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: 394QL

Calculation Name: 4KC0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KC0

Chain ID: A

ChEMBL ID:

UniProt ID: Q3TBT3

Base Structure: X-ray

Registration Date: 2023-06-26

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2041285.794944
FMO2-HF: Nuclear repulsion 1966447.422574
FMO2-HF: Total energy -74838.37237
FMO2-MP2: Total energy -75054.759037


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:152:LEU)


Summations of interaction energy for fragment #1(A:152:LEU)
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.
-6.843-2.3778.772-4.42-8.817-0.012
Interaction energy analysis for fragmet #1(A:152:LEU)
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 : -0.006
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].
3A154VAL00.021-0.0043.811-2.5130.267-0.036-1.419-1.3250.000
4A155ALA00.0380.0394.486-0.856-0.674-0.001-0.020-0.1610.000
5A156HIS00.0560.0325.988-0.610-0.6100.0000.0000.0000.000
6A157GLY00.0170.0047.664-0.265-0.2650.0000.0000.0000.000
7A158LEU0-0.025-0.0057.912-0.173-0.1730.0000.0000.0000.000
8A159ALA00.0380.01910.332-0.163-0.1630.0000.0000.0000.000
9A160TRP00.0470.01810.989-0.160-0.1600.0000.0000.0000.000
10A161SER0-0.068-0.04013.549-0.083-0.0830.0000.0000.0000.000
11A162TYR00.0570.03014.971-0.061-0.0610.0000.0000.0000.000
12A163TYR00.0870.03116.303-0.056-0.0560.0000.0000.0000.000
13A164ILE0-0.020-0.01217.862-0.045-0.0450.0000.0000.0000.000
14A165GLY00.000-0.00819.406-0.034-0.0340.0000.0000.0000.000
15A166TYR0-0.095-0.08020.338-0.023-0.0230.0000.0000.0000.000
16A167LEU00.0540.03318.461-0.027-0.0270.0000.0000.0000.000
17A168ARG10.8680.93321.707-0.183-0.1830.0000.0000.0000.000
18A169LEU0-0.104-0.05223.358-0.021-0.0210.0000.0000.0000.000
19A170ILE0-0.051-0.00624.791-0.015-0.0150.0000.0000.0000.000
20A171LEU0-0.015-0.01222.777-0.013-0.0130.0000.0000.0000.000
21A172PRO00.0040.01026.626-0.010-0.0100.0000.0000.0000.000
22A173GLY00.0150.01529.710-0.010-0.0100.0000.0000.0000.000
23A174LEU0-0.021-0.00428.374-0.007-0.0070.0000.0000.0000.000
24A175GLN00.033-0.01531.387-0.010-0.0100.0000.0000.0000.000
25A176ALA0-0.0210.00034.369-0.006-0.0060.0000.0000.0000.000
26A177ARG10.8440.89730.301-0.117-0.1170.0000.0000.0000.000
27A178ILE00.0430.03932.283-0.004-0.0040.0000.0000.0000.000
28A179ARG10.8860.94036.516-0.060-0.0600.0000.0000.0000.000
29A180MET0-0.062-0.03539.139-0.003-0.0030.0000.0000.0000.000
30A181PHE00.0430.01237.693-0.003-0.0030.0000.0000.0000.000
31A182ASN00.0270.00238.845-0.004-0.0040.0000.0000.0000.000
32A183GLN0-0.0230.00141.820-0.005-0.0050.0000.0000.0000.000
33A184LEU0-0.028-0.00341.933-0.002-0.0020.0000.0000.0000.000
34A185HIS10.8690.94841.136-0.068-0.0680.0000.0000.0000.000
35A186ASN00.002-0.00543.9890.0000.0000.0000.0000.0000.000
36A187ASN0-0.019-0.02542.7480.0020.0020.0000.0000.0000.000
37A188MET00.0300.06138.001-0.001-0.0010.0000.0000.0000.000
38A189LEU0-0.0030.01734.7130.0010.0010.0000.0000.0000.000
39A190SER0-0.008-0.02538.3610.0000.0000.0000.0000.0000.000
40A191GLY00.0320.02638.3610.0010.0010.0000.0000.0000.000
41A192ALA00.0380.02634.1240.0040.0040.0000.0000.0000.000
42A193GLY00.0940.03931.108-0.001-0.0010.0000.0000.0000.000
43A194SER0-0.049-0.02731.6960.0060.0060.0000.0000.0000.000
44A195ARG10.8140.88033.039-0.070-0.0700.0000.0000.0000.000
45A196ARG10.8650.94127.534-0.107-0.1070.0000.0000.0000.000
46A197LEU0-0.028-0.01024.543-0.006-0.0060.0000.0000.0000.000
47A198TYR0-0.039-0.05224.7490.0090.0090.0000.0000.0000.000
48A199ILE0-0.002-0.00518.960-0.001-0.0010.0000.0000.0000.000
49A200LEU00.0080.00320.5520.0120.0120.0000.0000.0000.000
50A201PHE00.001-0.02812.0460.0150.0150.0000.0000.0000.000
51A202PRO00.0450.03816.2140.0160.0160.0000.0000.0000.000
52A203LEU00.0410.00011.4390.0480.0480.0000.0000.0000.000
53A204ASP-1-0.811-0.89011.5500.2850.2850.0000.0000.0000.000
54A205CYS0-0.126-0.07610.9810.0430.0430.0000.0000.0000.000
55A206GLY00.0490.03713.734-0.006-0.0060.0000.0000.0000.000
56A207VAL0-0.081-0.03416.606-0.010-0.0100.0000.0000.0000.000
57A208PRO00.0230.01418.988-0.008-0.0080.0000.0000.0000.000
58A209ASP-1-0.871-0.93322.1380.1610.1610.0000.0000.0000.000
59A210ASN0-0.062-0.04623.1890.0030.0030.0000.0000.0000.000
60A211LEU0-0.049-0.02321.213-0.007-0.0070.0000.0000.0000.000
61A212SER0-0.042-0.01524.2090.0040.0040.0000.0000.0000.000
62A213VAL0-0.005-0.01125.5310.0040.0040.0000.0000.0000.000
63A214VAL0-0.029-0.01226.675-0.011-0.0110.0000.0000.0000.000
64A215ASP-1-0.789-0.90927.9510.0950.0950.0000.0000.0000.000
65A216PRO0-0.023-0.00830.076-0.002-0.0020.0000.0000.0000.000
66A217ASN0-0.073-0.03432.249-0.008-0.0080.0000.0000.0000.000
67A218ILE00.0130.00428.0730.0010.0010.0000.0000.0000.000
68A219ARG10.9130.96232.096-0.058-0.0580.0000.0000.0000.000
69A220PHE00.0180.01332.7770.0010.0010.0000.0000.0000.000
70A221ARG10.8090.89234.642-0.071-0.0710.0000.0000.0000.000
71A222ASP-1-0.833-0.92935.8590.0660.0660.0000.0000.0000.000
72A223MET0-0.020-0.00232.8380.0080.0080.0000.0000.0000.000
73A224LEU0-0.018-0.00331.542-0.006-0.0060.0000.0000.0000.000
74A225PRO0-0.0120.01334.9230.0010.0010.0000.0000.0000.000
75A226GLN00.0370.01033.1350.0080.0080.0000.0000.0000.000
76A227GLN00.0510.01535.590-0.001-0.0010.0000.0000.0000.000
77A228ASN0-0.0140.00036.2610.0050.0050.0000.0000.0000.000
78A229ILE0-0.0040.00837.3160.0020.0020.0000.0000.0000.000
79A230ASP-1-0.787-0.90633.8510.0800.0800.0000.0000.0000.000
80A231ARG10.8620.93232.661-0.086-0.0860.0000.0000.0000.000
81A232ALA0-0.016-0.00735.996-0.004-0.0040.0000.0000.0000.000
82A233GLY00.0020.00737.873-0.003-0.0030.0000.0000.0000.000
83A234ILE0-0.020-0.00633.542-0.002-0.0020.0000.0000.0000.000
84A235LYS10.9280.97333.932-0.081-0.0810.0000.0000.0000.000
85A236ASN0-0.017-0.02333.0770.0080.0080.0000.0000.0000.000
86A237ARG10.8910.94627.286-0.137-0.1370.0000.0000.0000.000
87A238VAL00.0230.00631.601-0.002-0.0020.0000.0000.0000.000
88A239TYR0-0.009-0.01926.8340.0090.0090.0000.0000.0000.000
89A240SER00.0340.02928.116-0.013-0.0130.0000.0000.0000.000
90A241ASN00.0540.00927.150-0.001-0.0010.0000.0000.0000.000
91A242SER00.0410.02829.287-0.011-0.0110.0000.0000.0000.000
92A243VAL0-0.007-0.00730.5890.0060.0060.0000.0000.0000.000
93A244TYR00.022-0.00528.330-0.005-0.0050.0000.0000.0000.000
94A245GLU-1-0.841-0.90533.5590.0630.0630.0000.0000.0000.000
95A246ILE0-0.0040.00031.2950.0010.0010.0000.0000.0000.000
96A247LEU0-0.042-0.01834.316-0.005-0.0050.0000.0000.0000.000
97A248GLU-1-0.732-0.83935.1800.0620.0620.0000.0000.0000.000
98A249ASN0-0.029-0.02237.400-0.003-0.0030.0000.0000.0000.000
99A250GLY00.0070.00839.288-0.003-0.0030.0000.0000.0000.000
100A251GLN0-0.020-0.00640.565-0.001-0.0010.0000.0000.0000.000
101A252PRO0-0.008-0.00638.9420.0030.0030.0000.0000.0000.000
102A253ALA0-0.0010.00536.585-0.003-0.0030.0000.0000.0000.000
103A254GLY00.0130.00335.7110.0000.0000.0000.0000.0000.000
104A255VAL0-0.062-0.01335.4360.0000.0000.0000.0000.0000.000
105A256CYS0-0.023-0.01629.9340.0040.0040.0000.0000.0000.000
106A257ILE0-0.0140.00928.774-0.002-0.0020.0000.0000.0000.000
107A258LEU00.0160.01026.1990.0070.0070.0000.0000.0000.000
108A259GLU-1-0.770-0.86023.0490.1820.1820.0000.0000.0000.000
109A260TYR00.0680.03719.5770.0040.0040.0000.0000.0000.000
110A261ALA00.0090.01915.847-0.006-0.0060.0000.0000.0000.000
111A262THR00.018-0.01516.2930.0310.0310.0000.0000.0000.000
112A263PRO0-0.0020.00112.972-0.006-0.0060.0000.0000.0000.000
113A264LEU00.0120.02111.4850.0810.0810.0000.0000.0000.000
114A265GLN00.0580.03312.6550.0050.0050.0000.0000.0000.000
115A266THR0-0.021-0.00811.298-0.053-0.0530.0000.0000.0000.000
116A267LEU00.0030.0016.7740.0110.0110.0000.0000.0000.000
117A268PHE00.009-0.0029.833-0.059-0.0590.0000.0000.0000.000
118A269ALA00.0200.00812.382-0.051-0.0510.0000.0000.0000.000
119A270MET0-0.026-0.0127.2080.0310.0310.0000.0000.0000.000
120A271SER0-0.060-0.0099.273-0.056-0.0560.0000.0000.0000.000
121A272GLN0-0.069-0.03910.641-0.058-0.0580.0000.0000.0000.000
122A273ASP-1-0.765-0.85212.6940.0650.0650.0000.0000.0000.000
123A274ALA0-0.025-0.01113.311-0.017-0.0170.0000.0000.0000.000
124A275LYS10.7860.87312.935-0.082-0.0820.0000.0000.0000.000
125A276ALA0-0.028-0.01010.650-0.023-0.0230.0000.0000.0000.000
126A277GLY0-0.018-0.0276.9010.0910.0910.0000.0000.0000.000
127A278PHE0-0.044-0.0122.499-0.9400.0360.814-0.413-1.377-0.004
128A279SER00.035-0.0056.7340.0840.0840.0000.0000.0000.000
129A280ARG10.9090.9147.8230.1130.1130.0000.0000.0000.000
130A281GLU-1-0.811-0.8988.173-0.027-0.0270.0000.0000.0000.000
131A282ASP-1-0.819-0.8693.689-1.704-1.1840.013-0.164-0.369-0.001
132A283ARG10.8250.8933.882-0.1950.0920.003-0.103-0.186-0.001
133A284LEU0-0.0070.0056.4210.2680.2680.0000.0000.0000.000
134A285GLU-1-0.894-0.9513.951-0.1300.0680.000-0.028-0.1700.000
135A286GLN0-0.012-0.0202.2911.5251.5855.050-1.412-3.698-0.010
136A287ALA00.0140.0054.7250.2540.283-0.001-0.015-0.0130.000
137A288LYS10.9020.9567.917-0.341-0.3410.0000.0000.0000.000
138A289LEU0-0.0030.0072.484-0.045-0.6112.930-0.846-1.5180.004
139A290PHE0-0.018-0.0056.567-0.406-0.4060.0000.0000.0000.000
140A291CYS0-0.050-0.0328.738-0.269-0.2690.0000.0000.0000.000
141A292ARG10.9420.9686.291-0.448-0.4480.0000.0000.0000.000
142A293THR0-0.029-0.0257.529-0.143-0.1430.0000.0000.0000.000
143A294LEU0-0.052-0.03310.062-0.148-0.1480.0000.0000.0000.000
144A295GLU-1-0.878-0.94713.3010.3030.3030.0000.0000.0000.000
145A296GLU-1-0.877-0.93710.7240.3330.3330.0000.0000.0000.000
146A297ILE0-0.0100.00812.752-0.046-0.0460.0000.0000.0000.000
147A298LEU0-0.042-0.03715.986-0.047-0.0470.0000.0000.0000.000
148A299GLU-1-0.909-0.93717.8780.1300.1300.0000.0000.0000.000
149A300ASP-1-0.910-0.93317.8050.1150.1150.0000.0000.0000.000
150A301VAL0-0.117-0.05420.627-0.017-0.0170.0000.0000.0000.000
151A302PRO00.0300.00223.1540.0080.0080.0000.0000.0000.000
152A303GLU-1-0.911-0.95625.7580.0980.0980.0000.0000.0000.000
153A304SER00.004-0.01322.7420.0040.0040.0000.0000.0000.000
154A305ARG10.9310.96220.752-0.141-0.1410.0000.0000.0000.000
155A306ASN0-0.015-0.00423.893-0.003-0.0030.0000.0000.0000.000
156A307ASN00.0010.00926.789-0.012-0.0120.0000.0000.0000.000
157A308CYS0-0.056-0.02322.6440.0090.0090.0000.0000.0000.000
158A309ARG10.8440.92922.762-0.129-0.1290.0000.0000.0000.000
159A310LEU00.0180.01716.2960.0030.0030.0000.0000.0000.000
160A311ILE00.0150.01420.164-0.018-0.0180.0000.0000.0000.000
161A312VAL00.0210.01315.0130.0170.0170.0000.0000.0000.000
162A313TYR0-0.007-0.00317.471-0.028-0.0280.0000.0000.0000.000
163A314GLN0-0.013-0.02514.0630.0600.0600.0000.0000.0000.000
164A315GLU-1-0.851-0.92117.2790.1050.1050.0000.0000.0000.000
165A316PRO0-0.057-0.01918.2660.0030.0030.0000.0000.0000.000
166A317THR0-0.024-0.03717.6950.0040.0040.0000.0000.0000.000
167A318ASP-1-0.929-0.94320.3950.0330.0330.0000.0000.0000.000
168A319GLY00.0160.01023.998-0.001-0.0010.0000.0000.0000.000
169A320ASN0-0.038-0.03426.5970.0090.0090.0000.0000.0000.000
170A321SER0-0.023-0.01025.3130.0010.0010.0000.0000.0000.000
171A322PHE0-0.0050.00622.9760.0000.0000.0000.0000.0000.000
172A323SER00.0340.01625.7590.0020.0020.0000.0000.0000.000
173A324LEU00.1000.05323.2350.0020.0020.0000.0000.0000.000
174A325SER00.0350.01726.1230.0040.0040.0000.0000.0000.000
175A326GLN0-0.031-0.03829.5830.0010.0010.0000.0000.0000.000
176A327GLU-1-0.815-0.89623.2900.1140.1140.0000.0000.0000.000
177A328VAL0-0.004-0.00726.0180.0050.0050.0000.0000.0000.000
178A329LEU0-0.023-0.01827.758-0.001-0.0010.0000.0000.0000.000
179A330ARG10.8420.92124.068-0.097-0.0970.0000.0000.0000.000
180A331HIS0-0.031-0.02522.8830.0090.0090.0000.0000.0000.000
181A332ILE0-0.012-0.00627.448-0.004-0.0040.0000.0000.0000.000
182A333ARG10.7770.84530.473-0.068-0.0680.0000.0000.0000.000
183A334GLN0-0.0230.00428.913-0.009-0.0090.0000.0000.0000.000
184A335GLU-1-0.803-0.86227.9720.1160.1160.0000.0000.0000.000
185A336GLU-1-1.021-0.99729.7720.0540.0540.0000.0000.0000.000