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: LZ6J9

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 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 -2047477.719857
FMO2-HF: Nuclear repulsion 1972638.924082
FMO2-HF: Total energy -74838.795775
FMO2-MP2: Total energy -75055.183748


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.
-7.701-2.4556.891-4.357-7.781-0.012
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 : 0.022 / q_NPA : 0.004
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].
3A154VAL00.006-0.0063.876-1.9330.362-0.024-1.210-1.0610.000
4A155ALA00.0350.0284.375-1.038-0.8480.000-0.029-0.1600.000
5A156HIS00.0650.0385.969-0.704-0.7040.0000.0000.0000.000
6A157GLY00.0160.0057.683-0.270-0.2700.0000.0000.0000.000
7A158LEU0-0.0190.0088.089-0.196-0.1960.0000.0000.0000.000
8A159ALA00.0330.02410.065-0.169-0.1690.0000.0000.0000.000
9A160TRP00.0440.01411.029-0.151-0.1510.0000.0000.0000.000
10A161SER0-0.078-0.05713.647-0.082-0.0820.0000.0000.0000.000
11A162TYR00.0470.02114.910-0.068-0.0680.0000.0000.0000.000
12A163TYR00.0890.03416.011-0.059-0.0590.0000.0000.0000.000
13A164ILE0-0.014-0.01017.672-0.044-0.0440.0000.0000.0000.000
14A165GLY00.007-0.00119.212-0.035-0.0350.0000.0000.0000.000
15A166TYR0-0.105-0.08120.528-0.022-0.0220.0000.0000.0000.000
16A167LEU00.0450.02718.217-0.028-0.0280.0000.0000.0000.000
17A168ARG10.8690.92821.505-0.189-0.1890.0000.0000.0000.000
18A169LEU0-0.075-0.03223.236-0.020-0.0200.0000.0000.0000.000
19A170ILE0-0.0250.02024.615-0.014-0.0140.0000.0000.0000.000
20A171LEU00.0170.00822.644-0.014-0.0140.0000.0000.0000.000
21A172PRO00.0130.01426.334-0.010-0.0100.0000.0000.0000.000
22A173GLY0-0.0040.00529.515-0.009-0.0090.0000.0000.0000.000
23A174LEU0-0.0240.00027.843-0.006-0.0060.0000.0000.0000.000
24A175GLN00.031-0.00930.856-0.008-0.0080.0000.0000.0000.000
25A176ALA0-0.0230.00733.742-0.006-0.0060.0000.0000.0000.000
26A177ARG10.8410.90130.284-0.115-0.1150.0000.0000.0000.000
27A178ILE00.0610.03931.478-0.004-0.0040.0000.0000.0000.000
28A179ARG10.8900.94335.829-0.057-0.0570.0000.0000.0000.000
29A180MET0-0.061-0.03638.783-0.003-0.0030.0000.0000.0000.000
30A181PHE00.0250.00637.365-0.003-0.0030.0000.0000.0000.000
31A182ASN00.010-0.00737.845-0.005-0.0050.0000.0000.0000.000
32A183GLN0-0.0110.01041.248-0.005-0.0050.0000.0000.0000.000
33A184LEU0-0.012-0.00141.959-0.002-0.0020.0000.0000.0000.000
34A185HIS10.8500.94441.362-0.065-0.0650.0000.0000.0000.000
35A186ASN00.014-0.00143.4650.0010.0010.0000.0000.0000.000
36A187ASN0-0.017-0.01742.2230.0010.0010.0000.0000.0000.000
37A188MET0-0.0030.04538.186-0.001-0.0010.0000.0000.0000.000
38A189LEU0-0.0050.01634.5830.0010.0010.0000.0000.0000.000
39A190SER0-0.007-0.02537.9100.0000.0000.0000.0000.0000.000
40A191GLY00.0350.02637.7830.0000.0000.0000.0000.0000.000
41A192ALA00.0260.02133.2630.0040.0040.0000.0000.0000.000
42A193GLY00.0850.03630.563-0.001-0.0010.0000.0000.0000.000
43A194SER0-0.035-0.01331.2740.0060.0060.0000.0000.0000.000
44A195ARG10.8190.86832.710-0.062-0.0620.0000.0000.0000.000
45A196ARG10.8550.93227.197-0.093-0.0930.0000.0000.0000.000
46A197LEU0-0.036-0.01324.177-0.005-0.0050.0000.0000.0000.000
47A198TYR0-0.048-0.06024.2230.0060.0060.0000.0000.0000.000
48A199ILE00.0090.00018.6850.0000.0000.0000.0000.0000.000
49A200LEU00.0230.01320.0600.0110.0110.0000.0000.0000.000
50A201PHE00.027-0.01111.8920.0170.0170.0000.0000.0000.000
51A202PRO00.0420.03916.2340.0010.0010.0000.0000.0000.000
52A203LEU00.023-0.00611.0540.0570.0570.0000.0000.0000.000
53A204ASP-1-0.778-0.88611.5350.2800.2800.0000.0000.0000.000
54A205CYS0-0.102-0.05311.1660.0560.0560.0000.0000.0000.000
55A206GLY00.0280.03613.863-0.003-0.0030.0000.0000.0000.000
56A207VAL0-0.052-0.03316.805-0.019-0.0190.0000.0000.0000.000
57A208PRO00.0320.01719.0980.0000.0000.0000.0000.0000.000
58A209ASP-1-0.869-0.93122.3030.1690.1690.0000.0000.0000.000
59A210ASN0-0.072-0.04523.2130.0010.0010.0000.0000.0000.000
60A211LEU0-0.038-0.01621.302-0.008-0.0080.0000.0000.0000.000
61A212SER0-0.045-0.02024.2640.0030.0030.0000.0000.0000.000
62A213VAL0-0.009-0.00925.8490.0050.0050.0000.0000.0000.000
63A214VAL0-0.028-0.01826.930-0.009-0.0090.0000.0000.0000.000
64A215ASP-1-0.721-0.86228.3700.0790.0790.0000.0000.0000.000
65A216PRO0-0.045-0.02430.181-0.001-0.0010.0000.0000.0000.000
66A217ASN0-0.075-0.03932.232-0.008-0.0080.0000.0000.0000.000
67A218ILE0-0.007-0.00728.2810.0000.0000.0000.0000.0000.000
68A219ARG10.9190.96832.366-0.053-0.0530.0000.0000.0000.000
69A220PHE00.0270.00032.8540.0000.0000.0000.0000.0000.000
70A221ARG10.8150.89134.844-0.066-0.0660.0000.0000.0000.000
71A222ASP-1-0.818-0.92636.1410.0640.0640.0000.0000.0000.000
72A223MET0-0.016-0.00133.5980.0090.0090.0000.0000.0000.000
73A224LEU00.0060.01631.358-0.006-0.0060.0000.0000.0000.000
74A225PRO0-0.0150.01035.0230.0010.0010.0000.0000.0000.000
75A226GLN00.0190.00233.2360.0090.0090.0000.0000.0000.000
76A227GLN00.025-0.00335.713-0.003-0.0030.0000.0000.0000.000
77A228ASN0-0.0030.00336.3210.0060.0060.0000.0000.0000.000
78A229ILE00.0000.01237.5570.0020.0020.0000.0000.0000.000
79A230ASP-1-0.783-0.89733.6380.0780.0780.0000.0000.0000.000
80A231ARG10.8370.91132.209-0.084-0.0840.0000.0000.0000.000
81A232ALA0-0.009-0.00235.807-0.004-0.0040.0000.0000.0000.000
82A233GLY00.0100.01237.711-0.004-0.0040.0000.0000.0000.000
83A234ILE0-0.028-0.00933.103-0.001-0.0010.0000.0000.0000.000
84A235LYS10.8820.94133.771-0.089-0.0890.0000.0000.0000.000
85A236ASN0-0.003-0.01633.0200.0080.0080.0000.0000.0000.000
86A237ARG10.9260.96627.457-0.147-0.1470.0000.0000.0000.000
87A238VAL00.0200.01331.958-0.004-0.0040.0000.0000.0000.000
88A239TYR0-0.064-0.06127.0850.0070.0070.0000.0000.0000.000
89A240SER00.0310.02528.597-0.013-0.0130.0000.0000.0000.000
90A241ASN00.028-0.00327.325-0.001-0.0010.0000.0000.0000.000
91A242SER00.0340.01929.655-0.011-0.0110.0000.0000.0000.000
92A243VAL0-0.009-0.00630.7540.0050.0050.0000.0000.0000.000
93A244TYR0-0.011-0.00428.306-0.004-0.0040.0000.0000.0000.000
94A245GLU-1-0.827-0.88634.0480.0570.0570.0000.0000.0000.000
95A246ILE0-0.012-0.01130.9710.0020.0020.0000.0000.0000.000
96A247LEU0-0.058-0.02834.458-0.005-0.0050.0000.0000.0000.000
97A248GLU-1-0.719-0.82835.3800.0500.0500.0000.0000.0000.000
98A249ASN0-0.037-0.02837.353-0.003-0.0030.0000.0000.0000.000
99A250GLY00.0190.01739.532-0.002-0.0020.0000.0000.0000.000
100A251GLN0-0.023-0.00540.9910.0000.0000.0000.0000.0000.000
101A252PRO0-0.011-0.01639.0920.0020.0020.0000.0000.0000.000
102A253ALA0-0.0040.00436.815-0.003-0.0030.0000.0000.0000.000
103A254GLY00.0290.00835.1530.0000.0000.0000.0000.0000.000
104A255VAL0-0.061-0.01735.1770.0000.0000.0000.0000.0000.000
105A256CYS0-0.060-0.01229.4920.0040.0040.0000.0000.0000.000
106A257ILE00.0180.00029.067-0.002-0.0020.0000.0000.0000.000
107A258LEU00.0090.01026.0240.0070.0070.0000.0000.0000.000
108A259GLU-1-0.730-0.83923.3500.1760.1760.0000.0000.0000.000
109A260TYR00.0720.03219.5700.0030.0030.0000.0000.0000.000
110A261ALA00.0090.01915.594-0.004-0.0040.0000.0000.0000.000
111A262THR00.005-0.01316.0100.0510.0510.0000.0000.0000.000
112A263PRO0-0.022-0.01313.319-0.003-0.0030.0000.0000.0000.000
113A264LEU00.0160.01711.8300.1110.1110.0000.0000.0000.000
114A265GLN00.0190.00612.5930.0170.0170.0000.0000.0000.000
115A266THR0-0.023-0.00911.022-0.065-0.0650.0000.0000.0000.000
116A267LEU00.0060.0006.6480.0170.0170.0000.0000.0000.000
117A268PHE00.0120.0089.465-0.074-0.0740.0000.0000.0000.000
118A269ALA00.0480.02812.158-0.056-0.0560.0000.0000.0000.000
119A270MET0-0.050-0.0277.6970.0320.0320.0000.0000.0000.000
120A271SER0-0.0170.0078.724-0.035-0.0350.0000.0000.0000.000
121A272GLN0-0.061-0.03510.355-0.064-0.0640.0000.0000.0000.000
122A273ASP-1-0.764-0.84913.3180.0820.0820.0000.0000.0000.000
123A274ALA0-0.035-0.01413.264-0.009-0.0090.0000.0000.0000.000
124A275LYS10.7930.86312.700-0.108-0.1080.0000.0000.0000.000
125A276ALA0-0.042-0.01710.565-0.024-0.0240.0000.0000.0000.000
126A277GLY0-0.001-0.0136.9530.1110.1110.0000.0000.0000.000
127A278PHE0-0.057-0.0142.702-0.8030.1180.364-0.309-0.976-0.002
128A279SER00.024-0.0146.4580.0890.0890.0000.0000.0000.000
129A280ARG10.8880.9027.6540.1890.1890.0000.0000.0000.000
130A281GLU-1-0.805-0.8858.055-0.062-0.0620.0000.0000.0000.000
131A282ASP-1-0.812-0.8723.256-3.098-1.8540.080-0.579-0.745-0.004
132A283ARG10.8060.8904.2330.1090.260-0.001-0.029-0.1220.000
133A284LEU0-0.0050.0086.5240.3150.3150.0000.0000.0000.000
134A285GLU-1-0.893-0.9544.334-0.347-0.210-0.001-0.014-0.1220.000
135A286GLN0-0.009-0.0182.5571.7342.8912.929-1.130-2.957-0.008
136A287ALA00.0110.0055.108-0.019-0.003-0.001-0.005-0.0100.000
137A288LYS10.8990.9507.486-0.215-0.2150.0000.0000.0000.000
138A289LEU0-0.0030.0032.193-0.398-1.2633.545-1.052-1.6280.002
139A290PHE0-0.023-0.0076.038-0.340-0.3400.0000.0000.0000.000
140A291CYS0-0.069-0.0388.331-0.260-0.2600.0000.0000.0000.000
141A292ARG10.9170.9476.463-0.143-0.1430.0000.0000.0000.000
142A293THR0-0.030-0.0287.403-0.123-0.1230.0000.0000.0000.000
143A294LEU0-0.043-0.02510.025-0.095-0.0950.0000.0000.0000.000
144A295GLU-1-0.878-0.94213.1300.2250.2250.0000.0000.0000.000
145A296GLU-1-0.836-0.90710.8130.1880.1880.0000.0000.0000.000
146A297ILE0-0.015-0.00412.509-0.032-0.0320.0000.0000.0000.000
147A298LEU0-0.045-0.04115.746-0.036-0.0360.0000.0000.0000.000
148A299GLU-1-0.884-0.93017.8520.0960.0960.0000.0000.0000.000
149A300ASP-1-0.919-0.93317.8830.1000.1000.0000.0000.0000.000
150A301VAL0-0.111-0.04720.424-0.012-0.0120.0000.0000.0000.000
151A302PRO00.0590.01223.0150.0070.0070.0000.0000.0000.000
152A303GLU-1-0.881-0.93125.3020.0950.0950.0000.0000.0000.000
153A304SER00.007-0.01322.2110.0020.0020.0000.0000.0000.000
154A305ARG10.8990.95020.404-0.109-0.1090.0000.0000.0000.000
155A306ASN00.0030.01823.369-0.007-0.0070.0000.0000.0000.000
156A307ASN0-0.002-0.01426.734-0.009-0.0090.0000.0000.0000.000
157A308CYS0-0.073-0.03022.1150.0080.0080.0000.0000.0000.000
158A309ARG10.8420.91322.204-0.115-0.1150.0000.0000.0000.000
159A310LEU00.0180.01915.6730.0090.0090.0000.0000.0000.000
160A311ILE0-0.012-0.00419.690-0.023-0.0230.0000.0000.0000.000
161A312VAL00.0230.01514.7950.0190.0190.0000.0000.0000.000
162A313TYR0-0.062-0.04517.172-0.027-0.0270.0000.0000.0000.000
163A314GLN0-0.014-0.01314.2840.0420.0420.0000.0000.0000.000
164A315GLU-1-0.796-0.89417.5300.0980.0980.0000.0000.0000.000
165A316PRO0-0.075-0.02118.365-0.001-0.0010.0000.0000.0000.000
166A317THR0-0.033-0.04917.8120.0070.0070.0000.0000.0000.000
167A318ASP-1-0.931-0.93820.4970.0160.0160.0000.0000.0000.000
168A319GLY00.0100.00724.186-0.001-0.0010.0000.0000.0000.000
169A320ASN0-0.030-0.03227.1610.0090.0090.0000.0000.0000.000
170A321SER0-0.019-0.00625.2790.0020.0020.0000.0000.0000.000
171A322PHE00.0080.00923.391-0.002-0.0020.0000.0000.0000.000
172A323SER00.0270.00726.5370.0010.0010.0000.0000.0000.000
173A324LEU00.0670.04723.6600.0000.0000.0000.0000.0000.000
174A325SER00.0260.01126.6610.0040.0040.0000.0000.0000.000
175A326GLN0-0.025-0.03629.7670.0010.0010.0000.0000.0000.000
176A327GLU-1-0.759-0.83823.1380.0830.0830.0000.0000.0000.000
177A328VAL00.002-0.00525.5840.0040.0040.0000.0000.0000.000
178A329LEU0-0.020-0.01427.146-0.001-0.0010.0000.0000.0000.000
179A330ARG10.7910.86623.411-0.072-0.0720.0000.0000.0000.000
180A331HIS0-0.019-0.01222.0820.0090.0090.0000.0000.0000.000
181A332ILE0-0.012-0.00726.696-0.004-0.0040.0000.0000.0000.000
182A333ARG10.7530.83829.681-0.056-0.0560.0000.0000.0000.000
183A334GLN0-0.0020.01728.479-0.008-0.0080.0000.0000.0000.000
184A335GLU-1-0.796-0.85127.4600.0980.0980.0000.0000.0000.000
185A336GLU-1-1.017-0.99929.6140.0400.0400.0000.0000.0000.000