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: 16NVZ

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 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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2681794.052717
FMO2-HF: Nuclear repulsion 2593547.646063
FMO2-HF: Total energy -88246.406654
FMO2-MP2: Total energy -88504.896384


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.
-30.857-24.18416.194-8.714-14.151-0.056
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 : 0.020 / q_NPA : -0.004
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].
3A12HIS00.0260.0082.269-6.288-4.2274.858-2.951-3.967-0.009
4A13LEU0-0.059-0.0242.5390.4181.7771.460-0.722-2.0980.001
5A14LEU0-0.013-0.0014.9900.8960.8960.0000.0000.0000.000
6A15ARG10.8650.9067.7900.4550.4550.0000.0000.0000.000
7A16ASP-1-0.809-0.8779.912-0.516-0.5160.0000.0000.0000.000
8A17VAL00.0560.03010.0840.0550.0550.0000.0000.0000.000
9A18TRP00.0400.0345.396-0.038-0.0380.0000.0000.0000.000
10A19SER0-0.076-0.0529.6510.1380.1380.0000.0000.0000.000
11A20LEU0-0.066-0.03412.9400.1200.1200.0000.0000.0000.000
12A21LEU0-0.0240.0099.7330.0920.0920.0000.0000.0000.000
13A22ASN00.0020.00412.893-0.022-0.0220.0000.0000.0000.000
14A23GLU-1-0.792-0.90211.486-1.260-1.2600.0000.0000.0000.000
15A24GLU-1-0.882-0.92111.143-0.817-0.8170.0000.0000.0000.000
16A25GLU-1-0.821-0.91811.997-0.945-0.9450.0000.0000.0000.000
17A26ARG10.7500.8587.8431.1091.1090.0000.0000.0000.000
18A27GLU-1-0.911-0.9546.898-1.711-1.7110.0000.0000.0000.000
19A28LEU0-0.026-0.0038.270-0.095-0.0950.0000.0000.0000.000
20A29LEU0-0.051-0.0305.755-0.050-0.0500.0000.0000.0000.000
21A30ASP-1-0.814-0.9341.973-19.755-19.7136.776-3.724-3.093-0.049
22A31LYS10.7550.8864.4731.2081.374-0.001-0.011-0.1540.000
23A32GLU-1-0.798-0.8837.219-0.470-0.4700.0000.0000.0000.000
24A33ILE0-0.095-0.0292.355-0.4630.3001.747-0.592-1.918-0.002
25A34GLN0-0.003-0.0083.852-0.1380.3550.005-0.136-0.362-0.001
26A35PRO0-0.018-0.0172.532-1.086-0.3641.159-0.349-1.5310.004
27A36PHE00.0330.0134.360-0.488-0.4070.000-0.017-0.0640.000
28A37PRO0-0.0130.0028.1040.0510.0510.0000.0000.0000.000
29A38CYS00.0200.01610.644-0.161-0.1610.0000.0000.0000.000
30A39LYS10.9650.98713.045-0.317-0.3170.0000.0000.0000.000
31A40LYS10.8870.93015.935-0.264-0.2640.0000.0000.0000.000
32A41ALA0-0.043-0.03618.9330.0020.0020.0000.0000.0000.000
33A42SER0-0.0190.00316.291-0.013-0.0130.0000.0000.0000.000
34A43THR0-0.002-0.02418.180-0.007-0.0070.0000.0000.0000.000
35A44VAL0-0.0110.00212.9550.0240.0240.0000.0000.0000.000
36A45PHE00.0230.02015.586-0.028-0.0280.0000.0000.0000.000
37A46SER0-0.048-0.03918.3320.0210.0210.0000.0000.0000.000
38A47GLU-1-0.865-0.94822.172-0.030-0.0300.0000.0000.0000.000
39A48GLY00.0280.01825.1410.0080.0080.0000.0000.0000.000
40A49ASP-1-0.800-0.88720.5300.0030.0030.0000.0000.0000.000
41A50ILE00.0600.03021.126-0.013-0.0130.0000.0000.0000.000
42A51PRO0-0.009-0.00918.5920.0090.0090.0000.0000.0000.000
43A52ASN00.0010.00115.794-0.019-0.0190.0000.0000.0000.000
44A53ASN0-0.025-0.01810.891-0.085-0.0850.0000.0000.0000.000
45A54LEU0-0.0010.02012.3010.0620.0620.0000.0000.0000.000
46A55PHE00.009-0.01210.381-0.025-0.0250.0000.0000.0000.000
47A56TYR0-0.003-0.0037.576-0.103-0.1030.0000.0000.0000.000
48A57LEU0-0.032-0.0099.1490.1690.1690.0000.0000.0000.000
49A58TYR00.0390.0316.795-0.048-0.0480.0000.0000.0000.000
50A59GLU-1-0.771-0.8818.7861.0131.0130.0000.0000.0000.000
51A60GLY00.0210.01711.1590.0280.0280.0000.0000.0000.000
52A61LYS10.7930.88314.336-0.255-0.2550.0000.0000.0000.000
53A62ILE00.0150.01914.0790.0250.0250.0000.0000.0000.000
54A63LYS10.8650.93217.866-0.138-0.1380.0000.0000.0000.000
55A64ILE00.0040.00818.4580.0060.0060.0000.0000.0000.000
56A65LEU0-0.046-0.03622.305-0.002-0.0020.0000.0000.0000.000
57A66ARG10.9030.95525.3790.0340.0340.0000.0000.0000.000
58A67GLU-1-0.804-0.93228.1660.0110.0110.0000.0000.0000.000
59A68GLY0-0.0110.02831.2000.0020.0020.0000.0000.0000.000
60A69VAL00.0270.00833.8890.0000.0000.0000.0000.0000.000
61A70TYR0-0.042-0.02336.3350.0010.0010.0000.0000.0000.000
62A71GLY00.0160.01537.8270.0010.0010.0000.0000.0000.000
63A72ARG10.7790.88035.759-0.005-0.0050.0000.0000.0000.000
64A73PHE00.0450.03430.020-0.002-0.0020.0000.0000.0000.000
65A74HIS0-0.009-0.01329.572-0.005-0.0050.0000.0000.0000.000
66A75ILE0-0.006-0.00625.281-0.002-0.0020.0000.0000.0000.000
67A76SER00.0050.00025.017-0.002-0.0020.0000.0000.0000.000
68A77ARG10.8130.88517.7450.1050.1050.0000.0000.0000.000
69A78ILE0-0.031-0.02420.6170.0140.0140.0000.0000.0000.000
70A79VAL0-0.0170.00815.500-0.013-0.0130.0000.0000.0000.000
71A80LYS10.8960.94317.1400.0900.0900.0000.0000.0000.000
72A81PRO0-0.003-0.01512.884-0.043-0.0430.0000.0000.0000.000
73A82GLY00.0290.02512.145-0.026-0.0260.0000.0000.0000.000
74A83GLN0-0.0250.00013.138-0.070-0.0700.0000.0000.0000.000
75A84PHE00.0930.04310.4640.0600.0600.0000.0000.0000.000
76A85PHE0-0.036-0.04512.2720.0590.0590.0000.0000.0000.000
77A86GLY00.0300.01314.645-0.035-0.0350.0000.0000.0000.000
78A87MET0-0.0070.00015.936-0.002-0.0020.0000.0000.0000.000
79A88ARG10.7950.90817.4770.0890.0890.0000.0000.0000.000
80A89PRO00.0330.02320.269-0.002-0.0020.0000.0000.0000.000
81A90TYR00.0560.02217.823-0.001-0.0010.0000.0000.0000.000
82A91PHE0-0.027-0.03217.367-0.009-0.0090.0000.0000.0000.000
83A92ALA0-0.042-0.01322.1310.0050.0050.0000.0000.0000.000
84A93GLU-1-0.942-0.95224.237-0.173-0.1730.0000.0000.0000.000
85A94GLU-1-0.969-0.97024.801-0.093-0.0930.0000.0000.0000.000
86A95THR00.010-0.00624.177-0.007-0.0070.0000.0000.0000.000
87A96CYS0-0.060-0.04220.489-0.007-0.0070.0000.0000.0000.000
88A97SER00.0570.03323.1060.0130.0130.0000.0000.0000.000
89A98SER0-0.072-0.05923.5580.0010.0010.0000.0000.0000.000
90A99THR00.0780.05122.013-0.012-0.0120.0000.0000.0000.000
91A100ALA0-0.0310.00217.807-0.008-0.0080.0000.0000.0000.000
92A101ILE00.017-0.00619.0060.0200.0200.0000.0000.0000.000
93A102ALA00.0250.02816.519-0.013-0.0130.0000.0000.0000.000
94A103VAL0-0.020-0.00818.040-0.004-0.0040.0000.0000.0000.000
95A104GLU-1-0.848-0.92216.6280.2350.2350.0000.0000.0000.000
96A105ASN00.0090.00814.754-0.023-0.0230.0000.0000.0000.000
97A106SER00.0060.00212.532-0.017-0.0170.0000.0000.0000.000
98A107LYS10.8000.8926.764-1.198-1.1980.0000.0000.0000.000
99A108VAL0-0.007-0.0108.493-0.133-0.1330.0000.0000.0000.000
100A109LEU0-0.0010.0122.994-0.5830.4030.190-0.212-0.9640.000
101A110ALA0-0.012-0.0126.117-0.169-0.1690.0000.0000.0000.000
102A111ILE00.0150.0026.970-0.187-0.1870.0000.0000.0000.000
103A112PRO00.0850.0589.0930.1080.1080.0000.0000.0000.000
104A113VAL00.0100.00712.256-0.092-0.0920.0000.0000.0000.000
105A114GLU-1-0.839-0.93315.196-0.395-0.3950.0000.0000.0000.000
106A115ALA00.0110.01611.002-0.018-0.0180.0000.0000.0000.000
107A116ILE0-0.035-0.02011.263-0.075-0.0750.0000.0000.0000.000
108A117GLU-1-0.800-0.89314.154-0.355-0.3550.0000.0000.0000.000
109A118ALA0-0.019-0.01115.2420.0230.0230.0000.0000.0000.000
110A119LEU00.0080.01010.7620.0150.0150.0000.0000.0000.000
111A120LEU0-0.080-0.05015.5070.0390.0390.0000.0000.0000.000
112A121LYS10.7970.88418.5050.4040.4040.0000.0000.0000.000
113A122GLY00.0200.03918.8460.0390.0390.0000.0000.0000.000
114A123ASN0-0.022-0.02015.9830.0990.0990.0000.0000.0000.000
115A124THR00.0740.01918.921-0.006-0.0060.0000.0000.0000.000
116A125SER0-0.040-0.02718.9040.0560.0560.0000.0000.0000.000
117A126PHE00.0320.02012.2640.0060.0060.0000.0000.0000.000
118A127CYS0-0.0110.00017.2080.0320.0320.0000.0000.0000.000
119A128ARG10.9200.94719.9560.3730.3730.0000.0000.0000.000
120A129TYR0-0.076-0.02914.4570.0390.0390.0000.0000.0000.000
121A130PHE00.0590.01613.1910.0630.0630.0000.0000.0000.000
122A131LEU00.0180.01818.9090.0470.0470.0000.0000.0000.000
123A132LYS10.9400.97121.2640.3150.3150.0000.0000.0000.000
124A133ALA0-0.022-0.01318.6220.0340.0340.0000.0000.0000.000
125A134LEU00.0200.00520.7070.0360.0360.0000.0000.0000.000
126A135ALA00.0330.02123.0330.0260.0260.0000.0000.0000.000
127A136LYS10.8800.94223.1030.1680.1680.0000.0000.0000.000
128A137GLU-1-0.788-0.89521.166-0.094-0.0940.0000.0000.0000.000
129A138LEU00.0300.03424.4910.0180.0180.0000.0000.0000.000
130A139GLY00.0730.04127.7220.0130.0130.0000.0000.0000.000
131A140TYR0-0.115-0.05223.1120.0140.0140.0000.0000.0000.000
132A141ALA00.0350.01527.7720.0130.0130.0000.0000.0000.000
133A142GLU-1-0.869-0.92429.507-0.081-0.0810.0000.0000.0000.000
134A143ARG10.8920.93729.6810.0790.0790.0000.0000.0000.000
135A144ARG10.8040.90128.7670.0220.0220.0000.0000.0000.000
136A145THR00.007-0.00532.7910.0080.0080.0000.0000.0000.000
137A146VAL00.0230.03635.0450.0050.0050.0000.0000.0000.000
138A147THR0-0.038-0.05535.2940.0050.0050.0000.0000.0000.000
139A148LEU0-0.074-0.05732.6600.0060.0060.0000.0000.0000.000
140A149THR0-0.043-0.03237.0800.0040.0040.0000.0000.0000.000
141A150GLN00.0050.01740.3450.0010.0010.0000.0000.0000.000
142A151LYS10.8050.90837.5280.0230.0230.0000.0000.0000.000
143A152HIS00.0720.03241.7140.0040.0040.0000.0000.0000.000
144A153VAL00.002-0.01341.0400.0000.0000.0000.0000.0000.000
145A154ARG10.8200.86439.972-0.011-0.0110.0000.0000.0000.000
146A155GLY00.0570.03539.6860.0010.0010.0000.0000.0000.000
147A156ARG10.8440.91636.881-0.001-0.0010.0000.0000.0000.000
148A157LEU0-0.0050.00834.3720.0010.0010.0000.0000.0000.000
149A158ALA00.0270.01434.8140.0030.0030.0000.0000.0000.000
150A159GLU-1-0.799-0.86933.360-0.023-0.0230.0000.0000.0000.000
151A160THR0-0.032-0.03030.424-0.002-0.0020.0000.0000.0000.000
152A161LEU0-0.005-0.01130.1010.0040.0040.0000.0000.0000.000
153A162LEU0-0.0010.01030.2250.0040.0040.0000.0000.0000.000
154A163ILE00.0020.00527.037-0.003-0.0030.0000.0000.0000.000
155A164LEU0-0.021-0.01025.5070.0000.0000.0000.0000.0000.000
156A165LYS10.8840.93425.4340.0060.0060.0000.0000.0000.000
157A166GLU-1-0.850-0.91025.874-0.010-0.0100.0000.0000.0000.000
158A167ASN0-0.116-0.06822.122-0.029-0.0290.0000.0000.0000.000
159A168PHE00.001-0.02719.2990.0070.0070.0000.0000.0000.000
160A169GLY00.0240.03722.2820.0170.0170.0000.0000.0000.000
161A170PHE0-0.063-0.05524.683-0.003-0.0030.0000.0000.0000.000
162A171GLU-1-0.763-0.86424.4900.1690.1690.0000.0000.0000.000
163A172ASN0-0.005-0.00924.617-0.013-0.0130.0000.0000.0000.000
164A173ASP-1-0.769-0.86127.8630.0790.0790.0000.0000.0000.000
165A174GLY0-0.0030.00829.689-0.008-0.0080.0000.0000.0000.000
166A175ALA0-0.0060.00230.818-0.009-0.0090.0000.0000.0000.000
167A176THR0-0.061-0.05629.201-0.005-0.0050.0000.0000.0000.000
168A177LEU0-0.0150.00527.4260.0040.0040.0000.0000.0000.000
169A178SER00.0130.00322.4460.0020.0020.0000.0000.0000.000
170A179ILE0-0.063-0.04922.3630.0170.0170.0000.0000.0000.000
171A180TYR0-0.030-0.00923.724-0.016-0.0160.0000.0000.0000.000
172A181LEU00.0090.00924.5400.0080.0080.0000.0000.0000.000
173A182SER0-0.049-0.05227.388-0.003-0.0030.0000.0000.0000.000
174A183ARG10.9060.94630.428-0.077-0.0770.0000.0000.0000.000
175A184GLU-1-0.792-0.91032.0450.0610.0610.0000.0000.0000.000
176A185GLU-1-0.785-0.83325.8480.1000.1000.0000.0000.0000.000
177A186LEU00.0330.01629.903-0.009-0.0090.0000.0000.0000.000
178A187ALA0-0.0180.00331.619-0.008-0.0080.0000.0000.0000.000
179A188THR0-0.024-0.01630.641-0.007-0.0070.0000.0000.0000.000
180A189LEU0-0.033-0.01427.258-0.007-0.0070.0000.0000.0000.000
181A190SER00.015-0.00530.706-0.009-0.0090.0000.0000.0000.000
182A191ASN00.0140.01434.1730.0000.0000.0000.0000.0000.000
183A192MET0-0.0410.00036.270-0.001-0.0010.0000.0000.0000.000
184A193THR00.0780.04337.5440.0030.0030.0000.0000.0000.000
185A194VAL00.0880.03336.212-0.001-0.0010.0000.0000.0000.000
186A195SER00.0310.01238.6450.0010.0010.0000.0000.0000.000
187A196ASN0-0.0030.00341.1910.0010.0010.0000.0000.0000.000
188A197ALA00.0920.05636.526-0.001-0.0010.0000.0000.0000.000
189A198ILE0-0.009-0.01537.9170.0010.0010.0000.0000.0000.000
190A199ARG10.9220.96839.805-0.026-0.0260.0000.0000.0000.000
191A200THR0-0.006-0.00340.025-0.002-0.0020.0000.0000.0000.000
192A201LEU0-0.005-0.00235.3270.0000.0000.0000.0000.0000.000
193A202SER00.0510.02039.5160.0010.0010.0000.0000.0000.000
194A203THR0-0.056-0.02142.711-0.001-0.0010.0000.0000.0000.000
195A204PHE00.024-0.00738.271-0.002-0.0020.0000.0000.0000.000
196A205VAL00.0110.01740.3630.0000.0000.0000.0000.0000.000
197A206SER0-0.021-0.01442.565-0.001-0.0010.0000.0000.0000.000
198A207GLU-1-0.800-0.87244.8620.0150.0150.0000.0000.0000.000
199A208ARG10.8990.96143.352-0.032-0.0320.0000.0000.0000.000
200A209MET0-0.0230.00140.417-0.003-0.0030.0000.0000.0000.000
201A210LEU0-0.022-0.01235.4150.0010.0010.0000.0000.0000.000
202A211ALA00.0320.02237.091-0.001-0.0010.0000.0000.0000.000
203A212LEU0-0.032-0.02735.7310.0020.0020.0000.0000.0000.000
204A213ASP-1-0.794-0.86334.1040.1000.1000.0000.0000.0000.000
205A214GLY00.0730.04333.2990.0080.0080.0000.0000.0000.000
206A215LYS10.8390.89226.942-0.130-0.1300.0000.0000.0000.000
207A216ARG10.8500.91829.054-0.121-0.1210.0000.0000.0000.000
208A217ILE0-0.007-0.00830.675-0.007-0.0070.0000.0000.0000.000
209A218LYS10.8510.92831.373-0.076-0.0760.0000.0000.0000.000
210A219ILE00.010-0.00131.973-0.005-0.0050.0000.0000.0000.000
211A220ILE0-0.015-0.01035.0450.0010.0010.0000.0000.0000.000
212A221ASP-1-0.805-0.87438.2180.0140.0140.0000.0000.0000.000
213A222CYS00.012-0.00934.560-0.001-0.0010.0000.0000.0000.000
214A223ASP-1-0.828-0.90537.127-0.002-0.0020.0000.0000.0000.000
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