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: 2K15R

Calculation Name: 1T3B-A-Xray310

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: 2021-09-06

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. 1.20200116
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 -2311348.025272
FMO2-HF: Nuclear repulsion 2230042.519401
FMO2-HF: Total energy -81305.50587
FMO2-MP2: Total energy -81544.515906


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.
0.6521.8850.009-0.652-0.5910.001
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 : 0.023 / 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 00.0190.0153.6500.3401.2370.005-0.445-0.4570.001
4A4ALA 00.0080.0084.673-0.184-0.1200.000-0.004-0.0600.000
5A5ILE 00.0450.0165.359-0.231-0.2310.0000.0000.0000.000
6A6LYS 10.9390.9668.2160.6660.6660.0000.0000.0000.000
7A7ARG 10.9450.98310.2210.1600.1600.0000.0000.0000.000
8A8LYS 10.8880.9369.5170.3660.3660.0000.0000.0000.000
9A9LEU 00.0290.02411.3980.0020.0020.0000.0000.0000.000
10A10GLN 00.0210.01514.9050.0090.0090.0000.0000.0000.000
11A11SER 0-0.062-0.02616.6530.0340.0340.0000.0000.0000.000
12A12PHE 0-0.027-0.03017.9130.0040.0040.0000.0000.0000.000
13A13ASN 0-0.0260.00119.706-0.006-0.0060.0000.0000.0000.000
14A14ILE 0-0.028-0.00116.204-0.008-0.0080.0000.0000.0000.000
15A15SER 0-0.017-0.02217.869-0.005-0.0050.0000.0000.0000.000
16A16ASN 0-0.050-0.05317.332-0.033-0.0330.0000.0000.0000.000
17A17ILE 0-0.0010.02811.274-0.045-0.0450.0000.0000.0000.000
18A18VAL 0-0.010-0.01312.181-0.014-0.0140.0000.0000.0000.000
19A19ILE 0-0.062-0.0196.455-0.027-0.0270.0000.0000.0000.000
20A20LYS 10.9530.9599.0450.4970.4970.0000.0000.0000.000
21A21SER 0-0.003-0.0069.088-0.199-0.1990.0000.0000.0000.000
22A22SER 00.024-0.0289.3770.1440.1440.0000.0000.0000.000
23A23PRO 0-0.054-0.02411.381-0.006-0.0060.0000.0000.0000.000
24A24ILE 0-0.010-0.01212.3360.0610.0610.0000.0000.0000.000
25A25SER 00.1150.0549.077-0.106-0.1060.0000.0000.0000.000
26A26GLY 0-0.004-0.0067.7570.0570.0570.0000.0000.0000.000
27A27ILE 00.0380.0298.470-0.089-0.0890.0000.0000.0000.000
28A28LYS 10.8360.9764.2412.7102.9090.000-0.101-0.0990.000
29A29THR 00.022-0.0018.6620.1070.1070.0000.0000.0000.000
30A30ALA 0-0.057-0.01211.262-0.029-0.0290.0000.0000.0000.000
31A31VAL 00.0250.01112.4620.0970.0970.0000.0000.0000.000
32A32THR 0-0.028-0.01414.7120.0080.0080.0000.0000.0000.000
33A33ASP -1-0.834-0.91516.942-0.169-0.1690.0000.0000.0000.000
34A34GLN 00.0670.03518.8460.0050.0050.0000.0000.0000.000
35A35GLY 00.0140.01719.9750.0160.0160.0000.0000.0000.000
36A36ILE 0-0.052-0.02216.524-0.038-0.0380.0000.0000.0000.000
37A37LEU 00.0150.03114.9940.0080.0080.0000.0000.0000.000
38A38TYR 00.020-0.00312.922-0.058-0.0580.0000.0000.0000.000
39A39VAL 0-0.021-0.0069.5530.0740.0740.0000.0000.0000.000
40A40SER 00.013-0.0199.302-0.141-0.1410.0000.0000.0000.000
41A41GLU -1-0.927-0.9553.860-3.090-3.0170.004-0.1020.0250.000
42A42ASP -1-0.824-0.8795.621-0.283-0.2830.0000.0000.0000.000
43A43GLY 00.018-0.0068.1500.0290.0290.0000.0000.0000.000
44A44LYS 10.8400.9149.9530.2480.2480.0000.0000.0000.000
45A45TYR 00.019-0.00712.9100.0460.0460.0000.0000.0000.000
46A46LEU 00.0530.01713.434-0.091-0.0910.0000.0000.0000.000
47A47PHE 0-0.0290.00514.3610.0520.0520.0000.0000.0000.000
48A48GLU -1-0.947-0.97817.567-0.236-0.2360.0000.0000.0000.000
49A49GLY 00.011-0.00119.7880.0260.0260.0000.0000.0000.000
50A50LYS 10.9280.95620.9770.1480.1480.0000.0000.0000.000
51A51LEU 0-0.0070.01016.1420.0140.0140.0000.0000.0000.000
52A52TYR 0-0.049-0.03219.9520.0020.0020.0000.0000.0000.000
53A53GLU -1-0.759-0.89420.918-0.135-0.1350.0000.0000.0000.000
54A54LEU 0-0.050-0.02423.3130.0040.0040.0000.0000.0000.000
55A55THR 0-0.018-0.01125.2740.0060.0060.0000.0000.0000.000
56A56ASN 0-0.087-0.04726.9590.0070.0070.0000.0000.0000.000
57A57ASN 00.0110.00630.3370.0010.0010.0000.0000.0000.000
58A58GLY 00.0750.04029.9000.0040.0040.0000.0000.0000.000
59A59PRO 0-0.040-0.01527.179-0.007-0.0070.0000.0000.0000.000
60A60VAL 00.0010.00824.110-0.004-0.0040.0000.0000.0000.000
61A61ASP -1-0.863-0.93021.435-0.222-0.2220.0000.0000.0000.000
62A62VAL 00.0700.03816.4710.0000.0000.0000.0000.0000.000
63A63ALA 0-0.050-0.05418.880-0.014-0.0140.0000.0000.0000.000
64A64GLY 00.0170.02219.7750.0110.0110.0000.0000.0000.000
65A65LYS 10.9300.94719.7160.1430.1430.0000.0000.0000.000
66A66ILE 0-0.0260.00015.127-0.008-0.0080.0000.0000.0000.000
67A67LEU 0-0.005-0.00718.9240.0020.0020.0000.0000.0000.000
68A68VAL 00.0030.01022.2090.0110.0110.0000.0000.0000.000
69A69ASP -1-0.873-0.93418.803-0.191-0.1910.0000.0000.0000.000
70A70LYS 10.9110.97021.3210.1870.1870.0000.0000.0000.000
71A71LEU 00.0190.05222.4150.0130.0130.0000.0000.0000.000
72A72ASN 00.0820.03124.5440.0160.0160.0000.0000.0000.000
73A73SER 0-0.143-0.09722.4260.0110.0110.0000.0000.0000.000
74A74TYR 00.053-0.00324.4390.0000.0000.0000.0000.0000.000
75A75LYS 10.9700.95227.8420.0670.0670.0000.0000.0000.000
76A76ASP -1-0.953-0.96629.578-0.055-0.0550.0000.0000.0000.000
77A77GLU -1-0.898-0.95729.298-0.080-0.0800.0000.0000.0000.000
78A78MET 0-0.092-0.02929.1860.0020.0020.0000.0000.0000.000
79A79ILE 0-0.0080.00934.3740.0040.0040.0000.0000.0000.000
80A80VAL 0-0.034-0.03535.4280.0000.0000.0000.0000.0000.000
81A81TYR 0-0.013-0.01338.3180.0030.0030.0000.0000.0000.000
82A82PRO 0-0.004-0.01038.815-0.001-0.0010.0000.0000.0000.000
83A83ALA 00.0640.05140.5500.0020.0020.0000.0000.0000.000
84A84LYS 10.7730.88742.1640.0280.0280.0000.0000.0000.000
85A85ASN 0-0.004-0.02540.092-0.001-0.0010.0000.0000.0000.000
86A86GLU -1-0.954-0.95835.178-0.047-0.0470.0000.0000.0000.000
87A87LYS 10.9040.95838.4740.0340.0340.0000.0000.0000.000
88A88HIS 10.8750.93436.1590.0460.0460.0000.0000.0000.000
89A89VAL 00.0540.03632.7950.0020.0020.0000.0000.0000.000
90A90VAL 00.0070.01833.325-0.006-0.0060.0000.0000.0000.000
91A91THR 00.0330.01131.7500.0030.0030.0000.0000.0000.000
92A92VAL 0-0.0110.00434.099-0.002-0.0020.0000.0000.0000.000
93A93PHE 0-0.023-0.00330.4890.0010.0010.0000.0000.0000.000
94A94MET 00.010-0.01336.5710.0030.0030.0000.0000.0000.000
95A95ASP -1-0.813-0.92739.756-0.053-0.0530.0000.0000.0000.000
96A96ILE 00.0980.02842.3620.0010.0010.0000.0000.0000.000
97A97THR 0-0.063-0.01645.4830.0020.0020.0000.0000.0000.000
98A101CYS 0-0.079-0.02143.619-0.001-0.0010.0000.0000.0000.000
99A99HIS 00.0330.02747.0920.0010.0010.0000.0000.0000.000
100A100TYR 00.0540.01846.3670.0010.0010.0000.0000.0000.000
101A102HIS 00.0280.02545.0900.0010.0010.0000.0000.0000.000
102A103LEU 0-0.023-0.01348.2230.0010.0010.0000.0000.0000.000
103A104LEU 0-0.029-0.03141.6130.0010.0010.0000.0000.0000.000
104A105HIS 00.0580.01644.4360.0010.0010.0000.0000.0000.000
105A106GLN 0-0.017-0.01446.6030.0010.0010.0000.0000.0000.000
106A107GLN 0-0.045-0.03548.0240.0020.0020.0000.0000.0000.000
107A108LEU 00.0060.03743.003-0.001-0.0010.0000.0000.0000.000
108A109LYS 10.8050.90046.0630.0290.0290.0000.0000.0000.000
109A110GLU -1-0.712-0.84248.276-0.030-0.0300.0000.0000.0000.000
110A111TYR 0-0.047-0.04243.0330.0000.0000.0000.0000.0000.000
111A112ASN 00.0410.00643.178-0.002-0.0020.0000.0000.0000.000
112A113ASP -1-0.909-0.94644.736-0.028-0.0280.0000.0000.0000.000
113A114LEU 0-0.048-0.01444.7230.0010.0010.0000.0000.0000.000
114A115GLY 0-0.061-0.02442.592-0.001-0.0010.0000.0000.0000.000
115A116ILE 00.019-0.00238.839-0.003-0.0030.0000.0000.0000.000
116A117THR 00.0150.00436.6110.0020.0020.0000.0000.0000.000
117A118VAL 0-0.0070.00437.450-0.004-0.0040.0000.0000.0000.000
118A119ARG 10.8850.93429.3140.0780.0780.0000.0000.0000.000
119A120TYR 00.0020.01435.757-0.004-0.0040.0000.0000.0000.000
120A121LEU 00.0150.02230.642-0.001-0.0010.0000.0000.0000.000
121A122ALA 00.0100.00434.8690.0030.0030.0000.0000.0000.000
122A123PHE 0-0.013-0.02533.947-0.005-0.0050.0000.0000.0000.000
123A124PRO 0-0.004-0.00436.8480.0030.0030.0000.0000.0000.000
124A125ARG 10.9420.98439.0940.0490.0490.0000.0000.0000.000
125A126ALA 00.0010.03340.556-0.002-0.0020.0000.0000.0000.000
126A127GLY 00.019-0.01038.9420.0020.0020.0000.0000.0000.000
127A128MET 00.0130.02135.9490.0020.0020.0000.0000.0000.000
128A129ASN 0-0.008-0.01839.5230.0020.0020.0000.0000.0000.000
129A130ASN 00.0530.01642.6490.0040.0040.0000.0000.0000.000
130A131GLN 00.0640.02744.881-0.002-0.0020.0000.0000.0000.000
131A132THR 00.0870.04444.3050.0010.0010.0000.0000.0000.000
132A133ALA 0-0.0220.00340.579-0.001-0.0010.0000.0000.0000.000
133A134LYS 10.8460.92641.1760.0460.0460.0000.0000.0000.000
134A135GLN 00.0680.02343.279-0.001-0.0010.0000.0000.0000.000
135A136MET 00.0060.02540.4030.0000.0000.0000.0000.0000.000
136A137GLU -1-0.755-0.86736.396-0.058-0.0580.0000.0000.0000.000
137A138ALA 0-0.058-0.00939.8600.0000.0000.0000.0000.0000.000
138A139ILE 00.001-0.02041.9600.0010.0010.0000.0000.0000.000
139A140TRP 0-0.024-0.03035.7680.0020.0020.0000.0000.0000.000
140A141THR 0-0.035-0.02036.4040.0000.0000.0000.0000.0000.000
141A142ALA 0-0.048-0.00838.7750.0030.0030.0000.0000.0000.000
142A143LYS 10.9580.96140.8640.0260.0260.0000.0000.0000.000
143A144ASP -1-0.877-0.94142.422-0.031-0.0310.0000.0000.0000.000
144A145PRO 00.0490.01338.8610.0010.0010.0000.0000.0000.000
145A146VAL 00.0750.05741.7140.0000.0000.0000.0000.0000.000
146A147PHE 0-0.036-0.00143.7730.0010.0010.0000.0000.0000.000
147A148ALA 0-0.011-0.01044.1470.0000.0000.0000.0000.0000.000
148A149LEU 00.0190.00041.7170.0000.0000.0000.0000.0000.000
149A150ASN 0-0.003-0.00345.222-0.001-0.0010.0000.0000.0000.000
150A151GLU -1-0.880-0.93548.011-0.026-0.0260.0000.0000.0000.000
151A152ALA 0-0.0030.00546.8660.0010.0010.0000.0000.0000.000
152A153GLU -1-0.892-0.96346.431-0.040-0.0400.0000.0000.0000.000
153A154LYS 10.8480.93549.5440.0280.0280.0000.0000.0000.000
154A155GLY 00.0090.01452.0440.0010.0010.0000.0000.0000.000
155A156ASN 0-0.115-0.06552.6250.0010.0010.0000.0000.0000.000
156A157LEU 0-0.002-0.00248.150-0.001-0.0010.0000.0000.0000.000
157A158PRO 0-0.060-0.02046.3630.0010.0010.0000.0000.0000.000
158A159LYS 10.9650.97349.6070.0230.0230.0000.0000.0000.000
159A160GLU -1-0.945-0.95246.398-0.034-0.0340.0000.0000.0000.000
160A161VAL 00.061-0.00244.741-0.001-0.0010.0000.0000.0000.000
161A162LYS 10.8770.98040.3140.0400.0400.0000.0000.0000.000
162A163THR 00.025-0.00738.3000.0000.0000.0000.0000.0000.000
163A164PRO 0-0.107-0.07137.757-0.002-0.0020.0000.0000.0000.000
164A165ASN 0-0.005-0.00832.175-0.006-0.0060.0000.0000.0000.000
165A166ILE 00.0550.03632.090-0.006-0.0060.0000.0000.0000.000
166A167VAL 00.0190.01732.743-0.005-0.0050.0000.0000.0000.000
167A168LYS 10.8660.89630.9380.0880.0880.0000.0000.0000.000
168A169LYS 10.9070.96626.4130.0900.0900.0000.0000.0000.000
169A170HIS 0-0.015-0.00929.306-0.006-0.0060.0000.0000.0000.000
170A171TYR 0-0.010-0.01031.530-0.005-0.0050.0000.0000.0000.000
171A172GLU -1-0.864-0.93328.426-0.110-0.1100.0000.0000.0000.000
172A173LEU 0-0.0210.00825.567-0.009-0.0090.0000.0000.0000.000
173A174GLY 00.0570.01228.133-0.004-0.0040.0000.0000.0000.000
174A175ILE 00.009-0.00130.201-0.001-0.0010.0000.0000.0000.000
175A176GLN 0-0.053-0.01322.7380.0030.0030.0000.0000.0000.000
176A177PHE 0-0.002-0.01226.385-0.007-0.0070.0000.0000.0000.000
177A178GLY 0-0.0220.00628.9800.0030.0030.0000.0000.0000.000
178A179VAL 0-0.067-0.02431.7970.0080.0080.0000.0000.0000.000
179A180ARG 10.9250.95134.5460.0760.0760.0000.0000.0000.000
180A181GLY 0-0.0050.00137.6260.0040.0040.0000.0000.0000.000
181A182THR 0-0.0460.01438.910-0.002-0.0020.0000.0000.0000.000
182A183PRO 00.049-0.00940.6460.0030.0030.0000.0000.0000.000
183A184SER 0-0.040-0.03036.2170.0000.0000.0000.0000.0000.000
184A185ILE 00.0180.02136.097-0.002-0.0020.0000.0000.0000.000
185A186VAL 00.003-0.00529.730-0.002-0.0020.0000.0000.0000.000
186A187THR 00.0450.04230.3470.0040.0040.0000.0000.0000.000
187A188SER 00.0460.01730.194-0.007-0.0070.0000.0000.0000.000
188A189THR 0-0.005-0.01727.708-0.005-0.0050.0000.0000.0000.000
189A190GLY 0-0.033-0.04226.491-0.008-0.0080.0000.0000.0000.000
190A191GLU -1-0.955-0.96527.501-0.084-0.0840.0000.0000.0000.000
191A192LEU 0-0.014-0.02630.352-0.002-0.0020.0000.0000.0000.000
192A193ILE 00.0250.03333.0570.0010.0010.0000.0000.0000.000
193A194GLY 0-0.035-0.02335.8460.0040.0040.0000.0000.0000.000
194A195GLY 00.0590.02937.4470.0010.0010.0000.0000.0000.000
195A196TYR 0-0.043-0.02541.1980.0010.0010.0000.0000.0000.000
196A197LEU 00.0550.02540.4900.0010.0010.0000.0000.0000.000
197A198LYS 10.9491.00844.4180.0340.0340.0000.0000.0000.000
198A199PRO 00.0480.01945.571-0.001-0.0010.0000.0000.0000.000
199A200ALA 00.031-0.00245.088-0.001-0.0010.0000.0000.0000.000
200A201ASP -1-0.889-0.95745.273-0.040-0.0400.0000.0000.0000.000
201A202LEU 0-0.0100.00139.004-0.002-0.0020.0000.0000.0000.000
202A203LEU 0-0.016-0.00940.696-0.003-0.0030.0000.0000.0000.000
203A204ARG 10.9981.00440.9480.0370.0370.0000.0000.0000.000
204A205ALA 00.0160.01739.328-0.002-0.0020.0000.0000.0000.000
205A206LEU 0-0.072-0.03635.466-0.004-0.0040.0000.0000.0000.000
206A207GLU -1-0.996-0.99836.678-0.041-0.0410.0000.0000.0000.000
207A208GLU -1-0.950-0.98138.185-0.044-0.0440.0000.0000.0000.000
208A209THR 0-0.052-0.01933.990-0.002-0.0020.0000.0000.0000.000
209A210ALA 00.0230.02933.268-0.001-0.0010.0000.0000.0000.000
210A211NME 0-0.087-0.05629.922-0.004-0.0040.0000.0000.0000.000