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: JLR39

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 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 -2040904.96004
FMO2-HF: Nuclear repulsion 1966067.582016
FMO2-HF: Total energy -74837.378023
FMO2-MP2: Total energy -75053.827864


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.
-9.031-5.86114.051-5.756-11.465-0.027
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 : -0.008 / q_NPA : -0.008
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].
3A154VAL00.016-0.0053.800-2.3290.480-0.034-1.364-1.4110.001
4A155ALA00.0310.0373.926-0.0600.161-0.001-0.031-0.1900.000
5A156HIS00.0620.0365.4100.2200.2200.0000.0000.0000.000
6A157GLY00.007-0.0017.310-0.056-0.0560.0000.0000.0000.000
7A158LEU0-0.030-0.0197.780-0.013-0.0130.0000.0000.0000.000
8A159ALA00.0430.0139.606-0.015-0.0150.0000.0000.0000.000
9A160TRP00.0410.02010.864-0.084-0.0840.0000.0000.0000.000
10A161SER0-0.069-0.02913.423-0.034-0.0340.0000.0000.0000.000
11A162TYR00.0730.03514.451-0.018-0.0180.0000.0000.0000.000
12A163TYR00.0870.03215.614-0.009-0.0090.0000.0000.0000.000
13A164ILE0-0.024-0.01217.332-0.017-0.0170.0000.0000.0000.000
14A165GLY0-0.008-0.01318.841-0.009-0.0090.0000.0000.0000.000
15A166TYR0-0.104-0.10719.771-0.011-0.0110.0000.0000.0000.000
16A167LEU00.0490.03317.8510.0010.0010.0000.0000.0000.000
17A168ARG10.8710.93321.084-0.088-0.0880.0000.0000.0000.000
18A169LEU0-0.116-0.05522.824-0.003-0.0030.0000.0000.0000.000
19A170ILE0-0.032-0.00123.907-0.003-0.0030.0000.0000.0000.000
20A171LEU0-0.039-0.02622.101-0.004-0.0040.0000.0000.0000.000
21A172PRO00.0070.02126.111-0.003-0.0030.0000.0000.0000.000
22A173GLY0-0.0160.00129.165-0.003-0.0030.0000.0000.0000.000
23A174LEU0-0.018-0.00427.604-0.005-0.0050.0000.0000.0000.000
24A175GLN00.020-0.01930.783-0.008-0.0080.0000.0000.0000.000
25A176ALA0-0.0170.00133.646-0.003-0.0030.0000.0000.0000.000
26A177ARG10.8680.90129.576-0.012-0.0120.0000.0000.0000.000
27A178ILE00.0370.03731.495-0.004-0.0040.0000.0000.0000.000
28A179ARG10.9350.97535.614-0.019-0.0190.0000.0000.0000.000
29A180MET0-0.077-0.04238.418-0.001-0.0010.0000.0000.0000.000
30A181PHE00.0430.01237.029-0.001-0.0010.0000.0000.0000.000
31A182ASN00.0310.00638.088-0.004-0.0040.0000.0000.0000.000
32A183GLN0-0.067-0.02940.9810.0010.0010.0000.0000.0000.000
33A184LEU0-0.034-0.00541.236-0.001-0.0010.0000.0000.0000.000
34A185HIS10.8880.95640.4210.0050.0050.0000.0000.0000.000
35A186ASN00.0150.00243.298-0.001-0.0010.0000.0000.0000.000
36A187ASN0-0.028-0.02841.8600.0000.0000.0000.0000.0000.000
37A188MET00.0230.05137.2520.0000.0000.0000.0000.0000.000
38A189LEU00.0040.01933.980-0.001-0.0010.0000.0000.0000.000
39A190SER0-0.027-0.02737.4970.0050.0050.0000.0000.0000.000
40A191GLY00.0480.03237.485-0.002-0.0020.0000.0000.0000.000
41A192ALA00.0430.04733.3050.0010.0010.0000.0000.0000.000
42A193GLY00.1060.03830.314-0.003-0.0030.0000.0000.0000.000
43A194SER0-0.079-0.06130.782-0.001-0.0010.0000.0000.0000.000
44A195ARG10.8260.88332.197-0.012-0.0120.0000.0000.0000.000
45A196ARG10.8870.94026.817-0.027-0.0270.0000.0000.0000.000
46A197LEU0-0.019-0.00423.398-0.005-0.0050.0000.0000.0000.000
47A198TYR0-0.048-0.04223.8270.0070.0070.0000.0000.0000.000
48A199ILE0-0.004-0.00418.150-0.006-0.0060.0000.0000.0000.000
49A200LEU0-0.013-0.00319.7470.0000.0000.0000.0000.0000.000
50A201PHE0-0.008-0.02911.3970.0020.0020.0000.0000.0000.000
51A202PRO00.0530.04115.754-0.007-0.0070.0000.0000.0000.000
52A203LEU00.031-0.00511.184-0.037-0.0370.0000.0000.0000.000
53A204ASP-1-0.837-0.91311.192-0.322-0.3220.0000.0000.0000.000
54A205CYS0-0.157-0.09510.661-0.046-0.0460.0000.0000.0000.000
55A206GLY00.0480.03413.4470.0150.0150.0000.0000.0000.000
56A207VAL0-0.088-0.03416.1960.0240.0240.0000.0000.0000.000
57A208PRO00.0120.00918.727-0.005-0.0050.0000.0000.0000.000
58A209ASP-1-0.860-0.92621.722-0.121-0.1210.0000.0000.0000.000
59A210ASN0-0.071-0.05123.0350.0020.0020.0000.0000.0000.000
60A211LEU0-0.050-0.02321.3410.0110.0110.0000.0000.0000.000
61A212SER0-0.047-0.01823.9540.0070.0070.0000.0000.0000.000
62A213VAL00.005-0.00625.161-0.008-0.0080.0000.0000.0000.000
63A214VAL0-0.039-0.01526.3670.0060.0060.0000.0000.0000.000
64A215ASP-1-0.802-0.91827.655-0.075-0.0750.0000.0000.0000.000
65A216PRO0-0.020-0.00429.7530.0060.0060.0000.0000.0000.000
66A217ASN0-0.059-0.02531.9530.0080.0080.0000.0000.0000.000
67A218ILE00.0110.00327.7930.0050.0050.0000.0000.0000.000
68A219ARG10.9600.99931.7370.0280.0280.0000.0000.0000.000
69A220PHE00.0300.01732.4990.0030.0030.0000.0000.0000.000
70A221ARG10.8020.89434.2900.0190.0190.0000.0000.0000.000
71A222ASP-1-0.838-0.92335.598-0.012-0.0120.0000.0000.0000.000
72A223MET0-0.032-0.01132.353-0.002-0.0020.0000.0000.0000.000
73A224LEU0-0.030-0.00930.8700.0030.0030.0000.0000.0000.000
74A225PRO0-0.0020.02234.433-0.001-0.0010.0000.0000.0000.000
75A226GLN00.0250.00232.6260.0050.0050.0000.0000.0000.000
76A227GLN00.0580.01135.0290.0010.0010.0000.0000.0000.000
77A228ASN0-0.013-0.00335.6600.0010.0010.0000.0000.0000.000
78A229ILE0-0.0060.00736.7450.0010.0010.0000.0000.0000.000
79A230ASP-1-0.794-0.88633.3590.0410.0410.0000.0000.0000.000
80A231ARG10.9560.95433.550-0.050-0.0500.0000.0000.0000.000
81A232ALA0-0.041-0.02135.794-0.001-0.0010.0000.0000.0000.000
82A233GLY00.0040.01137.5230.0000.0000.0000.0000.0000.000
83A234ILE0-0.028-0.01233.256-0.002-0.0020.0000.0000.0000.000
84A235LYS10.9240.97733.258-0.025-0.0250.0000.0000.0000.000
85A236ASN00.009-0.00432.0730.0060.0060.0000.0000.0000.000
86A237ARG10.8810.94027.094-0.019-0.0190.0000.0000.0000.000
87A238VAL00.0250.00731.4110.0010.0010.0000.0000.0000.000
88A239TYR0-0.002-0.01126.0700.0000.0000.0000.0000.0000.000
89A240SER00.0240.02728.0620.0000.0000.0000.0000.0000.000
90A241ASN00.0720.02426.4570.0030.0030.0000.0000.0000.000
91A242SER00.0270.02628.9760.0010.0010.0000.0000.0000.000
92A243VAL0-0.009-0.01030.1640.0010.0010.0000.0000.0000.000
93A244TYR00.0340.00228.411-0.003-0.0030.0000.0000.0000.000
94A245GLU-1-0.884-0.95133.186-0.018-0.0180.0000.0000.0000.000
95A246ILE0-0.0080.00130.649-0.004-0.0040.0000.0000.0000.000
96A247LEU0-0.042-0.02033.8890.0040.0040.0000.0000.0000.000
97A248GLU-1-0.773-0.88334.763-0.030-0.0300.0000.0000.0000.000
98A249ASN0-0.030-0.02436.9760.0000.0000.0000.0000.0000.000
99A250GLY00.0010.00538.8960.0020.0020.0000.0000.0000.000
100A251GLN0-0.024-0.01140.1610.0030.0030.0000.0000.0000.000
101A252PRO0-0.0070.00238.524-0.002-0.0020.0000.0000.0000.000
102A253ALA00.0080.00936.1170.0020.0020.0000.0000.0000.000
103A254GLY00.0110.00134.9070.0030.0030.0000.0000.0000.000
104A255VAL0-0.064-0.01534.801-0.003-0.0030.0000.0000.0000.000
105A256CYS0-0.003-0.00128.9720.0020.0020.0000.0000.0000.000
106A257ILE0-0.0140.00528.064-0.003-0.0030.0000.0000.0000.000
107A258LEU00.0220.00725.4510.0030.0030.0000.0000.0000.000
108A259GLU-1-0.780-0.84422.267-0.012-0.0120.0000.0000.0000.000
109A260TYR00.0720.03819.0220.0040.0040.0000.0000.0000.000
110A261ALA00.0030.01515.4240.0140.0140.0000.0000.0000.000
111A262THR00.028-0.01116.212-0.025-0.0250.0000.0000.0000.000
112A263PRO0-0.0010.00312.888-0.016-0.0160.0000.0000.0000.000
113A264LEU00.0120.01311.113-0.035-0.0350.0000.0000.0000.000
114A265GLN00.0700.03812.445-0.037-0.0370.0000.0000.0000.000
115A266THR0-0.019-0.00510.826-0.013-0.0130.0000.0000.0000.000
116A267LEU00.0080.0006.729-0.026-0.0260.0000.0000.0000.000
117A268PHE0-0.001-0.0029.722-0.064-0.0640.0000.0000.0000.000
118A269ALA00.0170.00312.310-0.011-0.0110.0000.0000.0000.000
119A270MET0-0.025-0.0106.0680.0070.0070.0000.0000.0000.000
120A271SER0-0.070-0.0259.242-0.026-0.0260.0000.0000.0000.000
121A272GLN0-0.070-0.03710.3740.0450.0450.0000.0000.0000.000
122A273ASP-1-0.798-0.89512.348-0.198-0.1980.0000.0000.0000.000
123A274ALA0-0.018-0.00513.176-0.031-0.0310.0000.0000.0000.000
124A275LYS10.8020.89313.0460.2120.2120.0000.0000.0000.000
125A276ALA0-0.0370.00010.706-0.057-0.0570.0000.0000.0000.000
126A277GLY00.025-0.0087.0310.0520.0520.0000.0000.0000.000
127A278PHE0-0.025-0.0012.782-1.721-0.6431.901-0.652-2.326-0.012
128A279SER00.0510.0276.6490.2280.2280.0000.0000.0000.000
129A280ARG10.9950.9707.7450.3620.3620.0000.0000.0000.000
130A281GLU-1-0.876-0.9398.022-0.677-0.6770.0000.0000.0000.000
131A282ASP-1-0.858-0.9143.330-3.095-2.5010.025-0.198-0.421-0.001
132A283ARG10.8990.9443.693-0.0660.3260.011-0.158-0.244-0.001
133A284LEU0-0.0040.0046.2720.0560.0560.0000.0000.0000.000
134A285GLU-1-0.896-0.9513.426-1.275-0.9620.010-0.055-0.2690.000
135A286GLN0-0.021-0.0282.035-0.951-2.5318.561-2.168-4.813-0.013
136A287ALA00.0140.0074.2550.3480.4350.000-0.042-0.0450.000
137A288LYS10.9410.9767.6140.5730.5730.0000.0000.0000.000
138A289LEU0-0.018-0.0012.1180.186-0.5583.578-1.088-1.746-0.001
139A290PHE0-0.012-0.0055.8020.3190.3190.0000.0000.0000.000
140A291CYS0-0.012-0.0037.7900.1280.1280.0000.0000.0000.000
141A292ARG11.0041.0036.198-0.949-0.9490.0000.0000.0000.000
142A293THR0-0.0140.0007.1690.1460.1460.0000.0000.0000.000
143A294LEU0-0.058-0.0359.859-0.041-0.0410.0000.0000.0000.000
144A295GLU-1-0.929-0.98812.7930.1150.1150.0000.0000.0000.000
145A296GLU-1-0.910-0.95611.2340.7370.7370.0000.0000.0000.000
146A297ILE0-0.0040.01012.734-0.036-0.0360.0000.0000.0000.000
147A298LEU0-0.070-0.05415.934-0.035-0.0350.0000.0000.0000.000
148A299GLU-1-1.006-0.99617.8510.1910.1910.0000.0000.0000.000
149A300ASP-1-0.920-0.93918.0950.2590.2590.0000.0000.0000.000
150A301VAL0-0.104-0.04720.676-0.020-0.0200.0000.0000.0000.000
151A302PRO00.0240.00623.114-0.010-0.0100.0000.0000.0000.000
152A303GLU-1-0.922-0.97525.6690.0570.0570.0000.0000.0000.000
153A304SER0-0.015-0.02322.268-0.007-0.0070.0000.0000.0000.000
154A305ARG11.0371.02921.705-0.125-0.1250.0000.0000.0000.000
155A306ASN00.0000.00123.514-0.011-0.0110.0000.0000.0000.000
156A307ASN00.0110.01826.290-0.014-0.0140.0000.0000.0000.000
157A308CYS0-0.032-0.00121.644-0.007-0.0070.0000.0000.0000.000
158A309ARG10.8940.95522.035-0.035-0.0350.0000.0000.0000.000
159A310LEU00.0300.02315.411-0.010-0.0100.0000.0000.0000.000
160A311ILE00.0180.01619.2870.0040.0040.0000.0000.0000.000
161A312VAL00.0180.00914.551-0.020-0.0200.0000.0000.0000.000
162A313TYR00.0340.01617.0060.0040.0040.0000.0000.0000.000
163A314GLN0-0.067-0.04813.782-0.024-0.0240.0000.0000.0000.000
164A315GLU-1-0.884-0.93516.881-0.115-0.1150.0000.0000.0000.000
165A316PRO0-0.065-0.02417.974-0.028-0.0280.0000.0000.0000.000
166A317THR0-0.018-0.02117.494-0.001-0.0010.0000.0000.0000.000
167A318ASP-1-0.934-0.95820.205-0.162-0.1620.0000.0000.0000.000
168A319GLY00.0170.01123.806-0.001-0.0010.0000.0000.0000.000
169A320ASN0-0.030-0.02926.344-0.001-0.0010.0000.0000.0000.000
170A321SER0-0.043-0.02225.0390.0060.0060.0000.0000.0000.000
171A322PHE00.0210.01922.3540.0070.0070.0000.0000.0000.000
172A323SER00.0270.01825.3980.0020.0020.0000.0000.0000.000
173A324LEU00.1150.05822.7860.0060.0060.0000.0000.0000.000
174A325SER00.0280.01125.7170.0050.0050.0000.0000.0000.000
175A326GLN00.018-0.00329.1200.0090.0090.0000.0000.0000.000
176A327GLU-1-0.889-0.94022.930-0.060-0.0600.0000.0000.0000.000
177A328VAL0-0.014-0.01725.4830.0080.0080.0000.0000.0000.000
178A329LEU0-0.026-0.01527.1630.0090.0090.0000.0000.0000.000
179A330ARG10.9070.96025.4340.0430.0430.0000.0000.0000.000
180A331HIS0-0.026-0.02122.0990.0130.0130.0000.0000.0000.000
181A332ILE0-0.0030.00426.7630.0070.0070.0000.0000.0000.000
182A333ARG10.7680.85229.6760.0240.0240.0000.0000.0000.000
183A334GLN0-0.0270.00128.367-0.001-0.0010.0000.0000.0000.000
184A335GLU-1-0.914-0.93027.3820.0220.0220.0000.0000.0000.000
185A336GLU-1-1.019-1.00029.3330.0220.0220.0000.0000.0000.000