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: R8968

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2556251.481686
FMO2-HF: Nuclear repulsion 2471293.199567
FMO2-HF: Total energy -84958.282119
FMO2-MP2: Total energy -85205.061225


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.
-1.1720.75-0.022-0.898-1.0030.004
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 : 0.000 / q_NPA : 0.001
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].
3A263PRO00.0010.0123.837-1.7650.157-0.022-0.898-1.0030.004
4A264SER00.0340.0246.5500.1890.1890.0000.0000.0000.000
5A265LEU00.1090.0479.1070.0000.0000.0000.0000.0000.000
6A266LYS10.9300.96612.7210.0780.0780.0000.0000.0000.000
7A267THR0-0.022-0.0208.0340.0160.0160.0000.0000.0000.000
8A268LEU0-0.014-0.0219.9620.0220.0220.0000.0000.0000.000
9A269GLN00.0040.01112.4540.0210.0210.0000.0000.0000.000
10A270GLU-1-0.893-0.93613.616-0.039-0.0390.0000.0000.0000.000
11A271LYS10.8520.9237.9780.3180.3180.0000.0000.0000.000
12A272GLY00.0670.04313.9930.0090.0090.0000.0000.0000.000
13A273LEU0-0.111-0.05210.990-0.005-0.0050.0000.0000.0000.000
14A274ILE0-0.021-0.00713.8910.0070.0070.0000.0000.0000.000
15A275LYS10.9230.96316.9310.0620.0620.0000.0000.0000.000
16A276ASP-1-0.918-0.96719.054-0.092-0.0920.0000.0000.0000.000
17A277GLN0-0.0490.00021.6110.0030.0030.0000.0000.0000.000
18A278ILE0-0.012-0.00824.9550.0050.0050.0000.0000.0000.000
19A279PHE0-0.025-0.03725.2150.0040.0040.0000.0000.0000.000
20A280GLY00.0680.05125.318-0.004-0.0040.0000.0000.0000.000
21A281SER0-0.074-0.02826.9000.0010.0010.0000.0000.0000.000
22A282HIS0-0.012-0.04028.8490.0010.0010.0000.0000.0000.000
23A283LEU00.0640.02932.431-0.001-0.0010.0000.0000.0000.000
24A284HIS10.8340.88035.1090.0190.0190.0000.0000.0000.000
25A285LYS10.9791.00627.9230.0360.0360.0000.0000.0000.000
26A286VAL00.0040.00730.715-0.001-0.0010.0000.0000.0000.000
27A287CYS0-0.049-0.01733.0580.0000.0000.0000.0000.0000.000
28A288GLU-1-0.896-0.94135.283-0.019-0.0190.0000.0000.0000.000
29A289ARG10.8100.91027.2460.0420.0420.0000.0000.0000.000
30A290GLU-1-0.857-0.93133.972-0.030-0.0300.0000.0000.0000.000
31A291ASN0-0.0350.00236.0460.0010.0010.0000.0000.0000.000
32A292SER0-0.057-0.02337.9170.0010.0010.0000.0000.0000.000
33A293THR0-0.046-0.08040.5490.0000.0000.0000.0000.0000.000
34A294VAL00.010-0.02239.9700.0000.0000.0000.0000.0000.000
35A295PRO00.0160.01434.8070.0000.0000.0000.0000.0000.000
36A296TRP00.0600.01435.0570.0010.0010.0000.0000.0000.000
37A297PHE00.0230.01431.2790.0000.0000.0000.0000.0000.000
38A298VAL00.0180.00134.4150.0010.0010.0000.0000.0000.000
39A299LYS10.9150.95837.1050.0220.0220.0000.0000.0000.000
40A300GLN00.0400.02033.9910.0000.0000.0000.0000.0000.000
41A301CYS0-0.040-0.00534.6360.0000.0000.0000.0000.0000.000
42A302ILE0-0.016-0.00437.3820.0010.0010.0000.0000.0000.000
43A303GLU-1-0.937-0.96340.563-0.021-0.0210.0000.0000.0000.000
44A304ALA00.0170.00738.3190.0010.0010.0000.0000.0000.000
45A305VAL0-0.029-0.02039.1300.0010.0010.0000.0000.0000.000
46A306GLU-1-0.867-0.94341.618-0.015-0.0150.0000.0000.0000.000
47A307LYS10.8350.92441.8140.0210.0210.0000.0000.0000.000
48A308ARG10.8440.91936.3140.0230.0230.0000.0000.0000.000
49A309GLY00.0240.00042.5570.0000.0000.0000.0000.0000.000
50A310LEU0-0.049-0.02043.3560.0000.0000.0000.0000.0000.000
51A311ASP-1-0.856-0.93946.705-0.013-0.0130.0000.0000.0000.000
52A312VAL00.0050.02041.5340.0000.0000.0000.0000.0000.000
53A313ASP-1-0.853-0.93644.970-0.013-0.0130.0000.0000.0000.000
54A314GLY0-0.060-0.04243.131-0.001-0.0010.0000.0000.0000.000
55A315ILE00.0220.03640.399-0.001-0.0010.0000.0000.0000.000
56A316TYR00.024-0.04038.8270.0000.0000.0000.0000.0000.000
57A317ARG10.8780.96139.0610.0130.0130.0000.0000.0000.000
58A318VAL0-0.0030.00037.2060.0000.0000.0000.0000.0000.000
59A319SER0-0.062-0.02332.823-0.001-0.0010.0000.0000.0000.000
60A320GLY00.0950.04732.6360.0010.0010.0000.0000.0000.000
61A321ASN00.0360.00926.938-0.002-0.0020.0000.0000.0000.000
62A322LEU00.0630.02925.251-0.002-0.0020.0000.0000.0000.000
63A323ALA00.0160.00422.865-0.003-0.0030.0000.0000.0000.000
64A324THR0-0.024-0.01323.733-0.002-0.0020.0000.0000.0000.000
65A325ILE00.0120.00826.361-0.002-0.0020.0000.0000.0000.000
66A326GLN0-0.002-0.00921.740-0.004-0.0040.0000.0000.0000.000
67A327LYS10.9450.97821.6610.0280.0280.0000.0000.0000.000
68A328LEU00.0220.02223.370-0.003-0.0030.0000.0000.0000.000
69A329ARG10.8200.88920.9260.0620.0620.0000.0000.0000.000
70A330PHE0-0.043-0.01617.230-0.002-0.0020.0000.0000.0000.000
71A331ILE00.0570.02422.418-0.003-0.0030.0000.0000.0000.000
72A332VAL0-0.0100.00024.3850.0000.0000.0000.0000.0000.000
73A333ASN00.0240.01422.1660.0060.0060.0000.0000.0000.000
74A334GLN0-0.056-0.03317.882-0.002-0.0020.0000.0000.0000.000
75A335GLU-1-0.860-0.94322.588-0.049-0.0490.0000.0000.0000.000
76A336GLU-1-0.918-0.94322.515-0.063-0.0630.0000.0000.0000.000
77A337LYS10.9250.95526.3840.0430.0430.0000.0000.0000.000
78A338LEU00.0270.01429.289-0.001-0.0010.0000.0000.0000.000
79A339ASN00.0460.02531.1130.0030.0030.0000.0000.0000.000
80A340LEU0-0.003-0.01732.9290.0000.0000.0000.0000.0000.000
81A341ASP-1-0.826-0.90035.237-0.021-0.0210.0000.0000.0000.000
82A342ASP-1-0.932-0.95031.825-0.031-0.0310.0000.0000.0000.000
83A343SER00.0290.00433.5280.0000.0000.0000.0000.0000.000
84A344GLN0-0.048-0.02426.1810.0000.0000.0000.0000.0000.000
85A345TRP0-0.061-0.04126.6360.0000.0000.0000.0000.0000.000
86A346GLU-1-0.888-0.94432.853-0.020-0.0200.0000.0000.0000.000
87A347ASP-1-0.870-0.92833.769-0.019-0.0190.0000.0000.0000.000
88A348ILE00.0410.00934.879-0.001-0.0010.0000.0000.0000.000
89A349HIS00.025-0.00235.561-0.001-0.0010.0000.0000.0000.000
90A350VAL0-0.034-0.01929.829-0.001-0.0010.0000.0000.0000.000
91A351VAL00.0190.02032.023-0.002-0.0020.0000.0000.0000.000
92A352THR00.0020.00534.354-0.001-0.0010.0000.0000.0000.000
93A353GLY0-0.014-0.01732.4690.0000.0000.0000.0000.0000.000
94A354ALA00.0210.01230.164-0.001-0.0010.0000.0000.0000.000
95A355LEU00.0180.01031.197-0.001-0.0010.0000.0000.0000.000
96A356LYS10.8470.89634.1840.0210.0210.0000.0000.0000.000
97A357MET0-0.028-0.00426.226-0.001-0.0010.0000.0000.0000.000
98A358PHE00.0250.02230.119-0.001-0.0010.0000.0000.0000.000
99A359PHE00.007-0.01631.3330.0000.0000.0000.0000.0000.000
100A360ARG10.8880.93531.3140.0250.0250.0000.0000.0000.000
101A361GLU-1-0.798-0.87824.583-0.053-0.0530.0000.0000.0000.000
102A362LEU0-0.0280.01328.924-0.001-0.0010.0000.0000.0000.000
103A363PRO00.0050.00829.5530.0010.0010.0000.0000.0000.000
104A364GLU-1-0.910-0.94931.009-0.017-0.0170.0000.0000.0000.000
105A365PRO0-0.0070.00734.804-0.001-0.0010.0000.0000.0000.000
106A366LEU0-0.014-0.00336.8440.0010.0010.0000.0000.0000.000
107A367PHE0-0.006-0.00639.2370.0010.0010.0000.0000.0000.000
108A368PRO0-0.0090.00540.1620.0000.0000.0000.0000.0000.000
109A369TYR00.1390.05034.2950.0010.0010.0000.0000.0000.000
110A370SER0-0.026-0.01241.2880.0010.0010.0000.0000.0000.000
111A371PHE0-0.018-0.02144.0170.0010.0010.0000.0000.0000.000
112A372PHE00.0230.01943.6560.0010.0010.0000.0000.0000.000
113A373GLU-1-0.872-0.93945.757-0.009-0.0090.0000.0000.0000.000
114A374GLN00.0310.00348.7230.0010.0010.0000.0000.0000.000
115A375PHE00.028-0.00546.4250.0000.0000.0000.0000.0000.000
116A376VAL0-0.0090.00148.1180.0000.0000.0000.0000.0000.000
117A377GLU-1-0.960-0.98150.759-0.007-0.0070.0000.0000.0000.000
118A378ALA0-0.062-0.02452.9830.0000.0000.0000.0000.0000.000
119A379ILE00.005-0.01350.6740.0000.0000.0000.0000.0000.000
120A380LYS10.8830.95152.6740.0080.0080.0000.0000.0000.000
121A381LYS10.8920.97356.4480.0080.0080.0000.0000.0000.000
122A382GLN00.0700.02159.4650.0000.0000.0000.0000.0000.000
123A383ASP-1-0.833-0.89962.766-0.007-0.0070.0000.0000.0000.000
124A384ASN00.017-0.01558.6510.0000.0000.0000.0000.0000.000
125A385ASN00.0540.02159.932-0.001-0.0010.0000.0000.0000.000
126A386THR0-0.009-0.00260.5830.0000.0000.0000.0000.0000.000
127A387ARG10.8160.92156.6390.0080.0080.0000.0000.0000.000
128A388ILE0-0.019-0.00156.5710.0000.0000.0000.0000.0000.000
129A389GLU-1-0.907-0.95356.695-0.009-0.0090.0000.0000.0000.000
130A390ALA0-0.024-0.00256.3590.0000.0000.0000.0000.0000.000
131A391VAL00.0380.00551.4380.0000.0000.0000.0000.0000.000
132A392LYS10.9580.98952.3840.0090.0090.0000.0000.0000.000
133A393SER0-0.032-0.02553.9580.0000.0000.0000.0000.0000.000
134A394LEU0-0.067-0.03050.1340.0000.0000.0000.0000.0000.000
135A395VAL00.0490.02448.8310.0000.0000.0000.0000.0000.000
136A396GLN0-0.031-0.03049.4490.0000.0000.0000.0000.0000.000
137A397LYS10.9100.96950.3930.0090.0090.0000.0000.0000.000
138A398LEU0-0.0430.01144.3360.0000.0000.0000.0000.0000.000
139A399PRO00.0040.00242.1750.0000.0000.0000.0000.0000.000
140A400PRO00.0580.01544.3270.0000.0000.0000.0000.0000.000
141A401PRO00.0520.02339.7850.0000.0000.0000.0000.0000.000
142A402ASN00.0170.02239.682-0.001-0.0010.0000.0000.0000.000
143A403ARG10.9490.98142.3770.0130.0130.0000.0000.0000.000
144A404ASP-1-0.831-0.87644.175-0.015-0.0150.0000.0000.0000.000
145A405THR0-0.006-0.02239.006-0.001-0.0010.0000.0000.0000.000
146A406MET0-0.058-0.01442.4070.0000.0000.0000.0000.0000.000
147A407LYS10.9480.99244.5390.0130.0130.0000.0000.0000.000
148A408VAL00.0110.00642.8750.0000.0000.0000.0000.0000.000
149A409LEU00.0140.01040.4750.0000.0000.0000.0000.0000.000
150A410PHE00.023-0.01243.6800.0000.0000.0000.0000.0000.000
151A411GLY00.0300.01846.8590.0010.0010.0000.0000.0000.000
152A412HIS00.0090.02142.9320.0000.0000.0000.0000.0000.000
153A413LEU00.001-0.00642.8930.0000.0000.0000.0000.0000.000
154A414THR0-0.038-0.03246.8140.0010.0010.0000.0000.0000.000
155A415LYS10.8930.94648.6280.0150.0150.0000.0000.0000.000
156A416ILE0-0.0240.00644.8940.0000.0000.0000.0000.0000.000
157A417VAL00.0140.01948.2970.0000.0000.0000.0000.0000.000
158A418ALA00.0110.01051.1410.0000.0000.0000.0000.0000.000
159A419LYS10.8310.91450.2770.0130.0130.0000.0000.0000.000
160A420ALA00.0790.05651.0120.0000.0000.0000.0000.0000.000
161A421SER0-0.082-0.04752.0200.0000.0000.0000.0000.0000.000
162A422LYS10.8740.94750.6680.0110.0110.0000.0000.0000.000
163A423ASN00.0510.01846.5800.0000.0000.0000.0000.0000.000
164A424LEU0-0.0040.00947.1910.0000.0000.0000.0000.0000.000
165A425MET0-0.085-0.02043.4260.0000.0000.0000.0000.0000.000
166A426SER00.0380.00648.2670.0000.0000.0000.0000.0000.000
167A427THR00.0480.00448.757-0.001-0.0010.0000.0000.0000.000
168A428GLN00.0140.01548.9750.0000.0000.0000.0000.0000.000
169A429SER0-0.050-0.03345.890-0.001-0.0010.0000.0000.0000.000
170A430LEU00.0280.01143.746-0.001-0.0010.0000.0000.0000.000
171A431GLY00.0520.02744.062-0.001-0.0010.0000.0000.0000.000
172A432ILE0-0.015-0.00942.3630.0000.0000.0000.0000.0000.000
173A433VAL0-0.060-0.01438.893-0.001-0.0010.0000.0000.0000.000
174A434PHE00.003-0.04439.237-0.001-0.0010.0000.0000.0000.000
175A435GLY00.0410.03841.2930.0000.0000.0000.0000.0000.000
176A436PRO00.0200.00038.2500.0000.0000.0000.0000.0000.000
177A437THR0-0.122-0.04835.993-0.001-0.0010.0000.0000.0000.000
178A438LEU0-0.027-0.00836.875-0.001-0.0010.0000.0000.0000.000
179A439LEU0-0.023-0.01339.5410.0000.0000.0000.0000.0000.000
180A440ARG10.8240.94332.5000.0260.0260.0000.0000.0000.000
181A441ALA00.0760.03438.1820.0000.0000.0000.0000.0000.000
182A442GLU-1-0.895-0.95837.375-0.017-0.0170.0000.0000.0000.000
183A443ASN00.007-0.02735.2910.0020.0020.0000.0000.0000.000
184A444GLU-1-0.895-0.91438.755-0.015-0.0150.0000.0000.0000.000
185A445THR00.017-0.00141.0320.0000.0000.0000.0000.0000.000
186A446GLY0-0.008-0.00243.0560.0000.0000.0000.0000.0000.000
187A447ASN0-0.004-0.00944.803-0.001-0.0010.0000.0000.0000.000
188A448MET00.0970.05539.1420.0000.0000.0000.0000.0000.000
189A449ALA00.0440.00544.0760.0000.0000.0000.0000.0000.000
190A450ILE0-0.009-0.00446.5090.0000.0000.0000.0000.0000.000
191A451HIS10.8490.93043.1330.0110.0110.0000.0000.0000.000
192A452MET0-0.0020.01542.291-0.001-0.0010.0000.0000.0000.000
193A453VAL00.0060.00744.8230.0000.0000.0000.0000.0000.000
194A454TYR00.009-0.01247.1770.0000.0000.0000.0000.0000.000
195A455GLN00.0350.00940.8460.0000.0000.0000.0000.0000.000
196A456ASN00.0510.01544.589-0.001-0.0010.0000.0000.0000.000
197A457GLN00.0120.01246.8220.0000.0000.0000.0000.0000.000
198A458ILE0-0.0150.00447.3150.0000.0000.0000.0000.0000.000
199A459ALA0-0.019-0.01445.2060.0000.0000.0000.0000.0000.000
200A460GLU-1-0.837-0.92947.285-0.011-0.0110.0000.0000.0000.000
201A461LEU0-0.0170.01150.3180.0000.0000.0000.0000.0000.000
202A462MET0-0.049-0.02547.2480.0000.0000.0000.0000.0000.000
203A463LEU0-0.039-0.00447.6440.0000.0000.0000.0000.0000.000
204A464SER0-0.066-0.05450.6200.0000.0000.0000.0000.0000.000
205A465GLU-1-0.838-0.92754.044-0.009-0.0090.0000.0000.0000.000
206A466TYR0-0.0010.01949.5300.0000.0000.0000.0000.0000.000
207A467SER0-0.006-0.01553.4670.0000.0000.0000.0000.0000.000
208A468LYS10.9380.97756.4590.0090.0090.0000.0000.0000.000
209A469ILE0-0.031-0.00252.0190.0000.0000.0000.0000.0000.000
210A470PHE0-0.016-0.02648.1860.0000.0000.0000.0000.0000.000
211A471GLY0-0.055-0.01553.4590.0000.0000.0000.0000.0000.000