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: R8678

Calculation Name: 1NA5-A-Xray372

Preferred Name: Integrin alpha M

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1NA5

Chain ID: A

ChEMBL ID: CHEMBL3826

UniProt ID: P11215

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2351077.017785
FMO2-HF: Nuclear repulsion 2274241.932103
FMO2-HF: Total energy -76835.085682
FMO2-MP2: Total energy -77063.507721


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:130:GLN)


Summations of interaction energy for fragment #1(A:130:GLN)
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.
-1.8950.4040.025-0.955-1.370.002
Interaction energy analysis for fragmet #1(A:130:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.022
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].
3A132ASP-1-0.823-0.8943.860-2.113-0.647-0.002-0.748-0.7160.002
4A133SER0-0.063-0.0356.1390.5040.5040.0000.0000.0000.000
5A134ASP-1-0.755-0.8438.2350.1300.1300.0000.0000.0000.000
6A135ILE00.015-0.0039.4080.0140.0140.0000.0000.0000.000
7A136ALA00.0170.01313.250-0.039-0.0390.0000.0000.0000.000
8A137PHE0-0.012-0.02115.5230.0410.0410.0000.0000.0000.000
9A138LEU0-0.0070.00319.683-0.030-0.0300.0000.0000.0000.000
10A139ILE0-0.023-0.01623.2450.0090.0090.0000.0000.0000.000
11A140ASP-1-0.719-0.84725.7030.1500.1500.0000.0000.0000.000
12A141GLY00.0280.00129.4000.0050.0050.0000.0000.0000.000
13A142SER00.0010.00132.024-0.013-0.0130.0000.0000.0000.000
14A143GLY0-0.049-0.03435.0740.0020.0020.0000.0000.0000.000
15A144SER0-0.082-0.05235.213-0.005-0.0050.0000.0000.0000.000
16A145ILE0-0.0150.01330.8290.0020.0020.0000.0000.0000.000
17A146ILE00.0570.04035.056-0.006-0.0060.0000.0000.0000.000
18A147PRO00.1020.03135.2160.0090.0090.0000.0000.0000.000
19A148HIS0-0.053-0.04134.075-0.001-0.0010.0000.0000.0000.000
20A149ASP-1-0.812-0.90532.4600.1640.1640.0000.0000.0000.000
21A150PHE00.0830.05229.5980.0150.0150.0000.0000.0000.000
22A151ARG10.8520.92829.499-0.115-0.1150.0000.0000.0000.000
23A152ARG10.7640.86328.848-0.143-0.1430.0000.0000.0000.000
24A153MET00.0320.03225.5470.0250.0250.0000.0000.0000.000
25A154LYS10.8270.91024.803-0.133-0.1330.0000.0000.0000.000
26A155GLU-1-0.831-0.87824.2230.2430.2430.0000.0000.0000.000
27A156PHE00.0280.01120.6740.0270.0270.0000.0000.0000.000
28A157VAL00.0230.00620.0870.0390.0390.0000.0000.0000.000
29A158SER0-0.034-0.03219.2100.0300.0300.0000.0000.0000.000
30A159THR0-0.002-0.00818.8820.0280.0280.0000.0000.0000.000
31A160VAL0-0.011-0.00415.9390.0580.0580.0000.0000.0000.000
32A161MET0-0.040-0.00814.7960.0810.0810.0000.0000.0000.000
33A162GLU-1-0.868-0.92413.9130.4050.4050.0000.0000.0000.000
34A163GLN0-0.025-0.01113.7260.1090.1090.0000.0000.0000.000
35A164LEU0-0.0030.00010.6950.1630.1630.0000.0000.0000.000
36A165LYS10.8530.9419.225-0.209-0.2090.0000.0000.0000.000
37A166LYS10.9380.9794.636-3.587-3.479-0.001-0.005-0.1020.000
38A167SER0-0.007-0.0114.916-0.121-0.029-0.001-0.007-0.0840.000
39A168LYS10.8560.9333.2682.1502.7830.029-0.195-0.4680.000
40A169THR0-0.0140.0046.0190.0410.0410.0000.0000.0000.000
41A170LEU0-0.0250.0088.072-0.036-0.0360.0000.0000.0000.000
42A171PHE00.013-0.01311.4300.0740.0740.0000.0000.0000.000
43A172SER0-0.046-0.04614.750-0.061-0.0610.0000.0000.0000.000
44A173LEU0-0.020-0.01018.2960.0340.0340.0000.0000.0000.000
45A174MET00.0040.00821.537-0.026-0.0260.0000.0000.0000.000
46A175GLN0-0.011-0.01424.6860.0150.0150.0000.0000.0000.000
47A176TYR0-0.038-0.03527.380-0.007-0.0070.0000.0000.0000.000
48A177SER00.038-0.00130.1300.0050.0050.0000.0000.0000.000
49A178GLU-1-0.757-0.84533.5980.0970.0970.0000.0000.0000.000
50A179GLU-1-0.835-0.87934.2930.0920.0920.0000.0000.0000.000
51A180PHE0-0.009-0.03529.8650.0100.0100.0000.0000.0000.000
52A181ARG10.8530.91929.500-0.117-0.1170.0000.0000.0000.000
53A182ILE00.0120.00923.7770.0150.0150.0000.0000.0000.000
54A183HIS0-0.012-0.01524.830-0.010-0.0100.0000.0000.0000.000
55A184PHE00.0300.01417.925-0.001-0.0010.0000.0000.0000.000
56A185THR0-0.023-0.01820.5760.0220.0220.0000.0000.0000.000
57A186PHE00.0370.01114.6100.0060.0060.0000.0000.0000.000
58A187LYS10.8850.93316.282-0.030-0.0300.0000.0000.0000.000
59A188GLU-1-0.814-0.87118.5000.0890.0890.0000.0000.0000.000
60A189PHE00.0050.01112.8150.0100.0100.0000.0000.0000.000
61A190GLN0-0.035-0.02713.7080.0060.0060.0000.0000.0000.000
62A191ASN0-0.027-0.01015.560-0.037-0.0370.0000.0000.0000.000
63A192ASN0-0.0030.00218.361-0.010-0.0100.0000.0000.0000.000
64A193PRO00.0840.06913.9040.0290.0290.0000.0000.0000.000
65A194ASN0-0.063-0.04915.6310.0810.0810.0000.0000.0000.000
66A195PRO00.0520.03016.301-0.031-0.0310.0000.0000.0000.000
67A196ARG10.8080.87119.009-0.305-0.3050.0000.0000.0000.000
68A197SER0-0.048-0.03421.553-0.022-0.0220.0000.0000.0000.000
69A198LEU00.0080.01419.516-0.018-0.0180.0000.0000.0000.000
70A199VAL0-0.007-0.00220.918-0.008-0.0080.0000.0000.0000.000
71A200LYS10.9050.95623.921-0.187-0.1870.0000.0000.0000.000
72A201PRO00.0110.00126.323-0.006-0.0060.0000.0000.0000.000
73A202ILE0-0.0310.01326.032-0.010-0.0100.0000.0000.0000.000
74A203THR00.0260.00429.5310.0050.0050.0000.0000.0000.000
75A204GLN0-0.051-0.02532.0500.0040.0040.0000.0000.0000.000
76A205LEU0-0.073-0.02331.375-0.007-0.0070.0000.0000.0000.000
77A206LEU00.0100.01434.776-0.008-0.0080.0000.0000.0000.000
78A207GLY00.0140.02636.6340.0010.0010.0000.0000.0000.000
79A208ARG10.7950.85237.706-0.090-0.0900.0000.0000.0000.000
80A209THR00.0210.00632.2610.0010.0010.0000.0000.0000.000
81A210HIS0-0.085-0.03833.358-0.005-0.0050.0000.0000.0000.000
82A211THR00.0670.00827.901-0.001-0.0010.0000.0000.0000.000
83A212ALA0-0.0090.00928.4020.0120.0120.0000.0000.0000.000
84A213THR0-0.023-0.04929.2260.0010.0010.0000.0000.0000.000
85A214GLY00.0240.00828.130-0.002-0.0020.0000.0000.0000.000
86A215ILE0-0.009-0.00624.0320.0070.0070.0000.0000.0000.000
87A216ARG10.8100.89624.977-0.121-0.1210.0000.0000.0000.000
88A217LYS10.8520.90826.622-0.118-0.1180.0000.0000.0000.000
89A218VAL00.003-0.01220.922-0.003-0.0030.0000.0000.0000.000
90A219VAL0-0.037-0.02021.7340.0030.0030.0000.0000.0000.000
91A220ARG10.8570.91022.515-0.125-0.1250.0000.0000.0000.000
92A221GLU-1-0.825-0.88524.3970.0990.0990.0000.0000.0000.000
93A222LEU00.0070.01419.919-0.011-0.0110.0000.0000.0000.000
94A223PHE0-0.038-0.03015.076-0.003-0.0030.0000.0000.0000.000
95A224ASN00.0090.01119.320-0.027-0.0270.0000.0000.0000.000
96A225ILE00.0610.03019.126-0.001-0.0010.0000.0000.0000.000
97A226THR0-0.023-0.01820.450-0.009-0.0090.0000.0000.0000.000
98A227ASN00.007-0.00721.380-0.018-0.0180.0000.0000.0000.000
99A228GLY0-0.051-0.03017.9160.0130.0130.0000.0000.0000.000
100A229ALA00.0070.02715.348-0.008-0.0080.0000.0000.0000.000
101A230ARG10.7610.8378.4640.0120.0120.0000.0000.0000.000
102A231LYS10.9470.96213.7550.0170.0170.0000.0000.0000.000
103A232ASN0-0.009-0.01412.914-0.028-0.0280.0000.0000.0000.000
104A233ALA00.0100.0299.8080.0190.0190.0000.0000.0000.000
105A234PHE00.002-0.0076.136-0.047-0.0470.0000.0000.0000.000
106A235LYS10.8440.94210.327-0.206-0.2060.0000.0000.0000.000
107A236ILE0-0.016-0.0029.3480.0350.0350.0000.0000.0000.000
108A237LEU00.001-0.00213.810-0.042-0.0420.0000.0000.0000.000
109A238VAL0-0.0090.00016.0340.0160.0160.0000.0000.0000.000
110A239VAL00.0090.00018.700-0.031-0.0310.0000.0000.0000.000
111A240ILE0-0.039-0.03021.8710.0150.0150.0000.0000.0000.000
112A241THR00.0450.01024.984-0.019-0.0190.0000.0000.0000.000
113A242ASP-1-0.821-0.90128.7080.1730.1730.0000.0000.0000.000
114A243GLY00.0050.00631.999-0.009-0.0090.0000.0000.0000.000
115A244GLU-1-0.946-0.96032.8630.1360.1360.0000.0000.0000.000
116A245LYS10.8510.93132.885-0.137-0.1370.0000.0000.0000.000
117A246PHE0-0.020-0.01034.702-0.008-0.0080.0000.0000.0000.000
118A247GLY00.005-0.02037.6410.0010.0010.0000.0000.0000.000
119A248ASP-1-0.770-0.86433.0650.1330.1330.0000.0000.0000.000
120A249PRO0-0.0090.00036.3370.0000.0000.0000.0000.0000.000
121A250LEU0-0.0310.00332.598-0.003-0.0030.0000.0000.0000.000
122A251GLY00.0480.02734.7130.0030.0030.0000.0000.0000.000
123A252TYR0-0.052-0.08229.0720.0100.0100.0000.0000.0000.000
124A253GLU-1-0.859-0.93730.1350.1460.1460.0000.0000.0000.000
125A254ASP-1-0.776-0.87432.0000.1150.1150.0000.0000.0000.000
126A255VAL0-0.074-0.03227.591-0.002-0.0020.0000.0000.0000.000
127A256ILE0-0.0010.01525.1320.0100.0100.0000.0000.0000.000
128A257PRO00.0240.00425.2080.0140.0140.0000.0000.0000.000
129A258GLU-1-0.872-0.91325.9820.1300.1300.0000.0000.0000.000
130A259ALA00.0370.00921.9350.0030.0030.0000.0000.0000.000
131A260ASP-1-0.855-0.90520.9350.3150.3150.0000.0000.0000.000
132A261ARG10.8910.95621.337-0.139-0.1390.0000.0000.0000.000
133A262GLU-1-0.923-0.96020.6250.1510.1510.0000.0000.0000.000
134A263GLY00.0270.02117.4520.0030.0030.0000.0000.0000.000
135A264VAL0-0.048-0.02516.0530.0450.0450.0000.0000.0000.000
136A265ILE00.0050.00412.086-0.012-0.0120.0000.0000.0000.000
137A266ARG10.7780.86116.045-0.288-0.2880.0000.0000.0000.000
138A267TYR0-0.027-0.04213.709-0.001-0.0010.0000.0000.0000.000
139A268VAL0-0.033-0.00719.043-0.023-0.0230.0000.0000.0000.000
140A269ILE0-0.015-0.01320.5830.0120.0120.0000.0000.0000.000
141A270GLY00.0360.02024.400-0.015-0.0150.0000.0000.0000.000
142A271VAL0-0.059-0.04427.5160.0030.0030.0000.0000.0000.000
143A272GLY00.0760.03829.851-0.010-0.0100.0000.0000.0000.000
144A273ASP-1-0.832-0.92433.4970.1490.1490.0000.0000.0000.000
145A274ALA00.0100.02234.258-0.002-0.0020.0000.0000.0000.000
146A275PHE00.0310.01231.3880.0030.0030.0000.0000.0000.000
147A276ARG10.8370.90633.022-0.145-0.1450.0000.0000.0000.000
148A277SER0-0.0010.01035.3920.0020.0020.0000.0000.0000.000
149A278GLU-1-0.763-0.88332.2460.2080.2080.0000.0000.0000.000
150A279LYS10.9410.96734.267-0.116-0.1160.0000.0000.0000.000
151A280SER00.0500.02834.659-0.002-0.0020.0000.0000.0000.000
152A281ARG10.8200.88929.558-0.195-0.1950.0000.0000.0000.000
153A282GLN0-0.018-0.00130.1210.0180.0180.0000.0000.0000.000
154A283GLU-1-0.739-0.82830.7980.1720.1720.0000.0000.0000.000
155A284LEU00.0100.00626.6700.0090.0090.0000.0000.0000.000
156A285ASN0-0.057-0.05826.1310.0350.0350.0000.0000.0000.000
157A286THR0-0.061-0.02026.9740.0040.0040.0000.0000.0000.000
158A287ILE00.0080.00123.9700.0040.0040.0000.0000.0000.000
159A288ALA0-0.0200.00022.1800.0160.0160.0000.0000.0000.000
160A289SER00.0300.03118.775-0.015-0.0150.0000.0000.0000.000
161A290LYS10.9480.97920.870-0.242-0.2420.0000.0000.0000.000
162A291PRO00.0360.00919.8350.0270.0270.0000.0000.0000.000
163A292PRO00.0860.03921.5660.0320.0320.0000.0000.0000.000
164A293ARG10.9010.92122.076-0.341-0.3410.0000.0000.0000.000
165A294ASP-1-0.830-0.88618.0290.5030.5030.0000.0000.0000.000
166A295HIS10.8350.92015.964-0.486-0.4860.0000.0000.0000.000
167A296VAL00.0260.02819.879-0.010-0.0100.0000.0000.0000.000
168A297PHE0-0.025-0.00818.5850.0120.0120.0000.0000.0000.000
169A298GLN0-0.016-0.01224.113-0.010-0.0100.0000.0000.0000.000
170A299VAL0-0.010-0.00226.1290.0070.0070.0000.0000.0000.000
171A300ASN00.0400.00628.853-0.012-0.0120.0000.0000.0000.000
172A301ASN00.0630.03931.281-0.002-0.0020.0000.0000.0000.000
173A302PHE00.1010.02828.8310.0170.0170.0000.0000.0000.000
174A303GLU-1-0.878-0.91228.9430.1710.1710.0000.0000.0000.000
175A304ALA00.0330.01428.9020.0110.0110.0000.0000.0000.000
176A305LEU00.0330.04424.2280.0190.0190.0000.0000.0000.000
177A306LYS10.8790.92523.696-0.189-0.1890.0000.0000.0000.000
178A307THR0-0.036-0.02623.2700.0240.0240.0000.0000.0000.000
179A308ILE00.0400.02321.6290.0180.0180.0000.0000.0000.000
180A309GLN0-0.036-0.00918.8700.0440.0440.0000.0000.0000.000
181A310ASN00.0590.03316.7990.0560.0560.0000.0000.0000.000
182A311GLN0-0.021-0.01416.2450.0680.0680.0000.0000.0000.000
183A312LEU00.0200.00515.8990.0450.0450.0000.0000.0000.000
184A313ARG10.8030.89011.895-0.794-0.7940.0000.0000.0000.000
185A314GLU-1-0.807-0.89311.7231.2741.2740.0000.0000.0000.000
186A315LYS10.8360.91012.223-0.446-0.4460.0000.0000.0000.000
187A316ILE0-0.0030.0189.582-0.018-0.0180.0000.0000.0000.000
188A317PHE0-0.013-0.0377.7360.3300.3300.0000.0000.0000.000
189A318ALA00.0110.0207.9160.3470.3470.0000.0000.0000.000
190A319ILE0-0.034-0.0128.653-0.114-0.1140.0000.0000.0000.000
191A320GLY00.0060.0137.4440.3550.3550.0000.0000.0000.000
192A321SER0-0.009-0.0046.6330.0910.0910.0000.0000.0000.000
193A322PRO00.0210.0128.751-0.188-0.1880.0000.0000.0000.000
194A323GLY0-0.009-0.00412.602-0.084-0.0840.0000.0000.0000.000
195A324ILE0-0.076-0.0298.238-0.233-0.2330.0000.0000.0000.000