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: 89LVY

Calculation Name: 3BUU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BUU

Chain ID: A

ChEMBL ID:

UniProt ID: Q82SR2

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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2872121.796915
FMO2-HF: Nuclear repulsion 2782081.597211
FMO2-HF: Total energy -90040.199704
FMO2-MP2: Total energy -90304.202601


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:34:ALA)


Summations of interaction energy for fragment #1(A:34: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.
-2.020.4810.025-1.279-1.2480.005
Interaction energy analysis for fragmet #1(A:34:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : 0.004
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].
3A36THR00.0140.0113.430-1.0231.4780.025-1.279-1.2480.005
4A37ALA00.0480.0125.7670.2380.2380.0000.0000.0000.000
5A38GLN00.0280.0049.239-0.051-0.0510.0000.0000.0000.000
6A39SER00.0140.0246.860-0.253-0.2530.0000.0000.0000.000
7A40ILE0-0.007-0.0068.1060.2080.2080.0000.0000.0000.000
8A41LEU0-0.020-0.01310.3800.1970.1970.0000.0000.0000.000
9A42GLU-1-0.909-0.95610.917-1.175-1.1750.0000.0000.0000.000
10A43LYS10.8730.9369.2301.2801.2800.0000.0000.0000.000
11A44ALA00.0280.01413.2630.1260.1260.0000.0000.0000.000
12A45ASP-1-0.746-0.86316.053-0.443-0.4430.0000.0000.0000.000
13A46GLU-1-0.892-0.93513.492-0.763-0.7630.0000.0000.0000.000
14A47ILE00.0120.03615.7280.0700.0700.0000.0000.0000.000
15A48ARG10.8660.93619.0770.3300.3300.0000.0000.0000.000
16A49PHE0-0.052-0.04621.4210.0510.0510.0000.0000.0000.000
17A50PRO00.0340.01921.412-0.034-0.0340.0000.0000.0000.000
18A51GLN0-0.012-0.00218.1800.0090.0090.0000.0000.0000.000
19A52ASP-1-0.858-0.93121.570-0.230-0.2300.0000.0000.0000.000
20A53SER0-0.066-0.03024.9410.0030.0030.0000.0000.0000.000
21A54PHE0-0.008-0.00825.7680.0120.0120.0000.0000.0000.000
22A55GLN00.0000.01330.1550.0060.0060.0000.0000.0000.000
23A56VAL0-0.019-0.00730.699-0.005-0.0050.0000.0000.0000.000
24A57ASN0-0.018-0.00233.2690.0050.0050.0000.0000.0000.000
25A58VAL00.0320.01133.151-0.007-0.0070.0000.0000.0000.000
26A59ALA0-0.013-0.00535.7200.0080.0080.0000.0000.0000.000
27A60ILE00.013-0.00335.538-0.008-0.0080.0000.0000.0000.000
28A61ARG10.8860.93438.1260.1150.1150.0000.0000.0000.000
29A62THR00.0760.04539.058-0.008-0.0080.0000.0000.0000.000
30A63ALA0-0.0020.01340.7030.0050.0050.0000.0000.0000.000
31A64ALA00.0350.01941.258-0.005-0.0050.0000.0000.0000.000
32A65PRO0-0.061-0.04342.9000.0020.0020.0000.0000.0000.000
33A66ASP-1-0.913-0.93645.884-0.059-0.0590.0000.0000.0000.000
34A67HIS0-0.089-0.05546.6910.0050.0050.0000.0000.0000.000
35A68ALA0-0.0100.00045.464-0.004-0.0040.0000.0000.0000.000
36A69GLU-1-0.893-0.93743.267-0.082-0.0820.0000.0000.0000.000
37A70ASP-1-0.914-0.95145.752-0.074-0.0740.0000.0000.0000.000
38A71LEU0-0.116-0.06441.448-0.005-0.0050.0000.0000.0000.000
39A72TYR00.009-0.01940.8800.0010.0010.0000.0000.0000.000
40A73ARG10.8080.87540.1010.0920.0920.0000.0000.0000.000
41A74TYR00.0520.02637.3230.0030.0030.0000.0000.0000.000
42A75GLN0-0.0040.00837.520-0.003-0.0030.0000.0000.0000.000
43A76VAL0-0.005-0.00832.0410.0030.0030.0000.0000.0000.000
44A77LEU0-0.056-0.02533.772-0.001-0.0010.0000.0000.0000.000
45A78SER00.0490.01028.0670.0010.0010.0000.0000.0000.000
46A79LYS10.8890.93228.5690.1840.1840.0000.0000.0000.000
47A80GLY00.0830.04025.015-0.002-0.0020.0000.0000.0000.000
48A81ASN00.021-0.00823.5120.0210.0210.0000.0000.0000.000
49A82GLU-1-0.886-0.92526.243-0.197-0.1970.0000.0000.0000.000
50A83ASN0-0.023-0.02128.4780.0240.0240.0000.0000.0000.000
51A84SER00.004-0.00830.802-0.005-0.0050.0000.0000.0000.000
52A85ILE0-0.028-0.01733.0730.0100.0100.0000.0000.0000.000
53A86VAL00.0200.02434.811-0.005-0.0050.0000.0000.0000.000
54A87MET0-0.021-0.01637.4310.0080.0080.0000.0000.0000.000
55A88ILE00.0030.02040.779-0.003-0.0030.0000.0000.0000.000
56A89THR0-0.002-0.01042.2120.0030.0030.0000.0000.0000.000
57A90GLU-1-0.866-0.89744.166-0.086-0.0860.0000.0000.0000.000
58A91PRO00.1530.07744.252-0.005-0.0050.0000.0000.0000.000
59A92ALA0-0.011-0.02647.799-0.001-0.0010.0000.0000.0000.000
60A93SER0-0.0040.00249.7820.0010.0010.0000.0000.0000.000
61A94GLU-1-0.828-0.89945.622-0.091-0.0910.0000.0000.0000.000
62A95ARG10.8520.92146.8560.0760.0760.0000.0000.0000.000
63A96GLY00.0030.00946.4420.0040.0040.0000.0000.0000.000
64A97GLN0-0.076-0.03144.8210.0020.0020.0000.0000.0000.000
65A98ALA00.000-0.00641.962-0.003-0.0030.0000.0000.0000.000
66A99ILE00.0140.00537.2590.0030.0030.0000.0000.0000.000
67A100LEU0-0.048-0.00237.000-0.004-0.0040.0000.0000.0000.000
68A101MET00.0120.03729.3110.0020.0020.0000.0000.0000.000
69A102LYS10.8910.93433.5340.1240.1240.0000.0000.0000.000
70A103GLY00.0170.00830.0640.0050.0050.0000.0000.0000.000
71A104ARG10.8240.89023.9560.2460.2460.0000.0000.0000.000
72A105ASP-1-0.873-0.90331.336-0.132-0.1320.0000.0000.0000.000
73A106LEU00.0000.00633.910-0.003-0.0030.0000.0000.0000.000
74A107TRP0-0.009-0.02137.2020.0110.0110.0000.0000.0000.000
75A108VAL00.0420.01340.463-0.004-0.0040.0000.0000.0000.000
76A109PHE0-0.016-0.02041.8510.0060.0060.0000.0000.0000.000
77A110MET00.0630.02745.811-0.002-0.0020.0000.0000.0000.000
78A111PRO00.0680.02848.6300.0020.0020.0000.0000.0000.000
79A112SER0-0.034-0.00152.0440.0020.0020.0000.0000.0000.000
80A113VAL0-0.031-0.01849.3540.0020.0020.0000.0000.0000.000
81A114SER00.0010.00151.774-0.001-0.0010.0000.0000.0000.000
82A115GLN0-0.056-0.03248.947-0.004-0.0040.0000.0000.0000.000
83A116PRO0-0.0110.01144.2450.0000.0000.0000.0000.0000.000
84A117ILE00.008-0.00243.8970.0020.0020.0000.0000.0000.000
85A118ARG10.7840.88036.8710.1180.1180.0000.0000.0000.000
86A119LEU00.0400.03339.4710.0040.0040.0000.0000.0000.000
87A120SER0-0.010-0.02535.096-0.003-0.0030.0000.0000.0000.000
88A121LEU00.0660.02129.4200.0020.0020.0000.0000.0000.000
89A122SER00.0330.02232.049-0.001-0.0010.0000.0000.0000.000
90A123GLN0-0.0370.00333.2410.0040.0040.0000.0000.0000.000
91A124ARG10.8820.93235.9200.1110.1110.0000.0000.0000.000
92A125LEU0-0.0260.00535.9720.0040.0040.0000.0000.0000.000
93A126THR0-0.001-0.00937.9980.0070.0070.0000.0000.0000.000
94A127GLY00.0520.04737.946-0.007-0.0070.0000.0000.0000.000
95A128GLN0-0.020-0.02634.438-0.006-0.0060.0000.0000.0000.000
96A129VAL0-0.0180.00332.925-0.013-0.0130.0000.0000.0000.000
97A130ALA0-0.001-0.00231.7570.0100.0100.0000.0000.0000.000
98A131ASN00.012-0.01933.312-0.004-0.0040.0000.0000.0000.000
99A132GLY0-0.003-0.01830.329-0.004-0.0040.0000.0000.0000.000
100A133ASP-1-0.755-0.84428.882-0.212-0.2120.0000.0000.0000.000
101A134ILE0-0.048-0.02229.573-0.006-0.0060.0000.0000.0000.000
102A135ALA0-0.014-0.00231.291-0.003-0.0030.0000.0000.0000.000
103A136ARG10.7560.85026.0370.2450.2450.0000.0000.0000.000
104A137ALA0-0.0200.00524.7320.0040.0040.0000.0000.0000.000
105A138ASN0-0.003-0.00620.351-0.006-0.0060.0000.0000.0000.000
106A139PHE0-0.011-0.01218.9740.0390.0390.0000.0000.0000.000
107A140THR0-0.001-0.03515.909-0.010-0.0100.0000.0000.0000.000
108A141GLY0-0.033-0.00818.2520.0410.0410.0000.0000.0000.000
109A142ASP-1-0.806-0.88520.204-0.243-0.2430.0000.0000.0000.000
110A143TYR0-0.004-0.01119.3220.0450.0450.0000.0000.0000.000
111A144HIS00.0040.01513.793-0.072-0.0720.0000.0000.0000.000
112A145PRO0-0.0180.00112.6010.0490.0490.0000.0000.0000.000
113A146GLN0-0.009-0.01612.099-0.055-0.0550.0000.0000.0000.000
114A147LEU0-0.0120.0039.0450.0140.0140.0000.0000.0000.000
115A148LEU0-0.068-0.02112.0590.0700.0700.0000.0000.0000.000
116A149ARG10.8100.87114.6000.2520.2520.0000.0000.0000.000
117A150ASN00.0710.03110.421-0.124-0.1240.0000.0000.0000.000
118A151GLU-1-0.791-0.87414.648-0.150-0.1500.0000.0000.0000.000
119A152SER00.0250.00117.726-0.022-0.0220.0000.0000.0000.000
120A153ILE0-0.095-0.04219.7880.0110.0110.0000.0000.0000.000
121A154ASP-1-0.944-0.98622.507-0.091-0.0910.0000.0000.0000.000
122A155ASP-1-0.955-0.96621.630-0.088-0.0880.0000.0000.0000.000
123A156GLU-1-0.880-0.92018.111-0.238-0.2380.0000.0000.0000.000
124A157ASP-1-0.860-0.90614.750-0.124-0.1240.0000.0000.0000.000
125A158TYR0-0.060-0.04215.278-0.072-0.0720.0000.0000.0000.000
126A159TYR00.0410.0188.087-0.041-0.0410.0000.0000.0000.000
127A160VAL0-0.018-0.00213.2830.0080.0080.0000.0000.0000.000
128A161LEU00.010-0.00411.282-0.006-0.0060.0000.0000.0000.000
129A162GLU-1-0.785-0.90315.044-0.184-0.1840.0000.0000.0000.000
130A163LEU0-0.029-0.01216.221-0.043-0.0430.0000.0000.0000.000
131A164THR0-0.008-0.00918.7470.0550.0550.0000.0000.0000.000
132A165GLY0-0.001-0.00120.977-0.023-0.0230.0000.0000.0000.000
133A166ILE0-0.021-0.01219.9680.0170.0170.0000.0000.0000.000
134A167ASP-1-0.779-0.86623.512-0.181-0.1810.0000.0000.0000.000
135A168ARG10.9360.95627.3460.1240.1240.0000.0000.0000.000
136A169SER0-0.109-0.06729.8220.0070.0070.0000.0000.0000.000
137A170VAL00.0120.02825.0470.0000.0000.0000.0000.0000.000
138A171THR0-0.036-0.02427.6910.0120.0120.0000.0000.0000.000
139A172TYR0-0.020-0.05225.8850.0210.0210.0000.0000.0000.000
140A173GLN0-0.050-0.04426.133-0.002-0.0020.0000.0000.0000.000
141A174LYS10.8620.92822.1420.2060.2060.0000.0000.0000.000
142A175VAL0-0.0130.00521.6550.0200.0200.0000.0000.0000.000
143A176LEU0-0.069-0.00419.402-0.024-0.0240.0000.0000.0000.000
144A177LEU00.0250.00717.0570.0260.0260.0000.0000.0000.000
145A178TRP0-0.048-0.02917.001-0.050-0.0500.0000.0000.0000.000
146A179VAL0-0.025-0.01713.5430.0110.0110.0000.0000.0000.000
147A180ASN00.0040.00314.602-0.038-0.0380.0000.0000.0000.000
148A181GLN00.000-0.01911.131-0.117-0.1170.0000.0000.0000.000
149A182SER0-0.034-0.01311.256-0.063-0.0630.0000.0000.0000.000
150A183ASN0-0.003-0.02513.237-0.044-0.0440.0000.0000.0000.000
151A184PHE00.007-0.0027.690-0.077-0.0770.0000.0000.0000.000
152A185ARG10.9741.00613.7930.2940.2940.0000.0000.0000.000
153A186PRO0-0.0220.00317.490-0.002-0.0020.0000.0000.0000.000
154A187TYR00.0160.00619.2040.0350.0350.0000.0000.0000.000
155A188LYS10.8900.93421.2250.2320.2320.0000.0000.0000.000
156A189ALA0-0.040-0.01421.462-0.036-0.0360.0000.0000.0000.000
157A190GLU-1-0.807-0.88523.262-0.166-0.1660.0000.0000.0000.000
158A191PHE00.001-0.00224.344-0.020-0.0200.0000.0000.0000.000
159A192TYR0-0.009-0.02824.3270.0250.0250.0000.0000.0000.000
160A193SER00.0040.00328.103-0.006-0.0060.0000.0000.0000.000
161A194VAL00.020-0.00829.503-0.005-0.0050.0000.0000.0000.000
162A195SER0-0.034-0.01430.8440.0000.0000.0000.0000.0000.000
163A196GLY00.0300.01528.3720.0070.0070.0000.0000.0000.000
164A197ARG10.8600.93429.3230.1040.1040.0000.0000.0000.000
165A198LEU00.0530.03127.636-0.007-0.0070.0000.0000.0000.000
166A199LEU0-0.055-0.03430.2150.0110.0110.0000.0000.0000.000
167A200LYS10.8660.93229.8270.1840.1840.0000.0000.0000.000
168A201THR0-0.022-0.00127.809-0.013-0.0130.0000.0000.0000.000
169A202SER0-0.010-0.00426.1040.0040.0040.0000.0000.0000.000
170A203ARG10.8710.91225.9560.1350.1350.0000.0000.0000.000
171A204TYR0-0.015-0.00422.9380.0040.0040.0000.0000.0000.000
172A205GLU-1-0.789-0.89925.477-0.151-0.1510.0000.0000.0000.000
173A206ASN0-0.016-0.01727.625-0.004-0.0040.0000.0000.0000.000
174A207PHE00.0060.00121.8070.0000.0000.0000.0000.0000.000
175A208ASP-1-0.867-0.93326.460-0.142-0.1420.0000.0000.0000.000
176A209ASN0-0.028-0.01425.345-0.033-0.0330.0000.0000.0000.000
177A210ILE00.012-0.00125.3660.0160.0160.0000.0000.0000.000
178A211LEU0-0.039-0.02624.832-0.020-0.0200.0000.0000.0000.000
179A212GLY00.0190.01022.105-0.020-0.0200.0000.0000.0000.000
180A213GLU-1-0.864-0.91817.275-0.467-0.4670.0000.0000.0000.000
181A214MET0-0.072-0.01920.9770.0390.0390.0000.0000.0000.000
182A215ARG10.8280.88920.9100.3070.3070.0000.0000.0000.000
183A216PRO0-0.051-0.00222.8250.0220.0220.0000.0000.0000.000
184A217THR0-0.017-0.02325.8210.0040.0040.0000.0000.0000.000
185A218ARG10.8650.90229.0130.1450.1450.0000.0000.0000.000
186A219ILE0-0.042-0.01126.376-0.015-0.0150.0000.0000.0000.000
187A220ILE0-0.050-0.01029.6110.0130.0130.0000.0000.0000.000
188A221MET0-0.022-0.01228.783-0.009-0.0090.0000.0000.0000.000
189A222GLU-1-0.865-0.92131.759-0.121-0.1210.0000.0000.0000.000
190A223ASP-1-0.759-0.85832.826-0.116-0.1160.0000.0000.0000.000
191A224ALA0-0.034-0.01032.0340.0020.0020.0000.0000.0000.000
192A225LEU0-0.101-0.04834.1760.0070.0070.0000.0000.0000.000
193A226LYS10.9260.94137.4460.0730.0730.0000.0000.0000.000
194A227SER0-0.052-0.04439.4470.0040.0040.0000.0000.0000.000
195A228GLY00.0280.01540.2210.0030.0030.0000.0000.0000.000
196A229GLU-1-0.890-0.93239.113-0.103-0.1030.0000.0000.0000.000
197A230VAL00.008-0.00435.223-0.007-0.0070.0000.0000.0000.000
198A231SER0-0.020-0.02235.2970.0050.0050.0000.0000.0000.000
199A232VAL0-0.020-0.01234.487-0.009-0.0090.0000.0000.0000.000
200A233LEU0-0.032-0.01731.2300.0050.0050.0000.0000.0000.000
201A234ASP-1-0.778-0.85132.588-0.138-0.1380.0000.0000.0000.000
202A235TYR0-0.005-0.00130.132-0.002-0.0020.0000.0000.0000.000
203A236SER00.003-0.00932.6890.0050.0050.0000.0000.0000.000
204A237ASP-1-0.846-0.92534.414-0.126-0.1260.0000.0000.0000.000
205A238MET00.0050.02226.863-0.003-0.0030.0000.0000.0000.000
206A239LYS10.8210.90631.1780.1280.1280.0000.0000.0000.000
207A240LEU00.0410.02226.353-0.002-0.0020.0000.0000.0000.000
208A241ARG10.8660.91630.4290.1420.1420.0000.0000.0000.000
209A242ASP-1-0.855-0.92531.907-0.151-0.1510.0000.0000.0000.000
210A243LEU0-0.060-0.02531.5590.0100.0100.0000.0000.0000.000
211A244PRO00.0400.01433.502-0.006-0.0060.0000.0000.0000.000
212A245ASP-1-0.811-0.92634.133-0.126-0.1260.0000.0000.0000.000
213A246LYS10.8680.92735.4970.1110.1110.0000.0000.0000.000
214A247ILE00.0050.01336.3760.0070.0070.0000.0000.0000.000
215A248PHE00.0060.02533.5760.0020.0020.0000.0000.0000.000
216A249THR0-0.029-0.02737.9680.0010.0010.0000.0000.0000.000
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