Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

tag_button

FMODB ID: YV912

Calculation Name: 2AR7-A-Xray372

Preferred Name: Adenylate kinase 4

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2AR7

Chain ID: A

ChEMBL ID: CHEMBL4926

UniProt ID: P27144

Base Structure: X-ray

Registration Date: 2023-09-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2557080.131572
FMO2-HF: Nuclear repulsion 2469997.921914
FMO2-HF: Total energy -87082.209658
FMO2-MP2: Total energy -87339.499357


3D Structure
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:4:LYS)


Summations of interaction energy for fragment #1(A:4:LYS)
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.
5.8837.96-0.013-0.94-1.1230.002
Interaction energy analysis for fragmet #1(A:4:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.019 / q_NPA : 1.017
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].
3A6LEU00.0250.0223.8673.2985.168-0.011-0.910-0.9490.002
4A7ARG10.7880.9095.89336.26536.2650.0000.0000.0000.000
5A8ALA00.0280.0168.4081.5091.5090.0000.0000.0000.000
6A9VAL0-0.0030.01111.3410.3220.3220.0000.0000.0000.000
7A10ILE0-0.003-0.00815.0980.4690.4690.0000.0000.0000.000
8A11LEU0-0.0010.00318.2530.4100.4100.0000.0000.0000.000
9A12GLY00.025-0.00321.5790.0740.0740.0000.0000.0000.000
10A13PRO00.0090.02925.129-0.077-0.0770.0000.0000.0000.000
11A14PRO00.0200.00528.670-0.215-0.2150.0000.0000.0000.000
12A15GLY00.0380.02630.4250.2650.2650.0000.0000.0000.000
13A16SER0-0.065-0.04526.510-0.128-0.1280.0000.0000.0000.000
14A17GLY00.0410.01726.858-0.148-0.1480.0000.0000.0000.000
15A18LYS10.8670.93022.17712.46512.4650.0000.0000.0000.000
16A19GLY00.0720.05422.096-0.551-0.5510.0000.0000.0000.000
17A20THR00.000-0.01123.185-0.427-0.4270.0000.0000.0000.000
18A21VAL0-0.0090.00119.755-0.209-0.2090.0000.0000.0000.000
19A22CYS0-0.027-0.00518.638-0.669-0.6690.0000.0000.0000.000
20A23GLN00.0410.02418.917-0.464-0.4640.0000.0000.0000.000
21A24ARG10.8850.94520.82711.99111.9910.0000.0000.0000.000
22A25ILE0-0.0020.01114.956-0.235-0.2350.0000.0000.0000.000
23A26ALA0-0.001-0.00516.262-0.900-0.9000.0000.0000.0000.000
24A27GLN0-0.020-0.01816.799-0.177-0.1770.0000.0000.0000.000
25A28ASN0-0.052-0.04418.2250.1180.1180.0000.0000.0000.000
26A29PHE0-0.018-0.01012.5470.1430.1430.0000.0000.0000.000
27A30GLY00.0270.02512.669-1.930-1.9300.0000.0000.0000.000
28A31LEU0-0.049-0.01110.570-1.529-1.5290.0000.0000.0000.000
29A32GLN00.0470.02013.0131.1331.1330.0000.0000.0000.000
30A33HIS0-0.036-0.04115.102-0.378-0.3780.0000.0000.0000.000
31A34LEU0-0.0310.00713.6690.3510.3510.0000.0000.0000.000
32A35SER00.0240.00118.2330.5700.5700.0000.0000.0000.000
33A36SER00.0910.03721.189-0.002-0.0020.0000.0000.0000.000
34A37GLY0-0.003-0.00523.5420.2580.2580.0000.0000.0000.000
35A38HIS0-0.069-0.03621.7430.7660.7660.0000.0000.0000.000
36A39PHE00.0940.02717.5540.2760.2760.0000.0000.0000.000
37A40LEU0-0.0040.01423.4930.2580.2580.0000.0000.0000.000
38A41ARG10.9720.98926.85611.88211.8820.0000.0000.0000.000
39A42GLU-1-0.897-0.93521.996-14.238-14.2380.0000.0000.0000.000
40A43ASN00.0060.00223.1300.3820.3820.0000.0000.0000.000
41A44ILE00.0070.00226.9480.2870.2870.0000.0000.0000.000
42A45LYS10.8380.92426.32112.13112.1310.0000.0000.0000.000
43A46ALA0-0.052-0.04027.611-0.004-0.0040.0000.0000.0000.000
44A47SER0-0.011-0.01029.6420.0030.0030.0000.0000.0000.000
45A48THR0-0.015-0.01525.8620.2340.2340.0000.0000.0000.000
46A49GLU-1-0.808-0.87228.884-10.603-10.6030.0000.0000.0000.000
47A50VAL00.028-0.00425.6190.2900.2900.0000.0000.0000.000
48A51GLY00.0280.02028.6970.1360.1360.0000.0000.0000.000
49A52GLU-1-0.757-0.87329.911-8.876-8.8760.0000.0000.0000.000
50A53MET0-0.064-0.01531.4240.2080.2080.0000.0000.0000.000
51A54ALA0-0.006-0.00930.2200.2420.2420.0000.0000.0000.000
52A55LYS10.8150.89532.3548.8148.8140.0000.0000.0000.000
53A56GLN00.0530.03234.9550.5040.5040.0000.0000.0000.000
54A57TYR0-0.011-0.01233.7670.1100.1100.0000.0000.0000.000
55A58ILE0-0.0250.00133.1460.1330.1330.0000.0000.0000.000
56A59GLU-1-0.845-0.93637.341-8.103-8.1030.0000.0000.0000.000
57A60LYS10.8700.93340.1468.0578.0570.0000.0000.0000.000
58A61SER0-0.045-0.03538.2230.1450.1450.0000.0000.0000.000
59A62LEU0-0.039-0.00338.712-0.027-0.0270.0000.0000.0000.000
60A63LEU00.0030.00433.125-0.161-0.1610.0000.0000.0000.000
61A64VAL0-0.0090.00430.2470.0440.0440.0000.0000.0000.000
62A65PRO00.0190.01631.341-0.195-0.1950.0000.0000.0000.000
63A66ASP-1-0.700-0.82527.296-11.252-11.2520.0000.0000.0000.000
64A67HIS00.0450.03626.450-0.623-0.6230.0000.0000.0000.000
65A68VAL00.0050.01426.859-0.426-0.4260.0000.0000.0000.000
66A69ILE00.0010.00024.098-0.509-0.5090.0000.0000.0000.000
67A70THR0-0.016-0.03521.797-0.676-0.6760.0000.0000.0000.000
68A71ARG10.8140.88222.20610.78110.7810.0000.0000.0000.000
69A72LEU0-0.0120.00322.586-0.479-0.4790.0000.0000.0000.000
70A73MET00.0010.01818.206-0.483-0.4830.0000.0000.0000.000
71A74MET0-0.0030.00616.956-1.111-1.1110.0000.0000.0000.000
72A75SER0-0.029-0.01217.331-0.883-0.8830.0000.0000.0000.000
73A76GLU-1-0.799-0.88817.554-16.708-16.7080.0000.0000.0000.000
74A77LEU0-0.028-0.00413.980-1.039-1.0390.0000.0000.0000.000
75A78GLU-1-0.753-0.84512.636-24.290-24.2900.0000.0000.0000.000
76A79ASN0-0.080-0.04712.464-1.823-1.8230.0000.0000.0000.000
77A80ARG10.8180.88611.07719.02619.0260.0000.0000.0000.000
78A81ARG10.8320.8928.40922.28822.2880.0000.0000.0000.000
79A82GLY0-0.0090.0005.197-4.229-4.2290.0000.0000.0000.000
80A83GLN0-0.0080.0025.182-4.808-4.756-0.001-0.002-0.0480.000
81A84HIS00.0620.0434.788-1.769-1.614-0.001-0.028-0.1260.000
82A85TRP0-0.040-0.0548.2353.2523.2520.0000.0000.0000.000
83A86LEU00.0180.01011.0980.0560.0560.0000.0000.0000.000
84A87LEU0-0.012-0.00113.7031.0721.0720.0000.0000.0000.000
85A88ASP-1-0.747-0.87616.293-13.031-13.0310.0000.0000.0000.000
86A89GLY0-0.096-0.07119.7520.5980.5980.0000.0000.0000.000
87A90PHE0-0.0060.01217.6100.6770.6770.0000.0000.0000.000
88A91PRO00.0480.02416.815-0.727-0.7270.0000.0000.0000.000
89A92ARG10.8270.86019.87111.18011.1800.0000.0000.0000.000
90A93THR00.0080.00223.1600.4170.4170.0000.0000.0000.000
91A94LEU00.0530.02022.427-0.473-0.4730.0000.0000.0000.000
92A95GLY00.0760.04222.099-0.428-0.4280.0000.0000.0000.000
93A96GLN0-0.065-0.04121.067-0.590-0.5900.0000.0000.0000.000
94A97ALA00.0180.00518.077-0.768-0.7680.0000.0000.0000.000
95A98GLU-1-0.873-0.93917.456-12.835-12.8350.0000.0000.0000.000
96A99ALA0-0.069-0.02618.764-0.299-0.2990.0000.0000.0000.000
97A100LEU00.0350.00213.253-0.721-0.7210.0000.0000.0000.000
98A101ASP-1-0.737-0.84013.773-17.669-17.6690.0000.0000.0000.000
99A102LYS10.8310.92314.28513.82113.8210.0000.0000.0000.000
100A103ILE0-0.057-0.02013.210-0.172-0.1720.0000.0000.0000.000
101A104CYS0-0.159-0.0688.690-2.495-2.4950.0000.0000.0000.000
102A105GLU-1-0.747-0.8457.957-17.315-17.3150.0000.0000.0000.000
103A106VAL0-0.021-0.0378.118-2.138-2.1380.0000.0000.0000.000
104A107ASP-1-0.801-0.9105.339-30.433-30.4330.0000.0000.0000.000
105A108LEU0-0.066-0.0358.3651.0161.0160.0000.0000.0000.000
106A109VAL00.0310.02311.326-0.169-0.1690.0000.0000.0000.000
107A110ILE00.0320.01814.9640.6210.6210.0000.0000.0000.000
108A111SER0-0.023-0.00317.8030.3100.3100.0000.0000.0000.000
109A112LEU00.010-0.00721.5420.2670.2670.0000.0000.0000.000
110A113ASN0-0.022-0.01024.3060.5280.5280.0000.0000.0000.000
111A114ILE00.000-0.00826.8840.2090.2090.0000.0000.0000.000
112A115PRO00.0250.01629.5800.1470.1470.0000.0000.0000.000
113A116PHE00.0320.01032.892-0.010-0.0100.0000.0000.0000.000
114A117GLU-1-0.782-0.87535.727-7.161-7.1610.0000.0000.0000.000
115A118THR00.013-0.00433.1950.0070.0070.0000.0000.0000.000
116A119LEU0-0.036-0.02331.611-0.022-0.0220.0000.0000.0000.000
117A120LYS10.8250.91335.5977.1217.1210.0000.0000.0000.000
118A121ASP-1-0.850-0.92539.300-7.097-7.0970.0000.0000.0000.000
119A122ARG10.8710.93833.0008.6468.6460.0000.0000.0000.000
120A123LEU0-0.0040.00137.255-0.005-0.0050.0000.0000.0000.000
121A124SER0-0.042-0.03440.5240.1810.1810.0000.0000.0000.000
122A125ARG10.8770.90443.0106.9156.9150.0000.0000.0000.000
123A126ARG10.8280.89939.0237.6667.6660.0000.0000.0000.000
124A127TRP0-0.0070.00544.0130.1810.1810.0000.0000.0000.000
125A128ILE0-0.027-0.01144.842-0.145-0.1450.0000.0000.0000.000
126A129HIS00.0760.04547.8800.0240.0240.0000.0000.0000.000
127A130PRO0-0.022-0.02049.889-0.082-0.0820.0000.0000.0000.000
128A131PRO0-0.013-0.00450.564-0.080-0.0800.0000.0000.0000.000
129A132SER0-0.041-0.04549.656-0.062-0.0620.0000.0000.0000.000
130A133GLY0-0.0050.00945.932-0.141-0.1410.0000.0000.0000.000
131A134ARG10.8230.89344.9266.2036.2030.0000.0000.0000.000
132A135VAL0-0.004-0.00741.4700.1020.1020.0000.0000.0000.000
133A136TYR0-0.007-0.02343.719-0.153-0.1530.0000.0000.0000.000
134A137ASN0-0.029-0.03339.4890.1880.1880.0000.0000.0000.000
135A138LEU00.0260.00042.982-0.037-0.0370.0000.0000.0000.000
136A139ASP-1-0.849-0.87641.070-6.977-6.9770.0000.0000.0000.000
137A140PHE0-0.126-0.06436.387-0.217-0.2170.0000.0000.0000.000
138A141ASN0-0.041-0.02740.723-0.108-0.1080.0000.0000.0000.000
139A142PRO00.0270.02143.1170.0520.0520.0000.0000.0000.000
140A143PRO00.0100.02046.650-0.062-0.0620.0000.0000.0000.000
141A144HIS0-0.053-0.04048.6360.1440.1440.0000.0000.0000.000
142A145VAL0-0.016-0.00951.8900.1120.1120.0000.0000.0000.000
143A146HIS0-0.001-0.00753.173-0.032-0.0320.0000.0000.0000.000
144A147GLY00.0140.01252.8520.0990.0990.0000.0000.0000.000
145A148ILE0-0.023-0.00554.1280.0440.0440.0000.0000.0000.000
146A149ASP-1-0.714-0.80650.943-6.383-6.3830.0000.0000.0000.000
147A150ASP-1-0.803-0.90248.951-6.365-6.3650.0000.0000.0000.000
148A151VAL0-0.090-0.03750.7140.0380.0380.0000.0000.0000.000
149A152THR0-0.035-0.03853.6610.0980.0980.0000.0000.0000.000
150A153GLY0-0.0040.00955.9590.1170.1170.0000.0000.0000.000
151A154GLU-1-0.863-0.92255.908-5.613-5.6130.0000.0000.0000.000
152A155PRO0-0.015-0.01955.561-0.098-0.0980.0000.0000.0000.000
153A156LEU0-0.0190.01549.684-0.082-0.0820.0000.0000.0000.000
154A157VAL0-0.028-0.01950.7160.1000.1000.0000.0000.0000.000
155A158GLN0-0.050-0.04247.070-0.050-0.0500.0000.0000.0000.000
156A159GLN0-0.004-0.01143.3330.1440.1440.0000.0000.0000.000
157A160GLU-1-0.883-0.95846.537-6.450-6.4500.0000.0000.0000.000
158A161ASP-1-0.849-0.91941.745-7.424-7.4240.0000.0000.0000.000
159A162ASP-1-0.782-0.85241.335-7.604-7.6040.0000.0000.0000.000
160A163LYS10.8850.95442.9866.3626.3620.0000.0000.0000.000
161A164PRO00.022-0.00642.351-0.118-0.1180.0000.0000.0000.000
162A165GLU-1-0.758-0.86841.740-7.171-7.1710.0000.0000.0000.000
163A166ALA00.0420.03842.147-0.117-0.1170.0000.0000.0000.000
164A167VAL0-0.030-0.02037.412-0.232-0.2320.0000.0000.0000.000
165A168ALA0-0.015-0.00937.467-0.251-0.2510.0000.0000.0000.000
166A169ALA0-0.0060.00037.752-0.183-0.1830.0000.0000.0000.000
167A170ARG10.8580.91835.9177.6087.6080.0000.0000.0000.000
168A171LEU0-0.050-0.02131.668-0.331-0.3310.0000.0000.0000.000
169A172ARG10.8410.90833.0127.1037.1030.0000.0000.0000.000
170A173GLN00.0670.03233.916-0.165-0.1650.0000.0000.0000.000
171A174TYR0-0.016-0.00925.041-0.329-0.3290.0000.0000.0000.000
172A175LYS10.8960.92929.2998.9588.9580.0000.0000.0000.000
173A176ASP-1-0.903-0.94129.728-8.645-8.6450.0000.0000.0000.000
174A177VAL0-0.047-0.02327.765-0.163-0.1630.0000.0000.0000.000
175A178ALA0-0.007-0.00125.521-0.345-0.3450.0000.0000.0000.000
176A179LYS10.8830.92824.9499.0829.0820.0000.0000.0000.000
177A180PRO00.012-0.00625.313-0.247-0.2470.0000.0000.0000.000
178A181VAL00.0280.02219.900-0.308-0.3080.0000.0000.0000.000
179A182ILE0-0.068-0.02920.530-0.477-0.4770.0000.0000.0000.000
180A183GLU-1-0.737-0.86121.316-10.688-10.6880.0000.0000.0000.000
181A184LEU0-0.0020.02018.542-0.103-0.1030.0000.0000.0000.000
182A185TYR00.008-0.01814.142-0.142-0.1420.0000.0000.0000.000
183A186LYS10.8030.89417.07210.61110.6110.0000.0000.0000.000
184A187SER0-0.086-0.05019.250-0.107-0.1070.0000.0000.0000.000
185A188ARG10.8010.86513.33316.50216.5020.0000.0000.0000.000
186A189GLY0-0.0010.01014.766-0.538-0.5380.0000.0000.0000.000
187A190VAL00.0030.00811.448-0.185-0.1850.0000.0000.0000.000
188A191LEU0-0.076-0.02713.765-0.288-0.2880.0000.0000.0000.000
189A192HIS00.0150.01714.1930.9840.9840.0000.0000.0000.000
190A193GLN0-0.001-0.03218.4930.1740.1740.0000.0000.0000.000
191A194PHE00.0120.02122.1490.3520.3520.0000.0000.0000.000
192A195SER0-0.013-0.02223.8530.2000.2000.0000.0000.0000.000
193A196GLY00.0110.02227.5310.3320.3320.0000.0000.0000.000
194A197THR00.0410.00329.446-0.153-0.1530.0000.0000.0000.000
195A198GLU-1-0.758-0.85130.404-9.067-9.0670.0000.0000.0000.000
196A199THR00.0480.01728.812-0.206-0.2060.0000.0000.0000.000
197A200ASN0-0.039-0.02227.985-0.281-0.2810.0000.0000.0000.000
198A201LYS10.8510.89526.4869.1659.1650.0000.0000.0000.000
199A202ILE0-0.0090.01123.095-0.366-0.3660.0000.0000.0000.000
200A203TRP00.002-0.00420.074-0.503-0.5030.0000.0000.0000.000
201A204PRO00.0430.02521.032-0.549-0.5490.0000.0000.0000.000
202A205TYR00.0260.03120.003-0.554-0.5540.0000.0000.0000.000
203A206VAL00.0140.00216.854-0.524-0.5240.0000.0000.0000.000
204A207TYR00.0280.01016.236-0.947-0.9470.0000.0000.0000.000
205A208THR0-0.021-0.03115.948-0.818-0.8180.0000.0000.0000.000
206A209LEU00.0110.01514.347-0.816-0.8160.0000.0000.0000.000
207A210PHE00.001-0.00911.633-1.047-1.0470.0000.0000.0000.000
208A211SER0-0.025-0.02211.094-1.247-1.2470.0000.0000.0000.000
209A212ASN0-0.067-0.02211.669-0.378-0.3780.0000.0000.0000.000
210A213LYS10.8260.9206.35622.97222.9720.0000.0000.0000.000
211A214ILE0-0.012-0.0026.103-3.309-3.3090.0000.0000.0000.000
212A215THR00.0390.0129.2441.4731.4730.0000.0000.0000.000
213A216PRO0-0.0100.00412.003-0.661-0.6610.0000.0000.0000.000
214A217ILE00.0200.01213.8390.0810.0810.0000.0000.0000.000
215A218GLN0-0.051-0.04016.9390.5520.5520.0000.0000.0000.000
216A219SER00.0190.02619.8290.6210.6210.0000.0000.0000.000
217A220LYS10.8850.94122.30311.24211.2420.0000.0000.0000.000
218A221GLU-1-0.837-0.92223.832-11.558-11.5580.0000.0000.0000.000
219A222ALA00.0050.02121.8770.1810.1810.0000.0000.0000.000
220A223TYR0-0.061-0.04120.9820.2910.2910.0000.0000.0000.000
221A224LEU00.0460.03926.7590.2400.2400.0000.0000.0000.000