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: 3Q8ML

Calculation Name: 1MBM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1MBM

Chain ID: A

ChEMBL ID:

UniProt ID: P19811

Base Structure: X-ray

Registration Date: 2023-06-19

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1921348.360732
FMO2-HF: Nuclear repulsion 1849710.802004
FMO2-HF: Total energy -71637.558728
FMO2-MP2: Total energy -71846.497241


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:7:LYS)


Summations of interaction energy for fragment #1(A:7: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.
-140.435-135.020.757-2.602-3.567-0.018
Interaction energy analysis for fragmet #1(A:7:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.982 / q_NPA : 0.971
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].
3A9ARG10.8910.9092.75614.35418.2140.695-2.166-2.389-0.016
4A10GLY0-0.007-0.0114.8411.2041.293-0.001-0.004-0.0830.000
5A11ASN0-0.047-0.0245.9760.1780.1780.0000.0000.0000.000
6A12VAL00.0060.0127.2003.3713.3710.0000.0000.0000.000
7A13GLY00.0030.0038.373-1.725-1.7250.0000.0000.0000.000
8A14PHE0-0.032-0.0108.5620.5690.5690.0000.0000.0000.000
9A15VAL00.0150.00212.8600.4800.4800.0000.0000.0000.000
10A16ALA0-0.012-0.00416.5630.2000.2000.0000.0000.0000.000
11A17GLY00.0520.01919.3960.2050.2050.0000.0000.0000.000
12A18SER0-0.124-0.05322.9470.3290.3290.0000.0000.0000.000
13A19SER0-0.0030.00821.3740.1690.1690.0000.0000.0000.000
14A20TYR0-0.018-0.01416.888-0.227-0.2270.0000.0000.0000.000
15A21GLY00.0290.00815.8040.2530.2530.0000.0000.0000.000
16A22THR0-0.032-0.01310.897-1.202-1.2020.0000.0000.0000.000
17A23GLY00.0270.00712.8241.4241.4240.0000.0000.0000.000
18A24SER0-0.0180.01312.142-1.738-1.7380.0000.0000.0000.000
19A25VAL00.0140.00812.6141.7141.7140.0000.0000.0000.000
20A26TRP00.001-0.02613.338-1.858-1.8580.0000.0000.0000.000
21A27THR00.0050.01016.0620.9480.9480.0000.0000.0000.000
22A28ARG10.7920.88418.80112.80712.8070.0000.0000.0000.000
23A29ASN00.0070.00122.2740.1760.1760.0000.0000.0000.000
24A30ASN0-0.038-0.02024.2300.1380.1380.0000.0000.0000.000
25A31GLU-1-0.860-0.90123.522-11.959-11.9590.0000.0000.0000.000
26A32VAL0-0.022-0.01517.878-0.526-0.5260.0000.0000.0000.000
27A33VAL0-0.011-0.01319.0940.6210.6210.0000.0000.0000.000
28A34VAL00.002-0.00516.758-1.175-1.1750.0000.0000.0000.000
29A35LEU0-0.013-0.00317.1970.9920.9920.0000.0000.0000.000
30A36THR00.014-0.01016.872-0.771-0.7710.0000.0000.0000.000
31A37ALA00.0530.04418.6940.4990.4990.0000.0000.0000.000
32A38SER0-0.048-0.05921.0010.0010.0010.0000.0000.0000.000
33A39HIS0-0.081-0.06921.2010.1460.1460.0000.0000.0000.000
34A40VAL00.0150.02818.4100.2310.2310.0000.0000.0000.000
35A41VAL0-0.0130.01121.6060.1930.1930.0000.0000.0000.000
36A42GLY00.0880.04723.6330.3010.3010.0000.0000.0000.000
37A43ARG10.9530.95626.9578.4308.4300.0000.0000.0000.000
38A44ALA0-0.037-0.02129.3970.1680.1680.0000.0000.0000.000
39A45ASN0-0.034-0.03627.891-0.238-0.2380.0000.0000.0000.000
40A46MET00.0210.02726.283-0.121-0.1210.0000.0000.0000.000
41A47ALA00.0080.00121.3470.0560.0560.0000.0000.0000.000
42A48THR0-0.0120.00019.2030.1250.1250.0000.0000.0000.000
43A49LEU00.0130.02613.781-0.313-0.3130.0000.0000.0000.000
44A50LYS10.9510.96912.01620.98520.9850.0000.0000.0000.000
45A51ILE00.008-0.0059.736-1.047-1.0470.0000.0000.0000.000
46A52GLY00.0020.0179.9190.7680.7680.0000.0000.0000.000
47A53ASP-1-0.918-0.96311.030-21.804-21.8040.0000.0000.0000.000
48A54ALA0-0.055-0.01814.2341.6071.6070.0000.0000.0000.000
49A55MET0-0.016-0.01915.525-0.558-0.5580.0000.0000.0000.000
50A56LEU00.0100.01518.2230.7150.7150.0000.0000.0000.000
51A57THR0-0.028-0.01720.310-0.212-0.2120.0000.0000.0000.000
52A58LEU0-0.006-0.00519.3890.2050.2050.0000.0000.0000.000
53A59THR00.001-0.00823.7490.3890.3890.0000.0000.0000.000
54A60PHE0-0.009-0.01020.233-0.139-0.1390.0000.0000.0000.000
55A61LYS10.9400.97325.92210.72710.7270.0000.0000.0000.000
56A62LYS10.8440.92626.49410.43310.4330.0000.0000.0000.000
57A63ASN0-0.0130.00527.5430.6050.6050.0000.0000.0000.000
58A64GLY00.0620.03627.751-0.253-0.2530.0000.0000.0000.000
59A65ASP-1-0.789-0.89322.851-12.399-12.3990.0000.0000.0000.000
60A66PHE00.0410.05821.221-0.558-0.5580.0000.0000.0000.000
61A67ALA0-0.005-0.01022.4250.6090.6090.0000.0000.0000.000
62A68GLU-1-0.830-0.92521.702-13.333-13.3330.0000.0000.0000.000
63A69ALA0-0.0120.00021.6420.6980.6980.0000.0000.0000.000
64A70VAL0-0.0050.00022.120-0.528-0.5280.0000.0000.0000.000
65A71THR00.0170.00620.6870.4460.4460.0000.0000.0000.000
66A72THR00.0470.01623.445-0.069-0.0690.0000.0000.0000.000
67A73GLN00.0720.00917.724-0.575-0.5750.0000.0000.0000.000
68A74SER0-0.044-0.02320.666-0.399-0.3990.0000.0000.0000.000
69A75GLU-1-0.963-0.96422.478-12.485-12.4850.0000.0000.0000.000
70A76LEU0-0.038-0.01815.684-0.449-0.4490.0000.0000.0000.000
71A77PRO00.0250.03116.978-0.412-0.4120.0000.0000.0000.000
72A78GLY00.0330.00313.818-1.304-1.3040.0000.0000.0000.000
73A79ASN0-0.064-0.02412.3362.2862.2860.0000.0000.0000.000
74A80TRP0-0.043-0.02410.640-2.582-2.5820.0000.0000.0000.000
75A81PRO00.0230.02111.4211.2441.2440.0000.0000.0000.000
76A82GLN00.026-0.00114.1290.2950.2950.0000.0000.0000.000
77A83LEU0-0.026-0.00917.067-0.507-0.5070.0000.0000.0000.000
78A84HIS00.0230.02118.6921.3471.3470.0000.0000.0000.000
79A85PHE0-0.012-0.00619.925-0.429-0.4290.0000.0000.0000.000
80A86ALA00.009-0.00222.1510.4030.4030.0000.0000.0000.000
81A87GLN0-0.058-0.02023.6870.0970.0970.0000.0000.0000.000
82A88PRO00.0240.01023.284-0.307-0.3070.0000.0000.0000.000
83A89THR0-0.012-0.00423.1640.7720.7720.0000.0000.0000.000
84A90THR0-0.035-0.01922.989-0.459-0.4590.0000.0000.0000.000
85A91GLY00.0240.01621.8200.2440.2440.0000.0000.0000.000
86A92PRO00.0220.02116.5780.0780.0780.0000.0000.0000.000
87A93ALA0-0.012-0.00115.9960.2120.2120.0000.0000.0000.000
88A94SER00.0070.01110.648-0.256-0.2560.0000.0000.0000.000
89A95TRP0-0.022-0.00611.5040.4300.4300.0000.0000.0000.000
90A96CYS0-0.053-0.0268.736-1.877-1.8770.0000.0000.0000.000
91A97THR00.013-0.0016.8840.7860.7860.0000.0000.0000.000
92A98ALA00.027-0.0096.899-3.515-3.5150.0000.0000.0000.000
93A99THR0-0.091-0.0484.151-2.445-2.2410.000-0.025-0.1780.000
94A100GLY00.0430.0353.081-2.031-1.2480.056-0.284-0.554-0.001
95A101ASP-1-0.830-0.8893.607-29.532-29.2440.007-0.061-0.234-0.001
96A102GLU-1-0.719-0.8486.754-21.251-21.2510.0000.0000.0000.000
97A103GLU-1-1.007-1.0149.362-18.260-18.2600.0000.0000.0000.000
98A104GLY00.0530.01712.1020.7340.7340.0000.0000.0000.000
99A105LEU0-0.033-0.01915.4580.0240.0240.0000.0000.0000.000
100A106LEU0-0.007-0.00718.9450.0630.0630.0000.0000.0000.000
101A107SER00.000-0.03020.6900.4010.4010.0000.0000.0000.000
102A108GLY00.011-0.00824.478-0.166-0.1660.0000.0000.0000.000
103A109GLU-1-0.898-0.95027.002-9.870-9.8700.0000.0000.0000.000
104A110VAL0-0.002-0.00123.9920.0540.0540.0000.0000.0000.000
105A111CYS0-0.0480.00319.944-0.376-0.3760.0000.0000.0000.000
106A112LEU0-0.0110.00219.3440.3400.3400.0000.0000.0000.000
107A113ALA00.0650.02514.129-0.664-0.6640.0000.0000.0000.000
108A114TRP0-0.0170.01810.4790.6030.6030.0000.0000.0000.000
109A115THR00.015-0.00612.474-0.877-0.8770.0000.0000.0000.000
110A116THR0-0.011-0.00912.9660.9140.9140.0000.0000.0000.000
111A117SER00.007-0.00815.359-0.311-0.3110.0000.0000.0000.000
112A118GLY00.0230.01614.3090.0570.0570.0000.0000.0000.000
113A119ASP-1-0.751-0.84011.110-20.620-20.6200.0000.0000.0000.000
114A120SER0-0.0030.00613.540-0.357-0.3570.0000.0000.0000.000
115A121GLY0-0.037-0.02816.182-0.344-0.3440.0000.0000.0000.000
116A122SER0-0.013-0.02712.018-0.917-0.9170.0000.0000.0000.000
117A123ALA0-0.0220.00513.4601.1771.1770.0000.0000.0000.000
118A124VAL00.0300.01413.438-1.074-1.0740.0000.0000.0000.000
119A125VAL0-0.032-0.03212.8050.6900.6900.0000.0000.0000.000
120A126GLN00.033-0.01015.6080.1350.1350.0000.0000.0000.000
121A127GLY0-0.0090.00516.2670.6240.6240.0000.0000.0000.000
122A128ASP-1-0.972-0.98914.987-17.763-17.7630.0000.0000.0000.000
123A129ALA00.0140.00516.3070.1520.1520.0000.0000.0000.000
124A130VAL0-0.033-0.01316.150-0.467-0.4670.0000.0000.0000.000
125A131VAL00.005-0.00318.3220.8960.8960.0000.0000.0000.000
126A132GLY0-0.009-0.03019.3170.9400.9400.0000.0000.0000.000
127A133VAL0-0.0550.00117.701-0.948-0.9480.0000.0000.0000.000
128A134HIS00.0330.01615.7430.6250.6250.0000.0000.0000.000
129A135THR0-0.0130.00417.697-0.008-0.0080.0000.0000.0000.000
130A136GLY00.0260.00420.1890.2850.2850.0000.0000.0000.000
131A137SER0-0.038-0.00818.720-0.050-0.0500.0000.0000.0000.000
132A138ASN00.027-0.00220.7960.5360.5360.0000.0000.0000.000
133A139THR0-0.014-0.01621.872-0.405-0.4050.0000.0000.0000.000
134A140SER0-0.007-0.00822.1660.1710.1710.0000.0000.0000.000
135A141GLY00.0420.03418.625-0.080-0.0800.0000.0000.0000.000
136A142VAL0-0.0020.02319.355-0.317-0.3170.0000.0000.0000.000
137A143ALA0-0.012-0.00918.090-0.289-0.2890.0000.0000.0000.000
138A144TYR00.0000.00220.1030.4830.4830.0000.0000.0000.000
139A145VAL00.0260.01118.741-0.537-0.5370.0000.0000.0000.000
140A146THR0-0.027-0.01321.3530.8290.8290.0000.0000.0000.000
141A147THR00.0230.00722.528-0.480-0.4800.0000.0000.0000.000
142A148PRO00.0600.02323.0680.3560.3560.0000.0000.0000.000
143A149SER0-0.081-0.04325.5090.2380.2380.0000.0000.0000.000
144A150GLY0-0.0070.00027.5680.3940.3940.0000.0000.0000.000
145A151LYS10.9010.96128.16110.05610.0560.0000.0000.0000.000
146A152LEU00.006-0.00124.913-0.379-0.3790.0000.0000.0000.000
147A153LEU0-0.036-0.02022.6230.3850.3850.0000.0000.0000.000
148A154GLY00.0170.00424.238-0.346-0.3460.0000.0000.0000.000
149A155ALA0-0.042-0.02425.1710.0650.0650.0000.0000.0000.000
150A156ASP-1-0.942-0.94228.466-9.019-9.0190.0000.0000.0000.000
151A157THR0-0.035-0.03029.748-0.123-0.1230.0000.0000.0000.000
152A158VAL00.0140.00628.1780.0690.0690.0000.0000.0000.000
153A159THR0-0.0020.01531.154-0.101-0.1010.0000.0000.0000.000
154A160LEU00.0830.03627.908-0.244-0.2440.0000.0000.0000.000
155A161SER0-0.058-0.03130.714-0.257-0.2570.0000.0000.0000.000
156A162SER0-0.086-0.03832.782-0.131-0.1310.0000.0000.0000.000
157A163LEU00.0640.02425.408-0.124-0.1240.0000.0000.0000.000
158A164SER00.001-0.04728.215-0.359-0.3590.0000.0000.0000.000
159A165LYS10.8690.94729.6608.7998.7990.0000.0000.0000.000
160A166HIS0-0.050-0.01626.850-0.053-0.0530.0000.0000.0000.000
161A167PHE00.0290.02721.661-0.469-0.4690.0000.0000.0000.000
162A168THR00.0150.01825.3950.3280.3280.0000.0000.0000.000
163A169GLY00.004-0.00426.219-0.311-0.3110.0000.0000.0000.000
164A170PRO0-0.031-0.01527.7500.2380.2380.0000.0000.0000.000
165A171LEU00.0360.00829.155-0.291-0.2910.0000.0000.0000.000
166A172THR0-0.049-0.02326.037-0.064-0.0640.0000.0000.0000.000
167A173SER00.014-0.00228.8310.1350.1350.0000.0000.0000.000
168A174ILE0-0.0010.01727.348-0.348-0.3480.0000.0000.0000.000
169A175PRO00.0220.02423.2140.2760.2760.0000.0000.0000.000
170A176LYS10.9040.94025.2949.9609.9600.0000.0000.0000.000
171A177ASP-1-0.937-0.96922.679-11.267-11.2670.0000.0000.0000.000
172A178ILE00.0070.02123.771-0.408-0.4080.0000.0000.0000.000
173A179PRO00.0360.00124.1100.3210.3210.0000.0000.0000.000
174A180ASP-1-0.884-0.94226.936-8.709-8.7090.0000.0000.0000.000
175A181ASN0-0.059-0.02628.3690.4380.4380.0000.0000.0000.000
176A182ILE0-0.019-0.00424.833-0.058-0.0580.0000.0000.0000.000
177A183ILE0-0.013-0.01229.3750.1450.1450.0000.0000.0000.000
178A184ALA00.024-0.00531.846-0.050-0.0500.0000.0000.0000.000
179A185ASP-1-0.794-0.87933.159-8.157-8.1570.0000.0000.0000.000
180A186VAL0-0.041-0.01732.7080.1770.1770.0000.0000.0000.000
181A187ASP-1-0.924-0.96634.062-8.112-8.1120.0000.0000.0000.000
182A188ALA0-0.028-0.02131.411-0.134-0.1340.0000.0000.0000.000
183A189VAL00.0180.00926.7300.0970.0970.0000.0000.0000.000
184A190PRO00.0100.00627.126-0.038-0.0380.0000.0000.0000.000
185A191ARG10.9620.97423.74910.89410.8940.0000.0000.0000.000
186A192SER0-0.030-0.02221.913-0.374-0.3740.0000.0000.0000.000
187A193LEU00.0360.02821.350-0.471-0.4710.0000.0000.0000.000
188A194ALA0-0.008-0.01622.251-0.251-0.2510.0000.0000.0000.000
189A195MET00.007-0.00918.4360.0360.0360.0000.0000.0000.000
190A196LEU0-0.0060.01016.582-0.513-0.5130.0000.0000.0000.000
191A197ILE0-0.023-0.01217.393-0.442-0.4420.0000.0000.0000.000
192A198ASP-1-0.936-0.98218.804-12.291-12.2910.0000.0000.0000.000
193A199GLY0-0.037-0.00215.440-0.188-0.1880.0000.0000.0000.000
194A200LEU0-0.052-0.01513.708-1.095-1.0950.0000.0000.0000.000
195A201SER0-0.051-0.03511.5990.1160.1160.0000.0000.0000.000
196A202ASN0-0.045-0.0129.537-1.273-1.2730.0000.0000.0000.000
197A203ARG10.7300.8555.27921.16121.1610.0000.0000.0000.000
198A204GLU-1-1.021-1.0073.919-27.317-27.1260.000-0.062-0.1290.000