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: ZY2VN

Calculation Name: 4HUD-A-Xray321

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: 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 219
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2663571.196285
FMO2-HF: Nuclear repulsion 2574615.789968
FMO2-HF: Total energy -88955.406316
FMO2-MP2: Total energy -89214.52973


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:2:ACE )


Summations of interaction energy for fragment #1(A:2: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.
1.2112.846-0.006-0.74-0.887-0.002
Interaction energy analysis for fragmet #1(A:2:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : -0.002
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].
3A4TYR 0-0.051-0.0343.7930.2641.829-0.006-0.736-0.822-0.002
4A5PHE 0-0.0130.0185.1780.1850.2550.000-0.004-0.0650.000
5A6TYR 0-0.071-0.0556.335-0.011-0.0110.0000.0000.0000.000
6A7ASN 0-0.001-0.0108.0300.0150.0150.0000.0000.0000.000
7A8SER 0-0.051-0.00810.916-0.020-0.0200.0000.0000.0000.000
8A9SER 00.0740.00312.8930.0270.0270.0000.0000.0000.000
9A10PHE 00.0120.01016.0940.0060.0060.0000.0000.0000.000
10A11ARG 10.9600.9868.9030.0550.0550.0000.0000.0000.000
11A12ARG 10.9070.98214.162-0.058-0.0580.0000.0000.0000.000
12A13TYR 00.0170.01015.9920.0070.0070.0000.0000.0000.000
13A14ALA 00.0030.00316.0720.0030.0030.0000.0000.0000.000
14A15THR 0-0.012-0.03214.319-0.002-0.0020.0000.0000.0000.000
15A16LEU 00.0110.01316.6790.0070.0070.0000.0000.0000.000
16A17MET 0-0.036-0.01619.8480.0020.0020.0000.0000.0000.000
17A18GLY 00.010-0.01219.203-0.001-0.0010.0000.0000.0000.000
18A19ASP -1-0.812-0.89418.7340.0840.0840.0000.0000.0000.000
19A20LEU 0-0.029-0.00920.6310.0030.0030.0000.0000.0000.000
20A21PHE 0-0.049-0.02823.537-0.001-0.0010.0000.0000.0000.000
21A22SER 00.0010.02020.189-0.001-0.0010.0000.0000.0000.000
22A23ASN 0-0.094-0.04122.663-0.002-0.0020.0000.0000.0000.000
23A24ILE 00.0770.04825.4360.0000.0000.0000.0000.0000.000
24A25GLN 0-0.036-0.03628.1990.0010.0010.0000.0000.0000.000
25A26ILE 00.0130.03930.567-0.001-0.0010.0000.0000.0000.000
26A27LYS 10.9040.95533.665-0.010-0.0100.0000.0000.0000.000
27A28ARG 10.8850.93234.6380.0010.0010.0000.0000.0000.000
28A29GLN 00.009-0.01537.8670.0010.0010.0000.0000.0000.000
29A30LEU 0-0.026-0.00537.568-0.002-0.0020.0000.0000.0000.000
30A31GLU -1-0.947-0.97241.8620.0060.0060.0000.0000.0000.000
31A32SER 0-0.034-0.01640.5650.0000.0000.0000.0000.0000.000
32A33GLY 00.0420.01641.8500.0020.0020.0000.0000.0000.000
33A34ASP -1-0.960-0.98339.3050.0120.0120.0000.0000.0000.000
34A35LYS 10.9480.98433.005-0.008-0.0080.0000.0000.0000.000
35A36PHE 00.001-0.00632.684-0.002-0.0020.0000.0000.0000.000
36A37ILE 0-0.062-0.03429.8900.0020.0020.0000.0000.0000.000
37A38ARG 10.9750.98424.821-0.037-0.0370.0000.0000.0000.000
38A39VAL 00.0060.00526.578-0.003-0.0030.0000.0000.0000.000
39A40PRO 0-0.0010.03122.5030.0030.0030.0000.0000.0000.000
40A41ILE 00.0300.00719.744-0.008-0.0080.0000.0000.0000.000
41A42THR 0-0.004-0.01418.5590.0000.0000.0000.0000.0000.000
42A43TYR 00.0200.00416.1460.0120.0120.0000.0000.0000.000
43A44ALA 0-0.036-0.02417.346-0.029-0.0290.0000.0000.0000.000
44A45SER 00.0350.02819.7760.0180.0180.0000.0000.0000.000
45A46LYS 10.9190.94022.5750.0460.0460.0000.0000.0000.000
46A47GLU -1-0.884-0.94525.780-0.071-0.0710.0000.0000.0000.000
47A48HIS 0-0.034-0.00818.3470.0150.0150.0000.0000.0000.000
48A49PHE 00.0140.00222.4100.0030.0030.0000.0000.0000.000
49A50MET 00.0500.01723.9160.0070.0070.0000.0000.0000.000
50A51MET 0-0.030-0.01224.6970.0030.0030.0000.0000.0000.000
51A52LYS 10.8850.94420.1160.1300.1300.0000.0000.0000.000
52A53LEU 0-0.0090.01624.8440.0060.0060.0000.0000.0000.000
53A54ASN 00.006-0.01827.1080.0110.0110.0000.0000.0000.000
54A55LYS 10.9290.97422.7770.1070.1070.0000.0000.0000.000
55A56TRP 0-0.051-0.01721.0390.0030.0030.0000.0000.0000.000
56A57THR 0-0.0130.00227.5860.0060.0060.0000.0000.0000.000
57A58SER 0-0.046-0.02630.5260.0030.0030.0000.0000.0000.000
58A59ILE 00.0200.01132.3220.0000.0000.0000.0000.0000.000
59A60ASN 0-0.045-0.01431.646-0.001-0.0010.0000.0000.0000.000
60A61SER 0-0.009-0.00733.3910.0020.0020.0000.0000.0000.000
61A62GLN 00.006-0.02135.9770.0020.0020.0000.0000.0000.000
62A63GLU -1-0.875-0.93130.328-0.028-0.0280.0000.0000.0000.000
63A64ASP -1-0.869-0.94531.450-0.039-0.0390.0000.0000.0000.000
64A65VAL 0-0.011-0.00433.4360.0010.0010.0000.0000.0000.000
65A66ALA 0-0.016-0.00535.0820.0010.0010.0000.0000.0000.000
66A67LYS 10.8760.92927.6900.0350.0350.0000.0000.0000.000
67A68VAL 00.0600.04830.467-0.001-0.0010.0000.0000.0000.000
68A69GLU -1-0.898-0.91031.898-0.013-0.0130.0000.0000.0000.000
69A70THR 0-0.092-0.04729.3480.0030.0030.0000.0000.0000.000
70A71ILE 0-0.0320.00226.6010.0000.0000.0000.0000.0000.000
71A72LEU 0-0.052-0.01127.862-0.001-0.0010.0000.0000.0000.000
72A73PRO 00.0140.01129.8800.0020.0020.0000.0000.0000.000
73A74ARG 10.8130.86222.0450.0360.0360.0000.0000.0000.000
74A75ILE 00.0300.02024.611-0.001-0.0010.0000.0000.0000.000
75A76ASN 00.0180.02822.241-0.008-0.0080.0000.0000.0000.000
76A77LEU 0-0.017-0.00920.6220.0050.0050.0000.0000.0000.000
77A78HIS 0-0.044-0.02818.762-0.022-0.0220.0000.0000.0000.000
78A79LEU 0-0.0150.01020.5190.0110.0110.0000.0000.0000.000
79A80VAL 0-0.032-0.02222.900-0.010-0.0100.0000.0000.0000.000
80A81ASP -1-0.884-0.94826.112-0.049-0.0490.0000.0000.0000.000
81A82PHE 0-0.034-0.01523.4170.0030.0030.0000.0000.0000.000
82A83SER 00.0000.01626.850-0.001-0.0010.0000.0000.0000.000
83A84TYR 0-0.006-0.01928.8480.0030.0030.0000.0000.0000.000
84A85ASN 0-0.040-0.03030.128-0.001-0.0010.0000.0000.0000.000
85A86ALA 0-0.008-0.01231.8110.0030.0030.0000.0000.0000.000
86A87PRO 00.0030.02734.5450.0010.0010.0000.0000.0000.000
87A88NME 00.000-0.00736.7510.0000.0000.0000.0000.0000.000
88A104ACE 00.005-0.00731.6890.0010.0010.0000.0000.0000.000
89A105VAL 0-0.012-0.02031.334-0.002-0.0020.0000.0000.0000.000
90A106VAL 00.0180.02626.889-0.003-0.0030.0000.0000.0000.000
91A107SER 0-0.047-0.05624.9000.0000.0000.0000.0000.0000.000
92A108GLN 00.0200.01820.197-0.004-0.0040.0000.0000.0000.000
93A109TYR 0-0.040-0.00818.8140.0070.0070.0000.0000.0000.000
94A110ASN 0-0.027-0.01525.0990.0020.0020.0000.0000.0000.000
95A111PRO 00.0080.02223.888-0.002-0.0020.0000.0000.0000.000
96A112SER 00.0150.00425.1730.0000.0000.0000.0000.0000.000
97A113PRO 00.0090.02426.0430.0000.0000.0000.0000.0000.000
98A114ILE 0-0.017-0.00923.221-0.005-0.0050.0000.0000.0000.000
99A115LYS 10.8660.94626.9990.0190.0190.0000.0000.0000.000
100A116MET 0-0.063-0.02622.252-0.008-0.0080.0000.0000.0000.000
101A117ILE 00.0250.02325.9350.0070.0070.0000.0000.0000.000
102A118TYR 00.007-0.01719.988-0.004-0.0040.0000.0000.0000.000
103A119GLU -1-0.848-0.91825.757-0.041-0.0410.0000.0000.0000.000
104A120LEU 0-0.024-0.01525.011-0.005-0.0050.0000.0000.0000.000
105A121SER 00.011-0.01626.5500.0010.0010.0000.0000.0000.000
106A122ILE 00.0110.00727.751-0.001-0.0010.0000.0000.0000.000
107A123PHE 00.0260.01027.402-0.002-0.0020.0000.0000.0000.000
108A124THR 00.015-0.00630.8940.0030.0030.0000.0000.0000.000
109A125ARG 10.9210.96933.5880.0180.0180.0000.0000.0000.000
110A126TYR 0-0.128-0.09836.2310.0000.0000.0000.0000.0000.000
111A127GLU -1-0.886-0.94837.864-0.010-0.0100.0000.0000.0000.000
112A128ASP -1-0.895-0.94839.4650.0010.0010.0000.0000.0000.000
113A129ASP -1-0.770-0.88934.472-0.003-0.0030.0000.0000.0000.000
114A130MET 0-0.044-0.02234.4330.0010.0010.0000.0000.0000.000
115A131PHE 00.0050.00335.9420.0010.0010.0000.0000.0000.000
116A132GLN 00.0550.03635.7240.0040.0040.0000.0000.0000.000
117A133ILE 00.0120.00430.6190.0020.0020.0000.0000.0000.000
118A134VAL 0-0.012-0.00633.2600.0020.0020.0000.0000.0000.000
119A135GLU -1-0.952-0.97034.8100.0050.0050.0000.0000.0000.000
120A136GLN 0-0.085-0.06332.2050.0050.0050.0000.0000.0000.000
121A137ILE 0-0.029-0.00329.5510.0020.0020.0000.0000.0000.000
122A138LEU 0-0.017-0.03232.5720.0020.0020.0000.0000.0000.000
123A139PRO 00.0090.02035.6780.0000.0000.0000.0000.0000.000
124A140TYR 0-0.074-0.02532.9650.0010.0010.0000.0000.0000.000
125A141PHE 0-0.014-0.01529.4710.0010.0010.0000.0000.0000.000
126A142GLN 0-0.0420.00935.407-0.003-0.0030.0000.0000.0000.000
127A143PRO 0-0.026-0.01837.6760.0010.0010.0000.0000.0000.000
128A144HIS 0-0.021-0.02034.455-0.001-0.0010.0000.0000.0000.000
129A145PHE 00.0780.05027.8340.0010.0010.0000.0000.0000.000
130A146ASN 0-0.047-0.03531.276-0.003-0.0030.0000.0000.0000.000
131A147THR 00.003-0.00426.3800.0040.0040.0000.0000.0000.000
132A148THR 0-0.037-0.01227.721-0.003-0.0030.0000.0000.0000.000
133A149MET 00.0080.00520.8860.0060.0060.0000.0000.0000.000
134A150TYR 0-0.024-0.02522.986-0.007-0.0070.0000.0000.0000.000
135A151GLU -1-0.735-0.82618.7100.0770.0770.0000.0000.0000.000
136A152GLN 0-0.033-0.05319.187-0.002-0.0020.0000.0000.0000.000
137A153PHE 00.0510.01817.2610.0240.0240.0000.0000.0000.000
138A154GLY 00.0790.04516.479-0.010-0.0100.0000.0000.0000.000
139A155ASN 0-0.062-0.05117.5000.0150.0150.0000.0000.0000.000
140A156ASP -1-0.909-0.92821.0290.0980.0980.0000.0000.0000.000
141A157ILE 0-0.021-0.00723.3080.0060.0060.0000.0000.0000.000
142A158PRO 0-0.009-0.00522.7550.0000.0000.0000.0000.0000.000
143A159PHE 00.0080.00521.691-0.015-0.0150.0000.0000.0000.000
144A160LYS 10.9600.98224.133-0.034-0.0340.0000.0000.0000.000
145A161ARG 10.7860.88022.050-0.059-0.0590.0000.0000.0000.000
146A162ASP -1-0.894-0.94726.1610.0340.0340.0000.0000.0000.000
147A163ILE 0-0.0130.00824.242-0.006-0.0060.0000.0000.0000.000
148A164LYS 10.9400.98127.716-0.008-0.0080.0000.0000.0000.000
149A165ILE 00.0260.01025.882-0.004-0.0040.0000.0000.0000.000
150A166VAL 0-0.001-0.02029.9470.0020.0020.0000.0000.0000.000
151A167LEU 0-0.0020.01032.303-0.003-0.0030.0000.0000.0000.000
152A168MET 0-0.063-0.03033.0460.0010.0010.0000.0000.0000.000
153A169SER 0-0.027-0.01734.7620.0000.0000.0000.0000.0000.000
154A170ALA 00.0250.01234.7510.0000.0000.0000.0000.0000.000
155A171ALA 0-0.009-0.00535.2840.0000.0000.0000.0000.0000.000
156A172ILE 0-0.023-0.01036.042-0.001-0.0010.0000.0000.0000.000
157A173ASP -1-0.844-0.91536.761-0.030-0.0300.0000.0000.0000.000
158A174GLU -1-0.971-0.98337.870-0.019-0.0190.0000.0000.0000.000
159A175ALA 00.011-0.01336.347-0.003-0.0030.0000.0000.0000.000
160A176ILE 0-0.041-0.01638.2720.0000.0000.0000.0000.0000.000
161A177ASP -1-0.898-0.98840.312-0.031-0.0310.0000.0000.0000.000
162A178GLY 00.0610.00642.1330.0010.0010.0000.0000.0000.000
163A179ASP -1-0.828-0.87144.885-0.014-0.0140.0000.0000.0000.000
164A180ASN 0-0.044-0.01444.6030.0010.0010.0000.0000.0000.000
165A181LEU 0-0.0640.02441.1020.0010.0010.0000.0000.0000.000
166A182SER 0-0.013-0.04139.898-0.002-0.0020.0000.0000.0000.000
167A183ARG 10.8040.88340.0690.0170.0170.0000.0000.0000.000
168A184ARG 10.9000.96035.1750.0350.0350.0000.0000.0000.000
169A185ARG 10.9180.94531.8910.0430.0430.0000.0000.0000.000
170A186ILE 00.0470.05236.100-0.001-0.0010.0000.0000.0000.000
171A187GLU -1-0.858-0.93131.781-0.040-0.0400.0000.0000.0000.000
172A188TRP 00.0410.01733.4230.0020.0020.0000.0000.0000.000
173A189SER 0-0.008-0.00931.248-0.002-0.0020.0000.0000.0000.000
174A190LEU 0-0.022-0.01030.6260.0020.0020.0000.0000.0000.000
175A191THR 00.0250.02630.058-0.005-0.0050.0000.0000.0000.000
176A192PHE 00.007-0.01327.9840.0040.0040.0000.0000.0000.000
177A193GLU -1-0.821-0.91628.704-0.016-0.0160.0000.0000.0000.000
178A194VAL 00.0060.01224.3280.0060.0060.0000.0000.0000.000
179A195ASN 0-0.089-0.05627.513-0.005-0.0050.0000.0000.0000.000
180A196GLY 00.0360.01224.8170.0060.0060.0000.0000.0000.000
181A197TRP 0-0.027-0.02723.549-0.002-0.0020.0000.0000.0000.000
182A198MET 0-0.0020.00919.7440.0000.0000.0000.0000.0000.000
183A199TYR 0-0.028-0.05317.2670.0060.0060.0000.0000.0000.000
184A200PRO 0-0.0100.00019.204-0.007-0.0070.0000.0000.0000.000
185A201PRO 00.0170.00113.9350.0150.0150.0000.0000.0000.000
186A202VAL 00.0440.03614.616-0.003-0.0030.0000.0000.0000.000
187A203ASP -1-0.810-0.90110.1070.0700.0700.0000.0000.0000.000
188A204ASP -1-0.734-0.8666.7000.2440.2440.0000.0000.0000.000
189A205ALA 0-0.095-0.0569.0680.1160.1160.0000.0000.0000.000
190A206GLU -1-1.014-0.99610.3840.0910.0910.0000.0000.0000.000
191A207GLY 0-0.033-0.01611.693-0.012-0.0120.0000.0000.0000.000
192A208LEU 0-0.036-0.0207.538-0.022-0.0220.0000.0000.0000.000
193A209ILE 0-0.046-0.01011.481-0.040-0.0400.0000.0000.0000.000
194A210ARG 10.9120.96613.808-0.212-0.2120.0000.0000.0000.000
195A211THR 00.0300.00116.007-0.038-0.0380.0000.0000.0000.000
196A212THR 0-0.0120.01618.2570.0040.0040.0000.0000.0000.000
197A213TYR 0-0.046-0.07920.759-0.013-0.0130.0000.0000.0000.000
198A214THR 0-0.0010.01724.0840.0020.0020.0000.0000.0000.000
199A215ASP -1-0.770-0.88226.1660.0470.0470.0000.0000.0000.000
200A216PHE 00.011-0.01527.587-0.002-0.0020.0000.0000.0000.000
201A217HIS 0-0.056-0.02430.600-0.006-0.0060.0000.0000.0000.000
202A218ALA 0-0.048-0.02231.0750.0010.0010.0000.0000.0000.000
203A219ASN 0-0.022-0.00929.4050.0030.0030.0000.0000.0000.000
204A220THR 0-0.054-0.03925.5110.0000.0000.0000.0000.0000.000
205A221ARG 10.9380.99920.598-0.076-0.0760.0000.0000.0000.000
206A222ASP -1-0.898-0.96819.2080.1570.1570.0000.0000.0000.000
207A223LEU 0-0.082-0.05415.572-0.004-0.0040.0000.0000.0000.000
208A224PRO 00.0030.02015.3530.0340.0340.0000.0000.0000.000
209A225ASP -1-0.790-0.8919.0920.5550.5550.0000.0000.0000.000
210A226GLY 0-0.016-0.02410.892-0.045-0.0450.0000.0000.0000.000
211A227GLU -1-1.012-1.0188.757-0.094-0.0940.0000.0000.0000.000
212A228GLY 0-0.0210.00410.869-0.005-0.0050.0000.0000.0000.000
213A229VAL 0-0.053-0.01013.963-0.016-0.0160.0000.0000.0000.000
214A230PHE 0-0.074-0.02814.559-0.015-0.0150.0000.0000.0000.000
215A231GLU -1-0.799-0.86514.984-0.034-0.0340.0000.0000.0000.000
216A232SER 0-0.025-0.02713.871-0.026-0.0260.0000.0000.0000.000
217A233VAL 00.0240.00615.5300.0100.0100.0000.0000.0000.000
218A234ASP -1-0.931-0.97114.354-0.261-0.2610.0000.0000.0000.000
219A235NME 0-0.029-0.01414.8830.0120.0120.0000.0000.0000.000