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

tag_button

FMODB ID: KG8N3

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 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 216
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2535459.531617
FMO2-HF: Nuclear repulsion 2452314.13834
FMO2-HF: Total energy -83145.393277
FMO2-MP2: Total energy -83389.809419


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.
-1.4080.289-0.027-0.944-0.7260.001
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 : -0.006 / q_NPA : -0.019
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].
3A8THR00.0360.0313.8170.7512.448-0.027-0.944-0.7260.001
4A9ASN00.0330.0006.8860.2150.2150.0000.0000.0000.000
5A10LEU00.0260.0239.2320.0600.0600.0000.0000.0000.000
6A11GLY00.0480.0158.4040.0200.0200.0000.0000.0000.000
7A12ARG10.9900.9846.025-1.017-1.0170.0000.0000.0000.000
8A13ASN00.0140.0158.8670.0990.0990.0000.0000.0000.000
9A14ILE00.0010.01212.1430.0110.0110.0000.0000.0000.000
10A15GLU-1-0.925-0.9568.5401.5991.5990.0000.0000.0000.000
11A16ASN0-0.021-0.02710.828-0.067-0.0670.0000.0000.0000.000
12A17LYS10.9590.99813.636-0.264-0.2640.0000.0000.0000.000
13A18SER00.019-0.00514.817-0.051-0.0510.0000.0000.0000.000
14A19PHE0-0.024-0.02611.4420.0280.0280.0000.0000.0000.000
15A20SER0-0.017-0.01316.470-0.022-0.0220.0000.0000.0000.000
16A21ILE0-0.022-0.00719.238-0.033-0.0330.0000.0000.0000.000
17A22ILE0-0.029-0.00217.263-0.014-0.0140.0000.0000.0000.000
18A23ASP-1-0.831-0.92419.5390.5230.5230.0000.0000.0000.000
19A24GLU-1-1.027-1.01722.1050.1920.1920.0000.0000.0000.000
20A25GLU-1-0.874-0.92724.2540.1840.1840.0000.0000.0000.000
21A26ALA0-0.085-0.04523.776-0.012-0.0120.0000.0000.0000.000
22A27GLY00.0020.00625.761-0.020-0.0200.0000.0000.0000.000
23A28PRO0-0.057-0.02527.4140.0210.0210.0000.0000.0000.000
24A29HIS00.0400.01023.869-0.019-0.0190.0000.0000.0000.000
25A30SER00.0010.00028.554-0.004-0.0040.0000.0000.0000.000
26A31PHE0-0.054-0.01123.4620.0060.0060.0000.0000.0000.000
27A32ALA00.0700.03323.552-0.001-0.0010.0000.0000.0000.000
28A33GLN00.008-0.01218.6550.0690.0690.0000.0000.0000.000
29A34GLU-1-0.801-0.91417.2890.7630.7630.0000.0000.0000.000
30A35GLU-1-0.843-0.94518.1220.5440.5440.0000.0000.0000.000
31A36TRP0-0.049-0.03419.6910.0100.0100.0000.0000.0000.000
32A37GLU-1-0.907-0.93513.4071.2521.2520.0000.0000.0000.000
33A38VAL0-0.014-0.00915.6620.0860.0860.0000.0000.0000.000
34A39VAL0-0.010-0.00617.316-0.018-0.0180.0000.0000.0000.000
35A40ARG10.8860.94914.739-0.811-0.8110.0000.0000.0000.000
36A41ARG10.9180.9669.789-1.533-1.5330.0000.0000.0000.000
37A42ILE0-0.012-0.00815.417-0.055-0.0550.0000.0000.0000.000
38A43ILE0-0.028-0.00518.235-0.051-0.0510.0000.0000.0000.000
39A44HIS00.0270.01111.906-0.037-0.0370.0000.0000.0000.000
40A45ALA0-0.056-0.02115.252-0.046-0.0460.0000.0000.0000.000
41A46THR0-0.062-0.03916.561-0.062-0.0620.0000.0000.0000.000
42A47ALA0-0.0020.01619.856-0.031-0.0310.0000.0000.0000.000
43A48ASP-1-0.793-0.88621.5420.1700.1700.0000.0000.0000.000
44A49PHE00.0740.00923.3440.0290.0290.0000.0000.0000.000
45A50ASP-1-0.862-0.91925.2760.1960.1960.0000.0000.0000.000
46A51TYR0-0.006-0.01623.130-0.002-0.0020.0000.0000.0000.000
47A52LYS10.8930.96924.885-0.219-0.2190.0000.0000.0000.000
48A53ASN00.003-0.00625.6750.0120.0120.0000.0000.0000.000
49A54ILE0-0.060-0.01626.881-0.007-0.0070.0000.0000.0000.000
50A55THR0-0.043-0.03922.529-0.003-0.0030.0000.0000.0000.000
51A56LYS10.8760.93525.875-0.220-0.2200.0000.0000.0000.000
52A57ILE00.008-0.00421.2530.0080.0080.0000.0000.0000.000
53A58HIS00.0480.05625.2850.0110.0110.0000.0000.0000.000
54A59PRO00.0740.03625.2990.0340.0340.0000.0000.0000.000
55A60GLN00.0330.00625.1970.0060.0060.0000.0000.0000.000
56A61ALA0-0.036-0.01422.7660.0190.0190.0000.0000.0000.000
57A62ILE00.0540.01917.5900.0370.0370.0000.0000.0000.000
58A63ASP-1-0.837-0.90819.2160.5170.5170.0000.0000.0000.000
59A64SER0-0.018-0.02420.960-0.001-0.0010.0000.0000.0000.000
60A65GLY00.0190.01619.077-0.006-0.0060.0000.0000.0000.000
61A66ILE0-0.027-0.01415.0350.0490.0490.0000.0000.0000.000
62A67GLN0-0.012-0.01117.356-0.011-0.0110.0000.0000.0000.000
63A68ALA00.0530.01720.143-0.026-0.0260.0000.0000.0000.000
64A69LEU00.009-0.01413.672-0.006-0.0060.0000.0000.0000.000
65A70LYS10.8630.94113.571-0.873-0.8730.0000.0000.0000.000
66A71LYS10.8970.95617.228-0.313-0.3130.0000.0000.0000.000
67A72GLY00.0440.02318.032-0.045-0.0450.0000.0000.0000.000
68A73CYS0-0.082-0.01919.031-0.027-0.0270.0000.0000.0000.000
69A74PRO0-0.019-0.00419.9220.0230.0230.0000.0000.0000.000
70A75ILE00.016-0.01616.4010.0300.0300.0000.0000.0000.000
71A76VAL00.0220.01120.458-0.034-0.0340.0000.0000.0000.000
72A77CYS0-0.023-0.00220.0200.0360.0360.0000.0000.0000.000
73A78ASP-1-0.714-0.86122.7700.1400.1400.0000.0000.0000.000
74A79VAL0-0.035-0.02722.386-0.028-0.0280.0000.0000.0000.000
75A80GLN00.1090.03618.9940.0330.0330.0000.0000.0000.000
76A81MET0-0.015-0.02218.2990.0030.0030.0000.0000.0000.000
77A82ILE00.0270.02416.9820.0020.0020.0000.0000.0000.000
78A83LEU00.0620.02715.8250.0460.0460.0000.0000.0000.000
79A84SER0-0.086-0.03214.485-0.001-0.0010.0000.0000.0000.000
80A85GLY00.0090.01812.392-0.085-0.0850.0000.0000.0000.000
81A86LEU0-0.084-0.05710.9870.1430.1430.0000.0000.0000.000
82A87ASN00.0160.0096.776-0.031-0.0310.0000.0000.0000.000
83A88PRO00.0700.0149.2230.2680.2680.0000.0000.0000.000
84A89GLU-1-0.889-0.9396.418-0.447-0.4470.0000.0000.0000.000
85A90ARG10.8360.9036.120-2.253-2.2530.0000.0000.0000.000
86A91LEU00.0150.0078.1130.0100.0100.0000.0000.0000.000
87A92LYS10.9810.99711.3530.0950.0950.0000.0000.0000.000
88A93VAL0-0.064-0.0298.840-0.064-0.0640.0000.0000.0000.000
89A94TYR0-0.034-0.04712.0640.0890.0890.0000.0000.0000.000
90A95GLY00.0040.01314.850-0.066-0.0660.0000.0000.0000.000
91A96CYS0-0.0590.00015.709-0.005-0.0050.0000.0000.0000.000
92A97LYS10.9280.98216.867-0.120-0.1200.0000.0000.0000.000
93A98THR00.0070.01216.2580.0140.0140.0000.0000.0000.000
94A99TYR00.0230.00319.380-0.035-0.0350.0000.0000.0000.000
95A100CYS0-0.033-0.01222.4500.0180.0180.0000.0000.0000.000
96A101PHE00.0530.03024.349-0.014-0.0140.0000.0000.0000.000
97A102ILE0-0.052-0.01225.953-0.010-0.0100.0000.0000.0000.000
98A103SER0-0.052-0.04627.044-0.008-0.0080.0000.0000.0000.000
99A104ASP-1-0.780-0.85928.8470.0160.0160.0000.0000.0000.000
100A105GLU-1-0.872-0.95130.996-0.008-0.0080.0000.0000.0000.000
101A106ASP-1-0.794-0.88133.8120.0290.0290.0000.0000.0000.000
102A107VAL0-0.0160.00231.6030.0040.0040.0000.0000.0000.000
103A108ILE0-0.013-0.00832.2040.0050.0050.0000.0000.0000.000
104A109GLU-1-0.840-0.92135.5890.0070.0070.0000.0000.0000.000
105A110ASN0-0.027-0.01937.3970.0000.0000.0000.0000.0000.000
106A111ALA00.0050.00836.3590.0020.0020.0000.0000.0000.000
107A112LYS10.7820.88138.483-0.006-0.0060.0000.0000.0000.000
108A113ARG10.8980.94340.990-0.021-0.0210.0000.0000.0000.000
109A114LYS10.8540.93139.953-0.053-0.0530.0000.0000.0000.000
110A115ASN0-0.0430.00642.8860.0010.0010.0000.0000.0000.000
111A116SER0-0.016-0.01838.8310.0030.0030.0000.0000.0000.000
112A117THR00.008-0.00934.683-0.003-0.0030.0000.0000.0000.000
113A118ARG11.0270.99831.968-0.016-0.0160.0000.0000.0000.000
114A119ALA00.007-0.00430.5350.0030.0030.0000.0000.0000.000
115A120ILE00.0080.00731.5040.0090.0090.0000.0000.0000.000
116A121GLU-1-0.768-0.87634.4320.0620.0620.0000.0000.0000.000
117A122SER0-0.047-0.01228.3490.0000.0000.0000.0000.0000.000
118A123ILE0-0.021-0.00928.7220.0050.0050.0000.0000.0000.000
119A124GLN00.0290.00431.325-0.002-0.0020.0000.0000.0000.000
120A125LYS10.7980.89130.981-0.035-0.0350.0000.0000.0000.000
121A126ALA00.0250.02528.341-0.002-0.0020.0000.0000.0000.000
122A127ASN00.0110.00030.0920.0110.0110.0000.0000.0000.000
123A128SER0-0.078-0.03432.843-0.004-0.0040.0000.0000.0000.000
124A129PHE0-0.006-0.01330.087-0.008-0.0080.0000.0000.0000.000
125A130ASN0-0.059-0.03330.9610.0060.0060.0000.0000.0000.000
126A131LEU0-0.044-0.02225.7430.0120.0120.0000.0000.0000.000
127A132LEU00.006-0.00226.8060.0190.0190.0000.0000.0000.000
128A133ASN00.0160.00128.2130.0280.0280.0000.0000.0000.000
129A134GLU-1-0.888-0.96126.0230.2420.2420.0000.0000.0000.000
130A135SER0-0.093-0.02123.5800.0260.0260.0000.0000.0000.000
131A136ILE00.0100.00518.2290.0170.0170.0000.0000.0000.000
132A137ILE00.006-0.00722.229-0.012-0.0120.0000.0000.0000.000
133A138VAL0-0.001-0.00319.3790.0220.0220.0000.0000.0000.000
134A139ILE0-0.008-0.00322.571-0.032-0.0320.0000.0000.0000.000
135A140GLY00.0360.00222.5100.0140.0140.0000.0000.0000.000
136A141ASN0-0.128-0.06523.495-0.018-0.0180.0000.0000.0000.000
137A142ALA00.1010.03426.317-0.007-0.0070.0000.0000.0000.000
138A143PRO00.0170.00029.6300.0070.0070.0000.0000.0000.000
139A144THR00.0200.01132.0290.0030.0030.0000.0000.0000.000
140A145ALA00.0300.02429.607-0.003-0.0030.0000.0000.0000.000
141A146LEU00.004-0.00229.0810.0070.0070.0000.0000.0000.000
142A147LEU0-0.001-0.01031.3450.0020.0020.0000.0000.0000.000
143A148GLU-1-0.883-0.92833.7390.0920.0920.0000.0000.0000.000
144A149ILE00.0090.00529.506-0.001-0.0010.0000.0000.0000.000
145A150GLU-1-0.875-0.94332.8330.1220.1220.0000.0000.0000.000
146A151LYS10.9140.92635.071-0.090-0.0900.0000.0000.0000.000
147A152LEU0-0.0040.00033.674-0.003-0.0030.0000.0000.0000.000
148A153ILE0-0.038-0.01231.648-0.001-0.0010.0000.0000.0000.000
149A154ARG10.8620.94135.730-0.109-0.1090.0000.0000.0000.000
150A155GLN0-0.079-0.03539.236-0.006-0.0060.0000.0000.0000.000
151A156GLU-1-0.869-0.94537.5030.0860.0860.0000.0000.0000.000
152A157GLY0-0.0420.01137.4950.0000.0000.0000.0000.0000.000
153A158ILE0-0.079-0.02731.3440.0070.0070.0000.0000.0000.000
154A159LYS10.9460.96330.152-0.197-0.1970.0000.0000.0000.000
155A160PRO0-0.0220.02326.6810.0050.0050.0000.0000.0000.000
156A161ALA00.0250.00623.4170.0020.0020.0000.0000.0000.000
157A162LEU0-0.057-0.03720.2900.0200.0200.0000.0000.0000.000
158A163ILE0-0.0060.01024.167-0.007-0.0070.0000.0000.0000.000
159A164VAL0-0.003-0.00319.9200.0150.0150.0000.0000.0000.000
160A165GLY00.0420.00723.299-0.023-0.0230.0000.0000.0000.000
161A166VAL0-0.025-0.01521.822-0.002-0.0020.0000.0000.0000.000
162A167PRO0-0.0110.01025.061-0.007-0.0070.0000.0000.0000.000
163A168VAL0-0.003-0.00426.5380.0030.0030.0000.0000.0000.000
164A169GLY0-0.019-0.02028.574-0.013-0.0130.0000.0000.0000.000
165A170PHE0-0.030-0.04632.1440.0070.0070.0000.0000.0000.000
166A171VAL0-0.0070.01135.653-0.002-0.0020.0000.0000.0000.000
167A172SER00.0720.03335.961-0.002-0.0020.0000.0000.0000.000
168A173ALA0-0.0310.00831.3560.0060.0060.0000.0000.0000.000
169A174LYS10.8830.93132.920-0.111-0.1110.0000.0000.0000.000
170A175GLU-1-0.822-0.92134.5150.1180.1180.0000.0000.0000.000
171A176SER0-0.036-0.04132.4580.0070.0070.0000.0000.0000.000
172A177LYS10.8900.96428.268-0.186-0.1860.0000.0000.0000.000
173A178GLU-1-0.845-0.90832.4230.1370.1370.0000.0000.0000.000
174A179SER0-0.070-0.04335.061-0.001-0.0010.0000.0000.0000.000
175A180ILE00.0400.01830.252-0.002-0.0020.0000.0000.0000.000
176A181LEU00.0170.00131.6820.0020.0020.0000.0000.0000.000
177A182LYS10.9380.97434.700-0.119-0.1190.0000.0000.0000.000
178A183LEU00.0210.01934.349-0.005-0.0050.0000.0000.0000.000
179A184GLU-1-0.842-0.91232.6820.2140.2140.0000.0000.0000.000
180A185TYR0-0.067-0.02736.033-0.005-0.0050.0000.0000.0000.000
181A186TYR0-0.068-0.04538.962-0.008-0.0080.0000.0000.0000.000
182A187ASN0-0.064-0.02538.2910.0000.0000.0000.0000.0000.000
183A188VAL0-0.0070.00638.741-0.005-0.0050.0000.0000.0000.000
184A189THR0-0.007-0.01934.1920.0020.0020.0000.0000.0000.000
185A190SER0-0.0100.00532.5040.0000.0000.0000.0000.0000.000
186A191ILE0-0.027-0.00728.3610.0130.0130.0000.0000.0000.000
187A192PRO0-0.0020.02125.2850.0020.0020.0000.0000.0000.000
188A193TYR0-0.011-0.03725.6770.0050.0050.0000.0000.0000.000
189A194ILE00.0220.00720.2480.0200.0200.0000.0000.0000.000
190A195LEU0-0.032-0.00824.283-0.014-0.0140.0000.0000.0000.000
191A196THR00.0310.03023.6680.0170.0170.0000.0000.0000.000
192A197MET0-0.035-0.01326.755-0.018-0.0180.0000.0000.0000.000
193A198GLY00.0510.03030.472-0.002-0.0020.0000.0000.0000.000
194A199ARG10.9540.95231.769-0.103-0.1030.0000.0000.0000.000
195A200LYS10.8520.92026.998-0.174-0.1740.0000.0000.0000.000
196A201GLY00.0530.02424.6800.0140.0140.0000.0000.0000.000
197A202GLY00.0340.00722.960-0.018-0.0180.0000.0000.0000.000
198A203SER00.003-0.00919.8140.0360.0360.0000.0000.0000.000
199A204THR00.0720.02616.4990.0310.0310.0000.0000.0000.000
200A205ILE00.0110.03316.8900.0640.0640.0000.0000.0000.000
201A206ALA00.016-0.00218.1030.0660.0660.0000.0000.0000.000
202A207VAL0-0.0090.00212.8870.0650.0650.0000.0000.0000.000
203A208ALA00.0020.00813.4490.1610.1610.0000.0000.0000.000
204A209ILE00.001-0.00214.1540.1570.1570.0000.0000.0000.000
205A210LEU00.0100.00614.2330.0970.0970.0000.0000.0000.000
206A211HIS00.006-0.0029.7940.3920.3920.0000.0000.0000.000
207A212ALA0-0.0150.01010.3020.4210.4210.0000.0000.0000.000
208A213LEU00.0160.01512.4890.1100.1100.0000.0000.0000.000
209A214LEU00.002-0.0059.1800.0620.0620.0000.0000.0000.000
210A215LEU0-0.018-0.0027.2910.3300.3300.0000.0000.0000.000
211A216LEU00.0300.0129.179-0.049-0.0490.0000.0000.0000.000
212A217SER00.0050.03211.631-0.134-0.1340.0000.0000.0000.000
213A218SER0-0.026-0.0277.231-0.339-0.3390.0000.0000.0000.000
214A219LYS10.9090.9549.950-1.229-1.2290.0000.0000.0000.000
215A220ARG10.6890.85211.448-0.847-0.8470.0000.0000.0000.000
216A221GLY0-0.029-0.00412.193-0.159-0.1590.0000.0000.0000.000