Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: V5ZQ1

Calculation Name: 1T06-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T06

Chain ID: A

ChEMBL ID:

UniProt ID: Q81BA8

Base Structure: X-ray

Registration Date: 2023-06-26

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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3012450.226234
FMO2-HF: Nuclear repulsion 2918027.148001
FMO2-HF: Total energy -94423.078233
FMO2-MP2: Total energy -94693.399074


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-21.794-15.97520.802-10.184-16.437-0.031
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.040 / q_NPA : -0.006
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].
3A3PHE00.0910.0473.865-0.7031.766-0.020-1.361-1.0880.005
4A4LYS10.9260.9646.8032.1422.1420.0000.0000.0000.000
5A5THR0-0.039-0.0622.367-3.251-1.3962.625-1.615-2.864-0.015
6A6VAL00.0110.0133.1330.9611.7560.048-0.171-0.672-0.001
7A7MET00.0050.0044.9700.7400.828-0.001-0.003-0.0840.000
8A8GLN0-0.036-0.0096.9840.1990.1990.0000.0000.0000.000
9A9GLU-1-0.812-0.9032.4132.3514.6671.572-1.706-2.182-0.023
10A10LEU0-0.030-0.0256.9460.1810.1810.0000.0000.0000.000
11A11GLU-1-0.977-0.9829.9400.1040.1040.0000.0000.0000.000
12A12ALA00.0480.0229.6520.0530.0530.0000.0000.0000.000
13A13LEU0-0.086-0.0399.2550.0900.0900.0000.0000.0000.000
14A14GLY0-0.0070.00612.618-0.014-0.0140.0000.0000.0000.000
15A15LYS10.8950.93915.617-0.645-0.6450.0000.0000.0000.000
16A16GLU-1-0.753-0.86819.0530.1080.1080.0000.0000.0000.000
17A17ARG10.9370.96422.323-0.331-0.3310.0000.0000.0000.000
18A18THR0-0.0050.00019.569-0.026-0.0260.0000.0000.0000.000
19A19LYS10.8630.92420.143-0.059-0.0590.0000.0000.0000.000
20A20LYS10.8630.91622.106-0.137-0.1370.0000.0000.0000.000
21A21ILE0-0.034-0.01224.843-0.018-0.0180.0000.0000.0000.000
22A22TYR0-0.013-0.04018.330-0.020-0.0200.0000.0000.0000.000
23A23ILE00.0220.01523.645-0.020-0.0200.0000.0000.0000.000
24A24SER0-0.0220.00725.998-0.011-0.0110.0000.0000.0000.000
25A25ASN0-0.049-0.03325.954-0.010-0.0100.0000.0000.0000.000
26A26GLY00.0300.01827.678-0.005-0.0050.0000.0000.0000.000
27A27ALA00.0000.01522.474-0.020-0.0200.0000.0000.0000.000
28A28HIS10.8650.91523.1720.1190.1190.0000.0000.0000.000
29A29GLU-1-0.780-0.86721.295-0.027-0.0270.0000.0000.0000.000
30A30PRO00.0020.01817.821-0.009-0.0090.0000.0000.0000.000
31A31VAL00.001-0.00917.8770.0030.0030.0000.0000.0000.000
32A32PHE00.0390.01512.147-0.002-0.0020.0000.0000.0000.000
33A33GLY0-0.035-0.01916.9760.0250.0250.0000.0000.0000.000
34A34VAL0-0.014-0.00912.5280.0460.0460.0000.0000.0000.000
35A35ALA0-0.0100.00315.615-0.042-0.0420.0000.0000.0000.000
36A36THR00.0700.03015.3470.1490.1490.0000.0000.0000.000
37A37GLY00.0070.00514.4720.1110.1110.0000.0000.0000.000
38A38ALA0-0.045-0.03112.8110.1510.1510.0000.0000.0000.000
39A39MET00.0570.0429.9850.3270.3270.0000.0000.0000.000
40A40LYS10.9600.9939.190-0.733-0.7330.0000.0000.0000.000
41A41PRO0-0.051-0.0368.1860.0620.0620.0000.0000.0000.000
42A42ILE00.0400.0204.3310.9921.4560.022-0.108-0.3790.000
43A43ALA00.0490.0185.0220.7210.9100.000-0.027-0.1620.000
44A44LYS10.8950.9516.750-2.209-2.2090.0000.0000.0000.000
45A45LYS10.7650.8722.314-16.307-21.19814.186-3.673-5.6220.014
46A46ILE0-0.015-0.0042.387-5.260-2.9322.372-1.492-3.209-0.011
47A47LYS10.8850.9444.5651.4471.572-0.001-0.019-0.1050.000
48A48LEU00.0050.0076.944-0.456-0.4560.0000.0000.0000.000
49A49ASN0-0.017-0.0046.0030.1900.1900.0000.0000.0000.000
50A50GLN00.1090.0479.2800.0120.0120.0000.0000.0000.000
51A51GLU-1-0.894-0.94710.944-1.170-1.1700.0000.0000.0000.000
52A52LEU00.0150.0044.719-0.133-0.052-0.001-0.009-0.0700.000
53A53ALA0-0.009-0.0059.2700.1980.1980.0000.0000.0000.000
54A54GLU-1-0.753-0.83611.211-0.400-0.4000.0000.0000.0000.000
55A55GLU-1-0.928-0.96010.089-2.085-2.0850.0000.0000.0000.000
56A56LEU0-0.031-0.0287.1430.1430.1430.0000.0000.0000.000
57A57TYR0-0.034-0.02811.6880.1730.1730.0000.0000.0000.000
58A58ALA00.0120.00215.0030.0860.0860.0000.0000.0000.000
59A59THR0-0.065-0.04613.4750.0750.0750.0000.0000.0000.000
60A60GLY00.0050.00716.5710.0500.0500.0000.0000.0000.000
61A61ASN0-0.004-0.00315.3460.1210.1210.0000.0000.0000.000
62A62TYR00.0560.01716.084-0.014-0.0140.0000.0000.0000.000
63A63ASP-1-0.746-0.87113.9390.2680.2680.0000.0000.0000.000
64A64ALA00.0180.01011.5170.1050.1050.0000.0000.0000.000
65A65MET0-0.0350.01512.089-0.034-0.0340.0000.0000.0000.000
66A66TYR0-0.009-0.04114.151-0.008-0.0080.0000.0000.0000.000
67A67PHE0-0.017-0.0325.8030.1710.1710.0000.0000.0000.000
68A68ALA0-0.0060.00710.4190.0110.0110.0000.0000.0000.000
69A69GLY00.0350.01011.370-0.053-0.0530.0000.0000.0000.000
70A70ILE0-0.101-0.06010.8070.0330.0330.0000.0000.0000.000
71A71ILE0-0.030-0.0116.4800.0540.0540.0000.0000.0000.000
72A72ALA00.0610.03710.036-0.265-0.2650.0000.0000.0000.000
73A73ASP-1-0.821-0.90113.059-0.314-0.3140.0000.0000.0000.000
74A74PRO00.0320.00814.945-0.009-0.0090.0000.0000.0000.000
75A75LYS10.7740.86616.2460.3520.3520.0000.0000.0000.000
76A76ALA0-0.031-0.01417.4270.0050.0050.0000.0000.0000.000
77A77MET0-0.0680.00417.777-0.019-0.0190.0000.0000.0000.000
78A78SER00.003-0.02920.3100.0530.0530.0000.0000.0000.000
79A79GLU-1-0.807-0.90923.975-0.144-0.1440.0000.0000.0000.000
80A80SER0-0.0110.00425.709-0.002-0.0020.0000.0000.0000.000
81A81ASP-1-0.771-0.84220.480-0.392-0.3920.0000.0000.0000.000
82A82PHE00.0460.00920.461-0.002-0.0020.0000.0000.0000.000
83A83ASP-1-0.802-0.88823.226-0.129-0.1290.0000.0000.0000.000
84A84ARG10.7680.83618.8280.4510.4510.0000.0000.0000.000
85A85TRP0-0.043-0.03314.1160.0370.0370.0000.0000.0000.000
86A86ILE0-0.041-0.00821.3470.0210.0210.0000.0000.0000.000
87A87ASP-1-0.820-0.89124.443-0.145-0.1450.0000.0000.0000.000
88A88GLY00.0050.01222.183-0.007-0.0070.0000.0000.0000.000
89A89ALA0-0.063-0.03822.5160.0110.0110.0000.0000.0000.000
90A90TYR0-0.027-0.02521.3550.0370.0370.0000.0000.0000.000
91A91PHE00.0320.00421.8760.0190.0190.0000.0000.0000.000
92A92TYR00.0680.02424.8200.0010.0010.0000.0000.0000.000
93A93MET0-0.088-0.01321.8210.0070.0070.0000.0000.0000.000
94A94LEU00.0080.01919.0080.0260.0260.0000.0000.0000.000
95A95SER00.0650.01221.683-0.006-0.0060.0000.0000.0000.000
96A96ASP-1-0.800-0.87524.2410.0390.0390.0000.0000.0000.000
97A97TYR0-0.038-0.03421.1840.0150.0150.0000.0000.0000.000
98A98VAL0-0.0350.00516.4580.0430.0430.0000.0000.0000.000
99A99VAL00.0150.00318.960-0.012-0.0120.0000.0000.0000.000
100A100ALA00.0330.03121.007-0.007-0.0070.0000.0000.0000.000
101A101VAL0-0.054-0.01418.8430.0010.0010.0000.0000.0000.000
102A102THR00.0530.04716.3290.0350.0350.0000.0000.0000.000
103A103LEU00.0340.04119.257-0.018-0.0180.0000.0000.0000.000
104A104SER0-0.013-0.02922.4990.0050.0050.0000.0000.0000.000
105A105GLU-1-0.871-0.91218.3650.1640.1640.0000.0000.0000.000
106A106SER0-0.0080.00621.166-0.020-0.0200.0000.0000.0000.000
107A107ASN0-0.028-0.03922.7090.0170.0170.0000.0000.0000.000
108A108ILE00.0220.02825.3650.0100.0100.0000.0000.0000.000
109A109ALA00.0070.00725.8620.0020.0020.0000.0000.0000.000
110A110GLN00.0360.00927.3340.0050.0050.0000.0000.0000.000
111A111ASP-1-0.857-0.91930.753-0.072-0.0720.0000.0000.0000.000
112A112VAL00.004-0.01126.592-0.003-0.0030.0000.0000.0000.000
113A113ALA00.0010.00129.2560.0020.0020.0000.0000.0000.000
114A114ASP-1-0.758-0.83330.569-0.026-0.0260.0000.0000.0000.000
115A115LYS10.7960.88030.1890.1360.1360.0000.0000.0000.000
116A116TRP0-0.016-0.03424.5170.0040.0040.0000.0000.0000.000
117A117ILE0-0.0210.00432.3560.0030.0030.0000.0000.0000.000
118A118ALA0-0.010-0.00834.9300.0030.0030.0000.0000.0000.000
119A119SER0-0.063-0.04333.906-0.003-0.0030.0000.0000.0000.000
120A120GLY00.0140.00136.021-0.004-0.0040.0000.0000.0000.000
121A121ASP-1-0.828-0.91131.597-0.067-0.0670.0000.0000.0000.000
122A122GLU-1-0.847-0.92032.894-0.005-0.0050.0000.0000.0000.000
123A123LEU00.011-0.00227.7870.0140.0140.0000.0000.0000.000
124A124LYS10.8110.88628.9310.1430.1430.0000.0000.0000.000
125A125MET0-0.0170.01430.0200.0090.0090.0000.0000.0000.000
126A126SER0-0.061-0.05429.1970.0120.0120.0000.0000.0000.000
127A127ALA0-0.0020.00226.0870.0160.0160.0000.0000.0000.000
128A128GLY00.0370.01927.6410.0050.0050.0000.0000.0000.000
129A129TRP00.0430.00530.1340.0090.0090.0000.0000.0000.000
130A130SER0-0.008-0.01626.7840.0170.0170.0000.0000.0000.000
131A131CYS0-0.081-0.01726.2730.0180.0180.0000.0000.0000.000
132A132TYR00.011-0.03827.2640.0120.0120.0000.0000.0000.000
133A133CYS0-0.070-0.00428.8690.0080.0080.0000.0000.0000.000
134A134TRP0-0.021-0.03424.2640.0290.0290.0000.0000.0000.000
135A135LEU0-0.036-0.01626.3010.0120.0120.0000.0000.0000.000
136A136LEU0-0.0050.00728.0580.0060.0060.0000.0000.0000.000
137A137GLY0-0.0080.00227.5960.0080.0080.0000.0000.0000.000
138A138ASN0-0.032-0.02222.9450.0470.0470.0000.0000.0000.000
139A139ARG10.8090.89924.9980.0000.0000.0000.0000.0000.000
140A140LYS10.9770.98329.184-0.107-0.1070.0000.0000.0000.000
141A141ASP-1-0.711-0.86532.5990.0670.0670.0000.0000.0000.000
142A142ASN0-0.028-0.03235.807-0.001-0.0010.0000.0000.0000.000
143A143ALA0-0.045-0.00432.278-0.007-0.0070.0000.0000.0000.000
144A144PHE0-0.021-0.01630.637-0.008-0.0080.0000.0000.0000.000
145A145SER00.0050.01236.3880.0050.0050.0000.0000.0000.000
146A146GLU-1-0.850-0.93340.0180.0310.0310.0000.0000.0000.000
147A147SER00.0200.00942.0490.0020.0020.0000.0000.0000.000
148A148LYS10.8480.91535.3580.0220.0220.0000.0000.0000.000
149A149ILE00.006-0.00235.9560.0000.0000.0000.0000.0000.000
150A150SER00.0280.00939.6840.0040.0040.0000.0000.0000.000
151A151ASP-1-0.896-0.95443.3060.0050.0050.0000.0000.0000.000
152A152MET0-0.071-0.02635.027-0.002-0.0020.0000.0000.0000.000
153A153LEU0-0.037-0.01739.7960.0020.0020.0000.0000.0000.000
154A154GLU-1-0.780-0.87441.8450.0220.0220.0000.0000.0000.000
155A155MET0-0.0060.00039.601-0.002-0.0020.0000.0000.0000.000
156A156VAL0-0.034-0.00538.580-0.001-0.0010.0000.0000.0000.000
157A157LYS10.8310.89941.673-0.018-0.0180.0000.0000.0000.000
158A158ASP-1-0.870-0.91245.0530.0140.0140.0000.0000.0000.000
159A159THR0-0.060-0.06442.472-0.003-0.0030.0000.0000.0000.000
160A160ILE0-0.0040.01038.900-0.001-0.0010.0000.0000.0000.000
161A161HIS0-0.038-0.04641.601-0.002-0.0020.0000.0000.0000.000
162A162HIS0-0.037-0.00843.951-0.001-0.0010.0000.0000.0000.000
163A163SER0-0.035-0.01738.989-0.006-0.0060.0000.0000.0000.000
164A164PRO00.0180.00136.4140.0050.0050.0000.0000.0000.000
165A165GLU-1-0.730-0.84536.5570.0300.0300.0000.0000.0000.000
166A166ARG10.8900.93929.638-0.053-0.0530.0000.0000.0000.000
167A167THR00.0460.01133.0530.0070.0070.0000.0000.0000.000
168A168LYS10.8520.93534.450-0.019-0.0190.0000.0000.0000.000
169A169SER0-0.037-0.02332.1070.0110.0110.0000.0000.0000.000
170A170ALA0-0.0180.00530.8610.0120.0120.0000.0000.0000.000
171A171MET00.0160.02632.3140.0050.0050.0000.0000.0000.000
172A172ASN0-0.001-0.00935.6220.0100.0100.0000.0000.0000.000
173A173ASN0-0.010-0.00428.8970.0150.0150.0000.0000.0000.000
174A174PHE00.0620.01433.2230.0080.0080.0000.0000.0000.000
175A175LEU00.0110.01134.6180.0030.0030.0000.0000.0000.000
176A176ASN0-0.026-0.03634.6160.0090.0090.0000.0000.0000.000
177A177THR0-0.022-0.02330.7850.0100.0100.0000.0000.0000.000
178A178VAL00.0130.00833.8830.0030.0030.0000.0000.0000.000
179A179ALA00.0190.01436.8260.0020.0020.0000.0000.0000.000
180A180ILE0-0.049-0.01234.0040.0040.0040.0000.0000.0000.000
181A181SER0-0.089-0.04932.2730.0130.0130.0000.0000.0000.000
182A182TYR00.0170.00334.164-0.003-0.0030.0000.0000.0000.000
183A183VAL00.0450.01836.907-0.004-0.0040.0000.0000.0000.000
184A184PRO0-0.048-0.01039.467-0.001-0.0010.0000.0000.0000.000
185A185LEU00.0080.01641.120-0.004-0.0040.0000.0000.0000.000
186A186HIS0-0.061-0.03140.9700.0000.0000.0000.0000.0000.000
187A187GLU-1-0.849-0.93742.3580.0630.0630.0000.0000.0000.000
188A188LYS10.8480.90844.820-0.029-0.0290.0000.0000.0000.000
189A189ALA00.0140.00940.488-0.002-0.0020.0000.0000.0000.000
190A190VAL0-0.042-0.01842.6080.0020.0020.0000.0000.0000.000
191A191GLU-1-0.881-0.93144.4580.0350.0350.0000.0000.0000.000
192A192ILE00.0410.01743.414-0.001-0.0010.0000.0000.0000.000
193A193ALA0-0.016-0.00841.804-0.001-0.0010.0000.0000.0000.000
194A194LYS10.8950.95343.601-0.047-0.0470.0000.0000.0000.000
195A195GLU-1-0.992-0.99647.0660.0290.0290.0000.0000.0000.000
196A196VAL0-0.0020.00642.413-0.002-0.0020.0000.0000.0000.000
197A197GLY00.0090.01645.629-0.001-0.0010.0000.0000.0000.000
198A198ILE0-0.074-0.05142.5960.0040.0040.0000.0000.0000.000
199A199VAL00.0300.02539.158-0.005-0.0050.0000.0000.0000.000
200A200GLU-1-0.841-0.88639.7140.0440.0440.0000.0000.0000.000
201A201VAL00.0140.01934.482-0.005-0.0050.0000.0000.0000.000
202A202LYS10.8200.86437.213-0.016-0.0160.0000.0000.0000.000
203A203ARG10.8500.90532.227-0.088-0.0880.0000.0000.0000.000
204A204ASP-1-0.843-0.91334.1400.0110.0110.0000.0000.0000.000
205A205ASN0-0.065-0.03934.9670.0070.0070.0000.0000.0000.000
206A206LYS10.8050.90130.580-0.083-0.0830.0000.0000.0000.000
207A207LYS10.9740.98737.099-0.077-0.0770.0000.0000.0000.000
208A208SER00.0130.01037.0700.0070.0070.0000.0000.0000.000
209A209SER0-0.065-0.04034.9110.0080.0080.0000.0000.0000.000
210A210LEU00.0310.01037.281-0.006-0.0060.0000.0000.0000.000
211A211LEU00.0100.00734.6790.0080.0080.0000.0000.0000.000
212A212ASN00.0430.01138.498-0.010-0.0100.0000.0000.0000.000
213A213ALA00.0600.04338.9490.0080.0080.0000.0000.0000.000
214A214SER00.0360.01940.0200.0050.0050.0000.0000.0000.000
215A215GLU-1-0.869-0.92140.6910.1090.1090.0000.0000.0000.000
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