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: 4JQYN

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 OptH
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 -2550246.589787
FMO2-HF: Nuclear repulsion 2463165.894496
FMO2-HF: Total energy -87080.695291
FMO2-MP2: Total energy -87337.927699


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.
7.95410.2220.018-0.993-1.292-0.002
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 : 0.996
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].
3A6LEU00.0500.0293.3562.6584.6550.021-0.962-1.056-0.002
4A7ARG10.7950.9025.47438.30538.3050.0000.0000.0000.000
5A8ALA00.0350.0107.8701.6611.6610.0000.0000.0000.000
6A9VAL00.0040.01210.8230.3080.3080.0000.0000.0000.000
7A10ILE00.0060.00614.4740.6000.6000.0000.0000.0000.000
8A11LEU00.003-0.00417.6900.4010.4010.0000.0000.0000.000
9A12GLY00.024-0.00620.8230.1070.1070.0000.0000.0000.000
10A13PRO0-0.0110.01324.396-0.104-0.1040.0000.0000.0000.000
11A14PRO00.008-0.01728.001-0.159-0.1590.0000.0000.0000.000
12A15GLY00.0290.01929.7720.2330.2330.0000.0000.0000.000
13A16SER0-0.0240.00025.937-0.044-0.0440.0000.0000.0000.000
14A17GLY00.0420.01926.582-0.037-0.0370.0000.0000.0000.000
15A18LYS10.9020.94921.60612.25112.2510.0000.0000.0000.000
16A19GLY00.0380.03621.777-0.564-0.5640.0000.0000.0000.000
17A20THR0-0.006-0.00223.305-0.239-0.2390.0000.0000.0000.000
18A21VAL00.002-0.01019.739-0.273-0.2730.0000.0000.0000.000
19A22CYS0-0.0060.00718.508-0.710-0.7100.0000.0000.0000.000
20A23GLN00.0440.03018.828-0.439-0.4390.0000.0000.0000.000
21A24ARG10.9090.96120.83711.88411.8840.0000.0000.0000.000
22A25ILE0-0.0100.01114.990-0.153-0.1530.0000.0000.0000.000
23A26ALA0-0.021-0.00516.062-0.945-0.9450.0000.0000.0000.000
24A27GLN0-0.004-0.00116.491-0.277-0.2770.0000.0000.0000.000
25A28ASN0-0.040-0.03618.1310.0370.0370.0000.0000.0000.000
26A29PHE0-0.034-0.01912.6660.0970.0970.0000.0000.0000.000
27A30GLY00.0200.02812.536-1.825-1.8250.0000.0000.0000.000
28A31LEU0-0.048-0.01110.397-1.783-1.7830.0000.0000.0000.000
29A32GLN00.0630.02512.9680.6090.6090.0000.0000.0000.000
30A33HIS0-0.067-0.05614.957-0.406-0.4060.0000.0000.0000.000
31A34LEU0-0.0160.00913.2870.5970.5970.0000.0000.0000.000
32A35SER00.0410.01018.0090.4880.4880.0000.0000.0000.000
33A36SER00.0850.03620.8830.0490.0490.0000.0000.0000.000
34A37GLY0-0.023-0.00823.1900.3100.3100.0000.0000.0000.000
35A38HIS0-0.021-0.01620.4790.8820.8820.0000.0000.0000.000
36A39PHE00.0960.03016.9660.1260.1260.0000.0000.0000.000
37A40LEU00.0000.01822.9500.2760.2760.0000.0000.0000.000
38A41ARG10.9590.97526.43011.78811.7880.0000.0000.0000.000
39A42GLU-1-0.928-0.95721.272-14.559-14.5590.0000.0000.0000.000
40A43ASN00.0210.01122.7640.5000.5000.0000.0000.0000.000
41A44ILE0-0.023-0.00226.5570.2660.2660.0000.0000.0000.000
42A45LYS10.8730.94426.53312.02512.0250.0000.0000.0000.000
43A46ALA0-0.070-0.05027.0740.1990.1990.0000.0000.0000.000
44A47SER0-0.0070.01629.0160.0710.0710.0000.0000.0000.000
45A48THR0-0.003-0.02025.3980.2420.2420.0000.0000.0000.000
46A49GLU-1-0.901-0.95328.400-10.502-10.5020.0000.0000.0000.000
47A50VAL0-0.022-0.03025.5650.3070.3070.0000.0000.0000.000
48A51GLY00.0180.01428.4460.1660.1660.0000.0000.0000.000
49A52GLU-1-0.840-0.93529.482-8.868-8.8680.0000.0000.0000.000
50A53MET0-0.052-0.01831.2780.2150.2150.0000.0000.0000.000
51A54ALA0-0.006-0.00629.9580.2690.2690.0000.0000.0000.000
52A55LYS10.9770.99732.1138.7308.7300.0000.0000.0000.000
53A56GLN00.0650.03734.6900.5260.5260.0000.0000.0000.000
54A57TYR0-0.013-0.01333.1790.1080.1080.0000.0000.0000.000
55A58ILE0-0.038-0.01132.5460.1770.1770.0000.0000.0000.000
56A59GLU-1-0.914-0.97036.824-7.918-7.9180.0000.0000.0000.000
57A60LYS10.8470.92639.7268.0858.0850.0000.0000.0000.000
58A61SER0-0.069-0.04137.8100.1400.1400.0000.0000.0000.000
59A62LEU00.0060.01938.420-0.005-0.0050.0000.0000.0000.000
60A63LEU0-0.014-0.01233.202-0.142-0.1420.0000.0000.0000.000
61A64VAL0-0.023-0.00329.6610.0140.0140.0000.0000.0000.000
62A65PRO00.0320.02031.107-0.145-0.1450.0000.0000.0000.000
63A66ASP-1-0.806-0.91726.879-10.962-10.9620.0000.0000.0000.000
64A67HIS00.0330.01626.209-0.639-0.6390.0000.0000.0000.000
65A68VAL00.0030.00626.759-0.378-0.3780.0000.0000.0000.000
66A69ILE00.0020.00223.541-0.486-0.4860.0000.0000.0000.000
67A70THR0-0.020-0.03321.546-0.682-0.6820.0000.0000.0000.000
68A71ARG10.9420.97621.93310.89810.8980.0000.0000.0000.000
69A72LEU00.0040.00022.030-0.461-0.4610.0000.0000.0000.000
70A73MET0-0.0060.01418.095-0.376-0.3760.0000.0000.0000.000
71A74MET0-0.0060.00617.231-1.233-1.2330.0000.0000.0000.000
72A75SER0-0.032-0.00816.890-0.817-0.8170.0000.0000.0000.000
73A76GLU-1-0.827-0.92017.155-16.855-16.8550.0000.0000.0000.000
74A77LEU0-0.044-0.03613.434-1.128-1.1280.0000.0000.0000.000
75A78GLU-1-0.802-0.88112.147-25.430-25.4300.0000.0000.0000.000
76A79ASN0-0.033-0.00112.367-1.711-1.7110.0000.0000.0000.000
77A80ARG10.8450.92410.56419.90719.9070.0000.0000.0000.000
78A81ARG10.8720.9287.97924.12724.1270.0000.0000.0000.000
79A82GLY0-0.023-0.0034.583-5.722-5.713-0.001-0.002-0.0060.000
80A83GLN0-0.008-0.0105.154-2.466-2.386-0.001-0.002-0.0770.000
81A84HIS00.0440.0544.779-0.786-0.604-0.001-0.027-0.1530.000
82A85TRP0-0.030-0.0427.9043.3743.3740.0000.0000.0000.000
83A86LEU00.0290.01010.4470.0910.0910.0000.0000.0000.000
84A87LEU0-0.032-0.01513.2120.9820.9820.0000.0000.0000.000
85A88ASP-1-0.760-0.89615.628-13.219-13.2190.0000.0000.0000.000
86A89GLY0-0.080-0.05918.9990.4220.4220.0000.0000.0000.000
87A90PHE0-0.0170.00417.3460.7510.7510.0000.0000.0000.000
88A91PRO00.0380.01716.475-0.732-0.7320.0000.0000.0000.000
89A92ARG10.9240.94919.62411.20011.2000.0000.0000.0000.000
90A93THR00.0010.01023.2390.2030.2030.0000.0000.0000.000
91A94LEU00.0810.01521.911-0.488-0.4880.0000.0000.0000.000
92A95GLY00.0530.03922.044-0.343-0.3430.0000.0000.0000.000
93A96GLN0-0.038-0.02920.973-0.547-0.5470.0000.0000.0000.000
94A97ALA00.0170.00217.968-0.727-0.7270.0000.0000.0000.000
95A98GLU-1-0.894-0.94017.359-12.879-12.8790.0000.0000.0000.000
96A99ALA0-0.121-0.06518.467-0.431-0.4310.0000.0000.0000.000
97A100LEU00.0230.00213.313-0.686-0.6860.0000.0000.0000.000
98A101ASP-1-0.765-0.89613.553-18.141-18.1410.0000.0000.0000.000
99A102LYS10.9050.96113.93813.67413.6740.0000.0000.0000.000
100A103ILE0-0.049-0.01512.993-0.358-0.3580.0000.0000.0000.000
101A104CYS0-0.145-0.0648.782-2.660-2.6600.0000.0000.0000.000
102A105GLU-1-0.857-0.9206.964-19.114-19.1140.0000.0000.0000.000
103A106VAL0-0.014-0.0187.271-1.972-1.9720.0000.0000.0000.000
104A107ASP-1-0.796-0.9015.211-30.557-30.5570.0000.0000.0000.000
105A108LEU0-0.075-0.0468.1131.1721.1720.0000.0000.0000.000
106A109VAL00.0170.02110.974-0.230-0.2300.0000.0000.0000.000
107A110ILE00.0370.02214.5390.7100.7100.0000.0000.0000.000
108A111SER0-0.040-0.01817.3440.2880.2880.0000.0000.0000.000
109A112LEU0-0.013-0.01420.8730.2530.2530.0000.0000.0000.000
110A113ASN0-0.046-0.03123.7880.3710.3710.0000.0000.0000.000
111A114ILE00.014-0.00326.6130.1890.1890.0000.0000.0000.000
112A115PRO00.0360.02629.4520.1200.1200.0000.0000.0000.000
113A116PHE00.0540.01332.597-0.004-0.0040.0000.0000.0000.000
114A117GLU-1-0.873-0.94535.280-7.164-7.1640.0000.0000.0000.000
115A118THR0-0.0080.00233.3910.0170.0170.0000.0000.0000.000
116A119LEU0-0.034-0.02931.4700.0050.0050.0000.0000.0000.000
117A120LYS10.9370.97435.4456.9716.9710.0000.0000.0000.000
118A121ASP-1-0.858-0.92039.010-7.105-7.1050.0000.0000.0000.000
119A122ARG10.8570.95433.8658.5438.5430.0000.0000.0000.000
120A123LEU0-0.015-0.01937.4230.0530.0530.0000.0000.0000.000
121A124SER0-0.015-0.01640.4340.1690.1690.0000.0000.0000.000
122A125ARG10.8900.93542.8466.8846.8840.0000.0000.0000.000
123A126ARG10.9130.97137.9267.7257.7250.0000.0000.0000.000
124A127TRP00.0000.00643.9640.1560.1560.0000.0000.0000.000
125A128ILE0-0.015-0.00844.965-0.145-0.1450.0000.0000.0000.000
126A129HIS00.0600.03747.5310.0250.0250.0000.0000.0000.000
127A130PRO0-0.027-0.02049.343-0.094-0.0940.0000.0000.0000.000
128A131PRO0-0.012-0.00349.890-0.086-0.0860.0000.0000.0000.000
129A132SER0-0.027-0.03749.165-0.099-0.0990.0000.0000.0000.000
130A133GLY00.0100.01445.725-0.142-0.1420.0000.0000.0000.000
131A134ARG10.8000.89044.5556.2686.2680.0000.0000.0000.000
132A135VAL00.0140.00740.8420.0840.0840.0000.0000.0000.000
133A136TYR00.009-0.00543.734-0.111-0.1110.0000.0000.0000.000
134A137ASN0-0.040-0.03239.6650.1160.1160.0000.0000.0000.000
135A138LEU00.018-0.00242.758-0.028-0.0280.0000.0000.0000.000
136A139ASP-1-0.884-0.92641.177-6.995-6.9950.0000.0000.0000.000
137A140PHE0-0.121-0.06636.417-0.210-0.2100.0000.0000.0000.000
138A141ASN0-0.037-0.02740.915-0.092-0.0920.0000.0000.0000.000
139A142PRO00.0150.01343.1280.0560.0560.0000.0000.0000.000
140A143PRO00.0180.01846.564-0.045-0.0450.0000.0000.0000.000
141A144HIS0-0.050-0.02648.1020.1340.1340.0000.0000.0000.000
142A145VAL0-0.0070.00551.7700.1010.1010.0000.0000.0000.000
143A146HIS00.013-0.00852.663-0.014-0.0140.0000.0000.0000.000
144A147GLY00.0010.00152.9170.0940.0940.0000.0000.0000.000
145A148ILE0-0.037-0.00753.9280.0410.0410.0000.0000.0000.000
146A149ASP-1-0.732-0.83150.762-6.396-6.3960.0000.0000.0000.000
147A150ASP-1-0.815-0.91449.018-6.353-6.3530.0000.0000.0000.000
148A151VAL0-0.093-0.04450.6450.0660.0660.0000.0000.0000.000
149A152THR0-0.008-0.02653.4240.1130.1130.0000.0000.0000.000
150A153GLY00.0080.01555.5450.1170.1170.0000.0000.0000.000
151A154GLU-1-0.893-0.93155.714-5.584-5.5840.0000.0000.0000.000
152A155PRO00.002-0.01055.113-0.097-0.0970.0000.0000.0000.000
153A156LEU0-0.0300.00449.436-0.095-0.0950.0000.0000.0000.000
154A157VAL0-0.033-0.02150.1810.1090.1090.0000.0000.0000.000
155A158GLN0-0.068-0.02846.777-0.010-0.0100.0000.0000.0000.000
156A159GLN0-0.014-0.01343.1760.2050.2050.0000.0000.0000.000
157A160GLU-1-0.929-0.98546.105-6.554-6.5540.0000.0000.0000.000
158A161ASP-1-0.877-0.93041.491-7.283-7.2830.0000.0000.0000.000
159A162ASP-1-0.863-0.93441.146-7.579-7.5790.0000.0000.0000.000
160A163LYS10.9460.98442.4256.2746.2740.0000.0000.0000.000
161A164PRO00.004-0.01941.860-0.141-0.1410.0000.0000.0000.000
162A165GLU-1-0.885-0.93841.507-6.993-6.9930.0000.0000.0000.000
163A166ALA00.0480.03142.047-0.111-0.1110.0000.0000.0000.000
164A167VAL0-0.042-0.02137.011-0.238-0.2380.0000.0000.0000.000
165A168ALA0-0.002-0.00937.095-0.263-0.2630.0000.0000.0000.000
166A169ALA0-0.0200.00037.462-0.161-0.1610.0000.0000.0000.000
167A170ARG10.9260.95135.4677.7067.7060.0000.0000.0000.000
168A171LEU0-0.055-0.02031.283-0.319-0.3190.0000.0000.0000.000
169A172ARG10.9760.97932.5517.2657.2650.0000.0000.0000.000
170A173GLN00.0520.03633.616-0.097-0.0970.0000.0000.0000.000
171A174TYR0-0.007-0.00624.493-0.342-0.3420.0000.0000.0000.000
172A175LYS10.9190.93528.7588.9008.9000.0000.0000.0000.000
173A176ASP-1-0.889-0.92329.106-8.743-8.7430.0000.0000.0000.000
174A177VAL0-0.075-0.03126.958-0.141-0.1410.0000.0000.0000.000
175A178ALA00.005-0.00324.788-0.304-0.3040.0000.0000.0000.000
176A179LYS10.9550.98624.2259.2239.2230.0000.0000.0000.000
177A180PRO00.0210.00024.837-0.210-0.2100.0000.0000.0000.000
178A181VAL00.0440.03719.376-0.289-0.2890.0000.0000.0000.000
179A182ILE0-0.051-0.02320.027-0.456-0.4560.0000.0000.0000.000
180A183GLU-1-0.933-0.98320.738-10.772-10.7720.0000.0000.0000.000
181A184LEU00.0020.01618.041-0.035-0.0350.0000.0000.0000.000
182A185TYR00.014-0.01414.276-0.211-0.2110.0000.0000.0000.000
183A186LYS10.9110.95516.77810.51210.5120.0000.0000.0000.000
184A187SER0-0.063-0.02919.076-0.131-0.1310.0000.0000.0000.000
185A188ARG10.8640.93613.87116.07116.0710.0000.0000.0000.000
186A189GLY00.0120.02614.331-0.591-0.5910.0000.0000.0000.000
187A190VAL0-0.0010.00311.029-0.272-0.2720.0000.0000.0000.000
188A191LEU0-0.081-0.03013.482-0.264-0.2640.0000.0000.0000.000
189A192HIS00.0120.01114.1210.9370.9370.0000.0000.0000.000
190A193GLN0-0.006-0.02018.2640.0780.0780.0000.0000.0000.000
191A194PHE0-0.0040.01421.7350.2600.2600.0000.0000.0000.000
192A195SER0-0.002-0.01623.8340.1820.1820.0000.0000.0000.000
193A196GLY00.0090.01527.2060.3270.3270.0000.0000.0000.000
194A197THR00.0600.01329.146-0.113-0.1130.0000.0000.0000.000
195A198GLU-1-0.913-0.94730.709-8.960-8.9600.0000.0000.0000.000
196A199THR00.0610.00529.095-0.214-0.2140.0000.0000.0000.000
197A200ASN0-0.020-0.00628.323-0.220-0.2200.0000.0000.0000.000
198A201LYS10.9510.96726.8619.4929.4920.0000.0000.0000.000
199A202ILE00.0040.01123.326-0.365-0.3650.0000.0000.0000.000
200A203TRP0-0.036-0.02619.934-0.490-0.4900.0000.0000.0000.000
201A204PRO00.0490.02521.431-0.528-0.5280.0000.0000.0000.000
202A205TYR00.0270.01919.968-0.566-0.5660.0000.0000.0000.000
203A206VAL00.015-0.00117.168-0.476-0.4760.0000.0000.0000.000
204A207TYR00.017-0.00216.659-0.936-0.9360.0000.0000.0000.000
205A208THR0-0.018-0.01716.545-0.816-0.8160.0000.0000.0000.000
206A209LEU00.0170.01814.369-0.654-0.6540.0000.0000.0000.000
207A210PHE0-0.008-0.01211.600-0.926-0.9260.0000.0000.0000.000
208A211SER0-0.053-0.02211.668-1.070-1.0700.0000.0000.0000.000
209A212ASN0-0.012-0.00211.6090.0120.0120.0000.0000.0000.000
210A213LYS10.8290.9396.97222.85422.8540.0000.0000.0000.000
211A214ILE0-0.0020.0026.058-2.720-2.7200.0000.0000.0000.000
212A215THR00.0340.0048.9851.4901.4900.0000.0000.0000.000
213A216PRO0-0.038-0.01511.753-0.807-0.8070.0000.0000.0000.000
214A217ILE00.0310.00914.118-0.214-0.2140.0000.0000.0000.000
215A218GLN0-0.046-0.02616.9130.3640.3640.0000.0000.0000.000
216A219SER00.0150.01819.8010.5150.5150.0000.0000.0000.000
217A220LYS10.9260.98122.39511.04211.0420.0000.0000.0000.000
218A221GLU-1-0.902-0.97324.076-11.663-11.6630.0000.0000.0000.000
219A222ALA00.0230.02921.934-0.018-0.0180.0000.0000.0000.000
220A223TYR0-0.031-0.02621.6200.3270.3270.0000.0000.0000.000
221A224LEU00.0380.03527.0410.0700.0700.0000.0000.0000.000