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: ZVG1N

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 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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2775434.047389
FMO2-HF: Nuclear repulsion 2684815.329075
FMO2-HF: Total energy -90618.718313
FMO2-MP2: Total energy -90874.260585


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.
-2.8760.0870.177-1.244-1.897-0.003
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 : 0.033 / q_NPA : 0.002
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].
3A3GLN00.021-0.0082.923-2.180-0.1690.051-0.838-1.2250.001
4A4PRO00.0320.0146.2970.4190.4190.0000.0000.0000.000
5A5ILE0-0.054-0.0269.373-0.009-0.0090.0000.0000.0000.000
6A6TYR0-0.032-0.00312.4050.0550.0550.0000.0000.0000.000
7A7LYS10.9460.96613.7410.1020.1020.0000.0000.0000.000
8A8ARG10.7680.87016.2790.0790.0790.0000.0000.0000.000
9A9ILE0-0.0130.00514.5380.0230.0230.0000.0000.0000.000
10A10LEU00.0000.01118.357-0.007-0.0070.0000.0000.0000.000
11A11LEU0-0.0030.00916.8240.0170.0170.0000.0000.0000.000
12A12LYS10.8350.90420.083-0.043-0.0430.0000.0000.0000.000
13A13LEU00.0530.02119.9770.0140.0140.0000.0000.0000.000
14A14SER0-0.079-0.07423.770-0.005-0.0050.0000.0000.0000.000
15A15GLY00.0750.03226.265-0.001-0.0010.0000.0000.0000.000
16A16GLU-1-0.761-0.87228.2280.0350.0350.0000.0000.0000.000
17A17ALA0-0.109-0.04422.8340.0060.0060.0000.0000.0000.000
18A18LEU00.0640.03123.6010.0020.0020.0000.0000.0000.000
19A19GLN0-0.0380.00225.821-0.006-0.0060.0000.0000.0000.000
20A20GLY00.0800.05527.1200.0050.0050.0000.0000.0000.000
21A21GLU-1-0.979-0.98528.9020.0450.0450.0000.0000.0000.000
22A22ASP-1-0.895-0.94630.0990.0280.0280.0000.0000.0000.000
23A23GLY0-0.072-0.04031.678-0.002-0.0020.0000.0000.0000.000
24A24LEU0-0.087-0.06232.491-0.002-0.0020.0000.0000.0000.000
25A25GLY00.0230.02432.171-0.001-0.0010.0000.0000.0000.000
26A26ILE0-0.024-0.03027.5560.0030.0030.0000.0000.0000.000
27A27ASP-1-0.781-0.89426.4510.0240.0240.0000.0000.0000.000
28A28PRO00.002-0.01625.744-0.001-0.0010.0000.0000.0000.000
29A29ALA00.0370.02223.502-0.007-0.0070.0000.0000.0000.000
30A30ILE0-0.047-0.01221.6340.0030.0030.0000.0000.0000.000
31A31LEU0-0.044-0.02820.7930.0010.0010.0000.0000.0000.000
32A32ASP-1-0.729-0.83720.956-0.045-0.0450.0000.0000.0000.000
33A33ARG10.7640.88315.777-0.109-0.1090.0000.0000.0000.000
34A34MET0-0.038-0.03316.200-0.008-0.0080.0000.0000.0000.000
35A35ALA00.0190.02116.684-0.016-0.0160.0000.0000.0000.000
36A36VAL00.0100.00313.044-0.028-0.0280.0000.0000.0000.000
37A37GLU-1-0.798-0.90111.9400.0750.0750.0000.0000.0000.000
38A38ILE0-0.033-0.02012.144-0.030-0.0300.0000.0000.0000.000
39A39LYS10.8330.90513.6830.1820.1820.0000.0000.0000.000
40A40GLU-1-0.857-0.9407.960-0.179-0.1790.0000.0000.0000.000
41A41LEU0-0.041-0.0239.428-0.112-0.1120.0000.0000.0000.000
42A42VAL00.0130.01111.035-0.041-0.0410.0000.0000.0000.000
43A43GLU-1-0.984-0.9809.807-0.511-0.5110.0000.0000.0000.000
44A44MET0-0.072-0.0284.976-0.182-0.1820.0000.0000.0000.000
45A45GLY0-0.107-0.0669.8380.0080.0080.0000.0000.0000.000
46A46VAL0-0.0030.01311.1010.0480.0480.0000.0000.0000.000
47A47GLU-1-0.808-0.88713.890-0.134-0.1340.0000.0000.0000.000
48A48VAL00.015-0.00215.1800.0230.0230.0000.0000.0000.000
49A49SER00.0260.01518.1480.0050.0050.0000.0000.0000.000
50A50VAL00.000-0.00820.0410.0090.0090.0000.0000.0000.000
51A51VAL0-0.0120.01322.578-0.001-0.0010.0000.0000.0000.000
52A52LEU00.0450.03024.4330.0080.0080.0000.0000.0000.000
53A53GLY0-0.020-0.01727.064-0.001-0.0010.0000.0000.0000.000
54A54GLY00.0530.01329.838-0.002-0.0020.0000.0000.0000.000
55A55GLY0-0.066-0.04132.049-0.001-0.0010.0000.0000.0000.000
56A56ASN00.0220.02330.2770.0020.0020.0000.0000.0000.000
57A57LEU0-0.025-0.00232.396-0.001-0.0010.0000.0000.0000.000
58A58PHE0-0.015-0.01235.235-0.001-0.0010.0000.0000.0000.000
59A59ARG10.8620.92132.882-0.028-0.0280.0000.0000.0000.000
60A60GLY00.0440.01838.762-0.001-0.0010.0000.0000.0000.000
61A61ALA0-0.0050.00441.485-0.001-0.0010.0000.0000.0000.000
62A62LYS10.9890.98543.316-0.019-0.0190.0000.0000.0000.000
63A63LEU00.0710.02544.7050.0000.0000.0000.0000.0000.000
64A64ALA00.0180.01345.231-0.001-0.0010.0000.0000.0000.000
65A65LYS10.9240.96447.169-0.019-0.0190.0000.0000.0000.000
66A66ALA0-0.044-0.02249.2380.0000.0000.0000.0000.0000.000
67A67GLY00.0270.02250.576-0.001-0.0010.0000.0000.0000.000
68A68MET0-0.059-0.01546.510-0.001-0.0010.0000.0000.0000.000
69A69ASN00.0240.00848.7520.0010.0010.0000.0000.0000.000
70A70ARG10.9160.92840.129-0.014-0.0140.0000.0000.0000.000
71A71VAL00.0460.03044.2430.0000.0000.0000.0000.0000.000
72A72VAL00.0190.01244.282-0.001-0.0010.0000.0000.0000.000
73A73GLY00.0270.00343.504-0.001-0.0010.0000.0000.0000.000
74A74ASP-1-0.784-0.88340.1760.0110.0110.0000.0000.0000.000
75A75HIS00.0290.00539.650-0.001-0.0010.0000.0000.0000.000
76A76MET0-0.036-0.01440.414-0.001-0.0010.0000.0000.0000.000
77A77GLY00.0090.00637.2660.0000.0000.0000.0000.0000.000
78A78MET0-0.0270.00935.705-0.001-0.0010.0000.0000.0000.000
79A79LEU00.0450.03635.498-0.002-0.0020.0000.0000.0000.000
80A80ALA00.0310.01934.960-0.002-0.0020.0000.0000.0000.000
81A81THR0-0.062-0.04531.141-0.001-0.0010.0000.0000.0000.000
82A82VAL00.0210.00731.007-0.003-0.0030.0000.0000.0000.000
83A83MET0-0.035-0.01032.229-0.003-0.0030.0000.0000.0000.000
84A84ASN00.020-0.01528.358-0.002-0.0020.0000.0000.0000.000
85A85GLY00.0270.01927.663-0.003-0.0030.0000.0000.0000.000
86A86LEU0-0.038-0.01827.862-0.006-0.0060.0000.0000.0000.000
87A87ALA00.0090.01628.339-0.004-0.0040.0000.0000.0000.000
88A88MET00.0370.01721.744-0.006-0.0060.0000.0000.0000.000
89A89ARG10.8920.93323.9320.0380.0380.0000.0000.0000.000
90A90ASP-1-0.878-0.93125.297-0.051-0.0510.0000.0000.0000.000
91A91SER00.001-0.02622.589-0.007-0.0070.0000.0000.0000.000
92A92LEU0-0.028-0.01718.966-0.008-0.0080.0000.0000.0000.000
93A93PHE0-0.030-0.00421.425-0.014-0.0140.0000.0000.0000.000
94A94ARG10.7560.84223.7550.0370.0370.0000.0000.0000.000
95A95ALA0-0.0200.01918.255-0.002-0.0020.0000.0000.0000.000
96A96ASP-1-0.871-0.92818.730-0.196-0.1960.0000.0000.0000.000
97A97VAL0-0.024-0.00817.209-0.023-0.0230.0000.0000.0000.000
98A98ASN0-0.041-0.02919.9230.0250.0250.0000.0000.0000.000
99A99ALA00.0470.02321.752-0.005-0.0050.0000.0000.0000.000
100A100LYN00.0030.00623.8060.0040.0040.0000.0000.0000.000
101A101LEU0-0.040-0.00926.4050.0020.0020.0000.0000.0000.000
102A102MET00.0070.02028.9420.0000.0000.0000.0000.0000.000
103A103SER0-0.016-0.01631.0910.0040.0040.0000.0000.0000.000
104A104ALA00.011-0.00133.897-0.002-0.0020.0000.0000.0000.000
105A105PHE0-0.042-0.01536.1200.0010.0010.0000.0000.0000.000
106A106GLN00.0660.04837.905-0.001-0.0010.0000.0000.0000.000
107A107LEU00.003-0.00136.5330.0020.0020.0000.0000.0000.000
108A108ASN00.004-0.02038.485-0.004-0.0040.0000.0000.0000.000
109A109GLY00.0130.00739.4320.0020.0020.0000.0000.0000.000
110A110ILE0-0.0340.00535.284-0.001-0.0010.0000.0000.0000.000
111A111CYS0-0.040-0.04132.467-0.001-0.0010.0000.0000.0000.000
112A112ASP-1-0.882-0.90931.801-0.051-0.0510.0000.0000.0000.000
113A113THR0-0.023-0.02534.1230.0040.0040.0000.0000.0000.000
114A114TYR0-0.041-0.07329.654-0.005-0.0050.0000.0000.0000.000
115A115ASN00.0290.00532.7130.0010.0010.0000.0000.0000.000
116A116TRP00.0870.04431.144-0.004-0.0040.0000.0000.0000.000
117A117SER00.0150.01430.189-0.005-0.0050.0000.0000.0000.000
118A118GLU-1-0.816-0.91330.614-0.064-0.0640.0000.0000.0000.000
119A119ALA0-0.0020.00127.631-0.006-0.0060.0000.0000.0000.000
120A120ILE00.0070.01326.096-0.009-0.0090.0000.0000.0000.000
121A121LYS10.7830.87925.7630.0510.0510.0000.0000.0000.000
122A122MET00.0260.01125.734-0.009-0.0090.0000.0000.0000.000
123A123LEU0-0.0040.00321.001-0.010-0.0100.0000.0000.0000.000
124A124ARG10.9460.98421.1890.0900.0900.0000.0000.0000.000
125A125GLU-1-0.960-0.97322.213-0.117-0.1170.0000.0000.0000.000
126A126LYS10.9100.95514.8200.3060.3060.0000.0000.0000.000
127A127ARG10.8210.93119.6410.0940.0940.0000.0000.0000.000
128A128VAL00.0230.01118.3800.0040.0040.0000.0000.0000.000
129A129VAL0-0.025-0.01221.0390.0090.0090.0000.0000.0000.000
130A130ILE0-0.020-0.00123.7700.0060.0060.0000.0000.0000.000
131A131PHE00.019-0.00525.5170.0010.0010.0000.0000.0000.000
132A132SER0-0.027-0.02728.3890.0060.0060.0000.0000.0000.000
133A133ALA0-0.003-0.01131.151-0.001-0.0010.0000.0000.0000.000
134A134GLY00.0170.00332.7870.0010.0010.0000.0000.0000.000
135A135THR00.0460.00633.768-0.003-0.0030.0000.0000.0000.000
136A136GLY00.0250.02036.110-0.001-0.0010.0000.0000.0000.000
137A137ASN0-0.075-0.03638.8510.0010.0010.0000.0000.0000.000
138A138PRO0-0.005-0.00139.3920.0010.0010.0000.0000.0000.000
139A139PHE0-0.068-0.05941.0840.0000.0000.0000.0000.0000.000
140A140PHE00.0190.02936.4860.0010.0010.0000.0000.0000.000
141A141THR0-0.029-0.03533.393-0.002-0.0020.0000.0000.0000.000
142A142THR00.033-0.00628.742-0.001-0.0010.0000.0000.0000.000
143A143ASP-1-0.766-0.86227.8080.0370.0370.0000.0000.0000.000
144A144SER00.0840.03229.633-0.001-0.0010.0000.0000.0000.000
145A145THR0-0.040-0.00629.847-0.004-0.0040.0000.0000.0000.000
146A146ALA0-0.011-0.00725.702-0.004-0.0040.0000.0000.0000.000
147A147CYS0-0.0080.00326.858-0.002-0.0020.0000.0000.0000.000
148A148LEU00.0480.02828.517-0.003-0.0030.0000.0000.0000.000
149A149ARG10.7980.88727.6680.0170.0170.0000.0000.0000.000
150A150GLY00.0460.02025.138-0.006-0.0060.0000.0000.0000.000
151A151ILE0-0.0020.00125.982-0.006-0.0060.0000.0000.0000.000
152A152GLU-1-0.814-0.85928.587-0.028-0.0280.0000.0000.0000.000
153A153ILE0-0.066-0.03823.787-0.004-0.0040.0000.0000.0000.000
154A154GLU-1-0.909-0.94925.221-0.075-0.0750.0000.0000.0000.000
155A155ALA0-0.033-0.01321.562-0.009-0.0090.0000.0000.0000.000
156A156ASP-1-0.794-0.89718.357-0.085-0.0850.0000.0000.0000.000
157A157VAL0-0.056-0.03517.0720.0160.0160.0000.0000.0000.000
158A158VAL0-0.0010.00120.526-0.010-0.0100.0000.0000.0000.000
159A159LEU00.007-0.00215.3330.0190.0190.0000.0000.0000.000
160A160LYS10.8110.88319.526-0.067-0.0670.0000.0000.0000.000
161A161ALA00.0480.02819.7440.0170.0170.0000.0000.0000.000
162A162THR0-0.117-0.06720.969-0.014-0.0140.0000.0000.0000.000
163A163LYS10.9030.93721.824-0.066-0.0660.0000.0000.0000.000
164A164VAL0-0.0130.00123.4630.0030.0030.0000.0000.0000.000
165A165ASP-1-0.792-0.89519.0190.2550.2550.0000.0000.0000.000
166A166GLY00.0440.01919.9320.0190.0190.0000.0000.0000.000
167A167VAL0-0.060-0.02922.431-0.014-0.0140.0000.0000.0000.000
168A168TYR0-0.007-0.00424.1460.0090.0090.0000.0000.0000.000
169A169ASP-1-0.776-0.87728.3190.0930.0930.0000.0000.0000.000
170A170CYS0-0.073-0.03030.658-0.004-0.0040.0000.0000.0000.000
171A178ALA0-0.021-0.01929.623-0.002-0.0020.0000.0000.0000.000
172A179LYS10.9710.98028.211-0.112-0.1120.0000.0000.0000.000
173A180LEU0-0.0220.01420.866-0.008-0.0080.0000.0000.0000.000
174A181TYR0-0.015-0.03225.4350.0030.0030.0000.0000.0000.000
175A182LYS10.8580.94317.232-0.269-0.2690.0000.0000.0000.000
176A183ASN0-0.023-0.02320.7360.0180.0180.0000.0000.0000.000
177A184LEU0-0.0210.00523.858-0.003-0.0030.0000.0000.0000.000
178A185SER00.0460.02126.497-0.005-0.0050.0000.0000.0000.000
179A186TYR00.027-0.03827.0680.0030.0030.0000.0000.0000.000
180A187ALA00.007-0.00131.038-0.001-0.0010.0000.0000.0000.000
181A188GLU-1-0.770-0.87829.9280.0820.0820.0000.0000.0000.000
182A189VAL0-0.049-0.02029.0450.0010.0010.0000.0000.0000.000
183A190ILE0-0.039-0.02232.108-0.001-0.0010.0000.0000.0000.000
184A191ASP-1-0.890-0.94035.6560.0410.0410.0000.0000.0000.000
185A192LYS10.7900.90030.820-0.082-0.0820.0000.0000.0000.000
186A193GLU-1-0.958-0.96735.9140.0460.0460.0000.0000.0000.000
187A194LEU0-0.0280.00129.8290.0030.0030.0000.0000.0000.000
188A195LYS10.9130.96029.703-0.085-0.0850.0000.0000.0000.000
189A196VAL0-0.001-0.00626.8670.0070.0070.0000.0000.0000.000
190A197MET0-0.048-0.03626.996-0.002-0.0020.0000.0000.0000.000
191A198ASP-1-0.802-0.86631.1790.0240.0240.0000.0000.0000.000
192A199LEU00.0960.03033.9620.0000.0000.0000.0000.0000.000
193A200SER00.0320.02935.8760.0000.0000.0000.0000.0000.000
194A201ALA0-0.036-0.00531.213-0.002-0.0020.0000.0000.0000.000
195A202PHE00.002-0.01728.403-0.001-0.0010.0000.0000.0000.000
196A203THR0-0.027-0.02431.9910.0010.0010.0000.0000.0000.000
197A204LEU00.0080.02032.105-0.002-0.0020.0000.0000.0000.000
198A205ALA00.009-0.01028.028-0.003-0.0030.0000.0000.0000.000
199A206ARG10.9370.97629.696-0.028-0.0280.0000.0000.0000.000
200A207ASP-1-0.920-0.95931.6890.0130.0130.0000.0000.0000.000
201A208HIS0-0.099-0.05630.674-0.006-0.0060.0000.0000.0000.000
202A209GLY00.0210.02829.001-0.004-0.0040.0000.0000.0000.000
203A210MET0-0.0420.00224.346-0.001-0.0010.0000.0000.0000.000
204A211PRO0-0.0070.01821.5270.0100.0100.0000.0000.0000.000
205A212ILE0-0.015-0.02222.409-0.005-0.0050.0000.0000.0000.000
206A213ARG10.8720.94513.647-0.205-0.2050.0000.0000.0000.000
207A214VAL0-0.057-0.02419.956-0.013-0.0130.0000.0000.0000.000
208A215PHE00.0750.02915.7860.0190.0190.0000.0000.0000.000
209A216ASN00.013-0.00418.040-0.043-0.0430.0000.0000.0000.000
210A217MET00.0410.01616.0690.0310.0310.0000.0000.0000.000
211A218GLY0-0.016-0.00118.013-0.010-0.0100.0000.0000.0000.000
212A219LYS10.7560.87815.186-0.375-0.3750.0000.0000.0000.000
213A220PRO00.0420.01814.3430.0100.0100.0000.0000.0000.000
214A221GLY00.0040.01610.1280.0560.0560.0000.0000.0000.000
215A222ALA00.0120.00410.2030.0890.0890.0000.0000.0000.000
216A223LEU00.0370.01312.1830.0220.0220.0000.0000.0000.000
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