Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 6YR8Z

Calculation Name: 2A1F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2A1F

Chain ID: A

ChEMBL ID:

UniProt ID: P43890

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 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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2774293.282997
FMO2-HF: Nuclear repulsion 2683675.551449
FMO2-HF: Total energy -90617.731547
FMO2-MP2: Total energy -90873.282378


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:1:LEU)


Summations of interaction energy for fragment #1(A:1:LEU)
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.
-2.7080.2320.114-1.271-1.783-0.002
Interaction energy analysis for fragmet #1(A:1:LEU)
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 : 0.007
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].
3A3GLN00.000-0.0313.301-1.8640.1550.021-0.873-1.1670.002
4A4PRO00.0320.0146.2970.4060.4060.0000.0000.0000.000
5A5ILE0-0.056-0.0229.466-0.035-0.0350.0000.0000.0000.000
6A6TYR0-0.0060.00412.5140.0350.0350.0000.0000.0000.000
7A7LYS10.9440.96613.8220.0660.0660.0000.0000.0000.000
8A8ARG10.8330.92116.3530.0390.0390.0000.0000.0000.000
9A9ILE0-0.0110.00614.7810.0220.0220.0000.0000.0000.000
10A10LEU0-0.0110.00618.437-0.012-0.0120.0000.0000.0000.000
11A11LEU00.0010.01017.1010.0180.0180.0000.0000.0000.000
12A12LYS10.8030.88120.156-0.080-0.0800.0000.0000.0000.000
13A13LEU00.0550.01519.9440.0150.0150.0000.0000.0000.000
14A14SER0-0.048-0.03623.832-0.007-0.0070.0000.0000.0000.000
15A15GLY00.0680.03126.3170.0000.0000.0000.0000.0000.000
16A16GLU-1-0.826-0.91728.2680.0560.0560.0000.0000.0000.000
17A17ALA0-0.117-0.05422.8560.0050.0050.0000.0000.0000.000
18A18LEU00.0510.02323.8190.0030.0030.0000.0000.0000.000
19A19GLN0-0.041-0.00125.849-0.010-0.0100.0000.0000.0000.000
20A20GLY00.0830.05827.1430.0060.0060.0000.0000.0000.000
21A21GLU-1-0.957-0.98128.9670.0530.0530.0000.0000.0000.000
22A22ASP-1-0.897-0.94430.1150.0400.0400.0000.0000.0000.000
23A23GLY0-0.098-0.05031.708-0.002-0.0020.0000.0000.0000.000
24A24LEU0-0.073-0.05632.529-0.002-0.0020.0000.0000.0000.000
25A25GLY00.0200.02132.188-0.001-0.0010.0000.0000.0000.000
26A26ILE0-0.028-0.02627.6090.0040.0040.0000.0000.0000.000
27A27ASP-1-0.793-0.90726.2950.0380.0380.0000.0000.0000.000
28A28PRO00.001-0.01325.7430.0010.0010.0000.0000.0000.000
29A29ALA00.0560.03723.467-0.004-0.0040.0000.0000.0000.000
30A30ILE0-0.059-0.01421.6290.0060.0060.0000.0000.0000.000
31A31LEU0-0.036-0.03220.7990.0050.0050.0000.0000.0000.000
32A32ASP-1-0.778-0.90420.981-0.014-0.0140.0000.0000.0000.000
33A33ARG10.8320.93816.063-0.142-0.1420.0000.0000.0000.000
34A34MET0-0.031-0.03116.195-0.003-0.0030.0000.0000.0000.000
35A35ALA00.0250.02516.694-0.009-0.0090.0000.0000.0000.000
36A36VAL0-0.003-0.00212.929-0.025-0.0250.0000.0000.0000.000
37A37GLU-1-0.848-0.94611.9420.1530.1530.0000.0000.0000.000
38A38ILE0-0.018-0.01312.161-0.016-0.0160.0000.0000.0000.000
39A39LYS10.8850.92913.5540.1490.1490.0000.0000.0000.000
40A40GLU-1-0.863-0.9418.1210.0020.0020.0000.0000.0000.000
41A41LEU0-0.044-0.0269.442-0.092-0.0920.0000.0000.0000.000
42A42VAL00.0130.01411.060-0.040-0.0400.0000.0000.0000.000
43A43GLU-1-0.990-0.9829.607-0.474-0.4740.0000.0000.0000.000
44A44MET0-0.091-0.0404.977-0.096-0.0960.0000.0000.0000.000
45A45GLY0-0.103-0.0669.8410.0100.0100.0000.0000.0000.000
46A46VAL0-0.0100.01011.1310.0410.0410.0000.0000.0000.000
47A47GLU-1-0.824-0.90613.936-0.099-0.0990.0000.0000.0000.000
48A48VAL00.0160.00215.2210.0240.0240.0000.0000.0000.000
49A49SER00.0220.01218.195-0.002-0.0020.0000.0000.0000.000
50A50VAL00.000-0.00620.1210.0120.0120.0000.0000.0000.000
51A51VAL00.0010.01822.630-0.005-0.0050.0000.0000.0000.000
52A52LEU00.0350.02424.3210.0090.0090.0000.0000.0000.000
53A53GLY0-0.012-0.00927.115-0.003-0.0030.0000.0000.0000.000
54A54GLY00.0470.01129.895-0.002-0.0020.0000.0000.0000.000
55A55GLY0-0.065-0.04432.101-0.002-0.0020.0000.0000.0000.000
56A56ASN00.0080.02130.3020.0010.0010.0000.0000.0000.000
57A57LEU0-0.0160.00132.435-0.002-0.0020.0000.0000.0000.000
58A58PHE00.0020.00035.269-0.002-0.0020.0000.0000.0000.000
59A59ARG10.8820.92333.022-0.044-0.0440.0000.0000.0000.000
60A60GLY00.0390.01338.815-0.002-0.0020.0000.0000.0000.000
61A61ALA0-0.0030.00641.536-0.001-0.0010.0000.0000.0000.000
62A62LYS10.9880.98443.378-0.028-0.0280.0000.0000.0000.000
63A63LEU00.0640.02344.677-0.001-0.0010.0000.0000.0000.000
64A64ALA00.0190.01545.295-0.001-0.0010.0000.0000.0000.000
65A65LYS10.9250.96547.233-0.027-0.0270.0000.0000.0000.000
66A66ALA0-0.043-0.02149.303-0.001-0.0010.0000.0000.0000.000
67A67GLY00.0240.02050.652-0.001-0.0010.0000.0000.0000.000
68A68MET0-0.060-0.01646.497-0.001-0.0010.0000.0000.0000.000
69A69ASN00.0310.01148.8160.0020.0020.0000.0000.0000.000
70A70ARG10.9880.98040.347-0.027-0.0270.0000.0000.0000.000
71A71VAL00.0370.03344.3100.0010.0010.0000.0000.0000.000
72A72VAL00.0170.01244.3440.0000.0000.0000.0000.0000.000
73A73GLY00.025-0.00343.5590.0000.0000.0000.0000.0000.000
74A74ASP-1-0.832-0.91840.2380.0250.0250.0000.0000.0000.000
75A75HIS00.0130.00239.7090.0000.0000.0000.0000.0000.000
76A76MET0-0.039-0.01940.462-0.001-0.0010.0000.0000.0000.000
77A77GLY00.0050.00537.3160.0000.0000.0000.0000.0000.000
78A78MET0-0.0130.01235.7540.0000.0000.0000.0000.0000.000
79A79LEU00.0460.03835.543-0.001-0.0010.0000.0000.0000.000
80A80ALA00.0290.02034.922-0.002-0.0020.0000.0000.0000.000
81A81THR0-0.066-0.04831.1770.0000.0000.0000.0000.0000.000
82A82VAL00.0190.00531.042-0.001-0.0010.0000.0000.0000.000
83A83MET0-0.033-0.00932.252-0.002-0.0020.0000.0000.0000.000
84A84ASN00.024-0.01328.375-0.002-0.0020.0000.0000.0000.000
85A85GLY00.0230.01327.688-0.001-0.0010.0000.0000.0000.000
86A86LEU0-0.042-0.01927.877-0.005-0.0050.0000.0000.0000.000
87A87ALA00.0130.02228.318-0.004-0.0040.0000.0000.0000.000
88A88MET00.0250.00921.663-0.006-0.0060.0000.0000.0000.000
89A89ARG10.9200.95123.9320.0210.0210.0000.0000.0000.000
90A90ASP-1-0.903-0.95625.286-0.034-0.0340.0000.0000.0000.000
91A91SER0-0.0010.00122.540-0.007-0.0070.0000.0000.0000.000
92A92LEU0-0.025-0.02118.971-0.007-0.0070.0000.0000.0000.000
93A93PHE0-0.0180.00121.396-0.014-0.0140.0000.0000.0000.000
94A94ARG10.8320.91423.7130.0170.0170.0000.0000.0000.000
95A95ALA0-0.0180.02418.166-0.003-0.0030.0000.0000.0000.000
96A96ASP-1-0.913-0.94618.682-0.140-0.1400.0000.0000.0000.000
97A97VAL0-0.049-0.02917.229-0.021-0.0210.0000.0000.0000.000
98A98ASN0-0.034-0.02319.8950.0220.0220.0000.0000.0000.000
99A99ALA00.0420.01821.748-0.001-0.0010.0000.0000.0000.000
100A100LYN00.0230.02523.8060.0000.0000.0000.0000.0000.000
101A101LEU0-0.041-0.01226.4240.0030.0030.0000.0000.0000.000
102A102MET00.0100.02028.9630.0000.0000.0000.0000.0000.000
103A103SER0-0.0010.00031.1280.0050.0050.0000.0000.0000.000
104A104ALA00.012-0.00333.936-0.002-0.0020.0000.0000.0000.000
105A105PHE0-0.026-0.01236.1690.0000.0000.0000.0000.0000.000
106A106GLN00.0220.01037.939-0.001-0.0010.0000.0000.0000.000
107A107LEU0-0.002-0.00336.3170.0020.0020.0000.0000.0000.000
108A108ASN00.0520.01338.500-0.003-0.0030.0000.0000.0000.000
109A109GLY0-0.010-0.00139.4370.0010.0010.0000.0000.0000.000
110A110ILE0-0.0320.00335.237-0.001-0.0010.0000.0000.0000.000
111A111CYS0-0.060-0.04932.518-0.001-0.0010.0000.0000.0000.000
112A112ASP-1-0.878-0.90732.037-0.032-0.0320.0000.0000.0000.000
113A113THR0-0.033-0.03034.1430.0040.0040.0000.0000.0000.000
114A114TYR0-0.049-0.07429.800-0.004-0.0040.0000.0000.0000.000
115A115ASN00.018-0.00432.7600.0000.0000.0000.0000.0000.000
116A116TRP00.0900.04831.200-0.004-0.0040.0000.0000.0000.000
117A117SER00.0110.01430.242-0.004-0.0040.0000.0000.0000.000
118A118GLU-1-0.901-0.96930.656-0.046-0.0460.0000.0000.0000.000
119A119ALA0-0.001-0.00327.612-0.005-0.0050.0000.0000.0000.000
120A120ILE0-0.0020.00826.149-0.007-0.0070.0000.0000.0000.000
121A121LYS10.8840.94125.8020.0350.0350.0000.0000.0000.000
122A122MET00.0350.02225.768-0.008-0.0080.0000.0000.0000.000
123A123LEU0-0.007-0.00121.024-0.008-0.0080.0000.0000.0000.000
124A124ARG10.9380.97721.2180.0650.0650.0000.0000.0000.000
125A125GLU-1-1.017-1.00222.187-0.091-0.0910.0000.0000.0000.000
126A126LYS10.9180.95314.9220.2420.2420.0000.0000.0000.000
127A127ARG10.8640.94919.6420.0770.0770.0000.0000.0000.000
128A128VAL00.0220.01018.3970.0050.0050.0000.0000.0000.000
129A129VAL0-0.015-0.00721.0580.0040.0040.0000.0000.0000.000
130A130ILE0-0.021-0.00623.7980.0080.0080.0000.0000.0000.000
131A131PHE00.017-0.00325.431-0.002-0.0020.0000.0000.0000.000
132A132SER0-0.028-0.02728.4360.0060.0060.0000.0000.0000.000
133A133ALA0-0.005-0.01131.196-0.002-0.0020.0000.0000.0000.000
134A134GLY00.006-0.00232.8480.0000.0000.0000.0000.0000.000
135A135THR00.030-0.00333.831-0.003-0.0030.0000.0000.0000.000
136A136GLY00.0070.00936.177-0.002-0.0020.0000.0000.0000.000
137A137ASN0-0.048-0.01938.918-0.001-0.0010.0000.0000.0000.000
138A138PRO0-0.007-0.00639.4620.0020.0020.0000.0000.0000.000
139A139PHE0-0.069-0.06041.1840.0000.0000.0000.0000.0000.000
140A140PHE00.0090.02236.6270.0020.0020.0000.0000.0000.000
141A141THR0-0.029-0.04433.522-0.001-0.0010.0000.0000.0000.000
142A142THR00.027-0.01128.714-0.001-0.0010.0000.0000.0000.000
143A143ASP-1-0.730-0.84828.2890.0660.0660.0000.0000.0000.000
144A144SER00.0670.01629.724-0.001-0.0010.0000.0000.0000.000
145A145THR0-0.043-0.00629.783-0.004-0.0040.0000.0000.0000.000
146A146ALA0-0.014-0.01025.761-0.004-0.0040.0000.0000.0000.000
147A147CYS00.0040.01026.942-0.001-0.0010.0000.0000.0000.000
148A148LEU00.0390.02528.609-0.003-0.0030.0000.0000.0000.000
149A149ARG10.8380.91927.702-0.007-0.0070.0000.0000.0000.000
150A150GLY00.0400.01925.218-0.005-0.0050.0000.0000.0000.000
151A151ILE00.0100.00626.066-0.005-0.0050.0000.0000.0000.000
152A152GLU-1-0.824-0.87928.676-0.005-0.0050.0000.0000.0000.000
153A153ILE0-0.070-0.03523.890-0.005-0.0050.0000.0000.0000.000
154A154GLU-1-0.962-0.97825.291-0.037-0.0370.0000.0000.0000.000
155A155ALA0-0.039-0.01621.658-0.007-0.0070.0000.0000.0000.000
156A156ASP-1-0.789-0.90218.587-0.024-0.0240.0000.0000.0000.000
157A157VAL0-0.062-0.03817.1780.0150.0150.0000.0000.0000.000
158A158VAL00.0040.00320.629-0.011-0.0110.0000.0000.0000.000
159A159LEU00.0090.00115.4010.0190.0190.0000.0000.0000.000
160A160LYS10.8380.91319.621-0.105-0.1050.0000.0000.0000.000
161A161ALA00.0500.02619.8080.0180.0180.0000.0000.0000.000
162A162THR0-0.125-0.06821.049-0.021-0.0210.0000.0000.0000.000
163A163LYS10.9210.94821.895-0.091-0.0910.0000.0000.0000.000
164A164VAL0-0.0180.00223.5150.0000.0000.0000.0000.0000.000
165A165ASP-1-0.846-0.94020.1830.2670.2670.0000.0000.0000.000
166A166GLY00.0330.00420.0330.0240.0240.0000.0000.0000.000
167A167VAL0-0.051-0.02322.535-0.016-0.0160.0000.0000.0000.000
168A168TYR0-0.009-0.00424.2630.0080.0080.0000.0000.0000.000
169A169ASP-1-0.802-0.90828.4260.1060.1060.0000.0000.0000.000
170A170CYS0-0.070-0.02830.754-0.004-0.0040.0000.0000.0000.000
171A178ALA0-0.014-0.01329.609-0.002-0.0020.0000.0000.0000.000
172A179LYS10.9700.98028.229-0.125-0.1250.0000.0000.0000.000
173A180LEU0-0.0160.01920.954-0.009-0.0090.0000.0000.0000.000
174A181TYR0-0.009-0.01725.5160.0010.0010.0000.0000.0000.000
175A182LYS10.8970.96317.476-0.301-0.3010.0000.0000.0000.000
176A183ASN0-0.025-0.02620.8970.0190.0190.0000.0000.0000.000
177A184LEU00.0030.01323.985-0.005-0.0050.0000.0000.0000.000
178A185SER00.0620.03726.624-0.003-0.0030.0000.0000.0000.000
179A186TYR00.015-0.05526.9890.0020.0020.0000.0000.0000.000
180A187ALA0-0.002-0.00431.162-0.001-0.0010.0000.0000.0000.000
181A188GLU-1-0.850-0.93129.9570.0990.0990.0000.0000.0000.000
182A189VAL0-0.046-0.01929.1980.0000.0000.0000.0000.0000.000
183A190ILE0-0.042-0.02032.229-0.002-0.0020.0000.0000.0000.000
184A191ASP-1-0.882-0.93835.7770.0540.0540.0000.0000.0000.000
185A192LYS10.8400.93331.598-0.098-0.0980.0000.0000.0000.000
186A193GLU-1-0.953-0.96436.0320.0590.0590.0000.0000.0000.000
187A194LEU0-0.038-0.00430.1900.0030.0030.0000.0000.0000.000
188A195LYS10.9180.96429.753-0.105-0.1050.0000.0000.0000.000
189A196VAL0-0.008-0.01127.0090.0090.0090.0000.0000.0000.000
190A197MET0-0.028-0.03126.7630.0000.0000.0000.0000.0000.000
191A198ASP-1-0.814-0.87031.2810.0430.0430.0000.0000.0000.000
192A199LEU00.0810.02634.0660.0010.0010.0000.0000.0000.000
193A200SER00.0340.02135.9840.0000.0000.0000.0000.0000.000
194A201ALA0-0.0170.01131.290-0.002-0.0020.0000.0000.0000.000
195A202PHE0-0.002-0.01028.7730.0000.0000.0000.0000.0000.000
196A203THR0-0.029-0.02332.1000.0020.0020.0000.0000.0000.000
197A204LEU00.0170.02232.438-0.002-0.0020.0000.0000.0000.000
198A205ALA0-0.003-0.02028.113-0.003-0.0030.0000.0000.0000.000
199A206ARG10.9360.97529.808-0.046-0.0460.0000.0000.0000.000
200A207ASP-1-0.922-0.95831.8050.0300.0300.0000.0000.0000.000
201A208HIS0-0.091-0.05030.828-0.007-0.0070.0000.0000.0000.000
202A209GLY00.0290.03429.115-0.003-0.0030.0000.0000.0000.000
203A210MET0-0.0400.00424.3900.0030.0030.0000.0000.0000.000
204A211PRO0-0.0030.02521.6700.0090.0090.0000.0000.0000.000
205A212ILE0-0.019-0.01822.531-0.003-0.0030.0000.0000.0000.000
206A213ARG10.8370.92613.464-0.298-0.2980.0000.0000.0000.000
207A214VAL0-0.051-0.01620.069-0.014-0.0140.0000.0000.0000.000
208A215PHE00.0740.02815.7370.0200.0200.0000.0000.0000.000
209A216ASN00.0200.01318.135-0.045-0.0450.0000.0000.0000.000
210A217MET00.0340.01316.1140.0320.0320.0000.0000.0000.000
211A218GLY0-0.030-0.01618.061-0.010-0.0100.0000.0000.0000.000
212A219LYS10.8800.95515.435-0.435-0.4350.0000.0000.0000.000
213A220PRO00.0380.01514.4260.0200.0200.0000.0000.0000.000
214A221GLY00.0110.02210.1650.0470.0470.0000.0000.0000.000
215A222ALA00.0040.00110.2690.1180.1180.0000.0000.0000.000
216A223LEU00.0400.01912.2710.0350.0350.0000.0000.0000.000
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