FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: JL8Q9

Calculation Name: 4LK4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LK4

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KSQ6

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 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 331
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4810114.194372
FMO2-HF: Nuclear repulsion 4684076.172592
FMO2-HF: Total energy -126038.02178
FMO2-MP2: Total energy -126406.062649


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:32:ARG)


Summations of interaction energy for fragment #1(A:32:ARG)
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.
-190.312-190.61636.048-17.452-18.29-0.173
Interaction energy analysis for fragmet #1(A:32:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.819 / q_NPA : 0.872
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].
3A34ILE00.0010.0012.440-1.9210.8550.610-1.070-2.3150.001
4A35ASN0-0.007-0.0034.4921.7421.963-0.001-0.027-0.1930.000
5A36GLY00.0410.0148.026-1.346-1.3460.0000.0000.0000.000
6A37SER0-0.015-0.0108.6901.0021.0020.0000.0000.0000.000
7A38ASN00.0260.02410.7380.0710.0710.0000.0000.0000.000
8A39ALA00.0210.01010.956-0.720-0.7200.0000.0000.0000.000
9A40ASN0-0.028-0.01311.1792.3042.3040.0000.0000.0000.000
10A41SER00.0430.00612.785-0.360-0.3600.0000.0000.0000.000
11A42ALA00.0040.00315.6930.2740.2740.0000.0000.0000.000
12A43GLU-1-0.888-0.9259.733-21.318-21.3180.0000.0000.0000.000
13A44TRP0-0.115-0.06010.021-0.284-0.2840.0000.0000.0000.000
14A45PRO00.0260.01816.0130.5570.5570.0000.0000.0000.000
15A46SER0-0.032-0.04019.0010.4130.4130.0000.0000.0000.000
16A47ILE0-0.0210.00816.5920.0350.0350.0000.0000.0000.000
17A48VAL0-0.019-0.02019.5040.7950.7950.0000.0000.0000.000
18A49ALA00.0160.03122.075-0.462-0.4620.0000.0000.0000.000
19A50LEU0-0.027-0.01923.8780.6290.6290.0000.0000.0000.000
20A51VAL00.0570.01226.855-0.133-0.1330.0000.0000.0000.000
21A52LYS10.9180.96529.3818.8808.8800.0000.0000.0000.000
22A53ARG10.8100.88532.8588.5868.5860.0000.0000.0000.000
23A54GLY0-0.042-0.02835.5360.1550.1550.0000.0000.0000.000
24A55ALA0-0.056-0.01433.6280.1610.1610.0000.0000.0000.000
25A56ASP-1-0.740-0.88330.969-9.936-9.9360.0000.0000.0000.000
26A57ALA0-0.022-0.00527.853-0.117-0.1170.0000.0000.0000.000
27A58TYR0-0.008-0.02724.573-0.139-0.1390.0000.0000.0000.000
28A59GLN0-0.052-0.03727.497-0.215-0.2150.0000.0000.0000.000
29A60GLY0-0.044-0.01630.2650.0160.0160.0000.0000.0000.000
30A61GLN0-0.048-0.02621.9110.0850.0850.0000.0000.0000.000
31A62PHE0-0.054-0.03726.5840.0890.0890.0000.0000.0000.000
32A63CYS0-0.069-0.01223.652-0.096-0.0960.0000.0000.0000.000
33A64GLY00.0910.06720.6970.1750.1750.0000.0000.0000.000
34A65GLY00.0070.00421.2580.4040.4040.0000.0000.0000.000
35A66SER0-0.039-0.03519.699-0.317-0.3170.0000.0000.0000.000
36A67PHE00.0130.00721.5630.5450.5450.0000.0000.0000.000
37A68LEU0-0.015-0.02323.494-0.354-0.3540.0000.0000.0000.000
38A69GLY00.0580.04125.7190.0910.0910.0000.0000.0000.000
39A70GLY0-0.008-0.00528.2710.1730.1730.0000.0000.0000.000
40A71ARG10.9190.95231.4258.3788.3780.0000.0000.0000.000
41A72TYR00.0020.00629.4830.1490.1490.0000.0000.0000.000
42A73VAL00.0300.02625.010-0.285-0.2850.0000.0000.0000.000
43A74LEU0-0.0230.00321.2530.3720.3720.0000.0000.0000.000
44A75THR00.011-0.01522.643-0.347-0.3470.0000.0000.0000.000
45A76ALA00.0400.02521.8500.0340.0340.0000.0000.0000.000
46A77ALA0-0.011-0.00423.7640.4470.4470.0000.0000.0000.000
47A78HIS10.8690.91722.04113.78813.7880.0000.0000.0000.000
48A80PHE0-0.025-0.03927.3260.3200.3200.0000.0000.0000.000
49A81ASP-1-0.722-0.83129.717-10.176-10.1760.0000.0000.0000.000
50A82SER0-0.072-0.03532.1940.2690.2690.0000.0000.0000.000
51A83ARG10.9230.98129.54710.59310.5930.0000.0000.0000.000
52A84SER00.0280.01434.880-0.056-0.0560.0000.0000.0000.000
53A85ALA00.0890.04335.388-0.054-0.0540.0000.0000.0000.000
54A86ALA00.0200.00836.307-0.101-0.1010.0000.0000.0000.000
55A87SER0-0.064-0.02936.4380.0670.0670.0000.0000.0000.000
56A88VAL0-0.014-0.01031.010-0.201-0.2010.0000.0000.0000.000
57A89ASP-1-0.723-0.84431.913-8.694-8.6940.0000.0000.0000.000
58A90VAL0-0.011-0.00527.464-0.332-0.3320.0000.0000.0000.000
59A91ILE00.0090.00025.9850.4270.4270.0000.0000.0000.000
60A92ILE00.0210.01624.433-0.556-0.5560.0000.0000.0000.000
61A93GLY00.0390.02521.5000.3580.3580.0000.0000.0000.000
62A94ALA0-0.048-0.01822.4560.1650.1650.0000.0000.0000.000
63A95TYR0-0.037-0.05614.956-0.217-0.2170.0000.0000.0000.000
64A96ASP-1-0.827-0.92320.037-12.182-12.1820.0000.0000.0000.000
65A97LEU0-0.038-0.03022.0700.5850.5850.0000.0000.0000.000
66A98ASN0-0.038-0.02024.7190.6810.6810.0000.0000.0000.000
67A99ASN0-0.0100.01825.2180.6960.6960.0000.0000.0000.000
68A100SER00.000-0.01326.924-0.159-0.1590.0000.0000.0000.000
69A101SER0-0.084-0.04428.2910.1520.1520.0000.0000.0000.000
70A102GLN00.0060.00722.156-0.346-0.3460.0000.0000.0000.000
71A103GLY00.0560.02525.586-0.101-0.1010.0000.0000.0000.000
72A104GLU-1-0.867-0.89726.131-9.366-9.3660.0000.0000.0000.000
73A105ARG10.7850.87628.9729.1549.1540.0000.0000.0000.000
74A106ILE0-0.022-0.00930.9610.3450.3450.0000.0000.0000.000
75A107ALA00.0010.01032.445-0.204-0.2040.0000.0000.0000.000
76A108ALA00.0120.01532.866-0.033-0.0330.0000.0000.0000.000
77A109GLN0-0.072-0.05834.5220.3850.3850.0000.0000.0000.000
78A110LYS10.8540.91235.9717.9647.9640.0000.0000.0000.000
79A111ILE0-0.009-0.00131.332-0.234-0.2340.0000.0000.0000.000
80A112TYR0-0.0390.00031.9770.3060.3060.0000.0000.0000.000
81A113ARG10.8440.88529.8549.7009.7000.0000.0000.0000.000
82A114HIS00.0750.04427.5600.5110.5110.0000.0000.0000.000
83A115LEU00.0200.01130.4120.0230.0230.0000.0000.0000.000
84A116SER0-0.015-0.01530.5170.2590.2590.0000.0000.0000.000
85A117TYR0-0.080-0.04626.712-0.302-0.3020.0000.0000.0000.000
86A118SER0-0.007-0.00128.9160.3990.3990.0000.0000.0000.000
87A119PRO00.009-0.00628.627-0.366-0.3660.0000.0000.0000.000
88A120SER0-0.053-0.01429.030-0.244-0.2440.0000.0000.0000.000
89A121ASN00.0340.00026.267-0.024-0.0240.0000.0000.0000.000
90A122LEU0-0.0130.01123.479-0.513-0.5130.0000.0000.0000.000
91A123LEU0-0.0020.01123.863-0.549-0.5490.0000.0000.0000.000
92A124ASN0-0.013-0.03324.6840.1850.1850.0000.0000.0000.000
93A125ASP-1-0.731-0.80022.739-12.866-12.8660.0000.0000.0000.000
94A126ILE0-0.042-0.01323.089-0.596-0.5960.0000.0000.0000.000
95A127ALA0-0.006-0.01425.0620.5720.5720.0000.0000.0000.000
96A128ILE0-0.0230.00326.510-0.405-0.4050.0000.0000.0000.000
97A129VAL00.0040.00028.3260.3740.3740.0000.0000.0000.000
98A130GLU-1-0.742-0.82430.680-8.657-8.6570.0000.0000.0000.000
99A131LEU0-0.001-0.00129.4770.1760.1760.0000.0000.0000.000
100A132ALA0-0.003-0.01433.9340.1820.1820.0000.0000.0000.000
101A133GLN0-0.034-0.02235.0220.3400.3400.0000.0000.0000.000
102A134THR0-0.020-0.01433.500-0.166-0.1660.0000.0000.0000.000
103A135SER0-0.025-0.03829.4000.0290.0290.0000.0000.0000.000
104A136SER0-0.056-0.04030.4950.0040.0040.0000.0000.0000.000
105A137LEU00.0080.01625.290-0.130-0.1300.0000.0000.0000.000
106A138PRO00.0280.00722.1920.0300.0300.0000.0000.0000.000
107A139ALA0-0.0030.02823.515-0.183-0.1830.0000.0000.0000.000
108A140ILE0-0.0070.00016.785-0.335-0.3350.0000.0000.0000.000
109A141THR00.0060.01419.3680.7670.7670.0000.0000.0000.000
110A142LEU0-0.025-0.00818.825-0.893-0.8930.0000.0000.0000.000
111A143ALA00.0520.02416.4320.2260.2260.0000.0000.0000.000
112A144GLY00.0280.02418.4940.8590.8590.0000.0000.0000.000
113A145PRO00.0360.01120.229-0.667-0.6670.0000.0000.0000.000
114A146ALA00.0340.02021.323-0.158-0.1580.0000.0000.0000.000
115A147THR00.0080.01115.160-0.052-0.0520.0000.0000.0000.000
116A148ARG10.9520.97014.05119.26719.2670.0000.0000.0000.000
117A149THR0-0.011-0.01515.249-0.967-0.9670.0000.0000.0000.000
118A150SER0-0.068-0.03116.6470.3750.3750.0000.0000.0000.000
119A151LEU0-0.0450.00110.901-0.463-0.4630.0000.0000.0000.000
120A152PRO00.0080.02010.3180.5660.5660.0000.0000.0000.000
121A153ALA00.017-0.0019.588-1.960-1.9600.0000.0000.0000.000
122A154LEU0-0.032-0.0354.4690.7420.837-0.001-0.004-0.0890.000
123A155THR0-0.015-0.0114.841-5.187-5.121-0.001-0.001-0.0630.000
124A156PRO0-0.005-0.0052.985-2.393-1.7100.067-0.160-0.5900.000
125A157LEU0-0.043-0.0194.2298.9639.062-0.001-0.012-0.0850.000
126A158THR0-0.031-0.0275.947-4.151-4.1510.0000.0000.0000.000
127A159VAL0-0.0170.0038.3472.9912.9910.0000.0000.0000.000
128A160ALA00.0340.00810.868-0.779-0.7790.0000.0000.0000.000
129A161GLY0-0.004-0.01013.3610.9100.9100.0000.0000.0000.000
130A162TRP00.003-0.01815.828-0.790-0.7900.0000.0000.0000.000
131A163GLY0-0.064-0.03218.4010.2190.2190.0000.0000.0000.000
132A164ILE0-0.099-0.02811.721-0.384-0.3840.0000.0000.0000.000
133A165THR0-0.032-0.02613.481-0.149-0.1490.0000.0000.0000.000
134A173PHE00.0590.03421.323-0.084-0.0840.0000.0000.0000.000
135A174THR0-0.017-0.00818.7060.8710.8710.0000.0000.0000.000
136A175PRO00.0210.01921.194-0.293-0.2930.0000.0000.0000.000
137A176ILE0-0.0040.01316.3800.2160.2160.0000.0000.0000.000
138A177LEU0-0.0120.03414.934-0.558-0.5580.0000.0000.0000.000
139A178GLN0-0.018-0.02013.041-1.160-1.1600.0000.0000.0000.000
140A179GLU-1-0.801-0.9228.140-24.940-24.9400.0000.0000.0000.000
141A180VAL0-0.004-0.0097.274-0.238-0.2380.0000.0000.0000.000
142A181ASP-1-0.796-0.8552.480-54.028-51.1021.925-2.307-2.545-0.023
143A182VAL0-0.043-0.0305.1830.9610.9610.0000.0000.0000.000
144A183ASP-1-0.773-0.8531.714-143.865-152.87530.199-12.770-8.420-0.153
145A184LEU0-0.027-0.0024.4707.5917.683-0.001-0.047-0.0440.000
146A185VAL00.0180.0207.663-1.803-1.8030.0000.0000.0000.000
147A186SER0-0.016-0.0139.9530.9990.9990.0000.0000.0000.000
148A187GLN00.0270.01613.060-0.800-0.8000.0000.0000.0000.000
149A188SER00.0320.00016.0420.1880.1880.0000.0000.0000.000
150A189LEU0-0.002-0.00312.3860.6040.6040.0000.0000.0000.000
151A190CYS00.0280.03412.6411.0301.0300.0000.0000.0000.000
152A191GLN00.001-0.00415.8130.5270.5270.0000.0000.0000.000
153A192ILE0-0.011-0.00718.8210.5940.5940.0000.0000.0000.000
154A193VAL0-0.048-0.02315.3350.5220.5220.0000.0000.0000.000
155A194MET00.0230.04516.3490.0840.0840.0000.0000.0000.000
156A195GLN0-0.021-0.00119.1951.2771.2770.0000.0000.0000.000
157A196HIS00.003-0.01122.4030.3330.3330.0000.0000.0000.000
158A197GLY0-0.010-0.00724.443-0.002-0.0020.0000.0000.0000.000
159A198ILE0-0.0190.00918.5370.0630.0630.0000.0000.0000.000
160A199SER00.0290.02021.9480.4240.4240.0000.0000.0000.000
161A200SER00.0340.00320.243-0.634-0.6340.0000.0000.0000.000
162A201ASP-1-0.888-0.94120.220-13.754-13.7540.0000.0000.0000.000
163A202PRO0-0.006-0.02117.210-0.238-0.2380.0000.0000.0000.000
164A203ASN0-0.063-0.01219.051-0.538-0.5380.0000.0000.0000.000
165A204SER0-0.027-0.03220.7190.6280.6280.0000.0000.0000.000
166A205THR00.0880.03320.678-0.445-0.4450.0000.0000.0000.000
167A206ASN0-0.0040.00518.445-0.147-0.1470.0000.0000.0000.000
168A207PHE00.0130.02111.0480.3380.3380.0000.0000.0000.000
169A209ALA00.000-0.0077.912-1.181-1.1810.0000.0000.0000.000
170A210ALA00.0030.0036.7612.7682.7680.0000.0000.0000.000
171A211ARG10.8950.9576.10019.75219.7520.0000.0000.0000.000
172A212LEU0-0.032-0.0252.550-0.3520.8793.185-0.927-3.4890.002
173A213THR0-0.002-0.0026.2581.0551.0550.0000.0000.0000.000
174A214LYS10.8480.9287.35437.57637.5760.0000.0000.0000.000
175A215ASH0-0.032-0.10911.7991.9001.9000.0000.0000.0000.000
176A216SER0-0.119-0.06211.839-1.650-1.6500.0000.0000.0000.000
177A217CYM-1-0.759-0.82312.759-18.985-18.9850.0000.0000.0000.000
178A218GLN00.050-0.00314.366-1.275-1.2750.0000.0000.0000.000
179A219GLY00.0820.05416.5760.7030.7030.0000.0000.0000.000
180A220ASP-1-0.807-0.89618.680-15.388-15.3880.0000.0000.0000.000
181A221ALA0-0.029-0.01419.138-0.697-0.6970.0000.0000.0000.000
182A222GLY00.028-0.01220.1260.4830.4830.0000.0000.0000.000
183A223GLY00.0160.02018.1010.2430.2430.0000.0000.0000.000
184A224PRO0-0.031-0.00215.487-0.292-0.2920.0000.0000.0000.000
185A225ILE0-0.0100.0129.081-0.957-0.9570.0000.0000.0000.000
186A226VAL0-0.035-0.02411.0161.3911.3910.0000.0000.0000.000
187A227VAL00.0180.0039.698-3.307-3.3070.0000.0000.0000.000
188A228LYS10.8470.9092.91642.34042.8570.067-0.127-0.4570.000
189A229THR0-0.032-0.0288.2980.8980.8980.0000.0000.0000.000
190A230GLY00.0310.01810.6430.4020.4020.0000.0000.0000.000
191A231ARG10.8210.9138.69525.62325.6230.0000.0000.0000.000
192A232GLU-1-0.847-0.91513.482-18.477-18.4770.0000.0000.0000.000
193A233GLN00.0060.00314.243-0.945-0.9450.0000.0000.0000.000
194A234LEU0-0.014-0.00911.4681.1101.1100.0000.0000.0000.000
195A235GLY00.028-0.02014.8890.6890.6890.0000.0000.0000.000
196A236ILE0-0.0320.00115.709-0.062-0.0620.0000.0000.0000.000
197A237VAL0-0.0120.00814.733-0.142-0.1420.0000.0000.0000.000
198A238SER0-0.036-0.04617.0061.1511.1510.0000.0000.0000.000
199A239TRP00.033-0.00618.2010.4800.4800.0000.0000.0000.000
200A240GLY00.0430.02717.234-1.013-1.0130.0000.0000.0000.000
201A241ASP-1-0.862-0.96312.703-23.609-23.6090.0000.0000.0000.000
202A242GLU-1-0.876-0.92916.307-14.034-14.0340.0000.0000.0000.000
203A243GLN0-0.117-0.05218.7690.5440.5440.0000.0000.0000.000
204A244CYM-1-0.648-0.67117.806-18.138-18.1380.0000.0000.0000.000
205A245ALA0-0.086-0.10019.0880.3070.3070.0000.0000.0000.000
206A246LYS10.8580.90815.99016.02716.0270.0000.0000.0000.000
207A247THR00.0250.02615.6210.2770.2770.0000.0000.0000.000
208A248GLY0-0.024-0.00714.723-1.375-1.3750.0000.0000.0000.000
209A249THR0-0.030-0.02414.9581.1211.1210.0000.0000.0000.000
210A250TYR0-0.082-0.05810.719-2.079-2.0790.0000.0000.0000.000
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