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: VK511

Calculation Name: 1AN8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AN8

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NKX2

Base Structure: X-ray

Registration Date: 2023-09-27

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2561183.121561
FMO2-HF: Nuclear repulsion 2477156.009199
FMO2-HF: Total energy -84027.112362
FMO2-MP2: Total energy -84275.361457


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:3:LYS)


Summations of interaction energy for fragment #1(A:3: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.
-122.709-116.8811.8-3.364-4.261-0.028
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.980 / 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].
3A5ASP-1-0.768-0.8582.558-68.871-63.8871.799-3.240-3.543-0.027
4A6ILE00.0010.0053.416-0.4880.0870.005-0.108-0.472-0.001
5A7SER0-0.051-0.0474.8987.5967.678-0.001-0.006-0.0750.000
6A8ASN0-0.022-0.0387.2975.2015.2010.0000.0000.0000.000
7A9VAL00.0230.0194.2663.1883.296-0.001-0.007-0.0990.000
8A10LYS10.8040.9057.45332.17132.1710.0000.0000.0000.000
9A11SER00.0280.0149.8603.2483.2480.0000.0000.0000.000
10A12ASP-1-0.787-0.86010.118-27.627-27.6270.0000.0000.0000.000
11A13LEU0-0.039-0.0108.9802.3552.3550.0000.0000.0000.000
12A14LEU0-0.007-0.00112.8421.8581.8580.0000.0000.0000.000
13A15TYR00.0170.02315.4111.7681.7680.0000.0000.0000.000
14A16ALA0-0.030-0.01215.2661.2091.2090.0000.0000.0000.000
15A17TYR00.023-0.02313.9360.8530.8530.0000.0000.0000.000
16A18THR0-0.055-0.02818.2591.0281.0280.0000.0000.0000.000
17A19ILE0-0.077-0.02920.7590.2460.2460.0000.0000.0000.000
18A20THR0-0.018-0.00923.2900.1330.1330.0000.0000.0000.000
19A21PRO0-0.0160.00025.457-0.035-0.0350.0000.0000.0000.000
20A22TYR0-0.034-0.03526.7620.2550.2550.0000.0000.0000.000
21A23ASP-1-0.802-0.92229.379-9.959-9.9590.0000.0000.0000.000
22A24TYR0-0.057-0.03531.9440.3420.3420.0000.0000.0000.000
23A25LYS10.8450.90833.8939.2789.2780.0000.0000.0000.000
24A26ASP-1-0.867-0.91937.083-7.314-7.3140.0000.0000.0000.000
25A27CYS0-0.0140.01736.9440.1740.1740.0000.0000.0000.000
26A28ARG10.8580.92239.3157.3317.3310.0000.0000.0000.000
27A29VAL0-0.0050.00036.779-0.092-0.0920.0000.0000.0000.000
28A30ASN00.0570.03639.0140.4230.4230.0000.0000.0000.000
29A31PHE0-0.060-0.03936.5560.2540.2540.0000.0000.0000.000
30A32SER00.0510.03435.091-0.195-0.1950.0000.0000.0000.000
31A33THR0-0.040-0.02632.5700.1260.1260.0000.0000.0000.000
32A34THR0-0.005-0.02730.4040.0400.0400.0000.0000.0000.000
33A35HIS00.0390.03727.048-0.037-0.0370.0000.0000.0000.000
34A36THR0-0.0110.00728.092-0.310-0.3100.0000.0000.0000.000
35A37LEU00.0250.02130.3610.3740.3740.0000.0000.0000.000
36A38ASN0-0.0070.00532.579-0.092-0.0920.0000.0000.0000.000
37A39ILE00.002-0.01533.1680.2160.2160.0000.0000.0000.000
38A40ASP-1-0.820-0.89236.724-7.666-7.6660.0000.0000.0000.000
39A41THR00.0510.00835.418-0.010-0.0100.0000.0000.0000.000
40A42GLN00.0160.00538.8340.0820.0820.0000.0000.0000.000
41A43LYS10.7940.90041.1707.7197.7190.0000.0000.0000.000
42A44TYR0-0.079-0.06838.1090.1010.1010.0000.0000.0000.000
43A45ARG10.7880.87232.8949.1999.1990.0000.0000.0000.000
44A46GLY00.0170.02839.6920.0430.0430.0000.0000.0000.000
45A47LYS10.8120.86142.5356.8076.8070.0000.0000.0000.000
46A48ASP-1-0.806-0.88642.215-7.197-7.1970.0000.0000.0000.000
47A49TYR0-0.0250.00035.830-0.135-0.1350.0000.0000.0000.000
48A50TYR0-0.068-0.02533.7350.1900.1900.0000.0000.0000.000
49A51ILE00.0120.01830.756-0.236-0.2360.0000.0000.0000.000
50A52SER0-0.051-0.02430.4670.1860.1860.0000.0000.0000.000
51A53SER0-0.015-0.03028.218-0.343-0.3430.0000.0000.0000.000
52A54GLU-1-0.755-0.86022.926-12.652-12.6520.0000.0000.0000.000
53A55MET0-0.058-0.02225.152-0.395-0.3950.0000.0000.0000.000
54A56SER0-0.018-0.02124.6170.2340.2340.0000.0000.0000.000
55A57TYR00.0130.00826.2560.3250.3250.0000.0000.0000.000
56A58GLU-1-0.802-0.90026.652-10.837-10.8370.0000.0000.0000.000
57A59ALA0-0.0120.00627.5760.2820.2820.0000.0000.0000.000
58A60SER0-0.042-0.04529.6380.3540.3540.0000.0000.0000.000
59A61GLN00.0230.00731.8420.3390.3390.0000.0000.0000.000
60A62LYS10.7930.90932.1559.1719.1710.0000.0000.0000.000
61A63PHE00.0100.00832.0080.1290.1290.0000.0000.0000.000
62A64LYS10.8260.89937.0817.3667.3660.0000.0000.0000.000
63A65ARG10.9320.95839.8327.1527.1520.0000.0000.0000.000
64A66ASP-1-0.826-0.92641.815-7.001-7.0010.0000.0000.0000.000
65A67ASP-1-0.835-0.88639.449-7.682-7.6820.0000.0000.0000.000
66A68HIS0-0.046-0.03940.7160.0250.0250.0000.0000.0000.000
67A69VAL0-0.026-0.01734.718-0.049-0.0490.0000.0000.0000.000
68A70ASP-1-0.834-0.90534.114-8.627-8.6270.0000.0000.0000.000
69A71VAL0-0.013-0.01230.455-0.227-0.2270.0000.0000.0000.000
70A72PHE0-0.008-0.01425.0920.0710.0710.0000.0000.0000.000
71A73GLY0-0.016-0.00825.267-0.299-0.2990.0000.0000.0000.000
72A74LEU0-0.0310.00120.2040.3250.3250.0000.0000.0000.000
73A75PHE00.0000.00623.662-0.235-0.2350.0000.0000.0000.000
74A76TYR0-0.040-0.05120.726-0.546-0.5460.0000.0000.0000.000
75A77ILE0-0.038-0.00422.363-0.215-0.2150.0000.0000.0000.000
76A78LEU00.0130.00025.0770.1020.1020.0000.0000.0000.000
77A79ASN0-0.037-0.02227.7340.2300.2300.0000.0000.0000.000
78A80SER00.008-0.00429.8700.0290.0290.0000.0000.0000.000
79A81HIS00.010-0.00731.9210.0200.0200.0000.0000.0000.000
80A82THR0-0.002-0.00235.792-0.017-0.0170.0000.0000.0000.000
81A83GLY00.0410.03533.4980.0890.0890.0000.0000.0000.000
82A84GLU-1-0.746-0.81230.819-10.018-10.0180.0000.0000.0000.000
83A85TYR00.0450.02126.9730.1460.1460.0000.0000.0000.000
84A86ILE00.0270.00824.960-0.450-0.4500.0000.0000.0000.000
85A87TYR0-0.023-0.02018.7670.4880.4880.0000.0000.0000.000
86A88GLY00.0310.01323.981-0.141-0.1410.0000.0000.0000.000
87A89GLY00.0300.02126.1880.2490.2490.0000.0000.0000.000
88A90ILE0-0.044-0.01127.4490.3470.3470.0000.0000.0000.000
89A91THR00.0040.00330.864-0.260-0.2600.0000.0000.0000.000
90A92PRO00.020-0.00333.1540.1460.1460.0000.0000.0000.000
91A93ALA0-0.0030.01536.385-0.158-0.1580.0000.0000.0000.000
92A94GLN0-0.026-0.01436.815-0.009-0.0090.0000.0000.0000.000
93A95ASN0-0.049-0.02238.7970.2940.2940.0000.0000.0000.000
94A96ASN0-0.063-0.02040.6920.1960.1960.0000.0000.0000.000
95A97LYS10.9860.98240.8836.8706.8700.0000.0000.0000.000
96A98VAL0-0.0020.00536.7130.1430.1430.0000.0000.0000.000
97A99ASN0-0.030-0.03436.340-0.142-0.1420.0000.0000.0000.000
98A100HIS00.0120.00032.841-0.020-0.0200.0000.0000.0000.000
99A101LYS10.9370.97532.2008.2708.2700.0000.0000.0000.000
100A102LEU0-0.0130.00326.4420.0700.0700.0000.0000.0000.000
101A103LEU00.0160.00329.4230.0960.0960.0000.0000.0000.000
102A104GLY00.0590.00625.415-0.265-0.2650.0000.0000.0000.000
103A105ASN0-0.075-0.03123.7040.8060.8060.0000.0000.0000.000
104A106LEU00.0080.00617.918-0.550-0.5500.0000.0000.0000.000
105A107PHE0-0.020-0.00418.2930.7560.7560.0000.0000.0000.000
106A108ILE00.0090.01215.863-1.387-1.3870.0000.0000.0000.000
107A109SER00.017-0.00214.2910.6170.6170.0000.0000.0000.000
108A110GLY0-0.016-0.00716.267-0.136-0.1360.0000.0000.0000.000
109A111GLU-1-0.826-0.88919.230-15.212-15.2120.0000.0000.0000.000
110A112SER0-0.0050.00121.7160.0730.0730.0000.0000.0000.000
111A113GLN0-0.016-0.01123.217-0.208-0.2080.0000.0000.0000.000
112A114GLN00.0150.02821.7590.7510.7510.0000.0000.0000.000
113A115ASN0-0.011-0.02224.728-0.017-0.0170.0000.0000.0000.000
114A116LEU0-0.017-0.01922.3020.0570.0570.0000.0000.0000.000
115A117ASN00.0490.02726.883-0.247-0.2470.0000.0000.0000.000
116A118ASN0-0.081-0.05430.0190.3230.3230.0000.0000.0000.000
117A119LYS10.9280.99127.02311.29311.2930.0000.0000.0000.000
118A120ILE00.0210.02523.696-0.087-0.0870.0000.0000.0000.000
119A121ILE0-0.013-0.00728.2310.2530.2530.0000.0000.0000.000
120A122LEU00.0320.01727.340-0.237-0.2370.0000.0000.0000.000
121A123GLU-1-0.877-0.93631.503-9.517-9.5170.0000.0000.0000.000
122A124LYS10.8900.93631.00010.30310.3030.0000.0000.0000.000
123A125ASP-1-0.792-0.89433.776-8.591-8.5910.0000.0000.0000.000
124A126ILE0-0.081-0.04232.173-0.092-0.0920.0000.0000.0000.000
125A127VAL00.0320.02427.8120.0950.0950.0000.0000.0000.000
126A128THR00.0660.03025.791-0.310-0.3100.0000.0000.0000.000
127A129PHE00.011-0.01720.971-0.018-0.0180.0000.0000.0000.000
128A130GLN00.0250.01721.485-0.580-0.5800.0000.0000.0000.000
129A131GLU-1-0.784-0.86122.497-11.028-11.0280.0000.0000.0000.000
130A132ILE0-0.016-0.01522.680-0.060-0.0600.0000.0000.0000.000
131A133ASP-1-0.777-0.84917.156-18.529-18.5290.0000.0000.0000.000
132A134PHE00.0240.01619.380-0.432-0.4320.0000.0000.0000.000
133A135LYS10.7740.87521.12010.81810.8180.0000.0000.0000.000
134A136ILE0-0.007-0.00618.5800.1330.1330.0000.0000.0000.000
135A137ARG10.8230.88912.39621.25021.2500.0000.0000.0000.000
136A138LYS10.8590.91618.22012.68112.6810.0000.0000.0000.000
137A139TYR00.0300.02121.0280.3180.3180.0000.0000.0000.000
138A140LEU00.0370.00816.1000.1590.1590.0000.0000.0000.000
139A141MET0-0.042-0.01716.827-0.527-0.5270.0000.0000.0000.000
140A142ASP-1-0.841-0.90518.821-13.141-13.1410.0000.0000.0000.000
141A143ASN0-0.115-0.06321.9580.7760.7760.0000.0000.0000.000
142A144TYR0-0.042-0.02918.1060.3020.3020.0000.0000.0000.000
143A145LYS10.8680.92717.53914.90914.9090.0000.0000.0000.000
144A146ILE00.007-0.00313.254-0.902-0.9020.0000.0000.0000.000
145A147TYR0-0.005-0.02011.086-1.110-1.1100.0000.0000.0000.000
146A148ASP-1-0.786-0.86913.379-17.287-17.2870.0000.0000.0000.000
147A149ALA00.0460.02012.790-1.515-1.5150.0000.0000.0000.000
148A150THR0-0.025-0.02212.649-1.608-1.6080.0000.0000.0000.000
149A151SER0-0.058-0.02012.427-0.156-0.1560.0000.0000.0000.000
150A152PRO00.0060.00111.956-1.890-1.8900.0000.0000.0000.000
151A153TYR0-0.044-0.02710.4680.5640.5640.0000.0000.0000.000
152A154VAL0-0.023-0.0154.622-2.066-2.026-0.001-0.001-0.0370.000
153A155SER0-0.044-0.0465.082-10.092-10.053-0.001-0.002-0.0350.000
154A156GLY00.0720.0277.5033.7093.7090.0000.0000.0000.000
155A157ARG10.7750.89110.43620.40920.4090.0000.0000.0000.000
156A158ILE00.0190.01313.2081.2601.2600.0000.0000.0000.000
157A159GLU-1-0.806-0.89116.748-18.393-18.3930.0000.0000.0000.000
158A160ILE0-0.006-0.00619.1660.8330.8330.0000.0000.0000.000
159A161GLY00.0720.04122.497-0.082-0.0820.0000.0000.0000.000
160A162THR0-0.049-0.05425.1340.2580.2580.0000.0000.0000.000
161A163LYS10.8370.89528.4649.2529.2520.0000.0000.0000.000
162A164ASP-1-0.830-0.87829.504-10.533-10.5330.0000.0000.0000.000
163A165GLY00.0040.01028.7880.0800.0800.0000.0000.0000.000
164A166LYS10.8670.92925.45110.42410.4240.0000.0000.0000.000
165A167HIS00.005-0.01121.3030.2560.2560.0000.0000.0000.000
166A168GLU-1-0.822-0.86320.639-14.017-14.0170.0000.0000.0000.000
167A169GLN0-0.060-0.04514.789-1.059-1.0590.0000.0000.0000.000
168A170ILE0-0.014-0.01215.1430.0720.0720.0000.0000.0000.000
169A171ASP-1-0.823-0.8998.621-34.932-34.9320.0000.0000.0000.000
170A172LEU0-0.013-0.00810.7311.3561.3560.0000.0000.0000.000
171A173PHE0-0.024-0.0196.1051.2421.2420.0000.0000.0000.000
172A174ASP-1-0.844-0.9096.398-33.747-33.7470.0000.0000.0000.000
173A175SER0-0.063-0.0617.2964.5734.5730.0000.0000.0000.000
174A176PRO00.0140.0127.556-2.603-2.6030.0000.0000.0000.000
175A177ASN0-0.081-0.0618.5310.5520.5520.0000.0000.0000.000
176A178GLU-1-0.897-0.9428.358-20.565-20.5650.0000.0000.0000.000
177A179GLY0-0.0160.00410.686-1.835-1.8350.0000.0000.0000.000
178A180THR0-0.033-0.03011.8371.0591.0590.0000.0000.0000.000
179A181ARG10.8850.93215.25014.69114.6910.0000.0000.0000.000
180A182SER0-0.0040.01317.8730.1780.1780.0000.0000.0000.000
181A183ASP-1-0.720-0.83012.526-19.481-19.4810.0000.0000.0000.000
182A184ILE0-0.016-0.00412.185-0.138-0.1380.0000.0000.0000.000
183A185PHE00.012-0.01014.244-0.023-0.0230.0000.0000.0000.000
184A186ALA00.0070.01815.8260.8240.8240.0000.0000.0000.000
185A187LYS10.8380.89912.73323.48023.4800.0000.0000.0000.000
186A188TYR0-0.013-0.02417.4200.3760.3760.0000.0000.0000.000
187A189LYS10.8480.92819.34615.01815.0180.0000.0000.0000.000
188A190ASP-1-0.841-0.93021.446-13.553-13.5530.0000.0000.0000.000
189A191ASN0-0.046-0.03123.2730.5260.5260.0000.0000.0000.000
190A192ARG10.8030.88721.97614.06514.0650.0000.0000.0000.000
191A193ILE0-0.024-0.01525.525-0.074-0.0740.0000.0000.0000.000
192A194ILE0-0.0070.00426.560-0.035-0.0350.0000.0000.0000.000
193A195ASN00.0440.02128.9280.3340.3340.0000.0000.0000.000
194A196MET00.0530.03229.469-0.197-0.1970.0000.0000.0000.000
195A197LYS10.8810.94232.7598.5598.5590.0000.0000.0000.000
196A198ASN00.0290.00331.7080.3710.3710.0000.0000.0000.000
197A199PHE00.0210.03225.735-0.171-0.1710.0000.0000.0000.000
198A200SER0-0.059-0.01628.5530.2740.2740.0000.0000.0000.000
199A201HIS10.8100.87424.51012.59712.5970.0000.0000.0000.000
200A202PHE00.0130.01422.080-0.210-0.2100.0000.0000.0000.000
201A203ASP-1-0.802-0.87420.831-12.951-12.9510.0000.0000.0000.000
202A204ILE00.0150.00216.584-0.554-0.5540.0000.0000.0000.000
203A205TYR00.0180.01014.4890.6740.6740.0000.0000.0000.000
204A206LEU00.0240.01112.598-1.381-1.3810.0000.0000.0000.000
205A207GLU-1-0.808-0.8779.668-25.660-25.6600.0000.0000.0000.000
206A208LYS10.8310.89410.24415.77815.7780.0000.0000.0000.000