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: ZY38N

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 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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2649488.393574
FMO2-HF: Nuclear repulsion 2560872.560924
FMO2-HF: Total energy -88615.83265
FMO2-MP2: Total energy -88873.835804


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.
2.0943.158-0.012-0.541-0.5110
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 : 0.005 / q_NPA : -0.011
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].
3A5PHE0-0.0280.0083.8631.7442.808-0.012-0.541-0.5110.000
4A6TYR0-0.015-0.0326.268-0.474-0.4740.0000.0000.0000.000
5A7ASN0-0.002-0.0197.847-0.266-0.2660.0000.0000.0000.000
6A8SER0-0.041-0.00910.386-0.056-0.0560.0000.0000.0000.000
7A9SER00.0580.00712.067-0.041-0.0410.0000.0000.0000.000
8A10PHE00.0250.01214.250-0.013-0.0130.0000.0000.0000.000
9A11ARG10.9050.9677.1920.9380.9380.0000.0000.0000.000
10A12ARG10.8580.94412.433-0.041-0.0410.0000.0000.0000.000
11A13TYR00.002-0.02814.817-0.002-0.0020.0000.0000.0000.000
12A14ALA00.0020.01014.4520.0050.0050.0000.0000.0000.000
13A15THR00.001-0.02212.905-0.030-0.0300.0000.0000.0000.000
14A16LEU0-0.0140.00115.2760.0160.0160.0000.0000.0000.000
15A17MET0-0.020-0.01518.7250.0160.0160.0000.0000.0000.000
16A18GLY00.0200.00917.7700.0050.0050.0000.0000.0000.000
17A19ASP-1-0.762-0.86817.738-0.124-0.1240.0000.0000.0000.000
18A20LEU0-0.052-0.01819.5430.0160.0160.0000.0000.0000.000
19A21PHE00.008-0.01622.0820.0130.0130.0000.0000.0000.000
20A22SER0-0.053-0.02218.6300.0090.0090.0000.0000.0000.000
21A23ASN0-0.063-0.02921.469-0.001-0.0010.0000.0000.0000.000
22A24ILE00.0380.04124.4270.0130.0130.0000.0000.0000.000
23A25GLN0-0.028-0.02326.869-0.010-0.0100.0000.0000.0000.000
24A26ILE00.0160.03529.5900.0030.0030.0000.0000.0000.000
25A27LYS10.7810.88032.6960.0520.0520.0000.0000.0000.000
26A28ARG10.8170.88533.3790.0860.0860.0000.0000.0000.000
27A29GLN00.024-0.00236.7670.0020.0020.0000.0000.0000.000
28A30LEU0-0.034-0.01736.905-0.002-0.0020.0000.0000.0000.000
29A31GLU-1-0.947-0.96941.280-0.040-0.0400.0000.0000.0000.000
30A32SER00.0190.00840.6700.0010.0010.0000.0000.0000.000
31A33GLY0-0.019-0.00641.8450.0010.0010.0000.0000.0000.000
32A34ASP-1-0.808-0.90338.341-0.055-0.0550.0000.0000.0000.000
33A35LYS10.9180.97232.9190.0740.0740.0000.0000.0000.000
34A36PHE00.0190.00932.1910.0000.0000.0000.0000.0000.000
35A37ILE0-0.058-0.02428.749-0.001-0.0010.0000.0000.0000.000
36A38ARG10.9490.96524.3280.1130.1130.0000.0000.0000.000
37A39VAL00.0160.01425.558-0.003-0.0030.0000.0000.0000.000
38A40PRO0-0.0110.01921.043-0.007-0.0070.0000.0000.0000.000
39A41ILE00.0380.01618.5000.0070.0070.0000.0000.0000.000
40A42THR0-0.015-0.01916.738-0.022-0.0220.0000.0000.0000.000
41A43TYR00.0260.00413.5840.0460.0460.0000.0000.0000.000
42A44ALA0-0.013-0.01014.482-0.070-0.0700.0000.0000.0000.000
43A45SER00.0200.02416.7240.0480.0480.0000.0000.0000.000
44A46LYS10.8350.88719.1100.1280.1280.0000.0000.0000.000
45A47GLU-1-0.862-0.93122.445-0.139-0.1390.0000.0000.0000.000
46A48HIS0-0.046-0.02914.9900.0430.0430.0000.0000.0000.000
47A49PHE00.0260.00919.6240.0030.0030.0000.0000.0000.000
48A50MET00.0120.01320.7530.0110.0110.0000.0000.0000.000
49A51MET0-0.052-0.02421.6760.0110.0110.0000.0000.0000.000
50A52LYS10.8420.91616.3250.3180.3180.0000.0000.0000.000
51A53LEU00.0050.01321.5720.0100.0100.0000.0000.0000.000
52A54ASN00.021-0.00324.3580.0150.0150.0000.0000.0000.000
53A55LYS10.9530.98721.3340.1780.1780.0000.0000.0000.000
54A56TRP0-0.0110.00218.3590.0130.0130.0000.0000.0000.000
55A57THR0-0.019-0.00924.9420.0090.0090.0000.0000.0000.000
56A58SER0-0.056-0.03327.6340.0110.0110.0000.0000.0000.000
57A59ILE00.015-0.00129.676-0.003-0.0030.0000.0000.0000.000
58A60ASN0-0.068-0.03028.7500.0080.0080.0000.0000.0000.000
59A61SER0-0.045-0.04131.2000.0070.0070.0000.0000.0000.000
60A62GLN00.036-0.00733.613-0.003-0.0030.0000.0000.0000.000
61A63GLU-1-0.852-0.90629.084-0.097-0.0970.0000.0000.0000.000
62A64ASP-1-0.796-0.87228.926-0.109-0.1090.0000.0000.0000.000
63A65VAL0-0.009-0.00431.368-0.003-0.0030.0000.0000.0000.000
64A66ALA0-0.019-0.00333.9040.0010.0010.0000.0000.0000.000
65A67LYS10.7960.87426.3860.1130.1130.0000.0000.0000.000
66A68VAL00.0230.02629.327-0.007-0.0070.0000.0000.0000.000
67A69GLU-1-0.781-0.87130.175-0.090-0.0900.0000.0000.0000.000
68A70THR0-0.101-0.06027.812-0.004-0.0040.0000.0000.0000.000
69A71ILE0-0.0190.01124.855-0.009-0.0090.0000.0000.0000.000
70A72LEU0-0.069-0.01326.136-0.010-0.0100.0000.0000.0000.000
71A73PRO00.0200.01228.8180.0060.0060.0000.0000.0000.000
72A74ARG10.7440.81820.3340.2010.2010.0000.0000.0000.000
73A75ILE00.0210.00923.0120.0110.0110.0000.0000.0000.000
74A76ASN00.0070.01219.378-0.047-0.0470.0000.0000.0000.000
75A77LEU0-0.0140.00818.6080.0210.0210.0000.0000.0000.000
76A78HIS0-0.037-0.03215.249-0.044-0.0440.0000.0000.0000.000
77A79LEU0-0.0200.01318.5200.0280.0280.0000.0000.0000.000
78A80VAL0-0.042-0.03320.548-0.011-0.0110.0000.0000.0000.000
79A81ASP-1-0.854-0.93523.528-0.075-0.0750.0000.0000.0000.000
80A82PHE0-0.045-0.02420.353-0.006-0.0060.0000.0000.0000.000
81A83SER00.0150.02024.3920.0070.0070.0000.0000.0000.000
82A84TYR0-0.019-0.01827.0570.0010.0010.0000.0000.0000.000
83A85ASN0-0.071-0.03628.713-0.001-0.0010.0000.0000.0000.000
84A86ALA00.0120.00130.5710.0040.0040.0000.0000.0000.000
85A87PRO0-0.0220.00533.519-0.002-0.0020.0000.0000.0000.000
86A105VAL00.018-0.01231.9340.0020.0020.0000.0000.0000.000
87A106VAL00.0060.01326.714-0.003-0.0030.0000.0000.0000.000
88A107SER00.000-0.00125.1250.0000.0000.0000.0000.0000.000
89A108GLN00.019-0.00220.9980.0080.0080.0000.0000.0000.000
90A109TYR0-0.033-0.01520.1400.0000.0000.0000.0000.0000.000
91A110ASN0-0.054-0.02825.261-0.002-0.0020.0000.0000.0000.000
92A111PRO0-0.0020.02723.8800.0050.0050.0000.0000.0000.000
93A112SER00.0200.00625.084-0.005-0.0050.0000.0000.0000.000
94A113PRO0-0.0070.01125.599-0.004-0.0040.0000.0000.0000.000
95A114ILE0-0.023-0.02321.9310.0000.0000.0000.0000.0000.000
96A115LYS10.8390.92726.0360.0510.0510.0000.0000.0000.000
97A116MET0-0.028-0.01321.099-0.006-0.0060.0000.0000.0000.000
98A117ILE00.0210.01924.0710.0010.0010.0000.0000.0000.000
99A118TYR00.034-0.00318.050-0.005-0.0050.0000.0000.0000.000
100A119GLU-1-0.840-0.90223.502-0.120-0.1200.0000.0000.0000.000
101A120LEU0-0.024-0.01223.114-0.021-0.0210.0000.0000.0000.000
102A121SER00.011-0.00424.5040.0100.0100.0000.0000.0000.000
103A122ILE00.0010.00125.372-0.014-0.0140.0000.0000.0000.000
104A123PHE00.0320.01124.9020.0070.0070.0000.0000.0000.000
105A124THR0-0.017-0.03528.693-0.002-0.0020.0000.0000.0000.000
106A125ARG10.8610.93631.3970.0830.0830.0000.0000.0000.000
107A126TYR0-0.069-0.05934.2670.0080.0080.0000.0000.0000.000
108A127GLU-1-0.865-0.94636.118-0.065-0.0650.0000.0000.0000.000
109A128ASP-1-0.882-0.92437.986-0.063-0.0630.0000.0000.0000.000
110A129ASP-1-0.749-0.88033.231-0.087-0.0870.0000.0000.0000.000
111A130MET0-0.022-0.00632.042-0.006-0.0060.0000.0000.0000.000
112A131PHE0-0.004-0.00134.430-0.001-0.0010.0000.0000.0000.000
113A132GLN00.0230.00434.688-0.002-0.0020.0000.0000.0000.000
114A133ILE00.0010.01329.259-0.001-0.0010.0000.0000.0000.000
115A134VAL00.0020.00031.602-0.001-0.0010.0000.0000.0000.000
116A135GLU-1-0.946-0.97133.427-0.056-0.0560.0000.0000.0000.000
117A136GLN0-0.093-0.06930.7440.0010.0010.0000.0000.0000.000
118A137ILE0-0.015-0.00528.252-0.003-0.0030.0000.0000.0000.000
119A138LEU0-0.002-0.00931.2410.0030.0030.0000.0000.0000.000
120A139PRO00.0120.00634.3100.0030.0030.0000.0000.0000.000
121A140TYR0-0.058-0.02531.7450.0050.0050.0000.0000.0000.000
122A141PHE0-0.027-0.01527.8680.0010.0010.0000.0000.0000.000
123A142GLN0-0.050-0.01534.0130.0040.0040.0000.0000.0000.000
124A143PRO0-0.032-0.01836.1080.0040.0040.0000.0000.0000.000
125A144HIS00.008-0.00732.981-0.005-0.0050.0000.0000.0000.000
126A145PHE00.0930.06126.8480.0020.0020.0000.0000.0000.000
127A146ASN0-0.033-0.01730.105-0.001-0.0010.0000.0000.0000.000
128A147THR00.010-0.01624.7770.0010.0010.0000.0000.0000.000
129A148THR0-0.037-0.01926.8210.0010.0010.0000.0000.0000.000
130A149MET0-0.0060.00719.770-0.006-0.0060.0000.0000.0000.000
131A150TYR0-0.014-0.02322.3180.0100.0100.0000.0000.0000.000
132A151GLU-1-0.732-0.83418.9080.0260.0260.0000.0000.0000.000
133A152GLN0-0.054-0.04519.4430.0010.0010.0000.0000.0000.000
134A153PHE00.0680.03217.3480.0120.0120.0000.0000.0000.000
135A154GLY00.0850.03317.734-0.015-0.0150.0000.0000.0000.000
136A155ASN0-0.065-0.02719.145-0.009-0.0090.0000.0000.0000.000
137A156ASP-1-0.873-0.91622.3920.1170.1170.0000.0000.0000.000
138A157ILE0-0.002-0.00824.516-0.007-0.0070.0000.0000.0000.000
139A158PRO0-0.012-0.00923.4440.0030.0030.0000.0000.0000.000
140A159PHE00.0240.01522.095-0.012-0.0120.0000.0000.0000.000
141A160LYS10.8410.91524.063-0.003-0.0030.0000.0000.0000.000
142A161ARG10.7930.89322.237-0.029-0.0290.0000.0000.0000.000
143A162ASP-1-0.784-0.87125.515-0.015-0.0150.0000.0000.0000.000
144A163ILE0-0.0070.01723.3340.0000.0000.0000.0000.0000.000
145A164LYS10.8340.91326.7440.0380.0380.0000.0000.0000.000
146A165ILE00.0160.01424.522-0.003-0.0030.0000.0000.0000.000
147A166VAL0-0.002-0.01828.3050.0050.0050.0000.0000.0000.000
148A167LEU00.0060.01930.416-0.006-0.0060.0000.0000.0000.000
149A168MET0-0.039-0.01531.0960.0070.0070.0000.0000.0000.000
150A169SER0-0.027-0.01432.8520.0030.0030.0000.0000.0000.000
151A170ALA00.0330.01432.834-0.005-0.0050.0000.0000.0000.000
152A171ALA0-0.027-0.00132.7390.0050.0050.0000.0000.0000.000
153A172ILE0-0.007-0.00933.756-0.005-0.0050.0000.0000.0000.000
154A173ASP-1-0.859-0.92134.051-0.078-0.0780.0000.0000.0000.000
155A174GLU-1-0.841-0.92135.297-0.074-0.0740.0000.0000.0000.000
156A175ALA00.0070.02032.9170.0020.0020.0000.0000.0000.000
157A176ILE00.0130.00134.934-0.002-0.0020.0000.0000.0000.000
158A177ASP-1-0.850-0.92337.327-0.074-0.0740.0000.0000.0000.000
159A178GLY00.0390.01739.1190.0000.0000.0000.0000.0000.000
160A179ASP-1-0.860-0.91742.170-0.056-0.0560.0000.0000.0000.000
161A180ASN0-0.090-0.04544.3340.0010.0010.0000.0000.0000.000
162A181LEU0-0.073-0.03440.4620.0020.0020.0000.0000.0000.000
163A182SER0-0.034-0.03537.018-0.001-0.0010.0000.0000.0000.000
164A183ARG10.7720.89037.1780.0680.0680.0000.0000.0000.000
165A184ARG10.8380.91433.6490.0900.0900.0000.0000.0000.000
166A185ARG10.8890.92629.0520.1180.1180.0000.0000.0000.000
167A186ILE00.0140.02833.9760.0000.0000.0000.0000.0000.000
168A187GLU-1-0.808-0.87228.954-0.129-0.1290.0000.0000.0000.000
169A188TRP00.0330.01031.1740.0080.0080.0000.0000.0000.000
170A189SER00.004-0.01928.646-0.013-0.0130.0000.0000.0000.000
171A190LEU0-0.041-0.01728.7400.0100.0100.0000.0000.0000.000
172A191THR0-0.006-0.00327.996-0.013-0.0130.0000.0000.0000.000
173A192PHE00.025-0.01225.9770.0080.0080.0000.0000.0000.000
174A193GLU-1-0.793-0.88326.399-0.063-0.0630.0000.0000.0000.000
175A194VAL00.0120.00422.5090.0070.0070.0000.0000.0000.000
176A195ASN0-0.077-0.04925.6560.0060.0060.0000.0000.0000.000
177A196GLY00.0550.00923.9200.0000.0000.0000.0000.0000.000
178A197TRP0-0.052-0.02823.0060.0080.0080.0000.0000.0000.000
179A198MET00.0160.02218.3090.0020.0020.0000.0000.0000.000
180A199TYR0-0.031-0.05918.0290.0070.0070.0000.0000.0000.000
181A200PRO0-0.010-0.00418.977-0.009-0.0090.0000.0000.0000.000
182A201PRO0-0.008-0.00613.659-0.002-0.0020.0000.0000.0000.000
183A202VAL00.0390.03214.914-0.003-0.0030.0000.0000.0000.000
184A203ASP-1-0.847-0.92411.6710.8240.8240.0000.0000.0000.000
185A204ASP-1-0.746-0.8767.4851.3081.3080.0000.0000.0000.000
186A205ALA0-0.071-0.04210.561-0.047-0.0470.0000.0000.0000.000
187A206GLU-1-0.999-0.99312.3600.1890.1890.0000.0000.0000.000
188A207GLY0-0.008-0.00813.792-0.069-0.0690.0000.0000.0000.000
189A208LEU0-0.052-0.0058.708-0.014-0.0140.0000.0000.0000.000
190A209ILE0-0.053-0.02012.542-0.065-0.0650.0000.0000.0000.000
191A210ARG10.8900.94614.542-0.160-0.1600.0000.0000.0000.000
192A211THR00.006-0.00715.538-0.007-0.0070.0000.0000.0000.000
193A212THR0-0.036-0.00517.818-0.013-0.0130.0000.0000.0000.000
194A213TYR0-0.043-0.05020.1890.0060.0060.0000.0000.0000.000
195A214THR00.0130.02423.3460.0020.0020.0000.0000.0000.000
196A215ASP-1-0.733-0.87026.117-0.063-0.0630.0000.0000.0000.000
197A216PHE00.003-0.00226.7410.0060.0060.0000.0000.0000.000
198A217HIS0-0.062-0.01629.7630.0050.0050.0000.0000.0000.000
199A218ALA0-0.039-0.01930.3610.0050.0050.0000.0000.0000.000
200A219ASN0-0.033-0.00728.4450.0090.0090.0000.0000.0000.000
201A220THR0-0.050-0.03225.163-0.003-0.0030.0000.0000.0000.000
202A221ARG10.8400.91919.9500.1090.1090.0000.0000.0000.000
203A222ASP-1-0.916-0.96718.800-0.034-0.0340.0000.0000.0000.000
204A223LEU0-0.036-0.01915.227-0.012-0.0120.0000.0000.0000.000
205A224PRO0-0.0040.00814.9550.0110.0110.0000.0000.0000.000
206A225ASP-1-0.735-0.8638.281-0.432-0.4320.0000.0000.0000.000
207A226GLY00.0480.01410.147-0.015-0.0150.0000.0000.0000.000
208A227GLU-1-0.978-0.9988.007-1.075-1.0750.0000.0000.0000.000
209A228GLY0-0.042-0.01810.1310.0550.0550.0000.0000.0000.000
210A229VAL0-0.074-0.01313.3870.0510.0510.0000.0000.0000.000
211A230PHE0-0.023-0.00513.0600.0430.0430.0000.0000.0000.000
212A231GLU-1-0.786-0.84814.102-0.284-0.2840.0000.0000.0000.000
213A232SER00.0470.01511.3630.0170.0170.0000.0000.0000.000
214A233VAL00.0160.01813.1260.0320.0320.0000.0000.0000.000
215A234ASP-1-0.920-0.95711.742-0.392-0.3920.0000.0000.0000.000