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: QV29Y

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2301798.702173
FMO2-HF: Nuclear repulsion 2220664.386184
FMO2-HF: Total energy -81134.315989
FMO2-MP2: Total energy -81372.800423


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.
-135.09-127.65712.233-7.471-12.1930.067
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 : -0.774 / q_NPA : -0.911
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].
3A4ALA00.001-0.0063.815-8.013-6.227-0.010-0.747-1.0300.004
4A5ILE00.0500.0192.440-0.3770.2030.963-0.497-1.0450.000
5A6LYS10.9440.9733.145-51.561-51.0550.011-0.157-0.3600.001
6A7ARG10.9400.9767.561-27.632-27.6320.0000.0000.0000.000
7A8LYS10.8780.9308.502-28.116-28.1160.0000.0000.0000.000
8A9LEU00.0320.0267.752-0.669-0.6690.0000.0000.0000.000
9A10GLN00.0350.02811.376-0.640-0.6400.0000.0000.0000.000
10A11SER0-0.061-0.03013.466-1.594-1.5940.0000.0000.0000.000
11A12PHE0-0.030-0.03114.689-0.385-0.3850.0000.0000.0000.000
12A13ASN0-0.029-0.00116.3190.1730.1730.0000.0000.0000.000
13A14ILE0-0.036-0.00712.028-0.070-0.0700.0000.0000.0000.000
14A15SER0-0.034-0.02913.4930.6410.6410.0000.0000.0000.000
15A16ASN0-0.059-0.05912.4361.6521.6520.0000.0000.0000.000
16A17ILE0-0.0130.0226.8101.5071.5070.0000.0000.0000.000
17A18VAL0-0.016-0.0106.7301.9181.9180.0000.0000.0000.000
18A19ILE0-0.074-0.0192.374-10.099-8.7196.513-3.002-4.8910.037
19A20LYS10.9620.9654.251-32.683-32.3300.002-0.077-0.2780.000
20A21SER0-0.004-0.0065.0482.3862.529-0.001-0.002-0.1400.000
21A22SER00.023-0.0247.433-4.882-4.8820.0000.0000.0000.000
22A23PRO0-0.060-0.0299.6880.3940.3940.0000.0000.0000.000
23A24ILE0-0.016-0.01511.372-2.030-2.0300.0000.0000.0000.000
24A25SER00.1170.0569.5862.1022.1020.0000.0000.0000.000
25A26GLY0-0.009-0.0089.091-1.739-1.7390.0000.0000.0000.000
26A27ILE00.0200.0148.3780.2400.2400.0000.0000.0000.000
27A28LYS10.8690.9952.136-63.490-61.0294.757-2.976-4.2410.025
28A29THR00.016-0.0036.741-3.118-3.1180.0000.0000.0000.000
29A30ALA0-0.046-0.0067.3172.8832.8830.0000.0000.0000.000
30A31VAL00.0170.0078.268-4.191-4.1910.0000.0000.0000.000
31A32THR0-0.019-0.00810.4280.2870.2870.0000.0000.0000.000
32A33ASP-1-0.836-0.91712.30917.37317.3730.0000.0000.0000.000
33A34GLN00.0570.03014.658-0.081-0.0810.0000.0000.0000.000
34A35GLY00.0100.01415.468-1.000-1.0000.0000.0000.0000.000
35A36ILE0-0.052-0.02212.2511.6671.6670.0000.0000.0000.000
36A37LEU00.0120.02911.268-0.744-0.7440.0000.0000.0000.000
37A38TYR00.017-0.00410.2882.3012.3010.0000.0000.0000.000
38A39VAL0-0.011-0.0026.979-2.278-2.2780.0000.0000.0000.000
39A40SER00.018-0.0217.7452.6612.6610.0000.0000.0000.000
40A41GLU-1-0.897-0.9524.51752.14652.364-0.001-0.012-0.2040.000
41A42ASP-1-0.815-0.8624.92726.20726.213-0.001-0.001-0.0040.000
42A43GLY00.006-0.0097.6150.2890.2890.0000.0000.0000.000
43A44LYS10.8220.9088.601-22.340-22.3400.0000.0000.0000.000
44A45TYR00.008-0.01211.397-1.483-1.4830.0000.0000.0000.000
45A46LEU00.0520.01811.4192.2652.2650.0000.0000.0000.000
46A47PHE0-0.0340.00212.890-1.644-1.6440.0000.0000.0000.000
47A48GLU-1-0.943-0.97614.68717.80117.8010.0000.0000.0000.000
48A49GLY00.006-0.00417.020-1.050-1.0500.0000.0000.0000.000
49A50LYS10.9270.95618.007-13.958-13.9580.0000.0000.0000.000
50A51LEU0-0.0030.01214.207-0.719-0.7190.0000.0000.0000.000
51A52TYR0-0.049-0.03217.7570.0220.0220.0000.0000.0000.000
52A53GLU-1-0.756-0.89219.29414.56714.5670.0000.0000.0000.000
53A54LEU0-0.052-0.02421.721-0.207-0.2070.0000.0000.0000.000
54A55THR0-0.027-0.01523.445-0.267-0.2670.0000.0000.0000.000
55A56ASN0-0.089-0.05025.499-0.212-0.2120.0000.0000.0000.000
56A57ASN00.0240.01227.794-0.298-0.2980.0000.0000.0000.000
57A58GLY00.0680.03727.723-0.389-0.3890.0000.0000.0000.000
58A59PRO0-0.041-0.01524.9850.4900.4900.0000.0000.0000.000
59A60VAL0-0.0020.00621.0020.1020.1020.0000.0000.0000.000
60A61ASP-1-0.865-0.93017.97617.98117.9810.0000.0000.0000.000
61A62VAL00.0710.03813.6920.2070.2070.0000.0000.0000.000
62A63ALA0-0.047-0.05114.5991.0221.0220.0000.0000.0000.000
63A64GLY00.0170.02015.578-0.275-0.2750.0000.0000.0000.000
64A65LYS10.9250.94415.697-15.494-15.4940.0000.0000.0000.000
65A66ILE0-0.0210.00410.4250.7720.7720.0000.0000.0000.000
66A67LEU0-0.005-0.00613.9440.3110.3110.0000.0000.0000.000
67A68VAL0-0.0020.00816.875-0.384-0.3840.0000.0000.0000.000
68A69ASP-1-0.873-0.93413.91820.55820.5580.0000.0000.0000.000
69A70LYS10.9170.97315.594-18.117-18.1170.0000.0000.0000.000
70A71LEU00.0170.05016.840-0.594-0.5940.0000.0000.0000.000
71A72ASN00.0790.02919.426-1.103-1.1030.0000.0000.0000.000
72A73SER0-0.141-0.09617.075-0.535-0.5350.0000.0000.0000.000
73A74TYR00.055-0.00119.152-0.018-0.0180.0000.0000.0000.000
74A75LYS10.9710.95222.424-13.103-13.1030.0000.0000.0000.000
75A76ASP-1-0.955-0.96824.48111.97011.9700.0000.0000.0000.000
76A77GLU-1-0.899-0.95623.89612.71812.7180.0000.0000.0000.000
77A78MET0-0.094-0.02923.853-0.390-0.3900.0000.0000.0000.000
78A79ILE0-0.0080.00928.961-0.152-0.1520.0000.0000.0000.000
79A80VAL0-0.032-0.03530.389-0.082-0.0820.0000.0000.0000.000
80A81TYR0-0.014-0.01333.138-0.217-0.2170.0000.0000.0000.000
81A82PRO0-0.002-0.01033.9930.0010.0010.0000.0000.0000.000
82A83ALA00.0620.05135.737-0.264-0.2640.0000.0000.0000.000
83A84LYS10.7740.88737.700-7.247-7.2470.0000.0000.0000.000
84A85ASN0-0.005-0.02636.1380.2620.2620.0000.0000.0000.000
85A86GLU-1-0.955-0.95930.84910.06910.0690.0000.0000.0000.000
86A87LYS10.9050.95934.411-8.263-8.2630.0000.0000.0000.000
87A88HIS10.8730.93331.733-9.194-9.1940.0000.0000.0000.000
88A89VAL00.0550.03628.035-0.171-0.1710.0000.0000.0000.000
89A90VAL00.0080.01928.4520.4380.4380.0000.0000.0000.000
90A91THR00.0350.01326.291-0.102-0.1020.0000.0000.0000.000
91A92VAL0-0.0100.00428.7790.0140.0140.0000.0000.0000.000
92A93PHE0-0.025-0.00324.8610.0020.0020.0000.0000.0000.000
93A94MET00.009-0.01430.953-0.285-0.2850.0000.0000.0000.000
94A95ASP-1-0.812-0.92634.0468.6848.6840.0000.0000.0000.000
95A96ILE00.0980.02836.644-0.093-0.0930.0000.0000.0000.000
96A97THR0-0.064-0.01839.763-0.222-0.2220.0000.0000.0000.000
97A98CYS0-0.077-0.02037.9870.0550.0550.0000.0000.0000.000
98A99HIS00.0340.02841.434-0.017-0.0170.0000.0000.0000.000
99A100TYR00.0510.01740.927-0.061-0.0610.0000.0000.0000.000
100A102HIS00.0310.02539.507-0.095-0.0950.0000.0000.0000.000
101A103LEU0-0.031-0.01542.629-0.010-0.0100.0000.0000.0000.000
102A104LEU0-0.025-0.03036.214-0.032-0.0320.0000.0000.0000.000
103A105HIS00.0580.01738.912-0.074-0.0740.0000.0000.0000.000
104A106GLN0-0.017-0.01541.153-0.054-0.0540.0000.0000.0000.000
105A107GLN0-0.045-0.03442.775-0.153-0.1530.0000.0000.0000.000
106A108LEU00.0040.03737.6920.0900.0900.0000.0000.0000.000
107A109LYS10.8060.89941.018-6.753-6.7530.0000.0000.0000.000
108A110GLU-1-0.713-0.84243.3777.0067.0060.0000.0000.0000.000
109A111TYR0-0.047-0.04238.0320.0320.0320.0000.0000.0000.000
110A112ASN00.0420.00638.2760.2980.2980.0000.0000.0000.000
111A113ASP-1-0.911-0.94739.8997.2817.2810.0000.0000.0000.000
112A114LEU0-0.049-0.01440.126-0.121-0.1210.0000.0000.0000.000
113A115GLY0-0.059-0.02338.2110.1290.1290.0000.0000.0000.000
114A116ILE00.019-0.00234.0410.3550.3550.0000.0000.0000.000
115A117THR00.0110.00331.659-0.289-0.2890.0000.0000.0000.000
116A118VAL0-0.0050.00432.4560.3200.3200.0000.0000.0000.000
117A119ARG10.8880.93524.212-12.141-12.1410.0000.0000.0000.000
118A120TYR0-0.0010.01330.3450.2100.2100.0000.0000.0000.000
119A121LEU00.0140.02225.0780.2240.2240.0000.0000.0000.000
120A122ALA00.0160.00629.237-0.342-0.3420.0000.0000.0000.000
121A123PHE0-0.016-0.02528.4140.3320.3320.0000.0000.0000.000
122A124PRO0-0.002-0.00331.109-0.269-0.2690.0000.0000.0000.000
123A125ARG10.9400.98333.475-8.179-8.1790.0000.0000.0000.000
124A126ALA0-0.0010.03235.0900.0950.0950.0000.0000.0000.000
125A127GLY00.022-0.00933.460-0.096-0.0960.0000.0000.0000.000
126A128MET00.0140.02130.270-0.160-0.1600.0000.0000.0000.000
127A129ASN0-0.008-0.01933.952-0.016-0.0160.0000.0000.0000.000
128A130ASN00.0510.01637.171-0.373-0.3730.0000.0000.0000.000
129A131GLN00.0620.02739.2430.1750.1750.0000.0000.0000.000
130A132THR00.0860.04338.5730.0210.0210.0000.0000.0000.000
131A133ALA0-0.0210.00434.9090.1560.1560.0000.0000.0000.000
132A134LYS10.8500.92935.513-8.412-8.4120.0000.0000.0000.000
133A135GLN00.0600.02037.6660.1340.1340.0000.0000.0000.000
134A136MET00.0070.02534.7010.0990.0990.0000.0000.0000.000
135A137GLU-1-0.749-0.86430.86010.33510.3350.0000.0000.0000.000
136A138ALA0-0.063-0.01134.2650.1130.1130.0000.0000.0000.000
137A139ILE0-0.001-0.02236.3970.0340.0340.0000.0000.0000.000
138A140TRP0-0.021-0.02930.214-0.156-0.1560.0000.0000.0000.000
139A141THR0-0.033-0.01831.0280.1390.1390.0000.0000.0000.000
140A142ALA0-0.050-0.00833.403-0.112-0.1120.0000.0000.0000.000
141A143LYS10.9570.96035.660-7.894-7.8940.0000.0000.0000.000
142A144ASP-1-0.876-0.94137.3438.2218.2210.0000.0000.0000.000
143A145PRO00.0520.01533.557-0.235-0.2350.0000.0000.0000.000
144A146VAL00.0750.05736.495-0.095-0.0950.0000.0000.0000.000
145A147PHE0-0.038-0.00238.452-0.187-0.1870.0000.0000.0000.000
146A148ALA0-0.012-0.01138.692-0.143-0.1430.0000.0000.0000.000
147A149LEU00.013-0.00136.173-0.101-0.1010.0000.0000.0000.000
148A150ASN00.001-0.00239.682-0.067-0.0670.0000.0000.0000.000
149A151GLU-1-0.880-0.93542.5336.5686.5680.0000.0000.0000.000
150A152ALA0-0.0010.00641.235-0.129-0.1290.0000.0000.0000.000
151A153GLU-1-0.890-0.96340.7777.6557.6550.0000.0000.0000.000
152A154LYS10.8450.93343.919-6.914-6.9140.0000.0000.0000.000
153A155GLY00.0090.01446.394-0.175-0.1750.0000.0000.0000.000
154A156ASN0-0.117-0.06547.050-0.159-0.1590.0000.0000.0000.000
155A157LEU00.000-0.00142.4610.1640.1640.0000.0000.0000.000
156A158PRO0-0.060-0.01940.779-0.143-0.1430.0000.0000.0000.000
157A159LYS10.9650.97244.044-6.285-6.2850.0000.0000.0000.000
158A160GLU-1-0.946-0.95441.0327.8067.8060.0000.0000.0000.000
159A161VAL00.061-0.00239.2270.0650.0650.0000.0000.0000.000
160A162LYS10.8760.98034.991-8.664-8.6640.0000.0000.0000.000
161A163THR00.025-0.00732.834-0.154-0.1540.0000.0000.0000.000
162A164PRO0-0.100-0.06932.1660.2250.2250.0000.0000.0000.000
163A165ASN0-0.006-0.00926.7580.4510.4510.0000.0000.0000.000
164A166ILE00.0520.03626.5110.4480.4480.0000.0000.0000.000
165A167VAL00.0160.01627.0740.2630.2630.0000.0000.0000.000
166A168LYS10.8650.89625.478-12.104-12.1040.0000.0000.0000.000
167A169LYS10.9080.96720.799-13.676-13.6760.0000.0000.0000.000
168A170HIS0-0.014-0.00923.5700.1330.1330.0000.0000.0000.000
169A171TYR0-0.013-0.01125.7940.1760.1760.0000.0000.0000.000
170A172GLU-1-0.857-0.93122.90813.19413.1940.0000.0000.0000.000
171A173LEU0-0.0220.00919.8640.4280.4280.0000.0000.0000.000
172A174GLY00.0540.01222.4710.1610.1610.0000.0000.0000.000
173A175ILE00.008-0.00224.961-0.085-0.0850.0000.0000.0000.000
174A176GLN0-0.048-0.01117.262-0.098-0.0980.0000.0000.0000.000
175A177PHE0-0.002-0.01221.0350.3510.3510.0000.0000.0000.000
176A178GLY0-0.0230.00723.779-0.254-0.2540.0000.0000.0000.000
177A179VAL0-0.064-0.02426.769-0.529-0.5290.0000.0000.0000.000
178A180ARG10.9230.95029.274-9.743-9.7430.0000.0000.0000.000
179A181GLY0-0.0050.00032.451-0.347-0.3470.0000.0000.0000.000
180A182THR0-0.0470.01433.3380.1950.1950.0000.0000.0000.000
181A183PRO00.048-0.00935.098-0.244-0.2440.0000.0000.0000.000
182A184SER0-0.039-0.03030.897-0.083-0.0830.0000.0000.0000.000
183A185ILE00.0150.01931.0200.2460.2460.0000.0000.0000.000
184A186VAL00.004-0.00324.4500.0450.0450.0000.0000.0000.000
185A187THR00.0350.04025.819-0.104-0.1040.0000.0000.0000.000
186A188SER00.0450.01525.3680.4130.4130.0000.0000.0000.000
187A189THR0-0.036-0.03023.4820.6900.6900.0000.0000.0000.000
188A190GLY0-0.004-0.02921.9050.4170.4170.0000.0000.0000.000
189A191GLU-1-0.940-0.96022.84211.01311.0130.0000.0000.0000.000
190A192LEU0-0.016-0.02825.8050.1480.1480.0000.0000.0000.000
191A193ILE00.0210.03228.331-0.155-0.1550.0000.0000.0000.000
192A194GLY0-0.032-0.02230.983-0.274-0.2740.0000.0000.0000.000
193A195GLY00.0560.02932.427-0.161-0.1610.0000.0000.0000.000
194A196TYR0-0.040-0.02536.105-0.018-0.0180.0000.0000.0000.000
195A197LEU00.0520.02435.705-0.093-0.0930.0000.0000.0000.000
196A198LYS10.9481.00839.459-6.855-6.8550.0000.0000.0000.000
197A199PRO00.0460.01840.6140.1340.1340.0000.0000.0000.000
198A200ALA00.032-0.00240.3600.1370.1370.0000.0000.0000.000
199A201ASP-1-0.891-0.95840.8037.5587.5580.0000.0000.0000.000
200A202LEU0-0.0090.00234.1320.1880.1880.0000.0000.0000.000
201A203LEU0-0.018-0.00936.1770.2810.2810.0000.0000.0000.000
202A204ARG10.9981.00436.771-7.340-7.3400.0000.0000.0000.000
203A205ALA00.0150.01735.0450.1660.1660.0000.0000.0000.000
204A206LEU0-0.071-0.03631.0880.3210.3210.0000.0000.0000.000
205A207GLU-1-0.997-0.99832.8118.5578.5570.0000.0000.0000.000
206A208GLU-1-0.952-0.98234.7588.4218.4210.0000.0000.0000.000
207A209THR0-0.085-0.03830.4280.2120.2120.0000.0000.0000.000
208A210ALA0-0.016-0.00127.3890.4300.4300.0000.0000.0000.000