FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 94772

Calculation Name: 2IM5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IM5

Chain ID: A

ChEMBL ID:

UniProt ID: Q7MXV0

Base Structure: X-ray

Registration Date: 2023-06-22

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 389
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7266958.222505
FMO2-HF: Nuclear repulsion 7109813.353295
FMO2-HF: Total energy -157144.86921
FMO2-MP2: Total energy -157605.549159


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:ILE)


Summations of interaction energy for fragment #1(A:3:ILE)
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.
-51.236-37.69525.518-15.094-23.968-0.108
Interaction energy analysis for fragmet #1(A:3:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.072 / q_NPA : -0.041
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].
3A5ARG10.8930.9432.847-15.223-10.7020.340-2.290-2.5720.028
4A6SER00.003-0.0056.108-0.112-0.1120.0000.0000.0000.000
5A7ILE00.0080.0058.358-0.204-0.2040.0000.0000.0000.000
6A8LEU0-0.011-0.00710.947-0.091-0.0910.0000.0000.0000.000
7A9ASP-1-0.755-0.8484.798-0.622-0.586-0.001-0.006-0.0290.000
8A10THR00.036-0.0157.321-0.187-0.1870.0000.0000.0000.000
9A11ASP-1-0.721-0.8049.826-0.271-0.2710.0000.0000.0000.000
10A12LEU00.0380.01712.9980.0020.0020.0000.0000.0000.000
11A13TYR0-0.047-0.04515.5490.0090.0090.0000.0000.0000.000
12A14LYS10.7290.87912.8560.3230.3230.0000.0000.0000.000
13A15PHE00.0570.02513.1170.0050.0050.0000.0000.0000.000
14A16THR00.0440.02417.7440.0060.0060.0000.0000.0000.000
15A17THR0-0.045-0.04219.9760.0140.0140.0000.0000.0000.000
16A18GLY00.0370.02919.4090.0020.0020.0000.0000.0000.000
17A19TYR00.010-0.00520.2980.0100.0100.0000.0000.0000.000
18A20ALA00.0130.00523.2010.0070.0070.0000.0000.0000.000
19A21TYR0-0.063-0.07320.5810.0120.0120.0000.0000.0000.000
20A22ALA0-0.002-0.00523.5980.0050.0050.0000.0000.0000.000
21A23LYS10.8400.93425.5090.0520.0520.0000.0000.0000.000
22A24LEU0-0.044-0.01628.5650.0050.0050.0000.0000.0000.000
23A25PHE0-0.037-0.01527.3570.0000.0000.0000.0000.0000.000
24A26PRO00.0240.01826.625-0.010-0.0100.0000.0000.0000.000
25A27ARG10.9020.94127.6520.0650.0650.0000.0000.0000.000
26A28ALA00.0310.02926.805-0.001-0.0010.0000.0000.0000.000
27A29TYR0-0.039-0.01324.614-0.002-0.0020.0000.0000.0000.000
28A30GLY00.011-0.00422.8700.0100.0100.0000.0000.0000.000
29A31GLU-1-0.758-0.86521.159-0.237-0.2370.0000.0000.0000.000
30A32PHE0-0.011-0.00516.7670.0160.0160.0000.0000.0000.000
31A33ARG10.8930.94517.6710.2020.2020.0000.0000.0000.000
32A34PHE00.001-0.00311.4820.0000.0000.0000.0000.0000.000
33A35ILE0-0.012-0.02115.9110.0390.0390.0000.0000.0000.000
34A36ASP-1-0.727-0.87114.762-0.396-0.3960.0000.0000.0000.000
35A37ARG10.7870.89416.3380.3050.3050.0000.0000.0000.000
36A38ASN0-0.020-0.01116.9290.0470.0470.0000.0000.0000.000
37A39ARG10.8400.92719.0780.2500.2500.0000.0000.0000.000
38A40GLN00.0700.04014.4340.0290.0290.0000.0000.0000.000
39A41GLY0-0.0020.01017.819-0.005-0.0050.0000.0000.0000.000
40A42PHE0-0.036-0.02711.076-0.023-0.0230.0000.0000.0000.000
41A43THR00.018-0.01514.4470.0120.0120.0000.0000.0000.000
42A44GLU-1-0.763-0.90313.727-0.485-0.4850.0000.0000.0000.000
43A45GLU-1-0.881-0.90312.110-0.386-0.3860.0000.0000.0000.000
44A46PHE00.0020.0107.412-0.110-0.1100.0000.0000.0000.000
45A47ALA00.0270.0158.930-0.169-0.1690.0000.0000.0000.000
46A48GLU-1-0.770-0.85410.314-0.630-0.6300.0000.0000.0000.000
47A49LEU0-0.014-0.0036.191-0.088-0.0880.0000.0000.0000.000
48A50VAL00.0120.0035.789-0.488-0.4880.0000.0000.0000.000
49A51ARG10.7190.8176.8310.3480.3480.0000.0000.0000.000
50A52GLY0-0.032-0.0137.7490.1180.1180.0000.0000.0000.000
51A53GLU-1-0.808-0.9171.988-24.461-23.56216.335-8.451-8.783-0.110
52A54ILE0-0.022-0.0135.2990.4020.423-0.001-0.002-0.0180.000
53A55ARG10.8240.8808.1490.8650.8650.0000.0000.0000.000
54A56ALA0-0.0060.0074.8710.2780.2780.0000.0000.0000.000
55A57MET0-0.016-0.0065.9070.3510.3510.0000.0000.0000.000
56A58ALA0-0.0130.0067.5320.1990.1990.0000.0000.0000.000
57A59ALA0-0.042-0.0198.8530.0700.0700.0000.0000.0000.000
58A60LEU0-0.067-0.0177.0130.1420.1420.0000.0000.0000.000
59A61SER0-0.009-0.02110.436-0.085-0.0850.0000.0000.0000.000
60A62LEU0-0.0290.00313.9070.0670.0670.0000.0000.0000.000
61A63THR00.019-0.02014.452-0.008-0.0080.0000.0000.0000.000
62A64ARG10.7870.83817.091-0.198-0.1980.0000.0000.0000.000
63A65ASP-1-0.822-0.90718.0970.2560.2560.0000.0000.0000.000
64A66GLU-1-0.770-0.84012.8800.2700.2700.0000.0000.0000.000
65A67LYS10.7630.86317.640-0.105-0.1050.0000.0000.0000.000
66A68GLU-1-0.838-0.91320.5500.1130.1130.0000.0000.0000.000
67A69PHE00.0120.01117.540-0.014-0.0140.0000.0000.0000.000
68A70LEU0-0.003-0.00617.404-0.021-0.0210.0000.0000.0000.000
69A71GLN0-0.055-0.03720.896-0.005-0.0050.0000.0000.0000.000
70A72ARG10.7670.88023.717-0.103-0.1030.0000.0000.0000.000
71A73GLU-1-0.892-0.94821.4170.0330.0330.0000.0000.0000.000
72A74LEU0-0.089-0.03518.294-0.016-0.0160.0000.0000.0000.000
73A75PRO00.0210.01522.775-0.006-0.0060.0000.0000.0000.000
74A76TYR00.0200.00922.022-0.006-0.0060.0000.0000.0000.000
75A77LEU0-0.050-0.01820.106-0.012-0.0120.0000.0000.0000.000
76A78PRO00.0250.00924.6450.0100.0100.0000.0000.0000.000
77A79PRO00.0360.00725.905-0.003-0.0030.0000.0000.0000.000
78A80ILE00.0480.02825.7760.0020.0020.0000.0000.0000.000
79A81TYR00.0380.01119.307-0.006-0.0060.0000.0000.0000.000
80A82ILE00.0180.01021.354-0.003-0.0030.0000.0000.0000.000
81A83ASP-1-0.863-0.92621.6150.0460.0460.0000.0000.0000.000
82A84PHE0-0.057-0.02619.0120.0030.0030.0000.0000.0000.000
83A85LEU00.011-0.00616.177-0.006-0.0060.0000.0000.0000.000
84A86ASP-1-0.755-0.83017.7740.1210.1210.0000.0000.0000.000
85A87GLY0-0.0170.00919.0350.0220.0220.0000.0000.0000.000
86A88PHE0-0.051-0.01913.570-0.001-0.0010.0000.0000.0000.000
87A89ARG10.8710.93214.331-0.027-0.0270.0000.0000.0000.000
88A90PHE00.0210.00210.463-0.033-0.0330.0000.0000.0000.000
89A91ASP-1-0.860-0.93813.385-0.191-0.1910.0000.0000.0000.000
90A92PRO0-0.007-0.01711.798-0.025-0.0250.0000.0000.0000.000
91A93GLU-1-0.947-0.95014.040-0.227-0.2270.0000.0000.0000.000
92A94GLU-1-0.802-0.86116.252-0.264-0.2640.0000.0000.0000.000
93A95VAL0-0.067-0.04312.4290.0000.0000.0000.0000.0000.000
94A96THR00.0120.02415.081-0.006-0.0060.0000.0000.0000.000
95A97VAL0-0.007-0.02110.948-0.027-0.0270.0000.0000.0000.000
96A98SER0-0.0100.00914.2320.0370.0370.0000.0000.0000.000
97A99ILE0-0.0050.00714.351-0.036-0.0360.0000.0000.0000.000
98A100ASP-1-0.793-0.89317.550-0.242-0.2420.0000.0000.0000.000
99A101ALA0-0.018-0.02120.7750.0050.0050.0000.0000.0000.000
100A102GLN0-0.105-0.05922.9180.0310.0310.0000.0000.0000.000
101A103GLY00.0170.02220.3380.0070.0070.0000.0000.0000.000
102A104HIS0-0.038-0.02017.803-0.001-0.0010.0000.0000.0000.000
103A105LEU00.0080.01610.3940.0000.0000.0000.0000.0000.000
104A106ASP-1-0.842-0.88115.014-0.321-0.3210.0000.0000.0000.000
105A107ILE00.0540.00810.654-0.028-0.0280.0000.0000.0000.000
106A108ARG10.7780.84714.9590.3270.3270.0000.0000.0000.000
107A109ALA00.0450.04514.974-0.005-0.0050.0000.0000.0000.000
108A110GLN0-0.077-0.05717.0280.0470.0470.0000.0000.0000.000
109A111GLY00.0730.03220.5270.0000.0000.0000.0000.0000.000
110A112LEU00.0020.00421.8480.0060.0060.0000.0000.0000.000
111A113LEU0-0.0100.00021.023-0.016-0.0160.0000.0000.0000.000
112A114TYR0-0.017-0.02220.370-0.017-0.0170.0000.0000.0000.000
113A115ARG10.7660.87016.5430.2150.2150.0000.0000.0000.000
114A116VAL0-0.002-0.00416.497-0.027-0.0270.0000.0000.0000.000
115A117THR0-0.018-0.03715.771-0.048-0.0480.0000.0000.0000.000
116A118LEU0-0.012-0.01113.367-0.031-0.0310.0000.0000.0000.000
117A119TRP00.013-0.0089.338-0.072-0.0720.0000.0000.0000.000
118A120GLU-1-0.812-0.85710.228-0.452-0.4520.0000.0000.0000.000
119A121THR0-0.028-0.0548.390-0.071-0.0710.0000.0000.0000.000
120A122PRO00.0370.0165.671-0.085-0.0850.0000.0000.0000.000
121A123ILE00.0370.0295.385-0.280-0.2800.0000.0000.0000.000
122A124LEU0-0.046-0.0296.952-0.125-0.1250.0000.0000.0000.000
123A125ALA00.0200.0134.715-0.125-0.026-0.001-0.010-0.0880.000
124A126VAL0-0.005-0.0022.413-2.343-0.5341.380-0.838-2.3510.002
125A127ILE0-0.003-0.0043.359-0.609-0.0480.051-0.014-0.598-0.003
126A128SER0-0.027-0.0366.1260.1780.1780.0000.0000.0000.000
127A129GLU-1-0.783-0.8812.337-5.340-2.0282.331-1.964-3.679-0.023
128A130LEU0-0.037-0.0282.405-0.797-0.1682.027-0.450-2.206-0.002
129A131TYR0-0.049-0.0433.9510.2200.2820.006-0.014-0.0550.000
130A132TYR0-0.012-0.0287.3540.1130.1130.0000.0000.0000.000
131A133ARG10.9150.9482.534-2.153-1.3693.002-0.862-2.925-0.001
132A134PHE0-0.053-0.0207.0950.1030.1030.0000.0000.0000.000
133A135ILE0-0.046-0.0228.8320.0770.0770.0000.0000.0000.000
134A136GLY0-0.024-0.00110.6460.0510.0510.0000.0000.0000.000
135A137ALA0-0.038-0.01211.1990.0520.0520.0000.0000.0000.000
136A138GLU-1-0.910-0.97210.7020.0340.0340.0000.0000.0000.000
137A139PRO0-0.060-0.01511.197-0.021-0.0210.0000.0000.0000.000
138A140ASP-1-0.807-0.91514.0030.0500.0500.0000.0000.0000.000
139A141TRP00.006-0.01711.420-0.028-0.0280.0000.0000.0000.000
140A142LYS10.7910.89117.500-0.017-0.0170.0000.0000.0000.000
141A143GLN0-0.002-0.00519.2190.0020.0020.0000.0000.0000.000
142A144VAL00.0040.00914.715-0.004-0.0040.0000.0000.0000.000
143A145GLU-1-0.741-0.83217.9570.0980.0980.0000.0000.0000.000
144A146GLU-1-0.810-0.88320.2810.0120.0120.0000.0000.0000.000
145A147VAL0-0.013-0.00820.145-0.003-0.0030.0000.0000.0000.000
146A148THR0-0.039-0.02417.700-0.015-0.0150.0000.0000.0000.000
147A149ARG10.8770.92420.537-0.034-0.0340.0000.0000.0000.000
148A150SER0-0.049-0.03323.503-0.002-0.0020.0000.0000.0000.000
149A151LYS10.7800.87119.5540.0860.0860.0000.0000.0000.000
150A152GLY00.0530.02623.489-0.003-0.0030.0000.0000.0000.000
151A153GLU-1-0.774-0.85524.3860.0210.0210.0000.0000.0000.000
152A154LEU00.0080.01927.6020.0000.0000.0000.0000.0000.000
153A155MET0-0.0290.00424.760-0.004-0.0040.0000.0000.0000.000
154A156ARG10.7970.88127.895-0.014-0.0140.0000.0000.0000.000
155A157GLU-1-0.896-0.93229.617-0.014-0.0140.0000.0000.0000.000
156A158HIS10.7510.86031.3220.0230.0230.0000.0000.0000.000
157A159ARG10.8120.87831.312-0.003-0.0030.0000.0000.0000.000
158A160ALA00.0100.01528.788-0.002-0.0020.0000.0000.0000.000
159A161THR0-0.006-0.01127.217-0.002-0.0020.0000.0000.0000.000
160A162PHE0-0.011-0.01220.297-0.008-0.0080.0000.0000.0000.000
161A163SER0-0.023-0.00619.9050.0130.0130.0000.0000.0000.000
162A164ILE00.0440.03814.436-0.015-0.0150.0000.0000.0000.000
163A165PHE0-0.023-0.02815.684-0.005-0.0050.0000.0000.0000.000
164A166GLY00.0470.00013.343-0.013-0.0130.0000.0000.0000.000
165A167MET0-0.0060.0585.5030.0040.0040.0000.0000.0000.000
166A168ARG10.7800.8738.2310.2540.2540.0000.0000.0000.000
167A169ARG10.8130.9249.5590.3350.3350.0000.0000.0000.000
168A170ARG10.7850.8843.0260.3830.8570.045-0.119-0.4000.001
169A171PHE00.0280.0347.788-0.176-0.1760.0000.0000.0000.000
170A172SER00.0750.0155.108-0.139-0.1390.0000.0000.0000.000
171A173LEU0-0.029-0.0173.573-0.0220.3120.004-0.074-0.2640.000
172A174GLU-1-0.906-0.9575.4550.6250.6250.0000.0000.0000.000
173A175VAL00.0170.0158.2290.0140.0140.0000.0000.0000.000
174A176GLU-1-0.786-0.9058.568-0.311-0.3110.0000.0000.0000.000
175A177ASP-1-0.814-0.8769.5660.3730.3730.0000.0000.0000.000
176A178ARG10.7880.84911.335-0.130-0.1300.0000.0000.0000.000
177A179VAL00.002-0.00113.185-0.005-0.0050.0000.0000.0000.000
178A180THR0-0.044-0.04213.226-0.011-0.0110.0000.0000.0000.000
179A181ASP-1-0.903-0.93615.5770.1480.1480.0000.0000.0000.000
180A182ILE0-0.0150.00217.000-0.009-0.0090.0000.0000.0000.000
181A183LEU0-0.005-0.01817.483-0.008-0.0080.0000.0000.0000.000
182A184LYS10.8170.89919.280-0.131-0.1310.0000.0000.0000.000
183A185GLN0-0.062-0.00721.511-0.006-0.0060.0000.0000.0000.000
184A186TYR0-0.011-0.02223.100-0.005-0.0050.0000.0000.0000.000
185A187ALA00.0230.01823.546-0.006-0.0060.0000.0000.0000.000
186A188GLY00.0080.01425.465-0.005-0.0050.0000.0000.0000.000
187A189GLU-1-0.811-0.88926.4550.0050.0050.0000.0000.0000.000
188A190SER0-0.078-0.03126.806-0.006-0.0060.0000.0000.0000.000
189A191LEU00.0210.02419.826-0.011-0.0110.0000.0000.0000.000
190A192PHE0-0.013-0.00723.0900.0110.0110.0000.0000.0000.000
191A193GLY00.0530.02320.6930.0130.0130.0000.0000.0000.000
192A194THR0-0.0020.00314.309-0.024-0.0240.0000.0000.0000.000
193A195SER0-0.005-0.02514.4160.0160.0160.0000.0000.0000.000
194A196ASN0-0.024-0.0178.2500.0600.0600.0000.0000.0000.000
195A197VAL00.0370.01712.2740.0480.0480.0000.0000.0000.000
196A198HIS00.0300.0218.5780.0340.0340.0000.0000.0000.000
197A199LEU0-0.002-0.0029.3070.0580.0580.0000.0000.0000.000
198A200ALA0-0.020-0.01312.9680.0160.0160.0000.0000.0000.000
199A201HIS0-0.0070.00014.964-0.002-0.0020.0000.0000.0000.000
200A202LYS10.8150.89312.669-0.360-0.3600.0000.0000.0000.000
201A203HIS0-0.031-0.01614.2750.0070.0070.0000.0000.0000.000
202A204GLY00.0230.03117.929-0.010-0.0100.0000.0000.0000.000
203A205LEU0-0.070-0.03517.813-0.015-0.0150.0000.0000.0000.000
204A206ARG10.9110.95020.076-0.006-0.0060.0000.0000.0000.000
205A207VAL00.0450.02317.124-0.008-0.0080.0000.0000.0000.000
206A208SER0-0.054-0.04318.6520.0020.0020.0000.0000.0000.000
207A209GLY00.015-0.00118.704-0.019-0.0190.0000.0000.0000.000
208A210THR0-0.028-0.01320.5960.0100.0100.0000.0000.0000.000
209A211HIS00.0540.03621.404-0.005-0.0050.0000.0000.0000.000
210A212PRO00.0090.02819.6640.0000.0000.0000.0000.0000.000
211A213HIS00.006-0.02521.772-0.002-0.0020.0000.0000.0000.000
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