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: 7GL7K

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 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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1873839.48306
FMO2-HF: Nuclear repulsion 1793373.898648
FMO2-HF: Total energy -80465.584412
FMO2-MP2: Total energy -80696.616891


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.
-2.153-0.1090.001-0.752-1.2940.001
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 : -0.002 / q_NPA : -0.009
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].
3A39ARG10.9570.9773.546-2.348-0.4190.002-0.744-1.1880.001
4A40ILE00.0260.0235.6470.4440.4440.0000.0000.0000.000
5A41ALA0-0.018-0.0138.737-0.066-0.0660.0000.0000.0000.000
6A42VAL0-0.0080.00110.3760.0450.0450.0000.0000.0000.000
7A43THR00.0450.03214.154-0.009-0.0090.0000.0000.0000.000
8A44GLY0-0.019-0.00517.123-0.008-0.0080.0000.0000.0000.000
9A45GLU-1-0.869-0.92720.018-0.005-0.0050.0000.0000.0000.000
10A46GLY0-0.027-0.01023.611-0.007-0.0070.0000.0000.0000.000
11A47MET0-0.0110.00826.2160.0050.0050.0000.0000.0000.000
12A48MET0-0.0130.00429.866-0.003-0.0030.0000.0000.0000.000
13A49THR00.001-0.03932.8420.0040.0040.0000.0000.0000.000
14A50ALA0-0.0020.00236.336-0.002-0.0020.0000.0000.0000.000
15A51SER00.0260.00139.7080.0020.0020.0000.0000.0000.000
16A52PRO0-0.045-0.01143.045-0.001-0.0010.0000.0000.0000.000
17A53ASP-1-0.808-0.88843.398-0.020-0.0200.0000.0000.0000.000
18A54MET0-0.083-0.03146.1590.0000.0000.0000.0000.0000.000
19A55ALA00.0200.01847.6030.0000.0000.0000.0000.0000.000
20A56ILE0-0.042-0.02345.617-0.001-0.0010.0000.0000.0000.000
21A57LEU00.0430.03849.6000.0010.0010.0000.0000.0000.000
22A58ASN00.005-0.00650.703-0.001-0.0010.0000.0000.0000.000
23A59LEU00.015-0.00452.6200.0000.0000.0000.0000.0000.000
24A60SER00.0270.00756.0210.0000.0000.0000.0000.0000.000
25A61VAL0-0.0070.02357.7170.0000.0000.0000.0000.0000.000
26A62LEU00.0280.00061.1360.0000.0000.0000.0000.0000.000
27A63ARG10.8610.92463.4880.0010.0010.0000.0000.0000.000
28A64GLN00.007-0.00366.4490.0000.0000.0000.0000.0000.000
29A65ALA0-0.0250.00669.0240.0000.0000.0000.0000.0000.000
30A66LYS10.9070.95171.498-0.002-0.0020.0000.0000.0000.000
31A67THR0-0.042-0.02571.2680.0000.0000.0000.0000.0000.000
32A68ALA00.0830.03566.2630.0000.0000.0000.0000.0000.000
33A69ARG10.9490.97467.7490.0000.0000.0000.0000.0000.000
34A70GLU-1-0.799-0.90769.3780.0010.0010.0000.0000.0000.000
35A71ALA00.0120.01367.5660.0000.0000.0000.0000.0000.000
36A72MET00.0060.00062.6950.0000.0000.0000.0000.0000.000
37A73THR0-0.010-0.00166.0830.0000.0000.0000.0000.0000.000
38A74ALA00.0520.02968.5360.0000.0000.0000.0000.0000.000
39A75ASN0-0.006-0.01761.7120.0000.0000.0000.0000.0000.000
40A76ASN00.009-0.00363.5350.0000.0000.0000.0000.0000.000
41A77GLU-1-0.931-0.95465.316-0.003-0.0030.0000.0000.0000.000
42A78ALA0-0.022-0.02266.0830.0000.0000.0000.0000.0000.000
43A79MET00.0100.01259.9870.0000.0000.0000.0000.0000.000
44A80THR0-0.024-0.02663.438-0.001-0.0010.0000.0000.0000.000
45A81LYN00.0010.02565.3690.0000.0000.0000.0000.0000.000
46A82VAL00.0240.01361.5770.0000.0000.0000.0000.0000.000
47A83LEU0-0.0040.00358.9290.0000.0000.0000.0000.0000.000
48A84ASP-1-0.843-0.93162.328-0.007-0.0070.0000.0000.0000.000
49A85ALA0-0.081-0.02365.1390.0000.0000.0000.0000.0000.000
50A86MET00.0130.00459.8340.0000.0000.0000.0000.0000.000
51A87LYS10.8670.93960.3060.0070.0070.0000.0000.0000.000
52A88LYS10.8660.93962.1570.0050.0050.0000.0000.0000.000
53A89ALA0-0.020-0.00162.3740.0000.0000.0000.0000.0000.000
54A90GLY0-0.057-0.01761.3340.0000.0000.0000.0000.0000.000
55A91ILE0-0.017-0.00856.071-0.001-0.0010.0000.0000.0000.000
56A92GLU-1-0.841-0.93253.814-0.013-0.0130.0000.0000.0000.000
57A93ASP-1-0.875-0.96355.638-0.010-0.0100.0000.0000.0000.000
58A94ARG10.8390.93348.2350.0170.0170.0000.0000.0000.000
59A95ASP-1-0.790-0.89750.823-0.014-0.0140.0000.0000.0000.000
60A96LEU0-0.0080.02052.5220.0010.0010.0000.0000.0000.000
61A97GLN00.0210.00550.0100.0000.0000.0000.0000.0000.000
62A98THR0-0.037-0.01353.1710.0010.0010.0000.0000.0000.000
63A99GLY00.0280.01152.9020.0000.0000.0000.0000.0000.000
64A100GLY0-0.013-0.00152.9630.0000.0000.0000.0000.0000.000
65A101ILE0-0.010-0.00453.6280.0000.0000.0000.0000.0000.000
66A102ASP-1-0.878-0.89256.2270.0030.0030.0000.0000.0000.000
67A103ILE00.025-0.00958.1730.0000.0000.0000.0000.0000.000
68A104GLN0-0.043-0.02059.0760.0010.0010.0000.0000.0000.000
69A105PRO0-0.018-0.01362.8320.0000.0000.0000.0000.0000.000
70A106ILE00.0070.02165.5850.0000.0000.0000.0000.0000.000
71A107TYR00.001-0.01364.4530.0000.0000.0000.0000.0000.000
72A108VAL0-0.0140.00470.3190.0000.0000.0000.0000.0000.000
73A109TYR00.0520.00165.8380.0000.0000.0000.0000.0000.000
74A110PRO0-0.0110.00371.8010.0000.0000.0000.0000.0000.000
75A111ASP-1-0.768-0.89174.1370.0060.0060.0000.0000.0000.000
76A112ASP-1-0.897-0.93876.7850.0060.0060.0000.0000.0000.000
77A113LYS10.7750.87479.827-0.005-0.0050.0000.0000.0000.000
78A114ASN0-0.043-0.02077.8480.0000.0000.0000.0000.0000.000
79A115ASN00.011-0.00379.3230.0000.0000.0000.0000.0000.000
80A116LEU0-0.067-0.00775.1050.0000.0000.0000.0000.0000.000
81A117LYS10.9010.94572.767-0.006-0.0060.0000.0000.0000.000
82A118GLU-1-0.881-0.94770.2030.0080.0080.0000.0000.0000.000
83A119PRO00.0170.02467.7340.0000.0000.0000.0000.0000.000
84A120THR0-0.045-0.03670.9960.0000.0000.0000.0000.0000.000
85A121ILE0-0.0130.00669.2050.0000.0000.0000.0000.0000.000
86A122THR0-0.014-0.01371.7120.0000.0000.0000.0000.0000.000
87A123GLY0-0.002-0.00871.4190.0000.0000.0000.0000.0000.000
88A124TYR0-0.023-0.00865.8610.0010.0010.0000.0000.0000.000
89A125SER00.0490.01463.8800.0000.0000.0000.0000.0000.000
90A126VAL0-0.043-0.03162.2030.0000.0000.0000.0000.0000.000
91A127SER0-0.021-0.03058.3500.0000.0000.0000.0000.0000.000
92A128THR00.0390.01857.6440.0000.0000.0000.0000.0000.000
93A129SER0-0.0250.00653.2620.0000.0000.0000.0000.0000.000
94A130LEU00.0180.00154.972-0.001-0.0010.0000.0000.0000.000
95A131THR0-0.077-0.03850.0760.0000.0000.0000.0000.0000.000
96A132VAL00.0410.00752.990-0.001-0.0010.0000.0000.0000.000
97A133ARG10.7560.87345.6010.0140.0140.0000.0000.0000.000
98A134VAL00.006-0.00151.2410.0000.0000.0000.0000.0000.000
99A135ARG10.8440.89847.9790.0150.0150.0000.0000.0000.000
100A136GLU-1-0.927-0.95751.370-0.013-0.0130.0000.0000.0000.000
101A137LEU00.0710.03549.3410.0010.0010.0000.0000.0000.000
102A138ALA00.0040.00652.6070.0010.0010.0000.0000.0000.000
103A139ASN0-0.031-0.02155.9740.0010.0010.0000.0000.0000.000
104A140VAL00.0040.00652.7860.0010.0010.0000.0000.0000.000
105A141GLY00.0050.00856.1640.0010.0010.0000.0000.0000.000
106A142LYS10.9330.95559.3730.0090.0090.0000.0000.0000.000
107A143ILE00.0380.01957.1160.0000.0000.0000.0000.0000.000
108A144LEU0-0.0060.00956.5240.0000.0000.0000.0000.0000.000
109A145ASP-1-0.876-0.93259.319-0.004-0.0040.0000.0000.0000.000
110A146GLU-1-0.910-0.95062.672-0.005-0.0050.0000.0000.0000.000
111A147SER0-0.095-0.06959.5790.0000.0000.0000.0000.0000.000
112A148VAL00.0040.00660.8390.0000.0000.0000.0000.0000.000
113A149THR0-0.060-0.05263.2360.0000.0000.0000.0000.0000.000
114A150LEU0-0.054-0.01763.7020.0000.0000.0000.0000.0000.000
115A151GLY0-0.038-0.01465.4740.0000.0000.0000.0000.0000.000
116A152VAL0-0.0170.00459.1630.0000.0000.0000.0000.0000.000
117A153ASN0-0.083-0.05460.3430.0000.0000.0000.0000.0000.000
118A154GLN0-0.029-0.00552.5110.0000.0000.0000.0000.0000.000
119A155GLY00.0760.03556.952-0.001-0.0010.0000.0000.0000.000
120A156GLY00.026-0.00554.1950.0000.0000.0000.0000.0000.000
121A157ASP-1-0.923-0.97450.4130.0000.0000.0000.0000.0000.000
122A158LEU0-0.061-0.01748.5380.0000.0000.0000.0000.0000.000
123A159ASN00.0320.03746.466-0.001-0.0010.0000.0000.0000.000
124A160LEU0-0.003-0.01546.425-0.001-0.0010.0000.0000.0000.000
125A161VAL0-0.002-0.00342.7600.0000.0000.0000.0000.0000.000
126A162ASN0-0.037-0.04240.1370.0000.0000.0000.0000.0000.000
127A163ASP-1-0.762-0.87841.494-0.016-0.0160.0000.0000.0000.000
128A164ASN0-0.058-0.02538.0210.0000.0000.0000.0000.0000.000
129A165PRO00.0470.02636.127-0.003-0.0030.0000.0000.0000.000
130A166SER0-0.006-0.00633.480-0.002-0.0020.0000.0000.0000.000
131A167ALA00.0210.01132.485-0.004-0.0040.0000.0000.0000.000
132A168VAL00.0350.01932.794-0.004-0.0040.0000.0000.0000.000
133A169ILE00.0460.02129.393-0.002-0.0020.0000.0000.0000.000
134A170ASN00.0100.00127.695-0.005-0.0050.0000.0000.0000.000
135A171GLU-1-0.844-0.88628.021-0.066-0.0660.0000.0000.0000.000
136A172ALA00.0250.01728.140-0.005-0.0050.0000.0000.0000.000
137A173ARG10.8600.90323.4270.0510.0510.0000.0000.0000.000
138A174LYS10.8590.91423.5520.0600.0600.0000.0000.0000.000
139A175ARG10.8680.92523.8040.0420.0420.0000.0000.0000.000
140A176ALA00.0440.03122.238-0.004-0.0040.0000.0000.0000.000
141A177VAL00.0030.00017.971-0.007-0.0070.0000.0000.0000.000
142A178ALA00.0000.00019.239-0.015-0.0150.0000.0000.0000.000
143A179ASN0-0.037-0.01921.181-0.010-0.0100.0000.0000.0000.000
144A180ALA00.0460.01816.452-0.003-0.0030.0000.0000.0000.000
145A181ILE00.0120.00316.291-0.018-0.0180.0000.0000.0000.000
146A182ALA0-0.038-0.02017.463-0.012-0.0120.0000.0000.0000.000
147A183LYS10.8840.94017.9900.0480.0480.0000.0000.0000.000
148A184ALA00.0220.00613.4630.0050.0050.0000.0000.0000.000
149A185LYS10.9350.97215.1720.1230.1230.0000.0000.0000.000
150A186THR00.0160.00817.1550.0020.0020.0000.0000.0000.000
151A187LEU0-0.023-0.01515.3160.0140.0140.0000.0000.0000.000
152A188ALA0-0.022-0.00813.6820.0020.0020.0000.0000.0000.000
153A189ASP-1-0.906-0.95514.820-0.142-0.1420.0000.0000.0000.000
154A190ALA0-0.058-0.02918.1420.0120.0120.0000.0000.0000.000
155A191ALA0-0.043-0.01214.2760.0200.0200.0000.0000.0000.000
156A192GLY0-0.0150.00715.5860.0030.0030.0000.0000.0000.000
157A193VAL0-0.066-0.04510.441-0.019-0.0190.0000.0000.0000.000
158A194GLY00.0270.01712.5490.0080.0080.0000.0000.0000.000
159A195LEU0-0.015-0.01210.942-0.090-0.0900.0000.0000.0000.000
160A196GLY00.0000.0069.1930.0430.0430.0000.0000.0000.000
161A197ARG10.9070.9498.3500.5230.5230.0000.0000.0000.000
162A198VAL00.0100.0058.559-0.111-0.1110.0000.0000.0000.000
163A199VAL0-0.053-0.0295.011-0.030-0.0300.0000.0000.0000.000
164A200GLU-1-0.906-0.9348.209-0.012-0.0120.0000.0000.0000.000
165A201ILE0-0.003-0.00710.7590.0010.0010.0000.0000.0000.000
166A202SER0-0.041-0.03413.6440.0150.0150.0000.0000.0000.000
167A203GLU-1-0.822-0.91116.132-0.042-0.0420.0000.0000.0000.000
168A204LEU00.005-0.00216.5430.0020.0020.0000.0000.0000.000
169A205SER0-0.039-0.01420.2740.0150.0150.0000.0000.0000.000
170A206ARG10.9560.98022.697-0.020-0.0200.0000.0000.0000.000
171A207PRO00.0220.00326.447-0.003-0.0030.0000.0000.0000.000
172A208PRO0-0.0100.01226.7980.0030.0030.0000.0000.0000.000
173A209MET0-0.007-0.01629.4650.0000.0000.0000.0000.0000.000
174A210PRO00.0090.00633.2020.0000.0000.0000.0000.0000.000
175A211MET0-0.0100.00832.9340.0040.0040.0000.0000.0000.000
176A212PRO00.0460.04536.482-0.002-0.0020.0000.0000.0000.000
177A213ILE0-0.0070.01037.8470.0030.0030.0000.0000.0000.000
178A214ALA00.0420.00340.3210.0000.0000.0000.0000.0000.000
179A215ARG10.9710.96641.990-0.004-0.0040.0000.0000.0000.000
180A216GLY0-0.0020.00841.7490.0000.0000.0000.0000.0000.000
181A217GLN00.0280.00936.0130.0030.0030.0000.0000.0000.000
182A218PHE00.0020.01338.013-0.001-0.0010.0000.0000.0000.000
183A219ARG10.9920.99235.162-0.011-0.0110.0000.0000.0000.000
184A220THR0-0.016-0.02534.024-0.002-0.0020.0000.0000.0000.000
185A221MET00.0520.03533.530-0.002-0.0020.0000.0000.0000.000
186A222LEU0-0.012-0.00734.429-0.002-0.0020.0000.0000.0000.000
187A223ALA0-0.049-0.02533.237-0.002-0.0020.0000.0000.0000.000
188A224ALA0-0.0070.00229.8220.0000.0000.0000.0000.0000.000
189A225ALA0-0.0260.00030.626-0.004-0.0040.0000.0000.0000.000
190A226PRO0-0.053-0.03930.741-0.001-0.0010.0000.0000.0000.000
191A227ASP-1-0.856-0.92431.257-0.030-0.0300.0000.0000.0000.000
192A228ASN0-0.110-0.06333.899-0.002-0.0020.0000.0000.0000.000
193A229SER0-0.0020.01835.293-0.001-0.0010.0000.0000.0000.000
194A230VAL0-0.007-0.00737.2630.0010.0010.0000.0000.0000.000
195A231PRO0-0.018-0.01139.3470.0000.0000.0000.0000.0000.000
196A232ILE0-0.0130.00738.0560.0000.0000.0000.0000.0000.000
197A233ALA0-0.007-0.00541.0900.0020.0020.0000.0000.0000.000
198A234ALA0-0.036-0.03142.4670.0000.0000.0000.0000.0000.000
199A235GLY0-0.010-0.00943.7770.0000.0000.0000.0000.0000.000
200A236GLU-1-0.796-0.87640.879-0.017-0.0170.0000.0000.0000.000
201A237ASN0-0.055-0.02138.4140.0030.0030.0000.0000.0000.000
202A238SER0-0.018-0.03334.460-0.002-0.0020.0000.0000.0000.000
203A239TYR0-0.018-0.03132.0860.0020.0020.0000.0000.0000.000
204A240ASN0-0.025-0.02427.879-0.004-0.0040.0000.0000.0000.000
205A241VAL0-0.023-0.00523.7060.0020.0020.0000.0000.0000.000
206A242SER0-0.004-0.00122.088-0.005-0.0050.0000.0000.0000.000
207A243VAL00.0030.01118.1810.0050.0050.0000.0000.0000.000
208A244ASN00.0230.00913.7590.0020.0020.0000.0000.0000.000
209A245VAL0-0.008-0.01312.745-0.016-0.0160.0000.0000.0000.000
210A246VAL0-0.011-0.0016.4600.0160.0160.0000.0000.0000.000
211A247PHE00.0470.0078.5410.0010.0010.0000.0000.0000.000
212A248GLU-1-0.874-0.9404.555-1.266-1.151-0.001-0.008-0.1060.000
213A249ILE0-0.033-0.0025.5940.3420.3420.0000.0000.0000.000
214A250LYS10.9490.9766.4510.4460.4460.0000.0000.0000.000