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: 982K2

Calculation Name: 2A4A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2A4A

Chain ID: A

ChEMBL ID:

UniProt ID: Q7RMC9

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 256
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3481358.138737
FMO2-HF: Nuclear repulsion 3381797.294566
FMO2-HF: Total energy -99560.84417
FMO2-MP2: Total energy -99853.354262


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:ASN)


Summations of interaction energy for fragment #1(A:3:ASN)
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.
-42.825-39.17814.379-8.225-9.799-0.029
Interaction energy analysis for fragmet #1(A:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.011
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].
3A5THR00.0320.0173.232-4.243-1.2870.106-1.369-1.6940.007
4A6GLU-1-0.868-0.9211.845-34.590-35.66214.080-6.096-6.911-0.043
5A7LYS10.8570.9203.185-5.663-3.9460.194-0.758-1.1520.007
6A8PHE00.0190.0135.660-0.314-0.3140.0000.0000.0000.000
7A9ALA00.0310.0257.369-0.325-0.3250.0000.0000.0000.000
8A10ALA00.019-0.0037.658-0.104-0.1040.0000.0000.0000.000
9A11TRP00.0440.0029.3420.0500.0500.0000.0000.0000.000
10A12SER0-0.028-0.02811.621-0.013-0.0130.0000.0000.0000.000
11A13VAL00.0120.00112.238-0.016-0.0160.0000.0000.0000.000
12A14ILE0-0.0050.01912.807-0.019-0.0190.0000.0000.0000.000
13A15CYS0-0.061-0.02915.4770.0270.0270.0000.0000.0000.000
14A16LEU0-0.0190.00316.3470.0260.0260.0000.0000.0000.000
15A17THR0-0.039-0.04116.964-0.056-0.0560.0000.0000.0000.000
16A18ASP-1-0.755-0.83619.583-0.114-0.1140.0000.0000.0000.000
17A19HIS0-0.028-0.01720.452-0.045-0.0450.0000.0000.0000.000
18A20THR0-0.070-0.04322.1210.0430.0430.0000.0000.0000.000
19A21PHE00.0530.01724.863-0.028-0.0280.0000.0000.0000.000
20A22LEU0-0.008-0.00627.5640.0210.0210.0000.0000.0000.000
21A23ASP-1-0.890-0.91928.737-0.263-0.2630.0000.0000.0000.000
22A24GLU-1-0.771-0.86731.705-0.183-0.1830.0000.0000.0000.000
23A25ASN0-0.037-0.03135.3600.0190.0190.0000.0000.0000.000
24A26GLY0-0.0120.02133.0820.0030.0030.0000.0000.0000.000
25A27THR0-0.038-0.06333.3060.0170.0170.0000.0000.0000.000
26A28GLU-1-0.704-0.86233.359-0.085-0.0850.0000.0000.0000.000
27A29ASP-1-0.843-0.91531.635-0.119-0.1190.0000.0000.0000.000
28A30ASP-1-0.834-0.87928.887-0.199-0.1990.0000.0000.0000.000
29A31ILE0-0.012-0.00627.774-0.012-0.0120.0000.0000.0000.000
30A32ARG10.7550.83928.3230.0960.0960.0000.0000.0000.000
31A33GLU-1-0.808-0.86823.001-0.204-0.2040.0000.0000.0000.000
32A34LEU0-0.039-0.01423.347-0.004-0.0040.0000.0000.0000.000
33A35CYS0-0.021-0.00423.6740.0020.0020.0000.0000.0000.000
34A36ASN00.0470.02623.7900.0280.0280.0000.0000.0000.000
35A37GLU-1-0.803-0.89819.501-0.342-0.3420.0000.0000.0000.000
36A38SER0-0.046-0.04619.381-0.002-0.0020.0000.0000.0000.000
37A39VAL0-0.012-0.02320.8530.0210.0210.0000.0000.0000.000
38A40LYS10.7710.86918.2550.2690.2690.0000.0000.0000.000
39A41THR0-0.021-0.01615.2020.0140.0140.0000.0000.0000.000
40A42CYS0-0.021-0.00816.056-0.009-0.0090.0000.0000.0000.000
41A43PRO00.0040.03113.311-0.006-0.0060.0000.0000.0000.000
42A44PHE00.0250.01416.540-0.065-0.0650.0000.0000.0000.000
43A45ALA00.0330.01519.1170.0150.0150.0000.0000.0000.000
44A46ALA0-0.0190.00519.9980.0340.0340.0000.0000.0000.000
45A47ALA0-0.027-0.01922.4360.0240.0240.0000.0000.0000.000
46A48VAL00.0130.01023.755-0.029-0.0290.0000.0000.0000.000
47A49CYS0-0.112-0.04926.2450.0140.0140.0000.0000.0000.000
48A50VAL00.0640.02028.040-0.021-0.0210.0000.0000.0000.000
49A51TYR0-0.001-0.03930.9930.0130.0130.0000.0000.0000.000
50A52PRO00.0720.00734.6160.0040.0040.0000.0000.0000.000
51A53LYS10.8100.92335.9980.1380.1380.0000.0000.0000.000
52A54PHE0-0.0130.00033.5760.0020.0020.0000.0000.0000.000
53A55VAL00.0020.01334.5200.0000.0000.0000.0000.0000.000
54A56LYS10.8710.93335.5370.0500.0500.0000.0000.0000.000
55A57PHE0-0.015-0.00631.7560.0060.0060.0000.0000.0000.000
56A58ILE00.048-0.00229.8520.0050.0050.0000.0000.0000.000
57A59ASN00.0200.00733.1250.0120.0120.0000.0000.0000.000
58A60GLU-1-0.819-0.87735.491-0.033-0.0330.0000.0000.0000.000
59A61LYS10.8410.91935.2220.0730.0730.0000.0000.0000.000
60A62ILE00.0230.01629.3460.0040.0040.0000.0000.0000.000
61A63LYS10.8540.93131.8460.0380.0380.0000.0000.0000.000
62A64GLN0-0.094-0.04233.4590.0120.0120.0000.0000.0000.000
63A65GLU-1-0.837-0.89531.645-0.066-0.0660.0000.0000.0000.000
64A66ILE0-0.042-0.01826.4200.0050.0050.0000.0000.0000.000
65A67ASN0-0.0080.01130.0860.0030.0030.0000.0000.0000.000
66A68PRO00.0030.00428.4970.0070.0070.0000.0000.0000.000
67A69PHE00.027-0.00926.3080.0040.0040.0000.0000.0000.000
68A70LYS10.8130.91322.042-0.003-0.0030.0000.0000.0000.000
69A71PRO0-0.068-0.03023.2130.0050.0050.0000.0000.0000.000
70A72LYS10.8910.94725.6230.0080.0080.0000.0000.0000.000
71A73ILE00.0100.00628.053-0.019-0.0190.0000.0000.0000.000
72A74ALA0-0.023-0.01128.6290.0080.0080.0000.0000.0000.000
73A75CYS00.0250.02230.635-0.015-0.0150.0000.0000.0000.000
74A76VAL0-0.024-0.00631.3150.0040.0040.0000.0000.0000.000
75A77ILE00.0300.00733.8500.0060.0060.0000.0000.0000.000
76A78ASN00.0040.00537.040-0.006-0.0060.0000.0000.0000.000
77A79PHE00.0020.02630.715-0.006-0.0060.0000.0000.0000.000
78A80PRO00.004-0.00933.8260.0040.0040.0000.0000.0000.000
79A81TYR00.029-0.01835.541-0.003-0.0030.0000.0000.0000.000
80A82GLY00.0730.03538.6800.0020.0020.0000.0000.0000.000
81A83THR0-0.048-0.02939.7430.0030.0030.0000.0000.0000.000
82A84ASP-1-0.812-0.89042.387-0.093-0.0930.0000.0000.0000.000
83A85SER00.000-0.00444.6920.0020.0020.0000.0000.0000.000
84A86MET00.018-0.00546.1410.0010.0010.0000.0000.0000.000
85A87GLU-1-0.916-0.95046.858-0.050-0.0500.0000.0000.0000.000
86A88LYS10.8520.92343.1000.0900.0900.0000.0000.0000.000
87A89VAL00.0060.00041.229-0.001-0.0010.0000.0000.0000.000
88A90LEU0-0.0170.00643.1620.0000.0000.0000.0000.0000.000
89A91ASN00.0240.00645.1910.0040.0040.0000.0000.0000.000
90A92ASP-1-0.870-0.93242.130-0.077-0.0770.0000.0000.0000.000
91A93THR0-0.073-0.06439.923-0.003-0.0030.0000.0000.0000.000
92A94GLU-1-0.946-0.97541.546-0.034-0.0340.0000.0000.0000.000
93A95LYS10.8760.93442.3000.0620.0620.0000.0000.0000.000
94A96ALA0-0.005-0.01238.295-0.001-0.0010.0000.0000.0000.000
95A97LEU0-0.047-0.03638.6900.0010.0010.0000.0000.0000.000
96A98ASP-1-0.899-0.93540.625-0.030-0.0300.0000.0000.0000.000
97A99ASP-1-0.909-0.94839.022-0.060-0.0600.0000.0000.0000.000
98A100GLY00.018-0.00537.826-0.001-0.0010.0000.0000.0000.000
99A101ALA0-0.025-0.01034.9290.0000.0000.0000.0000.0000.000
100A102ASP-1-0.832-0.89931.769-0.019-0.0190.0000.0000.0000.000
101A103GLU-1-0.789-0.87328.821-0.061-0.0610.0000.0000.0000.000
102A104ILE00.0220.01133.079-0.007-0.0070.0000.0000.0000.000
103A105ASP-1-0.751-0.85829.001-0.152-0.1520.0000.0000.0000.000
104A106LEU00.0560.03332.542-0.008-0.0080.0000.0000.0000.000
105A107VAL0-0.0490.00334.334-0.008-0.0080.0000.0000.0000.000
106A108ILE00.0020.01236.4100.0110.0110.0000.0000.0000.000
107A109ASN00.0450.00738.967-0.014-0.0140.0000.0000.0000.000
108A110TYR00.009-0.02635.3630.0060.0060.0000.0000.0000.000
109A111LYS10.8950.96539.3640.1230.1230.0000.0000.0000.000
110A112LYS10.9080.95141.7700.0710.0710.0000.0000.0000.000
111A113ILE0-0.064-0.03439.7800.0050.0050.0000.0000.0000.000
112A114ILE0-0.023-0.00138.4920.0010.0010.0000.0000.0000.000
113A115GLU-1-0.953-0.97142.791-0.098-0.0980.0000.0000.0000.000
114A116ASN0-0.058-0.05346.3450.0050.0050.0000.0000.0000.000
115A117THR00.0260.00743.2870.0030.0030.0000.0000.0000.000
116A118ASP-1-0.854-0.91945.608-0.054-0.0540.0000.0000.0000.000
117A119GLU-1-0.852-0.89648.054-0.058-0.0580.0000.0000.0000.000
118A120GLY00.0190.01244.9660.0010.0010.0000.0000.0000.000
119A121LEU00.0090.00441.026-0.001-0.0010.0000.0000.0000.000
120A122LYS10.8520.90543.8810.0540.0540.0000.0000.0000.000
121A123GLU-1-0.860-0.91545.682-0.070-0.0700.0000.0000.0000.000
122A124ALA00.0320.01740.4960.0010.0010.0000.0000.0000.000
123A125THR0-0.032-0.01641.9380.0000.0000.0000.0000.0000.000
124A126LYS10.9260.95843.3980.0460.0460.0000.0000.0000.000
125A127LEU00.0150.00941.6710.0030.0030.0000.0000.0000.000
126A128THR00.0130.00038.570-0.001-0.0010.0000.0000.0000.000
127A129GLN00.0140.02041.1640.0050.0050.0000.0000.0000.000
128A130SER0-0.097-0.05843.7600.0040.0040.0000.0000.0000.000
129A131VAL00.0640.01839.6320.0030.0030.0000.0000.0000.000
130A132LYS10.8170.89837.2190.0300.0300.0000.0000.0000.000
131A133LYS10.8890.94341.5380.0280.0280.0000.0000.0000.000
132A134LEU00.0180.02442.7550.0040.0040.0000.0000.0000.000
133A135LEU0-0.027-0.01637.4390.0000.0000.0000.0000.0000.000
134A136THR00.0350.01039.2850.0010.0010.0000.0000.0000.000
135A137ASN0-0.073-0.03737.6680.0000.0000.0000.0000.0000.000
136A138LYS10.8590.94535.3110.0310.0310.0000.0000.0000.000
137A139ILE0-0.0060.00029.688-0.001-0.0010.0000.0000.0000.000
138A140LEU00.0040.00533.512-0.009-0.0090.0000.0000.0000.000
139A141LYS10.7710.85427.3780.1130.1130.0000.0000.0000.000
140A142VAL0-0.012-0.01132.004-0.003-0.0030.0000.0000.0000.000
141A143ILE0-0.028-0.02230.601-0.009-0.0090.0000.0000.0000.000
142A144ILE00.010-0.01131.6630.0070.0070.0000.0000.0000.000
143A145GLU-1-0.722-0.83231.526-0.200-0.2000.0000.0000.0000.000
144A146VAL00.006-0.00928.1060.0030.0030.0000.0000.0000.000
145A147GLY0-0.012-0.00730.7430.0010.0010.0000.0000.0000.000
146A148GLU-1-0.849-0.92631.321-0.183-0.1830.0000.0000.0000.000
147A149LEU00.0180.01334.6390.0080.0080.0000.0000.0000.000
148A150LYS10.7690.88033.3890.1800.1800.0000.0000.0000.000
149A151THR0-0.0010.00234.1820.0000.0000.0000.0000.0000.000
150A152GLU-1-0.778-0.88733.357-0.109-0.1090.0000.0000.0000.000
151A153ASP-1-0.809-0.89534.779-0.079-0.0790.0000.0000.0000.000
152A154LEU00.0600.03537.7690.0060.0060.0000.0000.0000.000
153A155ILE0-0.0300.01131.3410.0020.0020.0000.0000.0000.000
154A156ILE00.0140.00934.3220.0040.0040.0000.0000.0000.000
155A157LYS10.8580.91435.8060.0830.0830.0000.0000.0000.000
156A158THR00.028-0.01136.3300.0060.0060.0000.0000.0000.000
157A159THR0-0.038-0.02732.6870.0010.0010.0000.0000.0000.000
158A160LEU0-0.0010.00135.4700.0070.0070.0000.0000.0000.000
159A161ALA0-0.0110.01638.4340.0070.0070.0000.0000.0000.000
160A162VAL00.0200.00935.4820.0050.0050.0000.0000.0000.000
161A163LEU0-0.0080.00133.8180.0050.0050.0000.0000.0000.000
162A164ASN0-0.035-0.03737.8770.0110.0110.0000.0000.0000.000
163A165GLY0-0.0220.00240.8570.0040.0040.0000.0000.0000.000
164A166ASN0-0.078-0.05239.3790.0040.0040.0000.0000.0000.000
165A167ALA00.0450.02234.9890.0020.0020.0000.0000.0000.000
166A168ASP-1-0.793-0.86733.296-0.025-0.0250.0000.0000.0000.000
167A169PHE0-0.024-0.01425.6950.0020.0020.0000.0000.0000.000
168A170ILE00.0100.02729.599-0.005-0.0050.0000.0000.0000.000
169A171LYS10.8310.90427.1310.1830.1830.0000.0000.0000.000
170A172THR0-0.0010.00225.0760.0030.0030.0000.0000.0000.000
171A173SER00.018-0.00826.2770.0090.0090.0000.0000.0000.000
172A174THR0-0.059-0.05428.078-0.014-0.0140.0000.0000.0000.000
173A175GLY0-0.029-0.00626.996-0.006-0.0060.0000.0000.0000.000
174A176LYS10.8090.88827.7100.2140.2140.0000.0000.0000.000
175A177VAL00.0180.03530.3180.0100.0100.0000.0000.0000.000
176A178GLN00.0160.00529.409-0.009-0.0090.0000.0000.0000.000
177A179ILE0-0.0210.00727.993-0.030-0.0300.0000.0000.0000.000
178A180ASN0-0.007-0.02825.0550.0230.0230.0000.0000.0000.000
179A181ALA00.0010.00822.6840.0120.0120.0000.0000.0000.000
180A182THR00.0440.02523.192-0.034-0.0340.0000.0000.0000.000
181A183PRO00.0400.01220.4340.0290.0290.0000.0000.0000.000
182A184SER00.0740.04422.9470.0210.0210.0000.0000.0000.000
183A185SER0-0.052-0.02826.0810.0180.0180.0000.0000.0000.000
184A186VAL00.0300.00722.9420.0180.0180.0000.0000.0000.000
185A187GLU-1-0.908-0.96424.876-0.149-0.1490.0000.0000.0000.000
186A188TYR0-0.049-0.02227.1080.0170.0170.0000.0000.0000.000
187A189ILE00.0360.02827.9170.0140.0140.0000.0000.0000.000
188A190ILE0-0.011-0.01324.1930.0180.0180.0000.0000.0000.000
189A191LYS10.7940.88428.7960.1260.1260.0000.0000.0000.000
190A192ALA00.0610.03831.8320.0120.0120.0000.0000.0000.000
191A193ILE00.0270.01029.1560.0080.0080.0000.0000.0000.000
192A194LYS10.8390.91628.3790.0390.0390.0000.0000.0000.000
193A195GLU-1-0.944-0.96533.393-0.039-0.0390.0000.0000.0000.000
194A196TYR00.0280.01736.0090.0060.0060.0000.0000.0000.000
195A197ILE0-0.003-0.00833.2310.0060.0060.0000.0000.0000.000
196A198LYS10.9070.95336.5420.0080.0080.0000.0000.0000.000
197A199ASN0-0.065-0.03438.5930.0060.0060.0000.0000.0000.000
198A200ASN0-0.0350.00339.248-0.001-0.0010.0000.0000.0000.000
199A201PRO00.0540.02138.5790.0010.0010.0000.0000.0000.000
200A202GLU-1-0.857-0.94137.9720.0130.0130.0000.0000.0000.000
201A203LYS10.8360.91536.2940.0130.0130.0000.0000.0000.000
202A204ASN00.0400.01832.635-0.005-0.0050.0000.0000.0000.000
203A205ASN0-0.082-0.05128.6170.0130.0130.0000.0000.0000.000
204A206LYS10.9030.97131.154-0.025-0.0250.0000.0000.0000.000
205A207ILE00.0160.02531.169-0.007-0.0070.0000.0000.0000.000
206A208GLY00.0230.01327.7590.0070.0070.0000.0000.0000.000
207A209LEU0-0.065-0.02323.801-0.010-0.0100.0000.0000.0000.000
208A210LYS10.7680.85024.0810.1840.1840.0000.0000.0000.000
209A211VAL00.0010.00520.950-0.002-0.0020.0000.0000.0000.000
210A212SER00.004-0.01221.746-0.021-0.0210.0000.0000.0000.000
211A213GLY00.0560.05023.0380.0200.0200.0000.0000.0000.000
212A214GLY00.002-0.00821.542-0.003-0.0030.0000.0000.0000.000
213A215ILE0-0.021-0.00216.487-0.075-0.0750.0000.0000.0000.000
214A216SER00.0310.01615.7990.0840.0840.0000.0000.0000.000
215A217ASP-1-0.816-0.87111.128-1.533-1.5330.0000.0000.0000.000
216A218LEU00.0520.0006.2300.2200.2200.0000.0000.0000.000
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218A220THR0-0.029-0.05710.4530.3260.3260.0000.0000.0000.000
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