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: 9GNZ2

Calculation Name: 1T3B-A-Xray319

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T3B

Chain ID: A

ChEMBL ID:

UniProt ID: P45111

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 210
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2311318.219155
FMO2-HF: Nuclear repulsion 2230012.712255
FMO2-HF: Total energy -81305.5069
FMO2-MP2: Total energy -81544.521759


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:ACE )


Summations of interaction energy for fragment #1(A:1:ACE )
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.
0.7892.1740.01-0.725-0.6670.001
Interaction energy analysis for fragmet #1(A:1:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.010
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].
3A3ALA 00.0260.0173.6460.2941.3140.005-0.508-0.5160.001
4A4ALA 00.0230.0144.678-0.163-0.0970.000-0.005-0.0600.000
5A5ILE 00.0250.0065.370-0.207-0.2070.0000.0000.0000.000
6A6LYS 10.9500.9768.2230.6960.6960.0000.0000.0000.000
7A7ARG 10.9380.98210.2460.1770.1770.0000.0000.0000.000
8A8LYS 10.8890.9298.8580.3980.3980.0000.0000.0000.000
9A9LEU 00.0270.02011.4060.0000.0000.0000.0000.0000.000
10A10GLN 00.0280.02214.9130.0210.0210.0000.0000.0000.000
11A11SER 0-0.062-0.02616.6600.0350.0350.0000.0000.0000.000
12A12PHE 0-0.023-0.02817.9190.0050.0050.0000.0000.0000.000
13A13ASN 0-0.031-0.00119.713-0.005-0.0050.0000.0000.0000.000
14A14ILE 0-0.029-0.00316.205-0.009-0.0090.0000.0000.0000.000
15A15SER 0-0.025-0.02917.871-0.006-0.0060.0000.0000.0000.000
16A16ASN 0-0.051-0.05117.332-0.034-0.0340.0000.0000.0000.000
17A17ILE 0-0.0070.02511.274-0.045-0.0450.0000.0000.0000.000
18A18VAL 0-0.008-0.01312.179-0.016-0.0160.0000.0000.0000.000
19A19ILE 0-0.065-0.0206.455-0.021-0.0210.0000.0000.0000.000
20A20LYS 10.9530.9589.0420.4950.4950.0000.0000.0000.000
21A21SER 0-0.001-0.0069.088-0.197-0.1970.0000.0000.0000.000
22A22SER 00.027-0.0249.3730.1390.1390.0000.0000.0000.000
23A23PRO 0-0.054-0.02411.380-0.005-0.0050.0000.0000.0000.000
24A24ILE 0-0.008-0.01012.3340.0610.0610.0000.0000.0000.000
25A25SER 00.1170.0539.076-0.101-0.1010.0000.0000.0000.000
26A26GLY 0-0.006-0.0057.7570.0540.0540.0000.0000.0000.000
27A27ILE 00.0220.0208.467-0.088-0.0880.0000.0000.0000.000
28A28LYS 10.8350.9754.2402.6252.8390.001-0.111-0.1030.000
29A29THR 00.021-0.0028.6610.1070.1070.0000.0000.0000.000
30A30ALA 0-0.054-0.01111.261-0.034-0.0340.0000.0000.0000.000
31A31VAL 00.0230.01112.4620.0980.0980.0000.0000.0000.000
32A32THR 0-0.024-0.01514.7120.0050.0050.0000.0000.0000.000
33A33ASP -1-0.830-0.91316.942-0.174-0.1740.0000.0000.0000.000
34A34GLN 00.0650.03418.8480.0050.0050.0000.0000.0000.000
35A35GLY 00.0100.01619.9760.0170.0170.0000.0000.0000.000
36A36ILE 0-0.049-0.02116.522-0.038-0.0380.0000.0000.0000.000
37A37LEU 00.0140.03014.9950.0090.0090.0000.0000.0000.000
38A38TYR 00.017-0.00312.920-0.060-0.0600.0000.0000.0000.000
39A39VAL 0-0.011-0.0049.5560.0690.0690.0000.0000.0000.000
40A40SER 00.022-0.0229.300-0.149-0.1490.0000.0000.0000.000
41A41GLU -1-0.901-0.9513.857-2.945-2.8600.004-0.1010.0120.000
42A42ASP -1-0.806-0.8535.635-0.240-0.2400.0000.0000.0000.000
43A43GLY 0-0.011-0.0078.1640.0180.0180.0000.0000.0000.000
44A44LYS 10.8460.9079.9650.2170.2170.0000.0000.0000.000
45A45TYR 00.004-0.01212.9180.0470.0470.0000.0000.0000.000
46A46LEU 00.0490.01413.432-0.088-0.0880.0000.0000.0000.000
47A47PHE 0-0.0330.00114.3600.0490.0490.0000.0000.0000.000
48A48GLU -1-0.951-0.97717.564-0.234-0.2340.0000.0000.0000.000
49A49GLY 00.013-0.00219.7850.0260.0260.0000.0000.0000.000
50A50LYS 10.9260.95620.9740.1450.1450.0000.0000.0000.000
51A51LEU 0-0.0080.00916.1410.0140.0140.0000.0000.0000.000
52A52TYR 0-0.050-0.03119.9510.0020.0020.0000.0000.0000.000
53A53GLU -1-0.753-0.89120.916-0.130-0.1300.0000.0000.0000.000
54A54LEU 0-0.048-0.02523.3110.0030.0030.0000.0000.0000.000
55A55THR 0-0.021-0.01325.2670.0050.0050.0000.0000.0000.000
56A56ASN 0-0.087-0.04626.9590.0070.0070.0000.0000.0000.000
57A57ASN 00.0140.00830.3440.0010.0010.0000.0000.0000.000
58A58GLY 00.0740.03829.9010.0040.0040.0000.0000.0000.000
59A59PRO 0-0.043-0.01427.178-0.006-0.0060.0000.0000.0000.000
60A60VAL 00.0010.00824.110-0.004-0.0040.0000.0000.0000.000
61A61ASP -1-0.858-0.92921.435-0.220-0.2200.0000.0000.0000.000
62A62VAL 00.0680.03916.4700.0000.0000.0000.0000.0000.000
63A63ALA 0-0.052-0.05518.880-0.014-0.0140.0000.0000.0000.000
64A64GLY 00.0160.02119.7740.0090.0090.0000.0000.0000.000
65A65LYS 10.9340.94619.7210.1420.1420.0000.0000.0000.000
66A66ILE 0-0.0250.00015.129-0.009-0.0090.0000.0000.0000.000
67A67LEU 0-0.008-0.00818.9240.0010.0010.0000.0000.0000.000
68A68VAL 00.0040.01022.2050.0110.0110.0000.0000.0000.000
69A69ASP -1-0.871-0.93118.789-0.195-0.1950.0000.0000.0000.000
70A70LYS 10.9080.97021.3110.1900.1900.0000.0000.0000.000
71A71LEU 00.0140.05022.4040.0130.0130.0000.0000.0000.000
72A72ASN 00.0870.03224.5290.0170.0170.0000.0000.0000.000
73A73SER 0-0.140-0.09722.4140.0110.0110.0000.0000.0000.000
74A74TYR 00.046-0.00424.4280.0000.0000.0000.0000.0000.000
75A75LYS 10.9730.95427.8310.0700.0700.0000.0000.0000.000
76A76ASP -1-0.953-0.96529.567-0.059-0.0590.0000.0000.0000.000
77A77GLU -1-0.899-0.95829.289-0.084-0.0840.0000.0000.0000.000
78A78MET 0-0.095-0.02929.1740.0030.0030.0000.0000.0000.000
79A79ILE 0-0.0080.00934.3630.0040.0040.0000.0000.0000.000
80A80VAL 0-0.035-0.03635.4150.0000.0000.0000.0000.0000.000
81A81TYR 0-0.014-0.01438.3050.0030.0030.0000.0000.0000.000
82A82PRO 0-0.001-0.01038.801-0.001-0.0010.0000.0000.0000.000
83A83ALA 00.0630.05240.5370.0020.0020.0000.0000.0000.000
84A84LYS 10.7640.88242.1490.0290.0290.0000.0000.0000.000
85A85ASN 0-0.005-0.02440.078-0.001-0.0010.0000.0000.0000.000
86A86GLU -1-0.955-0.95835.163-0.049-0.0490.0000.0000.0000.000
87A87LYS 10.9010.95638.4580.0350.0350.0000.0000.0000.000
88A88HIS 10.8750.93436.1440.0470.0470.0000.0000.0000.000
89A89VAL 00.0520.03632.7800.0020.0020.0000.0000.0000.000
90A90VAL 00.0080.01833.310-0.006-0.0060.0000.0000.0000.000
91A91THR 00.0320.01131.7380.0020.0020.0000.0000.0000.000
92A92VAL 0-0.0070.00634.086-0.002-0.0020.0000.0000.0000.000
93A93PHE 0-0.022-0.00330.4780.0010.0010.0000.0000.0000.000
94A94MET 00.003-0.01436.5590.0030.0030.0000.0000.0000.000
95A95ASP -1-0.812-0.92839.746-0.054-0.0540.0000.0000.0000.000
96A96ILE 00.1020.02942.3520.0010.0010.0000.0000.0000.000
97A97THR 0-0.067-0.01745.4740.0020.0020.0000.0000.0000.000
98A101CYS 0-0.081-0.02143.608-0.001-0.0010.0000.0000.0000.000
99A99HIS 00.0350.02947.0900.0010.0010.0000.0000.0000.000
100A100TYR 00.0540.01746.3640.0010.0010.0000.0000.0000.000
101A102HIS 00.0310.02445.0790.0010.0010.0000.0000.0000.000
102A103LEU 0-0.025-0.01448.2120.0010.0010.0000.0000.0000.000
103A104LEU 0-0.026-0.02941.6010.0010.0010.0000.0000.0000.000
104A105HIS 00.0610.01844.4250.0010.0010.0000.0000.0000.000
105A106GLN 0-0.020-0.01346.5910.0010.0010.0000.0000.0000.000
106A107GLN 0-0.043-0.03548.0110.0020.0020.0000.0000.0000.000
107A108LEU 00.0090.03842.990-0.001-0.0010.0000.0000.0000.000
108A109LYS 10.8030.89746.0500.0300.0300.0000.0000.0000.000
109A110GLU -1-0.716-0.84448.263-0.031-0.0310.0000.0000.0000.000
110A111TYR 0-0.043-0.04143.0190.0000.0000.0000.0000.0000.000
111A112ASN 00.0430.01043.164-0.002-0.0020.0000.0000.0000.000
112A113ASP -1-0.909-0.94544.721-0.028-0.0280.0000.0000.0000.000
113A114LEU 0-0.045-0.01544.7160.0010.0010.0000.0000.0000.000
114A115GLY 0-0.055-0.02242.576-0.001-0.0010.0000.0000.0000.000
115A116ILE 00.0240.00338.825-0.003-0.0030.0000.0000.0000.000
116A117THR 00.0150.00436.5960.0020.0020.0000.0000.0000.000
117A118VAL 0-0.0050.00437.435-0.004-0.0040.0000.0000.0000.000
118A119ARG 10.8840.93329.3010.0800.0800.0000.0000.0000.000
119A120TYR 00.0000.01335.744-0.004-0.0040.0000.0000.0000.000
120A121LEU 00.0140.02330.631-0.001-0.0010.0000.0000.0000.000
121A122ALA 00.0150.00634.8580.0030.0030.0000.0000.0000.000
122A123PHE 0-0.012-0.02633.946-0.005-0.0050.0000.0000.0000.000
123A124PRO 00.001-0.00136.8400.0030.0030.0000.0000.0000.000
124A125ARG 10.9370.98239.0920.0500.0500.0000.0000.0000.000
125A126ALA 00.0000.03140.555-0.002-0.0020.0000.0000.0000.000
126A127GLY 00.020-0.00938.9410.0010.0010.0000.0000.0000.000
127A128MET 00.0100.02135.9430.0020.0020.0000.0000.0000.000
128A129ASN 0-0.010-0.01939.5210.0020.0020.0000.0000.0000.000
129A130ASN 00.0520.01642.6480.0040.0040.0000.0000.0000.000
130A131GLN 00.0660.02744.874-0.002-0.0020.0000.0000.0000.000
131A132THR 00.0850.04244.2970.0010.0010.0000.0000.0000.000
132A133ALA 0-0.0190.00540.571-0.001-0.0010.0000.0000.0000.000
133A134LYS 10.8500.92941.1690.0480.0480.0000.0000.0000.000
134A135GLN 00.0640.02443.273-0.001-0.0010.0000.0000.0000.000
135A136MET 00.0050.02440.3930.0000.0000.0000.0000.0000.000
136A137GLU -1-0.756-0.87036.389-0.061-0.0610.0000.0000.0000.000
137A138ALA 0-0.061-0.01139.8530.0000.0000.0000.0000.0000.000
138A139ILE 00.008-0.01841.9500.0010.0010.0000.0000.0000.000
139A140TRP 0-0.023-0.02835.7590.0020.0020.0000.0000.0000.000
140A141THR 0-0.033-0.01936.3960.0000.0000.0000.0000.0000.000
141A142ALA 0-0.051-0.01038.7670.0030.0030.0000.0000.0000.000
142A143LYS 10.9560.96140.8560.0280.0280.0000.0000.0000.000
143A144ASP -1-0.873-0.94042.414-0.033-0.0330.0000.0000.0000.000
144A145PRO 00.0440.01238.8500.0010.0010.0000.0000.0000.000
145A146VAL 00.0730.05641.7020.0000.0000.0000.0000.0000.000
146A147PHE 0-0.038-0.00143.7620.0010.0010.0000.0000.0000.000
147A148ALA 0-0.005-0.00944.1370.0000.0000.0000.0000.0000.000
148A149LEU 00.0160.00041.7070.0000.0000.0000.0000.0000.000
149A150ASN 0-0.002-0.00345.210-0.001-0.0010.0000.0000.0000.000
150A151GLU -1-0.879-0.93348.000-0.027-0.0270.0000.0000.0000.000
151A152ALA 0-0.0020.00446.8560.0010.0010.0000.0000.0000.000
152A153GLU -1-0.895-0.96446.421-0.041-0.0410.0000.0000.0000.000
153A154LYS 10.8490.93549.5340.0290.0290.0000.0000.0000.000
154A155GLY 00.0100.01452.0340.0010.0010.0000.0000.0000.000
155A156ASN 0-0.116-0.06352.6160.0010.0010.0000.0000.0000.000
156A157LEU 0-0.003-0.00348.141-0.001-0.0010.0000.0000.0000.000
157A158PRO 0-0.059-0.01946.3550.0020.0020.0000.0000.0000.000
158A159LYS 10.9650.97349.5990.0240.0240.0000.0000.0000.000
159A160GLU -1-0.945-0.95446.391-0.035-0.0350.0000.0000.0000.000
160A161VAL 00.061-0.00244.734-0.001-0.0010.0000.0000.0000.000
161A162LYS 10.8760.97840.3080.0420.0420.0000.0000.0000.000
162A163THR 00.025-0.00738.2950.0000.0000.0000.0000.0000.000
163A164PRO 0-0.102-0.06937.752-0.002-0.0020.0000.0000.0000.000
164A165ASN 0-0.008-0.00832.170-0.007-0.0070.0000.0000.0000.000
165A166ILE 00.0550.03432.082-0.007-0.0070.0000.0000.0000.000
166A167VAL 00.0230.01832.735-0.005-0.0050.0000.0000.0000.000
167A168LYS 10.8700.89430.9370.0910.0910.0000.0000.0000.000
168A169LYS 10.9020.96726.4060.0950.0950.0000.0000.0000.000
169A170HIS 0-0.013-0.00729.298-0.005-0.0050.0000.0000.0000.000
170A171TYR 0-0.014-0.01031.521-0.004-0.0040.0000.0000.0000.000
171A172GLU -1-0.866-0.93428.425-0.113-0.1130.0000.0000.0000.000
172A173LEU 0-0.0230.00825.557-0.008-0.0080.0000.0000.0000.000
173A174GLY 00.0590.01328.131-0.003-0.0030.0000.0000.0000.000
174A175ILE 00.0140.00030.2020.0000.0000.0000.0000.0000.000
175A176GLN 0-0.055-0.01522.7380.0030.0030.0000.0000.0000.000
176A177PHE 0-0.001-0.01026.375-0.007-0.0070.0000.0000.0000.000
177A178GLY 0-0.0260.00628.9790.0040.0040.0000.0000.0000.000
178A179VAL 0-0.066-0.02531.7950.0080.0080.0000.0000.0000.000
179A180ARG 10.9250.95234.5450.0760.0760.0000.0000.0000.000
180A181GLY 0-0.0040.00037.6240.0040.0040.0000.0000.0000.000
181A182THR 0-0.0460.01438.908-0.002-0.0020.0000.0000.0000.000
182A183PRO 00.044-0.01140.6430.0030.0030.0000.0000.0000.000
183A184SER 0-0.035-0.02936.2170.0000.0000.0000.0000.0000.000
184A185ILE 00.0170.02136.098-0.002-0.0020.0000.0000.0000.000
185A186VAL 00.002-0.00529.730-0.002-0.0020.0000.0000.0000.000
186A187THR 00.0510.04130.3480.0040.0040.0000.0000.0000.000
187A188SER 00.0410.01730.181-0.007-0.0070.0000.0000.0000.000
188A189THR 0-0.006-0.01727.709-0.005-0.0050.0000.0000.0000.000
189A190GLY 0-0.036-0.04326.491-0.008-0.0080.0000.0000.0000.000
190A191GLU -1-0.955-0.96627.502-0.083-0.0830.0000.0000.0000.000
191A192LEU 0-0.015-0.02530.352-0.002-0.0020.0000.0000.0000.000
192A193ILE 00.0280.03333.0570.0010.0010.0000.0000.0000.000
193A194GLY 0-0.037-0.02235.8450.0040.0040.0000.0000.0000.000
194A195GLY 00.0590.02937.4470.0010.0010.0000.0000.0000.000
195A196TYR 0-0.042-0.02641.1980.0010.0010.0000.0000.0000.000
196A197LEU 00.0550.02540.4900.0010.0010.0000.0000.0000.000
197A198LYS 10.9421.00744.4180.0340.0340.0000.0000.0000.000
198A199PRO 00.0520.02045.571-0.001-0.0010.0000.0000.0000.000
199A200ALA 00.033-0.00145.089-0.001-0.0010.0000.0000.0000.000
200A201ASP -1-0.896-0.95945.274-0.040-0.0400.0000.0000.0000.000
201A202LEU 0-0.0120.00039.005-0.002-0.0020.0000.0000.0000.000
202A203LEU 0-0.017-0.00940.696-0.003-0.0030.0000.0000.0000.000
203A204ARG 11.0041.00540.9490.0370.0370.0000.0000.0000.000
204A205ALA 00.0110.01639.329-0.001-0.0010.0000.0000.0000.000
205A206LEU 0-0.072-0.03635.466-0.004-0.0040.0000.0000.0000.000
206A207GLU -1-0.993-0.99936.678-0.041-0.0410.0000.0000.0000.000
207A208GLU -1-0.949-0.98238.186-0.044-0.0440.0000.0000.0000.000
208A209THR 0-0.053-0.01833.990-0.002-0.0020.0000.0000.0000.000
209A210ALA 00.0240.03033.269-0.001-0.0010.0000.0000.0000.000
210A211NME 0-0.087-0.05729.923-0.004-0.0040.0000.0000.0000.000