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: 226QR

Calculation Name: 4HUD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HUD

Chain ID: A

ChEMBL ID:

UniProt ID: P11112

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2646823.646158
FMO2-HF: Nuclear repulsion 2558209.949828
FMO2-HF: Total energy -88613.696331
FMO2-MP2: Total energy -88871.727937


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:3:GLY)


Summations of interaction energy for fragment #1(A:3:GLY)
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.
1.8353.356-0.023-0.851-0.6470
Interaction energy analysis for fragmet #1(A:3:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.006
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].
3A5PHE0-0.0120.0183.8020.9912.512-0.023-0.851-0.6470.000
4A6TYR0-0.073-0.0566.757-0.458-0.4580.0000.0000.0000.000
5A7ASN00.004-0.0087.946-0.248-0.2480.0000.0000.0000.000
6A8SER0-0.053-0.00910.515-0.068-0.0680.0000.0000.0000.000
7A9SER00.0740.00312.274-0.021-0.0210.0000.0000.0000.000
8A10PHE00.0070.00814.308-0.017-0.0170.0000.0000.0000.000
9A11ARG10.9600.9867.5940.8040.8040.0000.0000.0000.000
10A12ARG10.9140.98412.743-0.073-0.0730.0000.0000.0000.000
11A13TYR00.0090.00715.0380.0030.0030.0000.0000.0000.000
12A14ALA00.0030.00214.4710.0020.0020.0000.0000.0000.000
13A15THR0-0.013-0.03213.295-0.030-0.0300.0000.0000.0000.000
14A16LEU00.0150.01615.5710.0120.0120.0000.0000.0000.000
15A17MET0-0.033-0.01618.8990.0100.0100.0000.0000.0000.000
16A18GLY00.005-0.01318.0520.0050.0050.0000.0000.0000.000
17A19ASP-1-0.810-0.89318.061-0.111-0.1110.0000.0000.0000.000
18A20LEU0-0.023-0.00719.8860.0130.0130.0000.0000.0000.000
19A21PHE0-0.053-0.02922.5910.0100.0100.0000.0000.0000.000
20A22SER0-0.0070.01819.532-0.004-0.0040.0000.0000.0000.000
21A23ASN0-0.086-0.03821.961-0.004-0.0040.0000.0000.0000.000
22A24ILE00.0760.04824.9700.0100.0100.0000.0000.0000.000
23A25GLN0-0.033-0.03527.571-0.010-0.0100.0000.0000.0000.000
24A26ILE00.0080.03730.0280.0040.0040.0000.0000.0000.000
25A27LYS10.9080.95733.0300.0440.0440.0000.0000.0000.000
26A28ARG10.8800.92933.8030.0750.0750.0000.0000.0000.000
27A29GLN00.012-0.01437.3510.0020.0020.0000.0000.0000.000
28A30LEU0-0.028-0.00637.276-0.001-0.0010.0000.0000.0000.000
29A31GLU-1-0.944-0.97141.557-0.035-0.0350.0000.0000.0000.000
30A32SER0-0.034-0.01640.5730.0010.0010.0000.0000.0000.000
31A33GLY00.0420.01641.8420.0020.0020.0000.0000.0000.000
32A34ASP-1-0.959-0.98339.068-0.046-0.0460.0000.0000.0000.000
33A35LYS10.9460.98432.8230.0710.0710.0000.0000.0000.000
34A36PHE00.003-0.00632.4390.0000.0000.0000.0000.0000.000
35A37ILE0-0.062-0.03429.417-0.002-0.0020.0000.0000.0000.000
36A38ARG10.9760.98424.6290.0970.0970.0000.0000.0000.000
37A39VAL00.0040.00425.556-0.004-0.0040.0000.0000.0000.000
38A40PRO0-0.0010.03121.585-0.005-0.0050.0000.0000.0000.000
39A41ILE00.0300.00618.7040.0030.0030.0000.0000.0000.000
40A42THR0-0.003-0.01317.168-0.020-0.0200.0000.0000.0000.000
41A43TYR00.0210.00413.8880.0430.0430.0000.0000.0000.000
42A44ALA0-0.034-0.02214.961-0.059-0.0590.0000.0000.0000.000
43A45SER00.0320.02817.0760.0370.0370.0000.0000.0000.000
44A46LYS10.9200.94119.4710.1100.1100.0000.0000.0000.000
45A47GLU-1-0.885-0.94622.854-0.127-0.1270.0000.0000.0000.000
46A48HIS0-0.030-0.00715.0580.0370.0370.0000.0000.0000.000
47A49PHE00.0140.00220.1020.0060.0060.0000.0000.0000.000
48A50MET00.0470.01621.1250.0070.0070.0000.0000.0000.000
49A51MET0-0.031-0.01321.2320.0110.0110.0000.0000.0000.000
50A52LYS10.8990.95117.4590.2760.2760.0000.0000.0000.000
51A53LEU0-0.0090.01522.0200.0080.0080.0000.0000.0000.000
52A54ASN00.007-0.01824.6460.0150.0150.0000.0000.0000.000
53A55LYS10.9290.97420.0780.1960.1960.0000.0000.0000.000
54A56TRP0-0.053-0.01818.8670.0080.0080.0000.0000.0000.000
55A57THR0-0.0120.00325.4170.0070.0070.0000.0000.0000.000
56A58SER0-0.046-0.02628.0710.0090.0090.0000.0000.0000.000
57A59ILE00.0210.01130.153-0.002-0.0020.0000.0000.0000.000
58A60ASN0-0.045-0.01429.2110.0070.0070.0000.0000.0000.000
59A61SER0-0.010-0.00631.6170.0050.0050.0000.0000.0000.000
60A62GLN00.007-0.02034.140-0.001-0.0010.0000.0000.0000.000
61A63GLU-1-0.874-0.93129.154-0.093-0.0930.0000.0000.0000.000
62A64ASP-1-0.870-0.94629.819-0.106-0.1060.0000.0000.0000.000
63A65VAL0-0.009-0.00431.921-0.002-0.0020.0000.0000.0000.000
64A66ALA0-0.016-0.00534.1910.0000.0000.0000.0000.0000.000
65A67LYS10.8750.92926.5020.1120.1120.0000.0000.0000.000
66A68VAL00.0610.04829.304-0.008-0.0080.0000.0000.0000.000
67A69GLU-1-0.898-0.91030.436-0.080-0.0800.0000.0000.0000.000
68A70THR0-0.092-0.04628.643-0.001-0.0010.0000.0000.0000.000
69A71ILE0-0.0280.00425.018-0.007-0.0070.0000.0000.0000.000
70A72LEU0-0.055-0.01226.619-0.007-0.0070.0000.0000.0000.000
71A73PRO00.0100.00928.9820.0050.0050.0000.0000.0000.000
72A74ARG10.8150.86220.7010.1810.1810.0000.0000.0000.000
73A75ILE00.0280.01923.2240.0100.0100.0000.0000.0000.000
74A76ASN00.0230.03020.015-0.037-0.0370.0000.0000.0000.000
75A77LEU0-0.012-0.00719.1520.0180.0180.0000.0000.0000.000
76A78HIS0-0.047-0.02915.894-0.030-0.0300.0000.0000.0000.000
77A79LEU0-0.0150.01018.2330.0240.0240.0000.0000.0000.000
78A80VAL0-0.030-0.02220.533-0.011-0.0110.0000.0000.0000.000
79A81ASP-1-0.887-0.94923.424-0.068-0.0680.0000.0000.0000.000
80A82PHE0-0.032-0.01420.788-0.002-0.0020.0000.0000.0000.000
81A83SER0-0.0020.01624.6850.0060.0060.0000.0000.0000.000
82A84TYR0-0.005-0.01827.1720.0010.0010.0000.0000.0000.000
83A85ASN0-0.042-0.03128.640-0.002-0.0020.0000.0000.0000.000
84A86ALA0-0.003-0.00430.5290.0040.0040.0000.0000.0000.000
85A87PRO00.0020.01533.684-0.002-0.0020.0000.0000.0000.000
86A105VAL00.005-0.01432.1900.0020.0020.0000.0000.0000.000
87A106VAL00.0100.01626.771-0.003-0.0030.0000.0000.0000.000
88A107SER0-0.053-0.06224.580-0.006-0.0060.0000.0000.0000.000
89A108GLN00.0210.01920.5530.0100.0100.0000.0000.0000.000
90A109TYR0-0.036-0.00819.4470.0030.0030.0000.0000.0000.000
91A110ASN0-0.023-0.01225.547-0.001-0.0010.0000.0000.0000.000
92A111PRO00.0080.02323.9730.0060.0060.0000.0000.0000.000
93A112SER00.0130.00324.831-0.006-0.0060.0000.0000.0000.000
94A113PRO00.0060.02325.421-0.003-0.0030.0000.0000.0000.000
95A114ILE0-0.018-0.01021.831-0.002-0.0020.0000.0000.0000.000
96A115LYS10.8660.94525.8300.0380.0380.0000.0000.0000.000
97A116MET0-0.064-0.02720.852-0.006-0.0060.0000.0000.0000.000
98A117ILE00.0250.02324.1160.0040.0040.0000.0000.0000.000
99A118TYR00.007-0.01718.249-0.005-0.0050.0000.0000.0000.000
100A119GLU-1-0.850-0.91823.678-0.103-0.1030.0000.0000.0000.000
101A120LEU0-0.024-0.01523.532-0.019-0.0190.0000.0000.0000.000
102A121SER00.007-0.01724.7580.0090.0090.0000.0000.0000.000
103A122ILE00.0130.00826.018-0.011-0.0110.0000.0000.0000.000
104A123PHE00.0320.01425.3320.0060.0060.0000.0000.0000.000
105A124THR00.017-0.00329.456-0.002-0.0020.0000.0000.0000.000
106A125ARG10.9350.99032.1230.0750.0750.0000.0000.0000.000
107A126TYR0-0.122-0.10034.7320.0060.0060.0000.0000.0000.000
108A127GLU-1-0.899-0.95336.692-0.056-0.0560.0000.0000.0000.000
109A128ASP-1-0.886-0.94438.297-0.056-0.0560.0000.0000.0000.000
110A129ASP-1-0.769-0.88833.439-0.078-0.0780.0000.0000.0000.000
111A130MET0-0.043-0.02233.050-0.005-0.0050.0000.0000.0000.000
112A131PHE00.0070.00434.787-0.001-0.0010.0000.0000.0000.000
113A132GLN00.0560.03734.9180.0000.0000.0000.0000.0000.000
114A133ILE00.0130.00529.5310.0000.0000.0000.0000.0000.000
115A134VAL0-0.011-0.00632.2530.0000.0000.0000.0000.0000.000
116A135GLU-1-0.954-0.97133.653-0.047-0.0470.0000.0000.0000.000
117A136GLN0-0.083-0.06331.5330.0020.0020.0000.0000.0000.000
118A137ILE0-0.028-0.00228.384-0.001-0.0010.0000.0000.0000.000
119A138LEU0-0.016-0.03231.5190.0040.0040.0000.0000.0000.000
120A139PRO00.0080.01934.5110.0030.0030.0000.0000.0000.000
121A140TYR0-0.074-0.02532.0170.0040.0040.0000.0000.0000.000
122A141PHE0-0.009-0.01328.3330.0000.0000.0000.0000.0000.000
123A142GLN0-0.0460.00734.2520.0020.0020.0000.0000.0000.000
124A143PRO0-0.023-0.01536.2490.0040.0040.0000.0000.0000.000
125A144HIS0-0.028-0.02533.194-0.005-0.0050.0000.0000.0000.000
126A145PHE00.0770.05126.9510.0020.0020.0000.0000.0000.000
127A146ASN0-0.043-0.03430.228-0.003-0.0030.0000.0000.0000.000
128A147THR00.004-0.00425.5870.0010.0010.0000.0000.0000.000
129A148THR0-0.036-0.01227.4820.0040.0040.0000.0000.0000.000
130A149MET00.0060.00420.272-0.006-0.0060.0000.0000.0000.000
131A150TYR0-0.023-0.02422.9610.0080.0080.0000.0000.0000.000
132A151GLU-1-0.742-0.82819.0840.0530.0530.0000.0000.0000.000
133A152GLN0-0.029-0.05119.8690.0000.0000.0000.0000.0000.000
134A153PHE00.0560.02018.0880.0130.0130.0000.0000.0000.000
135A154GLY00.0780.04417.945-0.006-0.0060.0000.0000.0000.000
136A155ASN0-0.063-0.05219.202-0.015-0.0150.0000.0000.0000.000
137A156ASP-1-0.909-0.92722.7190.1200.1200.0000.0000.0000.000
138A157ILE0-0.022-0.00824.654-0.005-0.0050.0000.0000.0000.000
139A158PRO0-0.006-0.00523.6490.0040.0040.0000.0000.0000.000
140A159PHE00.0100.00622.401-0.011-0.0110.0000.0000.0000.000
141A160LYS10.9560.98024.490-0.014-0.0140.0000.0000.0000.000
142A161ARG10.7870.88122.226-0.050-0.0500.0000.0000.0000.000
143A162ASP-1-0.894-0.94726.018-0.002-0.0020.0000.0000.0000.000
144A163ILE0-0.0140.00823.638-0.002-0.0020.0000.0000.0000.000
145A164LYS10.9390.98126.9560.0230.0230.0000.0000.0000.000
146A165ILE00.0270.01024.762-0.003-0.0030.0000.0000.0000.000
147A166VAL00.002-0.01928.6610.0040.0040.0000.0000.0000.000
148A167LEU0-0.0080.00830.770-0.006-0.0060.0000.0000.0000.000
149A168MET0-0.055-0.02831.2310.0060.0060.0000.0000.0000.000
150A169SER0-0.028-0.01733.0660.0030.0030.0000.0000.0000.000
151A170ALA00.0250.01233.050-0.005-0.0050.0000.0000.0000.000
152A171ALA0-0.009-0.00533.0770.0040.0040.0000.0000.0000.000
153A172ILE0-0.025-0.01233.992-0.005-0.0050.0000.0000.0000.000
154A173ASP-1-0.839-0.91234.346-0.070-0.0700.0000.0000.0000.000
155A174GLU-1-0.978-0.98735.697-0.064-0.0640.0000.0000.0000.000
156A175ALA00.009-0.01333.863-0.003-0.0030.0000.0000.0000.000
157A176ILE0-0.025-0.01135.839-0.003-0.0030.0000.0000.0000.000
158A177ASP-1-0.932-0.99437.740-0.068-0.0680.0000.0000.0000.000
159A178GLY00.0440.03439.6450.0000.0000.0000.0000.0000.000
160A179ASP-1-0.873-0.93742.762-0.050-0.0500.0000.0000.0000.000
161A180ASN0-0.085-0.04745.1670.0010.0010.0000.0000.0000.000
162A181LEU0-0.050-0.02041.0550.0010.0010.0000.0000.0000.000
163A182SER00.022-0.00137.551-0.003-0.0030.0000.0000.0000.000
164A183ARG10.8750.93738.2360.0610.0610.0000.0000.0000.000
165A184ARG10.8900.96132.7040.0860.0860.0000.0000.0000.000
166A185ARG10.8880.93229.4680.1070.1070.0000.0000.0000.000
167A186ILE00.0450.05134.2330.0010.0010.0000.0000.0000.000
168A187GLU-1-0.860-0.93129.576-0.109-0.1090.0000.0000.0000.000
169A188TRP00.0410.01831.6100.0060.0060.0000.0000.0000.000
170A189SER0-0.005-0.00929.145-0.011-0.0110.0000.0000.0000.000
171A190LEU0-0.023-0.01029.0840.0080.0080.0000.0000.0000.000
172A191THR00.0240.02628.316-0.010-0.0100.0000.0000.0000.000
173A192PHE00.006-0.01326.3860.0080.0080.0000.0000.0000.000
174A193GLU-1-0.818-0.91526.993-0.051-0.0510.0000.0000.0000.000
175A194VAL00.0080.01323.0720.0060.0060.0000.0000.0000.000
176A195ASN0-0.098-0.06026.1240.0050.0050.0000.0000.0000.000
177A196GLY00.0400.01323.8950.0030.0030.0000.0000.0000.000
178A197TRP0-0.026-0.02722.8890.0080.0080.0000.0000.0000.000
179A198MET00.0010.01018.5130.0030.0030.0000.0000.0000.000
180A199TYR0-0.028-0.05217.4770.0060.0060.0000.0000.0000.000
181A200PRO0-0.015-0.00218.704-0.006-0.0060.0000.0000.0000.000
182A201PRO00.0170.00113.3390.0000.0000.0000.0000.0000.000
183A202VAL00.0470.03714.8930.0020.0020.0000.0000.0000.000
184A203ASP-1-0.815-0.90311.1210.8550.8550.0000.0000.0000.000
185A204ASP-1-0.729-0.8657.3421.2991.2990.0000.0000.0000.000
186A205ALA0-0.096-0.05710.372-0.035-0.0350.0000.0000.0000.000
187A206GLU-1-1.017-0.99712.1670.2090.2090.0000.0000.0000.000
188A207GLY0-0.034-0.01713.496-0.076-0.0760.0000.0000.0000.000
189A208LEU0-0.033-0.0178.9190.0040.0040.0000.0000.0000.000
190A209ILE0-0.046-0.01012.898-0.072-0.0720.0000.0000.0000.000
191A210ARG10.9110.96514.487-0.153-0.1530.0000.0000.0000.000
192A211THR00.0330.00316.167-0.008-0.0080.0000.0000.0000.000
193A212THR0-0.0140.01518.435-0.014-0.0140.0000.0000.0000.000
194A213TYR0-0.043-0.07820.4420.0040.0040.0000.0000.0000.000
195A214THR0-0.0050.01623.7690.0010.0010.0000.0000.0000.000
196A215ASP-1-0.773-0.88325.812-0.047-0.0470.0000.0000.0000.000
197A216PHE00.012-0.01627.1320.0050.0050.0000.0000.0000.000
198A217HIS0-0.056-0.02530.0110.0040.0040.0000.0000.0000.000
199A218ALA0-0.049-0.02230.7300.0040.0040.0000.0000.0000.000
200A219ASN0-0.021-0.00929.3200.0090.0090.0000.0000.0000.000
201A220THR0-0.057-0.03925.679-0.002-0.0020.0000.0000.0000.000
202A221ARG10.9411.00020.5370.0840.0840.0000.0000.0000.000
203A222ASP-1-0.900-0.96919.5150.0000.0000.0000.0000.0000.000
204A223LEU0-0.083-0.05415.170-0.011-0.0110.0000.0000.0000.000
205A224PRO00.0050.02015.4450.0170.0170.0000.0000.0000.000
206A225ASP-1-0.789-0.8919.584-0.033-0.0330.0000.0000.0000.000
207A226GLY0-0.010-0.02210.207-0.040-0.0400.0000.0000.0000.000
208A227GLU-1-1.015-1.0208.356-0.812-0.8120.0000.0000.0000.000
209A228GLY0-0.0240.00310.3720.0380.0380.0000.0000.0000.000
210A229VAL0-0.056-0.01113.8070.0320.0320.0000.0000.0000.000
211A230PHE0-0.070-0.02813.3510.0270.0270.0000.0000.0000.000
212A231GLU-1-0.807-0.86814.100-0.259-0.2590.0000.0000.0000.000
213A232SER0-0.030-0.03712.1580.0010.0010.0000.0000.0000.000
214A233VAL00.0310.01514.0320.0470.0470.0000.0000.0000.000
215A234ASP-1-0.958-0.98111.320-0.481-0.4810.0000.0000.0000.000