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: 663YZ

Calculation Name: 4HVZ-A-Xray321

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HVZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q44642

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 215
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1877302.312351
FMO2-HF: Nuclear repulsion 1796690.36396
FMO2-HF: Total energy -80611.948391
FMO2-MP2: Total energy -80844.115988


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:36:ACE )


Summations of interaction energy for fragment #1(A:36:ACE )
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.
0.3160.8180-0.311-0.1920
Interaction energy analysis for fragmet #1(A:36:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.011
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].
3A38ALA 00.0160.0133.8570.0230.4530.000-0.295-0.1350.000
4A39ARG 10.9790.9684.3150.2640.3360.000-0.016-0.0570.000
5A40ILE 00.0100.0218.1990.0180.0180.0000.0000.0000.000
6A41ALA 0-0.009-0.00910.1480.0590.0590.0000.0000.0000.000
7A42VAL 00.0140.00812.0060.0010.0010.0000.0000.0000.000
8A43THR 00.0350.01815.6810.0210.0210.0000.0000.0000.000
9A44GLY 0-0.078-0.03818.288-0.018-0.0180.0000.0000.0000.000
10A45GLU -1-0.913-0.95221.7050.0170.0170.0000.0000.0000.000
11A46GLY 0-0.003-0.02225.001-0.007-0.0070.0000.0000.0000.000
12A47MET 0-0.039-0.00127.6010.0060.0060.0000.0000.0000.000
13A48MET 0-0.002-0.01031.135-0.003-0.0030.0000.0000.0000.000
14A49THR 00.0150.00234.3770.0040.0040.0000.0000.0000.000
15A50ALA 00.0210.00337.862-0.001-0.0010.0000.0000.0000.000
16A51SER 00.0330.02140.9220.0010.0010.0000.0000.0000.000
17A52PRO 0-0.023-0.00744.1740.0010.0010.0000.0000.0000.000
18A53ASP -1-0.886-0.92744.9140.0110.0110.0000.0000.0000.000
19A54MET 0-0.054-0.04847.3160.0000.0000.0000.0000.0000.000
20A55ALA 00.0530.03149.1700.0000.0000.0000.0000.0000.000
21A56ILE 0-0.061-0.02646.9970.0000.0000.0000.0000.0000.000
22A57LEU 00.0550.03750.5510.0000.0000.0000.0000.0000.000
23A58ASN 0-0.034-0.01751.0960.0000.0000.0000.0000.0000.000
24A59LEU 00.0300.01953.062-0.001-0.0010.0000.0000.0000.000
25A60SER 00.0130.00755.7150.0010.0010.0000.0000.0000.000
26A61VAL 0-0.004-0.00957.994-0.001-0.0010.0000.0000.0000.000
27A62LEU 00.0230.00960.9240.0000.0000.0000.0000.0000.000
28A63ARG 10.9090.95563.658-0.013-0.0130.0000.0000.0000.000
29A64GLN 0-0.001-0.02466.3210.0010.0010.0000.0000.0000.000
30A65ALA 0-0.0120.00668.696-0.001-0.0010.0000.0000.0000.000
31A66LYS 10.9700.97870.878-0.012-0.0120.0000.0000.0000.000
32A67THR 00.0150.00870.9870.0000.0000.0000.0000.0000.000
33A68ALA 00.0790.04466.4950.0000.0000.0000.0000.0000.000
34A69ARG 10.9630.98067.986-0.016-0.0160.0000.0000.0000.000
35A70GLU -1-0.865-0.95169.3120.0140.0140.0000.0000.0000.000
36A71ALA 00.0070.01767.1100.0000.0000.0000.0000.0000.000
37A72MET 00.016-0.00462.3170.0000.0000.0000.0000.0000.000
38A73THR 0-0.010-0.00265.9310.0000.0000.0000.0000.0000.000
39A74ALA 00.0380.02768.4460.0000.0000.0000.0000.0000.000
40A75ASN 0-0.021-0.01462.023-0.001-0.0010.0000.0000.0000.000
41A76ASN 0-0.009-0.00864.0100.0000.0000.0000.0000.0000.000
42A77GLU -1-0.940-0.98765.6220.0130.0130.0000.0000.0000.000
43A78ALA 0-0.004-0.02367.1880.0000.0000.0000.0000.0000.000
44A79MET 0-0.0170.00060.9450.0000.0000.0000.0000.0000.000
45A80THR 0-0.035-0.05764.4390.0000.0000.0000.0000.0000.000
46A81LYN 00.0180.04365.7210.0000.0000.0000.0000.0000.000
47A82VAL 00.0410.02762.2830.0000.0000.0000.0000.0000.000
48A83LEU 0-0.0020.02160.1270.0000.0000.0000.0000.0000.000
49A84ASP -1-0.923-0.94162.8550.0120.0120.0000.0000.0000.000
50A85ALA 0-0.019-0.03065.842-0.001-0.0010.0000.0000.0000.000
51A86MET 00.013-0.00960.9530.0000.0000.0000.0000.0000.000
52A87LYS 10.9420.97661.518-0.014-0.0140.0000.0000.0000.000
53A88LYS 10.8590.95063.130-0.010-0.0100.0000.0000.0000.000
54A89ALA 0-0.045-0.01363.2110.0000.0000.0000.0000.0000.000
55A90GLY 0-0.059-0.01262.4320.0000.0000.0000.0000.0000.000
56A91ILE 0-0.038-0.00557.4200.0000.0000.0000.0000.0000.000
57A92GLU -1-0.892-0.96256.0490.0130.0130.0000.0000.0000.000
58A93ASP -1-0.879-0.95157.0670.0150.0150.0000.0000.0000.000
59A94ARG 10.8610.94349.193-0.016-0.0160.0000.0000.0000.000
60A95ASP -1-0.882-0.95252.0990.0160.0160.0000.0000.0000.000
61A96LEU 00.0190.00953.6980.0000.0000.0000.0000.0000.000
62A97GLN 00.0040.00950.5860.0010.0010.0000.0000.0000.000
63A98THR 0-0.0050.00853.760-0.001-0.0010.0000.0000.0000.000
64A99GLY 00.0130.01053.3140.0010.0010.0000.0000.0000.000
65A100GLY 00.000-0.00853.1620.0000.0000.0000.0000.0000.000
66A101ILE 0-0.021-0.02553.761-0.001-0.0010.0000.0000.0000.000
67A102ASP -1-0.830-0.91455.9430.0210.0210.0000.0000.0000.000
68A103ILE 00.024-0.00657.851-0.001-0.0010.0000.0000.0000.000
69A104GLN 0-0.011-0.00159.0950.0010.0010.0000.0000.0000.000
70A105PRO 0-0.025-0.01662.228-0.001-0.0010.0000.0000.0000.000
71A106ILE 00.0360.02965.0560.0000.0000.0000.0000.0000.000
72A107TYR 0-0.033-0.02664.3970.0000.0000.0000.0000.0000.000
73A108VAL 00.0010.00869.4690.0000.0000.0000.0000.0000.000
74A109TYR 0-0.019-0.02165.2950.0000.0000.0000.0000.0000.000
75A110PRO 0-0.036-0.02870.9610.0000.0000.0000.0000.0000.000
76A111ASP -1-0.879-0.93073.4110.0110.0110.0000.0000.0000.000
77A112ASP -1-0.851-0.91576.1000.0100.0100.0000.0000.0000.000
78A113LYS 10.8500.92579.622-0.009-0.0090.0000.0000.0000.000
79A114ASN 00.0150.00076.3530.0000.0000.0000.0000.0000.000
80A115ASN 0-0.044-0.03378.4330.0000.0000.0000.0000.0000.000
81A116LEU 0-0.0630.01673.9360.0000.0000.0000.0000.0000.000
82A117LYS 10.9370.97572.021-0.015-0.0150.0000.0000.0000.000
83A118GLU -1-0.866-0.94869.2260.0150.0150.0000.0000.0000.000
84A119PRO 00.021-0.01367.4660.0000.0000.0000.0000.0000.000
85A120THR 0-0.045-0.03470.6300.0000.0000.0000.0000.0000.000
86A121ILE 0-0.009-0.00368.4710.0000.0000.0000.0000.0000.000
87A122THR 0-0.0140.00671.0720.0000.0000.0000.0000.0000.000
88A123GLY 0-0.028-0.01771.0470.0000.0000.0000.0000.0000.000
89A124TYR 0-0.037-0.02165.5930.0010.0010.0000.0000.0000.000
90A125SER 0-0.016-0.01963.909-0.001-0.0010.0000.0000.0000.000
91A126VAL 0-0.013-0.01161.9190.0010.0010.0000.0000.0000.000
92A127SER 00.0200.02758.374-0.001-0.0010.0000.0000.0000.000
93A128THR 0-0.0060.03157.6770.0010.0010.0000.0000.0000.000
94A129SER 0-0.0270.00453.796-0.001-0.0010.0000.0000.0000.000
95A130LEU 0-0.012-0.04955.3900.0000.0000.0000.0000.0000.000
96A131THR 0-0.068-0.01450.720-0.001-0.0010.0000.0000.0000.000
97A132VAL 00.0640.03153.7120.0000.0000.0000.0000.0000.000
98A133ARG 10.8600.94047.209-0.019-0.0190.0000.0000.0000.000
99A134VAL 00.0240.01352.6170.0000.0000.0000.0000.0000.000
100A135ARG 10.9350.94450.009-0.015-0.0150.0000.0000.0000.000
101A136GLU -1-0.928-0.95652.8280.0070.0070.0000.0000.0000.000
102A137LEU 00.0740.03450.2360.0000.0000.0000.0000.0000.000
103A138ALA 0-0.019-0.00553.8550.0000.0000.0000.0000.0000.000
104A139ASN 0-0.026-0.03556.997-0.001-0.0010.0000.0000.0000.000
105A140VAL 00.0180.01154.3100.0000.0000.0000.0000.0000.000
106A141GLY 00.0060.01357.5820.0000.0000.0000.0000.0000.000
107A142LYS 10.9620.98460.546-0.007-0.0070.0000.0000.0000.000
108A143ILE 00.0560.02858.2580.0000.0000.0000.0000.0000.000
109A144LEU 0-0.059-0.02657.3240.0000.0000.0000.0000.0000.000
110A145ASP -1-0.873-0.88559.9120.0090.0090.0000.0000.0000.000
111A146GLU -1-0.916-0.95163.3870.0100.0100.0000.0000.0000.000
112A147SER 0-0.135-0.12760.2830.0000.0000.0000.0000.0000.000
113A148VAL 00.0500.03061.8790.0000.0000.0000.0000.0000.000
114A149THR 0-0.107-0.03264.2130.0000.0000.0000.0000.0000.000
115A150LEU 0-0.001-0.00864.8400.0000.0000.0000.0000.0000.000
116A151GLY 0-0.080-0.03865.6340.0000.0000.0000.0000.0000.000
117A152VAL 0-0.012-0.01559.4120.0000.0000.0000.0000.0000.000
118A153ASN 0-0.094-0.03359.9800.0000.0000.0000.0000.0000.000
119A154GLN 00.0210.00253.980-0.001-0.0010.0000.0000.0000.000
120A155GLY 00.0810.03957.0740.0000.0000.0000.0000.0000.000
121A156GLY 00.028-0.00154.6460.0010.0010.0000.0000.0000.000
122A157ASP -1-0.921-0.97050.5940.0160.0160.0000.0000.0000.000
123A158LEU 0-0.094-0.05349.7040.0000.0000.0000.0000.0000.000
124A159ASN 00.0250.02046.985-0.001-0.0010.0000.0000.0000.000
125A160LEU 0-0.006-0.01047.3620.0000.0000.0000.0000.0000.000
126A161VAL 0-0.0200.00543.6350.0010.0010.0000.0000.0000.000
127A162ASN 00.021-0.00641.5230.0000.0000.0000.0000.0000.000
128A163ASP -1-0.927-0.95742.8770.0220.0220.0000.0000.0000.000
129A164ASN 0-0.047-0.04038.8680.0010.0010.0000.0000.0000.000
130A165PRO 00.0530.04536.794-0.002-0.0020.0000.0000.0000.000
131A166SER 00.0320.02634.881-0.002-0.0020.0000.0000.0000.000
132A167ALA 00.0330.00834.1380.0010.0010.0000.0000.0000.000
133A168VAL 00.0880.03934.822-0.001-0.0010.0000.0000.0000.000
134A169ILE 0-0.020-0.01630.973-0.001-0.0010.0000.0000.0000.000
135A170ASN 0-0.058-0.03230.4270.0030.0030.0000.0000.0000.000
136A171GLU -1-0.914-0.95730.0060.0000.0000.0000.0000.0000.000
137A172ALA 00.0250.00630.151-0.004-0.0040.0000.0000.0000.000
138A173ARG 10.8950.91025.123-0.047-0.0470.0000.0000.0000.000
139A174LYS 10.9090.96125.690-0.011-0.0110.0000.0000.0000.000
140A175ARG 10.8510.94726.3170.0000.0000.0000.0000.0000.000
141A176ALA 00.0600.03523.958-0.006-0.0060.0000.0000.0000.000
142A177VAL 0-0.0210.00820.464-0.006-0.0060.0000.0000.0000.000
143A178ALA 00.0340.00921.755-0.011-0.0110.0000.0000.0000.000
144A179ASN 0-0.0230.00123.420-0.017-0.0170.0000.0000.0000.000
145A180ALA 00.0540.00618.858-0.011-0.0110.0000.0000.0000.000
146A181ILE 00.001-0.00319.092-0.017-0.0170.0000.0000.0000.000
147A182ALA 0-0.109-0.08320.113-0.019-0.0190.0000.0000.0000.000
148A183LYS 10.9310.97519.6820.0380.0380.0000.0000.0000.000
149A184ALA 00.0330.02315.976-0.013-0.0130.0000.0000.0000.000
150A185LYS 10.9301.00017.8480.0570.0570.0000.0000.0000.000
151A186THR 00.0050.01320.479-0.008-0.0080.0000.0000.0000.000
152A187LEU 0-0.052-0.03416.447-0.006-0.0060.0000.0000.0000.000
153A188ALA 00.005-0.00616.815-0.018-0.0180.0000.0000.0000.000
154A189ASP -1-0.815-0.90217.690-0.162-0.1620.0000.0000.0000.000
155A190ALA 0-0.047-0.02121.132-0.011-0.0110.0000.0000.0000.000
156A191ALA 0-0.051-0.02417.1350.0010.0010.0000.0000.0000.000
157A192GLY 0-0.078-0.01318.459-0.021-0.0210.0000.0000.0000.000
158A193VAL 0-0.102-0.06214.221-0.028-0.0280.0000.0000.0000.000
159A194GLY 00.0560.03216.9500.0350.0350.0000.0000.0000.000
160A195LEU 0-0.033-0.01114.896-0.051-0.0510.0000.0000.0000.000
161A196GLY 00.0470.01713.9970.0350.0350.0000.0000.0000.000
162A197ARG 10.9260.95113.0650.1390.1390.0000.0000.0000.000
163A198VAL 00.0280.01013.056-0.031-0.0310.0000.0000.0000.000
164A199VAL 0-0.071-0.0298.0690.0250.0250.0000.0000.0000.000
165A200GLU -1-0.937-0.96710.0140.4130.4130.0000.0000.0000.000
166A201ILE 00.000-0.00612.291-0.048-0.0480.0000.0000.0000.000
167A202SER 0-0.036-0.01714.5270.0140.0140.0000.0000.0000.000
168A203GLU -1-0.787-0.87517.0260.0390.0390.0000.0000.0000.000
169A204LEU 00.023-0.00217.0550.0040.0040.0000.0000.0000.000
170A205SER 0-0.029-0.00420.8530.0010.0010.0000.0000.0000.000
171A206ARG 10.9440.97723.198-0.046-0.0460.0000.0000.0000.000
172A207PRO 00.0420.00426.755-0.006-0.0060.0000.0000.0000.000
173A208PRO 0-0.0130.02928.217-0.003-0.0030.0000.0000.0000.000
174A209MET 00.004-0.02530.2930.0000.0000.0000.0000.0000.000
175A210PRO 00.0100.01733.738-0.002-0.0020.0000.0000.0000.000
176A211MET 0-0.015-0.00433.8710.0000.0000.0000.0000.0000.000
177A212PRO 00.0550.04837.058-0.002-0.0020.0000.0000.0000.000
178A213ILE 0-0.0120.02238.7190.0000.0000.0000.0000.0000.000
179A214ALA 00.037-0.00241.267-0.001-0.0010.0000.0000.0000.000
180A215ARG 10.9690.96842.931-0.009-0.0090.0000.0000.0000.000
181A216GLY 00.0170.00942.360-0.001-0.0010.0000.0000.0000.000
182A217GLN 00.0250.01236.547-0.002-0.0020.0000.0000.0000.000
183A218PHE 0-0.0150.00038.910-0.001-0.0010.0000.0000.0000.000
184A219ARG 11.0080.99635.4670.0050.0050.0000.0000.0000.000
185A220THR 0-0.021-0.03234.652-0.002-0.0020.0000.0000.0000.000
186A221MET 00.0460.04934.2000.0000.0000.0000.0000.0000.000
187A222LEU 0-0.009-0.00335.300-0.001-0.0010.0000.0000.0000.000
188A223ALA 0-0.050-0.02534.671-0.002-0.0020.0000.0000.0000.000
189A224ALA 0-0.018-0.00130.995-0.003-0.0030.0000.0000.0000.000
190A225ALA 0-0.053-0.01631.7380.0010.0010.0000.0000.0000.000
191A226PRO 0-0.043-0.04732.712-0.002-0.0020.0000.0000.0000.000
192A227ASP -1-0.856-0.90233.701-0.023-0.0230.0000.0000.0000.000
193A228ASN 0-0.095-0.05936.124-0.001-0.0010.0000.0000.0000.000
194A229SER 00.0420.03837.2980.0000.0000.0000.0000.0000.000
195A230VAL 0-0.052-0.03339.291-0.001-0.0010.0000.0000.0000.000
196A231PRO 0-0.004-0.00340.9600.0000.0000.0000.0000.0000.000
197A232ILE 0-0.028-0.00939.0410.0010.0010.0000.0000.0000.000
198A233ALA 0-0.077-0.04042.144-0.001-0.0010.0000.0000.0000.000
199A234ALA 0-0.021-0.02343.9470.0010.0010.0000.0000.0000.000
200A235GLY 0-0.0130.00144.5340.0000.0000.0000.0000.0000.000
201A236GLU -1-0.782-0.87941.6050.0040.0040.0000.0000.0000.000
202A237ASN 0-0.014-0.01839.2640.0010.0010.0000.0000.0000.000
203A238SER 0-0.068-0.05635.694-0.002-0.0020.0000.0000.0000.000
204A239TYR 0-0.022-0.02233.0110.0040.0040.0000.0000.0000.000
205A240ASN 00.0320.00429.314-0.001-0.0010.0000.0000.0000.000
206A241VAL 0-0.032-0.00424.6330.0060.0060.0000.0000.0000.000
207A242SER 0-0.031-0.01722.622-0.006-0.0060.0000.0000.0000.000
208A243VAL 00.004-0.00818.6940.0110.0110.0000.0000.0000.000
209A244ASN 00.0120.00414.507-0.032-0.0320.0000.0000.0000.000
210A245VAL 0-0.023-0.01514.5480.0230.0230.0000.0000.0000.000
211A246VAL 00.0230.0238.394-0.030-0.0300.0000.0000.0000.000
212A247PHE 00.027-0.00511.5670.0450.0450.0000.0000.0000.000
213A248GLU -1-0.948-0.9738.851-0.396-0.3960.0000.0000.0000.000
214A249ILE 0-0.062-0.0129.5310.0780.0780.0000.0000.0000.000
215A250LYS 00.0400.01311.0210.0090.0090.0000.0000.0000.000