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: 5JVQZ

Calculation Name: 2IMH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IMH

Chain ID: A

ChEMBL ID:

UniProt ID: Q5LQD5

Base Structure: X-ray

Registration Date: 2023-09-23

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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2548086.419438
FMO2-HF: Nuclear repulsion 2462758.541427
FMO2-HF: Total energy -85327.878011
FMO2-MP2: Total energy -85577.280273


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:0:SER)


Summations of interaction energy for fragment #1(A:0:SER)
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.
-8.727-1.7755.13-3.942-8.1390.007
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.021
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].
3A2THR0-0.028-0.0253.1512.8875.6820.076-1.425-1.4460.004
4A3PHE00.0420.0065.250-0.405-0.319-0.001-0.012-0.0730.000
5A4SER0-0.035-0.0488.8860.3120.3120.0000.0000.0000.000
6A5ILE00.0060.00611.560-0.062-0.0620.0000.0000.0000.000
7A6LEU0-0.033-0.00315.3850.0480.0480.0000.0000.0000.000
8A7ALA00.029-0.01118.195-0.013-0.0130.0000.0000.0000.000
9A8HIS00.0270.00421.7700.0150.0150.0000.0000.0000.000
10A9ASP-1-0.782-0.86925.381-0.042-0.0420.0000.0000.0000.000
11A10PRO0-0.009-0.01827.9490.0060.0060.0000.0000.0000.000
12A11GLU-1-0.986-0.96631.400-0.023-0.0230.0000.0000.0000.000
13A12THR0-0.053-0.06129.9720.0050.0050.0000.0000.0000.000
14A13GLY00.0130.00431.2860.0040.0040.0000.0000.0000.000
15A14ALA0-0.052-0.00926.710-0.002-0.0020.0000.0000.0000.000
16A15ILE0-0.0070.00723.914-0.012-0.0120.0000.0000.0000.000
17A16GLY00.054-0.01220.9910.0210.0210.0000.0000.0000.000
18A17GLY00.0290.01717.121-0.039-0.0390.0000.0000.0000.000
19A18ALA0-0.027-0.00814.7350.0530.0530.0000.0000.0000.000
20A19ALA00.013-0.0049.373-0.123-0.1230.0000.0000.0000.000
21A20ALA00.0120.0118.0860.0990.0990.0000.0000.0000.000
22A21THR00.0130.0072.604-1.726-0.7020.781-0.636-1.1690.008
23A22GLY00.0500.0392.390-2.375-1.7241.593-0.885-1.3590.001
24A23SER0-0.022-0.0202.631-3.143-1.6822.539-0.737-3.263-0.006
25A24LEU00.0190.0294.123-1.167-1.0240.007-0.054-0.0950.000
26A25CYS0-0.047-0.0427.274-0.155-0.1550.0000.0000.0000.000
27A26VAL00.0360.0406.978-0.291-0.2910.0000.0000.0000.000
28A27GLY00.029-0.0068.426-0.237-0.2370.0000.0000.0000.000
29A28GLY0-0.067-0.02511.455-0.044-0.0440.0000.0000.0000.000
30A29TRP0-0.045-0.0167.639-0.227-0.2270.0000.0000.0000.000
31A30VAL0-0.0110.0178.037-0.081-0.0810.0000.0000.0000.000
32A31LEU0-0.039-0.01611.071-0.021-0.0210.0000.0000.0000.000
33A32ARG10.7710.87713.4200.2280.2280.0000.0000.0000.000
34A33GLY00.045-0.00117.695-0.023-0.0230.0000.0000.0000.000
35A34ASP-1-0.800-0.88821.206-0.039-0.0390.0000.0000.0000.000
36A35LEU00.0360.02424.934-0.009-0.0090.0000.0000.0000.000
37A36ASN0-0.077-0.02828.073-0.008-0.0080.0000.0000.0000.000
38A37ALA00.0010.00125.340-0.003-0.0030.0000.0000.0000.000
39A38GLY00.0400.01624.383-0.009-0.0090.0000.0000.0000.000
40A39MET0-0.063-0.01219.1390.0230.0230.0000.0000.0000.000
41A40SER0-0.036-0.03617.509-0.022-0.0220.0000.0000.0000.000
42A41ALA00.0340.01912.3480.0430.0430.0000.0000.0000.000
43A42SER0-0.054-0.03012.361-0.113-0.1130.0000.0000.0000.000
44A43GLN00.009-0.0017.3360.1990.1990.0000.0000.0000.000
45A44GLY00.0310.0066.3650.3740.3740.0000.0000.0000.000
46A45ALA0-0.026-0.0094.940-0.802-0.8020.0000.0000.0000.000
47A46ALA0-0.030-0.0185.9920.6010.6010.0000.0000.0000.000
48A47PRO00.0020.0237.0040.1480.1480.0000.0000.0000.000
49A48SER00.0210.0099.8630.1940.1940.0000.0000.0000.000
50A49THR00.0220.01513.607-0.034-0.0340.0000.0000.0000.000
51A50PHE00.0310.02315.2380.0000.0000.0000.0000.0000.000
52A51TRP00.0640.02413.617-0.022-0.0220.0000.0000.0000.000
53A52GLY00.0440.02116.377-0.003-0.0030.0000.0000.0000.000
54A53GLU-1-0.820-0.90417.192-0.106-0.1060.0000.0000.0000.000
55A54GLU-1-0.923-0.97820.464-0.188-0.1880.0000.0000.0000.000
56A55VAL0-0.017-0.00718.7480.0130.0130.0000.0000.0000.000
57A56LEU0-0.0090.00520.1890.0120.0120.0000.0000.0000.000
58A57GLN0-0.037-0.02423.2360.0180.0180.0000.0000.0000.000
59A58HIS00.0480.01624.2110.0120.0120.0000.0000.0000.000
60A59LEU0-0.0100.00523.3710.0040.0040.0000.0000.0000.000
61A60ARG10.7310.84525.0130.0940.0940.0000.0000.0000.000
62A61ASP-1-0.912-0.94029.547-0.089-0.0890.0000.0000.0000.000
63A62GLY0-0.032-0.01230.7330.0030.0030.0000.0000.0000.000
64A63SER0-0.067-0.02927.594-0.002-0.0020.0000.0000.0000.000
65A64HIS00.0590.04026.798-0.006-0.0060.0000.0000.0000.000
66A65PRO00.009-0.01523.345-0.010-0.0100.0000.0000.0000.000
67A66GLU-1-0.917-0.97023.138-0.263-0.2630.0000.0000.0000.000
68A67ASP-1-0.884-0.93724.023-0.187-0.1870.0000.0000.0000.000
69A68ALA00.0060.00423.816-0.005-0.0050.0000.0000.0000.000
70A69VAL00.003-0.00518.655-0.015-0.0150.0000.0000.0000.000
71A70ASN0-0.0130.00820.877-0.044-0.0440.0000.0000.0000.000
72A71HIS0-0.048-0.01123.2330.0010.0010.0000.0000.0000.000
73A72VAL00.0130.01618.7660.0000.0000.0000.0000.0000.000
74A73THR0-0.045-0.03317.077-0.008-0.0080.0000.0000.0000.000
75A74SER0-0.055-0.03819.5050.0040.0040.0000.0000.0000.000
76A75GLN0-0.0030.00222.6870.0130.0130.0000.0000.0000.000
77A76ASP-1-0.791-0.85116.941-0.338-0.3380.0000.0000.0000.000
78A77SER0-0.033-0.03319.426-0.034-0.0340.0000.0000.0000.000
79A78GLY0-0.005-0.00316.468-0.006-0.0060.0000.0000.0000.000
80A79ARG10.8420.89814.6760.2380.2380.0000.0000.0000.000
81A80ALA00.0210.00714.059-0.097-0.0970.0000.0000.0000.000
82A81TYR0-0.0100.00010.179-0.056-0.0560.0000.0000.0000.000
83A82ARG10.7950.8839.2980.2660.2660.0000.0000.0000.000
84A83GLN0-0.010-0.0129.055-0.247-0.2470.0000.0000.0000.000
85A84LEU0-0.036-0.00711.468-0.012-0.0120.0000.0000.0000.000
86A85ALA00.0320.02014.2260.0080.0080.0000.0000.0000.000
87A86ALA00.020-0.00316.3750.0240.0240.0000.0000.0000.000
88A87MET0-0.0290.00919.537-0.007-0.0070.0000.0000.0000.000
89A88ASP-1-0.728-0.84422.382-0.125-0.1250.0000.0000.0000.000
90A89LEU0-0.034-0.03325.8730.0030.0030.0000.0000.0000.000
91A90LEU0-0.063-0.02028.2020.0110.0110.0000.0000.0000.000
92A91GLY00.017-0.00125.4480.0030.0030.0000.0000.0000.000
93A92ASN0-0.104-0.04125.577-0.015-0.0150.0000.0000.0000.000
94A93ALA00.001-0.01621.235-0.002-0.0020.0000.0000.0000.000
95A94ALA0-0.0130.00921.3150.0040.0040.0000.0000.0000.000
96A95ALA00.010-0.00916.025-0.017-0.0170.0000.0000.0000.000
97A96PHE00.0260.02514.7210.0340.0340.0000.0000.0000.000
98A97THR0-0.023-0.02911.302-0.163-0.1630.0000.0000.0000.000
99A98GLY00.0010.02513.0270.0800.0800.0000.0000.0000.000
100A99SER0-0.025-0.05412.166-0.147-0.1470.0000.0000.0000.000
101A100GLU-1-0.850-0.89611.116-0.591-0.5910.0000.0000.0000.000
102A101ASN0-0.075-0.0377.411-0.435-0.4350.0000.0000.0000.000
103A102GLN00.0090.0044.5740.4790.579-0.001-0.005-0.0930.000
104A103ASP-1-0.817-0.8826.702-1.263-1.2630.0000.0000.0000.000
105A104ILE0-0.011-0.0138.372-0.162-0.1620.0000.0000.0000.000
106A105LYS10.8000.8789.4030.7640.7640.0000.0000.0000.000
107A106GLY00.0020.00111.3750.1400.1400.0000.0000.0000.000
108A107SER0-0.001-0.02212.944-0.063-0.0630.0000.0000.0000.000
109A108VAL0-0.0110.00415.6760.0280.0280.0000.0000.0000.000
110A109THR00.0290.02618.8810.0040.0040.0000.0000.0000.000
111A110PHE0-0.012-0.02419.3600.0110.0110.0000.0000.0000.000
112A111ALA0-0.008-0.01724.1030.0020.0020.0000.0000.0000.000
113A112SER0-0.0180.01625.3720.0080.0080.0000.0000.0000.000
114A113GLY00.0860.02421.9040.0140.0140.0000.0000.0000.000
115A114ILE0-0.048-0.00917.474-0.014-0.0140.0000.0000.0000.000
116A115ALA00.0320.03015.3730.0200.0200.0000.0000.0000.000
117A116SER0-0.035-0.02912.562-0.064-0.0640.0000.0000.0000.000
118A117GLY00.0450.0078.9950.0870.0870.0000.0000.0000.000
119A118ASN0-0.052-0.0204.824-0.945-0.886-0.001-0.009-0.0490.000
120A119MET0-0.0120.0242.934-0.648-0.1150.138-0.176-0.4960.000
121A120LEU0-0.0060.0105.6520.3620.3620.0000.0000.0000.000
122A121GLY00.0230.0108.8190.1020.1020.0000.0000.0000.000
123A122ASP-1-0.769-0.86710.852-0.330-0.3300.0000.0000.0000.000
124A123ASN0-0.043-0.03213.618-0.090-0.0900.0000.0000.0000.000
125A124SER0-0.057-0.05415.8760.0100.0100.0000.0000.0000.000
126A125VAL0-0.0070.01911.0700.0330.0330.0000.0000.0000.000
127A126LEU00.0330.00712.2720.0570.0570.0000.0000.0000.000
128A127GLY0-0.0210.00915.6020.0530.0530.0000.0000.0000.000
129A128ALA00.0690.02517.4790.0310.0310.0000.0000.0000.000
130A129MET0-0.069-0.01012.445-0.001-0.0010.0000.0000.0000.000
131A130THR0-0.031-0.03117.0610.0280.0280.0000.0000.0000.000
132A131GLU-1-0.973-0.98919.961-0.111-0.1110.0000.0000.0000.000
133A132ALA0-0.002-0.01019.8380.0190.0190.0000.0000.0000.000
134A133PHE0-0.029-0.01420.2200.0200.0200.0000.0000.0000.000
135A134VAL0-0.041-0.03122.1080.0110.0110.0000.0000.0000.000
136A135ALA0-0.029-0.00225.1170.0080.0080.0000.0000.0000.000
137A136SER0-0.062-0.01624.9000.0150.0150.0000.0000.0000.000
138A137ASP-1-0.881-0.95326.796-0.020-0.0200.0000.0000.0000.000
139A138LEU0-0.058-0.01625.1460.0080.0080.0000.0000.0000.000
140A139THR00.0460.00727.054-0.007-0.0070.0000.0000.0000.000
141A140PHE00.0140.01522.8740.0050.0050.0000.0000.0000.000
142A141GLU-1-0.796-0.91622.1200.0090.0090.0000.0000.0000.000
143A142ARG10.8590.91121.178-0.043-0.0430.0000.0000.0000.000
144A143ARG10.8570.95221.9520.0500.0500.0000.0000.0000.000
145A144LEU0-0.031-0.00718.126-0.012-0.0120.0000.0000.0000.000
146A145LEU0-0.025-0.02017.2470.0090.0090.0000.0000.0000.000
147A146ALA00.0230.01017.5320.0150.0150.0000.0000.0000.000
148A147ALA00.0200.01817.118-0.008-0.0080.0000.0000.0000.000
149A148LEU0-0.030-0.01411.661-0.025-0.0250.0000.0000.0000.000
150A149ILE00.0190.00313.8080.0110.0110.0000.0000.0000.000
151A150ALA0-0.0100.00016.191-0.005-0.0050.0000.0000.0000.000
152A151ALA0-0.023-0.01312.200-0.033-0.0330.0000.0000.0000.000
153A152GLU-1-0.906-0.97611.3870.3350.3350.0000.0000.0000.000
154A153GLY0-0.040-0.01812.521-0.020-0.0200.0000.0000.0000.000
155A154ALA0-0.0250.00215.074-0.005-0.0050.0000.0000.0000.000
156A155GLY0-0.0270.00111.704-0.088-0.0880.0000.0000.0000.000
157A156SER0-0.036-0.0378.477-0.086-0.0860.0000.0000.0000.000
158A157ASP-1-0.812-0.9139.158-0.002-0.0020.0000.0000.0000.000
159A158PHE0-0.025-0.0169.8500.0720.0720.0000.0000.0000.000
160A159ARG10.7800.8605.0091.0311.0310.0000.0000.0000.000
161A160GLY00.0000.0195.1440.1100.210-0.001-0.003-0.0960.000
162A161LEU0-0.021-0.0175.3580.2040.2040.0000.0000.0000.000
163A162LEU0-0.042-0.0235.617-0.406-0.4060.0000.0000.0000.000
164A163SER0-0.033-0.0376.478-0.550-0.5500.0000.0000.0000.000
165A164ALA00.0230.0028.0080.1590.1590.0000.0000.0000.000
166A165ALA0-0.036-0.01810.622-0.050-0.0500.0000.0000.0000.000
167A166MET00.0330.01513.306-0.049-0.0490.0000.0000.0000.000
168A167LEU0-0.0200.00616.4870.0200.0200.0000.0000.0000.000
169A168VAL00.0070.00218.770-0.027-0.0270.0000.0000.0000.000
170A169LEU0-0.021-0.00622.3020.0140.0140.0000.0000.0000.000
171A170HIS00.0550.00225.254-0.004-0.0040.0000.0000.0000.000
172A171PRO00.0340.01528.9690.0060.0060.0000.0000.0000.000
173A172ASP-1-0.820-0.88832.098-0.005-0.0050.0000.0000.0000.000
174A173ARG10.8490.91927.4320.0010.0010.0000.0000.0000.000
175A174PRO00.0350.03028.300-0.005-0.0050.0000.0000.0000.000
176A175PRO0-0.021-0.02823.9500.0000.0000.0000.0000.0000.000
177A176VAL00.0220.02122.2770.0160.0160.0000.0000.0000.000
178A177THR0-0.030-0.00619.150-0.005-0.0050.0000.0000.0000.000
179A178LEU0-0.035-0.01718.4460.0160.0160.0000.0000.0000.000
180A179ARG10.8300.87514.078-0.273-0.2730.0000.0000.0000.000
181A180ILE0-0.0340.00512.681-0.029-0.0290.0000.0000.0000.000
182A181ASP-1-0.748-0.85311.2380.6170.6170.0000.0000.0000.000
183A182TYR00.024-0.0039.9530.1210.1210.0000.0000.0000.000
184A183HIS0-0.0160.00810.978-0.124-0.1240.0000.0000.0000.000
185A184PRO0-0.048-0.01410.8570.1540.1540.0000.0000.0000.000
186A185ASP-1-0.909-0.96411.8140.4450.4450.0000.0000.0000.000
187A186ASN00.0360.01512.694-0.013-0.0130.0000.0000.0000.000
188A187PRO00.0530.0199.332-0.090-0.0900.0000.0000.0000.000
189A188ILE00.0320.02111.001-0.057-0.0570.0000.0000.0000.000
190A189GLY00.0480.02514.100-0.067-0.0670.0000.0000.0000.000
191A190ALA0-0.057-0.03115.409-0.041-0.0410.0000.0000.0000.000
192A191LEU00.0090.01014.130-0.034-0.0340.0000.0000.0000.000
193A192GLU-1-0.767-0.86216.9850.0600.0600.0000.0000.0000.000
194A193GLN0-0.001-0.00920.086-0.030-0.0300.0000.0000.0000.000
195A194LEU0-0.0300.00418.220-0.019-0.0190.0000.0000.0000.000
196A195TYR00.0600.01620.806-0.021-0.0210.0000.0000.0000.000
197A196GLN0-0.026-0.01422.484-0.021-0.0210.0000.0000.0000.000
198A197LYS10.8150.91523.772-0.184-0.1840.0000.0000.0000.000
199A198ALA0-0.014-0.00623.931-0.009-0.0090.0000.0000.0000.000
200A199THR0-0.046-0.03225.411-0.013-0.0130.0000.0000.0000.000
201A200THR0-0.026-0.01828.098-0.010-0.0100.0000.0000.0000.000
202A201GLY00.0170.00131.0550.0040.0040.0000.0000.0000.000
203A202ASP-1-0.800-0.90033.7770.0730.0730.0000.0000.0000.000
204A203TYR00.0130.01526.4050.0020.0020.0000.0000.0000.000
205A204ALA00.0160.01231.318-0.003-0.0030.0000.0000.0000.000
206A205ASP-1-0.846-0.91432.2290.0370.0370.0000.0000.0000.000
207A206TRP00.0060.00529.381-0.002-0.0020.0000.0000.0000.000
208A207ALA0-0.008-0.00730.278-0.004-0.0040.0000.0000.0000.000
209A208ARG10.7460.82932.165-0.038-0.0380.0000.0000.0000.000
210A209GLN00.001-0.00435.012-0.006-0.0060.0000.0000.0000.000
211A210VAL0-0.0280.00231.4530.0000.0000.0000.0000.0000.000
212A211PRO0-0.043-0.02034.159-0.003-0.0030.0000.0000.0000.000
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