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: KG413

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 OptHSide
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 -2301090.874573
FMO2-HF: Nuclear repulsion 2219954.76331
FMO2-HF: Total energy -81136.111263
FMO2-MP2: Total energy -81374.426896


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.
-140.837-133.76414.043-8.226-12.8890.07
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 : -0.771 / q_NPA : -0.915
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].
3A4ALA00.000-0.0073.815-7.821-6.017-0.009-0.752-1.0430.004
4A5ILE00.0620.0182.495-0.5440.1300.790-0.459-1.005-0.001
5A6LYS10.9330.9753.145-52.561-52.0380.012-0.172-0.3630.001
6A7ARG10.9400.9787.577-27.724-27.7240.0000.0000.0000.000
7A8LYS10.8630.9228.409-28.421-28.4210.0000.0000.0000.000
8A9LEU00.0360.0198.103-0.774-0.7740.0000.0000.0000.000
9A10GLN00.0320.02811.391-0.606-0.6060.0000.0000.0000.000
10A11SER0-0.062-0.02913.480-1.622-1.6220.0000.0000.0000.000
11A12PHE0-0.034-0.03114.621-0.388-0.3880.0000.0000.0000.000
12A13ASN0-0.037-0.00716.3340.1330.1330.0000.0000.0000.000
13A14ILE0-0.0100.01211.966-0.047-0.0470.0000.0000.0000.000
14A15SER0-0.017-0.02913.5930.7720.7720.0000.0000.0000.000
15A16ASN0-0.065-0.06012.5441.7681.7680.0000.0000.0000.000
16A17ILE0-0.0170.0216.9921.4111.4110.0000.0000.0000.000
17A18VAL0-0.017-0.0106.8091.8241.8240.0000.0000.0000.000
18A19ILE0-0.059-0.0222.586-7.707-5.2754.136-2.397-4.1710.030
19A20LYS10.9610.9654.407-32.048-31.7460.000-0.044-0.2580.000
20A21SER00.0220.0065.1802.3552.488-0.001-0.001-0.1300.000
21A22SER00.0330.0297.585-5.120-5.1200.0000.0000.0000.000
22A23PRO0-0.063-0.0339.7990.4800.4800.0000.0000.0000.000
23A24ILE0-0.005-0.00711.385-1.973-1.9730.0000.0000.0000.000
24A25SER00.1060.0499.5551.9041.9040.0000.0000.0000.000
25A26GLY0-0.033-0.0129.032-1.929-1.9290.0000.0000.0000.000
26A27ILE0-0.021-0.0248.4020.0770.0770.0000.0000.0000.000
27A28LYS10.8140.9272.024-69.698-68.6909.117-4.394-5.7310.036
28A29THR00.021-0.0016.645-2.999-2.9990.0000.0000.0000.000
29A30ALA0-0.038-0.0047.4132.7272.7270.0000.0000.0000.000
30A31VAL00.0050.0028.370-4.216-4.2160.0000.0000.0000.000
31A32THR0-0.009-0.00810.4160.3320.3320.0000.0000.0000.000
32A33ASP-1-0.834-0.91512.35417.37217.3720.0000.0000.0000.000
33A34GLN00.0350.01915.032-0.433-0.4330.0000.0000.0000.000
34A35GLY00.0020.01215.532-0.994-0.9940.0000.0000.0000.000
35A36ILE0-0.055-0.03412.0041.6421.6420.0000.0000.0000.000
36A37LEU00.0290.03211.412-0.747-0.7470.0000.0000.0000.000
37A38TYR00.015-0.00810.2412.2832.2830.0000.0000.0000.000
38A39VAL0-0.0180.0006.875-2.318-2.3180.0000.0000.0000.000
39A40SER00.039-0.0017.7452.9592.9590.0000.0000.0000.000
40A41GLU-1-0.852-0.9344.78052.26452.449-0.001-0.006-0.1780.000
41A42ASP-1-0.809-0.8614.92025.38025.392-0.001-0.001-0.0100.000
42A43GLY00.0260.0147.5680.4300.4300.0000.0000.0000.000
43A44LYS10.8140.9008.619-22.057-22.0570.0000.0000.0000.000
44A45TYR00.011-0.00811.419-1.564-1.5640.0000.0000.0000.000
45A46LEU00.0210.01611.3852.2972.2970.0000.0000.0000.000
46A47PHE0-0.022-0.00212.957-1.692-1.6920.0000.0000.0000.000
47A48GLU-1-0.950-0.97514.68617.91917.9190.0000.0000.0000.000
48A49GLY00.009-0.00117.023-1.055-1.0550.0000.0000.0000.000
49A50LYS10.8650.91618.148-14.758-14.7580.0000.0000.0000.000
50A51LEU0-0.0090.01414.434-0.677-0.6770.0000.0000.0000.000
51A52TYR0-0.036-0.03317.9140.1860.1860.0000.0000.0000.000
52A53GLU-1-0.775-0.91219.43414.73114.7310.0000.0000.0000.000
53A54LEU0-0.059-0.03121.871-0.190-0.1900.0000.0000.0000.000
54A55THR0-0.0160.00123.545-0.304-0.3040.0000.0000.0000.000
55A56ASN0-0.075-0.03625.628-0.319-0.3190.0000.0000.0000.000
56A57ASN00.0180.01027.907-0.248-0.2480.0000.0000.0000.000
57A58GLY00.0650.03927.878-0.385-0.3850.0000.0000.0000.000
58A59PRO0-0.035-0.01525.1610.4840.4840.0000.0000.0000.000
59A60VAL00.0070.01121.1570.1150.1150.0000.0000.0000.000
60A61ASP-1-0.840-0.91118.16317.65817.6580.0000.0000.0000.000
61A62VAL00.0610.03113.9110.1700.1700.0000.0000.0000.000
62A63ALA0-0.036-0.03814.7250.9750.9750.0000.0000.0000.000
63A64GLY00.0180.01915.715-0.278-0.2780.0000.0000.0000.000
64A65LYS10.9200.94015.958-15.305-15.3050.0000.0000.0000.000
65A66ILE0-0.0230.00710.5870.7090.7090.0000.0000.0000.000
66A67LEU0-0.0030.00514.0580.3320.3320.0000.0000.0000.000
67A68VAL00.0110.00316.973-0.355-0.3550.0000.0000.0000.000
68A69ASP-1-0.864-0.91613.55821.22521.2250.0000.0000.0000.000
69A70LYS10.9230.96515.448-17.934-17.9340.0000.0000.0000.000
70A71LEU00.0150.03116.896-0.555-0.5550.0000.0000.0000.000
71A72ASN00.0930.04219.518-1.168-1.1680.0000.0000.0000.000
72A73SER0-0.113-0.05917.052-0.443-0.4430.0000.0000.0000.000
73A74TYR00.026-0.02018.702-0.098-0.0980.0000.0000.0000.000
74A75LYS10.8790.90322.444-13.019-13.0190.0000.0000.0000.000
75A76ASP-1-0.886-0.92424.48511.85011.8500.0000.0000.0000.000
76A77GLU-1-0.817-0.87524.23212.76512.7650.0000.0000.0000.000
77A78MET0-0.081-0.03324.166-0.399-0.3990.0000.0000.0000.000
78A79ILE0-0.0090.01128.989-0.148-0.1480.0000.0000.0000.000
79A80VAL0-0.033-0.03830.215-0.091-0.0910.0000.0000.0000.000
80A81TYR00.007-0.00833.175-0.208-0.2080.0000.0000.0000.000
81A82PRO00.014-0.00334.068-0.012-0.0120.0000.0000.0000.000
82A83ALA00.0310.03235.785-0.276-0.2760.0000.0000.0000.000
83A84LYS10.8010.89537.755-7.250-7.2500.0000.0000.0000.000
84A85ASN0-0.001-0.02036.4550.1060.1060.0000.0000.0000.000
85A86GLU-1-0.887-0.89730.9709.9759.9750.0000.0000.0000.000
86A87LYS10.8240.91234.465-8.545-8.5450.0000.0000.0000.000
87A88HIS10.8060.88531.821-9.116-9.1160.0000.0000.0000.000
88A89VAL00.0470.03228.340-0.161-0.1610.0000.0000.0000.000
89A90VAL00.0070.01928.5340.4390.4390.0000.0000.0000.000
90A91THR00.0270.01626.215-0.062-0.0620.0000.0000.0000.000
91A92VAL0-0.0010.00928.8530.0170.0170.0000.0000.0000.000
92A93PHE0-0.0110.00324.873-0.005-0.0050.0000.0000.0000.000
93A94MET0-0.004-0.01331.021-0.273-0.2730.0000.0000.0000.000
94A95ASP-1-0.766-0.88834.0978.6078.6070.0000.0000.0000.000
95A96ILE00.0910.02436.697-0.099-0.0990.0000.0000.0000.000
96A97THR0-0.061-0.01839.807-0.223-0.2230.0000.0000.0000.000
97A98CYS0-0.067-0.00738.0310.0510.0510.0000.0000.0000.000
98A99HIS00.0340.02341.498-0.033-0.0330.0000.0000.0000.000
99A100TYR00.0580.01941.085-0.065-0.0650.0000.0000.0000.000
100A102HIS00.0320.01639.578-0.134-0.1340.0000.0000.0000.000
101A103LEU0-0.007-0.00642.693-0.007-0.0070.0000.0000.0000.000
102A104LEU0-0.026-0.01636.288-0.037-0.0370.0000.0000.0000.000
103A105HIS00.0520.01938.774-0.094-0.0940.0000.0000.0000.000
104A106GLN0-0.072-0.03541.216-0.088-0.0880.0000.0000.0000.000
105A107GLN0-0.056-0.04642.929-0.186-0.1860.0000.0000.0000.000
106A108LEU00.0110.03137.4910.1030.1030.0000.0000.0000.000
107A109LYS10.8080.88841.084-6.764-6.7640.0000.0000.0000.000
108A110GLU-1-0.732-0.84543.4476.9786.9780.0000.0000.0000.000
109A111TYR0-0.034-0.04738.1220.0130.0130.0000.0000.0000.000
110A112ASN00.013-0.00338.4670.2350.2350.0000.0000.0000.000
111A113ASP-1-0.888-0.93839.9687.2587.2580.0000.0000.0000.000
112A114LEU0-0.056-0.01640.416-0.122-0.1220.0000.0000.0000.000
113A115GLY0-0.017-0.00638.2990.1310.1310.0000.0000.0000.000
114A116ILE0-0.003-0.01434.1970.3610.3610.0000.0000.0000.000
115A117THR0-0.001-0.02731.773-0.288-0.2880.0000.0000.0000.000
116A118VAL0-0.0080.00532.5260.3180.3180.0000.0000.0000.000
117A119ARG10.8750.92024.272-12.185-12.1850.0000.0000.0000.000
118A120TYR00.0040.01230.4050.2180.2180.0000.0000.0000.000
119A121LEU00.0170.02525.0290.2310.2310.0000.0000.0000.000
120A122ALA00.0270.00929.283-0.342-0.3420.0000.0000.0000.000
121A123PHE0-0.013-0.02828.1860.3220.3220.0000.0000.0000.000
122A124PRO0-0.008-0.00531.035-0.285-0.2850.0000.0000.0000.000
123A125ARG10.8640.92633.520-8.122-8.1220.0000.0000.0000.000
124A126ALA0-0.0070.02635.1420.0930.0930.0000.0000.0000.000
125A127GLY00.025-0.00933.497-0.108-0.1080.0000.0000.0000.000
126A128MET00.0030.00430.485-0.146-0.1460.0000.0000.0000.000
127A129ASN0-0.011-0.01733.970-0.027-0.0270.0000.0000.0000.000
128A130ASN00.0740.03637.185-0.280-0.2800.0000.0000.0000.000
129A131GLN00.0650.02539.2550.1530.1530.0000.0000.0000.000
130A132THR00.0890.03939.6040.0210.0210.0000.0000.0000.000
131A133ALA0-0.0290.00234.9280.1640.1640.0000.0000.0000.000
132A134LYS10.8380.92235.524-8.372-8.3720.0000.0000.0000.000
133A135GLN00.0450.01937.6690.1250.1250.0000.0000.0000.000
134A136MET00.0190.02434.7300.0810.0810.0000.0000.0000.000
135A137GLU-1-0.715-0.82830.90110.41610.4160.0000.0000.0000.000
136A138ALA0-0.088-0.02134.2660.1070.1070.0000.0000.0000.000
137A139ILE0-0.017-0.02136.2770.0250.0250.0000.0000.0000.000
138A140TRP0-0.002-0.02330.193-0.167-0.1670.0000.0000.0000.000
139A141THR0-0.055-0.02731.0160.1680.1680.0000.0000.0000.000
140A142ALA0-0.040-0.00133.390-0.112-0.1120.0000.0000.0000.000
141A143LYS10.9300.94835.643-8.005-8.0050.0000.0000.0000.000
142A144ASP-1-0.863-0.94137.3118.2158.2150.0000.0000.0000.000
143A145PRO00.0470.01533.517-0.238-0.2380.0000.0000.0000.000
144A146VAL00.0740.05836.407-0.097-0.0970.0000.0000.0000.000
145A147PHE0-0.0320.00338.470-0.194-0.1940.0000.0000.0000.000
146A148ALA0-0.013-0.01438.701-0.147-0.1470.0000.0000.0000.000
147A149LEU00.0160.00236.184-0.103-0.1030.0000.0000.0000.000
148A150ASN00.0140.00839.707-0.036-0.0360.0000.0000.0000.000
149A151GLU-1-0.843-0.91042.5636.5856.5850.0000.0000.0000.000
150A152ALA00.0030.00741.240-0.131-0.1310.0000.0000.0000.000
151A153GLU-1-0.853-0.93440.6197.6507.6500.0000.0000.0000.000
152A154LYS10.7950.89643.959-6.917-6.9170.0000.0000.0000.000
153A155GLY00.0040.00946.428-0.175-0.1750.0000.0000.0000.000
154A156ASN0-0.108-0.05347.255-0.153-0.1530.0000.0000.0000.000
155A157LEU0-0.0020.00242.7520.1710.1710.0000.0000.0000.000
156A158PRO0-0.032-0.00940.759-0.142-0.1420.0000.0000.0000.000
157A159LYS10.9610.96644.045-6.272-6.2720.0000.0000.0000.000
158A160GLU-1-0.871-0.91340.8007.9237.9230.0000.0000.0000.000
159A161VAL00.000-0.01439.7180.0560.0560.0000.0000.0000.000
160A162LYS10.8880.94435.359-8.403-8.4030.0000.0000.0000.000
161A163THR00.030-0.00333.156-0.184-0.1840.0000.0000.0000.000
162A164PRO0-0.097-0.06231.9990.2370.2370.0000.0000.0000.000
163A165ASN0-0.018-0.01626.9480.3860.3860.0000.0000.0000.000
164A166ILE00.0500.02926.5030.4790.4790.0000.0000.0000.000
165A167VAL00.0140.00127.0870.2830.2830.0000.0000.0000.000
166A168LYS10.7990.87624.983-12.385-12.3850.0000.0000.0000.000
167A169LYS10.8400.91120.917-13.634-13.6340.0000.0000.0000.000
168A170HIS0-0.040-0.03423.6020.1370.1370.0000.0000.0000.000
169A171TYR00.003-0.00125.8290.1760.1760.0000.0000.0000.000
170A172GLU-1-0.802-0.89522.82513.04413.0440.0000.0000.0000.000
171A173LEU0-0.0320.00119.9000.4180.4180.0000.0000.0000.000
172A174GLY00.0630.02122.5300.1650.1650.0000.0000.0000.000
173A175ILE0-0.004-0.00525.050-0.079-0.0790.0000.0000.0000.000
174A176GLN0-0.035-0.00417.0400.0830.0830.0000.0000.0000.000
175A177PHE0-0.002-0.01521.1340.3490.3490.0000.0000.0000.000
176A178GLY0-0.0240.00723.878-0.250-0.2500.0000.0000.0000.000
177A179VAL0-0.072-0.03126.870-0.521-0.5210.0000.0000.0000.000
178A180ARG10.9360.95429.365-9.704-9.7040.0000.0000.0000.000
179A181GLY0-0.0060.00132.542-0.346-0.3460.0000.0000.0000.000
180A182THR0-0.0570.00333.3830.1960.1960.0000.0000.0000.000
181A183PRO00.059-0.00335.174-0.248-0.2480.0000.0000.0000.000
182A184SER0-0.044-0.02830.838-0.051-0.0510.0000.0000.0000.000
183A185ILE00.0000.00931.1050.2390.2390.0000.0000.0000.000
184A186VAL00.0170.00724.5100.0520.0520.0000.0000.0000.000
185A187THR00.0450.01427.274-0.095-0.0950.0000.0000.0000.000
186A188SER00.0360.02425.4670.3980.3980.0000.0000.0000.000
187A189THR0-0.013-0.00923.5950.6360.6360.0000.0000.0000.000
188A190GLY0-0.016-0.03522.0210.4230.4230.0000.0000.0000.000
189A191GLU-1-0.956-0.96322.95611.09711.0970.0000.0000.0000.000
190A192LEU0-0.003-0.02125.9190.1590.1590.0000.0000.0000.000
191A193ILE00.0000.02328.446-0.169-0.1690.0000.0000.0000.000
192A194GLY0-0.023-0.01631.084-0.280-0.2800.0000.0000.0000.000
193A195GLY00.0590.02832.532-0.165-0.1650.0000.0000.0000.000
194A196TYR0-0.037-0.02136.207-0.013-0.0130.0000.0000.0000.000
195A197LEU00.0560.02635.908-0.094-0.0940.0000.0000.0000.000
196A198LYS10.9471.01439.562-6.845-6.8450.0000.0000.0000.000
197A199PRO00.0490.01140.6740.1270.1270.0000.0000.0000.000
198A200ALA00.0320.00440.4610.1380.1380.0000.0000.0000.000
199A201ASP-1-0.842-0.92340.9397.5247.5240.0000.0000.0000.000
200A202LEU0-0.0070.00634.1780.1850.1850.0000.0000.0000.000
201A203LEU0-0.019-0.00536.2860.2670.2670.0000.0000.0000.000
202A204ARG10.9130.95036.884-7.366-7.3660.0000.0000.0000.000
203A205ALA00.0140.01535.2420.1830.1830.0000.0000.0000.000
204A206LEU0-0.067-0.03231.3210.3610.3610.0000.0000.0000.000
205A207GLU-1-0.890-0.93932.9318.6798.6790.0000.0000.0000.000
206A208GLU-1-0.945-0.97534.8858.3228.3220.0000.0000.0000.000
207A209THR0-0.060-0.02630.5920.2330.2330.0000.0000.0000.000
208A210ALA0-0.044-0.01928.2800.7100.7100.0000.0000.0000.000