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: 9GJ92

Calculation Name: 4HVZ-A-Xray372

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: 2023-06-20

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1873159.335584
FMO2-HF: Nuclear repulsion 1792698.520316
FMO2-HF: Total energy -80460.815268
FMO2-MP2: Total energy -80692.569413


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:37:PRO)


Summations of interaction energy for fragment #1(A:37: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.
-3.639-0.722-0.016-1.304-1.5980.004
Interaction energy analysis for fragmet #1(A:37:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : 0.005
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].
3A39ARG10.9850.9673.664-3.495-0.704-0.015-1.297-1.4790.004
4A40ILE00.0040.0176.0310.0910.0910.0000.0000.0000.000
5A41ALA0-0.006-0.0079.637-0.023-0.0230.0000.0000.0000.000
6A42VAL00.0170.01011.521-0.006-0.0060.0000.0000.0000.000
7A43THR00.0380.02015.052-0.006-0.0060.0000.0000.0000.000
8A44GLY0-0.080-0.04018.002-0.001-0.0010.0000.0000.0000.000
9A45GLU-1-0.911-0.95020.9880.0500.0500.0000.0000.0000.000
10A46GLY0-0.009-0.02524.439-0.003-0.0030.0000.0000.0000.000
11A47MET0-0.034-0.00126.6580.0000.0000.0000.0000.0000.000
12A48MET0-0.005-0.01130.293-0.003-0.0030.0000.0000.0000.000
13A49THR00.0220.00433.4090.0010.0010.0000.0000.0000.000
14A50ALA00.0210.00437.043-0.001-0.0010.0000.0000.0000.000
15A51SER00.0300.02140.0740.0010.0010.0000.0000.0000.000
16A52PRO0-0.020-0.00743.4180.0000.0000.0000.0000.0000.000
17A53ASP-1-0.887-0.92744.0800.0070.0070.0000.0000.0000.000
18A54MET0-0.051-0.04746.541-0.001-0.0010.0000.0000.0000.000
19A55ALA00.0510.03148.8550.0010.0010.0000.0000.0000.000
20A56ILE0-0.067-0.02946.892-0.001-0.0010.0000.0000.0000.000
21A57LEU00.0610.04050.4890.0010.0010.0000.0000.0000.000
22A58ASN0-0.032-0.01751.313-0.001-0.0010.0000.0000.0000.000
23A59LEU00.0290.01953.2380.0000.0000.0000.0000.0000.000
24A60SER00.0110.00656.0650.0000.0000.0000.0000.0000.000
25A61VAL0-0.009-0.01258.2980.0000.0000.0000.0000.0000.000
26A62LEU00.0230.01061.4290.0000.0000.0000.0000.0000.000
27A63ARG10.9150.95664.054-0.004-0.0040.0000.0000.0000.000
28A64GLN0-0.003-0.02666.7890.0000.0000.0000.0000.0000.000
29A65ALA0-0.0100.00669.2090.0000.0000.0000.0000.0000.000
30A66LYS10.9700.97871.487-0.004-0.0040.0000.0000.0000.000
31A67THR00.0160.00971.6280.0000.0000.0000.0000.0000.000
32A68ALA00.0810.04567.0590.0000.0000.0000.0000.0000.000
33A69ARG10.9600.97868.468-0.003-0.0030.0000.0000.0000.000
34A70GLU-1-0.866-0.95269.6980.0040.0040.0000.0000.0000.000
35A71ALA00.0050.01667.6020.0000.0000.0000.0000.0000.000
36A72MET00.016-0.00562.6680.0000.0000.0000.0000.0000.000
37A73THR0-0.009-0.00166.2200.0000.0000.0000.0000.0000.000
38A74ALA00.0390.02768.7030.0000.0000.0000.0000.0000.000
39A75ASN0-0.019-0.01362.2810.0000.0000.0000.0000.0000.000
40A76ASN0-0.013-0.00964.2010.0000.0000.0000.0000.0000.000
41A77GLU-1-0.939-0.98765.7790.0030.0030.0000.0000.0000.000
42A78ALA0-0.004-0.02167.3880.0000.0000.0000.0000.0000.000
43A79MET0-0.019-0.00161.0460.0000.0000.0000.0000.0000.000
44A80THR0-0.034-0.05764.5290.0000.0000.0000.0000.0000.000
45A81LYN00.0190.04365.6820.0000.0000.0000.0000.0000.000
46A82VAL00.0410.02762.3270.0000.0000.0000.0000.0000.000
47A83LEU0-0.0030.02260.0090.0000.0000.0000.0000.0000.000
48A84ASP-1-0.923-0.94162.7220.0020.0020.0000.0000.0000.000
49A85ALA0-0.020-0.03065.7350.0000.0000.0000.0000.0000.000
50A86MET00.013-0.00860.7320.0000.0000.0000.0000.0000.000
51A87LYS10.9410.97561.148-0.002-0.0020.0000.0000.0000.000
52A88LYS10.8600.95062.779-0.003-0.0030.0000.0000.0000.000
53A89ALA0-0.043-0.01362.9540.0000.0000.0000.0000.0000.000
54A90GLY0-0.058-0.01361.9270.0000.0000.0000.0000.0000.000
55A91ILE0-0.034-0.00257.0700.0000.0000.0000.0000.0000.000
56A92GLU-1-0.895-0.96155.3880.0020.0020.0000.0000.0000.000
57A93ASP-1-0.879-0.95256.6610.0020.0020.0000.0000.0000.000
58A94ARG10.8610.94248.457-0.001-0.0010.0000.0000.0000.000
59A95ASP-1-0.882-0.95251.6900.0030.0030.0000.0000.0000.000
60A96LEU00.0170.00853.3400.0010.0010.0000.0000.0000.000
61A97GLN00.0060.01050.4480.0000.0000.0000.0000.0000.000
62A98THR0-0.0070.00753.6570.0000.0000.0000.0000.0000.000
63A99GLY00.0130.01053.3770.0000.0000.0000.0000.0000.000
64A100GLY00.002-0.00853.4850.0000.0000.0000.0000.0000.000
65A101ILE0-0.025-0.02654.0830.0000.0000.0000.0000.0000.000
66A102ASP-1-0.827-0.91356.4150.0070.0070.0000.0000.0000.000
67A103ILE00.028-0.00558.3820.0000.0000.0000.0000.0000.000
68A104GLN0-0.016-0.00159.8840.0000.0000.0000.0000.0000.000
69A105PRO0-0.023-0.01562.9690.0000.0000.0000.0000.0000.000
70A106ILE00.0370.02965.8460.0000.0000.0000.0000.0000.000
71A107TYR0-0.034-0.02765.3480.0000.0000.0000.0000.0000.000
72A108VAL00.0000.00970.3960.0000.0000.0000.0000.0000.000
73A109TYR0-0.018-0.02166.3220.0000.0000.0000.0000.0000.000
74A110PRO0-0.039-0.02972.1070.0000.0000.0000.0000.0000.000
75A111ASP-1-0.877-0.92974.5870.0070.0070.0000.0000.0000.000
76A112ASP-1-0.851-0.91577.2720.0060.0060.0000.0000.0000.000
77A113LYS10.8520.92680.815-0.005-0.0050.0000.0000.0000.000
78A114ASN00.0140.00077.6260.0000.0000.0000.0000.0000.000
79A115ASN0-0.043-0.03379.6660.0000.0000.0000.0000.0000.000
80A116LEU0-0.0630.01675.0850.0000.0000.0000.0000.0000.000
81A117LYS10.9360.97573.182-0.006-0.0060.0000.0000.0000.000
82A118GLU-1-0.863-0.94770.4550.0080.0080.0000.0000.0000.000
83A119PRO00.023-0.01568.5800.0000.0000.0000.0000.0000.000
84A120THR0-0.048-0.03171.7340.0000.0000.0000.0000.0000.000
85A121ILE0-0.014-0.00869.3360.0000.0000.0000.0000.0000.000
86A122THR0-0.0110.00671.9800.0000.0000.0000.0000.0000.000
87A123GLY0-0.030-0.01871.8020.0000.0000.0000.0000.0000.000
88A124TYR0-0.037-0.02066.3140.0000.0000.0000.0000.0000.000
89A125SER0-0.016-0.02064.6080.0000.0000.0000.0000.0000.000
90A126VAL0-0.016-0.01162.3550.0000.0000.0000.0000.0000.000
91A127SER00.0200.02858.7970.0000.0000.0000.0000.0000.000
92A128THR0-0.0020.03257.9570.0000.0000.0000.0000.0000.000
93A129SER0-0.0310.00254.0470.0000.0000.0000.0000.0000.000
94A130LEU0-0.009-0.04755.4750.0000.0000.0000.0000.0000.000
95A131THR0-0.069-0.01450.8100.0000.0000.0000.0000.0000.000
96A132VAL00.0610.03053.731-0.001-0.0010.0000.0000.0000.000
97A133ARG10.8590.93946.887-0.004-0.0040.0000.0000.0000.000
98A134VAL00.0290.01552.389-0.001-0.0010.0000.0000.0000.000
99A135ARG10.9330.94249.493-0.003-0.0030.0000.0000.0000.000
100A136GLU-1-0.928-0.95552.0190.0040.0040.0000.0000.0000.000
101A137LEU00.0720.03249.7090.0000.0000.0000.0000.0000.000
102A138ALA0-0.020-0.00553.2250.0000.0000.0000.0000.0000.000
103A139ASN0-0.024-0.03456.3600.0000.0000.0000.0000.0000.000
104A140VAL00.0180.01254.0990.0000.0000.0000.0000.0000.000
105A141GLY00.0040.01257.3030.0000.0000.0000.0000.0000.000
106A142LYS10.9640.98460.339-0.004-0.0040.0000.0000.0000.000
107A143ILE00.0550.02758.0770.0000.0000.0000.0000.0000.000
108A144LEU0-0.061-0.02657.3700.0000.0000.0000.0000.0000.000
109A145ASP-1-0.873-0.88659.8900.0060.0060.0000.0000.0000.000
110A146GLU-1-0.917-0.95163.2950.0040.0040.0000.0000.0000.000
111A147SER0-0.133-0.12760.3440.0000.0000.0000.0000.0000.000
112A148VAL00.0480.03062.0500.0000.0000.0000.0000.0000.000
113A149THR0-0.103-0.03264.3680.0000.0000.0000.0000.0000.000
114A150LEU0-0.003-0.00964.8280.0000.0000.0000.0000.0000.000
115A151GLY0-0.080-0.03765.8730.0000.0000.0000.0000.0000.000
116A152VAL0-0.014-0.01659.6220.0000.0000.0000.0000.0000.000
117A153ASN0-0.090-0.03260.2890.0010.0010.0000.0000.0000.000
118A154GLN00.0200.00354.4200.0000.0000.0000.0000.0000.000
119A155GLY00.0830.04057.3000.0000.0000.0000.0000.0000.000
120A156GLY00.024-0.00254.7750.0000.0000.0000.0000.0000.000
121A157ASP-1-0.918-0.96950.9020.0110.0110.0000.0000.0000.000
122A158LEU0-0.094-0.05349.8540.0010.0010.0000.0000.0000.000
123A159ASN00.0240.02047.0990.0000.0000.0000.0000.0000.000
124A160LEU0-0.004-0.01047.341-0.001-0.0010.0000.0000.0000.000
125A161VAL0-0.0220.00543.4890.0010.0010.0000.0000.0000.000
126A162ASN00.022-0.00641.1060.0000.0000.0000.0000.0000.000
127A163ASP-1-0.926-0.95642.4660.0050.0050.0000.0000.0000.000
128A164ASN0-0.046-0.03937.8990.0000.0000.0000.0000.0000.000
129A165PRO00.0540.04636.2680.0000.0000.0000.0000.0000.000
130A166SER00.0310.02534.1300.0000.0000.0000.0000.0000.000
131A167ALA00.0320.00733.0870.0000.0000.0000.0000.0000.000
132A168VAL00.0870.04033.4670.0000.0000.0000.0000.0000.000
133A169ILE0-0.015-0.01430.3670.0010.0010.0000.0000.0000.000
134A170ASN0-0.061-0.03329.1430.0020.0020.0000.0000.0000.000
135A171GLU-1-0.915-0.95828.6290.0070.0070.0000.0000.0000.000
136A172ALA00.0280.00728.7580.0010.0010.0000.0000.0000.000
137A173ARG10.8930.91024.171-0.014-0.0140.0000.0000.0000.000
138A174LYS10.9130.96224.2890.0010.0010.0000.0000.0000.000
139A175ARG10.8430.94524.414-0.015-0.0150.0000.0000.0000.000
140A176ALA00.0700.03923.0830.0010.0010.0000.0000.0000.000
141A177VAL0-0.0290.00418.5220.0040.0040.0000.0000.0000.000
142A178ALA00.0380.00919.8490.0020.0020.0000.0000.0000.000
143A179ASN0-0.0230.00321.4800.0030.0030.0000.0000.0000.000
144A180ALA00.0590.00817.6020.0020.0020.0000.0000.0000.000
145A181ILE0-0.003-0.00516.5620.0050.0050.0000.0000.0000.000
146A182ALA0-0.114-0.08517.6490.0000.0000.0000.0000.0000.000
147A183LYS10.9390.97818.225-0.077-0.0770.0000.0000.0000.000
148A184ALA00.0330.02313.6100.0090.0090.0000.0000.0000.000
149A185LYS10.9230.99515.686-0.011-0.0110.0000.0000.0000.000
150A186THR00.0090.01517.7290.0000.0000.0000.0000.0000.000
151A187LEU0-0.041-0.02815.4690.0030.0030.0000.0000.0000.000
152A188ALA0-0.005-0.01213.5660.0040.0040.0000.0000.0000.000
153A189ASP-1-0.823-0.90614.8260.0190.0190.0000.0000.0000.000
154A190ALA0-0.034-0.01517.9820.0020.0020.0000.0000.0000.000
155A191ALA0-0.042-0.01914.7430.0050.0050.0000.0000.0000.000
156A192GLY0-0.069-0.00615.3110.0000.0000.0000.0000.0000.000
157A193VAL0-0.093-0.0589.972-0.009-0.0090.0000.0000.0000.000
158A194GLY00.0490.02312.3140.0020.0020.0000.0000.0000.000
159A195LEU0-0.034-0.01710.899-0.013-0.0130.0000.0000.0000.000
160A196GLY00.0050.0019.7600.0000.0000.0000.0000.0000.000
161A197ARG10.9530.9659.0850.1950.1950.0000.0000.0000.000
162A198VAL00.0340.0139.4890.0010.0010.0000.0000.0000.000
163A199VAL0-0.066-0.0285.333-0.024-0.0240.0000.0000.0000.000
164A200GLU-1-0.935-0.9658.6120.1530.1530.0000.0000.0000.000
165A201ILE0-0.002-0.00711.0260.0180.0180.0000.0000.0000.000
166A202SER0-0.030-0.01414.516-0.008-0.0080.0000.0000.0000.000
167A203GLU-1-0.791-0.87716.7150.0360.0360.0000.0000.0000.000
168A204LEU00.0280.00017.426-0.006-0.0060.0000.0000.0000.000
169A205SER0-0.029-0.00321.0810.0010.0010.0000.0000.0000.000
170A206ARG10.9450.97823.585-0.051-0.0510.0000.0000.0000.000
171A207PRO00.0420.00427.0730.0010.0010.0000.0000.0000.000
172A208PRO0-0.0150.02828.1030.0010.0010.0000.0000.0000.000
173A209MET00.005-0.02430.274-0.003-0.0030.0000.0000.0000.000
174A210PRO00.0110.01833.8200.0020.0020.0000.0000.0000.000
175A211MET0-0.016-0.00434.1900.0000.0000.0000.0000.0000.000
176A212PRO00.0560.04837.2720.0000.0000.0000.0000.0000.000
177A213ILE0-0.0120.02138.4200.0020.0020.0000.0000.0000.000
178A214ALA00.036-0.00141.384-0.001-0.0010.0000.0000.0000.000
179A215ARG10.9700.96843.272-0.017-0.0170.0000.0000.0000.000
180A216GLY00.0190.00942.9990.0000.0000.0000.0000.0000.000
181A217GLN00.0320.01737.1600.0010.0010.0000.0000.0000.000
182A218PHE0-0.018-0.00439.1110.0010.0010.0000.0000.0000.000
183A219ARG11.0110.99735.860-0.034-0.0340.0000.0000.0000.000
184A220THR0-0.011-0.02735.0600.0000.0000.0000.0000.0000.000
185A221MET00.0230.03834.2560.0020.0020.0000.0000.0000.000
186A222LEU0-0.006-0.00134.9010.0010.0010.0000.0000.0000.000
187A223ALA0-0.046-0.02434.4420.0000.0000.0000.0000.0000.000
188A224ALA0-0.021-0.00330.7140.0020.0020.0000.0000.0000.000
189A225ALA0-0.050-0.01531.0820.0000.0000.0000.0000.0000.000
190A226PRO0-0.043-0.04631.6440.0000.0000.0000.0000.0000.000
191A227ASP-1-0.858-0.90232.1520.0230.0230.0000.0000.0000.000
192A228ASN0-0.094-0.05834.538-0.001-0.0010.0000.0000.0000.000
193A229SER00.0400.03835.641-0.002-0.0020.0000.0000.0000.000
194A230VAL0-0.053-0.03437.5810.0000.0000.0000.0000.0000.000
195A231PRO0-0.002-0.00339.6320.0010.0010.0000.0000.0000.000
196A232ILE0-0.029-0.01138.2420.0000.0000.0000.0000.0000.000
197A233ALA0-0.076-0.03841.3110.0000.0000.0000.0000.0000.000
198A234ALA0-0.021-0.02343.5000.0000.0000.0000.0000.0000.000
199A235GLY0-0.0120.00244.444-0.001-0.0010.0000.0000.0000.000
200A236GLU-1-0.782-0.88041.0710.0140.0140.0000.0000.0000.000
201A237ASN0-0.015-0.01939.0810.0020.0020.0000.0000.0000.000
202A238SER0-0.067-0.05735.3690.0000.0000.0000.0000.0000.000
203A239TYR0-0.022-0.02232.5910.0010.0010.0000.0000.0000.000
204A240ASN00.0330.00429.157-0.002-0.0020.0000.0000.0000.000
205A241VAL0-0.029-0.00324.0810.0000.0000.0000.0000.0000.000
206A242SER0-0.031-0.01822.7900.0030.0030.0000.0000.0000.000
207A243VAL00.006-0.00817.872-0.002-0.0020.0000.0000.0000.000
208A244ASN00.0120.00514.756-0.004-0.0040.0000.0000.0000.000
209A245VAL0-0.025-0.01612.776-0.012-0.0120.0000.0000.0000.000
210A246VAL00.0300.0277.3400.0390.0390.0000.0000.0000.000
211A247PHE00.026-0.0049.102-0.059-0.0590.0000.0000.0000.000
212A248GLU-1-0.936-0.9654.769-0.597-0.471-0.001-0.007-0.1190.000
213A249ILE0-0.0470.0025.8920.0740.0740.0000.0000.0000.000
214A250LYS10.9550.9726.0430.0300.0300.0000.0000.0000.000