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: 3Q3KL

Calculation Name: 3T8K-A-Xray318

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: 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 185
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2055567.822587
FMO2-HF: Nuclear repulsion 1980822.232812
FMO2-HF: Total energy -74745.589775
FMO2-MP2: Total energy -74962.590822


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.
-2.289-0.4823.084-1.861-3.0280.001
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 : -0.008 / 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].
3A0ALA 00.1550.0703.8060.0151.406-0.009-0.575-0.8070.000
4A1MET 0-0.091-0.0461.9760.7470.2193.071-1.064-1.4780.001
5A2SER 0-0.092-0.0413.0341.6412.1840.020-0.126-0.4370.000
6A3GLU -1-0.971-0.9785.109-1.450-1.3810.000-0.003-0.0650.000
7A4TYR 0-0.006-0.0047.2770.5560.5560.0000.0000.0000.000
8A5ARG 10.9270.9687.9200.1220.1220.0000.0000.0000.000
9A6THR 00.013-0.00810.3050.1150.1150.0000.0000.0000.000
10A7VAL 00.0420.00611.747-0.091-0.0910.0000.0000.0000.000
11A8SER 0-0.064-0.06812.919-0.051-0.0510.0000.0000.0000.000
12A9ALA 0-0.011-0.00612.585-0.012-0.0120.0000.0000.0000.000
13A10ALA 00.0630.03110.142-0.035-0.0350.0000.0000.0000.000
14A11ALA 0-0.028-0.01712.0290.0030.0030.0000.0000.0000.000
15A12MET 0-0.049-0.01415.3320.0290.0290.0000.0000.0000.000
16A13LEU 0-0.061-0.03214.0790.0170.0170.0000.0000.0000.000
17A14GLY 00.0350.04212.093-0.043-0.0430.0000.0000.0000.000
18A15THR 00.002-0.00610.9450.1600.1600.0000.0000.0000.000
19A16TYR 0-0.005-0.02112.8100.0180.0180.0000.0000.0000.000
20A17GLU -1-0.879-0.9579.703-0.204-0.2040.0000.0000.0000.000
21A18ASP -1-0.776-0.8888.149-1.126-1.1260.0000.0000.0000.000
22A19PHE 0-0.023-0.0268.6580.0790.0790.0000.0000.0000.000
23A20LEU 0-0.030-0.01811.0480.1050.1050.0000.0000.0000.000
24A21GLU -1-0.939-0.9634.145-0.342-0.0100.002-0.093-0.2410.000
25A22LEU 0-0.020-0.0176.5320.3320.3320.0000.0000.0000.000
26A23PHE 0-0.068-0.0308.5880.1360.1360.0000.0000.0000.000
27A24GLU -1-0.932-0.9799.9260.4820.4820.0000.0000.0000.000
28A25LYS 10.9130.9535.102-3.354-3.3540.0000.0000.0000.000
29A26GLY 00.0150.0198.3390.0870.0870.0000.0000.0000.000
30A27TYR 0-0.053-0.0339.2630.0160.0160.0000.0000.0000.000
31A28GLU -1-0.900-0.94112.196-0.051-0.0510.0000.0000.0000.000
32A29ASP -1-0.840-0.91614.5730.2240.2240.0000.0000.0000.000
33A30LYS 10.9280.95214.441-0.400-0.4000.0000.0000.0000.000
34A31GLU -1-0.898-0.95217.4970.0840.0840.0000.0000.0000.000
35A32SER 0-0.060-0.03419.654-0.027-0.0270.0000.0000.0000.000
36A33VAL 00.0020.00515.654-0.025-0.0250.0000.0000.0000.000
37A34LEU 0-0.0100.01919.066-0.028-0.0280.0000.0000.0000.000
38A35LYS 10.9380.97021.511-0.085-0.0850.0000.0000.0000.000
39A36SER 0-0.039-0.01820.883-0.016-0.0160.0000.0000.0000.000
40A37ASN 00.1010.08423.3500.0030.0030.0000.0000.0000.000
41A38ILE 00.0440.03116.885-0.017-0.0170.0000.0000.0000.000
42A39LEU 00.0420.01120.748-0.023-0.0230.0000.0000.0000.000
43A40TYR 0-0.021-0.01822.815-0.009-0.0090.0000.0000.0000.000
44A41ASP -1-0.827-0.87019.174-0.140-0.1400.0000.0000.0000.000
45A42VAL 00.0130.02118.429-0.021-0.0210.0000.0000.0000.000
46A43LEU 0-0.063-0.03020.261-0.014-0.0140.0000.0000.0000.000
47A44ARG 10.7970.87022.2250.1420.1420.0000.0000.0000.000
48A45ASN 0-0.0180.00116.433-0.014-0.0140.0000.0000.0000.000
49A46ASN 0-0.025-0.01920.4710.0380.0380.0000.0000.0000.000
50A47ASN 00.0110.02617.1710.0430.0430.0000.0000.0000.000
51A48ASP -1-0.806-0.91420.540-0.146-0.1460.0000.0000.0000.000
52A49GLU -1-0.852-0.91719.178-0.182-0.1820.0000.0000.0000.000
53A50ALA 0-0.005-0.00916.6060.0170.0170.0000.0000.0000.000
54A51ARG 10.9110.96718.3050.1480.1480.0000.0000.0000.000
55A52TYR 0-0.009-0.00421.0390.0250.0250.0000.0000.0000.000
56A53LYS 10.8790.92618.1640.1660.1660.0000.0000.0000.000
57A54ILE 00.0240.01115.2760.0330.0330.0000.0000.0000.000
58A55SER 0-0.030-0.01418.4280.0290.0290.0000.0000.0000.000
59A56MET 0-0.035-0.01121.8900.0230.0230.0000.0000.0000.000
60A57PHE 0-0.0200.00016.2740.0170.0170.0000.0000.0000.000
61A58LEU 00.018-0.00517.8050.0250.0250.0000.0000.0000.000
62A59ILE 0-0.007-0.00120.8960.0140.0140.0000.0000.0000.000
63A60ASN 0-0.047-0.02823.2620.0050.0050.0000.0000.0000.000
64A61LYS 10.8780.95218.826-0.141-0.1410.0000.0000.0000.000
65A62GLY 0-0.016-0.00122.8870.0100.0100.0000.0000.0000.000
66A63ALA 0-0.030-0.00822.189-0.001-0.0010.0000.0000.0000.000
67A64ASP -1-0.836-0.92624.149-0.006-0.0060.0000.0000.0000.000
68A65ILE 00.0020.00126.717-0.011-0.0110.0000.0000.0000.000
69A66LYS 10.8420.93129.134-0.008-0.0080.0000.0000.0000.000
70A67SER 0-0.094-0.07727.463-0.004-0.0040.0000.0000.0000.000
71A68ARG 10.8340.90630.1710.0190.0190.0000.0000.0000.000
72A69THR 00.0130.02128.6850.0040.0040.0000.0000.0000.000
73A70LYS 11.0231.00830.6940.0590.0590.0000.0000.0000.000
74A71GLU -1-0.942-0.97332.226-0.059-0.0590.0000.0000.0000.000
75A72GLY 0-0.093-0.05334.2400.0020.0020.0000.0000.0000.000
76A73THR 0-0.016-0.00631.8360.0040.0040.0000.0000.0000.000
77A74THR 00.0700.03631.730-0.002-0.0020.0000.0000.0000.000
78A75LEU 00.1180.04226.643-0.008-0.0080.0000.0000.0000.000
79A76PHE 00.031-0.00129.573-0.007-0.0070.0000.0000.0000.000
80A77PHE 0-0.013-0.00131.171-0.004-0.0040.0000.0000.0000.000
81A78PRO 0-0.0080.00226.554-0.004-0.0040.0000.0000.0000.000
82A79LEU 00.0140.02728.192-0.008-0.0080.0000.0000.0000.000
83A80PHE 00.025-0.01129.150-0.003-0.0030.0000.0000.0000.000
84A81GLN 0-0.061-0.02630.0510.0040.0040.0000.0000.0000.000
85A82GLY 00.0450.02127.451-0.004-0.0040.0000.0000.0000.000
86A83GLY 0-0.007-0.00327.869-0.008-0.0080.0000.0000.0000.000
87A84GLY 0-0.026-0.01429.6280.0050.0050.0000.0000.0000.000
88A85ASN 0-0.030-0.01027.9180.0130.0130.0000.0000.0000.000
89A86ASP -1-0.791-0.88226.798-0.102-0.1020.0000.0000.0000.000
90A87ILE 00.0310.01729.4580.0050.0050.0000.0000.0000.000
91A88THR 00.0300.02330.8090.0090.0090.0000.0000.0000.000
92A89GLY 00.0460.02728.0840.0070.0070.0000.0000.0000.000
93A90THR 0-0.034-0.03629.0120.0030.0030.0000.0000.0000.000
94A91THR 0-0.061-0.04730.5060.0070.0070.0000.0000.0000.000
95A92GLU -1-0.899-0.96029.853-0.024-0.0240.0000.0000.0000.000
96A93LEU 00.0260.01725.5240.0060.0060.0000.0000.0000.000
97A94CYS 0-0.057-0.01129.7130.0070.0070.0000.0000.0000.000
98A95LYS 10.8980.94832.9800.0220.0220.0000.0000.0000.000
99A96ILE 00.0400.02528.8250.0060.0060.0000.0000.0000.000
100A97PHE 0-0.007-0.02226.7990.0050.0050.0000.0000.0000.000
101A98LEU 0-0.043-0.02232.1410.0040.0040.0000.0000.0000.000
102A99GLU -1-0.900-0.93934.527-0.007-0.0070.0000.0000.0000.000
103A100LYS 10.8980.95529.191-0.006-0.0060.0000.0000.0000.000
104A101GLY 0-0.025-0.02133.8020.0030.0030.0000.0000.0000.000
105A102ALA 0-0.0130.00632.5240.0000.0000.0000.0000.0000.000
106A103ASP -1-0.814-0.90434.602-0.023-0.0230.0000.0000.0000.000
107A104ILE 0-0.006-0.00636.942-0.004-0.0040.0000.0000.0000.000
108A105THR 0-0.073-0.04938.159-0.002-0.0020.0000.0000.0000.000
109A106ALA 0-0.030-0.00338.1790.0000.0000.0000.0000.0000.000
110A107LEU 0-0.023-0.01439.139-0.003-0.0030.0000.0000.0000.000
111A108TYR 00.0270.02033.4620.0000.0000.0000.0000.0000.000
112A109LYS 10.9650.94537.8140.0310.0310.0000.0000.0000.000
113A110PRO 00.0030.02235.6230.0020.0020.0000.0000.0000.000
114A111TYR 0-0.001-0.01437.157-0.001-0.0010.0000.0000.0000.000
115A112LYS 10.8970.96940.8600.0340.0340.0000.0000.0000.000
116A113ILE 00.0340.02837.6960.0010.0010.0000.0000.0000.000
117A114VAL 00.0340.01340.3410.0000.0000.0000.0000.0000.000
118A115VAL 00.0200.01934.744-0.004-0.0040.0000.0000.0000.000
119A116PHE 00.0750.02635.880-0.005-0.0050.0000.0000.0000.000
120A117LYS 10.9060.97137.6560.0530.0530.0000.0000.0000.000
121A118ASN 00.0260.00533.3750.0030.0030.0000.0000.0000.000
122A119ILE 00.0310.02435.576-0.002-0.0020.0000.0000.0000.000
123A120PHE 0-0.077-0.04037.5760.0010.0010.0000.0000.0000.000
124A121ASN 0-0.024-0.03137.5770.0040.0040.0000.0000.0000.000
125A122TYR 0-0.051-0.02532.892-0.003-0.0030.0000.0000.0000.000
126A123PHE 00.0090.00936.4510.0060.0060.0000.0000.0000.000
127A124VAL 00.0470.01835.235-0.003-0.0030.0000.0000.0000.000
128A125ASP -1-0.851-0.92438.409-0.047-0.0470.0000.0000.0000.000
129A126GLU -1-0.716-0.88940.877-0.044-0.0440.0000.0000.0000.000
130A127ASN 0-0.028-0.00642.8620.0040.0040.0000.0000.0000.000
131A128GLU -1-0.923-0.97436.871-0.064-0.0640.0000.0000.0000.000
132A129MET 0-0.043-0.00237.652-0.002-0.0020.0000.0000.0000.000
133A130ILE 0-0.0180.00340.0300.0030.0030.0000.0000.0000.000
134A131PRO 0-0.007-0.00538.3540.0030.0030.0000.0000.0000.000
135A132LEU 00.0690.03235.5620.0030.0030.0000.0000.0000.000
136A133TYR 0-0.028-0.04538.6500.0010.0010.0000.0000.0000.000
137A134LYS 10.9350.96342.0760.0290.0290.0000.0000.0000.000
138A135LEU 0-0.0090.03436.4190.0030.0030.0000.0000.0000.000
139A136ILE 00.0440.01238.0910.0030.0030.0000.0000.0000.000
140A137PHE 0-0.030-0.02341.2130.0020.0020.0000.0000.0000.000
141A138SER 0-0.063-0.04443.3890.0030.0030.0000.0000.0000.000
142A139GLN 0-0.0320.00540.6620.0040.0040.0000.0000.0000.000
143A140SER 00.0000.02744.115-0.002-0.0020.0000.0000.0000.000
144A141GLY 00.0660.02345.3060.0000.0000.0000.0000.0000.000
145A142LEU 0-0.029-0.01642.468-0.002-0.0020.0000.0000.0000.000
146A143GLN 0-0.037-0.02643.6920.0010.0010.0000.0000.0000.000
147A144LEU 00.001-0.01545.716-0.002-0.0020.0000.0000.0000.000
148A145LEU 0-0.003-0.00148.051-0.001-0.0010.0000.0000.0000.000
149A146ILE 00.0170.01647.4020.0010.0010.0000.0000.0000.000
150A147LYS 10.8620.93848.0950.0270.0270.0000.0000.0000.000
151A148ASP -1-0.767-0.89344.365-0.044-0.0440.0000.0000.0000.000
152A149LYS 10.8340.91541.9020.0530.0530.0000.0000.0000.000
153A150TRP 0-0.040-0.03541.3360.0000.0000.0000.0000.0000.000
154A151GLY 0-0.0080.00848.2560.0010.0010.0000.0000.0000.000
155A152LEU 0-0.035-0.01146.3650.0010.0010.0000.0000.0000.000
156A153THR 00.0140.01647.744-0.001-0.0010.0000.0000.0000.000
157A154ALA 00.005-0.00945.193-0.002-0.0020.0000.0000.0000.000
158A155LEU 00.0430.01746.571-0.001-0.0010.0000.0000.0000.000
159A156GLU -1-0.915-0.99049.623-0.034-0.0340.0000.0000.0000.000
160A157PHE 0-0.024-0.01141.9750.0000.0000.0000.0000.0000.000
161A158VAL 00.0390.01945.063-0.001-0.0010.0000.0000.0000.000
162A159LYS 10.9210.97547.3290.0320.0320.0000.0000.0000.000
163A160ARG 10.9130.96348.5940.0440.0440.0000.0000.0000.000
164A161CYS 0-0.0230.02344.829-0.003-0.0030.0000.0000.0000.000
165A162GLN 00.0300.00046.2840.0030.0030.0000.0000.0000.000
166A163LYS 10.8390.93240.8100.0590.0590.0000.0000.0000.000
167A164PRO 00.0590.03046.8900.0020.0020.0000.0000.0000.000
168A165ILE 0-0.004-0.00246.2610.0030.0030.0000.0000.0000.000
169A166ALA 00.0220.00644.7250.0020.0020.0000.0000.0000.000
170A167LEU 0-0.014-0.00346.6990.0020.0020.0000.0000.0000.000
171A168LYS 10.8950.95249.9270.0260.0260.0000.0000.0000.000
172A169MET 0-0.014-0.01045.8540.0010.0010.0000.0000.0000.000
173A170MET 0-0.031-0.00347.1170.0010.0010.0000.0000.0000.000
174A171GLU -1-0.927-0.96949.582-0.027-0.0270.0000.0000.0000.000
175A172ASP -1-0.869-0.92952.042-0.022-0.0220.0000.0000.0000.000
176A173TYR 0-0.083-0.05946.6730.0020.0020.0000.0000.0000.000
177A174ILE 00.013-0.00651.3420.0020.0020.0000.0000.0000.000
178A175LYS 10.9480.98053.5060.0190.0190.0000.0000.0000.000
179A176LYS 10.9090.96750.3660.0170.0170.0000.0000.0000.000
180A177TYR 0-0.028-0.02749.5950.0010.0010.0000.0000.0000.000
181A178ASN 0-0.022-0.00154.4730.0000.0000.0000.0000.0000.000
182A179LEU 0-0.012-0.00150.7810.0000.0000.0000.0000.0000.000
183A180LYS 10.8990.94355.1800.0170.0170.0000.0000.0000.000
184A181GLU -1-0.874-0.94554.287-0.028-0.0280.0000.0000.0000.000
185A182NME 0-0.0080.01353.6200.0010.0010.0000.0000.0000.000