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: 6YMYZ

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1741239.313565
FMO2-HF: Nuclear repulsion 1671019.718145
FMO2-HF: Total energy -70219.595421
FMO2-MP2: Total energy -70425.254115


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.
-12.327-14.19618.923-9.019-8.037-0.04
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 : 0.027 / q_NPA : -0.003
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].
3A3HIS0-0.0160.0042.415-4.246-1.6263.680-3.174-3.127-0.005
4A4MET0-0.040-0.0142.2661.5632.3051.631-0.773-1.6010.002
5A5ALA00.1080.0475.690-0.630-0.6300.0000.0000.0000.000
6A6ALA00.0140.0095.9470.1270.1270.0000.0000.0000.000
7A7ALA0-0.038-0.0044.8540.1400.1400.0000.0000.0000.000
8A8GLU-1-0.931-0.9646.537-0.945-0.9450.0000.0000.0000.000
9A9SER0-0.062-0.0329.6210.2430.2430.0000.0000.0000.000
10A10SER0-0.052-0.0317.1830.0830.0830.0000.0000.0000.000
11A11ILE0-0.030-0.0098.781-0.170-0.1700.0000.0000.0000.000
12A12GLN00.0050.0111.878-9.673-14.90413.612-5.072-3.309-0.037
13A13VAL0-0.041-0.0016.098-0.146-0.1460.0000.0000.0000.000
14A14LYS10.9230.9366.1801.3851.3850.0000.0000.0000.000
15A15ASN0-0.097-0.0587.7490.4160.4160.0000.0000.0000.000
16A16LYS10.9480.97311.176-0.349-0.3490.0000.0000.0000.000
17A17GLY00.000-0.00713.886-0.054-0.0540.0000.0000.0000.000
18A18SER0-0.052-0.02116.7210.0250.0250.0000.0000.0000.000
19A19ILE00.0540.02613.542-0.038-0.0380.0000.0000.0000.000
20A20LYS10.8310.90017.5400.1220.1220.0000.0000.0000.000
21A21LEU00.0150.01018.319-0.038-0.0380.0000.0000.0000.000
22A22SER0-0.005-0.01320.9180.0350.0350.0000.0000.0000.000
23A23ASN0-0.004-0.01123.044-0.007-0.0070.0000.0000.0000.000
24A24VAL00.0070.02122.140-0.020-0.0200.0000.0000.0000.000
25A25LYS10.9720.99724.5990.1670.1670.0000.0000.0000.000
26A26SER0-0.020-0.01022.834-0.019-0.0190.0000.0000.0000.000
27A27VAL00.0110.02024.5080.0160.0160.0000.0000.0000.000
28A28VAL0-0.018-0.00424.349-0.014-0.0140.0000.0000.0000.000
29A29ASN00.0310.02422.5560.0210.0210.0000.0000.0000.000
30A30SER00.018-0.02926.0130.0140.0140.0000.0000.0000.000
31A31SER0-0.035-0.00322.8610.0090.0090.0000.0000.0000.000
32A32GLY00.0090.01722.9760.0080.0080.0000.0000.0000.000
33A33LYS10.8170.88818.0680.0790.0790.0000.0000.0000.000
34A34LEU00.0300.02819.7680.0000.0000.0000.0000.0000.000
35A35VAL00.0170.02519.798-0.035-0.0350.0000.0000.0000.000
36A36ILE00.0160.00418.2210.0310.0310.0000.0000.0000.000
37A37THR00.004-0.00722.006-0.010-0.0100.0000.0000.0000.000
38A38SER0-0.025-0.03523.9270.0230.0230.0000.0000.0000.000
39A39ARG10.9660.97423.7390.2250.2250.0000.0000.0000.000
40A40ASN00.0280.01623.806-0.030-0.0300.0000.0000.0000.000
41A41THR0-0.0080.00319.9610.0050.0050.0000.0000.0000.000
42A42GLU-1-0.835-0.89618.819-0.296-0.2960.0000.0000.0000.000
43A43LEU00.0080.01713.5400.0510.0510.0000.0000.0000.000
44A44LYS10.8810.92116.1090.1570.1570.0000.0000.0000.000
45A45LEU0-0.0120.02412.6130.0210.0210.0000.0000.0000.000
46A46ILE0-0.015-0.01215.898-0.006-0.0060.0000.0000.0000.000
47A47ASP-1-0.753-0.85918.6030.0760.0760.0000.0000.0000.000
48A48GLU-1-0.783-0.90918.7140.1350.1350.0000.0000.0000.000
49A49PHE0-0.068-0.02922.0220.0000.0000.0000.0000.0000.000
50A50GLY00.0190.01623.257-0.011-0.0110.0000.0000.0000.000
51A51ARG10.8270.89521.614-0.066-0.0660.0000.0000.0000.000
52A52THR0-0.016-0.01218.2680.0020.0020.0000.0000.0000.000
53A53LYS10.8160.90614.962-0.114-0.1140.0000.0000.0000.000
54A54GLU-1-0.746-0.84310.296-0.351-0.3510.0000.0000.0000.000
55A55SER0-0.009-0.01714.4670.0640.0640.0000.0000.0000.000
56A56TYR0-0.0060.0049.705-0.174-0.1740.0000.0000.0000.000
57A57LYS10.8340.90615.3660.4030.4030.0000.0000.0000.000
58A58VAL00.022-0.00515.093-0.085-0.0850.0000.0000.0000.000
59A59PRO00.0160.02216.1590.0680.0680.0000.0000.0000.000
60A60TYR0-0.016-0.01519.0950.0180.0180.0000.0000.0000.000
61A61GLY00.010-0.01121.238-0.020-0.0200.0000.0000.0000.000
62A62ALA0-0.042-0.00216.012-0.008-0.0080.0000.0000.0000.000
63A63VAL0-0.023-0.00816.0570.0630.0630.0000.0000.0000.000
64A64LEU0-0.016-0.01415.010-0.071-0.0710.0000.0000.0000.000
65A65ALA0-0.035-0.02412.9990.0350.0350.0000.0000.0000.000
66A66LYS10.7830.87914.478-0.135-0.1350.0000.0000.0000.000
67A67GLY00.0150.00117.239-0.044-0.0440.0000.0000.0000.000
68A68ASP-1-0.854-0.92619.503-0.094-0.0940.0000.0000.0000.000
69A69GLY00.0130.01020.9210.0150.0150.0000.0000.0000.000
70A70GLU-1-0.849-0.91518.3330.0750.0750.0000.0000.0000.000
71A71GLN0-0.020-0.01717.8110.0200.0200.0000.0000.0000.000
72A72VAL0-0.0080.00212.6710.0050.0050.0000.0000.0000.000
73A73ALA0-0.009-0.01411.942-0.009-0.0090.0000.0000.0000.000
74A74GLY00.0140.0109.219-0.076-0.0760.0000.0000.0000.000
75A75GLY0-0.009-0.0085.3040.4450.4450.0000.0000.0000.000
76A76GLU-1-0.778-0.8685.5870.5530.5530.0000.0000.0000.000
77A77THR00.010-0.0115.870-0.344-0.3440.0000.0000.0000.000
78A78VAL0-0.004-0.0027.7200.1490.1490.0000.0000.0000.000
79A79ALA0-0.012-0.00610.5160.0860.0860.0000.0000.0000.000
80A80ASN00.0210.00110.463-0.346-0.3460.0000.0000.0000.000
81A81TRP0-0.008-0.00512.2490.1530.1530.0000.0000.0000.000
82A82ASP-1-0.755-0.86714.049-0.538-0.5380.0000.0000.0000.000
83A83PRO0-0.010-0.00513.5690.0230.0230.0000.0000.0000.000
84A84HIS00.0540.03715.2790.0600.0600.0000.0000.0000.000
85A85THR0-0.015-0.01519.2120.0740.0740.0000.0000.0000.000
86A86MET0-0.036-0.00420.947-0.030-0.0300.0000.0000.0000.000
87A87PRO0-0.0030.00321.5360.0260.0260.0000.0000.0000.000
88A88VAL0-0.005-0.00624.2420.0060.0060.0000.0000.0000.000
89A89ILE0-0.046-0.02223.4550.0020.0020.0000.0000.0000.000
90A90THR00.0150.01428.0610.0040.0040.0000.0000.0000.000
91A91GLU-1-0.955-0.99530.074-0.122-0.1220.0000.0000.0000.000
92A92VAL0-0.025-0.01732.0860.0060.0060.0000.0000.0000.000
93A93SER00.0190.01033.385-0.006-0.0060.0000.0000.0000.000
94A94GLY0-0.0160.00334.8580.0020.0020.0000.0000.0000.000
95A95PHE0-0.035-0.01236.4910.0020.0020.0000.0000.0000.000
96A96VAL0-0.0030.00634.144-0.002-0.0020.0000.0000.0000.000
97A97ARG10.8730.94937.2540.0660.0660.0000.0000.0000.000
98A98PHE00.005-0.01236.038-0.006-0.0060.0000.0000.0000.000
99A99THR0-0.020-0.01640.5470.0060.0060.0000.0000.0000.000
100A100ASP-1-0.783-0.89041.332-0.089-0.0890.0000.0000.0000.000
101A101MET0-0.0450.01835.823-0.006-0.0060.0000.0000.0000.000
102A102ILE0-0.005-0.01041.1180.0050.0050.0000.0000.0000.000
103A103ASP-1-0.830-0.92839.888-0.093-0.0930.0000.0000.0000.000
104A104GLY0-0.0050.00341.0650.0050.0050.0000.0000.0000.000
105A105GLN0-0.064-0.01342.7460.0010.0010.0000.0000.0000.000
106A106THR0-0.037-0.06140.942-0.002-0.0020.0000.0000.0000.000
107A107ILE0-0.0050.00936.323-0.008-0.0080.0000.0000.0000.000
108A108THR00.0310.02235.3220.0090.0090.0000.0000.0000.000
109A109ARG10.7960.85532.7140.0940.0940.0000.0000.0000.000
110A110GLN0-0.012-0.00230.888-0.001-0.0010.0000.0000.0000.000
111A111THR0-0.012-0.03730.6490.0000.0000.0000.0000.0000.000
112A112ASP-1-0.794-0.85724.570-0.169-0.1690.0000.0000.0000.000
113A113GLU-1-0.916-0.96927.736-0.133-0.1330.0000.0000.0000.000
114A114LEU0-0.073-0.02622.7480.0120.0120.0000.0000.0000.000
115A115THR0-0.088-0.07523.4530.0160.0160.0000.0000.0000.000
116A116GLY0-0.0210.00126.6810.0120.0120.0000.0000.0000.000
117A117LEU0-0.027-0.00824.7660.0060.0060.0000.0000.0000.000
118A118SER00.0190.01128.760-0.006-0.0060.0000.0000.0000.000
119A119SER0-0.0190.00228.536-0.001-0.0010.0000.0000.0000.000
120A120LEU00.0080.00630.9100.0010.0010.0000.0000.0000.000
121A121VAL0-0.009-0.00430.514-0.012-0.0120.0000.0000.0000.000
122A122VAL0-0.036-0.01732.9660.0120.0120.0000.0000.0000.000
123A123LEU00.0160.02434.661-0.008-0.0080.0000.0000.0000.000
124A124ASP-1-0.792-0.92535.427-0.146-0.1460.0000.0000.0000.000
125A125SER0-0.029-0.01937.3870.0060.0060.0000.0000.0000.000
126A126ALA0-0.034-0.00939.5140.0090.0090.0000.0000.0000.000
127A127GLU-1-0.857-0.93335.899-0.138-0.1380.0000.0000.0000.000
128A128ARG10.7800.92338.5680.1210.1210.0000.0000.0000.000
129A129THR00.032-0.00342.7440.0010.0010.0000.0000.0000.000
130A130ALA0-0.001-0.01846.408-0.002-0.0020.0000.0000.0000.000
131A131GLY00.0050.00449.2790.0000.0000.0000.0000.0000.000
132A132GLY00.0510.03145.1170.0000.0000.0000.0000.0000.000
133A133LYS10.7500.86743.8530.0960.0960.0000.0000.0000.000
134A134ASP-1-0.852-0.92744.920-0.090-0.0900.0000.0000.0000.000
135A135LEU0-0.0170.01844.6030.0000.0000.0000.0000.0000.000
136A136ARG10.7600.84941.6720.0910.0910.0000.0000.0000.000
137A137PRO00.0090.01538.1790.0010.0010.0000.0000.0000.000
138A138ALA00.005-0.00437.477-0.008-0.0080.0000.0000.0000.000
139A139LEU00.0090.01332.9220.0060.0060.0000.0000.0000.000
140A140LYS10.8400.92236.8430.0700.0700.0000.0000.0000.000
141A141ILE0-0.017-0.00334.7100.0000.0000.0000.0000.0000.000
142A142VAL0-0.018-0.00838.7160.0030.0030.0000.0000.0000.000
143A143ASP-1-0.742-0.89340.341-0.045-0.0450.0000.0000.0000.000
144A144ALA0-0.017-0.00442.5030.0000.0000.0000.0000.0000.000
145A145GLN0-0.074-0.03743.7550.0030.0030.0000.0000.0000.000
146A146GLY0-0.027-0.00144.8310.0000.0000.0000.0000.0000.000
147A147ASN0-0.038-0.02945.875-0.001-0.0010.0000.0000.0000.000
148A148ASP-1-0.785-0.89843.828-0.067-0.0670.0000.0000.0000.000
149A149VAL0-0.028-0.00138.6160.0030.0030.0000.0000.0000.000
150A150LEU0-0.0130.00041.256-0.004-0.0040.0000.0000.0000.000
151A151ILE00.0110.00637.137-0.002-0.0020.0000.0000.0000.000
152A152PRO0-0.017-0.02135.6800.0050.0050.0000.0000.0000.000
153A153GLY0-0.025-0.00539.003-0.002-0.0020.0000.0000.0000.000
154A154THR0-0.061-0.03041.385-0.001-0.0010.0000.0000.0000.000
155A155ASP-1-0.870-0.94143.848-0.058-0.0580.0000.0000.0000.000
156A156MET0-0.023-0.00841.8780.0020.0020.0000.0000.0000.000
157A157PRO00.002-0.00242.049-0.002-0.0020.0000.0000.0000.000
158A158ALA0-0.0090.00137.111-0.005-0.0050.0000.0000.0000.000
159A159GLN0-0.012-0.01738.6120.0070.0070.0000.0000.0000.000
160A160TYR00.0150.01833.216-0.003-0.0030.0000.0000.0000.000
161A161PHE00.011-0.00535.7330.0000.0000.0000.0000.0000.000
162A162LEU0-0.017-0.00232.131-0.011-0.0110.0000.0000.0000.000
163A163PRO0-0.025-0.00631.7510.0070.0070.0000.0000.0000.000
164A164GLY00.040-0.00133.9890.0020.0020.0000.0000.0000.000
165A165LYS10.8270.89930.1110.1860.1860.0000.0000.0000.000
166A166ALA0-0.032-0.00129.628-0.013-0.0130.0000.0000.0000.000
167A167ILE00.0260.02225.6190.0150.0150.0000.0000.0000.000
168A168VAL00.015-0.00528.517-0.008-0.0080.0000.0000.0000.000
169A169GLN0-0.055-0.02324.470-0.024-0.0240.0000.0000.0000.000
170A170LEU0-0.0130.00228.4520.0090.0090.0000.0000.0000.000
171A171GLU-1-0.779-0.86431.348-0.102-0.1020.0000.0000.0000.000
172A172ASP-1-0.819-0.92234.830-0.069-0.0690.0000.0000.0000.000
173A173GLY00.0000.00638.4550.0030.0030.0000.0000.0000.000
174A174VAL0-0.042-0.01232.4780.0050.0050.0000.0000.0000.000
175A175GLN0-0.012-0.00135.115-0.001-0.0010.0000.0000.0000.000
176A176ILE0-0.021-0.00931.679-0.005-0.0050.0000.0000.0000.000
177A177SER0-0.014-0.03229.8710.0100.0100.0000.0000.0000.000
178A178SER00.0010.00930.069-0.008-0.0080.0000.0000.0000.000
179A179GLY00.022-0.01426.5560.0030.0030.0000.0000.0000.000
180A180ASP-1-0.786-0.86325.450-0.125-0.1250.0000.0000.0000.000
181A181THR0-0.044-0.03923.726-0.011-0.0110.0000.0000.0000.000
182A182LEU00.0340.03026.1800.0030.0030.0000.0000.0000.000
183A183ALA00.007-0.00228.1750.0080.0080.0000.0000.0000.000
184A184ARG10.8180.88719.3890.3030.3030.0000.0000.0000.000
185A185ILE0-0.0010.00225.6050.0180.0180.0000.0000.0000.000
186A186PRO00.0260.01424.241-0.030-0.0300.0000.0000.0000.000
187A187GLN0-0.041-0.01719.6730.0110.0110.0000.0000.0000.000
188A188GLU-1-0.838-0.90624.797-0.214-0.2140.0000.0000.0000.000
189A189SER0-0.040-0.00724.853-0.014-0.0140.0000.0000.0000.000