FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: 9G1R2

Calculation Name: 3T8K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3T8K

Chain ID: A

ChEMBL ID:

UniProt ID: C7NDE2

Base Structure: X-ray

Registration Date: 2023-06-20

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2053327.263383
FMO2-HF: Nuclear repulsion 1978600.78421
FMO2-HF: Total energy -74726.479173
FMO2-MP2: Total energy -74943.384289


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:-2:SER)


Summations of interaction energy for fragment #1(A:-2:SER)
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.
-2.4-0.573.052-1.836-3.0450.002
Interaction energy analysis for fragmet #1(A:-2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.030
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].
3A0ALA00.1550.0713.806-0.0321.377-0.012-0.574-0.8230.000
4A1MET0-0.090-0.0481.9780.7740.2493.045-1.040-1.4800.002
5A2SER0-0.094-0.0423.0341.6812.2280.019-0.129-0.4370.000
6A3GLU-1-0.971-0.9785.109-1.510-1.439-0.001-0.002-0.0680.000
7A4TYR0-0.005-0.0037.2770.5500.5500.0000.0000.0000.000
8A5ARG10.9270.9687.9200.1060.1060.0000.0000.0000.000
9A6THR00.013-0.00810.3050.1120.1120.0000.0000.0000.000
10A7VAL00.0420.00711.747-0.092-0.0920.0000.0000.0000.000
11A8SER0-0.065-0.06812.919-0.051-0.0510.0000.0000.0000.000
12A9ALA0-0.011-0.00612.585-0.010-0.0100.0000.0000.0000.000
13A10ALA00.0640.03210.142-0.034-0.0340.0000.0000.0000.000
14A11ALA0-0.022-0.01512.0290.0000.0000.0000.0000.0000.000
15A12MET0-0.054-0.01515.3320.0300.0300.0000.0000.0000.000
16A13LEU0-0.062-0.03214.0790.0200.0200.0000.0000.0000.000
17A14GLY00.0320.04212.093-0.042-0.0420.0000.0000.0000.000
18A15THR00.001-0.00510.9450.1610.1610.0000.0000.0000.000
19A16TYR0-0.005-0.02112.8100.0170.0170.0000.0000.0000.000
20A17GLU-1-0.877-0.9579.703-0.211-0.2110.0000.0000.0000.000
21A18ASP-1-0.777-0.8898.149-1.147-1.1470.0000.0000.0000.000
22A19PHE0-0.021-0.0258.6580.0770.0770.0000.0000.0000.000
23A20LEU0-0.026-0.01711.0480.1030.1030.0000.0000.0000.000
24A21GLU-1-0.947-0.9654.145-0.372-0.0440.001-0.091-0.2370.000
25A22LEU0-0.017-0.0156.5320.3370.3370.0000.0000.0000.000
26A23PHE0-0.070-0.0328.5880.1350.1350.0000.0000.0000.000
27A24GLU-1-0.928-0.9789.9260.4810.4810.0000.0000.0000.000
28A25LYS10.9090.9535.102-3.366-3.3660.0000.0000.0000.000
29A26GLY00.0190.0208.3390.0980.0980.0000.0000.0000.000
30A27TYR0-0.056-0.0349.2630.0160.0160.0000.0000.0000.000
31A28GLU-1-0.904-0.94312.196-0.046-0.0460.0000.0000.0000.000
32A29ASP-1-0.836-0.91414.5730.2280.2280.0000.0000.0000.000
33A30LYS10.9280.95214.441-0.404-0.4040.0000.0000.0000.000
34A31GLU-1-0.901-0.95417.4970.0860.0860.0000.0000.0000.000
35A32SER0-0.060-0.03519.654-0.026-0.0260.0000.0000.0000.000
36A33VAL00.0050.00715.655-0.025-0.0250.0000.0000.0000.000
37A34LEU0-0.0120.01819.066-0.028-0.0280.0000.0000.0000.000
38A35LYS10.9340.96821.511-0.086-0.0860.0000.0000.0000.000
39A36SER0-0.037-0.01720.883-0.016-0.0160.0000.0000.0000.000
40A37ASN00.1030.08523.3500.0030.0030.0000.0000.0000.000
41A38ILE00.0410.03016.885-0.017-0.0170.0000.0000.0000.000
42A39LEU00.0440.01220.748-0.023-0.0230.0000.0000.0000.000
43A40TYR0-0.021-0.01822.815-0.008-0.0080.0000.0000.0000.000
44A41ASP-1-0.826-0.87119.174-0.141-0.1410.0000.0000.0000.000
45A42VAL00.0160.02218.429-0.021-0.0210.0000.0000.0000.000
46A43LEU0-0.063-0.03120.261-0.015-0.0150.0000.0000.0000.000
47A44ARG10.7990.87022.2250.1450.1450.0000.0000.0000.000
48A45ASN0-0.023-0.00116.433-0.013-0.0130.0000.0000.0000.000
49A46ASN0-0.026-0.02020.4710.0390.0390.0000.0000.0000.000
50A47ASN00.0140.02817.1710.0440.0440.0000.0000.0000.000
51A48ASP-1-0.807-0.91420.540-0.151-0.1510.0000.0000.0000.000
52A49GLU-1-0.851-0.91719.178-0.187-0.1870.0000.0000.0000.000
53A50ALA0-0.009-0.01016.6060.0180.0180.0000.0000.0000.000
54A51ARG10.9130.96718.3050.1500.1500.0000.0000.0000.000
55A52TYR0-0.007-0.00421.0390.0250.0250.0000.0000.0000.000
56A53LYS10.8790.92618.1640.1720.1720.0000.0000.0000.000
57A54ILE00.0240.01215.2760.0330.0330.0000.0000.0000.000
58A55SER0-0.032-0.01518.4280.0280.0280.0000.0000.0000.000
59A56MET0-0.032-0.01021.8900.0220.0220.0000.0000.0000.000
60A57PHE0-0.021-0.00116.2740.0160.0160.0000.0000.0000.000
61A58LEU00.020-0.00417.8060.0250.0250.0000.0000.0000.000
62A59ILE0-0.011-0.00320.8960.0140.0140.0000.0000.0000.000
63A60ASN0-0.044-0.02723.2620.0050.0050.0000.0000.0000.000
64A61LYS10.8830.95418.827-0.142-0.1420.0000.0000.0000.000
65A62GLY0-0.022-0.00322.8870.0100.0100.0000.0000.0000.000
66A63ALA0-0.028-0.00622.189-0.001-0.0010.0000.0000.0000.000
67A64ASP-1-0.840-0.92824.149-0.006-0.0060.0000.0000.0000.000
68A65ILE00.0060.00326.717-0.010-0.0100.0000.0000.0000.000
69A66LYS10.8410.93029.134-0.008-0.0080.0000.0000.0000.000
70A67SER0-0.092-0.07627.462-0.004-0.0040.0000.0000.0000.000
71A68ARG10.8330.90630.1710.0200.0200.0000.0000.0000.000
72A69THR00.0180.02428.6850.0040.0040.0000.0000.0000.000
73A70LYS11.0171.00530.6940.0600.0600.0000.0000.0000.000
74A71GLU-1-0.939-0.97232.226-0.059-0.0590.0000.0000.0000.000
75A72GLY0-0.096-0.05434.2380.0020.0020.0000.0000.0000.000
76A73THR0-0.019-0.00831.8360.0050.0050.0000.0000.0000.000
77A74THR00.0700.03831.730-0.002-0.0020.0000.0000.0000.000
78A75LEU00.1240.04526.643-0.008-0.0080.0000.0000.0000.000
79A76PHE00.029-0.00229.573-0.007-0.0070.0000.0000.0000.000
80A77PHE0-0.0110.00031.170-0.004-0.0040.0000.0000.0000.000
81A78PRO0-0.013-0.00126.554-0.004-0.0040.0000.0000.0000.000
82A79LEU00.0190.02928.192-0.009-0.0090.0000.0000.0000.000
83A80PHE00.023-0.01229.150-0.003-0.0030.0000.0000.0000.000
84A81GLN0-0.060-0.02630.0510.0040.0040.0000.0000.0000.000
85A82GLY00.0410.01927.451-0.003-0.0030.0000.0000.0000.000
86A83GLY0-0.007-0.00127.869-0.008-0.0080.0000.0000.0000.000
87A84GLY0-0.024-0.01429.6280.0050.0050.0000.0000.0000.000
88A85ASN0-0.031-0.01027.9180.0140.0140.0000.0000.0000.000
89A86ASP-1-0.792-0.88226.798-0.105-0.1050.0000.0000.0000.000
90A87ILE00.0300.01829.4580.0050.0050.0000.0000.0000.000
91A88THR00.0280.02130.8090.0090.0090.0000.0000.0000.000
92A89GLY00.0480.03028.0840.0070.0070.0000.0000.0000.000
93A90THR0-0.031-0.03429.0120.0030.0030.0000.0000.0000.000
94A91THR0-0.063-0.04830.5060.0070.0070.0000.0000.0000.000
95A92GLU-1-0.898-0.95929.854-0.026-0.0260.0000.0000.0000.000
96A93LEU00.0280.01825.5230.0060.0060.0000.0000.0000.000
97A94CYS0-0.060-0.01229.7130.0070.0070.0000.0000.0000.000
98A95LYS10.8950.94732.9800.0230.0230.0000.0000.0000.000
99A96ILE00.0420.02628.8090.0060.0060.0000.0000.0000.000
100A97PHE0-0.005-0.02126.7990.0050.0050.0000.0000.0000.000
101A98LEU0-0.042-0.02232.1410.0040.0040.0000.0000.0000.000
102A99GLU-1-0.903-0.94034.527-0.007-0.0070.0000.0000.0000.000
103A100LYS10.9010.95729.192-0.005-0.0050.0000.0000.0000.000
104A101GLY0-0.026-0.02133.8020.0030.0030.0000.0000.0000.000
105A102ALA0-0.0120.00732.5230.0000.0000.0000.0000.0000.000
106A103ASP-1-0.812-0.90334.602-0.023-0.0230.0000.0000.0000.000
107A104ILE0-0.003-0.00536.942-0.003-0.0030.0000.0000.0000.000
108A105THR0-0.077-0.05038.159-0.002-0.0020.0000.0000.0000.000
109A106ALA0-0.030-0.00338.1790.0000.0000.0000.0000.0000.000
110A107LEU0-0.020-0.01239.139-0.003-0.0030.0000.0000.0000.000
111A108TYR00.0230.01833.4610.0000.0000.0000.0000.0000.000
112A109LYS10.9660.94537.8140.0310.0310.0000.0000.0000.000
113A110PRO00.0040.02235.6230.0020.0020.0000.0000.0000.000
114A111TYR0-0.001-0.01437.157-0.001-0.0010.0000.0000.0000.000
115A112LYS10.8960.96940.8600.0350.0350.0000.0000.0000.000
116A113ILE00.0360.02937.6960.0010.0010.0000.0000.0000.000
117A114VAL00.0300.01240.3410.0000.0000.0000.0000.0000.000
118A115VAL00.0200.01734.744-0.004-0.0040.0000.0000.0000.000
119A116PHE00.0770.02835.880-0.005-0.0050.0000.0000.0000.000
120A117LYS10.9050.97037.6560.0540.0540.0000.0000.0000.000
121A118ASN00.0260.00633.3750.0030.0030.0000.0000.0000.000
122A119ILE00.0330.02535.576-0.002-0.0020.0000.0000.0000.000
123A120PHE0-0.077-0.04137.5760.0010.0010.0000.0000.0000.000
124A121ASN0-0.025-0.03137.5770.0050.0050.0000.0000.0000.000
125A122TYR0-0.052-0.02532.892-0.003-0.0030.0000.0000.0000.000
126A123PHE00.0090.00836.4510.0060.0060.0000.0000.0000.000
127A124VAL00.0480.01935.235-0.003-0.0030.0000.0000.0000.000
128A125ASP-1-0.850-0.92438.409-0.048-0.0480.0000.0000.0000.000
129A126GLU-1-0.715-0.88940.877-0.046-0.0460.0000.0000.0000.000
130A127ASN0-0.029-0.00742.8620.0040.0040.0000.0000.0000.000
131A128GLU-1-0.924-0.97436.871-0.066-0.0660.0000.0000.0000.000
132A129MET0-0.042-0.00137.645-0.002-0.0020.0000.0000.0000.000
133A130ILE0-0.0200.00240.0300.0030.0030.0000.0000.0000.000
134A131PRO0-0.004-0.00438.3540.0030.0030.0000.0000.0000.000
135A132LEU00.0660.03235.5620.0030.0030.0000.0000.0000.000
136A133TYR0-0.025-0.04338.6500.0010.0010.0000.0000.0000.000
137A134LYS10.9340.96342.0760.0300.0300.0000.0000.0000.000
138A135LEU0-0.0110.03336.4190.0030.0030.0000.0000.0000.000
139A136ILE00.0430.01238.0910.0030.0030.0000.0000.0000.000
140A137PHE0-0.028-0.02341.2130.0020.0020.0000.0000.0000.000
141A138SER0-0.066-0.04543.3890.0030.0030.0000.0000.0000.000
142A139GLN0-0.0300.00740.6620.0040.0040.0000.0000.0000.000
143A140SER0-0.0030.02644.115-0.002-0.0020.0000.0000.0000.000
144A141GLY00.0690.02445.3060.0000.0000.0000.0000.0000.000
145A142LEU0-0.030-0.01642.468-0.002-0.0020.0000.0000.0000.000
146A143GLN0-0.039-0.02843.6920.0020.0020.0000.0000.0000.000
147A144LEU00.002-0.01645.719-0.002-0.0020.0000.0000.0000.000
148A145LEU0-0.008-0.00648.051-0.001-0.0010.0000.0000.0000.000
149A146ILE00.0200.02247.4020.0010.0010.0000.0000.0000.000
150A147LYS10.8540.93448.0950.0270.0270.0000.0000.0000.000
151A148ASP-1-0.765-0.89344.365-0.045-0.0450.0000.0000.0000.000
152A149LYS10.8310.91341.9020.0530.0530.0000.0000.0000.000
153A150TRP0-0.038-0.03541.3360.0000.0000.0000.0000.0000.000
154A151GLY0-0.0100.00848.2560.0010.0010.0000.0000.0000.000
155A152LEU0-0.033-0.01046.3650.0010.0010.0000.0000.0000.000
156A153THR00.0170.01847.744-0.001-0.0010.0000.0000.0000.000
157A154ALA00.002-0.01145.193-0.002-0.0020.0000.0000.0000.000
158A155LEU00.0470.01946.571-0.002-0.0020.0000.0000.0000.000
159A156GLU-1-0.917-0.99149.623-0.034-0.0340.0000.0000.0000.000
160A157PHE0-0.024-0.01041.9750.0000.0000.0000.0000.0000.000
161A158VAL00.0330.01745.063-0.002-0.0020.0000.0000.0000.000
162A159LYS10.9310.97947.3290.0330.0330.0000.0000.0000.000
163A160ARG10.9080.96048.5950.0450.0450.0000.0000.0000.000
164A161CYS0-0.0230.02444.829-0.003-0.0030.0000.0000.0000.000
165A162GLN00.029-0.00146.2840.0030.0030.0000.0000.0000.000
166A163LYS10.8400.93340.8100.0600.0600.0000.0000.0000.000
167A164PRO00.0600.03046.8900.0020.0020.0000.0000.0000.000
168A165ILE0-0.006-0.00246.2620.0030.0030.0000.0000.0000.000
169A166ALA00.0220.00744.7260.0020.0020.0000.0000.0000.000
170A167LEU0-0.016-0.00446.6990.0020.0020.0000.0000.0000.000
171A168LYS10.8930.95149.9270.0270.0270.0000.0000.0000.000
172A169MET0-0.013-0.01045.8620.0010.0010.0000.0000.0000.000
173A170MET0-0.031-0.00247.0980.0010.0010.0000.0000.0000.000
174A171GLU-1-0.923-0.96849.583-0.027-0.0270.0000.0000.0000.000
175A172ASP-1-0.872-0.92952.042-0.023-0.0230.0000.0000.0000.000
176A173TYR0-0.080-0.05846.6730.0020.0020.0000.0000.0000.000
177A174ILE00.014-0.00551.3390.0020.0020.0000.0000.0000.000
178A175LYS10.9440.97853.5060.0190.0190.0000.0000.0000.000
179A176LYS10.9100.96850.3660.0180.0180.0000.0000.0000.000
180A177TYR0-0.022-0.02449.5950.0010.0010.0000.0000.0000.000
181A178ASN0-0.027-0.00354.4730.0000.0000.0000.0000.0000.000
182A179LEU0-0.0120.00050.7810.0000.0000.0000.0000.0000.000
183A180LYS10.9010.94855.1800.0170.0170.0000.0000.0000.000
184A181GLU-1-0.867-0.92954.287-0.028-0.0280.0000.0000.0000.000