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: 2NYNR

Calculation Name: 2AUK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AUK

Chain ID: A

ChEMBL ID:

UniProt ID: P0A8T7

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1740567.904989
FMO2-HF: Nuclear repulsion 1670348.757385
FMO2-HF: Total energy -70219.147604
FMO2-MP2: Total energy -70424.82837


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:1:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-12.834-12.02216.113-8.548-8.376-0.032
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : -0.002
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].
3A3HIS00.0080.0062.561-4.983-1.9153.503-3.428-3.1430.000
4A4MET0-0.090-0.0252.5440.8291.6662.099-1.002-1.9340.000
5A5ALA00.1150.0475.131-0.474-0.504-0.001-0.0040.0360.000
6A6ALA00.0420.0105.6750.0750.0750.0000.0000.0000.000
7A7ALA0-0.059-0.0154.1440.0000.092-0.001-0.043-0.0470.000
8A8GLU-1-0.929-0.9585.899-0.994-0.9940.0000.0000.0000.000
9A9SER0-0.062-0.0349.3920.2640.2640.0000.0000.0000.000
10A10SER0-0.039-0.0256.9410.0010.0010.0000.0000.0000.000
11A11ILE0-0.020-0.0048.186-0.281-0.2810.0000.0000.0000.000
12A12GLN0-0.0250.0011.958-8.492-11.64710.513-4.071-3.288-0.032
13A13VAL0-0.0220.0035.914-0.154-0.1540.0000.0000.0000.000
14A14LYS10.9210.9416.8081.4961.4960.0000.0000.0000.000
15A15ASN0-0.115-0.0568.2860.3710.3710.0000.0000.0000.000
16A16LYS10.9620.97711.540-0.235-0.2350.0000.0000.0000.000
17A17GLY00.005-0.00614.030-0.040-0.0400.0000.0000.0000.000
18A18SER0-0.044-0.01516.8980.0220.0220.0000.0000.0000.000
19A19ILE00.0450.02213.546-0.042-0.0420.0000.0000.0000.000
20A20LYS10.8290.90717.5660.1880.1880.0000.0000.0000.000
21A21LEU0-0.016-0.00517.905-0.043-0.0430.0000.0000.0000.000
22A22SER0-0.019-0.01121.0260.0350.0350.0000.0000.0000.000
23A23ASN0-0.036-0.03323.429-0.004-0.0040.0000.0000.0000.000
24A24VAL00.0080.01021.744-0.016-0.0160.0000.0000.0000.000
25A25LYS10.9640.98824.3890.1960.1960.0000.0000.0000.000
26A26SER0-0.025-0.01022.979-0.017-0.0170.0000.0000.0000.000
27A27VAL00.0180.02924.5070.0160.0160.0000.0000.0000.000
28A28VAL00.0050.01424.385-0.016-0.0160.0000.0000.0000.000
29A29ASN00.0380.03122.4940.0200.0200.0000.0000.0000.000
30A30SER00.022-0.01826.0830.0130.0130.0000.0000.0000.000
31A31SER0-0.040-0.00722.6250.0110.0110.0000.0000.0000.000
32A32GLY0-0.019-0.01322.9210.0110.0110.0000.0000.0000.000
33A33LYS10.8330.91418.1370.0750.0750.0000.0000.0000.000
34A34LEU00.0400.03219.8030.0020.0020.0000.0000.0000.000
35A35VAL00.011-0.00219.626-0.039-0.0390.0000.0000.0000.000
36A36ILE00.0180.01517.8510.0260.0260.0000.0000.0000.000
37A37THR00.0230.00021.703-0.013-0.0130.0000.0000.0000.000
38A38SER0-0.020-0.02723.7110.0220.0220.0000.0000.0000.000
39A39ARG10.9480.95923.4420.2330.2330.0000.0000.0000.000
40A40ASN0-0.016-0.00623.534-0.032-0.0320.0000.0000.0000.000
41A41THR00.0430.04519.7120.0270.0270.0000.0000.0000.000
42A42GLU-1-0.847-0.89718.805-0.365-0.3650.0000.0000.0000.000
43A43LEU00.0130.01413.7510.0520.0520.0000.0000.0000.000
44A44LYS10.9100.94316.0160.2190.2190.0000.0000.0000.000
45A45LEU00.0080.02912.5830.0210.0210.0000.0000.0000.000
46A46ILE0-0.056-0.02615.8590.0000.0000.0000.0000.0000.000
47A47ASP-1-0.763-0.87318.451-0.025-0.0250.0000.0000.0000.000
48A48GLU-1-0.836-0.95019.2860.0320.0320.0000.0000.0000.000
49A49PHE0-0.079-0.03522.1770.0030.0030.0000.0000.0000.000
50A50GLY00.0020.00923.078-0.005-0.0050.0000.0000.0000.000
51A51ARG10.8310.89521.7280.0210.0210.0000.0000.0000.000
52A52THR0-0.012-0.00618.667-0.005-0.0050.0000.0000.0000.000
53A53LYS10.9030.95815.2590.0390.0390.0000.0000.0000.000
54A54GLU-1-0.744-0.83510.532-0.645-0.6450.0000.0000.0000.000
55A55SER00.009-0.01014.6010.0820.0820.0000.0000.0000.000
56A56TYR0-0.025-0.0229.928-0.186-0.1860.0000.0000.0000.000
57A57LYS10.8790.93515.1500.4740.4740.0000.0000.0000.000
58A58VAL00.023-0.00615.106-0.089-0.0890.0000.0000.0000.000
59A59PRO00.0170.01615.7540.0770.0770.0000.0000.0000.000
60A60TYR0-0.033-0.02518.6580.0150.0150.0000.0000.0000.000
61A61GLY00.005-0.01020.636-0.018-0.0180.0000.0000.0000.000
62A62ALA0-0.0410.00315.5750.0000.0000.0000.0000.0000.000
63A63VAL0-0.003-0.00115.7120.0640.0640.0000.0000.0000.000
64A64LEU0-0.034-0.02614.966-0.079-0.0790.0000.0000.0000.000
65A65ALA0-0.050-0.03212.9610.0480.0480.0000.0000.0000.000
66A66LYS10.7990.88114.550-0.030-0.0300.0000.0000.0000.000
67A67GLY00.0140.00617.401-0.046-0.0460.0000.0000.0000.000
68A68ASP-1-0.796-0.89919.613-0.159-0.1590.0000.0000.0000.000
69A69GLY0-0.004-0.00120.7740.0220.0220.0000.0000.0000.000
70A70GLU-1-0.865-0.92318.5340.0040.0040.0000.0000.0000.000
71A71GLN0-0.020-0.01717.9900.0040.0040.0000.0000.0000.000
72A72VAL0-0.014-0.00512.7540.0060.0060.0000.0000.0000.000
73A73ALA0-0.012-0.00912.297-0.006-0.0060.0000.0000.0000.000
74A74GLY00.0360.0189.788-0.090-0.0900.0000.0000.0000.000
75A75GLY0-0.031-0.0195.5880.3420.3420.0000.0000.0000.000
76A76GLU-1-0.770-0.8695.6690.3450.3450.0000.0000.0000.000
77A77THR0-0.004-0.0125.484-0.178-0.1780.0000.0000.0000.000
78A78VAL00.001-0.0037.8170.1870.1870.0000.0000.0000.000
79A79ALA0-0.0090.00410.3180.1100.1100.0000.0000.0000.000
80A80ASN00.0200.00110.271-0.348-0.3480.0000.0000.0000.000
81A81TRP00.002-0.00612.0290.1170.1170.0000.0000.0000.000
82A82ASP-1-0.784-0.89213.622-0.527-0.5270.0000.0000.0000.000
83A83PRO00.007-0.00113.1340.0240.0240.0000.0000.0000.000
84A84HIS00.0390.02914.7700.0540.0540.0000.0000.0000.000
85A85THR0-0.022-0.00718.6630.0720.0720.0000.0000.0000.000
86A86MET0-0.0170.00720.441-0.034-0.0340.0000.0000.0000.000
87A87PRO0-0.0160.00021.4530.0290.0290.0000.0000.0000.000
88A88VAL00.0070.00624.2590.0010.0010.0000.0000.0000.000
89A89ILE0-0.046-0.03023.2560.0050.0050.0000.0000.0000.000
90A90THR00.0100.02327.8390.0030.0030.0000.0000.0000.000
91A91GLU-1-0.937-0.98830.039-0.127-0.1270.0000.0000.0000.000
92A92VAL0-0.022-0.01732.1280.0050.0050.0000.0000.0000.000
93A93SER00.0180.00633.647-0.007-0.0070.0000.0000.0000.000
94A94GLY0-0.016-0.00434.8410.0020.0020.0000.0000.0000.000
95A95PHE0-0.029-0.00936.5920.0030.0030.0000.0000.0000.000
96A96VAL0-0.0040.01233.669-0.003-0.0030.0000.0000.0000.000
97A97ARG10.9030.96936.9350.0620.0620.0000.0000.0000.000
98A98PHE00.012-0.00935.429-0.005-0.0050.0000.0000.0000.000
99A99THR0-0.018-0.00340.1030.0050.0050.0000.0000.0000.000
100A100ASP-1-0.801-0.91741.249-0.083-0.0830.0000.0000.0000.000
101A101MET0-0.0540.00735.245-0.007-0.0070.0000.0000.0000.000
102A102ILE00.001-0.01040.5510.0050.0050.0000.0000.0000.000
103A103ASP-1-0.839-0.92739.609-0.077-0.0770.0000.0000.0000.000
104A104GLY0-0.011-0.00140.5960.0040.0040.0000.0000.0000.000
105A105GLN0-0.062-0.01742.319-0.001-0.0010.0000.0000.0000.000
106A106THR0-0.048-0.06040.058-0.002-0.0020.0000.0000.0000.000
107A107ILE00.0040.01535.871-0.009-0.0090.0000.0000.0000.000
108A108THR00.0510.03934.9940.0090.0090.0000.0000.0000.000
109A109ARG10.7990.86432.7340.0700.0700.0000.0000.0000.000
110A110GLN0-0.004-0.00130.2120.0020.0020.0000.0000.0000.000
111A111THR0-0.022-0.03730.515-0.004-0.0040.0000.0000.0000.000
112A112ASP-1-0.812-0.86024.398-0.123-0.1230.0000.0000.0000.000
113A113GLU-1-0.929-0.97727.627-0.093-0.0930.0000.0000.0000.000
114A114LEU0-0.071-0.03322.5320.0140.0140.0000.0000.0000.000
115A115THR0-0.065-0.06322.9730.0150.0150.0000.0000.0000.000
116A116GLY0-0.0190.00526.0740.0100.0100.0000.0000.0000.000
117A117LEU0-0.032-0.00824.7560.0030.0030.0000.0000.0000.000
118A118SER00.0220.00428.656-0.004-0.0040.0000.0000.0000.000
119A119SER0-0.020-0.00627.780-0.005-0.0050.0000.0000.0000.000
120A120LEU00.0000.01530.1550.0020.0020.0000.0000.0000.000
121A121VAL0-0.013-0.01329.870-0.011-0.0110.0000.0000.0000.000
122A122VAL0-0.037-0.01732.3930.0110.0110.0000.0000.0000.000
123A123LEU00.0220.03233.993-0.008-0.0080.0000.0000.0000.000
124A124ASP-1-0.850-0.95734.733-0.139-0.1390.0000.0000.0000.000
125A125SER00.009-0.01636.7090.0060.0060.0000.0000.0000.000
126A126ALA0-0.0190.00438.9720.0080.0080.0000.0000.0000.000
127A127GLU-1-0.851-0.92735.536-0.122-0.1220.0000.0000.0000.000
128A128ARG10.8230.95137.9020.1130.1130.0000.0000.0000.000
129A129THR00.021-0.00142.2260.0010.0010.0000.0000.0000.000
130A130ALA00.010-0.01745.811-0.002-0.0020.0000.0000.0000.000
131A131GLY00.0140.00148.666-0.001-0.0010.0000.0000.0000.000
132A132GLY00.0550.03144.9740.0010.0010.0000.0000.0000.000
133A133LYS10.7570.87143.4210.0870.0870.0000.0000.0000.000
134A134ASP-1-0.900-0.94844.604-0.083-0.0830.0000.0000.0000.000
135A135LEU0-0.0330.01244.1330.0000.0000.0000.0000.0000.000
136A136ARG10.7980.87341.3460.0900.0900.0000.0000.0000.000
137A137PRO00.0200.02637.7120.0010.0010.0000.0000.0000.000
138A138ALA0-0.008-0.01037.319-0.008-0.0080.0000.0000.0000.000
139A139LEU00.0030.01232.9310.0060.0060.0000.0000.0000.000
140A140LYS10.8550.93036.9630.0670.0670.0000.0000.0000.000
141A141ILE0-0.018-0.01034.6350.0010.0010.0000.0000.0000.000
142A142VAL0-0.030-0.01138.5620.0020.0020.0000.0000.0000.000
143A143ASP-1-0.757-0.91740.178-0.047-0.0470.0000.0000.0000.000
144A144ALA0-0.024-0.01242.1240.0010.0010.0000.0000.0000.000
145A145GLN0-0.036-0.00743.5550.0040.0040.0000.0000.0000.000
146A146GLY0-0.048-0.01544.9570.0010.0010.0000.0000.0000.000
147A147ASN0-0.056-0.03045.836-0.001-0.0010.0000.0000.0000.000
148A148ASP-1-0.767-0.88643.689-0.067-0.0670.0000.0000.0000.000
149A149VAL00.0050.01838.6870.0030.0030.0000.0000.0000.000
150A150LEU0-0.022-0.00240.995-0.004-0.0040.0000.0000.0000.000
151A151ILE00.0050.01136.767-0.001-0.0010.0000.0000.0000.000
152A152PRO0-0.025-0.02435.7500.0050.0050.0000.0000.0000.000
153A153GLY0-0.0140.00039.019-0.003-0.0030.0000.0000.0000.000
154A154THR0-0.047-0.02241.216-0.001-0.0010.0000.0000.0000.000
155A155ASP-1-0.878-0.93643.852-0.060-0.0600.0000.0000.0000.000
156A156MET0-0.030-0.02941.1960.0020.0020.0000.0000.0000.000
157A157PRO0-0.0070.00441.659-0.002-0.0020.0000.0000.0000.000
158A158ALA0-0.007-0.01037.109-0.005-0.0050.0000.0000.0000.000
159A159GLN0-0.018-0.02038.4920.0080.0080.0000.0000.0000.000
160A160TYR0-0.010-0.00633.325-0.004-0.0040.0000.0000.0000.000
161A161PHE00.0110.00335.7580.0020.0020.0000.0000.0000.000
162A162LEU0-0.011-0.00831.876-0.011-0.0110.0000.0000.0000.000
163A163PRO0-0.013-0.00131.1530.0070.0070.0000.0000.0000.000
164A164GLY00.026-0.00433.0990.0010.0010.0000.0000.0000.000
165A165LYS10.8520.90429.7640.1770.1770.0000.0000.0000.000
166A166ALA0-0.050-0.00728.884-0.010-0.0100.0000.0000.0000.000
167A167ILE00.0460.01224.9600.0150.0150.0000.0000.0000.000
168A168VAL0-0.003-0.00827.751-0.011-0.0110.0000.0000.0000.000
169A169GLN0-0.059-0.01524.176-0.008-0.0080.0000.0000.0000.000
170A170LEU0-0.014-0.00228.0670.0110.0110.0000.0000.0000.000
171A171GLU-1-0.778-0.86731.097-0.082-0.0820.0000.0000.0000.000
172A172ASP-1-0.843-0.93234.471-0.064-0.0640.0000.0000.0000.000
173A173GLY00.0010.00238.1020.0040.0040.0000.0000.0000.000
174A174VAL0-0.039-0.00832.2280.0050.0050.0000.0000.0000.000
175A175GLN0-0.0100.00034.7870.0000.0000.0000.0000.0000.000
176A176ILE0-0.035-0.01431.474-0.004-0.0040.0000.0000.0000.000
177A177SER0-0.008-0.02129.6830.0110.0110.0000.0000.0000.000
178A178SER00.0020.00730.025-0.007-0.0070.0000.0000.0000.000
179A179GLY00.009-0.02526.7300.0020.0020.0000.0000.0000.000
180A180ASP-1-0.788-0.86625.388-0.123-0.1230.0000.0000.0000.000
181A181THR0-0.058-0.04423.755-0.014-0.0140.0000.0000.0000.000
182A182LEU00.0360.02326.1030.0080.0080.0000.0000.0000.000
183A183ALA00.001-0.01027.9240.0100.0100.0000.0000.0000.000
184A184ARG10.8210.90419.0610.2720.2720.0000.0000.0000.000
185A185ILE0-0.0010.00025.3520.0170.0170.0000.0000.0000.000
186A186PRO00.0230.01623.864-0.030-0.0300.0000.0000.0000.000
187A187GLN0-0.010-0.00519.3910.0020.0020.0000.0000.0000.000
188A188GLU-1-0.863-0.92124.345-0.198-0.1980.0000.0000.0000.000
189A189SER0-0.032-0.00824.723-0.021-0.0210.0000.0000.0000.000