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: K92G3

Calculation Name: 3K66-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K66

Chain ID: A

ChEMBL ID:

UniProt ID: Q10651

Base Structure: X-ray

Registration Date: 2023-06-22

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2437025.436492
FMO2-HF: Nuclear repulsion 2345571.216409
FMO2-HF: Total energy -91454.220083
FMO2-MP2: Total energy -91720.868935


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:234:SER)


Summations of interaction energy for fragment #1(A:234:SER)
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.
1.3534.1880.021-1.654-1.2020.006
Interaction energy analysis for fragmet #1(A:234:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.018
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].
3A236ASP-1-0.752-0.8423.4480.8583.6930.021-1.654-1.2020.006
4A237PRO00.008-0.0055.917-0.272-0.2720.0000.0000.0000.000
5A238TYR0-0.005-0.0367.049-0.176-0.1760.0000.0000.0000.000
6A239PHE00.017-0.0058.126-0.031-0.0310.0000.0000.0000.000
7A240LYS10.8450.9264.9500.0230.0230.0000.0000.0000.000
8A241ILE0-0.0190.01310.1770.0600.0600.0000.0000.0000.000
9A242ALA00.0470.01312.891-0.042-0.0420.0000.0000.0000.000
10A243ASN00.0590.07016.183-0.023-0.0230.0000.0000.0000.000
11A244TRP0-0.007-0.01115.481-0.018-0.0180.0000.0000.0000.000
12A245THR00.048-0.01219.162-0.016-0.0160.0000.0000.0000.000
13A246ASN0-0.038-0.01319.932-0.020-0.0200.0000.0000.0000.000
14A247GLU-1-0.658-0.79017.3550.0130.0130.0000.0000.0000.000
15A248HIS0-0.043-0.02319.084-0.007-0.0070.0000.0000.0000.000
16A249ASP-1-0.782-0.88619.7720.1270.1270.0000.0000.0000.000
17A250ASP-1-0.873-0.95514.8340.2010.2010.0000.0000.0000.000
18A251PHE0-0.0100.00315.2790.0130.0130.0000.0000.0000.000
19A252LYS10.9210.96316.904-0.085-0.0850.0000.0000.0000.000
20A253LYS10.8270.91515.154-0.208-0.2080.0000.0000.0000.000
21A254ALA0-0.016-0.01812.5520.0100.0100.0000.0000.0000.000
22A255GLU-1-0.829-0.90013.852-0.144-0.1440.0000.0000.0000.000
23A256MET0-0.0140.00316.548-0.023-0.0230.0000.0000.0000.000
24A257ARG10.8380.8919.408-0.339-0.3390.0000.0000.0000.000
25A258MET0-0.037-0.00112.999-0.080-0.0800.0000.0000.0000.000
26A259ASP-1-0.837-0.91513.843-0.183-0.1830.0000.0000.0000.000
27A260GLU-1-0.892-0.94715.398-0.036-0.0360.0000.0000.0000.000
28A261LYS10.9500.9767.7031.2171.2170.0000.0000.0000.000
29A262HIS0-0.007-0.01513.996-0.072-0.0720.0000.0000.0000.000
30A263ARG10.9390.94616.3560.0950.0950.0000.0000.0000.000
31A264LYS10.8480.93414.8060.1390.1390.0000.0000.0000.000
32A265LYS10.8160.89112.6060.6830.6830.0000.0000.0000.000
33A266VAL00.0120.00517.5070.0140.0140.0000.0000.0000.000
34A267ASP-1-0.877-0.92820.920-0.119-0.1190.0000.0000.0000.000
35A268LYS10.8420.90818.4380.2800.2800.0000.0000.0000.000
36A269VAL0-0.018-0.01220.3890.0100.0100.0000.0000.0000.000
37A270MET00.0310.01222.8760.0160.0160.0000.0000.0000.000
38A271LYS10.8610.91924.4070.1090.1090.0000.0000.0000.000
39A272GLU-1-0.784-0.86821.979-0.216-0.2160.0000.0000.0000.000
40A273TRP0-0.043-0.02526.1810.0110.0110.0000.0000.0000.000
41A274GLY00.0790.04428.8240.0090.0090.0000.0000.0000.000
42A275ASP-1-0.837-0.88228.415-0.089-0.0890.0000.0000.0000.000
43A276LEU0-0.063-0.04327.9790.0060.0060.0000.0000.0000.000
44A277GLU-1-0.772-0.87931.727-0.077-0.0770.0000.0000.0000.000
45A278THR0-0.028-0.02434.0980.0080.0080.0000.0000.0000.000
46A279ARG10.8080.88034.6570.0740.0740.0000.0000.0000.000
47A280TYR0-0.058-0.05436.4500.0040.0040.0000.0000.0000.000
48A281ASN0-0.035-0.03738.1000.0080.0080.0000.0000.0000.000
49A282GLU-1-0.821-0.86838.241-0.055-0.0550.0000.0000.0000.000
50A283GLN0-0.007-0.01239.9120.0050.0050.0000.0000.0000.000
51A284LYS10.9120.97342.1030.0600.0600.0000.0000.0000.000
52A285ALA00.0330.00943.8660.0000.0000.0000.0000.0000.000
53A286LYS10.8770.95042.3220.0530.0530.0000.0000.0000.000
54A287ASP-1-0.835-0.93242.873-0.059-0.0590.0000.0000.0000.000
55A288PRO00.0300.03544.202-0.004-0.0040.0000.0000.0000.000
56A289LYS10.9500.97344.7350.0500.0500.0000.0000.0000.000
57A290GLY00.0090.00542.191-0.003-0.0030.0000.0000.0000.000
58A291ALA0-0.032-0.03440.233-0.005-0.0050.0000.0000.0000.000
59A292GLU-1-0.818-0.89639.565-0.075-0.0750.0000.0000.0000.000
60A293LYS10.9010.96639.2040.0690.0690.0000.0000.0000.000
61A294PHE00.0060.00533.149-0.007-0.0070.0000.0000.0000.000
62A295LYS10.8830.93835.1640.0740.0740.0000.0000.0000.000
63A296SER00.0060.00435.323-0.006-0.0060.0000.0000.0000.000
64A297GLN0-0.048-0.03633.328-0.002-0.0020.0000.0000.0000.000
65A298MET00.011-0.00430.305-0.015-0.0150.0000.0000.0000.000
66A299ASN0-0.0040.02230.441-0.012-0.0120.0000.0000.0000.000
67A300ALA00.0650.04530.497-0.011-0.0110.0000.0000.0000.000
68A301ARG10.7920.88423.6910.1810.1810.0000.0000.0000.000
69A302PHE00.0320.01326.324-0.020-0.0200.0000.0000.0000.000
70A303GLN00.015-0.00826.605-0.010-0.0100.0000.0000.0000.000
71A304LYS10.9600.97425.3440.1630.1630.0000.0000.0000.000
72A305THR0-0.023-0.01921.190-0.013-0.0130.0000.0000.0000.000
73A306VAL00.0070.00721.986-0.027-0.0270.0000.0000.0000.000
74A307SER00.0530.02322.656-0.016-0.0160.0000.0000.0000.000
75A308SER0-0.0200.00419.339-0.026-0.0260.0000.0000.0000.000
76A309LEU00.001-0.01517.243-0.041-0.0410.0000.0000.0000.000
77A310GLU-1-0.895-0.93618.974-0.230-0.2300.0000.0000.0000.000
78A311GLU-1-0.944-0.96820.036-0.291-0.2910.0000.0000.0000.000
79A312GLU-1-0.810-0.87813.622-0.747-0.7470.0000.0000.0000.000
80A313HIS0-0.002-0.00316.209-0.011-0.0110.0000.0000.0000.000
81A314LYS10.8870.92617.5620.2620.2620.0000.0000.0000.000
82A315ARG10.7910.86112.1120.7710.7710.0000.0000.0000.000
83A316MET0-0.087-0.07010.454-0.007-0.0070.0000.0000.0000.000
84A317ARG10.8090.90014.9370.1820.1820.0000.0000.0000.000
85A318LYS10.8960.93317.7750.2300.2300.0000.0000.0000.000
86A319GLU-1-0.850-0.87211.941-0.818-0.8180.0000.0000.0000.000
87A320ILE0-0.020-0.02113.3700.0380.0380.0000.0000.0000.000
88A321GLU-1-0.852-0.92215.671-0.117-0.1170.0000.0000.0000.000
89A322ALA0-0.023-0.00218.4600.0320.0320.0000.0000.0000.000
90A323VAL00.0270.01514.1760.0230.0230.0000.0000.0000.000
91A324HIS10.8600.94417.4080.0850.0850.0000.0000.0000.000
92A325GLU-1-0.896-0.96819.010-0.052-0.0520.0000.0000.0000.000
93A326GLU-1-0.933-0.96318.716-0.054-0.0540.0000.0000.0000.000
94A327ARG10.8660.92512.7760.0170.0170.0000.0000.0000.000
95A328VAL0-0.029-0.01020.7680.0150.0150.0000.0000.0000.000
96A329GLN00.0400.02923.6380.0010.0010.0000.0000.0000.000
97A330ALA00.0250.03522.9040.0060.0060.0000.0000.0000.000
98A331MET00.003-0.00522.5310.0050.0050.0000.0000.0000.000
99A332LEU0-0.079-0.04325.3840.0050.0050.0000.0000.0000.000
100A333ASN0-0.050-0.05028.2990.0030.0030.0000.0000.0000.000
101A334GLU-1-0.913-0.93426.4040.0410.0410.0000.0000.0000.000
102A335LYS10.9520.98629.310-0.014-0.0140.0000.0000.0000.000
103A336LYS10.7750.87531.4460.0170.0170.0000.0000.0000.000
104A337ARG10.8830.95330.746-0.022-0.0220.0000.0000.0000.000
105A338ASP-1-0.809-0.91831.8010.0280.0280.0000.0000.0000.000
106A339ALA0-0.029-0.01334.3790.0010.0010.0000.0000.0000.000
107A340THR0-0.050-0.04936.684-0.002-0.0020.0000.0000.0000.000
108A341HIS0-0.058-0.01237.296-0.002-0.0020.0000.0000.0000.000
109A342ASP-1-0.841-0.92437.5480.0280.0280.0000.0000.0000.000
110A343TYR0-0.074-0.06340.2520.0000.0000.0000.0000.0000.000
111A344ARG10.9910.96742.314-0.006-0.0060.0000.0000.0000.000
112A345GLN00.0360.04141.0470.0000.0000.0000.0000.0000.000
113A346ALA0-0.022-0.00544.3280.0000.0000.0000.0000.0000.000
114A347LEU00.0350.00746.1830.0000.0000.0000.0000.0000.000
115A348ALA00.0320.02347.6160.0000.0000.0000.0000.0000.000
116A349THR0-0.104-0.08547.2520.0010.0010.0000.0000.0000.000
117A350HIS0-0.045-0.05249.9290.0020.0020.0000.0000.0000.000
118A351VAL0-0.0170.01752.2970.0000.0000.0000.0000.0000.000
119A352ASN0-0.101-0.02252.1560.0000.0000.0000.0000.0000.000
120A353LYS10.9910.99050.819-0.020-0.0200.0000.0000.0000.000
121A354PRO00.026-0.00953.3560.0010.0010.0000.0000.0000.000
122A355ASN00.0070.04546.8880.0020.0020.0000.0000.0000.000
123A356LYS10.9590.96549.747-0.015-0.0150.0000.0000.0000.000
124A357HIS00.0090.00345.760-0.001-0.0010.0000.0000.0000.000
125A358SER00.0240.01544.7980.0010.0010.0000.0000.0000.000
126A359VAL00.0410.02245.2120.0000.0000.0000.0000.0000.000
127A360LEU00.0290.01845.648-0.001-0.0010.0000.0000.0000.000
128A361GLN0-0.017-0.01441.749-0.002-0.0020.0000.0000.0000.000
129A362SER00.0280.01841.3720.0010.0010.0000.0000.0000.000
130A363LEU00.0030.01241.054-0.001-0.0010.0000.0000.0000.000
131A364LYS10.9130.96041.817-0.015-0.0150.0000.0000.0000.000
132A365ALA0-0.0110.01037.455-0.001-0.0010.0000.0000.0000.000
133A366TYR00.010-0.02537.325-0.001-0.0010.0000.0000.0000.000
134A367ILE00.002-0.00638.062-0.002-0.0020.0000.0000.0000.000
135A368ARG10.8990.95336.207-0.019-0.0190.0000.0000.0000.000
136A369ALA0-0.075-0.04433.880-0.002-0.0020.0000.0000.0000.000
137A370GLU-1-0.645-0.77134.031-0.016-0.0160.0000.0000.0000.000
138A371GLU-1-0.724-0.84135.749-0.017-0.0170.0000.0000.0000.000
139A372LYS10.8800.93127.864-0.008-0.0080.0000.0000.0000.000
140A373ASP-1-0.814-0.90031.327-0.032-0.0320.0000.0000.0000.000
141A374ARG10.8870.96432.6830.0140.0140.0000.0000.0000.000
142A375MET0-0.0050.01130.570-0.003-0.0030.0000.0000.0000.000
143A376HIS00.0370.02326.7060.0040.0040.0000.0000.0000.000
144A377THR0-0.019-0.00430.389-0.010-0.0100.0000.0000.0000.000
145A378LEU00.0130.00132.007-0.007-0.0070.0000.0000.0000.000
146A379ASN00.0260.00230.518-0.005-0.0050.0000.0000.0000.000
147A380ARG10.8790.94924.3550.0980.0980.0000.0000.0000.000
148A381TYR00.013-0.00729.713-0.006-0.0060.0000.0000.0000.000
149A382ARG10.8660.92932.8830.0450.0450.0000.0000.0000.000
150A383HIS00.0320.00627.326-0.005-0.0050.0000.0000.0000.000
151A384LEU0-0.010-0.01027.169-0.006-0.0060.0000.0000.0000.000
152A385LEU0-0.020-0.01230.394-0.004-0.0040.0000.0000.0000.000
153A386LYS10.7790.87932.2790.0620.0620.0000.0000.0000.000
154A387ALA0-0.0330.00427.591-0.003-0.0030.0000.0000.0000.000
155A388ASP-1-0.830-0.91527.796-0.152-0.1520.0000.0000.0000.000
156A389SER00.0090.00030.8790.0060.0060.0000.0000.0000.000
157A390LYS10.8640.92630.4030.1330.1330.0000.0000.0000.000
158A391GLU-1-0.779-0.89226.722-0.160-0.1600.0000.0000.0000.000
159A392ALA00.0140.02131.2010.0040.0040.0000.0000.0000.000
160A393ALA00.0280.00033.4310.0070.0070.0000.0000.0000.000
161A394ALA0-0.069-0.02132.5300.0050.0050.0000.0000.0000.000
162A395TYR00.008-0.00630.803-0.002-0.0020.0000.0000.0000.000
163A396LYS10.9760.99733.7270.0560.0560.0000.0000.0000.000
164A397PRO00.0210.01436.8360.0050.0050.0000.0000.0000.000
165A398THR00.0330.00132.4400.0050.0050.0000.0000.0000.000
166A399VAL0-0.0190.00234.0330.0050.0050.0000.0000.0000.000
167A400ILE00.000-0.01136.0920.0050.0050.0000.0000.0000.000
168A401HIS0-0.022-0.00437.4850.0030.0030.0000.0000.0000.000
169A402ARG10.9110.92728.6270.0570.0570.0000.0000.0000.000
170A403LEU0-0.003-0.00636.7240.0040.0040.0000.0000.0000.000
171A404ARG10.9721.00039.0600.0360.0360.0000.0000.0000.000
172A405TYR00.013-0.00438.8340.0030.0030.0000.0000.0000.000
173A406ILE0-0.0370.01035.2810.0030.0030.0000.0000.0000.000
174A407ASP-1-0.738-0.84939.411-0.014-0.0140.0000.0000.0000.000
175A408LEU0-0.039-0.00943.0180.0020.0020.0000.0000.0000.000
176A409ARG10.8340.88936.3220.0210.0210.0000.0000.0000.000
177A410ILE00.0290.03339.9710.0030.0030.0000.0000.0000.000
178A411ASN0-0.036-0.03543.1680.0030.0030.0000.0000.0000.000
179A412GLY00.0050.00445.8140.0010.0010.0000.0000.0000.000
180A413THR0-0.025-0.03842.6370.0020.0020.0000.0000.0000.000
181A414LEU0-0.019-0.00745.2300.0020.0020.0000.0000.0000.000
182A415ALA0-0.015-0.00948.1880.0010.0010.0000.0000.0000.000
183A416MET0-0.060-0.00944.0070.0020.0020.0000.0000.0000.000
184A417LEU0-0.013-0.01248.6390.0010.0010.0000.0000.0000.000
185A418ARG10.9250.97351.9720.0050.0050.0000.0000.0000.000
186A419ASP-1-0.889-0.92954.1130.0010.0010.0000.0000.0000.000
187A420PHE0-0.036-0.01351.6520.0010.0010.0000.0000.0000.000
188A421PRO00.0540.04656.0210.0000.0000.0000.0000.0000.000
189A422ASP-1-0.854-0.93757.3470.0080.0080.0000.0000.0000.000
190A423LEU00.007-0.01451.3640.0000.0000.0000.0000.0000.000
191A424GLU-1-0.944-0.98853.8940.0000.0000.0000.0000.0000.000
192A425LYS10.9070.95755.280-0.005-0.0050.0000.0000.0000.000
193A426TYR0-0.004-0.01656.3100.0000.0000.0000.0000.0000.000
194A427VAL00.0020.00349.8070.0000.0000.0000.0000.0000.000
195A428ARG11.0021.00751.2100.0020.0020.0000.0000.0000.000
196A429PRO00.0140.01551.318-0.001-0.0010.0000.0000.0000.000
197A430ILE00.0050.01049.4120.0000.0000.0000.0000.0000.000
198A431ALA00.000-0.00646.8970.0000.0000.0000.0000.0000.000
199A432VAL0-0.005-0.00846.978-0.001-0.0010.0000.0000.0000.000
200A433THR00.0150.00948.293-0.001-0.0010.0000.0000.0000.000
201A434TYR00.0330.03640.7240.0010.0010.0000.0000.0000.000
202A435TRP0-0.069-0.02841.9010.0000.0000.0000.0000.0000.000
203A436LYS10.8390.91244.0940.0050.0050.0000.0000.0000.000
204A437ASP-1-0.869-0.95545.5010.0000.0000.0000.0000.0000.000
205A438TYR0-0.039-0.03636.1870.0000.0000.0000.0000.0000.000
206A439ARG10.7180.80140.6610.0140.0140.0000.0000.0000.000
207A440ASP-1-0.832-0.90141.229-0.009-0.0090.0000.0000.0000.000
208A441GLU-1-0.979-0.98440.3220.0060.0060.0000.0000.0000.000
209A442VAL0-0.052-0.03035.175-0.001-0.0010.0000.0000.0000.000
210A443SER0-0.109-0.06036.611-0.003-0.0030.0000.0000.0000.000
211A444PRO00.0410.01238.513-0.001-0.0010.0000.0000.0000.000
212A445ASP-1-0.946-0.96041.796-0.022-0.0220.0000.0000.0000.000
213A446ILE0-0.035-0.01639.704-0.003-0.0030.0000.0000.0000.000
214A447SER00.0500.01743.1980.0000.0000.0000.0000.0000.000
215A448VAL0-0.050-0.01741.482-0.001-0.0010.0000.0000.0000.000
216A449GLU-1-0.761-0.84938.934-0.053-0.0530.0000.0000.0000.000
217A450ASP-1-0.955-0.97042.169-0.042-0.0420.0000.0000.0000.000