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: QYQYY

Calculation Name: 1KAC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KAC

Chain ID: A

ChEMBL ID:

UniProt ID: P78310

Base Structure: X-ray

Registration Date: 2023-09-20

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1899074.796648
FMO2-HF: Nuclear repulsion 1828625.999742
FMO2-HF: Total energy -70448.796907
FMO2-MP2: Total energy -70653.06431


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:403:THR)


Summations of interaction energy for fragment #1(A:403:THR)
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.
-18.334-10.8256.489-6.206-7.791-0.026
Interaction energy analysis for fragmet #1(A:403:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / 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].
3A405TYR00.000-0.0032.391-6.262-0.4071.221-2.993-4.0820.015
4A406ASP-1-0.805-0.9042.139-16.067-15.1465.055-2.974-3.002-0.041
5A407PRO0-0.027-0.0212.7431.0231.7560.213-0.239-0.7070.000
6A408LEU00.0070.0085.6870.8850.8850.0000.0000.0000.000
7A409THR0-0.005-0.0168.0720.4690.4690.0000.0000.0000.000
8A410LEU0-0.053-0.0079.083-0.076-0.0760.0000.0000.0000.000
9A411TRP0-0.033-0.02011.475-0.020-0.0200.0000.0000.0000.000
10A412THR00.0440.03714.0380.0320.0320.0000.0000.0000.000
11A413THR0-0.092-0.03914.1180.0560.0560.0000.0000.0000.000
12A414PRO0-0.024-0.03915.2710.0410.0410.0000.0000.0000.000
13A415ASP-1-0.916-0.95917.936-0.410-0.4100.0000.0000.0000.000
14A416PRO0-0.0290.01819.3740.0320.0320.0000.0000.0000.000
15A417PRO00.021-0.00720.9880.0160.0160.0000.0000.0000.000
16A418PRO0-0.032-0.03324.246-0.005-0.0050.0000.0000.0000.000
17A419ASN00.0400.02221.0830.0220.0220.0000.0000.0000.000
18A420CYS0-0.0080.00124.6960.0060.0060.0000.0000.0000.000
19A421SER00.0590.04027.286-0.006-0.0060.0000.0000.0000.000
20A422LEU0-0.077-0.02928.8740.0070.0070.0000.0000.0000.000
21A423ILE0-0.043-0.01832.2830.0080.0080.0000.0000.0000.000
22A424GLN0-0.038-0.02434.7950.0080.0080.0000.0000.0000.000
23A425GLU-1-0.911-0.96432.478-0.053-0.0530.0000.0000.0000.000
24A426LEU0-0.081-0.05027.286-0.005-0.0050.0000.0000.0000.000
25A427ASP-1-0.748-0.87530.291-0.105-0.1050.0000.0000.0000.000
26A428ALA00.001-0.01529.251-0.006-0.0060.0000.0000.0000.000
27A429LYS10.9360.99025.1810.2250.2250.0000.0000.0000.000
28A430LEU00.0190.00822.309-0.002-0.0020.0000.0000.0000.000
29A431THR0-0.0120.00319.700-0.016-0.0160.0000.0000.0000.000
30A432LEU0-0.002-0.01718.4140.0140.0140.0000.0000.0000.000
31A433CYS0-0.034-0.01914.834-0.083-0.0830.0000.0000.0000.000
32A434LEU00.0050.00214.7000.0590.0590.0000.0000.0000.000
33A435THR00.0260.01212.478-0.092-0.0920.0000.0000.0000.000
34A436LYS10.8350.92311.6070.4140.4140.0000.0000.0000.000
35A437ASN0-0.0070.00012.346-0.122-0.1220.0000.0000.0000.000
36A438GLY00.0350.01814.1980.0700.0700.0000.0000.0000.000
37A439SER0-0.009-0.02316.0970.0030.0030.0000.0000.0000.000
38A440ILE00.0110.02118.2240.0330.0330.0000.0000.0000.000
39A441VAL0-0.0170.01815.856-0.054-0.0540.0000.0000.0000.000
40A442ASN0-0.035-0.01616.6580.1010.1010.0000.0000.0000.000
41A443GLY00.031-0.00117.323-0.064-0.0640.0000.0000.0000.000
42A444ILE0-0.017-0.02019.4380.0320.0320.0000.0000.0000.000
43A445VAL00.004-0.00120.526-0.024-0.0240.0000.0000.0000.000
44A446SER0-0.0110.00323.0440.0160.0160.0000.0000.0000.000
45A447LEU00.0200.01624.934-0.003-0.0030.0000.0000.0000.000
46A448VAL0-0.0040.00127.6320.0060.0060.0000.0000.0000.000
47A449GLY00.0160.00529.9030.0020.0020.0000.0000.0000.000
48A450VAL0-0.049-0.03929.805-0.005-0.0050.0000.0000.0000.000
49A451LYS10.9520.97432.9660.0880.0880.0000.0000.0000.000
50A452GLY00.0350.01035.5920.0010.0010.0000.0000.0000.000
51A453ASN00.0490.00338.540-0.003-0.0030.0000.0000.0000.000
52A454LEU00.0060.03432.539-0.003-0.0030.0000.0000.0000.000
53A455LEU0-0.0260.00735.334-0.009-0.0090.0000.0000.0000.000
54A456ASN0-0.052-0.00937.796-0.004-0.0040.0000.0000.0000.000
55A457ILE00.0050.00937.8680.0050.0050.0000.0000.0000.000
56A458GLN0-0.001-0.00740.8900.0000.0000.0000.0000.0000.000
57A459SER00.021-0.02543.759-0.002-0.0020.0000.0000.0000.000
58A460THR00.0140.00345.869-0.002-0.0020.0000.0000.0000.000
59A461THR0-0.0250.00139.1660.0010.0010.0000.0000.0000.000
60A462THR00.0250.00941.542-0.003-0.0030.0000.0000.0000.000
61A463THR0-0.019-0.03235.721-0.006-0.0060.0000.0000.0000.000
62A464VAL00.0190.03632.4350.0060.0060.0000.0000.0000.000
63A465GLY00.025-0.02231.309-0.008-0.0080.0000.0000.0000.000
64A466VAL0-0.0230.00726.3910.0060.0060.0000.0000.0000.000
65A467HIS00.009-0.02226.853-0.004-0.0040.0000.0000.0000.000
66A468LEU0-0.0160.00820.313-0.002-0.0020.0000.0000.0000.000
67A469VAL00.0370.01423.658-0.004-0.0040.0000.0000.0000.000
68A470PHE00.002-0.01317.481-0.001-0.0010.0000.0000.0000.000
69A471ASP-1-0.744-0.86919.8500.1460.1460.0000.0000.0000.000
70A472GLU-1-0.907-0.98521.1640.1300.1300.0000.0000.0000.000
71A473GLN0-0.086-0.04617.0150.0440.0440.0000.0000.0000.000
72A474GLY0-0.020-0.02216.4310.0080.0080.0000.0000.0000.000
73A475ARG10.8370.92314.763-0.310-0.3100.0000.0000.0000.000
74A476LEU0-0.0100.00117.102-0.005-0.0050.0000.0000.0000.000
75A477ILE00.0200.01719.1500.0320.0320.0000.0000.0000.000
76A478THR00.0030.01620.892-0.014-0.0140.0000.0000.0000.000
77A479SER00.0360.00823.5810.0110.0110.0000.0000.0000.000
78A480THR00.0020.04627.299-0.008-0.0080.0000.0000.0000.000
79A481PRO0-0.019-0.03628.9200.0110.0110.0000.0000.0000.000
80A482THR0-0.050-0.05422.905-0.019-0.0190.0000.0000.0000.000
81A483ALA0-0.003-0.00425.5210.0040.0040.0000.0000.0000.000
82A484LEU0-0.040-0.01519.420-0.002-0.0020.0000.0000.0000.000
83A485VAL0-0.0020.00223.5150.0200.0200.0000.0000.0000.000
84A486PRO0-0.001-0.02022.518-0.008-0.0080.0000.0000.0000.000
85A487GLN00.0380.01621.1800.0170.0170.0000.0000.0000.000
86A488ALA0-0.051-0.01620.327-0.019-0.0190.0000.0000.0000.000
87A489SER00.0000.00015.2610.0420.0420.0000.0000.0000.000
88A490TRP00.020-0.00814.872-0.069-0.0690.0000.0000.0000.000
89A491GLY00.0310.01911.3070.1310.1310.0000.0000.0000.000
90A492TYR0-0.005-0.0275.910-0.025-0.0250.0000.0000.0000.000
91A493ARG10.9420.9977.6901.7251.7250.0000.0000.0000.000
92A494GLN00.0440.0046.301-0.576-0.5760.0000.0000.0000.000
93A495GLY00.0130.0207.7820.4260.4260.0000.0000.0000.000
94A496GLN00.010-0.01510.351-0.030-0.0300.0000.0000.0000.000
95A497SER00.0710.04211.9710.1510.1510.0000.0000.0000.000
96A498VAL00.014-0.00210.328-0.239-0.2390.0000.0000.0000.000
97A499SER0-0.034-0.0016.4770.2030.2030.0000.0000.0000.000
98A500THR00.007-0.0088.5550.0530.0530.0000.0000.0000.000
99A501ASN0-0.022-0.0046.634-0.135-0.1350.0000.0000.0000.000
100A502THR00.0110.0119.236-0.275-0.2750.0000.0000.0000.000
101A503VAL0-0.002-0.0169.8310.2020.2020.0000.0000.0000.000
102A504THR0-0.007-0.0079.615-0.064-0.0640.0000.0000.0000.000
103A505ASN00.0410.0578.6480.0630.0630.0000.0000.0000.000
104A506GLY00.1110.04211.941-0.138-0.1380.0000.0000.0000.000
105A507LEU00.0460.02814.151-0.083-0.0830.0000.0000.0000.000
106A508GLY0-0.033-0.01413.979-0.023-0.0230.0000.0000.0000.000
107A509PHE0-0.001-0.0179.819-0.052-0.0520.0000.0000.0000.000
108A510MET0-0.0390.02915.910-0.002-0.0020.0000.0000.0000.000
109A511PRO00.0320.02219.311-0.004-0.0040.0000.0000.0000.000
110A512ASN00.0370.01122.5330.0350.0350.0000.0000.0000.000
111A513VAL00.0120.00023.959-0.004-0.0040.0000.0000.0000.000
112A514SER0-0.025-0.00526.8160.0080.0080.0000.0000.0000.000
113A515ALA0-0.092-0.04626.848-0.001-0.0010.0000.0000.0000.000
114A516TYR0-0.027-0.01824.687-0.012-0.0120.0000.0000.0000.000
115A517PRO00.0120.02329.0190.0040.0040.0000.0000.0000.000
116A518ARG10.9280.96325.834-0.021-0.0210.0000.0000.0000.000
117A519PRO0-0.0110.00331.335-0.004-0.0040.0000.0000.0000.000
118A520ASN00.0530.00533.3310.0030.0030.0000.0000.0000.000
119A521ALA00.0390.05332.812-0.007-0.0070.0000.0000.0000.000
120A522SER0-0.014-0.01233.736-0.008-0.0080.0000.0000.0000.000
121A523GLU-1-0.965-0.97735.103-0.048-0.0480.0000.0000.0000.000
122A524ALA00.0160.00034.717-0.006-0.0060.0000.0000.0000.000
123A525LYS10.9680.98830.6230.0610.0610.0000.0000.0000.000
124A526SER0-0.057-0.02230.225-0.008-0.0080.0000.0000.0000.000
125A527GLN0-0.005-0.00830.295-0.009-0.0090.0000.0000.0000.000
126A528MET00.0110.03726.146-0.008-0.0080.0000.0000.0000.000
127A529VAL0-0.043-0.03630.251-0.004-0.0040.0000.0000.0000.000
128A530SER0-0.0080.00931.043-0.004-0.0040.0000.0000.0000.000
129A531LEU00.0130.00333.1880.0060.0060.0000.0000.0000.000
130A532THR00.001-0.01031.329-0.011-0.0110.0000.0000.0000.000
131A533TYR00.0360.01633.8630.0100.0100.0000.0000.0000.000
132A534LEU00.0470.04734.375-0.011-0.0110.0000.0000.0000.000
133A535GLN0-0.011-0.02534.715-0.002-0.0020.0000.0000.0000.000
134A536GLY0-0.048-0.01633.556-0.009-0.0090.0000.0000.0000.000
135A537ASP-1-0.855-0.90534.234-0.137-0.1370.0000.0000.0000.000
136A538THR00.000-0.01837.3610.0060.0060.0000.0000.0000.000
137A539SER0-0.064-0.04839.2420.0080.0080.0000.0000.0000.000
138A540LYS10.8000.88639.4360.1330.1330.0000.0000.0000.000
139A541PRO0-0.0110.00738.648-0.008-0.0080.0000.0000.0000.000
140A542ILE00.0010.01833.8640.0070.0070.0000.0000.0000.000
141A543THR0-0.009-0.00435.688-0.007-0.0070.0000.0000.0000.000
142A544MET00.0110.01527.194-0.001-0.0010.0000.0000.0000.000
143A545LYS10.8640.93531.9620.0950.0950.0000.0000.0000.000
144A546VAL00.0130.00925.4510.0010.0010.0000.0000.0000.000
145A547ALA0-0.023-0.01228.7870.0060.0060.0000.0000.0000.000
146A548PHE0-0.022-0.02024.759-0.007-0.0070.0000.0000.0000.000
147A549ASN0-0.034-0.05425.1060.0140.0140.0000.0000.0000.000
148A550GLY00.058-0.00427.7260.0100.0100.0000.0000.0000.000
149A551ILE0-0.055-0.00527.9150.0070.0070.0000.0000.0000.000
150A552THR0-0.042-0.01326.9140.0060.0060.0000.0000.0000.000
151A553SER00.0530.03527.6130.0030.0030.0000.0000.0000.000
152A554LEU00.047-0.01528.675-0.005-0.0050.0000.0000.0000.000
153A555ASN0-0.034-0.00126.1250.0040.0040.0000.0000.0000.000
154A556GLY00.0240.02724.3190.0090.0090.0000.0000.0000.000
155A557TYR0-0.009-0.01221.584-0.013-0.0130.0000.0000.0000.000
156A558SER0-0.0140.00423.9260.0010.0010.0000.0000.0000.000
157A559LEU00.0210.03020.368-0.006-0.0060.0000.0000.0000.000
158A560THR0-0.0020.01424.7180.0110.0110.0000.0000.0000.000
159A561PHE00.0210.01522.755-0.009-0.0090.0000.0000.0000.000
160A562MET00.0000.02428.7080.0080.0080.0000.0000.0000.000
161A563TRP00.0500.01426.941-0.002-0.0020.0000.0000.0000.000
162A564SER0-0.010-0.02833.8510.0100.0100.0000.0000.0000.000
163A565GLY0-0.003-0.00337.549-0.006-0.0060.0000.0000.0000.000
164A566LEU0-0.014-0.01136.455-0.001-0.0010.0000.0000.0000.000
165A567SER0-0.002-0.00640.6130.0020.0020.0000.0000.0000.000
166A568ASN0-0.0100.01244.1950.0030.0030.0000.0000.0000.000
167A569TYR0-0.035-0.03240.461-0.002-0.0020.0000.0000.0000.000
168A570ILE00.0580.04342.8020.0010.0010.0000.0000.0000.000
169A571ASN0-0.042-0.02944.083-0.002-0.0020.0000.0000.0000.000
170A572GLN00.0670.06839.958-0.010-0.0100.0000.0000.0000.000
171A573PRO00.0300.02836.0030.0040.0040.0000.0000.0000.000
172A574PHE0-0.006-0.02831.207-0.003-0.0030.0000.0000.0000.000
173A575SER00.007-0.00731.913-0.011-0.0110.0000.0000.0000.000
174A576THR00.0290.03128.4400.0080.0080.0000.0000.0000.000
175A577PRO00.0180.01929.470-0.012-0.0120.0000.0000.0000.000
176A578SER0-0.005-0.00323.967-0.012-0.0120.0000.0000.0000.000
177A579CYS0-0.049-0.03125.7080.0110.0110.0000.0000.0000.000
178A580SER00.0130.01123.606-0.011-0.0110.0000.0000.0000.000
179A581PHE0-0.019-0.01121.0440.0310.0310.0000.0000.0000.000
180A582SER00.0280.00421.675-0.032-0.0320.0000.0000.0000.000
181A583TYR0-0.030-0.02818.3890.0210.0210.0000.0000.0000.000
182A584ILE00.0380.01621.029-0.025-0.0250.0000.0000.0000.000
183A585THR00.001-0.01216.8750.0000.0000.0000.0000.0000.000
184A586GLN00.0070.00319.8680.0000.0000.0000.0000.0000.000
185A587GLU-1-0.965-0.97216.1440.1430.1430.0000.0000.0000.000