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: 857VY

Calculation Name: 3HZR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HZR

Chain ID: A

ChEMBL ID:

UniProt ID: C4LUB5

Base Structure: X-ray

Registration Date: 2023-06-22

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 OptH
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 374
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6488536.147303
FMO2-HF: Nuclear repulsion 6340484.131743
FMO2-HF: Total energy -148052.015559
FMO2-MP2: Total energy -148488.826379


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:8:PRO)


Summations of interaction energy for fragment #1(A:8:PRO)
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.
-6.068-1.330.629-2.246-3.122-0.014
Interaction energy analysis for fragmet #1(A:8:PRO)
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 : -0.019
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].
3A10GLN00.0290.0052.724-5.106-1.2850.599-2.044-2.376-0.014
4A11LEU00.0890.0555.3420.2980.318-0.001-0.003-0.0160.000
5A12LEU00.0250.0228.028-0.060-0.0600.0000.0000.0000.000
6A13GLN0-0.110-0.0607.568-0.057-0.0570.0000.0000.0000.000
7A14SER00.0270.0096.800-0.127-0.1270.0000.0000.0000.000
8A15PHE0-0.016-0.0227.8500.0740.0740.0000.0000.0000.000
9A16THR0-0.0290.0089.5610.0000.0000.0000.0000.0000.000
10A17THR00.008-0.00312.5160.0000.0000.0000.0000.0000.000
11A18ARG10.8620.91316.2510.0540.0540.0000.0000.0000.000
12A19THR0-0.010-0.01918.2210.0070.0070.0000.0000.0000.000
13A20THR00.014-0.00713.725-0.008-0.0080.0000.0000.0000.000
14A21ASP-1-0.834-0.90112.984-0.059-0.0590.0000.0000.0000.000
15A22TYR00.0390.00912.7490.0180.0180.0000.0000.0000.000
16A23ASN00.0680.03512.4520.0220.0220.0000.0000.0000.000
17A24GLN00.021-0.00210.271-0.001-0.0010.0000.0000.0000.000
18A25LEU0-0.071-0.0057.625-0.043-0.0430.0000.0000.0000.000
19A26ILE00.013-0.0128.1580.0190.0190.0000.0000.0000.000
20A27ASN0-0.035-0.0229.9620.0580.0580.0000.0000.0000.000
21A28SER0-0.056-0.0484.709-0.0340.023-0.001-0.003-0.0530.000
22A29VAL0-0.050-0.0224.357-0.283-0.068-0.001-0.016-0.1990.000
23A30GLY0-0.0190.0156.0190.2020.2020.0000.0000.0000.000
24A31ILE0-0.057-0.0408.4520.0660.0660.0000.0000.0000.000
25A32ASN00.0140.01911.598-0.050-0.0500.0000.0000.0000.000
26A33ALA00.0220.00314.9700.0070.0070.0000.0000.0000.000
27A34ILE0-0.044-0.03117.1380.0020.0020.0000.0000.0000.000
28A35THR00.0180.01620.412-0.012-0.0120.0000.0000.0000.000
29A36PRO00.0650.00122.7450.0020.0020.0000.0000.0000.000
30A37GLN00.0110.00326.2690.0030.0030.0000.0000.0000.000
31A38GLN00.0360.03420.491-0.004-0.0040.0000.0000.0000.000
32A39ILE00.0040.00424.8420.0000.0000.0000.0000.0000.000
33A40GLN00.0090.00327.5300.0000.0000.0000.0000.0000.000
34A41ARG10.8310.91527.029-0.062-0.0620.0000.0000.0000.000
35A42ILE00.0100.00425.7820.0000.0000.0000.0000.0000.000
36A43GLU-1-0.908-0.94630.1410.0250.0250.0000.0000.0000.000
37A44LYS10.8850.92833.221-0.032-0.0320.0000.0000.0000.000
38A45LEU0-0.043-0.02331.014-0.001-0.0010.0000.0000.0000.000
39A46SER0-0.083-0.02633.109-0.001-0.0010.0000.0000.0000.000
40A47GLY00.0030.01034.975-0.001-0.0010.0000.0000.0000.000
41A48LYS10.7910.87336.545-0.032-0.0320.0000.0000.0000.000
42A49ALA00.0350.01635.8210.0010.0010.0000.0000.0000.000
43A50PRO0-0.0060.00230.9030.0020.0020.0000.0000.0000.000
44A51HIS0-0.010-0.00229.409-0.002-0.0020.0000.0000.0000.000
45A52HIS00.0730.02729.7930.0020.0020.0000.0000.0000.000
46A53TYR0-0.022-0.02325.791-0.001-0.0010.0000.0000.0000.000
47A54LEU00.0060.01124.1910.0020.0020.0000.0000.0000.000
48A55SER00.0300.00825.766-0.001-0.0010.0000.0000.0000.000
49A56ARG10.7710.88926.924-0.016-0.0160.0000.0000.0000.000
50A57GLY00.0020.02222.945-0.003-0.0030.0000.0000.0000.000
51A58VAL0-0.055-0.00521.731-0.002-0.0020.0000.0000.0000.000
52A59PHE00.002-0.01820.3370.0020.0020.0000.0000.0000.000
53A60LEU00.0070.01815.483-0.004-0.0040.0000.0000.0000.000
54A61ALA00.0120.01614.348-0.002-0.0020.0000.0000.0000.000
55A62GLU-1-0.854-0.94515.7880.1280.1280.0000.0000.0000.000
56A63LYS10.8880.98511.246-0.434-0.4340.0000.0000.0000.000
57A64SER0-0.025-0.04315.7110.0000.0000.0000.0000.0000.000
58A65LEU00.0270.01718.915-0.009-0.0090.0000.0000.0000.000
59A66ASP-1-0.822-0.91921.6370.0730.0730.0000.0000.0000.000
60A67LYS10.9660.97819.576-0.156-0.1560.0000.0000.0000.000
61A68PHE00.002-0.00423.365-0.005-0.0050.0000.0000.0000.000
62A69LEU0-0.012-0.00525.061-0.007-0.0070.0000.0000.0000.000
63A70ASP-1-0.821-0.89526.7930.0670.0670.0000.0000.0000.000
64A71ASP-1-0.887-0.94927.0810.0840.0840.0000.0000.0000.000
65A72VAL0-0.0110.00329.019-0.005-0.0050.0000.0000.0000.000
66A73GLU-1-0.874-0.94831.2500.0430.0430.0000.0000.0000.000
67A74ALA0-0.043-0.01132.555-0.004-0.0040.0000.0000.0000.000
68A75LYS10.7930.88934.356-0.048-0.0480.0000.0000.0000.000
69A76LYS10.9670.99830.171-0.071-0.0710.0000.0000.0000.000
70A77PRO0-0.037-0.01231.7520.0000.0000.0000.0000.0000.000
71A78THR00.010-0.01328.0810.0050.0050.0000.0000.0000.000
72A79PHE0-0.058-0.03825.660-0.006-0.0060.0000.0000.0000.000
73A80ILE00.0430.04025.7330.0080.0080.0000.0000.0000.000
74A81PHE0-0.004-0.02121.838-0.006-0.0060.0000.0000.0000.000
75A82ILE0-0.008-0.00823.2540.0030.0030.0000.0000.0000.000
76A83GLN0-0.035-0.00819.6740.0060.0060.0000.0000.0000.000
77A84LYS10.8270.91323.315-0.054-0.0540.0000.0000.0000.000
78A85TYR00.032-0.00523.0140.0010.0010.0000.0000.0000.000
79A86PRO0-0.0080.02225.122-0.005-0.0050.0000.0000.0000.000
80A87GLN00.047-0.02724.388-0.006-0.0060.0000.0000.0000.000
81A88LYS10.9370.96229.175-0.009-0.0090.0000.0000.0000.000
82A89GLU-1-0.878-0.94929.9880.0010.0010.0000.0000.0000.000
83A90VAL00.0120.00729.3020.0020.0020.0000.0000.0000.000
84A91ALA00.0490.02426.227-0.002-0.0020.0000.0000.0000.000
85A92LEU00.006-0.00927.8460.0030.0030.0000.0000.0000.000
86A93GLU-1-0.906-0.96021.5680.0240.0240.0000.0000.0000.000
87A94GLU-1-0.885-0.93924.8240.0470.0470.0000.0000.0000.000
88A95TYR00.015-0.00926.5700.0050.0050.0000.0000.0000.000
89A96ILE00.0090.01523.2460.0020.0020.0000.0000.0000.000
90A97THR00.0340.00122.085-0.002-0.0020.0000.0000.0000.000
91A98LEU0-0.0070.00925.1530.0020.0020.0000.0000.0000.000
92A99GLU-1-0.743-0.86128.7510.0320.0320.0000.0000.0000.000
93A100PHE00.004-0.00523.962-0.001-0.0010.0000.0000.0000.000
94A101ALA00.0450.02627.2870.0020.0020.0000.0000.0000.000
95A102ARG10.8210.91928.563-0.033-0.0330.0000.0000.0000.000
96A103TYR0-0.014-0.01529.226-0.001-0.0010.0000.0000.0000.000
97A104LEU00.0250.00625.6640.0000.0000.0000.0000.0000.000
98A105GLN0-0.023-0.00830.273-0.003-0.0030.0000.0000.0000.000
99A106ASP-1-0.904-0.93732.7000.0320.0320.0000.0000.0000.000
100A107ALA0-0.0270.00332.163-0.001-0.0010.0000.0000.0000.000
101A108PHE00.019-0.00728.3300.0000.0000.0000.0000.0000.000
102A109ASN0-0.048-0.01933.8490.0000.0000.0000.0000.0000.000
103A110ILE0-0.011-0.00429.6270.0000.0000.0000.0000.0000.000
104A111GLN00.001-0.01232.051-0.002-0.0020.0000.0000.0000.000
105A112VAL00.0250.02329.4250.0050.0050.0000.0000.0000.000
106A113ILE0-0.042-0.01228.256-0.004-0.0040.0000.0000.0000.000
107A114ILE0-0.023-0.02427.6590.0050.0050.0000.0000.0000.000
108A115GLN0-0.0170.00324.2950.0030.0030.0000.0000.0000.000
109A116ILE0-0.025-0.02126.9260.0000.0000.0000.0000.0000.000
110A117LEU00.011-0.00322.718-0.001-0.0010.0000.0000.0000.000
111A118ASP-1-0.789-0.91426.9600.0430.0430.0000.0000.0000.000
112A119ASP-1-0.804-0.91927.6400.0590.0590.0000.0000.0000.000
113A120ILE0-0.001-0.01522.233-0.004-0.0040.0000.0000.0000.000
114A121LYS10.8050.89725.239-0.026-0.0260.0000.0000.0000.000
115A122VAL0-0.070-0.03026.983-0.005-0.0050.0000.0000.0000.000
116A123LEU0-0.031-0.00625.481-0.005-0.0050.0000.0000.0000.000
117A124ASN0-0.022-0.01021.890-0.003-0.0030.0000.0000.0000.000
118A125ARG10.9250.95124.917-0.015-0.0150.0000.0000.0000.000
119A126GLU-1-0.775-0.83624.1980.0150.0150.0000.0000.0000.000
120A127ALA0-0.013-0.01128.725-0.001-0.0010.0000.0000.0000.000
121A128THR00.0140.00731.9040.0020.0020.0000.0000.0000.000
122A129ILE00.0910.03334.2090.0010.0010.0000.0000.0000.000
123A130ASN0-0.025-0.01335.3300.0020.0020.0000.0000.0000.000
124A131GLU-1-0.897-0.93534.7500.0130.0130.0000.0000.0000.000
125A132ALA00.0610.02331.8030.0000.0000.0000.0000.0000.000
126A133SER0-0.0010.02433.3250.0010.0010.0000.0000.0000.000
127A134LYS10.9240.95136.011-0.015-0.0150.0000.0000.0000.000
128A135MET0-0.0050.04330.5660.0000.0000.0000.0000.0000.000
129A136SER00.0450.00932.5300.0020.0020.0000.0000.0000.000
130A137ASN0-0.039-0.02333.6710.0030.0030.0000.0000.0000.000
131A138ASP-1-0.936-0.96435.7420.0200.0200.0000.0000.0000.000
132A139LEU0-0.009-0.01329.2600.0000.0000.0000.0000.0000.000
133A140MET00.0250.00833.6290.0000.0000.0000.0000.0000.000
134A141LYS10.8600.93235.444-0.020-0.0200.0000.0000.0000.000
135A142TYR00.014-0.00233.565-0.001-0.0010.0000.0000.0000.000
136A143ILE00.0130.01530.7660.0000.0000.0000.0000.0000.000
137A144LEU0-0.001-0.01433.8010.0000.0000.0000.0000.0000.000
138A145ALA0-0.0110.01436.881-0.001-0.0010.0000.0000.0000.000
139A146PHE0-0.053-0.02931.514-0.001-0.0010.0000.0000.0000.000
140A147GLY0-0.044-0.00536.0390.0000.0000.0000.0000.0000.000
141A148PHE0-0.015-0.00631.2000.0000.0000.0000.0000.0000.000
142A149ASN00.0390.01636.669-0.003-0.0030.0000.0000.0000.000
143A150GLU-1-0.805-0.88937.6790.0320.0320.0000.0000.0000.000
144A151ASP-1-0.901-0.94039.3290.0330.0330.0000.0000.0000.000
145A152LYS10.7900.90835.795-0.042-0.0420.0000.0000.0000.000
146A153THR00.0620.01033.0440.0040.0040.0000.0000.0000.000
147A154PHE0-0.0110.03132.265-0.004-0.0040.0000.0000.0000.000
148A155ILE00.0180.01631.9870.0040.0040.0000.0000.0000.000
149A156TYR0-0.067-0.04227.473-0.003-0.0030.0000.0000.0000.000
150A157THR00.0180.00531.2910.0020.0020.0000.0000.0000.000
151A158ASP-1-0.702-0.85227.1860.0750.0750.0000.0000.0000.000
152A159TYR0-0.050-0.03430.682-0.001-0.0010.0000.0000.0000.000
153A160GLN0-0.075-0.02633.553-0.002-0.0020.0000.0000.0000.000
154A161TYR0-0.038-0.05030.726-0.005-0.0050.0000.0000.0000.000
155A162PHE00.0820.04228.1750.0020.0020.0000.0000.0000.000
156A163GLY00.0300.00832.2750.0030.0030.0000.0000.0000.000
157A164LYS10.8270.91434.103-0.045-0.0450.0000.0000.0000.000
158A165MET00.0390.02828.1590.0020.0020.0000.0000.0000.000
159A166TYR00.0100.02129.0720.0040.0040.0000.0000.0000.000
160A167ARG10.9940.98829.330-0.052-0.0520.0000.0000.0000.000
161A168THR0-0.0310.00027.1450.0060.0060.0000.0000.0000.000
162A169ILE00.0800.04524.9060.0100.0100.0000.0000.0000.000
163A170SER0-0.056-0.03224.7060.0080.0080.0000.0000.0000.000
164A171LEU0-0.024-0.02825.1580.0020.0020.0000.0000.0000.000
165A172VAL00.0250.00519.9280.0100.0100.0000.0000.0000.000
166A173GLU-1-0.920-0.96020.5580.1050.1050.0000.0000.0000.000
167A174LYS10.8720.94021.288-0.088-0.0880.0000.0000.0000.000
168A175ALA0-0.0130.00319.2760.0000.0000.0000.0000.0000.000
169A176THR0-0.051-0.02416.0960.0360.0360.0000.0000.0000.000
170A177ALA00.0200.03114.802-0.032-0.0320.0000.0000.0000.000
171A178TYR00.0660.01615.1430.0320.0320.0000.0000.0000.000
172A179ASN0-0.014-0.02212.4160.0480.0480.0000.0000.0000.000
173A180VAL00.0210.02410.271-0.009-0.0090.0000.0000.0000.000
174A181VAL00.014-0.00310.1870.1090.1090.0000.0000.0000.000
175A182GLN0-0.061-0.05512.132-0.019-0.0190.0000.0000.0000.000
176A183PRO0-0.0030.0337.737-0.049-0.0490.0000.0000.0000.000
177A184PHE0-0.0010.0098.661-0.051-0.0510.0000.0000.0000.000
178A185PHE0-0.008-0.0089.879-0.027-0.0270.0000.0000.0000.000
179A186ASN0-0.019-0.01611.736-0.018-0.0180.0000.0000.0000.000
180A187PHE0-0.0260.00014.0700.0040.0040.0000.0000.0000.000
181A188GLU-1-0.851-0.93916.673-0.059-0.0590.0000.0000.0000.000
182A189TYR0-0.118-0.04419.064-0.003-0.0030.0000.0000.0000.000
183A190SER0-0.0090.00621.6080.0040.0040.0000.0000.0000.000
184A191ASP-1-0.859-0.94119.7160.0060.0060.0000.0000.0000.000
185A192ASN0-0.095-0.05723.0310.0070.0070.0000.0000.0000.000
186A193ILE00.1050.02523.9450.0040.0040.0000.0000.0000.000
187A194GLY00.0000.00924.0760.0070.0070.0000.0000.0000.000
188A195LYS10.9320.96620.044-0.011-0.0110.0000.0000.0000.000
189A196LEU0-0.0240.04019.1280.0110.0110.0000.0000.0000.000
190A197ALA00.0380.02419.5800.0160.0160.0000.0000.0000.000
191A198SER0-0.027-0.07220.3710.0080.0080.0000.0000.0000.000
192A199PRO0-0.007-0.00316.7570.0070.0070.0000.0000.0000.000
193A200SER00.0530.01018.9210.0220.0220.0000.0000.0000.000
194A201ILE0-0.063-0.00321.2420.0020.0020.0000.0000.0000.000
195A202MET0-0.058-0.02218.794-0.002-0.0020.0000.0000.0000.000
196A203THR00.0950.04816.625-0.003-0.0030.0000.0000.0000.000
197A204ALA00.0450.01919.642-0.002-0.0020.0000.0000.0000.000
198A205SER0-0.030-0.01023.043-0.003-0.0030.0000.0000.0000.000
199A206MET0-0.0030.01617.6580.0000.0000.0000.0000.0000.000
200A207PHE00.0310.01018.9700.0030.0030.0000.0000.0000.000
201A208SER0-0.0150.00424.410-0.012-0.0120.0000.0000.0000.000
202A209GLN00.0490.00926.659-0.003-0.0030.0000.0000.0000.000
203A210SER0-0.038-0.02026.038-0.007-0.0070.0000.0000.0000.000
204A211TYR0-0.039-0.01026.344-0.010-0.0100.0000.0000.0000.000
205A212SER00.0430.02331.659-0.003-0.0030.0000.0000.0000.000
206A213HIS10.8380.93434.407-0.049-0.0490.0000.0000.0000.000
207A214PHE00.005-0.01333.420-0.003-0.0030.0000.0000.0000.000
208A215PHE0-0.0190.00630.181-0.001-0.0010.0000.0000.0000.000
209A216SER00.0190.00434.293-0.001-0.0010.0000.0000.0000.000
210A217SER0-0.017-0.00132.999-0.002-0.0020.0000.0000.0000.000
211A218PRO0-0.013-0.01327.8510.0010.0010.0000.0000.0000.000
212A219ALA00.0050.00728.428-0.004-0.0040.0000.0000.0000.000
213A220ARG10.9070.95421.877-0.115-0.1150.0000.0000.0000.000
214A221CYS0-0.0150.01022.429-0.007-0.0070.0000.0000.0000.000
215A222LEU0-0.0040.00621.6090.0120.0120.0000.0000.0000.000
216A223VAL00.0060.00118.848-0.012-0.0120.0000.0000.0000.000
217A224LEU0-0.027-0.01020.1510.0000.0000.0000.0000.0000.000
218A225ASP-1-0.788-0.88716.6270.1500.1500.0000.0000.0000.000
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