Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: QVYZY

Calculation Name: 3BYI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BYI

Chain ID: A

ChEMBL ID:

UniProt ID: Q53QZ3

Base Structure: X-ray

Registration Date: 2023-09-21

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2557444.423873
FMO2-HF: Nuclear repulsion 2472485.173878
FMO2-HF: Total energy -84959.249995
FMO2-MP2: Total energy -85206.127189


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:261:MET)


Summations of interaction energy for fragment #1(A:261:MET)
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.
-0.2841.424-0.021-0.75-0.9370.003
Interaction energy analysis for fragmet #1(A:261:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.007
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].
3A263PRO0-0.0030.0083.837-1.2660.442-0.021-0.750-0.9370.003
4A264SER00.0290.0056.5490.3790.3790.0000.0000.0000.000
5A265LEU00.0890.0399.097-0.096-0.0960.0000.0000.0000.000
6A266LYS10.9290.95812.705-0.032-0.0320.0000.0000.0000.000
7A267THR0-0.011-0.0048.053-0.024-0.0240.0000.0000.0000.000
8A268LEU0-0.007-0.01010.100-0.057-0.0570.0000.0000.0000.000
9A269GLN0-0.0080.00512.607-0.002-0.0020.0000.0000.0000.000
10A270GLU-1-0.874-0.92013.751-0.073-0.0730.0000.0000.0000.000
11A271LYS10.8580.9208.0650.9400.9400.0000.0000.0000.000
12A272GLY00.0700.04814.052-0.012-0.0120.0000.0000.0000.000
13A273LEU0-0.114-0.05211.015-0.017-0.0170.0000.0000.0000.000
14A274ILE0-0.029-0.01213.9620.0230.0230.0000.0000.0000.000
15A275LYS10.8740.92616.9770.1320.1320.0000.0000.0000.000
16A276ASP-1-0.857-0.94318.7390.0020.0020.0000.0000.0000.000
17A277GLN0-0.056-0.00721.5910.0030.0030.0000.0000.0000.000
18A278ILE0-0.015-0.00824.9550.0070.0070.0000.0000.0000.000
19A279PHE0-0.015-0.02825.2280.0070.0070.0000.0000.0000.000
20A280GLY00.0690.04825.2910.0000.0000.0000.0000.0000.000
21A281SER0-0.051-0.01826.8720.0020.0020.0000.0000.0000.000
22A282HIS0-0.022-0.04328.831-0.002-0.0020.0000.0000.0000.000
23A283LEU00.0770.03632.414-0.005-0.0050.0000.0000.0000.000
24A284HIS10.8570.89635.088-0.008-0.0080.0000.0000.0000.000
25A285LYS10.9580.99727.6620.0040.0040.0000.0000.0000.000
26A286VAL0-0.012-0.00230.711-0.005-0.0050.0000.0000.0000.000
27A287CYS0-0.059-0.02233.043-0.003-0.0030.0000.0000.0000.000
28A288GLU-1-0.890-0.93835.397-0.019-0.0190.0000.0000.0000.000
29A289ARG10.7950.88226.9640.0610.0610.0000.0000.0000.000
30A290GLU-1-0.849-0.89534.120-0.031-0.0310.0000.0000.0000.000
31A291ASN0-0.051-0.01336.066-0.001-0.0010.0000.0000.0000.000
32A292SER0-0.047-0.03537.9680.0020.0020.0000.0000.0000.000
33A293THR0-0.030-0.04840.5620.0010.0010.0000.0000.0000.000
34A294VAL00.022-0.02040.0300.0030.0030.0000.0000.0000.000
35A295PRO00.0280.01534.779-0.003-0.0030.0000.0000.0000.000
36A296TRP00.054-0.01435.2220.0030.0030.0000.0000.0000.000
37A297PHE00.0350.02331.4380.0010.0010.0000.0000.0000.000
38A298VAL00.0290.00834.4150.0030.0030.0000.0000.0000.000
39A299LYS10.8740.96037.1050.0230.0230.0000.0000.0000.000
40A300GLN00.0260.01334.2340.0000.0000.0000.0000.0000.000
41A301CYS0-0.048-0.01434.8030.0010.0010.0000.0000.0000.000
42A302ILE0-0.019-0.01237.3970.0020.0020.0000.0000.0000.000
43A303GLU-1-0.932-0.95640.552-0.024-0.0240.0000.0000.0000.000
44A304ALA00.0160.00238.4580.0000.0000.0000.0000.0000.000
45A305VAL0-0.021-0.01439.3930.0010.0010.0000.0000.0000.000
46A306GLU-1-0.813-0.90241.861-0.005-0.0050.0000.0000.0000.000
47A307LYS10.8160.91241.5870.0250.0250.0000.0000.0000.000
48A308ARG10.7950.88036.4580.0150.0150.0000.0000.0000.000
49A309GLY00.0310.00342.8850.0010.0010.0000.0000.0000.000
50A310LEU0-0.041-0.01143.6690.0020.0020.0000.0000.0000.000
51A311ASP-1-0.829-0.91147.0700.0010.0010.0000.0000.0000.000
52A312VAL00.0180.03241.9950.0010.0010.0000.0000.0000.000
53A313ASP-1-0.859-0.93645.3540.0130.0130.0000.0000.0000.000
54A314GLY0-0.054-0.04243.7510.0020.0020.0000.0000.0000.000
55A315ILE00.0130.03140.8550.0030.0030.0000.0000.0000.000
56A316TYR00.025-0.03138.8750.0010.0010.0000.0000.0000.000
57A317ARG10.8690.94739.457-0.019-0.0190.0000.0000.0000.000
58A318VAL0-0.009-0.00237.9140.0050.0050.0000.0000.0000.000
59A319SER0-0.058-0.02533.4740.0000.0000.0000.0000.0000.000
60A320GLY00.0990.05133.180-0.001-0.0010.0000.0000.0000.000
61A321ASN00.0220.00827.5880.0080.0080.0000.0000.0000.000
62A322LEU00.0650.03325.726-0.005-0.0050.0000.0000.0000.000
63A323ALA00.0170.00323.422-0.001-0.0010.0000.0000.0000.000
64A324THR0-0.010-0.01724.147-0.010-0.0100.0000.0000.0000.000
65A325ILE00.0010.00426.710-0.009-0.0090.0000.0000.0000.000
66A326GLN00.008-0.00422.170-0.015-0.0150.0000.0000.0000.000
67A327LYS10.9010.96322.0560.0090.0090.0000.0000.0000.000
68A328LEU00.0100.01423.578-0.014-0.0140.0000.0000.0000.000
69A329ARG10.8080.87720.969-0.035-0.0350.0000.0000.0000.000
70A330PHE0-0.034-0.01417.300-0.005-0.0050.0000.0000.0000.000
71A331ILE00.0450.01822.418-0.013-0.0130.0000.0000.0000.000
72A332VAL00.0000.00424.531-0.008-0.0080.0000.0000.0000.000
73A333ASN00.004-0.00122.072-0.004-0.0040.0000.0000.0000.000
74A334GLN0-0.028-0.02117.9780.0060.0060.0000.0000.0000.000
75A335GLU-1-0.856-0.90422.679-0.094-0.0940.0000.0000.0000.000
76A336GLU-1-0.916-0.94422.634-0.135-0.1350.0000.0000.0000.000
77A337LYS10.9270.95926.5060.1100.1100.0000.0000.0000.000
78A338LEU00.0300.01729.445-0.002-0.0020.0000.0000.0000.000
79A339ASN00.018-0.01331.2670.0060.0060.0000.0000.0000.000
80A340LEU00.003-0.00433.0170.0010.0010.0000.0000.0000.000
81A341ASP-1-0.816-0.88635.230-0.024-0.0240.0000.0000.0000.000
82A342ASP-1-0.894-0.92631.844-0.057-0.0570.0000.0000.0000.000
83A343SER00.0420.01033.3090.0030.0030.0000.0000.0000.000
84A344GLN0-0.023-0.00926.0790.0090.0090.0000.0000.0000.000
85A345TRP0-0.048-0.03326.5430.0100.0100.0000.0000.0000.000
86A346GLU-1-0.856-0.92132.907-0.014-0.0140.0000.0000.0000.000
87A347ASP-1-0.833-0.90634.0510.0170.0170.0000.0000.0000.000
88A348ILE00.0430.00735.1690.0010.0010.0000.0000.0000.000
89A349HIS00.027-0.00136.2360.0010.0010.0000.0000.0000.000
90A350VAL0-0.048-0.02530.1420.0050.0050.0000.0000.0000.000
91A351VAL00.0210.02332.4160.0010.0010.0000.0000.0000.000
92A352THR00.0040.00534.6700.0030.0030.0000.0000.0000.000
93A353GLY0-0.020-0.02632.9090.0020.0020.0000.0000.0000.000
94A354ALA00.0250.01430.3700.0040.0040.0000.0000.0000.000
95A355LEU00.0100.00831.4210.0000.0000.0000.0000.0000.000
96A356LYS10.8410.90734.137-0.027-0.0270.0000.0000.0000.000
97A357MET0-0.020-0.00426.5500.0020.0020.0000.0000.0000.000
98A358PHE00.0190.02130.0720.0030.0030.0000.0000.0000.000
99A359PHE00.012-0.01131.2900.0010.0010.0000.0000.0000.000
100A360ARG10.8700.91731.343-0.041-0.0410.0000.0000.0000.000
101A361GLU-1-0.787-0.86424.6730.0420.0420.0000.0000.0000.000
102A362LEU0-0.0200.01828.890-0.001-0.0010.0000.0000.0000.000
103A363PRO00.0080.01529.4210.0050.0050.0000.0000.0000.000
104A364GLU-1-0.903-0.93730.9830.0240.0240.0000.0000.0000.000
105A365PRO0-0.0200.00134.778-0.003-0.0030.0000.0000.0000.000
106A366LEU0-0.010-0.00336.811-0.003-0.0030.0000.0000.0000.000
107A367PHE00.0140.00239.204-0.003-0.0030.0000.0000.0000.000
108A368PRO0-0.0080.00640.1350.0020.0020.0000.0000.0000.000
109A369TYR00.1350.04934.1720.0000.0000.0000.0000.0000.000
110A370SER0-0.023-0.00941.2610.0000.0000.0000.0000.0000.000
111A371PHE0-0.025-0.02543.995-0.001-0.0010.0000.0000.0000.000
112A372PHE00.0290.02343.623-0.001-0.0010.0000.0000.0000.000
113A373GLU-1-0.875-0.94845.7250.0270.0270.0000.0000.0000.000
114A374GLN00.007-0.00248.687-0.002-0.0020.0000.0000.0000.000
115A375PHE00.026-0.00646.311-0.001-0.0010.0000.0000.0000.000
116A376VAL00.0050.00548.022-0.001-0.0010.0000.0000.0000.000
117A377GLU-1-0.866-0.93550.7210.0170.0170.0000.0000.0000.000
118A378ALA0-0.059-0.02052.932-0.001-0.0010.0000.0000.0000.000
119A379ILE00.005-0.01150.851-0.001-0.0010.0000.0000.0000.000
120A380LYS10.8740.95852.399-0.025-0.0250.0000.0000.0000.000
121A381LYS10.8120.92456.406-0.016-0.0160.0000.0000.0000.000
122A382GLN00.0880.02959.4250.0000.0000.0000.0000.0000.000
123A383ASP-1-0.785-0.86862.7230.0110.0110.0000.0000.0000.000
124A384ASN00.0490.00458.3750.0010.0010.0000.0000.0000.000
125A385ASN0-0.012-0.01359.890-0.001-0.0010.0000.0000.0000.000
126A386THR0-0.006-0.01360.729-0.001-0.0010.0000.0000.0000.000
127A387ARG10.8050.92156.561-0.015-0.0150.0000.0000.0000.000
128A388ILE0-0.018-0.00156.5340.0000.0000.0000.0000.0000.000
129A389GLU-1-0.772-0.87456.6590.0050.0050.0000.0000.0000.000
130A390ALA0-0.0120.00856.4110.0000.0000.0000.0000.0000.000
131A391VAL00.027-0.00251.2440.0000.0000.0000.0000.0000.000
132A392LYS10.8440.91452.352-0.005-0.0050.0000.0000.0000.000
133A393SER0-0.025-0.02653.930-0.001-0.0010.0000.0000.0000.000
134A394LEU0-0.070-0.02250.279-0.001-0.0010.0000.0000.0000.000
135A395VAL00.0640.02848.7430.0000.0000.0000.0000.0000.000
136A396GLN0-0.029-0.01749.425-0.001-0.0010.0000.0000.0000.000
137A397LYS10.9060.96350.345-0.010-0.0100.0000.0000.0000.000
138A398LEU0-0.0420.00944.4460.0000.0000.0000.0000.0000.000
139A399PRO00.0140.00542.175-0.002-0.0020.0000.0000.0000.000
140A400PRO00.0630.01544.3070.0010.0010.0000.0000.0000.000
141A401PRO00.0450.02339.7550.0000.0000.0000.0000.0000.000
142A402ASN0-0.014-0.00239.711-0.002-0.0020.0000.0000.0000.000
143A403ARG10.9240.95942.3510.0000.0000.0000.0000.0000.000
144A404ASP-1-0.828-0.90044.239-0.005-0.0050.0000.0000.0000.000
145A405THR00.003-0.01039.015-0.001-0.0010.0000.0000.0000.000
146A406MET0-0.062-0.01942.3760.0010.0010.0000.0000.0000.000
147A407LYS10.9250.97044.5040.0030.0030.0000.0000.0000.000
148A408VAL00.0180.01842.9390.0000.0000.0000.0000.0000.000
149A409LEU00.0030.00640.2080.0000.0000.0000.0000.0000.000
150A410PHE00.021-0.01343.6390.0010.0010.0000.0000.0000.000
151A411GLY00.0270.01846.8150.0000.0000.0000.0000.0000.000
152A412HIS00.0060.00743.3540.0020.0020.0000.0000.0000.000
153A413LEU00.0120.00043.0720.0000.0000.0000.0000.0000.000
154A414THR0-0.042-0.03146.9120.0010.0010.0000.0000.0000.000
155A415LYS10.8150.89148.1410.0050.0050.0000.0000.0000.000
156A416ILE0-0.0250.00244.9700.0000.0000.0000.0000.0000.000
157A417VAL00.0110.01448.6170.0010.0010.0000.0000.0000.000
158A418ALA00.0050.00951.4350.0000.0000.0000.0000.0000.000
159A419LYS10.7890.87750.6640.0010.0010.0000.0000.0000.000
160A420ALA00.0710.05551.5140.0000.0000.0000.0000.0000.000
161A421SER0-0.033-0.01952.5730.0010.0010.0000.0000.0000.000
162A422LYS10.8580.93351.140-0.003-0.0030.0000.0000.0000.000
163A423ASN00.020-0.00247.1130.0020.0020.0000.0000.0000.000
164A424LEU00.0030.01347.7710.0020.0020.0000.0000.0000.000
165A425MET0-0.0650.00044.3740.0030.0030.0000.0000.0000.000
166A426SER00.0400.01648.752-0.001-0.0010.0000.0000.0000.000
167A427THR00.0490.00049.0430.0000.0000.0000.0000.0000.000
168A428GLN00.0120.01249.1250.0000.0000.0000.0000.0000.000
169A429SER0-0.046-0.03946.2610.0020.0020.0000.0000.0000.000
170A430LEU00.0160.00844.1590.0020.0020.0000.0000.0000.000
171A431GLY00.0440.02244.1860.0010.0010.0000.0000.0000.000
172A432ILE0-0.014-0.01342.7940.0020.0020.0000.0000.0000.000
173A433VAL0-0.043-0.00139.1420.0030.0030.0000.0000.0000.000
174A434PHE00.010-0.02339.3670.0020.0020.0000.0000.0000.000
175A435GLY00.0390.03541.244-0.001-0.0010.0000.0000.0000.000
176A436PRO00.0290.00238.2190.0000.0000.0000.0000.0000.000
177A437THR0-0.139-0.06435.8150.0030.0030.0000.0000.0000.000
178A438LEU0-0.028-0.00536.830-0.001-0.0010.0000.0000.0000.000
179A439LEU0-0.029-0.01239.498-0.002-0.0020.0000.0000.0000.000
180A440ARG10.8170.92832.270-0.039-0.0390.0000.0000.0000.000
181A441ALA00.0730.02938.1390.0020.0020.0000.0000.0000.000
182A442GLU-1-0.883-0.94537.1470.0480.0480.0000.0000.0000.000
183A443ASN0-0.006-0.03236.0260.0010.0010.0000.0000.0000.000
184A444GLU-1-0.878-0.90838.7990.0440.0440.0000.0000.0000.000
185A445THR00.0150.00440.9950.0000.0000.0000.0000.0000.000
186A446GLY0-0.004-0.00143.021-0.003-0.0030.0000.0000.0000.000
187A447ASN0-0.001-0.00244.7610.0030.0030.0000.0000.0000.000
188A448MET00.0870.04838.757-0.002-0.0020.0000.0000.0000.000
189A449ALA00.0450.01344.026-0.001-0.0010.0000.0000.0000.000
190A450ILE0-0.004-0.00746.456-0.002-0.0020.0000.0000.0000.000
191A451HIS10.8310.91742.967-0.041-0.0410.0000.0000.0000.000
192A452MET00.0020.00742.261-0.001-0.0010.0000.0000.0000.000
193A453VAL00.0080.01044.771-0.002-0.0020.0000.0000.0000.000
194A454TYR0-0.004-0.01947.187-0.002-0.0020.0000.0000.0000.000
195A455GLN00.0340.00740.546-0.003-0.0030.0000.0000.0000.000
196A456ASN00.0420.01244.455-0.001-0.0010.0000.0000.0000.000
197A457GLN00.0080.01146.770-0.001-0.0010.0000.0000.0000.000
198A458ILE0-0.0190.00147.351-0.002-0.0020.0000.0000.0000.000
199A459ALA0-0.024-0.01245.194-0.002-0.0020.0000.0000.0000.000
200A460GLU-1-0.807-0.91447.2370.0180.0180.0000.0000.0000.000
201A461LEU0-0.0320.01550.268-0.002-0.0020.0000.0000.0000.000
202A462MET0-0.044-0.01747.487-0.002-0.0020.0000.0000.0000.000
203A463LEU0-0.029-0.00347.801-0.002-0.0020.0000.0000.0000.000
204A464SER0-0.056-0.05850.572-0.001-0.0010.0000.0000.0000.000
205A465GLU-1-0.790-0.88453.9810.0070.0070.0000.0000.0000.000
206A466TYR0-0.0170.00649.310-0.001-0.0010.0000.0000.0000.000
207A467SER0-0.002-0.01053.425-0.001-0.0010.0000.0000.0000.000
208A468LYS10.8460.90556.418-0.007-0.0070.0000.0000.0000.000
209A469ILE0-0.040-0.00952.0270.0000.0000.0000.0000.0000.000
210A470PHE00.000-0.01548.137-0.001-0.0010.0000.0000.0000.000
211A471GLY0-0.0270.01053.425-0.002-0.0020.0000.0000.0000.000