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: ZVK4N

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 OptHSide
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 -2347393.560466
FMO2-HF: Nuclear repulsion 2270558.961094
FMO2-HF: Total energy -76834.599372
FMO2-MP2: Total energy -77063.117445


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.
-2.0580.5130.016-1.03-1.5590.003
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 : 0.013 / q_NPA : 0.010
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-1-0.833-0.9033.770-1.1860.618-0.025-0.861-0.9190.003
4A133SER0-0.043-0.0156.0620.3410.3410.0000.0000.0000.000
5A134ASP-1-0.765-0.8358.4080.2220.2220.0000.0000.0000.000
6A135ILE0-0.006-0.0249.7010.0170.0170.0000.0000.0000.000
7A136ALA00.0100.00413.547-0.042-0.0420.0000.0000.0000.000
8A137PHE0-0.007-0.01415.6970.0320.0320.0000.0000.0000.000
9A138LEU00.0090.01319.940-0.028-0.0280.0000.0000.0000.000
10A139ILE0-0.029-0.03423.3970.0090.0090.0000.0000.0000.000
11A140ASP-1-0.735-0.85125.9110.1500.1500.0000.0000.0000.000
12A141GLY00.015-0.01329.4780.0030.0030.0000.0000.0000.000
13A142SER00.0310.02132.010-0.014-0.0140.0000.0000.0000.000
14A143GLY0-0.044-0.03035.1030.0020.0020.0000.0000.0000.000
15A144SER0-0.096-0.05835.315-0.004-0.0040.0000.0000.0000.000
16A145ILE0-0.0140.02131.1910.0030.0030.0000.0000.0000.000
17A146ILE00.0290.02935.479-0.006-0.0060.0000.0000.0000.000
18A147PRO00.1020.02335.5410.0080.0080.0000.0000.0000.000
19A148HIS0-0.059-0.04334.1300.0000.0000.0000.0000.0000.000
20A149ASP-1-0.756-0.88332.9290.1540.1540.0000.0000.0000.000
21A150PHE00.0600.04729.7780.0140.0140.0000.0000.0000.000
22A151ARG10.8740.93329.703-0.108-0.1080.0000.0000.0000.000
23A152ARG10.7850.87028.919-0.135-0.1350.0000.0000.0000.000
24A153MET00.0310.03225.8930.0240.0240.0000.0000.0000.000
25A154LYS10.8120.90225.048-0.128-0.1280.0000.0000.0000.000
26A155GLU-1-0.857-0.88824.1310.2410.2410.0000.0000.0000.000
27A156PHE00.0280.01420.7610.0260.0260.0000.0000.0000.000
28A157VAL00.0200.00520.0960.0400.0400.0000.0000.0000.000
29A158SER0-0.036-0.03419.2080.0320.0320.0000.0000.0000.000
30A159THR0-0.011-0.00918.8510.0240.0240.0000.0000.0000.000
31A160VAL0-0.008-0.00816.0130.0560.0560.0000.0000.0000.000
32A161MET0-0.039-0.00714.7580.0820.0820.0000.0000.0000.000
33A162GLU-1-0.879-0.93613.7620.3770.3770.0000.0000.0000.000
34A163GLN0-0.044-0.02513.7910.0910.0910.0000.0000.0000.000
35A164LEU0-0.022-0.00310.8530.1560.1560.0000.0000.0000.000
36A165LYS10.8580.9479.291-0.145-0.1450.0000.0000.0000.000
37A166LYS10.9490.9824.469-4.439-4.324-0.001-0.006-0.1080.000
38A167SER0-0.003-0.0055.274-0.011-0.0110.0000.0000.0000.000
39A168LYS10.8630.9413.0831.6512.3030.042-0.163-0.5320.000
40A169THR00.0030.0046.1960.0970.0970.0000.0000.0000.000
41A170LEU0-0.0260.0088.162-0.090-0.0900.0000.0000.0000.000
42A171PHE00.012-0.01411.5920.0580.0580.0000.0000.0000.000
43A172SER0-0.045-0.04014.827-0.060-0.0600.0000.0000.0000.000
44A173LEU0-0.034-0.01518.3190.0330.0330.0000.0000.0000.000
45A174MET00.0030.00621.427-0.024-0.0240.0000.0000.0000.000
46A175GLN0-0.045-0.04824.6910.0120.0120.0000.0000.0000.000
47A176TYR0-0.047-0.02727.522-0.006-0.0060.0000.0000.0000.000
48A177SER00.0980.03730.1560.0050.0050.0000.0000.0000.000
49A178GLU-1-0.733-0.83633.6720.0960.0960.0000.0000.0000.000
50A179GLU-1-0.967-0.95834.8200.0920.0920.0000.0000.0000.000
51A180PHE00.002-0.04029.7800.0100.0100.0000.0000.0000.000
52A181ARG10.9280.97829.329-0.118-0.1180.0000.0000.0000.000
53A182ILE00.0290.01723.7510.0150.0150.0000.0000.0000.000
54A183HIS0-0.026-0.01324.559-0.010-0.0100.0000.0000.0000.000
55A184PHE00.0470.01918.074-0.004-0.0040.0000.0000.0000.000
56A185THR0-0.015-0.01520.6530.0220.0220.0000.0000.0000.000
57A186PHE00.0440.01214.6310.0050.0050.0000.0000.0000.000
58A187LYS10.9100.95316.537-0.054-0.0540.0000.0000.0000.000
59A188GLU-1-0.812-0.87518.7010.0980.0980.0000.0000.0000.000
60A189PHE0-0.0030.00413.1110.0100.0100.0000.0000.0000.000
61A190GLN0-0.014-0.01914.022-0.001-0.0010.0000.0000.0000.000
62A191ASN0-0.030-0.01515.861-0.032-0.0320.0000.0000.0000.000
63A192ASN00.0050.01318.763-0.016-0.0160.0000.0000.0000.000
64A193PRO00.0520.06114.4640.0280.0280.0000.0000.0000.000
65A194ASN0-0.061-0.05316.2540.0520.0520.0000.0000.0000.000
66A195PRO00.0550.02116.054-0.024-0.0240.0000.0000.0000.000
67A196ARG10.8390.88518.855-0.275-0.2750.0000.0000.0000.000
68A197SER0-0.082-0.04121.863-0.022-0.0220.0000.0000.0000.000
69A198LEU00.0170.01119.269-0.015-0.0150.0000.0000.0000.000
70A199VAL0-0.0040.00121.154-0.010-0.0100.0000.0000.0000.000
71A200LYS10.9660.98324.019-0.151-0.1510.0000.0000.0000.000
72A201PRO00.004-0.00426.346-0.006-0.0060.0000.0000.0000.000
73A202ILE0-0.0240.02225.865-0.010-0.0100.0000.0000.0000.000
74A203THR00.009-0.00229.4160.0040.0040.0000.0000.0000.000
75A204GLN0-0.061-0.03932.1150.0020.0020.0000.0000.0000.000
76A205LEU0-0.067-0.01931.377-0.007-0.0070.0000.0000.0000.000
77A206LEU0-0.0020.01334.929-0.008-0.0080.0000.0000.0000.000
78A207GLY00.0220.01936.8410.0010.0010.0000.0000.0000.000
79A208ARG10.8230.87437.925-0.087-0.0870.0000.0000.0000.000
80A209THR00.0520.02932.5030.0000.0000.0000.0000.0000.000
81A210HIS0-0.075-0.03333.622-0.004-0.0040.0000.0000.0000.000
82A211THR00.0680.00528.2130.0000.0000.0000.0000.0000.000
83A212ALA0-0.0190.00628.6740.0120.0120.0000.0000.0000.000
84A213THR0-0.013-0.04229.2050.0030.0030.0000.0000.0000.000
85A214GLY00.0150.01128.1860.0000.0000.0000.0000.0000.000
86A215ILE00.001-0.00823.9200.0100.0100.0000.0000.0000.000
87A216ARG10.8980.95124.791-0.122-0.1220.0000.0000.0000.000
88A217LYS10.8500.90426.261-0.121-0.1210.0000.0000.0000.000
89A218VAL00.0040.00520.785-0.001-0.0010.0000.0000.0000.000
90A219VAL0-0.028-0.01821.5210.0030.0030.0000.0000.0000.000
91A220ARG10.8240.87322.414-0.130-0.1300.0000.0000.0000.000
92A221GLU-1-0.815-0.89624.7050.1100.1100.0000.0000.0000.000
93A222LEU00.0060.01719.977-0.010-0.0100.0000.0000.0000.000
94A223PHE0-0.055-0.03014.840-0.001-0.0010.0000.0000.0000.000
95A224ASN00.0200.01519.414-0.023-0.0230.0000.0000.0000.000
96A225ILE00.0580.02319.5070.0000.0000.0000.0000.0000.000
97A226THR0-0.016-0.00820.689-0.008-0.0080.0000.0000.0000.000
98A227ASN0-0.030-0.04021.441-0.017-0.0170.0000.0000.0000.000
99A228GLY0-0.063-0.04018.0370.0140.0140.0000.0000.0000.000
100A229ALA00.0060.03615.6300.0000.0000.0000.0000.0000.000
101A230ARG10.7800.8408.674-0.097-0.0970.0000.0000.0000.000
102A231LYS10.9390.96514.215-0.011-0.0110.0000.0000.0000.000
103A232ASN0-0.025-0.03312.743-0.021-0.0210.0000.0000.0000.000
104A233ALA00.0170.0429.6910.0040.0040.0000.0000.0000.000
105A234PHE00.0080.0045.4020.0000.0000.0000.0000.0000.000
106A235LYS10.8670.94810.155-0.252-0.2520.0000.0000.0000.000
107A236ILE0-0.017-0.0059.4980.0240.0240.0000.0000.0000.000
108A237LEU00.0170.01213.971-0.036-0.0360.0000.0000.0000.000
109A238VAL0-0.016-0.00316.1980.0160.0160.0000.0000.0000.000
110A239VAL00.007-0.00518.865-0.028-0.0280.0000.0000.0000.000
111A240ILE0-0.023-0.01322.1350.0110.0110.0000.0000.0000.000
112A241THR00.025-0.00525.037-0.017-0.0170.0000.0000.0000.000
113A242ASP-1-0.817-0.90728.5920.1630.1630.0000.0000.0000.000
114A243GLY00.0140.01131.838-0.009-0.0090.0000.0000.0000.000
115A244GLU-1-0.987-0.97532.7860.1320.1320.0000.0000.0000.000
116A245LYS10.8050.90632.511-0.138-0.1380.0000.0000.0000.000
117A246PHE0-0.014-0.02334.599-0.008-0.0080.0000.0000.0000.000
118A247GLY0-0.002-0.01437.7890.0000.0000.0000.0000.0000.000
119A248ASP-1-0.763-0.86333.2420.1320.1320.0000.0000.0000.000
120A249PRO0-0.0120.00136.494-0.001-0.0010.0000.0000.0000.000
121A250LEU0-0.0180.00332.407-0.002-0.0020.0000.0000.0000.000
122A251GLY00.0580.03334.5150.0040.0040.0000.0000.0000.000
123A252TYR0-0.021-0.07428.9740.0070.0070.0000.0000.0000.000
124A253GLU-1-0.884-0.94730.0410.1430.1430.0000.0000.0000.000
125A254ASP-1-0.846-0.91031.9300.1160.1160.0000.0000.0000.000
126A255VAL0-0.110-0.06127.597-0.002-0.0020.0000.0000.0000.000
127A256ILE00.0030.01325.0180.0100.0100.0000.0000.0000.000
128A257PRO00.0210.01125.0220.0120.0120.0000.0000.0000.000
129A258GLU-1-0.847-0.88725.3350.1430.1430.0000.0000.0000.000
130A259ALA00.0440.02021.9350.0060.0060.0000.0000.0000.000
131A260ASP-1-0.848-0.90620.7310.2980.2980.0000.0000.0000.000
132A261ARG10.9020.96020.748-0.139-0.1390.0000.0000.0000.000
133A262GLU-1-0.931-0.96520.1260.1670.1670.0000.0000.0000.000
134A263GLY00.0180.01516.9070.0070.0070.0000.0000.0000.000
135A264VAL0-0.042-0.01915.6830.0450.0450.0000.0000.0000.000
136A265ILE0-0.0140.00111.999-0.017-0.0170.0000.0000.0000.000
137A266ARG10.7910.85916.087-0.284-0.2840.0000.0000.0000.000
138A267TYR00.000-0.01013.8290.0060.0060.0000.0000.0000.000
139A268VAL0-0.0180.00319.132-0.019-0.0190.0000.0000.0000.000
140A269ILE0-0.013-0.01520.5080.0100.0100.0000.0000.0000.000
141A270GLY00.0210.01824.323-0.014-0.0140.0000.0000.0000.000
142A271VAL0-0.052-0.04627.7240.0040.0040.0000.0000.0000.000
143A272GLY00.0730.03830.028-0.009-0.0090.0000.0000.0000.000
144A273ASP-1-0.852-0.94933.6580.1420.1420.0000.0000.0000.000
145A274ALA00.0190.03534.334-0.003-0.0030.0000.0000.0000.000
146A275PHE00.001-0.01431.2430.0020.0020.0000.0000.0000.000
147A276ARG10.8470.92532.876-0.137-0.1370.0000.0000.0000.000
148A277SER0-0.019-0.01435.1830.0020.0020.0000.0000.0000.000
149A278GLU-1-0.810-0.91032.3260.1920.1920.0000.0000.0000.000
150A279LYS10.9790.97834.107-0.109-0.1090.0000.0000.0000.000
151A280SER00.0600.03634.567-0.001-0.0010.0000.0000.0000.000
152A281ARG10.8480.92929.292-0.185-0.1850.0000.0000.0000.000
153A282GLN0-0.0040.00730.1700.0170.0170.0000.0000.0000.000
154A283GLU-1-0.739-0.82430.7470.1690.1690.0000.0000.0000.000
155A284LEU0-0.0010.00026.7900.0090.0090.0000.0000.0000.000
156A285ASN0-0.048-0.04926.1020.0340.0340.0000.0000.0000.000
157A286THR0-0.070-0.02926.3930.0050.0050.0000.0000.0000.000
158A287ILE0-0.0050.01023.9080.0040.0040.0000.0000.0000.000
159A288ALA0-0.026-0.00821.8560.0160.0160.0000.0000.0000.000
160A289SER00.0340.02818.681-0.010-0.0100.0000.0000.0000.000
161A290LYS10.9540.99420.772-0.232-0.2320.0000.0000.0000.000
162A291PRO00.009-0.01319.4600.0230.0230.0000.0000.0000.000
163A292PRO00.1200.04621.4000.0310.0310.0000.0000.0000.000
164A293ARG10.9140.95621.993-0.306-0.3060.0000.0000.0000.000
165A294ASP-1-0.835-0.90517.8570.4580.4580.0000.0000.0000.000
166A295HIS10.8400.91215.964-0.444-0.4440.0000.0000.0000.000
167A296VAL00.0100.02019.791-0.002-0.0020.0000.0000.0000.000
168A297PHE0-0.026-0.00818.2290.0110.0110.0000.0000.0000.000
169A298GLN0-0.004-0.00423.939-0.010-0.0100.0000.0000.0000.000
170A299VAL0-0.0100.00626.1240.0020.0020.0000.0000.0000.000
171A300ASN00.038-0.00528.897-0.009-0.0090.0000.0000.0000.000
172A301ASN00.0550.03031.313-0.002-0.0020.0000.0000.0000.000
173A302PHE00.1100.03629.2250.0160.0160.0000.0000.0000.000
174A303GLU-1-0.906-0.92229.1460.1570.1570.0000.0000.0000.000
175A304ALA00.0210.01129.1810.0080.0080.0000.0000.0000.000
176A305LEU00.0360.05224.5000.0170.0170.0000.0000.0000.000
177A306LYS10.8990.92723.737-0.177-0.1770.0000.0000.0000.000
178A307THR0-0.073-0.04823.4250.0220.0220.0000.0000.0000.000
179A308ILE00.0230.01121.7530.0100.0100.0000.0000.0000.000
180A309GLN0-0.006-0.00119.2080.0300.0300.0000.0000.0000.000
181A310ASN00.0370.02317.2270.0610.0610.0000.0000.0000.000
182A311GLN00.008-0.00316.3660.0710.0710.0000.0000.0000.000
183A312LEU00.0130.01015.8870.0480.0480.0000.0000.0000.000
184A313ARG10.8230.90412.037-0.729-0.7290.0000.0000.0000.000
185A314GLU-1-0.834-0.91011.6961.1371.1370.0000.0000.0000.000
186A315LYS10.8380.91612.027-0.416-0.4160.0000.0000.0000.000
187A316ILE00.001-0.0019.6170.0480.0480.0000.0000.0000.000
188A317PHE0-0.005-0.0267.6410.3870.3870.0000.0000.0000.000
189A318ALA00.0240.0297.5340.3730.3730.0000.0000.0000.000
190A319ILE0-0.055-0.0198.471-0.129-0.1290.0000.0000.0000.000
191A320GLY0-0.0060.0067.0330.2320.2320.0000.0000.0000.000
192A321SER0-0.012-0.0126.6090.3280.3280.0000.0000.0000.000
193A322PRO00.0330.0178.665-0.129-0.1290.0000.0000.0000.000
194A323GLY0-0.027-0.00212.353-0.056-0.0560.0000.0000.0000.000
195A324ILE0-0.062-0.0277.933-0.224-0.2240.0000.0000.0000.000