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: 4979N

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1894288.422394
FMO2-HF: Nuclear repulsion 1823838.21298
FMO2-HF: Total energy -70450.209414
FMO2-MP2: Total energy -70654.185982


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.
-22.395-20.63417.512-9.612-9.66-0.029
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 : 0.015 / q_NPA : 0.000
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].
3A405TYR0-0.022-0.0062.109-7.152-1.6513.605-4.141-4.9640.027
4A406ASP-1-0.766-0.8521.764-18.689-23.16913.403-5.130-3.793-0.055
5A407PRO0-0.015-0.0122.4430.9131.6530.504-0.341-0.903-0.001
6A408LEU0-0.002-0.0055.4770.9490.9490.0000.0000.0000.000
7A409THR0-0.015-0.0337.8270.4820.4820.0000.0000.0000.000
8A410LEU0-0.055-0.0078.752-0.114-0.1140.0000.0000.0000.000
9A411TRP0-0.019-0.04211.303-0.012-0.0120.0000.0000.0000.000
10A412THR00.0280.00713.7020.0400.0400.0000.0000.0000.000
11A413THR0-0.045-0.00113.9770.0610.0610.0000.0000.0000.000
12A414PRO0-0.017-0.00115.2390.0240.0240.0000.0000.0000.000
13A415ASP-1-0.870-0.94717.804-0.338-0.3380.0000.0000.0000.000
14A416PRO00.0150.03219.1580.0330.0330.0000.0000.0000.000
15A417PRO00.033-0.00420.7980.0130.0130.0000.0000.0000.000
16A418PRO0-0.022-0.01823.837-0.007-0.0070.0000.0000.0000.000
17A419ASN00.0130.01220.9940.0220.0220.0000.0000.0000.000
18A420CYS0-0.0060.00424.5460.0060.0060.0000.0000.0000.000
19A421SER00.019-0.02027.129-0.004-0.0040.0000.0000.0000.000
20A422LEU0-0.062-0.02528.7950.0070.0070.0000.0000.0000.000
21A423ILE0-0.054-0.02532.3620.0050.0050.0000.0000.0000.000
22A424GLN0-0.042-0.03134.7090.0060.0060.0000.0000.0000.000
23A425GLU-1-0.837-0.89831.400-0.042-0.0420.0000.0000.0000.000
24A426LEU0-0.056-0.02627.258-0.003-0.0030.0000.0000.0000.000
25A427ASP-1-0.762-0.88430.281-0.085-0.0850.0000.0000.0000.000
26A428ALA00.0320.00829.007-0.004-0.0040.0000.0000.0000.000
27A429LYS10.8370.93223.9330.2240.2240.0000.0000.0000.000
28A430LEU00.0220.00322.3110.0010.0010.0000.0000.0000.000
29A431THR0-0.0120.00819.1950.0050.0050.0000.0000.0000.000
30A432LEU00.009-0.01517.9540.0170.0170.0000.0000.0000.000
31A433CYS0-0.027-0.01114.417-0.080-0.0800.0000.0000.0000.000
32A434LEU0-0.0030.00514.4210.0650.0650.0000.0000.0000.000
33A435THR00.003-0.00412.413-0.092-0.0920.0000.0000.0000.000
34A436LYS10.8390.90911.4120.3940.3940.0000.0000.0000.000
35A437ASN0-0.042-0.02312.410-0.108-0.1080.0000.0000.0000.000
36A438GLY00.0640.03514.3690.0690.0690.0000.0000.0000.000
37A439SER00.0160.00016.104-0.004-0.0040.0000.0000.0000.000
38A440ILE0-0.0160.01618.1000.0340.0340.0000.0000.0000.000
39A441VAL0-0.0010.02215.180-0.052-0.0520.0000.0000.0000.000
40A442ASN00.007-0.01315.8210.1080.1080.0000.0000.0000.000
41A443GLY00.0170.01416.995-0.071-0.0710.0000.0000.0000.000
42A444ILE0-0.030-0.02119.1080.0290.0290.0000.0000.0000.000
43A445VAL0-0.010-0.00219.997-0.021-0.0210.0000.0000.0000.000
44A446SER0-0.057-0.02422.6560.0080.0080.0000.0000.0000.000
45A447LEU00.0190.01324.574-0.003-0.0030.0000.0000.0000.000
46A448VAL0-0.003-0.00627.2810.0060.0060.0000.0000.0000.000
47A449GLY00.0150.01229.4310.0020.0020.0000.0000.0000.000
48A450VAL0-0.047-0.03929.556-0.005-0.0050.0000.0000.0000.000
49A451LYS10.8780.94132.6700.0700.0700.0000.0000.0000.000
50A452GLY00.0320.01435.3660.0000.0000.0000.0000.0000.000
51A453ASN0-0.001-0.02838.428-0.003-0.0030.0000.0000.0000.000
52A454LEU00.0160.02932.519-0.003-0.0030.0000.0000.0000.000
53A455LEU0-0.032-0.00435.321-0.009-0.0090.0000.0000.0000.000
54A456ASN0-0.087-0.05237.722-0.002-0.0020.0000.0000.0000.000
55A457ILE00.0210.02137.5650.0060.0060.0000.0000.0000.000
56A458GLN00.0740.03740.8710.0020.0020.0000.0000.0000.000
57A459SER00.0280.00243.838-0.002-0.0020.0000.0000.0000.000
58A460THR00.0160.01245.585-0.001-0.0010.0000.0000.0000.000
59A461THR0-0.030-0.01639.0630.0010.0010.0000.0000.0000.000
60A462THR00.0410.01341.675-0.005-0.0050.0000.0000.0000.000
61A463THR0-0.016-0.01135.829-0.006-0.0060.0000.0000.0000.000
62A464VAL00.0130.02132.5050.0060.0060.0000.0000.0000.000
63A465GLY00.003-0.01630.946-0.007-0.0070.0000.0000.0000.000
64A466VAL0-0.0050.01226.0080.0060.0060.0000.0000.0000.000
65A467HIS0-0.001-0.02026.840-0.002-0.0020.0000.0000.0000.000
66A468LEU0-0.0060.00320.276-0.003-0.0030.0000.0000.0000.000
67A469VAL00.0350.01323.472-0.006-0.0060.0000.0000.0000.000
68A470PHE0-0.001-0.00317.1220.0010.0010.0000.0000.0000.000
69A471ASP-1-0.720-0.86219.6200.1420.1420.0000.0000.0000.000
70A472GLU-1-0.871-0.93421.1030.1030.1030.0000.0000.0000.000
71A473GLN0-0.055-0.03717.1580.0560.0560.0000.0000.0000.000
72A474GLY0-0.007-0.01816.4620.0010.0010.0000.0000.0000.000
73A475ARG10.8440.91614.867-0.261-0.2610.0000.0000.0000.000
74A476LEU0-0.023-0.01017.021-0.002-0.0020.0000.0000.0000.000
75A477ILE00.0250.01019.0560.0290.0290.0000.0000.0000.000
76A478THR00.0120.02020.503-0.011-0.0110.0000.0000.0000.000
77A479SER00.026-0.00123.2750.0110.0110.0000.0000.0000.000
78A480THR00.0100.02127.088-0.007-0.0070.0000.0000.0000.000
79A481PRO0-0.015-0.01428.8570.0090.0090.0000.0000.0000.000
80A482THR0-0.056-0.04322.865-0.019-0.0190.0000.0000.0000.000
81A483ALA00.0000.00025.6410.0060.0060.0000.0000.0000.000
82A484LEU0-0.036-0.01319.512-0.002-0.0020.0000.0000.0000.000
83A485VAL00.0220.01423.5160.0170.0170.0000.0000.0000.000
84A486PRO0-0.002-0.01722.606-0.006-0.0060.0000.0000.0000.000
85A487GLN00.0190.01521.3450.0220.0220.0000.0000.0000.000
86A488ALA0-0.041-0.01420.396-0.017-0.0170.0000.0000.0000.000
87A489SER0-0.009-0.00815.4320.0370.0370.0000.0000.0000.000
88A490TRP00.0210.00314.889-0.071-0.0710.0000.0000.0000.000
89A491GLY00.0360.01111.2710.1170.1170.0000.0000.0000.000
90A492TYR00.001-0.0075.812-0.004-0.0040.0000.0000.0000.000
91A493ARG10.8980.9647.9041.4781.4780.0000.0000.0000.000
92A494GLN00.0700.0346.194-0.450-0.4500.0000.0000.0000.000
93A495GLY00.0260.0177.5900.3250.3250.0000.0000.0000.000
94A496GLN00.0230.0019.865-0.126-0.1260.0000.0000.0000.000
95A497SER00.0460.02011.5550.1300.1300.0000.0000.0000.000
96A498VAL00.0060.02110.323-0.213-0.2130.0000.0000.0000.000
97A499SER0-0.043-0.0326.6260.2900.2900.0000.0000.0000.000
98A500THR00.0170.0048.672-0.061-0.0610.0000.0000.0000.000
99A501ASN0-0.061-0.0226.100-0.357-0.3570.0000.0000.0000.000
100A502THR00.0160.0079.147-0.242-0.2420.0000.0000.0000.000
101A503VAL00.001-0.0149.8810.1700.1700.0000.0000.0000.000
102A504THR00.0020.0019.442-0.088-0.0880.0000.0000.0000.000
103A505ASN00.0250.0258.7920.0580.0580.0000.0000.0000.000
104A506GLY00.0980.04812.071-0.118-0.1180.0000.0000.0000.000
105A507LEU00.0040.01714.217-0.070-0.0700.0000.0000.0000.000
106A508GLY0-0.0040.00813.753-0.018-0.0180.0000.0000.0000.000
107A509PHE0-0.025-0.0219.798-0.050-0.0500.0000.0000.0000.000
108A510MET0-0.0240.04815.7970.0020.0020.0000.0000.0000.000
109A511PRO00.0130.00619.206-0.003-0.0030.0000.0000.0000.000
110A512ASN00.0140.02122.3940.0360.0360.0000.0000.0000.000
111A513VAL00.0070.00123.864-0.003-0.0030.0000.0000.0000.000
112A514SER0-0.006-0.00426.6460.0090.0090.0000.0000.0000.000
113A515ALA0-0.091-0.04126.408-0.001-0.0010.0000.0000.0000.000
114A516TYR00.0180.00224.303-0.007-0.0070.0000.0000.0000.000
115A517PRO00.0570.03128.7020.0030.0030.0000.0000.0000.000
116A518ARG10.9110.95525.705-0.012-0.0120.0000.0000.0000.000
117A519PRO0-0.013-0.00531.301-0.003-0.0030.0000.0000.0000.000
118A520ASN0-0.023-0.01333.7360.0030.0030.0000.0000.0000.000
119A521ALA00.0640.05232.710-0.008-0.0080.0000.0000.0000.000
120A522SER0-0.004-0.01133.751-0.008-0.0080.0000.0000.0000.000
121A523GLU-1-0.919-0.94634.728-0.050-0.0500.0000.0000.0000.000
122A524ALA0-0.005-0.00334.415-0.006-0.0060.0000.0000.0000.000
123A525LYS10.8850.95330.8330.0540.0540.0000.0000.0000.000
124A526SER0-0.035-0.03230.126-0.009-0.0090.0000.0000.0000.000
125A527GLN0-0.010-0.00930.115-0.005-0.0050.0000.0000.0000.000
126A528MET0-0.0080.01825.974-0.010-0.0100.0000.0000.0000.000
127A529VAL0-0.022-0.01030.010-0.004-0.0040.0000.0000.0000.000
128A530SER0-0.022-0.00231.009-0.008-0.0080.0000.0000.0000.000
129A531LEU00.004-0.00433.0280.0090.0090.0000.0000.0000.000
130A532THR0-0.002-0.00830.733-0.011-0.0110.0000.0000.0000.000
131A533TYR00.0430.02633.4550.0090.0090.0000.0000.0000.000
132A534LEU00.0340.02734.004-0.010-0.0100.0000.0000.0000.000
133A535GLN0-0.029-0.04334.226-0.002-0.0020.0000.0000.0000.000
134A536GLY0-0.028-0.00233.548-0.008-0.0080.0000.0000.0000.000
135A537ASP-1-0.826-0.87334.121-0.119-0.1190.0000.0000.0000.000
136A538THR00.041-0.00137.3760.0030.0030.0000.0000.0000.000
137A539SER0-0.103-0.07139.2600.0070.0070.0000.0000.0000.000
138A540LYS10.8230.90539.4950.1150.1150.0000.0000.0000.000
139A541PRO0-0.0030.00838.235-0.007-0.0070.0000.0000.0000.000
140A542ILE0-0.021-0.00133.7800.0080.0080.0000.0000.0000.000
141A543THR0-0.020-0.01635.811-0.006-0.0060.0000.0000.0000.000
142A544MET00.0080.00227.206-0.003-0.0030.0000.0000.0000.000
143A545LYS10.8590.93231.9180.0850.0850.0000.0000.0000.000
144A546VAL00.0180.01525.1670.0010.0010.0000.0000.0000.000
145A547ALA0-0.022-0.01728.0660.0090.0090.0000.0000.0000.000
146A548PHE0-0.005-0.00924.449-0.008-0.0080.0000.0000.0000.000
147A549ASN0-0.008-0.03524.9510.0100.0100.0000.0000.0000.000
148A550GLY00.0090.00627.3890.0120.0120.0000.0000.0000.000
149A551ILE0-0.0020.01128.2170.0050.0050.0000.0000.0000.000
150A552THR0-0.044-0.01226.4830.0010.0010.0000.0000.0000.000
151A553SER00.0280.02827.7710.0030.0030.0000.0000.0000.000
152A554LEU00.027-0.00728.968-0.006-0.0060.0000.0000.0000.000
153A555ASN0-0.025-0.01726.069-0.006-0.0060.0000.0000.0000.000
154A556GLY00.0050.01523.9160.0030.0030.0000.0000.0000.000
155A557TYR0-0.034-0.01921.772-0.013-0.0130.0000.0000.0000.000
156A558SER0-0.018-0.03523.3880.0020.0020.0000.0000.0000.000
157A559LEU00.0090.02619.906-0.009-0.0090.0000.0000.0000.000
158A560THR0-0.011-0.00324.2680.0190.0190.0000.0000.0000.000
159A561PHE00.0180.01622.220-0.009-0.0090.0000.0000.0000.000
160A562MET00.0080.01828.2680.0070.0070.0000.0000.0000.000
161A563TRP00.0360.00926.746-0.001-0.0010.0000.0000.0000.000
162A564SER0-0.013-0.02733.6860.0090.0090.0000.0000.0000.000
163A565GLY00.0340.02237.454-0.005-0.0050.0000.0000.0000.000
164A566LEU0-0.013-0.01036.077-0.001-0.0010.0000.0000.0000.000
165A567SER0-0.0040.00040.4370.0020.0020.0000.0000.0000.000
166A568ASN0-0.029-0.00643.6860.0060.0060.0000.0000.0000.000
167A569TYR0-0.068-0.04540.1720.0000.0000.0000.0000.0000.000
168A570ILE00.0070.01041.948-0.002-0.0020.0000.0000.0000.000
169A571ASN0-0.0100.00543.890-0.002-0.0020.0000.0000.0000.000
170A572GLN00.0140.01439.713-0.007-0.0070.0000.0000.0000.000
171A573PRO00.0440.03835.3970.0040.0040.0000.0000.0000.000
172A574PHE00.0140.00530.707-0.002-0.0020.0000.0000.0000.000
173A575SER00.0380.00931.248-0.009-0.0090.0000.0000.0000.000
174A576THR00.0220.02127.8900.0080.0080.0000.0000.0000.000
175A577PRO00.0510.02428.623-0.014-0.0140.0000.0000.0000.000
176A578SER00.0130.01023.5300.0070.0070.0000.0000.0000.000
177A579CYS0-0.043-0.00625.2540.0040.0040.0000.0000.0000.000
178A580SER00.0170.00623.275-0.014-0.0140.0000.0000.0000.000
179A581PHE0-0.031-0.02420.7420.0300.0300.0000.0000.0000.000
180A582SER00.008-0.00821.521-0.030-0.0300.0000.0000.0000.000
181A583TYR0-0.024-0.02918.3000.0180.0180.0000.0000.0000.000
182A584ILE00.0450.01720.921-0.025-0.0250.0000.0000.0000.000
183A585THR0-0.004-0.02316.9450.0120.0120.0000.0000.0000.000
184A586GLN00.0330.00519.8940.0010.0010.0000.0000.0000.000
185A587GLU-1-0.949-0.96815.9920.0670.0670.0000.0000.0000.000