Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: VKQZ1

Calculation Name: 2GAU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GAU

Chain ID: A

ChEMBL ID:

UniProt ID: Q7MAW7

Base Structure: X-ray

Registration Date: 2023-09-27

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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2677656.358955
FMO2-HF: Nuclear repulsion 2589410.356058
FMO2-HF: Total energy -88246.002897
FMO2-MP2: Total energy -88504.573458


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:10:LEU)


Summations of interaction energy for fragment #1(A:10:LEU)
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.
-22.123-12.087.228-5.722-11.547-0.027
Interaction energy analysis for fragmet #1(A:10:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.009
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].
3A12HIS00.0270.0052.685-2.8400.3330.604-1.559-2.218-0.004
4A13LEU0-0.072-0.0312.6510.1521.4891.187-0.544-1.9800.001
5A14LEU0-0.016-0.0025.0350.8500.8500.0000.0000.0000.000
6A15ARG10.8700.9137.8430.3550.3550.0000.0000.0000.000
7A16ASP-1-0.868-0.92110.151-0.448-0.4480.0000.0000.0000.000
8A17VAL00.0520.01710.1200.0500.0500.0000.0000.0000.000
9A18TRP00.0520.0445.431-0.003-0.0030.0000.0000.0000.000
10A19SER0-0.078-0.0529.9040.1030.1030.0000.0000.0000.000
11A20LEU0-0.080-0.03913.0750.1230.1230.0000.0000.0000.000
12A21LEU0-0.0450.0029.7320.0560.0560.0000.0000.0000.000
13A22ASN00.0060.00413.011-0.019-0.0190.0000.0000.0000.000
14A23GLU-1-0.815-0.92511.161-1.127-1.1270.0000.0000.0000.000
15A24GLU-1-0.879-0.92611.486-0.721-0.7210.0000.0000.0000.000
16A25GLU-1-0.844-0.92912.070-0.897-0.8970.0000.0000.0000.000
17A26ARG10.8070.8937.9670.9410.9410.0000.0000.0000.000
18A27GLU-1-0.911-0.9467.005-1.569-1.5690.0000.0000.0000.000
19A28LEU0-0.0240.0037.949-0.161-0.1610.0000.0000.0000.000
20A29LEU0-0.037-0.0295.751-0.060-0.0600.0000.0000.0000.000
21A30ASP-1-0.841-0.9492.665-14.097-11.3371.465-2.201-2.023-0.024
22A31LYS10.7640.8864.2360.8100.974-0.001-0.023-0.1400.000
23A32GLU-1-0.821-0.9017.077-0.472-0.4720.0000.0000.0000.000
24A33ILE0-0.097-0.0322.301-0.6960.3411.252-0.561-1.728-0.005
25A34GLN00.0030.0014.063-0.0730.3130.002-0.099-0.2890.000
26A35PRO0-0.018-0.0112.332-0.575-0.4942.143-0.440-1.7840.005
27A36PHE00.0190.0104.238-0.477-0.3870.001-0.021-0.0700.000
28A37PRO0-0.0080.0037.9210.0150.0150.0000.0000.0000.000
29A38CYS00.0240.00510.253-0.148-0.1480.0000.0000.0000.000
30A39LYS10.9901.01212.637-0.279-0.2790.0000.0000.0000.000
31A40LYS10.8950.93115.775-0.221-0.2210.0000.0000.0000.000
32A41ALA0-0.070-0.04918.6800.0010.0010.0000.0000.0000.000
33A42SER0-0.029-0.00416.142-0.013-0.0130.0000.0000.0000.000
34A43THR0-0.017-0.03318.282-0.003-0.0030.0000.0000.0000.000
35A44VAL0-0.0050.00513.0540.0140.0140.0000.0000.0000.000
36A45PHE00.0180.01015.666-0.022-0.0220.0000.0000.0000.000
37A46SER0-0.042-0.03718.4060.0190.0190.0000.0000.0000.000
38A47GLU-1-0.845-0.93722.191-0.037-0.0370.0000.0000.0000.000
39A48GLY00.016-0.00225.0810.0080.0080.0000.0000.0000.000
40A49ASP-1-0.813-0.89520.538-0.025-0.0250.0000.0000.0000.000
41A50ILE00.0360.01221.720-0.012-0.0120.0000.0000.0000.000
42A51PRO0-0.044-0.03018.8140.0050.0050.0000.0000.0000.000
43A52ASN00.0350.02615.952-0.016-0.0160.0000.0000.0000.000
44A53ASN0-0.014-0.01111.318-0.105-0.1050.0000.0000.0000.000
45A54LEU00.0120.02112.6010.0670.0670.0000.0000.0000.000
46A55PHE0-0.001-0.00610.513-0.050-0.0500.0000.0000.0000.000
47A56TYR00.0150.0157.200-0.046-0.0460.0000.0000.0000.000
48A57LEU0-0.044-0.0208.8350.1450.1450.0000.0000.0000.000
49A58TYR00.0330.0276.762-0.017-0.0170.0000.0000.0000.000
50A59GLU-1-0.774-0.8868.8950.8380.8380.0000.0000.0000.000
51A60GLY00.0270.02211.0900.0270.0270.0000.0000.0000.000
52A61LYS10.8060.88214.320-0.226-0.2260.0000.0000.0000.000
53A62ILE00.0260.03013.8890.0230.0230.0000.0000.0000.000
54A63LYS10.8570.92817.813-0.105-0.1050.0000.0000.0000.000
55A64ILE00.0000.00418.6040.0010.0010.0000.0000.0000.000
56A65LEU0-0.054-0.04122.385-0.002-0.0020.0000.0000.0000.000
57A66ARG10.9320.97625.4470.0490.0490.0000.0000.0000.000
58A67GLU-1-0.791-0.90828.170-0.003-0.0030.0000.0000.0000.000
59A68GLY0-0.0070.01931.1490.0040.0040.0000.0000.0000.000
60A69VAL00.0200.00733.5500.0000.0000.0000.0000.0000.000
61A70TYR0-0.045-0.02736.1440.0010.0010.0000.0000.0000.000
62A71GLY00.0120.01437.6850.0020.0020.0000.0000.0000.000
63A72ARG10.8200.90635.5420.0040.0040.0000.0000.0000.000
64A73PHE00.0660.04729.3020.0000.0000.0000.0000.0000.000
65A74HIS0-0.019-0.01929.323-0.005-0.0050.0000.0000.0000.000
66A75ILE00.0040.00225.3330.0000.0000.0000.0000.0000.000
67A76SER0-0.034-0.02525.125-0.007-0.0070.0000.0000.0000.000
68A77ARG10.8340.89818.0040.1180.1180.0000.0000.0000.000
69A78ILE0-0.027-0.01620.6080.0130.0130.0000.0000.0000.000
70A79VAL0-0.031-0.00615.605-0.011-0.0110.0000.0000.0000.000
71A80LYS10.9160.94817.2420.1010.1010.0000.0000.0000.000
72A81PRO00.007-0.01112.781-0.042-0.0420.0000.0000.0000.000
73A82GLY00.0220.01711.785-0.019-0.0190.0000.0000.0000.000
74A83GLN0-0.038-0.00512.761-0.045-0.0450.0000.0000.0000.000
75A84PHE00.0910.03510.3750.0550.0550.0000.0000.0000.000
76A85PHE0-0.061-0.05812.3650.0530.0530.0000.0000.0000.000
77A86GLY00.0380.00714.892-0.020-0.0200.0000.0000.0000.000
78A87MET00.0040.02016.134-0.017-0.0170.0000.0000.0000.000
79A88ARG10.8480.92717.7550.1090.1090.0000.0000.0000.000
80A89PRO0-0.0050.01120.0380.0000.0000.0000.0000.0000.000
81A90TYR00.0790.03018.334-0.008-0.0080.0000.0000.0000.000
82A91PHE0-0.013-0.02118.111-0.004-0.0040.0000.0000.0000.000
83A92ALA0-0.055-0.02022.4180.0060.0060.0000.0000.0000.000
84A93GLU-1-0.932-0.94424.244-0.183-0.1830.0000.0000.0000.000
85A94GLU-1-0.976-0.97924.836-0.100-0.1000.0000.0000.0000.000
86A95THR00.0150.00024.400-0.010-0.0100.0000.0000.0000.000
87A96CYS0-0.094-0.04620.953-0.007-0.0070.0000.0000.0000.000
88A97SER00.0360.01823.5330.0090.0090.0000.0000.0000.000
89A98SER0-0.075-0.06123.4520.0030.0030.0000.0000.0000.000
90A99THR00.0950.05121.984-0.007-0.0070.0000.0000.0000.000
91A100ALA0-0.047-0.00417.581-0.002-0.0020.0000.0000.0000.000
92A101ILE00.0260.00718.6140.0170.0170.0000.0000.0000.000
93A102ALA00.0340.03416.004-0.014-0.0140.0000.0000.0000.000
94A103VAL0-0.026-0.01517.738-0.003-0.0030.0000.0000.0000.000
95A104GLU-1-0.835-0.90716.4510.2110.2110.0000.0000.0000.000
96A105ASN00.0060.00114.516-0.034-0.0340.0000.0000.0000.000
97A106SER0-0.003-0.00812.562-0.028-0.0280.0000.0000.0000.000
98A107LYS10.8030.9016.748-0.986-0.9860.0000.0000.0000.000
99A108VAL0-0.007-0.0098.166-0.133-0.1330.0000.0000.0000.000
100A109LEU00.0140.0112.794-0.7490.2660.575-0.274-1.3150.000
101A110ALA0-0.004-0.0056.108-0.174-0.1740.0000.0000.0000.000
102A111ILE00.015-0.0017.211-0.228-0.2280.0000.0000.0000.000
103A112PRO00.0930.0629.1600.1310.1310.0000.0000.0000.000
104A113VAL00.008-0.00412.203-0.092-0.0920.0000.0000.0000.000
105A114GLU-1-0.864-0.93115.263-0.408-0.4080.0000.0000.0000.000
106A115ALA00.0160.01011.097-0.014-0.0140.0000.0000.0000.000
107A116ILE0-0.047-0.02811.460-0.053-0.0530.0000.0000.0000.000
108A117GLU-1-0.818-0.91814.048-0.340-0.3400.0000.0000.0000.000
109A118ALA0-0.015-0.00515.2430.0320.0320.0000.0000.0000.000
110A119LEU00.0060.00610.7100.0230.0230.0000.0000.0000.000
111A120LEU0-0.076-0.04615.3990.0470.0470.0000.0000.0000.000
112A121LYS10.8220.90318.4430.3950.3950.0000.0000.0000.000
113A122GLY00.0190.03318.9650.0430.0430.0000.0000.0000.000
114A123ASN0-0.001-0.00116.3070.0740.0740.0000.0000.0000.000
115A124THR00.0510.00819.381-0.008-0.0080.0000.0000.0000.000
116A125SER0-0.019-0.01418.6780.0460.0460.0000.0000.0000.000
117A126PHE00.0390.02912.660-0.001-0.0010.0000.0000.0000.000
118A127CYS00.0010.00517.4880.0270.0270.0000.0000.0000.000
119A128ARG10.9250.94420.3640.3350.3350.0000.0000.0000.000
120A129TYR0-0.035-0.00114.4740.0310.0310.0000.0000.0000.000
121A130PHE00.0560.00813.4750.0580.0580.0000.0000.0000.000
122A131LEU00.0140.02119.1900.0440.0440.0000.0000.0000.000
123A132LYS10.9510.98021.4900.2830.2830.0000.0000.0000.000
124A133ALA0-0.025-0.01018.5700.0330.0330.0000.0000.0000.000
125A134LEU00.0340.00420.6080.0340.0340.0000.0000.0000.000
126A135ALA00.0250.02522.8900.0250.0250.0000.0000.0000.000
127A136LYS10.8960.94122.9820.1640.1640.0000.0000.0000.000
128A137GLU-1-0.818-0.90221.222-0.105-0.1050.0000.0000.0000.000
129A138LEU00.0330.03324.4520.0170.0170.0000.0000.0000.000
130A139GLY00.0480.02527.7710.0130.0130.0000.0000.0000.000
131A140TYR0-0.123-0.07422.9020.0160.0160.0000.0000.0000.000
132A141ALA00.0230.01227.7530.0130.0130.0000.0000.0000.000
133A142GLU-1-0.883-0.94029.394-0.083-0.0830.0000.0000.0000.000
134A143ARG10.9330.96329.1870.0820.0820.0000.0000.0000.000
135A144ARG10.8020.89928.9420.0330.0330.0000.0000.0000.000
136A145THR00.0210.01532.6920.0080.0080.0000.0000.0000.000
137A146VAL00.0200.03835.2070.0050.0050.0000.0000.0000.000
138A147THR0-0.033-0.05634.8900.0050.0050.0000.0000.0000.000
139A148LEU0-0.078-0.05532.6880.0060.0060.0000.0000.0000.000
140A149THR0-0.039-0.04037.0580.0040.0040.0000.0000.0000.000
141A150GLN00.0030.01640.2090.0020.0020.0000.0000.0000.000
142A151LYS10.8120.91337.3600.0260.0260.0000.0000.0000.000
143A152HIS00.0750.03541.6820.0030.0030.0000.0000.0000.000
144A153VAL0-0.002-0.02041.2580.0000.0000.0000.0000.0000.000
145A154ARG10.8330.87440.310-0.006-0.0060.0000.0000.0000.000
146A155GLY00.0390.02640.0350.0010.0010.0000.0000.0000.000
147A156ARG10.8510.92337.0670.0060.0060.0000.0000.0000.000
148A157LEU0-0.0080.00734.7590.0000.0000.0000.0000.0000.000
149A158ALA00.0300.01435.0110.0030.0030.0000.0000.0000.000
150A159GLU-1-0.822-0.87433.102-0.029-0.0290.0000.0000.0000.000
151A160THR0-0.025-0.02630.440-0.002-0.0020.0000.0000.0000.000
152A161LEU0-0.002-0.00730.2050.0030.0030.0000.0000.0000.000
153A162LEU0-0.0030.00430.3950.0030.0030.0000.0000.0000.000
154A163ILE0-0.0030.00226.826-0.003-0.0030.0000.0000.0000.000
155A164LEU0-0.034-0.01225.569-0.001-0.0010.0000.0000.0000.000
156A165LYS10.9230.95525.5250.0080.0080.0000.0000.0000.000
157A166GLU-1-0.946-0.95925.880-0.024-0.0240.0000.0000.0000.000
158A167ASN0-0.047-0.02422.087-0.018-0.0180.0000.0000.0000.000
159A168PHE0-0.015-0.03419.2070.0020.0020.0000.0000.0000.000
160A169GLY00.0260.04522.3660.0150.0150.0000.0000.0000.000
161A170PHE0-0.058-0.04424.7710.0000.0000.0000.0000.0000.000
162A171GLU-1-0.743-0.84224.1080.1520.1520.0000.0000.0000.000
163A172ASN00.019-0.00624.793-0.013-0.0130.0000.0000.0000.000
164A173ASP-1-0.769-0.85427.5830.0690.0690.0000.0000.0000.000
165A174GLY00.0030.01029.318-0.007-0.0070.0000.0000.0000.000
166A175ALA0-0.015-0.00830.461-0.008-0.0080.0000.0000.0000.000
167A176THR0-0.110-0.08528.901-0.006-0.0060.0000.0000.0000.000
168A177LEU0-0.031-0.00427.4500.0030.0030.0000.0000.0000.000
169A178SER0-0.001-0.00422.2770.0040.0040.0000.0000.0000.000
170A179ILE0-0.066-0.03622.4850.0150.0150.0000.0000.0000.000
171A180TYR0-0.055-0.04223.723-0.013-0.0130.0000.0000.0000.000
172A181LEU0-0.018-0.00124.6210.0060.0060.0000.0000.0000.000
173A182SER0-0.062-0.06727.435-0.002-0.0020.0000.0000.0000.000
174A183ARG10.9590.96730.271-0.065-0.0650.0000.0000.0000.000
175A184GLU-1-0.805-0.91531.6690.0500.0500.0000.0000.0000.000
176A185GLU-1-0.791-0.83525.6970.0790.0790.0000.0000.0000.000
177A186LEU00.0190.00929.805-0.009-0.0090.0000.0000.0000.000
178A187ALA0-0.0150.00531.724-0.007-0.0070.0000.0000.0000.000
179A188THR0-0.019-0.01130.869-0.006-0.0060.0000.0000.0000.000
180A189LEU0-0.038-0.01527.458-0.007-0.0070.0000.0000.0000.000
181A190SER00.0170.00330.929-0.008-0.0080.0000.0000.0000.000
182A191ASN0-0.0030.00834.2450.0000.0000.0000.0000.0000.000
183A192MET0-0.0380.00036.4030.0000.0000.0000.0000.0000.000
184A193THR00.0810.04537.4820.0030.0030.0000.0000.0000.000
185A194VAL00.1090.03836.001-0.001-0.0010.0000.0000.0000.000
186A195SER00.0130.01738.4980.0010.0010.0000.0000.0000.000
187A196ASN00.015-0.01141.6870.0020.0020.0000.0000.0000.000
188A197ALA00.0700.05436.861-0.001-0.0010.0000.0000.0000.000
189A198ILE0-0.017-0.01738.1810.0010.0010.0000.0000.0000.000
190A199ARG10.9490.98940.200-0.019-0.0190.0000.0000.0000.000
191A200THR0-0.018-0.03240.379-0.002-0.0020.0000.0000.0000.000
192A201LEU0-0.007-0.00435.5140.0000.0000.0000.0000.0000.000
193A202SER00.0380.02639.8040.0020.0020.0000.0000.0000.000
194A203THR0-0.041-0.01642.9450.0000.0000.0000.0000.0000.000
195A204PHE00.017-0.00438.226-0.001-0.0010.0000.0000.0000.000
196A205VAL00.0040.01140.0180.0000.0000.0000.0000.0000.000
197A206SER0-0.024-0.00842.3800.0000.0000.0000.0000.0000.000
198A207GLU-1-0.816-0.87744.6840.0110.0110.0000.0000.0000.000
199A208ARG10.9310.97243.146-0.027-0.0270.0000.0000.0000.000
200A209MET0-0.0300.00040.336-0.001-0.0010.0000.0000.0000.000
201A210LEU0-0.034-0.02335.5000.0010.0010.0000.0000.0000.000
202A211ALA00.0340.01837.038-0.001-0.0010.0000.0000.0000.000
203A212LEU0-0.032-0.02135.5870.0020.0020.0000.0000.0000.000
204A213ASP-1-0.780-0.86434.2510.0870.0870.0000.0000.0000.000
205A214GLY00.0740.04733.3040.0070.0070.0000.0000.0000.000
206A215LYS10.8490.90427.198-0.111-0.1110.0000.0000.0000.000
207A216ARG10.8500.92229.249-0.107-0.1070.0000.0000.0000.000
208A217ILE0-0.007-0.00630.644-0.006-0.0060.0000.0000.0000.000
209A218LYS10.9010.96231.455-0.066-0.0660.0000.0000.0000.000
210A219ILE0-0.009-0.02331.872-0.005-0.0050.0000.0000.0000.000
211A220ILE0-0.021-0.01234.9720.0010.0010.0000.0000.0000.000
212A221ASP-1-0.805-0.87738.0720.0110.0110.0000.0000.0000.000
213A222CYS00.002-0.01434.616-0.002-0.0020.0000.0000.0000.000
214A223ASP-1-0.832-0.91137.117-0.004-0.0040.0000.0000.0000.000
215A224ARG10.8220.88639.834-0.017-0.0170.0000.0000.0000.000
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