0000.0000.000
168A167ARG10.7650.84616.51915.70615.7060.0000.0000.0000.000
169A168GLY00.0300.02223.372-0.299-0.2990.0000.0000.0000.000
170A169ILE0-0.035-0.01119.384-0.016-0.0160.0000.0000.0000.000
171A170VAL0-0.0110.00123.331-0.307-0.3070.0000.0000.0000.000
172A171ARG10.9140.95425.98511.33211.3320.0000.0000.0000.000
173A172LYS10.8850.94528.0818.8028.8020.0000.0000.0000.000
174A173VAL0-0.023-0.00530.8740.1630.1630.0000.0000.0000.000
175A174ASN00.0450.02133.142-0.028-0.0280.0000.0000.0000.000
176A175ALA00.018-0.00334.089-0.026-0.0260.0000.0000.0000.000
177A176GLU-1-0.759-0.84936.105-7.748-7.7480.0000.0000.0000.000
178A177GLY0-0.0060.00739.676-0.055-0.0550.0000.0000.0000.000
179A178SER00.004-0.00440.823-0.132-0.1320.0000.0000.0000.000
180A179VAL00.0550.01735.192-0.125-0.1250.0000.0000.0000.000
181A180ASP-1-0.809-0.90136.249-8.603-8.6030.0000.0000.0000.000
182A181SER0-0.044-0.02837.727-0.044-0.0440.0000.0000.0000.000
183A182VAL00.0040.01633.493-0.090-0.0900.0000.0000.0000.000
184A183PHE00.0400.00329.960-0.154-0.1540.0000.0000.0000.000
185A184SER00.0180.02033.413-0.251-0.2510.0000.0000.0000.000
186A185GLN0-0.0010.00034.281-0.159-0.1590.0000.0000.0000.000
187A186VAL0-0.014-0.00928.406-0.233-0.2330.0000.0000.0000.000
188A187CYS0-0.038-0.01729.644-0.344-0.3440.0000.0000.0000.000
189A188THR0-0.019-0.01430.869-0.095-0.0950.0000.0000.0000.000
190A189HIS0-0.036-0.02328.322-0.249-0.2490.0000.0000.0000.000
191A190LEU0-0.038-0.01124.254-0.372-0.3720.0000.0000.0000.000
192A191ASP-1-0.772-0.87326.693-10.806-10.8060.0000.0000.0000.000
193A192ALA0-0.069-0.02229.1000.1370.1370.0000.0000.0000.000
194A193LEU0-0.114-0.06823.353-0.082-0.0820.0000.0000.0000.000
195A194LEU-1-0.976-0.95521.586-13.154-13.1540.0000.0000.0000.000