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

tag_button

FMODB ID: KG9J3

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2564450.718662
FMO2-HF: Nuclear repulsion 2479491.16237
FMO2-HF: Total energy -84959.556291
FMO2-MP2: Total energy -85206.487214


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.
-0.2561.189-0.007-0.612-0.8260.003
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 : 0.014 / q_NPA : -0.005
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].
3A263PRO00.0180.0193.861-1.2080.237-0.007-0.612-0.8260.003
4A264SER00.0420.0276.3840.4050.4050.0000.0000.0000.000
5A265LEU00.0680.0298.775-0.105-0.1050.0000.0000.0000.000
6A266LYS10.9130.94712.3920.0050.0050.0000.0000.0000.000
7A267THR0-0.024-0.0258.033-0.050-0.0500.0000.0000.0000.000
8A268LEU0-0.031-0.02410.022-0.081-0.0810.0000.0000.0000.000
9A269GLN0-0.016-0.00512.7160.0050.0050.0000.0000.0000.000
10A270GLU-1-0.847-0.90513.990-0.115-0.1150.0000.0000.0000.000
11A271LYS10.8720.9428.5110.9420.9420.0000.0000.0000.000
12A272GLY00.0460.02714.456-0.018-0.0180.0000.0000.0000.000
13A273LEU0-0.070-0.03511.400-0.013-0.0130.0000.0000.0000.000
14A274ILE0-0.022-0.00914.1970.0250.0250.0000.0000.0000.000
15A275LYS10.8470.89817.3140.1320.1320.0000.0000.0000.000
16A276ASP-1-0.825-0.91618.820-0.003-0.0030.0000.0000.0000.000
17A277GLN0-0.052-0.00821.7020.0030.0030.0000.0000.0000.000
18A278ILE0-0.021-0.00625.1510.0050.0050.0000.0000.0000.000
19A279PHE00.013-0.01225.4310.0070.0070.0000.0000.0000.000
20A280GLY00.0720.04925.158-0.002-0.0020.0000.0000.0000.000
21A281SER0-0.047-0.02026.2430.0000.0000.0000.0000.0000.000
22A282HIS0-0.010-0.03328.468-0.002-0.0020.0000.0000.0000.000
23A283LEU00.0750.03732.058-0.005-0.0050.0000.0000.0000.000
24A284HIS10.8500.90534.767-0.005-0.0050.0000.0000.0000.000
25A285LYS10.9590.98727.3480.0140.0140.0000.0000.0000.000
26A286VAL0-0.0150.00530.908-0.005-0.0050.0000.0000.0000.000
27A287CYS0-0.045-0.01233.210-0.003-0.0030.0000.0000.0000.000
28A288GLU-1-0.891-0.93935.158-0.024-0.0240.0000.0000.0000.000
29A289ARG10.8080.88327.3460.0690.0690.0000.0000.0000.000
30A290GLU-1-0.846-0.88934.162-0.032-0.0320.0000.0000.0000.000
31A291ASN0-0.040-0.00736.374-0.001-0.0010.0000.0000.0000.000
32A292SER0-0.059-0.04838.2950.0020.0020.0000.0000.0000.000
33A293THR0-0.032-0.05240.7370.0010.0010.0000.0000.0000.000
34A294VAL00.045-0.00240.1370.0030.0030.0000.0000.0000.000
35A295PRO00.0430.02234.747-0.003-0.0030.0000.0000.0000.000
36A296TRP00.017-0.02835.1460.0040.0040.0000.0000.0000.000
37A297PHE00.0380.02431.6070.0010.0010.0000.0000.0000.000
38A298VAL00.0220.00634.3010.0030.0030.0000.0000.0000.000
39A299LYS10.8420.94037.0700.0250.0250.0000.0000.0000.000
40A300GLN00.0390.02334.4270.0010.0010.0000.0000.0000.000
41A301CYS0-0.044-0.01934.8270.0020.0020.0000.0000.0000.000
42A302ILE0-0.037-0.01737.4410.0020.0020.0000.0000.0000.000
43A303GLU-1-0.908-0.95340.308-0.024-0.0240.0000.0000.0000.000
44A304ALA00.009-0.00238.5250.0000.0000.0000.0000.0000.000
45A305VAL0-0.016-0.01039.6850.0020.0020.0000.0000.0000.000
46A306GLU-1-0.803-0.89742.139-0.005-0.0050.0000.0000.0000.000
47A307LYS10.8130.90141.3740.0250.0250.0000.0000.0000.000
48A308ARG10.7680.87236.5810.0120.0120.0000.0000.0000.000
49A309GLY00.0270.00942.9060.0020.0020.0000.0000.0000.000
50A310LEU0-0.037-0.01143.6440.0030.0030.0000.0000.0000.000
51A311ASP-1-0.805-0.90147.0360.0020.0020.0000.0000.0000.000
52A312VAL00.0040.01242.1240.0010.0010.0000.0000.0000.000
53A313ASP-1-0.872-0.94344.9560.0150.0150.0000.0000.0000.000
54A314GLY0-0.035-0.03043.4460.0020.0020.0000.0000.0000.000
55A315ILE00.0090.01840.7560.0030.0030.0000.0000.0000.000
56A316TYR00.017-0.02638.8510.0010.0010.0000.0000.0000.000
57A317ARG10.8390.92539.289-0.020-0.0200.0000.0000.0000.000
58A318VAL0-0.0050.00637.9310.0050.0050.0000.0000.0000.000
59A319SER0-0.040-0.03933.533-0.002-0.0020.0000.0000.0000.000
60A320GLY00.0760.04633.3660.0020.0020.0000.0000.0000.000
61A321ASN0-0.0010.00227.4780.0070.0070.0000.0000.0000.000
62A322LEU00.0740.03425.631-0.005-0.0050.0000.0000.0000.000
63A323ALA00.0090.00623.1690.0010.0010.0000.0000.0000.000
64A324THR0-0.017-0.02424.060-0.011-0.0110.0000.0000.0000.000
65A325ILE0-0.0090.00326.630-0.009-0.0090.0000.0000.0000.000
66A326GLN00.0180.00322.010-0.015-0.0150.0000.0000.0000.000
67A327LYS10.8780.94822.523-0.004-0.0040.0000.0000.0000.000
68A328LEU00.0190.01823.853-0.014-0.0140.0000.0000.0000.000
69A329ARG10.7690.86220.921-0.030-0.0300.0000.0000.0000.000
70A330PHE0-0.030-0.01317.241-0.007-0.0070.0000.0000.0000.000
71A331ILE00.0480.01522.454-0.012-0.0120.0000.0000.0000.000
72A332VAL00.0050.00424.751-0.009-0.0090.0000.0000.0000.000
73A333ASN0-0.036-0.01222.377-0.006-0.0060.0000.0000.0000.000
74A334GLN00.0270.01018.0720.0020.0020.0000.0000.0000.000
75A335GLU-1-0.849-0.88823.011-0.103-0.1030.0000.0000.0000.000
76A336GLU-1-0.928-0.95722.558-0.131-0.1310.0000.0000.0000.000
77A337LYS10.9290.95426.6380.1070.1070.0000.0000.0000.000
78A338LEU00.0250.01929.938-0.001-0.0010.0000.0000.0000.000
79A339ASN00.016-0.00931.1470.0050.0050.0000.0000.0000.000
80A340LEU0-0.010-0.00533.3660.0020.0020.0000.0000.0000.000
81A341ASP-1-0.774-0.85735.569-0.022-0.0220.0000.0000.0000.000
82A342ASP-1-0.864-0.91431.656-0.053-0.0530.0000.0000.0000.000
83A343SER00.0320.00433.6290.0040.0040.0000.0000.0000.000
84A344GLN0-0.025-0.00126.3790.0090.0090.0000.0000.0000.000
85A345TRP0-0.044-0.03926.8760.0100.0100.0000.0000.0000.000
86A346GLU-1-0.854-0.91333.154-0.010-0.0100.0000.0000.0000.000
87A347ASP-1-0.806-0.91433.7740.0220.0220.0000.0000.0000.000
88A348ILE00.0670.02335.0950.0010.0010.0000.0000.0000.000
89A349HIS00.0420.01336.2670.0010.0010.0000.0000.0000.000
90A350VAL0-0.053-0.02330.2230.0050.0050.0000.0000.0000.000
91A351VAL00.0060.02032.4930.0010.0010.0000.0000.0000.000
92A352THR00.002-0.00134.5240.0020.0020.0000.0000.0000.000
93A353GLY0-0.004-0.00932.7660.0030.0030.0000.0000.0000.000
94A354ALA00.0140.00230.2520.0040.0040.0000.0000.0000.000
95A355LEU00.0050.00431.2420.0000.0000.0000.0000.0000.000
96A356LYS10.8260.90234.207-0.030-0.0300.0000.0000.0000.000
97A357MET0-0.036-0.00826.3500.0020.0020.0000.0000.0000.000
98A358PHE00.0160.01030.0760.0020.0020.0000.0000.0000.000
99A359PHE00.022-0.00631.0760.0000.0000.0000.0000.0000.000
100A360ARG10.8850.93831.283-0.042-0.0420.0000.0000.0000.000
101A361GLU-1-0.804-0.88024.5280.0400.0400.0000.0000.0000.000
102A362LEU0-0.0190.01628.554-0.002-0.0020.0000.0000.0000.000
103A363PRO00.0010.00529.2400.0050.0050.0000.0000.0000.000
104A364GLU-1-0.871-0.92230.9340.0200.0200.0000.0000.0000.000
105A365PRO0-0.0070.01334.787-0.002-0.0020.0000.0000.0000.000
106A366LEU0-0.0060.00536.928-0.003-0.0030.0000.0000.0000.000
107A367PHE00.002-0.01039.205-0.003-0.0030.0000.0000.0000.000
108A368PRO00.0070.00139.9510.0020.0020.0000.0000.0000.000
109A369TYR00.0790.02933.8040.0010.0010.0000.0000.0000.000
110A370SER0-0.023-0.01040.8260.0000.0000.0000.0000.0000.000
111A371PHE0-0.015-0.01443.829-0.001-0.0010.0000.0000.0000.000
112A372PHE00.0310.02643.2220.0000.0000.0000.0000.0000.000
113A373GLU-1-0.801-0.92245.3110.0250.0250.0000.0000.0000.000
114A374GLN0-0.009-0.00548.023-0.002-0.0020.0000.0000.0000.000
115A375PHE00.032-0.00646.387-0.001-0.0010.0000.0000.0000.000
116A376VAL0-0.026-0.00247.7560.0000.0000.0000.0000.0000.000
117A377GLU-1-0.815-0.90550.4780.0160.0160.0000.0000.0000.000
118A378ALA0-0.046-0.01652.682-0.001-0.0010.0000.0000.0000.000
119A379ILE0-0.008-0.01450.685-0.001-0.0010.0000.0000.0000.000
120A380LYS10.8360.92952.039-0.023-0.0230.0000.0000.0000.000
121A381LYS10.7710.89856.170-0.015-0.0150.0000.0000.0000.000
122A382GLN00.0780.02659.3290.0010.0010.0000.0000.0000.000
123A383ASP-1-0.758-0.84862.5070.0100.0100.0000.0000.0000.000
124A384ASN00.0550.02158.0230.0010.0010.0000.0000.0000.000
125A385ASN0-0.033-0.02959.689-0.001-0.0010.0000.0000.0000.000
126A386THR0-0.019-0.03360.6770.0000.0000.0000.0000.0000.000
127A387ARG10.8090.92156.229-0.015-0.0150.0000.0000.0000.000
128A388ILE0-0.0210.00056.2230.0000.0000.0000.0000.0000.000
129A389GLU-1-0.762-0.87456.4160.0040.0040.0000.0000.0000.000
130A390ALA0-0.0100.02156.104-0.001-0.0010.0000.0000.0000.000
131A391VAL00.032-0.00350.9060.0000.0000.0000.0000.0000.000
132A392LYS10.8180.90552.232-0.004-0.0040.0000.0000.0000.000
133A393SER0-0.020-0.02253.694-0.001-0.0010.0000.0000.0000.000
134A394LEU0-0.068-0.01549.993-0.001-0.0010.0000.0000.0000.000
135A395VAL00.0520.00948.761-0.001-0.0010.0000.0000.0000.000
136A396GLN0-0.021-0.01549.516-0.001-0.0010.0000.0000.0000.000
137A397LYS10.8970.95250.380-0.007-0.0070.0000.0000.0000.000
138A398LEU0-0.0330.01444.3440.0000.0000.0000.0000.0000.000
139A399PRO00.0190.00542.245-0.002-0.0020.0000.0000.0000.000
140A400PRO00.0410.01644.3000.0010.0010.0000.0000.0000.000
141A401PRO00.0280.00639.3730.0010.0010.0000.0000.0000.000
142A402ASN0-0.0110.00839.528-0.001-0.0010.0000.0000.0000.000
143A403ARG10.9100.95642.1590.0020.0020.0000.0000.0000.000
144A404ASP-1-0.799-0.89344.302-0.006-0.0060.0000.0000.0000.000
145A405THR00.010-0.00739.017-0.001-0.0010.0000.0000.0000.000
146A406MET0-0.047-0.01142.3740.0010.0010.0000.0000.0000.000
147A407LYS10.8940.94744.4690.0040.0040.0000.0000.0000.000
148A408VAL00.0150.01643.1320.0000.0000.0000.0000.0000.000
149A409LEU00.0090.01440.2040.0000.0000.0000.0000.0000.000
150A410PHE00.018-0.01043.6550.0010.0010.0000.0000.0000.000
151A411GLY00.0390.02346.8140.0000.0000.0000.0000.0000.000
152A412HIS0-0.021-0.01043.4030.0020.0020.0000.0000.0000.000
153A413LEU00.010-0.00343.1490.0000.0000.0000.0000.0000.000
154A414THR0-0.051-0.03646.9490.0010.0010.0000.0000.0000.000
155A415LYS10.8120.89947.8910.0050.0050.0000.0000.0000.000
156A416ILE00.0040.00745.0450.0000.0000.0000.0000.0000.000
157A417VAL00.0160.01348.6700.0010.0010.0000.0000.0000.000
158A418ALA0-0.016-0.00451.5900.0000.0000.0000.0000.0000.000
159A419LYS10.7840.88150.475-0.001-0.0010.0000.0000.0000.000
160A420ALA00.0710.04551.2050.0000.0000.0000.0000.0000.000
161A421SER0-0.054-0.02752.2510.0010.0010.0000.0000.0000.000
162A422LYS10.8440.93751.080-0.005-0.0050.0000.0000.0000.000
163A423ASN00.0410.01746.8680.0030.0030.0000.0000.0000.000
164A424LEU00.0250.02447.4500.0020.0020.0000.0000.0000.000
165A425MET0-0.0380.01044.4730.0030.0030.0000.0000.0000.000
166A426SER00.0310.01548.608-0.001-0.0010.0000.0000.0000.000
167A427THR00.0430.01448.9510.0010.0010.0000.0000.0000.000
168A428GLN00.0330.01949.0160.0010.0010.0000.0000.0000.000
169A429SER0-0.028-0.02646.1520.0020.0020.0000.0000.0000.000
170A430LEU00.0170.00544.1610.0020.0020.0000.0000.0000.000
171A431GLY00.0550.01744.1500.0010.0010.0000.0000.0000.000
172A432ILE0-0.028-0.02042.7570.0020.0020.0000.0000.0000.000
173A433VAL0-0.034-0.00139.3040.0030.0030.0000.0000.0000.000
174A434PHE00.007-0.00639.3840.0020.0020.0000.0000.0000.000
175A435GLY00.0590.03240.844-0.001-0.0010.0000.0000.0000.000
176A436PRO00.0240.00337.932-0.001-0.0010.0000.0000.0000.000
177A437THR0-0.125-0.06335.7330.0030.0030.0000.0000.0000.000
178A438LEU0-0.031-0.00436.696-0.002-0.0020.0000.0000.0000.000
179A439LEU0-0.052-0.02739.341-0.002-0.0020.0000.0000.0000.000
180A440ARG10.8210.92032.434-0.037-0.0370.0000.0000.0000.000
181A441ALA00.0720.03337.7930.0030.0030.0000.0000.0000.000
182A442GLU-1-0.867-0.93937.0140.0470.0470.0000.0000.0000.000
183A443ASN0-0.013-0.02635.9580.0030.0030.0000.0000.0000.000
184A444GLU-1-0.899-0.92638.5220.0400.0400.0000.0000.0000.000
185A445THR00.016-0.00140.8570.0000.0000.0000.0000.0000.000
186A446GLY00.0040.00643.068-0.003-0.0030.0000.0000.0000.000
187A447ASN0-0.001-0.00244.6900.0030.0030.0000.0000.0000.000
188A448MET00.1000.05438.358-0.002-0.0020.0000.0000.0000.000
189A449ALA00.0170.00943.650-0.001-0.0010.0000.0000.0000.000
190A450ILE00.005-0.00346.004-0.002-0.0020.0000.0000.0000.000
191A451HIS10.8330.92042.971-0.039-0.0390.0000.0000.0000.000
192A452MET00.0020.00941.999-0.001-0.0010.0000.0000.0000.000
193A453VAL00.0130.01044.569-0.002-0.0020.0000.0000.0000.000
194A454TYR00.004-0.01647.206-0.002-0.0020.0000.0000.0000.000
195A455GLN00.018-0.00240.410-0.003-0.0030.0000.0000.0000.000
196A456ASN00.0180.00944.607-0.001-0.0010.0000.0000.0000.000
197A457GLN0-0.010-0.01846.786-0.001-0.0010.0000.0000.0000.000
198A458ILE0-0.0200.00047.123-0.002-0.0020.0000.0000.0000.000
199A459ALA0-0.015-0.00245.124-0.002-0.0020.0000.0000.0000.000
200A460GLU-1-0.813-0.91447.1690.0170.0170.0000.0000.0000.000
201A461LEU0-0.0320.01550.334-0.002-0.0020.0000.0000.0000.000
202A462MET0-0.043-0.01847.344-0.002-0.0020.0000.0000.0000.000
203A463LEU0-0.0250.00247.810-0.002-0.0020.0000.0000.0000.000
204A464SER0-0.065-0.06350.467-0.001-0.0010.0000.0000.0000.000
205A465GLU-1-0.770-0.87354.1170.0060.0060.0000.0000.0000.000
206A466TYR0-0.035-0.00949.315-0.001-0.0010.0000.0000.0000.000
207A467SER00.011-0.01653.429-0.001-0.0010.0000.0000.0000.000
208A468LYS10.8140.89056.534-0.007-0.0070.0000.0000.0000.000
209A469ILE0-0.037-0.01351.9250.0000.0000.0000.0000.0000.000
210A470PHE00.004-0.00448.086-0.001-0.0010.0000.0000.0000.000
211A471GLY0-0.0060.02553.491-0.002-0.0020.0000.0000.0000.000