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: YZ7V2

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 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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3005240.471873
FMO2-HF: Nuclear repulsion 2910817.690565
FMO2-HF: Total energy -94422.781308
FMO2-MP2: Total energy -94693.2201


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.
-24.654-21.89426.065-12.263-16.564-0.012
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 : -0.038 / q_NPA : 0.005
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].
3A3PHE00.1010.0383.808-0.8701.588-0.026-1.299-1.1330.006
4A4LYS10.9340.9746.6212.3312.3310.0000.0000.0000.000
5A5THR0-0.030-0.0542.316-3.424-1.7323.208-1.808-3.093-0.016
6A6VAL00.0100.0193.0141.0741.8740.066-0.161-0.706-0.001
7A7MET0-0.0010.0015.0060.8320.924-0.001-0.003-0.0870.000
8A8GLN0-0.046-0.0126.5310.1350.1350.0000.0000.0000.000
9A9GLU-1-0.808-0.9152.4313.3556.4021.629-2.121-2.555-0.028
10A10LEU0-0.023-0.0216.8550.1930.1930.0000.0000.0000.000
11A11GLU-1-0.980-0.9819.7520.1680.1680.0000.0000.0000.000
12A12ALA00.0300.0179.5120.0400.0400.0000.0000.0000.000
13A13LEU0-0.089-0.0439.3440.0350.0350.0000.0000.0000.000
14A14GLY0-0.0300.00612.350-0.035-0.0350.0000.0000.0000.000
15A15LYS10.9140.94315.432-0.699-0.6990.0000.0000.0000.000
16A16GLU-1-0.735-0.86018.8920.1330.1330.0000.0000.0000.000
17A17ARG10.9340.96322.266-0.371-0.3710.0000.0000.0000.000
18A18THR0-0.005-0.01019.365-0.030-0.0300.0000.0000.0000.000
19A19LYS10.8850.93520.085-0.091-0.0910.0000.0000.0000.000
20A20LYS10.8500.90921.979-0.171-0.1710.0000.0000.0000.000
21A21ILE0-0.029-0.00524.643-0.020-0.0200.0000.0000.0000.000
22A22TYR0-0.005-0.03618.287-0.031-0.0310.0000.0000.0000.000
23A23ILE00.0270.01923.602-0.021-0.0210.0000.0000.0000.000
24A24SER0-0.0210.01026.014-0.015-0.0150.0000.0000.0000.000
25A25ASN0-0.098-0.06425.475-0.017-0.0170.0000.0000.0000.000
26A26GLY00.0440.02827.590-0.008-0.0080.0000.0000.0000.000
27A27ALA0-0.0220.01422.408-0.021-0.0210.0000.0000.0000.000
28A28HIS10.8910.91923.5730.1040.1040.0000.0000.0000.000
29A29GLU-1-0.810-0.87121.249-0.005-0.0050.0000.0000.0000.000
30A30PRO00.0120.01017.956-0.012-0.0120.0000.0000.0000.000
31A31VAL00.011-0.01117.9570.0060.0060.0000.0000.0000.000
32A32PHE00.0310.00712.097-0.002-0.0020.0000.0000.0000.000
33A33GLY0-0.018-0.00916.8940.0290.0290.0000.0000.0000.000
34A34VAL0-0.017-0.00512.5060.0550.0550.0000.0000.0000.000
35A35ALA0-0.0160.00815.935-0.056-0.0560.0000.0000.0000.000
36A36THR00.0840.02715.1510.1580.1580.0000.0000.0000.000
37A37GLY0-0.006-0.00214.3100.1250.1250.0000.0000.0000.000
38A38ALA0-0.043-0.02612.7840.1470.1470.0000.0000.0000.000
39A39MET00.0620.0419.7660.3620.3620.0000.0000.0000.000
40A40LYS10.9560.9899.217-0.849-0.8490.0000.0000.0000.000
41A41PRO0-0.043-0.0288.011-0.017-0.0170.0000.0000.0000.000
42A42ILE00.0520.0123.8170.3961.0080.118-0.174-0.5570.000
43A43ALA00.0390.0184.860-0.0770.020-0.001-0.012-0.0830.000
44A44LYS10.8880.9496.813-2.095-2.0950.0000.0000.0000.000
45A45LYS10.7640.8762.204-20.179-28.11119.260-5.597-5.7310.031
46A46ILE0-0.0090.0062.345-3.828-2.1401.814-1.066-2.437-0.004
47A47LYS10.8910.9554.7351.5551.680-0.001-0.013-0.1110.000
48A48LEU00.0100.0027.396-0.377-0.3770.0000.0000.0000.000
49A49ASN0-0.0150.0016.6940.1490.1490.0000.0000.0000.000
50A50GLN00.1110.0459.4930.0320.0320.0000.0000.0000.000
51A51GLU-1-0.883-0.94211.142-1.184-1.1840.0000.0000.0000.000
52A52LEU0-0.010-0.0074.718-0.131-0.050-0.001-0.009-0.0710.000
53A53ALA0-0.002-0.0019.2780.2060.2060.0000.0000.0000.000
54A54GLU-1-0.753-0.83911.217-0.406-0.4060.0000.0000.0000.000
55A55GLU-1-0.918-0.95310.526-1.924-1.9240.0000.0000.0000.000
56A56LEU0-0.031-0.0327.2730.1540.1540.0000.0000.0000.000
57A57TYR0-0.035-0.03011.7180.1760.1760.0000.0000.0000.000
58A58ALA00.0030.00115.0400.0880.0880.0000.0000.0000.000
59A59THR0-0.066-0.04613.1220.0780.0780.0000.0000.0000.000
60A60GLY00.0200.01816.2550.0480.0480.0000.0000.0000.000
61A61ASN0-0.030-0.01415.1480.1250.1250.0000.0000.0000.000
62A62TYR00.0760.02415.867-0.008-0.0080.0000.0000.0000.000
63A63ASP-1-0.729-0.86614.0230.3050.3050.0000.0000.0000.000
64A64ALA00.0230.01211.4630.1060.1060.0000.0000.0000.000
65A65MET0-0.0320.00712.051-0.038-0.0380.0000.0000.0000.000
66A66TYR0-0.040-0.05314.101-0.010-0.0100.0000.0000.0000.000
67A67PHE0-0.037-0.0375.6510.1610.1610.0000.0000.0000.000
68A68ALA00.0120.01710.481-0.013-0.0130.0000.0000.0000.000
69A69GLY00.0360.01011.683-0.059-0.0590.0000.0000.0000.000
70A70ILE0-0.097-0.05910.8340.0290.0290.0000.0000.0000.000
71A71ILE0-0.039-0.0176.6490.0210.0210.0000.0000.0000.000
72A72ALA00.0420.03610.249-0.253-0.2530.0000.0000.0000.000
73A73ASP-1-0.818-0.90813.078-0.350-0.3500.0000.0000.0000.000
74A74PRO00.0470.01014.964-0.014-0.0140.0000.0000.0000.000
75A75LYS10.7830.87916.2840.3750.3750.0000.0000.0000.000
76A76ALA0-0.039-0.02017.4290.0080.0080.0000.0000.0000.000
77A77MET0-0.0750.00518.071-0.020-0.0200.0000.0000.0000.000
78A78SER0-0.005-0.03220.6410.0520.0520.0000.0000.0000.000
79A79GLU-1-0.804-0.91724.157-0.151-0.1510.0000.0000.0000.000
80A80SER0-0.0110.00125.892-0.002-0.0020.0000.0000.0000.000
81A81ASP-1-0.766-0.84820.692-0.404-0.4040.0000.0000.0000.000
82A82PHE00.027-0.00220.790-0.002-0.0020.0000.0000.0000.000
83A83ASP-1-0.798-0.89523.466-0.132-0.1320.0000.0000.0000.000
84A84ARG10.7910.86319.0850.4590.4590.0000.0000.0000.000
85A85TRP0-0.055-0.04814.4270.0460.0460.0000.0000.0000.000
86A86ILE0-0.049-0.01021.5880.0230.0230.0000.0000.0000.000
87A87ASP-1-0.817-0.88824.615-0.150-0.1500.0000.0000.0000.000
88A88GLY0-0.026-0.00322.3960.0010.0010.0000.0000.0000.000
89A89ALA0-0.072-0.04422.5670.0130.0130.0000.0000.0000.000
90A90TYR00.0180.00421.5650.0310.0310.0000.0000.0000.000
91A91PHE00.0210.00122.0250.0190.0190.0000.0000.0000.000
92A92TYR00.0680.01125.103-0.001-0.0010.0000.0000.0000.000
93A93MET0-0.099-0.01321.8080.0070.0070.0000.0000.0000.000
94A94LEU0-0.0040.01118.9020.0240.0240.0000.0000.0000.000
95A95SER00.0820.02821.807-0.009-0.0090.0000.0000.0000.000
96A96ASP-1-0.819-0.89224.4960.0400.0400.0000.0000.0000.000
97A97TYR0-0.017-0.02621.1840.0120.0120.0000.0000.0000.000
98A98VAL0-0.0440.00216.5960.0390.0390.0000.0000.0000.000
99A99VAL00.0130.00119.276-0.011-0.0110.0000.0000.0000.000
100A100ALA00.0480.03721.066-0.011-0.0110.0000.0000.0000.000
101A101VAL0-0.046-0.02118.8700.0020.0020.0000.0000.0000.000
102A102THR00.0460.04216.5550.0340.0340.0000.0000.0000.000
103A103LEU00.0210.03519.450-0.015-0.0150.0000.0000.0000.000
104A104SER0-0.053-0.04022.4490.0050.0050.0000.0000.0000.000
105A105GLU-1-0.893-0.94718.4770.1250.1250.0000.0000.0000.000
106A106SER0-0.0050.01021.508-0.023-0.0230.0000.0000.0000.000
107A107ASN0-0.051-0.05322.9920.0150.0150.0000.0000.0000.000
108A108ILE00.0510.02925.7170.0080.0080.0000.0000.0000.000
109A109ALA0-0.030-0.00326.2120.0050.0050.0000.0000.0000.000
110A110GLN00.0580.01027.6250.0030.0030.0000.0000.0000.000
111A111ASP-1-0.869-0.91531.225-0.076-0.0760.0000.0000.0000.000
112A112VAL00.018-0.00127.013-0.001-0.0010.0000.0000.0000.000
113A113ALA0-0.016-0.01129.4100.0040.0040.0000.0000.0000.000
114A114ASP-1-0.725-0.82330.649-0.027-0.0270.0000.0000.0000.000
115A115LYS10.7930.89330.5080.1380.1380.0000.0000.0000.000
116A116TRP0-0.023-0.04624.7040.0060.0060.0000.0000.0000.000
117A117ILE0-0.0420.00332.5200.0040.0040.0000.0000.0000.000
118A118ALA0-0.005-0.00134.9490.0050.0050.0000.0000.0000.000
119A119SER0-0.057-0.04234.101-0.003-0.0030.0000.0000.0000.000
120A120GLY00.0270.01036.284-0.003-0.0030.0000.0000.0000.000
121A121ASP-1-0.863-0.93031.945-0.066-0.0660.0000.0000.0000.000
122A122GLU-1-0.839-0.91832.900-0.001-0.0010.0000.0000.0000.000
123A123LEU00.0260.00228.2130.0130.0130.0000.0000.0000.000
124A124LYS10.8300.90829.2140.1390.1390.0000.0000.0000.000
125A125MET0-0.0340.00330.3200.0060.0060.0000.0000.0000.000
126A126SER0-0.063-0.05729.2550.0120.0120.0000.0000.0000.000
127A127ALA00.0040.00926.4290.0150.0150.0000.0000.0000.000
128A128GLY00.0350.01827.8680.0060.0060.0000.0000.0000.000
129A129TRP00.0530.00730.3290.0080.0080.0000.0000.0000.000
130A130SER0-0.007-0.01526.9260.0170.0170.0000.0000.0000.000
131A131CYS0-0.085-0.02326.4960.0160.0160.0000.0000.0000.000
132A132TYR0-0.015-0.05527.5160.0120.0120.0000.0000.0000.000
133A133CYS0-0.079-0.01028.9580.0080.0080.0000.0000.0000.000
134A134TRP0-0.009-0.02024.4820.0320.0320.0000.0000.0000.000
135A135LEU0-0.015-0.00726.7280.0110.0110.0000.0000.0000.000
136A136LEU0-0.0030.01328.3420.0050.0050.0000.0000.0000.000
137A137GLY00.0000.00627.8390.0080.0080.0000.0000.0000.000
138A138ASN0-0.045-0.02423.5400.0430.0430.0000.0000.0000.000
139A139ARG10.8520.93525.6100.0080.0080.0000.0000.0000.000
140A140LYS10.9900.99329.610-0.099-0.0990.0000.0000.0000.000
141A141ASP-1-0.714-0.86632.9100.0650.0650.0000.0000.0000.000
142A142ASN0-0.035-0.03536.002-0.001-0.0010.0000.0000.0000.000
143A143ALA0-0.057-0.01132.505-0.007-0.0070.0000.0000.0000.000
144A144PHE0-0.037-0.02030.798-0.008-0.0080.0000.0000.0000.000
145A145SER00.0130.01536.4710.0030.0030.0000.0000.0000.000
146A146GLU-1-0.865-0.94639.9710.0310.0310.0000.0000.0000.000
147A147SER00.0390.00642.0980.0020.0020.0000.0000.0000.000
148A148LYS10.8510.92035.6570.0230.0230.0000.0000.0000.000
149A149ILE00.008-0.00836.0210.0000.0000.0000.0000.0000.000
150A150SER00.0230.00439.8410.0040.0040.0000.0000.0000.000
151A151ASP-1-0.908-0.94743.3670.0030.0030.0000.0000.0000.000
152A152MET0-0.077-0.03335.252-0.001-0.0010.0000.0000.0000.000
153A153LEU0-0.042-0.02239.9850.0020.0020.0000.0000.0000.000
154A154GLU-1-0.762-0.86942.0750.0240.0240.0000.0000.0000.000
155A155MET00.0120.01739.836-0.002-0.0020.0000.0000.0000.000
156A156VAL0-0.036-0.01538.6890.0000.0000.0000.0000.0000.000
157A157LYS10.8170.89341.744-0.019-0.0190.0000.0000.0000.000
158A158ASP-1-0.876-0.91545.0450.0140.0140.0000.0000.0000.000
159A159THR0-0.055-0.05642.636-0.003-0.0030.0000.0000.0000.000
160A160ILE0-0.0220.00038.763-0.001-0.0010.0000.0000.0000.000
161A161HIS0-0.041-0.05141.477-0.001-0.0010.0000.0000.0000.000
162A162HIS0-0.048-0.01643.941-0.001-0.0010.0000.0000.0000.000
163A163SER0-0.039-0.01038.801-0.006-0.0060.0000.0000.0000.000
164A164PRO00.0330.01236.3160.0040.0040.0000.0000.0000.000
165A165GLU-1-0.698-0.84536.1100.0360.0360.0000.0000.0000.000
166A166ARG10.9170.94430.087-0.060-0.0600.0000.0000.0000.000
167A167THR00.0420.01232.7860.0060.0060.0000.0000.0000.000
168A168LYS10.8400.93834.594-0.023-0.0230.0000.0000.0000.000
169A169SER0-0.033-0.02432.0750.0100.0100.0000.0000.0000.000
170A170ALA0-0.0220.00831.0460.0100.0100.0000.0000.0000.000
171A171MET00.0230.02632.3860.0050.0050.0000.0000.0000.000
172A172ASN00.011-0.00135.7250.0110.0110.0000.0000.0000.000
173A173ASN0-0.029-0.01129.0920.0160.0160.0000.0000.0000.000
174A174PHE00.0590.01033.3850.0080.0080.0000.0000.0000.000
175A175LEU00.0110.01134.7200.0030.0030.0000.0000.0000.000
176A176ASN0-0.027-0.03534.6990.0070.0070.0000.0000.0000.000
177A177THR0-0.015-0.01931.3250.0090.0090.0000.0000.0000.000
178A178VAL00.0070.02634.1660.0030.0030.0000.0000.0000.000
179A179ALA00.0180.01437.0440.0010.0010.0000.0000.0000.000
180A180ILE0-0.058-0.01534.1850.0040.0040.0000.0000.0000.000
181A181SER0-0.062-0.05732.3670.0080.0080.0000.0000.0000.000
182A182TYR0-0.014-0.00334.483-0.004-0.0040.0000.0000.0000.000
183A183VAL00.0400.00437.152-0.004-0.0040.0000.0000.0000.000
184A184PRO0-0.0190.01639.527-0.001-0.0010.0000.0000.0000.000
185A185LEU00.0090.01041.110-0.004-0.0040.0000.0000.0000.000
186A186HIS0-0.077-0.04540.9800.0010.0010.0000.0000.0000.000
187A187GLU-1-0.848-0.93942.6410.0640.0640.0000.0000.0000.000
188A188LYS10.8600.92745.135-0.030-0.0300.0000.0000.0000.000
189A189ALA00.0020.00840.847-0.001-0.0010.0000.0000.0000.000
190A190VAL0-0.040-0.02042.9640.0020.0020.0000.0000.0000.000
191A191GLU-1-0.879-0.93444.6030.0380.0380.0000.0000.0000.000
192A192ILE00.0410.00343.656-0.001-0.0010.0000.0000.0000.000
193A193ALA0-0.036-0.00942.209-0.001-0.0010.0000.0000.0000.000
194A194LYS10.8990.94943.936-0.050-0.0500.0000.0000.0000.000
195A195GLU-1-0.969-0.98847.2950.0310.0310.0000.0000.0000.000
196A196VAL0-0.038-0.00342.413-0.002-0.0020.0000.0000.0000.000
197A197GLY00.0060.01645.805-0.002-0.0020.0000.0000.0000.000
198A198ILE0-0.068-0.05142.6170.0030.0030.0000.0000.0000.000
199A199VAL00.0290.02339.186-0.005-0.0050.0000.0000.0000.000
200A200GLU-1-0.840-0.89239.9760.0500.0500.0000.0000.0000.000
201A201VAL00.0060.00634.264-0.005-0.0050.0000.0000.0000.000
202A202LYS10.8220.88437.315-0.020-0.0200.0000.0000.0000.000
203A203ARG10.8270.89832.154-0.100-0.1000.0000.0000.0000.000
204A204ASP-1-0.845-0.92133.9200.0150.0150.0000.0000.0000.000
205A205ASN0-0.062-0.02934.7410.0070.0070.0000.0000.0000.000
206A206LYS10.8330.90030.268-0.094-0.0940.0000.0000.0000.000
207A207LYS10.9710.98936.904-0.087-0.0870.0000.0000.0000.000
208A208SER00.0100.00637.0100.0090.0090.0000.0000.0000.000
209A209SER0-0.060-0.03134.6000.0070.0070.0000.0000.0000.000
210A210LEU00.0230.01337.030-0.007-0.0070.0000.0000.0000.000
211A211LEU0-0.014-0.00234.7260.0090.0090.0000.0000.0000.000
212A212ASN00.0670.02238.620-0.012-0.0120.0000.0000.0000.000
213A213ALA00.0580.03038.8250.0080.0080.0000.0000.0000.000
214A214SER00.0730.03839.8660.0040.0040.0000.0000.0000.000
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