FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 4J67N

Calculation Name: 2AFR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AFR

Chain ID: A

ChEMBL ID:

UniProt ID: Q8EXP7

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:

Apendix: None


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 216
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2535890.372814
FMO2-HF: Nuclear repulsion 2452743.936137
FMO2-HF: Total energy -83146.436678
FMO2-MP2: Total energy -83390.734899


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:6:GLN)


Summations of interaction energy for fragment #1(A:6: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.
-1.190.517-0.026-0.948-0.7320.002
Interaction energy analysis for fragmet #1(A:6:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.017
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].
3A8THR00.0400.0293.8170.6492.356-0.026-0.948-0.7320.002
4A9ASN00.0550.0196.9510.0740.0740.0000.0000.0000.000
5A10LEU00.0340.0279.3430.0420.0420.0000.0000.0000.000
6A11GLY00.0410.0178.4880.0300.0300.0000.0000.0000.000
7A12ARG10.9700.9655.731-0.150-0.1500.0000.0000.0000.000
8A13ASN0-0.0010.0059.0230.1060.1060.0000.0000.0000.000
9A14ILE00.0190.01912.3070.0380.0380.0000.0000.0000.000
10A15GLU-1-0.865-0.9338.9441.1411.1410.0000.0000.0000.000
11A16ASN0-0.027-0.02810.562-0.014-0.0140.0000.0000.0000.000
12A17LYS10.9570.99713.550-0.115-0.1150.0000.0000.0000.000
13A18SER00.011-0.01414.790-0.023-0.0230.0000.0000.0000.000
14A19PHE0-0.031-0.02110.9720.0120.0120.0000.0000.0000.000
15A20SER0-0.030-0.01616.405-0.009-0.0090.0000.0000.0000.000
16A21ILE0-0.017-0.00619.164-0.021-0.0210.0000.0000.0000.000
17A22ILE0-0.0010.00617.239-0.005-0.0050.0000.0000.0000.000
18A23ASP-1-0.829-0.90019.3290.3990.3990.0000.0000.0000.000
19A24GLU-1-1.025-1.01222.0480.1230.1230.0000.0000.0000.000
20A25GLU-1-0.902-0.94524.1790.1240.1240.0000.0000.0000.000
21A26ALA0-0.049-0.02823.700-0.005-0.0050.0000.0000.0000.000
22A27GLY00.0170.02525.714-0.013-0.0130.0000.0000.0000.000
23A28PRO0-0.030-0.01727.3680.0190.0190.0000.0000.0000.000
24A29HIS00.0310.00823.839-0.011-0.0110.0000.0000.0000.000
25A30SER00.0060.00128.548-0.005-0.0050.0000.0000.0000.000
26A31PHE0-0.044-0.00423.4150.0090.0090.0000.0000.0000.000
27A32ALA00.0620.03223.759-0.005-0.0050.0000.0000.0000.000
28A33GLN00.0470.00318.2390.0830.0830.0000.0000.0000.000
29A34GLU-1-0.778-0.87517.1300.7280.7280.0000.0000.0000.000
30A35GLU-1-0.833-0.93417.9950.5290.5290.0000.0000.0000.000
31A36TRP0-0.046-0.04619.9040.0160.0160.0000.0000.0000.000
32A37GLU-1-0.853-0.90714.2420.9780.9780.0000.0000.0000.000
33A38VAL0-0.024-0.01415.5710.0800.0800.0000.0000.0000.000
34A39VAL0-0.019-0.01017.154-0.019-0.0190.0000.0000.0000.000
35A40ARG10.8210.90615.177-0.632-0.6320.0000.0000.0000.000
36A41ARG10.9130.9669.244-1.325-1.3250.0000.0000.0000.000
37A42ILE0-0.014-0.00715.400-0.050-0.0500.0000.0000.0000.000
38A43ILE0-0.030-0.00218.227-0.049-0.0490.0000.0000.0000.000
39A44HIS00.0260.01411.939-0.037-0.0370.0000.0000.0000.000
40A45ALA0-0.060-0.02215.222-0.048-0.0480.0000.0000.0000.000
41A46THR0-0.078-0.05816.544-0.053-0.0530.0000.0000.0000.000
42A47ALA0-0.0020.01519.816-0.028-0.0280.0000.0000.0000.000
43A48ASP-1-0.785-0.87821.5050.1450.1450.0000.0000.0000.000
44A49PHE00.0760.01623.2010.0320.0320.0000.0000.0000.000
45A50ASP-1-0.814-0.87725.2440.1690.1690.0000.0000.0000.000
46A51TYR00.008-0.01023.1150.0080.0080.0000.0000.0000.000
47A52LYS10.8270.93024.858-0.175-0.1750.0000.0000.0000.000
48A53ASN0-0.012-0.01025.6560.0080.0080.0000.0000.0000.000
49A54ILE0-0.062-0.02726.893-0.005-0.0050.0000.0000.0000.000
50A55THR0-0.041-0.03422.3650.0020.0020.0000.0000.0000.000
51A56LYS10.8750.94025.804-0.214-0.2140.0000.0000.0000.000
52A57ILE00.009-0.00320.8720.0100.0100.0000.0000.0000.000
53A58HIS00.0190.03225.0340.0110.0110.0000.0000.0000.000
54A59PRO00.0590.02725.0230.0330.0330.0000.0000.0000.000
55A60GLN00.0410.02324.9430.0080.0080.0000.0000.0000.000
56A61ALA0-0.021-0.00622.3880.0260.0260.0000.0000.0000.000
57A62ILE00.0370.01117.3160.0500.0500.0000.0000.0000.000
58A63ASP-1-0.820-0.89218.8920.5270.5270.0000.0000.0000.000
59A64SER0-0.035-0.03520.6090.0080.0080.0000.0000.0000.000
60A65GLY00.0170.01218.6880.0030.0030.0000.0000.0000.000
61A66ILE0-0.048-0.00614.4630.0680.0680.0000.0000.0000.000
62A67GLN0-0.011-0.00916.9790.0150.0150.0000.0000.0000.000
63A68ALA00.0410.00919.710-0.019-0.0190.0000.0000.0000.000
64A69LEU00.018-0.01213.4680.0040.0040.0000.0000.0000.000
65A70LYS10.8620.93613.084-0.976-0.9760.0000.0000.0000.000
66A71LYS10.8960.95616.788-0.370-0.3700.0000.0000.0000.000
67A72GLY00.0490.02217.516-0.049-0.0490.0000.0000.0000.000
68A73CYS0-0.095-0.02518.520-0.033-0.0330.0000.0000.0000.000
69A74PRO0-0.008-0.00519.3930.0350.0350.0000.0000.0000.000
70A75ILE00.001-0.01715.7950.0250.0250.0000.0000.0000.000
71A76VAL00.0190.00920.110-0.031-0.0310.0000.0000.0000.000
72A77CYS0-0.0170.01019.7800.0350.0350.0000.0000.0000.000
73A78ASP-1-0.715-0.85322.4700.1710.1710.0000.0000.0000.000
74A79VAL0-0.020-0.02622.253-0.029-0.0290.0000.0000.0000.000
75A80GLN00.1120.04018.9000.0420.0420.0000.0000.0000.000
76A81MET0-0.0100.00818.2860.0120.0120.0000.0000.0000.000
77A82ILE00.0210.01716.9900.0050.0050.0000.0000.0000.000
78A83LEU00.0680.03215.8370.0610.0610.0000.0000.0000.000
79A84SER0-0.082-0.04014.4920.0190.0190.0000.0000.0000.000
80A85GLY00.0150.02112.399-0.092-0.0920.0000.0000.0000.000
81A86LEU0-0.086-0.05011.0000.1640.1640.0000.0000.0000.000
82A87ASN00.0150.0056.2450.2270.2270.0000.0000.0000.000
83A88PRO00.0680.0168.9760.3570.3570.0000.0000.0000.000
84A89GLU-1-0.898-0.9486.275-0.059-0.0590.0000.0000.0000.000
85A90ARG10.8700.9275.607-2.794-2.7940.0000.0000.0000.000
86A91LEU00.0190.0107.940-0.078-0.0780.0000.0000.0000.000
87A92LYS10.9780.99511.197-0.168-0.1680.0000.0000.0000.000
88A93VAL0-0.065-0.0288.339-0.096-0.0960.0000.0000.0000.000
89A94TYR0-0.004-0.02511.7480.0550.0550.0000.0000.0000.000
90A95GLY00.0060.01814.512-0.096-0.0960.0000.0000.0000.000
91A96CYS0-0.0660.00215.277-0.023-0.0230.0000.0000.0000.000
92A97LYS10.9250.97916.674-0.217-0.2170.0000.0000.0000.000
93A98THR00.0260.02216.0270.0190.0190.0000.0000.0000.000
94A99TYR0-0.003-0.01219.128-0.050-0.0500.0000.0000.0000.000
95A100CYS0-0.041-0.02322.2930.0140.0140.0000.0000.0000.000
96A101PHE00.0470.03124.151-0.013-0.0130.0000.0000.0000.000
97A102ILE0-0.042-0.00925.743-0.014-0.0140.0000.0000.0000.000
98A103SER0-0.053-0.04726.768-0.011-0.0110.0000.0000.0000.000
99A104ASP-1-0.773-0.85528.6360.0640.0640.0000.0000.0000.000
100A105GLU-1-0.880-0.95130.9980.0190.0190.0000.0000.0000.000
101A106ASP-1-0.833-0.90333.8160.0640.0640.0000.0000.0000.000
102A107VAL0-0.013-0.00231.4770.0020.0020.0000.0000.0000.000
103A108ILE0-0.015-0.01131.9990.0020.0020.0000.0000.0000.000
104A109GLU-1-0.791-0.88635.5930.0270.0270.0000.0000.0000.000
105A110ASN00.0170.01937.231-0.006-0.0060.0000.0000.0000.000
106A111ALA0-0.0010.00836.3590.0010.0010.0000.0000.0000.000
107A112LYS10.7730.86638.491-0.027-0.0270.0000.0000.0000.000
108A113ARG10.8710.92340.996-0.044-0.0440.0000.0000.0000.000
109A114LYS10.8040.88639.218-0.077-0.0770.0000.0000.0000.000
110A115ASN0-0.057-0.00542.8400.0010.0010.0000.0000.0000.000
111A116SER0-0.001-0.00938.9870.0030.0030.0000.0000.0000.000
112A117THR00.022-0.00534.690-0.002-0.0020.0000.0000.0000.000
113A118ARG11.0271.00431.671-0.040-0.0400.0000.0000.0000.000
114A119ALA00.003-0.00630.5460.0060.0060.0000.0000.0000.000
115A120ILE0-0.0110.00331.5150.0110.0110.0000.0000.0000.000
116A121GLU-1-0.760-0.85034.2770.0840.0840.0000.0000.0000.000
117A122SER0-0.036-0.00628.1180.0030.0030.0000.0000.0000.000
118A123ILE0-0.020-0.01328.2420.0080.0080.0000.0000.0000.000
119A124GLN00.003-0.02131.035-0.001-0.0010.0000.0000.0000.000
120A125LYS10.7950.87931.013-0.076-0.0760.0000.0000.0000.000
121A126ALA00.0270.01928.0700.0000.0000.0000.0000.0000.000
122A127ASN00.0120.00229.8280.0140.0140.0000.0000.0000.000
123A128SER0-0.073-0.02532.584-0.004-0.0040.0000.0000.0000.000
124A129PHE0-0.015-0.01929.493-0.008-0.0080.0000.0000.0000.000
125A130ASN0-0.049-0.02930.7400.0070.0070.0000.0000.0000.000
126A131LEU0-0.035-0.01625.5080.0150.0150.0000.0000.0000.000
127A132LEU00.0150.00126.3610.0230.0230.0000.0000.0000.000
128A133ASN00.0160.01227.7120.0180.0180.0000.0000.0000.000
129A134GLU-1-0.851-0.92025.6510.2740.2740.0000.0000.0000.000
130A135SER0-0.083-0.02423.0920.0330.0330.0000.0000.0000.000
131A136ILE00.0210.00517.8480.0110.0110.0000.0000.0000.000
132A137ILE0-0.009-0.01121.749-0.006-0.0060.0000.0000.0000.000
133A138VAL0-0.003-0.00618.8940.0170.0170.0000.0000.0000.000
134A139ILE0-0.010-0.00722.124-0.031-0.0310.0000.0000.0000.000
135A140GLY00.0390.00422.5560.0100.0100.0000.0000.0000.000
136A141ASN0-0.121-0.06623.538-0.025-0.0250.0000.0000.0000.000
137A142ALA00.0940.03126.333-0.010-0.0100.0000.0000.0000.000
138A143PRO00.0380.01029.6440.0090.0090.0000.0000.0000.000
139A144THR00.0390.01032.0740.0020.0020.0000.0000.0000.000
140A145ALA0-0.0110.00929.428-0.002-0.0020.0000.0000.0000.000
141A146LEU00.0120.00328.3840.0080.0080.0000.0000.0000.000
142A147LEU0-0.002-0.00731.0290.0010.0010.0000.0000.0000.000
143A148GLU-1-0.840-0.89733.5100.1110.1110.0000.0000.0000.000
144A149ILE00.0100.00329.0220.0000.0000.0000.0000.0000.000
145A150GLU-1-0.830-0.90332.3720.1330.1330.0000.0000.0000.000
146A151LYS10.8690.94534.635-0.113-0.1130.0000.0000.0000.000
147A152LEU0-0.048-0.02333.096-0.004-0.0040.0000.0000.0000.000
148A153ILE0-0.044-0.01931.051-0.001-0.0010.0000.0000.0000.000
149A154ARG10.8260.89835.270-0.121-0.1210.0000.0000.0000.000
150A155GLN0-0.071-0.04338.787-0.005-0.0050.0000.0000.0000.000
151A156GLU-1-0.806-0.92537.1490.1070.1070.0000.0000.0000.000
152A157GLY0-0.0110.02537.0280.0000.0000.0000.0000.0000.000
153A158ILE0-0.081-0.02830.9290.0080.0080.0000.0000.0000.000
154A159LYS10.8950.91128.813-0.243-0.2430.0000.0000.0000.000
155A160PRO0-0.0190.02126.1620.0080.0080.0000.0000.0000.000
156A161ALA00.001-0.00522.988-0.002-0.0020.0000.0000.0000.000
157A162LEU0-0.060-0.03119.7270.0150.0150.0000.0000.0000.000
158A163ILE0-0.0010.01123.719-0.002-0.0020.0000.0000.0000.000
159A164VAL0-0.002-0.00419.5140.0090.0090.0000.0000.0000.000
160A165GLY00.0470.00722.906-0.019-0.0190.0000.0000.0000.000
161A166VAL0-0.016-0.01421.762-0.007-0.0070.0000.0000.0000.000
162A167PRO0-0.0120.01725.092-0.008-0.0080.0000.0000.0000.000
163A168VAL00.0020.01126.327-0.001-0.0010.0000.0000.0000.000
164A169GLY0-0.018-0.02328.599-0.011-0.0110.0000.0000.0000.000
165A170PHE0-0.023-0.04632.1690.0050.0050.0000.0000.0000.000
166A171VAL0-0.0020.01535.673-0.002-0.0020.0000.0000.0000.000
167A172SER00.0710.03035.991-0.002-0.0020.0000.0000.0000.000
168A173ALA0-0.0270.01031.3340.0070.0070.0000.0000.0000.000
169A174LYS10.8520.91632.951-0.105-0.1050.0000.0000.0000.000
170A175GLU-1-0.798-0.90234.5390.1190.1190.0000.0000.0000.000
171A176SER0-0.023-0.03232.4490.0080.0080.0000.0000.0000.000
172A177LYS10.8450.93428.502-0.185-0.1850.0000.0000.0000.000
173A178GLU-1-0.862-0.92532.1910.1340.1340.0000.0000.0000.000
174A179SER0-0.082-0.04934.696-0.002-0.0020.0000.0000.0000.000
175A180ILE00.0390.01929.851-0.001-0.0010.0000.0000.0000.000
176A181LEU00.0130.00231.2170.0010.0010.0000.0000.0000.000
177A182LYS10.9440.97734.367-0.127-0.1270.0000.0000.0000.000
178A183LEU00.0130.02034.207-0.005-0.0050.0000.0000.0000.000
179A184GLU-1-0.795-0.87232.4850.2180.2180.0000.0000.0000.000
180A185TYR0-0.060-0.02435.684-0.006-0.0060.0000.0000.0000.000
181A186TYR0-0.057-0.04438.639-0.007-0.0070.0000.0000.0000.000
182A187ASN0-0.075-0.02937.9220.0000.0000.0000.0000.0000.000
183A188VAL0-0.0050.00538.409-0.004-0.0040.0000.0000.0000.000
184A189THR0-0.004-0.01633.8590.0040.0040.0000.0000.0000.000
185A190SER00.0010.00831.666-0.005-0.0050.0000.0000.0000.000
186A191ILE0-0.045-0.01328.0370.0150.0150.0000.0000.0000.000
187A192PRO00.0310.03324.786-0.001-0.0010.0000.0000.0000.000
188A193TYR0-0.042-0.06425.3180.0080.0080.0000.0000.0000.000
189A194ILE00.0240.00619.7540.0170.0170.0000.0000.0000.000
190A195LEU0-0.032-0.00623.962-0.010-0.0100.0000.0000.0000.000
191A196THR00.0290.02423.6760.0140.0140.0000.0000.0000.000
192A197MET0-0.036-0.01726.770-0.015-0.0150.0000.0000.0000.000
193A198GLY00.0530.03030.481-0.004-0.0040.0000.0000.0000.000
194A199ARG10.9560.95931.788-0.094-0.0940.0000.0000.0000.000
195A200LYS10.8020.86326.960-0.156-0.1560.0000.0000.0000.000
196A201GLY00.0790.03824.6960.0140.0140.0000.0000.0000.000
197A202GLY00.0130.00822.958-0.022-0.0220.0000.0000.0000.000
198A203SER00.000-0.02119.5790.0350.0350.0000.0000.0000.000
199A204THR00.0460.01016.4210.0430.0430.0000.0000.0000.000
200A205ILE00.0200.02716.9090.0610.0610.0000.0000.0000.000
201A206ALA00.0220.00218.1270.0660.0660.0000.0000.0000.000
202A207VAL0-0.0120.00113.0250.0750.0750.0000.0000.0000.000
203A208ALA0-0.0010.00813.4650.1760.1760.0000.0000.0000.000
204A209ILE00.0020.00014.1340.1460.1460.0000.0000.0000.000
205A210LEU00.0050.00113.8790.0980.0980.0000.0000.0000.000
206A211HIS0-0.009-0.0129.6150.5340.5340.0000.0000.0000.000
207A212ALA0-0.0070.01310.0080.4190.4190.0000.0000.0000.000
208A213LEU00.0180.01512.2450.0960.0960.0000.0000.0000.000
209A214LEU00.004-0.0048.7590.0560.0560.0000.0000.0000.000
210A215LEU0-0.016-0.0016.8410.3670.3670.0000.0000.0000.000
211A216LEU00.0170.0058.944-0.107-0.1070.0000.0000.0000.000
212A217SER00.0240.00611.205-0.166-0.1660.0000.0000.0000.000
213A218SER0-0.049-0.0346.764-0.368-0.3680.0000.0000.0000.000
214A219LYS10.8820.9459.731-1.101-1.1010.0000.0000.0000.000
215A220ARG10.6640.80411.342-0.835-0.8350.0000.0000.0000.000
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