Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: MNGJZ

Calculation Name: 4HYN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HYN

Chain ID: A

ChEMBL ID:

UniProt ID: G4FDE4

Base Structure: X-ray

Registration Date: 2023-09-24

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2208998.516587
FMO2-HF: Nuclear repulsion 2129895.779272
FMO2-HF: Total energy -79102.737315
FMO2-MP2: Total energy -79326.975568


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:1:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-3.676-2.301-0.001-0.58-0.7930.001
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.078 / q_NPA : -0.060
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].
3A24VAL0-0.033-0.0353.7580.2501.468-0.003-0.551-0.6640.001
4A25LEU0-0.0070.0035.7380.5910.5910.0000.0000.0000.000
5A26THR0-0.043-0.0439.0960.2280.2280.0000.0000.0000.000
6A27PRO0-0.009-0.03110.819-0.041-0.0410.0000.0000.0000.000
7A28GLU-1-0.833-0.88813.887-0.052-0.0520.0000.0000.0000.000
8A29GLU-1-0.824-0.88711.448-0.524-0.5240.0000.0000.0000.000
9A30LYS10.7850.8718.9700.4080.4080.0000.0000.0000.000
10A31ASP-1-0.878-0.93915.446-0.023-0.0230.0000.0000.0000.000
11A32MET0-0.0350.01017.1400.0060.0060.0000.0000.0000.000
12A33ILE0-0.038-0.02316.3020.0040.0040.0000.0000.0000.000
13A34GLY00.0580.02719.2970.0090.0090.0000.0000.0000.000
14A35GLU-1-0.951-0.96721.485-0.062-0.0620.0000.0000.0000.000
15A36ILE0-0.030-0.02621.7800.0070.0070.0000.0000.0000.000
16A37GLY00.0070.01423.2590.0020.0020.0000.0000.0000.000
17A38ASN0-0.022-0.04324.3770.0120.0120.0000.0000.0000.000
18A39ILE0-0.044-0.00627.2870.0070.0070.0000.0000.0000.000
19A40ALA00.0150.00826.5950.0040.0040.0000.0000.0000.000
20A41MET00.006-0.00226.6390.0020.0020.0000.0000.0000.000
21A42GLY00.0630.03828.7240.0070.0070.0000.0000.0000.000
22A43SER0-0.021-0.01231.3800.0090.0090.0000.0000.0000.000
23A44ALA0-0.023-0.01831.0420.0040.0040.0000.0000.0000.000
24A45ALA00.0240.01132.5180.0030.0030.0000.0000.0000.000
25A46THR0-0.001-0.00334.2350.0070.0070.0000.0000.0000.000
26A47THR0-0.013-0.00736.6430.0030.0030.0000.0000.0000.000
27A48LEU00.002-0.00135.4690.0030.0030.0000.0000.0000.000
28A49SER0-0.034-0.04237.8860.0040.0040.0000.0000.0000.000
29A50MET0-0.051-0.02039.8850.0040.0040.0000.0000.0000.000
30A51ILE0-0.066-0.02339.4190.0020.0020.0000.0000.0000.000
31A52LEU0-0.035-0.00839.3850.0020.0020.0000.0000.0000.000
32A53GLY0-0.021-0.01443.1930.0010.0010.0000.0000.0000.000
33A54ARG10.8460.92641.5060.0360.0360.0000.0000.0000.000
34A55ASP-1-0.874-0.90440.055-0.037-0.0370.0000.0000.0000.000
35A56ILE0-0.069-0.05434.4040.0000.0000.0000.0000.0000.000
36A57HIS0-0.0130.01231.772-0.004-0.0040.0000.0000.0000.000
37A58ILE0-0.013-0.02027.948-0.002-0.0020.0000.0000.0000.000
38A59THR0-0.0220.00326.3240.0060.0060.0000.0000.0000.000
39A60VAL00.0070.00421.144-0.007-0.0070.0000.0000.0000.000
40A61PRO0-0.064-0.01722.4750.0030.0030.0000.0000.0000.000
41A62THR0-0.011-0.02316.6170.0180.0180.0000.0000.0000.000
42A63VAL00.0160.00914.547-0.026-0.0260.0000.0000.0000.000
43A64ARG10.7400.85011.1330.2630.2630.0000.0000.0000.000
44A65GLU-1-0.767-0.8536.871-1.702-1.7020.0000.0000.0000.000
45A66GLU-1-0.822-0.8898.225-0.346-0.3460.0000.0000.0000.000
46A67LYS10.9280.9583.6510.8781.0350.002-0.029-0.1290.000
47A68MET00.0230.0128.0860.2010.2010.0000.0000.0000.000
48A69LYS10.7580.8488.4630.4260.4260.0000.0000.0000.000
49A70ASN0-0.079-0.0468.5930.1180.1180.0000.0000.0000.000
50A71VAL00.0550.04412.3210.0480.0480.0000.0000.0000.000
51A72LYS10.8130.88914.4880.1710.1710.0000.0000.0000.000
52A73SER0-0.044-0.03014.7160.0220.0220.0000.0000.0000.000
53A74ASP-1-0.834-0.89914.158-0.188-0.1880.0000.0000.0000.000
54A75PHE0-0.068-0.02717.2410.0170.0170.0000.0000.0000.000
55A76SER00.0190.00420.8560.0030.0030.0000.0000.0000.000
56A77GLY0-0.0030.00223.9030.0000.0000.0000.0000.0000.000
57A78GLU-1-0.899-0.94226.626-0.078-0.0780.0000.0000.0000.000
58A79GLN0-0.039-0.03824.3230.0000.0000.0000.0000.0000.000
59A80VAL00.0000.00328.099-0.002-0.0020.0000.0000.0000.000
60A81VAL0-0.025-0.01123.749-0.007-0.0070.0000.0000.0000.000
61A82VAL00.0190.00126.4020.0060.0060.0000.0000.0000.000
62A83SER0-0.024-0.01224.808-0.013-0.0130.0000.0000.0000.000
63A84VAL00.0020.00525.4270.0150.0150.0000.0000.0000.000
64A85GLU-1-0.931-0.97723.705-0.250-0.2500.0000.0000.0000.000
65A86TYR0-0.037-0.02422.4010.0220.0220.0000.0000.0000.000
66A87THR00.001-0.04125.533-0.011-0.0110.0000.0000.0000.000
67A88GLU-1-0.853-0.90127.794-0.125-0.1250.0000.0000.0000.000
68A89GLY00.0620.04926.5800.0080.0080.0000.0000.0000.000
69A90LEU0-0.051-0.03821.037-0.017-0.0170.0000.0000.0000.000
70A91GLU-1-0.945-0.96721.932-0.210-0.2100.0000.0000.0000.000
71A92GLY00.0060.00120.163-0.040-0.0400.0000.0000.0000.000
72A93LEU00.0090.02320.0850.0260.0260.0000.0000.0000.000
73A94ASN0-0.019-0.01620.025-0.046-0.0460.0000.0000.0000.000
74A95VAL0-0.020-0.01220.7160.0260.0260.0000.0000.0000.000
75A96LEU00.0270.01521.815-0.010-0.0100.0000.0000.0000.000
76A97VAL0-0.038-0.02021.0780.0050.0050.0000.0000.0000.000
77A98LEU00.0460.01324.2190.0060.0060.0000.0000.0000.000
78A99ASP-1-0.811-0.91227.408-0.066-0.0660.0000.0000.0000.000
79A100LYS10.8760.91728.8390.0660.0660.0000.0000.0000.000
80A101LYS10.8540.90332.1630.0450.0450.0000.0000.0000.000
81A102LEU00.0210.02629.2480.0030.0030.0000.0000.0000.000
82A103VAL0-0.014-0.01431.2820.0010.0010.0000.0000.0000.000
83A104ALA0-0.010-0.00933.8430.0020.0020.0000.0000.0000.000
84A105VAL0-0.0110.00835.8150.0020.0020.0000.0000.0000.000
85A106ILE00.0180.00132.7680.0020.0020.0000.0000.0000.000
86A107ALA0-0.017-0.00737.1640.0010.0010.0000.0000.0000.000
87A108ASP-1-0.869-0.94839.318-0.037-0.0370.0000.0000.0000.000
88A109LEU0-0.007-0.00138.9810.0020.0020.0000.0000.0000.000
89A110MET0-0.056-0.02239.0950.0000.0000.0000.0000.0000.000
90A111MET0-0.089-0.04042.1770.0000.0000.0000.0000.0000.000
91A112GLY0-0.057-0.01945.0820.0020.0020.0000.0000.0000.000
92A113GLY0-0.0250.00545.6080.0020.0020.0000.0000.0000.000
93A114SER0-0.108-0.09345.159-0.001-0.0010.0000.0000.0000.000
94A115GLY00.0620.02741.0950.0000.0000.0000.0000.0000.000
95A116GLU-1-0.923-0.94740.215-0.029-0.0290.0000.0000.0000.000
96A117VAL0-0.0080.01339.9640.0020.0020.0000.0000.0000.000
97A118GLU-1-0.964-0.99240.213-0.027-0.0270.0000.0000.0000.000
98A119THR0-0.085-0.06939.4560.0010.0010.0000.0000.0000.000
99A120GLU-1-0.827-0.89333.571-0.051-0.0510.0000.0000.0000.000
100A121GLU-1-0.897-0.93036.558-0.046-0.0460.0000.0000.0000.000
101A122LEU0-0.0270.00333.8790.0000.0000.0000.0000.0000.000
102A123ASP-1-0.812-0.91138.661-0.051-0.0510.0000.0000.0000.000
103A124GLU-1-0.876-0.95738.713-0.071-0.0710.0000.0000.0000.000
104A125ILE0-0.044-0.01840.813-0.002-0.0020.0000.0000.0000.000
105A126LYS10.8730.92339.1890.0460.0460.0000.0000.0000.000
106A127LEU00.007-0.00934.802-0.002-0.0020.0000.0000.0000.000
107A128SER0-0.027-0.00436.986-0.004-0.0040.0000.0000.0000.000
108A129ALA0-0.021-0.00539.547-0.001-0.0010.0000.0000.0000.000
109A130VAL00.0040.00133.517-0.001-0.0010.0000.0000.0000.000
110A131GLY00.0160.01034.733-0.005-0.0050.0000.0000.0000.000
111A132GLU-1-0.838-0.90935.816-0.075-0.0750.0000.0000.0000.000
112A133ALA00.0150.00735.817-0.001-0.0010.0000.0000.0000.000
113A134MET0-0.045-0.03230.438-0.005-0.0050.0000.0000.0000.000
114A135ASN0-0.071-0.03132.880-0.012-0.0120.0000.0000.0000.000
115A136GLN0-0.005-0.01534.928-0.005-0.0050.0000.0000.0000.000
116A137MET0-0.056-0.01031.787-0.001-0.0010.0000.0000.0000.000
117A138MET00.022-0.00626.779-0.001-0.0010.0000.0000.0000.000
118A139GLY00.0390.03330.654-0.007-0.0070.0000.0000.0000.000
119A140SER00.0050.00933.3310.0000.0000.0000.0000.0000.000
120A141ALA0-0.0040.01128.0270.0000.0000.0000.0000.0000.000
121A142ALA00.0350.01928.569-0.005-0.0050.0000.0000.0000.000
122A143THR0-0.020-0.01229.605-0.001-0.0010.0000.0000.0000.000
123A144SER0-0.007-0.00130.4640.0020.0020.0000.0000.0000.000
124A145LEU00.015-0.00323.8810.0010.0010.0000.0000.0000.000
125A146SER0-0.021-0.02427.914-0.004-0.0040.0000.0000.0000.000
126A147GLU-1-0.958-0.97829.827-0.078-0.0780.0000.0000.0000.000
127A148LEU0-0.049-0.01125.7850.0030.0030.0000.0000.0000.000
128A149LEU00.017-0.00323.1360.0030.0030.0000.0000.0000.000
129A150GLY0-0.095-0.03027.0120.0000.0000.0000.0000.0000.000
130A151ILE0-0.053-0.02526.0990.0010.0010.0000.0000.0000.000
131A152THR0-0.010-0.00929.6070.0010.0010.0000.0000.0000.000
132A153ILE0-0.0060.01225.937-0.009-0.0090.0000.0000.0000.000
133A154ASN0-0.066-0.03229.2720.0130.0130.0000.0000.0000.000
134A155ILE00.0090.00027.916-0.014-0.0140.0000.0000.0000.000
135A156SER0-0.0300.00429.2030.0100.0100.0000.0000.0000.000
136A157PRO00.004-0.01131.3760.0000.0000.0000.0000.0000.000
137A158PRO00.0370.01430.458-0.005-0.0050.0000.0000.0000.000
138A159LYS10.7860.89427.7110.1580.1580.0000.0000.0000.000
139A160VAL0-0.005-0.01029.687-0.008-0.0080.0000.0000.0000.000
140A161GLU-1-0.828-0.89027.355-0.140-0.1400.0000.0000.0000.000
141A162ILE00.0110.00729.462-0.004-0.0040.0000.0000.0000.000
142A163LEU0-0.010-0.00523.250-0.001-0.0010.0000.0000.0000.000
143A164ASN00.007-0.01927.2760.0020.0020.0000.0000.0000.000
144A165PHE00.0080.00620.453-0.007-0.0070.0000.0000.0000.000
145A166ASP-1-0.823-0.89523.683-0.069-0.0690.0000.0000.0000.000
146A167ASP-1-0.858-0.90826.251-0.080-0.0800.0000.0000.0000.000
147A168PRO0-0.053-0.02923.894-0.012-0.0120.0000.0000.0000.000
148A169ASN0-0.097-0.06523.666-0.009-0.0090.0000.0000.0000.000
149A170THR0-0.0260.00324.634-0.013-0.0130.0000.0000.0000.000
150A171GLN0-0.018-0.00920.792-0.019-0.0190.0000.0000.0000.000
151A172PHE00.0470.02417.9470.0120.0120.0000.0000.0000.000
152A173PRO00.0430.01920.034-0.013-0.0130.0000.0000.0000.000
153A174PRO0-0.003-0.00518.342-0.027-0.0270.0000.0000.0000.000
154A175VAL0-0.0160.00415.764-0.009-0.0090.0000.0000.0000.000
155A176THR0-0.018-0.01111.636-0.015-0.0150.0000.0000.0000.000
156A177ASP-1-0.859-0.91514.799-0.469-0.4690.0000.0000.0000.000
157A178ASN0-0.020-0.02411.300-0.007-0.0070.0000.0000.0000.000
158A179PRO00.0470.01611.686-0.087-0.0870.0000.0000.0000.000
159A180GLU-1-0.818-0.8907.086-0.532-0.5320.0000.0000.0000.000
160A181LYS10.8050.9076.5990.3230.3230.0000.0000.0000.000
161A182ASP-1-0.853-0.9425.574-2.726-2.7260.0000.0000.0000.000
162A183VAL0-0.045-0.0188.4280.2080.2080.0000.0000.0000.000
163A184ALA00.0100.01210.784-0.085-0.0850.0000.0000.0000.000
164A185VAL00.003-0.01113.3380.0500.0500.0000.0000.0000.000
165A186VAL0-0.014-0.01815.5000.0220.0220.0000.0000.0000.000
166A187GLU-1-0.826-0.87318.431-0.070-0.0700.0000.0000.0000.000
167A188PHE00.003-0.00821.0170.0050.0050.0000.0000.0000.000
168A189GLU-1-0.886-0.94424.654-0.032-0.0320.0000.0000.0000.000
169A190MET0-0.013-0.01327.453-0.002-0.0020.0000.0000.0000.000
170A191GLU-1-0.890-0.95730.874-0.027-0.0270.0000.0000.0000.000
171A192ILE00.0470.02134.237-0.001-0.0010.0000.0000.0000.000
172A193GLU-1-0.848-0.93037.297-0.026-0.0260.0000.0000.0000.000
173A194GLY0-0.021-0.01440.700-0.001-0.0010.0000.0000.0000.000
174A195LEU0-0.037-0.00138.2370.0010.0010.0000.0000.0000.000
175A196PRO0-0.044-0.02035.5850.0010.0010.0000.0000.0000.000
176A197LYS10.8120.89730.5610.0250.0250.0000.0000.0000.000
177A198SER0-0.0380.00330.634-0.001-0.0010.0000.0000.0000.000
178A199LYS10.8920.92723.5170.0690.0690.0000.0000.0000.000
179A200PHE0-0.0080.01225.1110.0020.0020.0000.0000.0000.000
180A201TYR0-0.014-0.02919.5050.0030.0030.0000.0000.0000.000
181A202GLN00.0410.03920.4420.0170.0170.0000.0000.0000.000
182A203VAL0-0.054-0.01515.421-0.018-0.0180.0000.0000.0000.000
183A204ILE00.0530.03116.3950.0210.0210.0000.0000.0000.000
184A205SER00.0670.02613.709-0.058-0.0580.0000.0000.0000.000
185A206ALA00.0280.00610.0900.0620.0620.0000.0000.0000.000
186A207ASP-1-0.896-0.95011.959-0.760-0.7600.0000.0000.0000.000
187A208LEU00.0050.00313.7610.0650.0650.0000.0000.0000.000
188A209VAL00.0210.01113.7200.0530.0530.0000.0000.0000.000
189A210LYS10.9360.96211.8520.5390.5390.0000.0000.0000.000
190A211LYS10.8080.92114.4520.3160.3160.0000.0000.0000.000
191A212MET00.014-0.00317.8790.0390.0390.0000.0000.0000.000
192A213TYR00.031-0.01915.5190.0310.0310.0000.0000.0000.000
193A214GLU-1-0.872-0.91417.075-0.282-0.2820.0000.0000.0000.000
194A215TYR0-0.086-0.06419.6520.0290.0290.0000.0000.0000.000
195A216PHE00.0100.00220.6400.0170.0170.0000.0000.0000.000
196A217THR00.008-0.00918.8430.0220.0220.0000.0000.0000.000
197A218LYS10.8140.90422.0150.1110.1110.0000.0000.0000.000
198A219LYS10.8670.90524.7820.1100.1100.0000.0000.0000.000
199A220GLN0-0.0120.01622.4900.0050.0050.0000.0000.0000.000
200A221SER0-0.059-0.03124.6560.0130.0130.0000.0000.0000.000
201A222GLU-1-0.932-0.93227.098-0.071-0.0710.0000.0000.0000.000
202A223ALA0-0.018-0.00630.4450.0000.0000.0000.0000.0000.000