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

tag_button

FMODB ID: 4J1MN

Calculation Name: 1T3B-A-Xray372

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: 2023-09-24

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 OptAll
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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2299871.053824
FMO2-HF: Nuclear repulsion 2218733.499731
FMO2-HF: Total energy -81137.554094
FMO2-MP2: Total energy -81375.572464


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:ASP)


Summations of interaction energy for fragment #1(A:2:ASP)
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.
-150.933-142.0649.579-7.029-11.4170.073
Interaction energy analysis for fragmet #1(A:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.746 / q_NPA : -0.905
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].
3A4ALA0-0.013-0.0163.457-8.114-6.005-0.002-0.977-1.1290.004
4A5ILE00.0090.0222.429-4.252-3.5791.776-0.859-1.590-0.001
5A6LYS10.9680.9643.150-58.406-57.6940.022-0.248-0.4860.001
6A7ARG10.9620.9926.936-29.023-29.0230.0000.0000.0000.000
7A8LYS10.8530.9258.131-29.348-29.3480.0000.0000.0000.000
8A9LEU00.0380.0217.550-1.047-1.0470.0000.0000.0000.000
9A10GLN00.0030.00210.845-0.983-0.9830.0000.0000.0000.000
10A11SER0-0.084-0.04812.931-1.710-1.7100.0000.0000.0000.000
11A12PHE0-0.013-0.00714.118-0.825-0.8250.0000.0000.0000.000
12A13ASN0-0.034-0.00715.772-0.351-0.3510.0000.0000.0000.000
13A14ILE0-0.0180.00211.3570.0150.0150.0000.0000.0000.000
14A15SER0-0.007-0.01213.7960.3980.3980.0000.0000.0000.000
15A16ASN0-0.056-0.05012.6091.3511.3510.0000.0000.0000.000
16A17ILE0-0.0120.0046.8181.3131.3130.0000.0000.0000.000
17A18VAL0-0.033-0.0116.6973.1703.1700.0000.0000.0000.000
18A19ILE0-0.041-0.0202.473-8.987-5.8402.987-2.446-3.6890.032
19A20LYS10.8790.9314.427-27.666-27.4160.000-0.039-0.2110.000
20A21SER00.0370.0135.5951.1401.243-0.0010.000-0.1010.000
21A22SER00.0070.0087.612-3.758-3.7580.0000.0000.0000.000
22A23PRO0-0.004-0.0109.9600.3900.3900.0000.0000.0000.000
23A24ILE0-0.0010.01711.644-1.708-1.7080.0000.0000.0000.000
24A25SER00.0320.0169.7371.6791.6790.0000.0000.0000.000
25A26GLY00.0110.0049.085-2.760-2.7600.0000.0000.0000.000
26A27ILE0-0.038-0.0278.6160.4410.4410.0000.0000.0000.000
27A28LYS10.8050.9252.290-70.116-68.2714.798-2.455-4.1880.037
28A29THR00.017-0.0266.621-4.497-4.4970.0000.0000.0000.000
29A30ALA0-0.029-0.0157.1524.9214.9210.0000.0000.0000.000
30A31VAL00.0000.0008.363-4.389-4.3890.0000.0000.0000.000
31A32THR0-0.036-0.0259.8951.4381.4380.0000.0000.0000.000
32A33ASP-1-0.816-0.90912.49918.00918.0090.0000.0000.0000.000
33A34GLN00.0360.02215.214-0.202-0.2020.0000.0000.0000.000
34A35GLY00.0080.00815.454-1.005-1.0050.0000.0000.0000.000
35A36ILE0-0.065-0.02812.0471.7101.7100.0000.0000.0000.000
36A37LEU00.0510.04211.776-0.942-0.9420.0000.0000.0000.000
37A38TYR00.0270.00410.3042.6572.6570.0000.0000.0000.000
38A39VAL0-0.010-0.0037.004-2.367-2.3670.0000.0000.0000.000
39A40SER0-0.008-0.0217.5754.0904.0900.0000.0000.0000.000
40A41GLU-1-0.825-0.9124.85951.45851.4580.0000.0000.0000.000
41A42ASP-1-0.797-0.8634.57527.23527.265-0.001-0.005-0.0230.000
42A43GLY00.0150.0076.977-1.019-1.0190.0000.0000.0000.000
43A44LYS10.8250.9197.755-22.481-22.4810.0000.0000.0000.000
44A45TYR00.010-0.00111.002-1.719-1.7190.0000.0000.0000.000
45A46LEU00.0300.00611.0752.7112.7110.0000.0000.0000.000
46A47PHE0-0.006-0.00112.964-1.777-1.7770.0000.0000.0000.000
47A48GLU-1-0.938-0.96914.96718.54518.5450.0000.0000.0000.000
48A49GLY00.0130.00016.700-1.254-1.2540.0000.0000.0000.000
49A50LYS10.8310.91417.962-15.160-15.1600.0000.0000.0000.000
50A51LEU00.0040.01514.037-0.291-0.2910.0000.0000.0000.000
51A52TYR0-0.012-0.02417.8200.0730.0730.0000.0000.0000.000
52A53GLU-1-0.800-0.90219.84214.30714.3070.0000.0000.0000.000
53A54LEU0-0.033-0.01321.786-0.258-0.2580.0000.0000.0000.000
54A55THR0-0.045-0.02323.835-0.257-0.2570.0000.0000.0000.000
55A56ASN0-0.071-0.03725.771-0.357-0.3570.0000.0000.0000.000
56A57ASN00.0250.00928.375-0.179-0.1790.0000.0000.0000.000
57A58GLY00.0490.04228.462-0.381-0.3810.0000.0000.0000.000
58A59PRO0-0.037-0.03725.1190.3980.3980.0000.0000.0000.000
59A60VAL00.0270.03021.3220.0520.0520.0000.0000.0000.000
60A61ASP-1-0.829-0.91418.68817.45317.4530.0000.0000.0000.000
61A62VAL00.0200.00714.2330.1340.1340.0000.0000.0000.000
62A63ALA0-0.009-0.01715.0410.9270.9270.0000.0000.0000.000
63A64GLY00.0370.02016.077-0.037-0.0370.0000.0000.0000.000
64A65LYS10.9030.94816.351-15.277-15.2770.0000.0000.0000.000
65A66ILE0-0.019-0.00810.9470.4690.4690.0000.0000.0000.000
66A67LEU00.0010.00814.3190.4790.4790.0000.0000.0000.000
67A68VAL00.0320.01417.213-0.629-0.6290.0000.0000.0000.000
68A69ASP-1-0.843-0.89113.97820.98820.9880.0000.0000.0000.000
69A70LYS10.8830.94515.490-18.223-18.2230.0000.0000.0000.000
70A71LEU00.0050.01516.888-0.590-0.5900.0000.0000.0000.000
71A72ASN00.016-0.00319.709-1.308-1.3080.0000.0000.0000.000
72A73SER0-0.077-0.03917.068-0.380-0.3800.0000.0000.0000.000
73A74TYR00.0580.01018.446-0.127-0.1270.0000.0000.0000.000
74A75LYS10.8750.90922.522-13.007-13.0070.0000.0000.0000.000
75A76ASP-1-0.859-0.91224.61611.80811.8080.0000.0000.0000.000
76A77GLU-1-0.804-0.87024.22112.76512.7650.0000.0000.0000.000
77A78MET0-0.054-0.01724.275-0.366-0.3660.0000.0000.0000.000
78A79ILE00.0010.01129.028-0.171-0.1710.0000.0000.0000.000
79A80VAL0-0.026-0.02330.134-0.066-0.0660.0000.0000.0000.000
80A81TYR00.011-0.01133.113-0.204-0.2040.0000.0000.0000.000
81A82PRO00.0110.00134.5010.0410.0410.0000.0000.0000.000
82A83ALA00.0130.02236.055-0.298-0.2980.0000.0000.0000.000
83A84LYS10.7630.87538.026-7.231-7.2310.0000.0000.0000.000
84A85ASN00.0360.00137.2860.0130.0130.0000.0000.0000.000
85A86GLU-1-0.881-0.88431.2219.9459.9450.0000.0000.0000.000
86A87LYS10.8280.89734.638-8.606-8.6060.0000.0000.0000.000
87A88HIS10.8100.90132.065-9.118-9.1180.0000.0000.0000.000
88A89VAL00.0260.02628.555-0.181-0.1810.0000.0000.0000.000
89A90VAL0-0.009-0.00129.0030.3830.3830.0000.0000.0000.000
90A91THR00.0100.00126.046-0.018-0.0180.0000.0000.0000.000
91A92VAL0-0.011-0.00128.9140.0620.0620.0000.0000.0000.000
92A93PHE00.0170.02524.819-0.078-0.0780.0000.0000.0000.000
93A94MET0-0.008-0.01130.915-0.306-0.3060.0000.0000.0000.000
94A95ASP-1-0.752-0.87934.0308.6268.6260.0000.0000.0000.000
95A96ILE00.0450.02236.756-0.111-0.1110.0000.0000.0000.000
96A97THR0-0.043-0.02439.968-0.236-0.2360.0000.0000.0000.000
97A98CYS0-0.0200.01038.0920.1160.1160.0000.0000.0000.000
98A99HIS00.0190.01841.510-0.051-0.0510.0000.0000.0000.000
99A100TYR00.0600.01641.103-0.045-0.0450.0000.0000.0000.000
100A102HIS00.0350.03539.843-0.121-0.1210.0000.0000.0000.000
101A103LEU0-0.024-0.00642.995-0.049-0.0490.0000.0000.0000.000
102A104LEU0-0.009-0.00136.464-0.048-0.0480.0000.0000.0000.000
103A105HIS00.0310.00239.118-0.137-0.1370.0000.0000.0000.000
104A106GLN0-0.035-0.03441.644-0.092-0.0920.0000.0000.0000.000
105A107GLN0-0.074-0.05043.341-0.193-0.1930.0000.0000.0000.000
106A108LEU0-0.0180.01237.8640.1040.1040.0000.0000.0000.000
107A109LYS10.8110.89541.437-6.744-6.7440.0000.0000.0000.000
108A110GLU-1-0.717-0.85043.5736.9846.9840.0000.0000.0000.000
109A111TYR0-0.052-0.04338.4720.0120.0120.0000.0000.0000.000
110A112ASN0-0.008-0.01738.0430.1580.1580.0000.0000.0000.000
111A113ASP-1-0.849-0.92840.1387.1357.1350.0000.0000.0000.000
112A114LEU0-0.045-0.01141.000-0.088-0.0880.0000.0000.0000.000
113A115GLY0-0.0060.00838.6340.1360.1360.0000.0000.0000.000
114A116ILE0-0.010-0.02734.5730.3350.3350.0000.0000.0000.000
115A117THR0-0.002-0.02432.015-0.286-0.2860.0000.0000.0000.000
116A118VAL0-0.0060.01032.7890.3300.3300.0000.0000.0000.000
117A119ARG10.8590.91324.395-12.222-12.2220.0000.0000.0000.000
118A120TYR00.0160.01330.2410.2690.2690.0000.0000.0000.000
119A121LEU00.0030.00225.2660.2300.2300.0000.0000.0000.000
120A122ALA00.0260.01829.506-0.308-0.3080.0000.0000.0000.000
121A123PHE0-0.022-0.03028.2930.3430.3430.0000.0000.0000.000
122A124PRO00.012-0.00231.353-0.280-0.2800.0000.0000.0000.000
123A125ARG10.8380.90233.877-8.147-8.1470.0000.0000.0000.000
124A126ALA0-0.022-0.00235.3340.0670.0670.0000.0000.0000.000
125A127GLY00.0460.03433.280-0.090-0.0900.0000.0000.0000.000
126A128MET0-0.011-0.00330.261-0.153-0.1530.0000.0000.0000.000
127A129ASN0-0.008-0.01033.691-0.004-0.0040.0000.0000.0000.000
128A130ASN00.0580.04237.123-0.272-0.2720.0000.0000.0000.000
129A131GLN00.0520.01839.1350.1280.1280.0000.0000.0000.000
130A132THR00.0830.03939.3720.0400.0400.0000.0000.0000.000
131A133ALA00.0020.00434.8330.1450.1450.0000.0000.0000.000
132A134LYS10.8470.91535.531-8.513-8.5130.0000.0000.0000.000
133A135GLN0-0.004-0.00937.5260.0760.0760.0000.0000.0000.000
134A136MET0-0.0090.01034.5500.1150.1150.0000.0000.0000.000
135A137GLU-1-0.707-0.84030.69610.50310.5030.0000.0000.0000.000
136A138ALA0-0.0650.00134.3350.0850.0850.0000.0000.0000.000
137A139ILE0-0.005-0.00436.191-0.048-0.0480.0000.0000.0000.000
138A140TRP00.002-0.02330.190-0.143-0.1430.0000.0000.0000.000
139A141THR0-0.062-0.03831.2940.1880.1880.0000.0000.0000.000
140A142ALA0-0.0040.01733.676-0.139-0.1390.0000.0000.0000.000
141A143LYS10.9140.93535.875-7.920-7.9200.0000.0000.0000.000
142A144ASP-1-0.862-0.93137.4588.1318.1310.0000.0000.0000.000
143A145PRO00.0590.02933.426-0.210-0.2100.0000.0000.0000.000
144A146VAL00.0430.03736.087-0.074-0.0740.0000.0000.0000.000
145A147PHE0-0.040-0.01938.226-0.185-0.1850.0000.0000.0000.000
146A148ALA00.002-0.00738.680-0.147-0.1470.0000.0000.0000.000
147A149LEU00.0020.00036.400-0.097-0.0970.0000.0000.0000.000
148A150ASN00.0110.00939.788-0.056-0.0560.0000.0000.0000.000
149A151GLU-1-0.817-0.87942.8246.5606.5600.0000.0000.0000.000
150A152ALA00.002-0.00341.304-0.125-0.1250.0000.0000.0000.000
151A153GLU-1-0.825-0.92740.7157.6517.6510.0000.0000.0000.000
152A154LYS10.7800.88043.988-6.881-6.8810.0000.0000.0000.000
153A155GLY00.0140.01746.488-0.169-0.1690.0000.0000.0000.000
154A156ASN0-0.103-0.04547.423-0.139-0.1390.0000.0000.0000.000
155A157LEU0-0.017-0.01342.9290.1620.1620.0000.0000.0000.000
156A158PRO0-0.029-0.00140.589-0.149-0.1490.0000.0000.0000.000
157A159LYS10.9800.97543.824-6.297-6.2970.0000.0000.0000.000
158A160GLU-1-0.865-0.91140.6337.9287.9280.0000.0000.0000.000
159A161VAL0-0.008-0.01839.8610.0740.0740.0000.0000.0000.000
160A162LYS10.8720.94035.270-8.416-8.4160.0000.0000.0000.000
161A163THR00.026-0.00732.613-0.153-0.1530.0000.0000.0000.000
162A164PRO0-0.098-0.05231.5360.2380.2380.0000.0000.0000.000
163A165ASN0-0.028-0.01926.3690.4190.4190.0000.0000.0000.000
164A166ILE00.0370.02926.3320.5030.5030.0000.0000.0000.000
165A167VAL00.022-0.00926.9150.3010.3010.0000.0000.0000.000
166A168LYS10.7850.87324.537-12.637-12.6370.0000.0000.0000.000
167A169LYS10.8390.90920.968-13.689-13.6890.0000.0000.0000.000
168A170HIS0-0.053-0.03423.6190.1730.1730.0000.0000.0000.000
169A171TYR00.0260.00925.9340.1970.1970.0000.0000.0000.000
170A172GLU-1-0.795-0.89122.88113.14313.1430.0000.0000.0000.000
171A173LEU0-0.0180.00220.0650.4440.4440.0000.0000.0000.000
172A174GLY00.0450.01022.7470.1650.1650.0000.0000.0000.000
173A175ILE0-0.023-0.01724.651-0.081-0.0810.0000.0000.0000.000
174A176GLN0-0.024-0.00616.8650.2090.2090.0000.0000.0000.000
175A177PHE0-0.008-0.01221.4640.3530.3530.0000.0000.0000.000
176A178GLY0-0.0090.01223.997-0.296-0.2960.0000.0000.0000.000
177A179VAL0-0.065-0.02826.780-0.530-0.5300.0000.0000.0000.000
178A180ARG10.9410.95829.348-9.762-9.7620.0000.0000.0000.000
179A181GLY00.0030.00632.587-0.344-0.3440.0000.0000.0000.000
180A182THR0-0.0370.01333.4450.2160.2160.0000.0000.0000.000
181A183PRO00.036-0.00835.256-0.256-0.2560.0000.0000.0000.000
182A184SER0-0.038-0.02930.918-0.073-0.0730.0000.0000.0000.000
183A185ILE0-0.025-0.00931.1560.2450.2450.0000.0000.0000.000
184A186VAL00.0120.01624.3800.0600.0600.0000.0000.0000.000
185A187THR00.0440.02027.675-0.221-0.2210.0000.0000.0000.000
186A188SER00.0200.01025.3640.4710.4710.0000.0000.0000.000
187A189THR00.0320.01423.6930.6720.6720.0000.0000.0000.000
188A190GLY0-0.025-0.02922.1460.6200.6200.0000.0000.0000.000
189A191GLU-1-0.919-0.94923.11211.14411.1440.0000.0000.0000.000
190A192LEU0-0.013-0.02026.345-0.008-0.0080.0000.0000.0000.000
191A193ILE00.0480.03328.504-0.238-0.2380.0000.0000.0000.000
192A194GLY0-0.007-0.00632.046-0.146-0.1460.0000.0000.0000.000
193A195GLY00.000-0.01232.652-0.176-0.1760.0000.0000.0000.000
194A196TYR0-0.013-0.00836.294-0.001-0.0010.0000.0000.0000.000
195A197LEU00.0270.02636.751-0.124-0.1240.0000.0000.0000.000
196A198LYS10.9290.97739.941-6.936-6.9360.0000.0000.0000.000
197A199PRO00.0310.01041.0340.0970.0970.0000.0000.0000.000
198A200ALA00.0370.00540.9260.1470.1470.0000.0000.0000.000
199A201ASP-1-0.839-0.89541.6397.3207.3200.0000.0000.0000.000
200A202LEU00.0040.00234.5920.1690.1690.0000.0000.0000.000
201A203LEU0-0.016-0.00936.7780.2280.2280.0000.0000.0000.000
202A204ARG10.9330.95937.352-7.374-7.3740.0000.0000.0000.000
203A205ALA0-0.0160.00135.5840.1630.1630.0000.0000.0000.000
204A206LEU0-0.057-0.02631.7190.3840.3840.0000.0000.0000.000
205A207GLU-1-0.905-0.94433.5878.6038.6030.0000.0000.0000.000
206A208GLU-1-0.884-0.94835.6428.2388.2380.0000.0000.0000.000
207A209THR0-0.059-0.01230.9200.0380.0380.0000.0000.0000.000
208A210ALA0-0.077-0.03628.9830.7480.7480.0000.0000.0000.000