FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 667MZ

Calculation Name: 2HY7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HY7

Chain ID: A

ChEMBL ID:

UniProt ID: Q8GCH2

Base Structure: X-ray

Registration Date: 2023-03-13

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 373
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6248137.876985
FMO2-HF: Nuclear repulsion 6101182.100749
FMO2-HF: Total energy -146955.776236
FMO2-MP2: Total energy -147386.034625


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:13:ARG)


Summations of interaction energy for fragment #1(A:13:ARG)
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.
-71.081-67.69213.909-6.919-10.378-0.078
Interaction energy analysis for fragmet #1(A:13:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.908 / q_NPA : 0.960
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].
3A15PRO00.0410.0242.245-12.113-10.3423.912-2.377-3.306-0.030
4A16CYS0-0.096-0.0312.972-5.397-4.4570.035-0.300-0.675-0.001
5A17TYR00.0680.0184.6285.9616.101-0.001-0.013-0.1260.000
6A18LEU00.0240.0168.032-1.825-1.8250.0000.0000.0000.000
7A19VAL0-0.0090.00410.3031.9581.9580.0000.0000.0000.000
8A20LEU00.0000.00213.7190.0600.0600.0000.0000.0000.000
9A21SER00.018-0.02916.4680.9990.9990.0000.0000.0000.000
10A22SER0-0.0250.00419.5420.1150.1150.0000.0000.0000.000
11A23HIS0-0.0030.00120.5460.8350.8350.0000.0000.0000.000
12A24ASP-1-0.727-0.82118.401-17.548-17.5480.0000.0000.0000.000
13A25PHE00.001-0.00114.3310.7950.7950.0000.0000.0000.000
14A26ARG10.8710.88416.74517.06017.0600.0000.0000.0000.000
15A27THR0-0.092-0.03819.3580.7060.7060.0000.0000.0000.000
16A28PRO0-0.001-0.00122.741-0.189-0.1890.0000.0000.0000.000
17A29ARG10.8150.89624.74111.31311.3130.0000.0000.0000.000
18A30ARG10.8830.95118.70615.14815.1480.0000.0000.0000.000
19A31ALA00.0550.03022.8960.6070.6070.0000.0000.0000.000
20A32ASN0-0.007-0.03322.429-0.752-0.7520.0000.0000.0000.000
21A33ILE00.0360.03018.056-0.545-0.5450.0000.0000.0000.000
22A34HIS00.0030.01618.011-0.985-0.9850.0000.0000.0000.000
23A35PHE00.0370.01917.391-0.744-0.7440.0000.0000.0000.000
24A36ILE00.0220.01815.831-0.511-0.5110.0000.0000.0000.000
25A37THR0-0.005-0.02213.002-1.418-1.4180.0000.0000.0000.000
26A38ASP-1-0.862-0.93412.662-19.383-19.3830.0000.0000.0000.000
27A39GLN00.0060.00612.881-1.362-1.3620.0000.0000.0000.000
28A40LEU0-0.022-0.00410.366-0.881-0.8810.0000.0000.0000.000
29A41ALA00.0280.0178.394-2.935-2.9350.0000.0000.0000.000
30A42LEU0-0.038-0.0048.000-1.882-1.8820.0000.0000.0000.000
31A43ARG10.7640.8558.52820.29320.2930.0000.0000.0000.000
32A44GLY00.0190.0074.343-1.501-1.466-0.001-0.021-0.0130.000
33A45THR0-0.0180.0121.876-18.269-18.6369.965-3.925-5.672-0.046
34A46THR00.0410.0274.2393.1333.4580.001-0.191-0.134-0.001
35A47ARG10.7750.8694.18549.68849.9440.000-0.043-0.2130.000
36A48PHE00.0120.0008.8841.8571.8570.0000.0000.0000.000
37A49PHE00.001-0.00512.6490.7580.7580.0000.0000.0000.000
38A50SER0-0.018-0.03814.4431.1291.1290.0000.0000.0000.000
39A51LEU00.003-0.01218.1710.4080.4080.0000.0000.0000.000
40A52ARG10.9050.93920.91511.87811.8780.0000.0000.0000.000
41A53TYR00.003-0.01222.8950.5200.5200.0000.0000.0000.000
42A54SER0-0.026-0.00124.7040.0180.0180.0000.0000.0000.000
43A55ARG11.0210.99827.15610.73110.7310.0000.0000.0000.000
44A56LEU00.0000.00129.9340.2350.2350.0000.0000.0000.000
45A57SER0-0.006-0.00727.9160.2450.2450.0000.0000.0000.000
46A58ARG10.9310.95329.49910.29510.2950.0000.0000.0000.000
47A59MET0-0.035-0.01132.3820.1330.1330.0000.0000.0000.000
48A60LYS10.8410.93132.3529.6889.6880.0000.0000.0000.000
49A61GLY00.0370.04233.2410.1140.1140.0000.0000.0000.000
50A62ASP-1-0.801-0.88526.740-11.869-11.8690.0000.0000.0000.000
51A63MET00.0580.01327.2600.0260.0260.0000.0000.0000.000
52A64ARG10.7900.85221.74912.98212.9820.0000.0000.0000.000
53A65LEU0-0.040-0.00524.978-0.234-0.2340.0000.0000.0000.000
54A66PRO00.0080.00126.123-0.021-0.0210.0000.0000.0000.000
55A67LEU00.0050.01620.461-0.179-0.1790.0000.0000.0000.000
56A68ASP-1-0.797-0.84722.570-12.179-12.1790.0000.0000.0000.000
57A69ASP-1-0.927-0.95724.169-11.656-11.6560.0000.0000.0000.000
58A70THR0-0.061-0.03819.053-0.588-0.5880.0000.0000.0000.000
59A71ALA0-0.030-0.01419.088-0.841-0.8410.0000.0000.0000.000
60A72ASN0-0.070-0.04718.120-0.181-0.1810.0000.0000.0000.000
61A73THR0-0.019-0.00815.876-0.356-0.3560.0000.0000.0000.000
62A74VAL00.008-0.0049.6120.2110.2110.0000.0000.0000.000
63A75VAL0-0.019-0.00113.0620.6560.6560.0000.0000.0000.000
64A76SER00.0090.01010.044-0.542-0.5420.0000.0000.0000.000
65A77HIS00.012-0.00812.4451.6361.6360.0000.0000.0000.000
66A78ASN0-0.006-0.01413.424-0.579-0.5790.0000.0000.0000.000
67A79GLY00.0260.0189.979-0.099-0.0990.0000.0000.0000.000
68A80VAL0-0.0170.0078.648-3.263-3.2630.0000.0000.0000.000
69A81ASP-1-0.861-0.9026.123-38.971-38.9710.0000.0000.0000.000
70A82CYS0-0.057-0.0329.5640.7990.7990.0000.0000.0000.000
71A83TYR00.0040.00712.8920.4100.4100.0000.0000.0000.000
72A84LEU00.0160.02414.6750.2740.2740.0000.0000.0000.000
73A85TRP0-0.022-0.00118.0610.2540.2540.0000.0000.0000.000
74A86ARG10.8640.93019.49612.95712.9570.0000.0000.0000.000
75A87THR0-0.016-0.01223.133-0.041-0.0410.0000.0000.0000.000
76A88THR00.029-0.00925.4200.0870.0870.0000.0000.0000.000
77A89VAL00.0290.00429.1550.2390.2390.0000.0000.0000.000
78A90HIS0-0.0020.01027.160-0.248-0.2480.0000.0000.0000.000
79A91PRO00.0130.02027.1290.3920.3920.0000.0000.0000.000
80A92PHE0-0.008-0.03029.577-0.224-0.2240.0000.0000.0000.000
81A93ASN0-0.011-0.01432.1370.3730.3730.0000.0000.0000.000
82A94THR0-0.025-0.04535.0550.1440.1440.0000.0000.0000.000
83A95ARG10.9160.96238.2198.2228.2220.0000.0000.0000.000
84A96ARG10.9450.99040.2937.5117.5110.0000.0000.0000.000
85A97SER00.0260.00541.833-0.124-0.1240.0000.0000.0000.000
86A98TRP00.0750.02043.332-0.114-0.1140.0000.0000.0000.000
87A99LEU0-0.0100.00140.198-0.014-0.0140.0000.0000.0000.000
88A100ARG10.9680.99438.3077.8437.8430.0000.0000.0000.000
89A101PRO00.0590.02837.787-0.255-0.2550.0000.0000.0000.000
90A102VAL00.0220.01837.240-0.178-0.1780.0000.0000.0000.000
91A103GLU-1-0.789-0.87934.831-8.847-8.8470.0000.0000.0000.000
92A104ASP-1-0.804-0.87733.346-9.358-9.3580.0000.0000.0000.000
93A105ALA0-0.028-0.00132.733-0.295-0.2950.0000.0000.0000.000
94A106MET0-0.011-0.01231.742-0.231-0.2310.0000.0000.0000.000
95A107PHE0-0.013-0.02327.963-0.405-0.4050.0000.0000.0000.000
96A108ARG10.9410.96627.7498.8708.8700.0000.0000.0000.000
97A109TRP00.0270.01527.812-0.362-0.3620.0000.0000.0000.000
98A110TYR00.013-0.00223.053-0.384-0.3840.0000.0000.0000.000
99A111ALA00.0440.02123.336-0.504-0.5040.0000.0000.0000.000
100A112ALA0-0.030-0.00623.004-0.491-0.4910.0000.0000.0000.000
101A113HIS10.7730.88523.27011.60211.6020.0000.0000.0000.000
102A114PRO00.0270.03617.967-0.026-0.0260.0000.0000.0000.000
103A115PRO00.0180.01516.4480.1230.1230.0000.0000.0000.000
104A116LYS10.9410.92412.57321.15421.1540.0000.0000.0000.000
105A117GLN00.0060.0149.361-0.382-0.3820.0000.0000.0000.000
106A118LEU00.0240.02111.457-1.838-1.8380.0000.0000.0000.000
107A119LEU00.0060.00512.490-1.047-1.0470.0000.0000.0000.000
108A120ASP-1-0.803-0.8828.888-24.663-24.6630.0000.0000.0000.000
109A121TRP00.0510.0087.352-1.267-1.2670.0000.0000.0000.000
110A122MET0-0.0100.0168.501-1.371-1.3710.0000.0000.0000.000
111A123ARG10.8710.9298.64826.75126.7510.0000.0000.0000.000
112A124GLU-1-0.905-0.9394.282-51.413-51.215-0.001-0.029-0.1680.000
113A125SER0-0.049-0.0275.742-4.754-4.7540.0000.0000.0000.000
114A126ASP-1-0.818-0.8984.304-37.649-37.558-0.001-0.020-0.0710.000
115A127VAL0-0.045-0.0237.4673.4913.4910.0000.0000.0000.000
116A128ILE0-0.014-0.00810.183-1.730-1.7300.0000.0000.0000.000
117A129VAL0-0.0030.00112.8341.5771.5770.0000.0000.0000.000
118A130PHE0-0.004-0.01915.552-0.235-0.2350.0000.0000.0000.000
119A131GLU-1-0.733-0.81118.774-13.686-13.6860.0000.0000.0000.000
120A132SER00.0180.01821.2330.1830.1830.0000.0000.0000.000
121A133GLY00.0220.00224.8770.0720.0720.0000.0000.0000.000
122A134ILE0-0.038-0.03322.538-0.024-0.0240.0000.0000.0000.000
123A135ALA00.0280.01019.673-0.054-0.0540.0000.0000.0000.000
124A136VAL00.0410.02721.263-0.419-0.4190.0000.0000.0000.000
125A137ALA0-0.054-0.02323.7650.0160.0160.0000.0000.0000.000
126A138PHE0-0.042-0.03518.7960.0930.0930.0000.0000.0000.000
127A139ILE00.0520.04119.238-0.791-0.7910.0000.0000.0000.000
128A140GLU-1-0.801-0.88320.089-12.960-12.9600.0000.0000.0000.000
129A141LEU0-0.057-0.03217.949-0.123-0.1230.0000.0000.0000.000
130A142ALA00.0440.00915.894-0.481-0.4810.0000.0000.0000.000
131A143LYS10.9420.98816.27815.72015.7200.0000.0000.0000.000
132A144ARG10.9150.95918.34013.56113.5610.0000.0000.0000.000
133A145VAL0-0.088-0.03713.323-0.051-0.0510.0000.0000.0000.000
134A146ASN0-0.008-0.0229.6710.6430.6430.0000.0000.0000.000
135A147PRO00.0060.01014.169-0.042-0.0420.0000.0000.0000.000
136A148ALA0-0.020-0.01111.9710.7450.7450.0000.0000.0000.000
137A149ALA0-0.0150.01911.040-0.338-0.3380.0000.0000.0000.000
138A150LYS10.8320.90411.59319.63519.6350.0000.0000.0000.000
139A151LEU0-0.050-0.03713.429-0.961-0.9610.0000.0000.0000.000
140A152VAL00.008-0.00914.9981.0391.0390.0000.0000.0000.000
141A153TYR00.0340.02217.422-0.399-0.3990.0000.0000.0000.000
142A154ARG10.8420.92019.72713.60913.6090.0000.0000.0000.000
143A155ALA00.000-0.00521.6400.0790.0790.0000.0000.0000.000
144A156SER0-0.012-0.06023.7520.1750.1750.0000.0000.0000.000
145A157ASP-1-0.851-0.89026.171-10.182-10.1820.0000.0000.0000.000
146A158GLY00.0270.01528.878-0.242-0.2420.0000.0000.0000.000
147A159LEU00.018-0.02027.6840.0410.0410.0000.0000.0000.000
148A160SER00.014-0.02531.4270.0320.0320.0000.0000.0000.000
149A161THR0-0.011-0.00433.6410.2330.2330.0000.0000.0000.000
150A162ILE0-0.050-0.01328.3900.0700.0700.0000.0000.0000.000
151A163ASN0-0.020-0.00632.6850.0460.0460.0000.0000.0000.000
152A164VAL0-0.0030.01629.187-0.019-0.0190.0000.0000.0000.000
153A165ALA0-0.002-0.00732.1450.2900.2900.0000.0000.0000.000
154A166SER00.0440.02433.034-0.142-0.1420.0000.0000.0000.000
155A167TYR00.002-0.00927.9710.0470.0470.0000.0000.0000.000
156A168ILE0-0.026-0.01526.889-0.207-0.2070.0000.0000.0000.000
157A169GLU-1-0.870-0.93529.855-9.100-9.1000.0000.0000.0000.000
158A170ARG10.8660.89932.1358.9138.9130.0000.0000.0000.000
159A171GLU-1-0.822-0.87726.590-11.461-11.4610.0000.0000.0000.000
160A172PHE0-0.022-0.02325.238-0.347-0.3470.0000.0000.0000.000
161A173ASP-1-0.868-0.94128.301-9.621-9.6210.0000.0000.0000.000
162A174ARG10.6660.79526.33111.27411.2740.0000.0000.0000.000
163A175VAL0-0.014-0.01624.380-0.089-0.0890.0000.0000.0000.000
164A176ALA00.0360.04625.004-0.431-0.4310.0000.0000.0000.000
165A177PRO00.014-0.00325.105-0.384-0.3840.0000.0000.0000.000
166A178THR0-0.098-0.06122.979-0.295-0.2950.0000.0000.0000.000
167A179LEU0-0.0250.00120.063-0.672-0.6720.0000.0000.0000.000
168A180ASP-1-0.801-0.87217.105-15.623-15.6230.0000.0000.0000.000
169A181VAL0-0.048-0.01718.1920.6290.6290.0000.0000.0000.000
170A182ILE0-0.0060.02020.446-0.367-0.3670.0000.0000.0000.000
171A183ALA00.0230.00421.2240.4190.4190.0000.0000.0000.000
172A184LEU0-0.005-0.01123.165-0.170-0.1700.0000.0000.0000.000
173A185VAL0-0.0090.00325.8810.0360.0360.0000.0000.0000.000
174A186SER0-0.012-0.05727.5910.2420.2420.0000.0000.0000.000
175A187PRO00.0520.01931.078-0.089-0.0890.0000.0000.0000.000
176A188ALA0-0.017-0.00332.6610.1300.1300.0000.0000.0000.000
177A189MET0-0.080-0.02729.2590.0220.0220.0000.0000.0000.000
178A190ALA00.006-0.00231.714-0.081-0.0810.0000.0000.0000.000
179A191ALA0-0.023-0.00232.6830.0190.0190.0000.0000.0000.000
180A192GLU-1-0.888-0.90834.031-8.667-8.6670.0000.0000.0000.000
181A193VAL0-0.053-0.02028.583-0.276-0.2760.0000.0000.0000.000
182A194VAL0-0.0050.01331.5650.1560.1560.0000.0000.0000.000
183A195SER0-0.031-0.05227.372-0.054-0.0540.0000.0000.0000.000
184A196ARG10.9360.96329.8208.7108.7100.0000.0000.0000.000
185A197ASP-1-0.869-0.93327.807-10.003-10.0030.0000.0000.0000.000
186A198ASN0-0.078-0.03423.3140.2270.2270.0000.0000.0000.000
187A199VAL0-0.0020.00724.303-0.460-0.4600.0000.0000.0000.000
188A200PHE0-0.003-0.01522.8310.2350.2350.0000.0000.0000.000
189A201HIS0-0.049-0.02226.1750.0720.0720.0000.0000.0000.000
190A202VAL0-0.005-0.00822.046-0.070-0.0700.0000.0000.0000.000
191A203GLY00.0510.03625.230-0.176-0.1760.0000.0000.0000.000
192A204HIS0-0.038-0.03724.977-0.892-0.8920.0000.0000.0000.000
193A205GLY00.0630.03623.5950.2570.2570.0000.0000.0000.000
194A206VAL0-0.044-0.02024.6230.2170.2170.0000.0000.0000.000
195A207ASP-1-0.876-0.96722.942-13.558-13.5580.0000.0000.0000.000
196A208HIS00.0040.00121.0330.6920.6920.0000.0000.0000.000
197A209ASN0-0.0080.00223.6270.5090.5090.0000.0000.0000.000
198A210LEU00.0540.02926.3010.2700.2700.0000.0000.0000.000
199A211ASP-1-0.768-0.87328.868-8.787-8.7870.0000.0000.0000.000
200A212GLN0-0.057-0.03528.5770.3590.3590.0000.0000.0000.000
201A213LEU0-0.038-0.00726.2260.0720.0720.0000.0000.0000.000
202A214GLY0-0.007-0.00230.5640.1500.1500.0000.0000.0000.000
203A215ASP-1-0.963-0.95134.081-7.920-7.9200.0000.0000.0000.000
204A216PRO00.0420.02034.411-0.227-0.2270.0000.0000.0000.000
205A217SER0-0.005-0.01737.586-0.163-0.1630.0000.0000.0000.000
206A218PRO0-0.039-0.01738.4260.0720.0720.0000.0000.0000.000
207A219TYR0-0.102-0.06440.4570.0900.0900.0000.0000.0000.000
208A220ALA00.0470.03144.093-0.002-0.0020.0000.0000.0000.000
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