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

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FMODB ID: 5JR5Z

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 OptHSide
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 -2551453.700368
FMO2-HF: Nuclear repulsion 2464371.934081
FMO2-HF: Total energy -87081.766287
FMO2-MP2: Total energy -87339.025555


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.
6.0458.670-1.292-1.3340.004
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 : 1.029 / q_NPA : 1.022
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].
3A6LEU00.0340.0243.6231.6864.1290.001-1.256-1.1890.004
4A7ARG10.7940.9115.78536.51136.5110.0000.0000.0000.000
5A8ALA00.0290.0078.1671.5221.5220.0000.0000.0000.000
6A9VAL0-0.0080.01011.1620.4120.4120.0000.0000.0000.000
7A10ILE00.0110.00414.8390.5440.5440.0000.0000.0000.000
8A11LEU00.000-0.00117.9310.4180.4180.0000.0000.0000.000
9A12GLY00.023-0.00521.1250.0750.0750.0000.0000.0000.000
10A13PRO0-0.0070.01924.629-0.079-0.0790.0000.0000.0000.000
11A14PRO00.0210.00528.283-0.176-0.1760.0000.0000.0000.000
12A15GLY00.0280.01930.0000.2300.2300.0000.0000.0000.000
13A16SER0-0.035-0.02426.344-0.049-0.0490.0000.0000.0000.000
14A17GLY00.0310.01226.615-0.047-0.0470.0000.0000.0000.000
15A18LYS10.8980.94221.80312.47712.4770.0000.0000.0000.000
16A19GLY00.0520.04121.918-0.577-0.5770.0000.0000.0000.000
17A20THR0-0.009-0.00723.454-0.287-0.2870.0000.0000.0000.000
18A21VAL00.004-0.00819.567-0.278-0.2780.0000.0000.0000.000
19A22CYS0-0.020-0.00218.583-0.715-0.7150.0000.0000.0000.000
20A23GLN00.0420.02918.889-0.479-0.4790.0000.0000.0000.000
21A24ARG10.8700.93120.99112.12912.1290.0000.0000.0000.000
22A25ILE00.0040.01614.854-0.176-0.1760.0000.0000.0000.000
23A26ALA0-0.027-0.00616.236-0.978-0.9780.0000.0000.0000.000
24A27GLN0-0.008-0.00616.749-0.192-0.1920.0000.0000.0000.000
25A28ASN0-0.044-0.03418.1360.0600.0600.0000.0000.0000.000
26A29PHE0-0.027-0.02112.3930.0650.0650.0000.0000.0000.000
27A30GLY00.0180.02812.738-1.854-1.8540.0000.0000.0000.000
28A31LEU0-0.055-0.01510.672-1.699-1.6990.0000.0000.0000.000
29A32GLN00.0670.02613.2960.8020.8020.0000.0000.0000.000
30A33HIS0-0.066-0.05915.296-0.405-0.4050.0000.0000.0000.000
31A34LEU0-0.0200.01213.6780.6150.6150.0000.0000.0000.000
32A35SER00.0460.00818.2990.4830.4830.0000.0000.0000.000
33A36SER00.0970.04021.150-0.003-0.0030.0000.0000.0000.000
34A37GLY0-0.032-0.01323.3980.3120.3120.0000.0000.0000.000
35A38HIS0-0.059-0.03821.5420.7350.7350.0000.0000.0000.000
36A39PHE00.0840.02317.5290.1510.1510.0000.0000.0000.000
37A40LEU0-0.0040.02123.4560.2610.2610.0000.0000.0000.000
38A41ARG10.9700.97926.87111.76011.7600.0000.0000.0000.000
39A42GLU-1-0.887-0.92622.058-14.208-14.2080.0000.0000.0000.000
40A43ASN00.0160.00123.1440.4420.4420.0000.0000.0000.000
41A44ILE0-0.015-0.00227.0350.2450.2450.0000.0000.0000.000
42A45LYS10.8540.93226.64312.03312.0330.0000.0000.0000.000
43A46ALA0-0.070-0.04627.4830.1880.1880.0000.0000.0000.000
44A47SER0-0.0010.00329.4520.0340.0340.0000.0000.0000.000
45A48THR0-0.013-0.01825.7470.2280.2280.0000.0000.0000.000
46A49GLU-1-0.789-0.88528.876-10.451-10.4510.0000.0000.0000.000
47A50VAL00.008-0.01325.8070.3040.3040.0000.0000.0000.000
48A51GLY00.0160.01328.9170.1590.1590.0000.0000.0000.000
49A52GLU-1-0.817-0.90529.969-8.893-8.8930.0000.0000.0000.000
50A53MET0-0.066-0.02931.7590.1970.1970.0000.0000.0000.000
51A54ALA0-0.003-0.00830.4820.2590.2590.0000.0000.0000.000
52A55LYS10.8980.93632.6228.6068.6060.0000.0000.0000.000
53A56GLN00.0520.03235.1940.5040.5040.0000.0000.0000.000
54A57TYR0-0.006-0.00933.8970.1070.1070.0000.0000.0000.000
55A58ILE0-0.035-0.00133.0400.1760.1760.0000.0000.0000.000
56A59GLU-1-0.852-0.91537.201-7.993-7.9930.0000.0000.0000.000
57A60LYS10.8630.93340.2338.0168.0160.0000.0000.0000.000
58A61SER0-0.060-0.04538.2370.1210.1210.0000.0000.0000.000
59A62LEU0-0.0110.01238.582-0.008-0.0080.0000.0000.0000.000
60A63LEU0-0.004-0.00933.283-0.138-0.1380.0000.0000.0000.000
61A64VAL0-0.0180.00029.8810.0210.0210.0000.0000.0000.000
62A65PRO00.0210.01931.252-0.160-0.1600.0000.0000.0000.000
63A66ASP-1-0.697-0.83027.138-11.206-11.2060.0000.0000.0000.000
64A67HIS00.0470.03426.289-0.611-0.6110.0000.0000.0000.000
65A68VAL00.0110.01126.769-0.367-0.3670.0000.0000.0000.000
66A69ILE0-0.001-0.00123.591-0.482-0.4820.0000.0000.0000.000
67A70THR0-0.032-0.04321.611-0.653-0.6530.0000.0000.0000.000
68A71ARG10.8260.90521.95310.77710.7770.0000.0000.0000.000
69A72LEU00.0060.00322.520-0.465-0.4650.0000.0000.0000.000
70A73MET0-0.0040.00818.085-0.387-0.3870.0000.0000.0000.000
71A74MET0-0.0030.00816.818-1.132-1.1320.0000.0000.0000.000
72A75SER0-0.0190.00117.370-0.733-0.7330.0000.0000.0000.000
73A76GLU-1-0.792-0.88517.619-16.766-16.7660.0000.0000.0000.000
74A77LEU0-0.037-0.02713.876-1.022-1.0220.0000.0000.0000.000
75A78GLU-1-0.770-0.84812.641-24.407-24.4070.0000.0000.0000.000
76A79ASN0-0.090-0.04012.787-1.407-1.4070.0000.0000.0000.000
77A80ARG10.8200.89310.98919.07319.0730.0000.0000.0000.000
78A81ARG10.8530.9048.33222.79022.7900.0000.0000.0000.000
79A82GLY0-0.022-0.0015.002-4.943-4.9430.0000.0000.0000.000
80A83GLN0-0.006-0.0075.540-2.633-2.6330.0000.0000.0000.000
81A84HIS00.0470.0444.599-1.051-0.869-0.001-0.036-0.1450.000
82A85TRP0-0.030-0.0438.0773.3503.3500.0000.0000.0000.000
83A86LEU00.0230.01110.804-0.066-0.0660.0000.0000.0000.000
84A87LEU0-0.022-0.01113.5821.0111.0110.0000.0000.0000.000
85A88ASP-1-0.738-0.87215.941-13.250-13.2500.0000.0000.0000.000
86A89GLY0-0.104-0.07619.3540.4690.4690.0000.0000.0000.000
87A90PHE0-0.0020.01517.5780.7200.7200.0000.0000.0000.000
88A91PRO00.0240.01216.770-0.774-0.7740.0000.0000.0000.000
89A92ARG10.8520.87219.82411.12711.1270.0000.0000.0000.000
90A93THR00.0060.00523.4640.2320.2320.0000.0000.0000.000
91A94LEU00.0730.01821.939-0.487-0.4870.0000.0000.0000.000
92A95GLY00.0590.04222.106-0.337-0.3370.0000.0000.0000.000
93A96GLN0-0.069-0.04721.056-0.573-0.5730.0000.0000.0000.000
94A97ALA00.0180.00218.068-0.715-0.7150.0000.0000.0000.000
95A98GLU-1-0.850-0.92117.391-12.730-12.7300.0000.0000.0000.000
96A99ALA0-0.110-0.05018.400-0.426-0.4260.0000.0000.0000.000
97A100LEU00.0380.00713.317-0.650-0.6500.0000.0000.0000.000
98A101ASP-1-0.735-0.83713.516-17.841-17.8410.0000.0000.0000.000
99A102LYS10.8520.92513.79313.79513.7950.0000.0000.0000.000
100A103ILE0-0.045-0.01413.163-0.294-0.2940.0000.0000.0000.000
101A104CYS0-0.149-0.0638.772-2.437-2.4370.0000.0000.0000.000
102A105GLU-1-0.805-0.9057.139-18.394-18.3940.0000.0000.0000.000
103A106VAL0-0.030-0.0197.348-2.124-2.1240.0000.0000.0000.000
104A107ASP-1-0.786-0.8965.207-31.552-31.5520.0000.0000.0000.000
105A108LEU0-0.074-0.0478.3671.0401.0400.0000.0000.0000.000
106A109VAL00.0170.02311.034-0.140-0.1400.0000.0000.0000.000
107A110ILE00.0360.02214.7100.6810.6810.0000.0000.0000.000
108A111SER0-0.043-0.01217.3540.3230.3230.0000.0000.0000.000
109A112LEU0-0.003-0.01520.9550.2390.2390.0000.0000.0000.000
110A113ASN0-0.023-0.01723.7840.4660.4660.0000.0000.0000.000
111A114ILE00.020-0.00126.6120.1880.1880.0000.0000.0000.000
112A115PRO00.0360.02729.3710.1280.1280.0000.0000.0000.000
113A116PHE00.0520.01832.503-0.014-0.0140.0000.0000.0000.000
114A117GLU-1-0.783-0.88635.282-7.170-7.1700.0000.0000.0000.000
115A118THR0-0.0020.00033.1550.0200.0200.0000.0000.0000.000
116A119LEU0-0.031-0.02331.4030.0090.0090.0000.0000.0000.000
117A120LYS10.8230.90835.4347.1297.1290.0000.0000.0000.000
118A121ASP-1-0.861-0.93038.926-7.123-7.1230.0000.0000.0000.000
119A122ARG10.8510.92833.1198.6548.6540.0000.0000.0000.000
120A123LEU0-0.006-0.01237.1720.0570.0570.0000.0000.0000.000
121A124SER0-0.011-0.00240.4700.1830.1830.0000.0000.0000.000
122A125ARG10.8600.89442.8076.9366.9360.0000.0000.0000.000
123A126ARG10.8340.90538.7417.6877.6870.0000.0000.0000.000
124A127TRP0-0.030-0.01144.0070.1660.1660.0000.0000.0000.000
125A128ILE0-0.006-0.00544.941-0.145-0.1450.0000.0000.0000.000
126A129HIS00.0600.04147.7010.0220.0220.0000.0000.0000.000
127A130PRO0-0.022-0.02149.603-0.088-0.0880.0000.0000.0000.000
128A131PRO0-0.016-0.00150.228-0.086-0.0860.0000.0000.0000.000
129A132SER0-0.022-0.03849.403-0.093-0.0930.0000.0000.0000.000
130A133GLY00.0030.01246.044-0.142-0.1420.0000.0000.0000.000
131A134ARG10.7980.87544.8106.2416.2410.0000.0000.0000.000
132A135VAL00.0080.00040.9600.0810.0810.0000.0000.0000.000
133A136TYR00.010-0.00643.818-0.106-0.1060.0000.0000.0000.000
134A137ASN0-0.042-0.03439.5530.1310.1310.0000.0000.0000.000
135A138LEU00.0270.00642.724-0.030-0.0300.0000.0000.0000.000
136A139ASP-1-0.853-0.88340.991-6.997-6.9970.0000.0000.0000.000
137A140PHE0-0.106-0.05936.409-0.209-0.2090.0000.0000.0000.000
138A141ASN0-0.043-0.02840.755-0.091-0.0910.0000.0000.0000.000
139A142PRO00.0180.01643.0360.0580.0580.0000.0000.0000.000
140A143PRO00.0110.01746.462-0.046-0.0460.0000.0000.0000.000
141A144HIS0-0.051-0.03048.3210.1390.1390.0000.0000.0000.000
142A145VAL0-0.011-0.00151.6800.1000.1000.0000.0000.0000.000
143A146HIS00.010-0.00552.997-0.025-0.0250.0000.0000.0000.000
144A147GLY00.0010.00152.8700.0950.0950.0000.0000.0000.000
145A148ILE0-0.032-0.00753.9120.0420.0420.0000.0000.0000.000
146A149ASP-1-0.729-0.80250.921-6.399-6.3990.0000.0000.0000.000
147A150ASP-1-0.817-0.91348.954-6.374-6.3740.0000.0000.0000.000
148A151VAL0-0.085-0.03850.7850.0640.0640.0000.0000.0000.000
149A152THR0-0.018-0.04153.5500.1080.1080.0000.0000.0000.000
150A153GLY00.0080.01755.6520.1170.1170.0000.0000.0000.000
151A154GLU-1-0.877-0.92555.807-5.602-5.6020.0000.0000.0000.000
152A155PRO0-0.005-0.01655.232-0.099-0.0990.0000.0000.0000.000
153A156LEU0-0.0280.00749.446-0.090-0.0900.0000.0000.0000.000
154A157VAL0-0.028-0.01850.4590.1060.1060.0000.0000.0000.000
155A158GLN0-0.041-0.02246.930-0.064-0.0640.0000.0000.0000.000
156A159GLN0-0.004-0.01043.3560.1820.1820.0000.0000.0000.000
157A160GLU-1-0.898-0.97546.320-6.492-6.4920.0000.0000.0000.000
158A161ASP-1-0.861-0.93041.762-7.413-7.4130.0000.0000.0000.000
159A162ASP-1-0.802-0.86640.977-7.678-7.6780.0000.0000.0000.000
160A163LYS10.9030.96742.6126.3636.3630.0000.0000.0000.000
161A164PRO00.028-0.00641.981-0.140-0.1400.0000.0000.0000.000
162A165GLU-1-0.837-0.92741.682-7.088-7.0880.0000.0000.0000.000
163A166ALA00.0370.03342.339-0.103-0.1030.0000.0000.0000.000
164A167VAL0-0.033-0.02037.185-0.236-0.2360.0000.0000.0000.000
165A168ALA0-0.007-0.00937.336-0.265-0.2650.0000.0000.0000.000
166A169ALA0-0.022-0.00237.738-0.161-0.1610.0000.0000.0000.000
167A170ARG10.8860.93335.8167.6537.6530.0000.0000.0000.000
168A171LEU0-0.057-0.02231.434-0.326-0.3260.0000.0000.0000.000
169A172ARG10.9300.96232.8727.1687.1680.0000.0000.0000.000
170A173GLN00.0620.04233.909-0.136-0.1360.0000.0000.0000.000
171A174TYR0-0.011-0.00624.734-0.324-0.3240.0000.0000.0000.000
172A175LYS10.8830.91129.0299.0519.0510.0000.0000.0000.000
173A176ASP-1-0.889-0.92529.378-8.726-8.7260.0000.0000.0000.000
174A177VAL0-0.073-0.02627.093-0.139-0.1390.0000.0000.0000.000
175A178ALA0-0.009-0.01225.128-0.316-0.3160.0000.0000.0000.000
176A179LYS10.9040.95124.4809.1899.1890.0000.0000.0000.000
177A180PRO00.0280.00425.065-0.229-0.2290.0000.0000.0000.000
178A181VAL00.0340.03119.670-0.301-0.3010.0000.0000.0000.000
179A182ILE0-0.050-0.02520.246-0.466-0.4660.0000.0000.0000.000
180A183GLU-1-0.794-0.89020.993-10.700-10.7000.0000.0000.0000.000
181A184LEU00.0100.02118.120-0.040-0.0400.0000.0000.0000.000
182A185TYR00.004-0.01914.131-0.183-0.1830.0000.0000.0000.000
183A186LYS10.8340.90116.98910.60310.6030.0000.0000.0000.000
184A187SER0-0.097-0.04919.155-0.063-0.0630.0000.0000.0000.000
185A188ARG10.8100.88013.10416.53416.5340.0000.0000.0000.000
186A189GLY00.0070.02214.439-0.609-0.6090.0000.0000.0000.000
187A190VAL0-0.004-0.00111.234-0.356-0.3560.0000.0000.0000.000
188A191LEU0-0.080-0.02713.486-0.313-0.3130.0000.0000.0000.000
189A192HIS00.0080.00913.7570.9720.9720.0000.0000.0000.000
190A193GLN0-0.002-0.02218.0630.1470.1470.0000.0000.0000.000
191A194PHE0-0.0060.01621.5930.2700.2700.0000.0000.0000.000
192A195SER0-0.005-0.01823.5950.1990.1990.0000.0000.0000.000
193A196GLY00.0110.01626.8990.3370.3370.0000.0000.0000.000
194A197THR00.0580.01128.802-0.109-0.1090.0000.0000.0000.000
195A198GLU-1-0.861-0.92630.192-9.041-9.0410.0000.0000.0000.000
196A199THR00.0760.02128.818-0.202-0.2020.0000.0000.0000.000
197A200ASN0-0.010-0.00428.018-0.255-0.2550.0000.0000.0000.000
198A201LYS10.8970.95126.2879.3499.3490.0000.0000.0000.000
199A202ILE0-0.0050.00523.062-0.375-0.3750.0000.0000.0000.000
200A203TRP0-0.010-0.00719.956-0.461-0.4610.0000.0000.0000.000
201A204PRO00.0500.02420.971-0.549-0.5490.0000.0000.0000.000
202A205TYR00.0250.02219.813-0.605-0.6050.0000.0000.0000.000
203A206VAL00.0210.00216.753-0.493-0.4930.0000.0000.0000.000
204A207TYR00.0080.00016.198-1.004-1.0040.0000.0000.0000.000
205A208THR0-0.002-0.01915.893-0.872-0.8720.0000.0000.0000.000
206A209LEU00.0040.01613.932-0.742-0.7420.0000.0000.0000.000
207A210PHE0-0.003-0.01011.414-1.106-1.1060.0000.0000.0000.000
208A211SER0-0.047-0.02411.065-1.235-1.2350.0000.0000.0000.000
209A212ASN0-0.040-0.01211.207-0.140-0.1400.0000.0000.0000.000
210A213LYS10.8420.9436.18424.11924.1190.0000.0000.0000.000
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