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: M3K6Z

Calculation Name: 5KDM-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5KDM

Chain ID: D

ChEMBL ID:

UniProt ID: Q9UER7

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1805658.095227
FMO2-HF: Nuclear repulsion 1736798.727242
FMO2-HF: Total energy -68859.367985
FMO2-MP2: Total energy -69057.30178


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(D:383:LEU)


Summations of interaction energy for fragment #1(D:383: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.
-2.1553.9265.031-3.527-7.5830
Interaction energy analysis for fragmet #1(D:383:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.012
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].
3D385THR0-0.074-0.0412.912-2.9490.8000.358-1.936-2.171-0.002
4D386VAL0-0.063-0.0264.7530.5240.612-0.001-0.010-0.0760.000
5D387ARG10.9710.9567.7330.8960.8960.0000.0000.0000.000
6D388TYR00.025-0.0649.0640.0020.0020.0000.0000.0000.000
7D389ASP-1-0.959-0.96410.596-0.246-0.2460.0000.0000.0000.000
8D390TYR00.0510.03113.7020.0050.0050.0000.0000.0000.000
9D391GLY00.0210.01616.161-0.014-0.0140.0000.0000.0000.000
10D392HIS10.7510.8789.4570.3570.3570.0000.0000.0000.000
11D393TYR00.0490.01411.9610.0090.0090.0000.0000.0000.000
12D394LEU00.0050.01311.010-0.003-0.0030.0000.0000.0000.000
13D395ILE0-0.031-0.0267.9550.0010.0010.0000.0000.0000.000
14D396MET0-0.030-0.00510.3800.0270.0270.0000.0000.0000.000
15D397LEU0-0.021-0.0128.157-0.013-0.0130.0000.0000.0000.000
16D398GLY00.0630.00911.5440.0440.0440.0000.0000.0000.000
17D399PRO0-0.0120.00114.554-0.033-0.0330.0000.0000.0000.000
18D400PHE00.0310.03317.9560.0000.0000.0000.0000.0000.000
19D413TYR00.0580.02319.2000.0040.0040.0000.0000.0000.000
20D414ALA0-0.031-0.03120.888-0.002-0.0020.0000.0000.0000.000
21D415GLU-1-0.860-0.91921.5060.3210.3210.0000.0000.0000.000
22D416SER0-0.028-0.02217.2330.0360.0360.0000.0000.0000.000
23D417SER0-0.042-0.03216.6130.0760.0760.0000.0000.0000.000
24D418TRP00.0180.00917.3620.0500.0500.0000.0000.0000.000
25D419ALA00.0270.01416.3110.0490.0490.0000.0000.0000.000
26D420GLN0-0.013-0.00111.9570.1130.1130.0000.0000.0000.000
27D421ALA00.0080.00112.4070.1410.1410.0000.0000.0000.000
28D422ALA00.0400.02813.3700.0820.0820.0000.0000.0000.000
29D423VAL00.003-0.0049.9070.0980.0980.0000.0000.0000.000
30D424GLN0-0.014-0.0247.5330.0450.0450.0000.0000.0000.000
31D425THR00.0530.0558.4030.2960.2960.0000.0000.0000.000
32D426ALA00.017-0.00610.1990.0700.0700.0000.0000.0000.000
33D427LEU0-0.049-0.0234.466-0.223-0.075-0.001-0.008-0.1390.000
34D428GLU-1-0.917-0.9506.6262.0702.0700.0000.0000.0000.000
35D429LEU0-0.029-0.0107.600-0.340-0.3400.0000.0000.0000.000
36D430PHE00.001-0.0186.552-0.297-0.2970.0000.0000.0000.000
37D431SER0-0.039-0.0204.693-0.197-0.104-0.001-0.005-0.0870.000
38D432ALA0-0.012-0.0016.927-0.297-0.2970.0000.0000.0000.000
39D433LEU0-0.115-0.05310.327-0.163-0.1630.0000.0000.0000.000
40D434TYR0-0.021-0.0409.679-0.104-0.1040.0000.0000.0000.000
41D435PRO0-0.0090.0338.812-0.060-0.0600.0000.0000.0000.000
42D436ALA00.018-0.0069.522-0.131-0.1310.0000.0000.0000.000
43D437PRO00.0110.0076.7440.0740.0740.0000.0000.0000.000
44D438CYS0-0.030-0.0137.1680.0080.0080.0000.0000.0000.000
45D439ILE00.0320.0082.349-1.0340.0951.087-0.419-1.7970.002
46D440SER0-0.077-0.0493.790-0.963-0.7450.006-0.097-0.1270.000
47D441GLY00.0700.0554.7260.1560.231-0.001-0.008-0.0660.000
48D442TYR00.0130.0052.273-0.668-0.3353.583-1.028-2.8870.000
49D443ALA00.019-0.0163.945-0.496-0.3890.002-0.008-0.1010.000
50D444ARG10.9430.9846.997-0.461-0.4610.0000.0000.0000.000
51D445PRO0-0.0580.0128.093-0.024-0.0240.0000.0000.0000.000
52D446PRO00.0610.01810.899-0.019-0.0190.0000.0000.0000.000
53D447GLY0-0.064-0.01913.4410.0620.0620.0000.0000.0000.000
54D448PRO0-0.025-0.01815.050-0.007-0.0070.0000.0000.0000.000
55D449SER00.0560.00216.092-0.021-0.0210.0000.0000.0000.000
56D450ALA00.0230.01617.3620.0250.0250.0000.0000.0000.000
57D451VAL00.0490.02916.402-0.002-0.0020.0000.0000.0000.000
58D452ILE0-0.012-0.00616.4320.0030.0030.0000.0000.0000.000
59D453GLU-1-0.917-0.97217.2870.0590.0590.0000.0000.0000.000
60D454HIS0-0.056-0.02111.767-0.049-0.0490.0000.0000.0000.000
61D455LEU0-0.014-0.02012.344-0.004-0.0040.0000.0000.0000.000
62D456GLY00.0160.02213.941-0.034-0.0340.0000.0000.0000.000
63D457SER0-0.081-0.03210.952-0.044-0.0440.0000.0000.0000.000
64D458LEU0-0.022-0.0157.568-0.050-0.0500.0000.0000.0000.000
65D459VAL0-0.021-0.0029.812-0.067-0.0670.0000.0000.0000.000
66D460PRO0-0.068-0.02510.846-0.009-0.0090.0000.0000.0000.000
67D461LYS10.8780.94513.7990.3390.3390.0000.0000.0000.000
68D462GLY0-0.0040.00916.2370.0010.0010.0000.0000.0000.000
69D463GLY00.0660.03417.3850.0050.0050.0000.0000.0000.000
70D464LEU0-0.044-0.01713.326-0.008-0.0080.0000.0000.0000.000
71D465LEU0-0.0110.00617.5730.0040.0040.0000.0000.0000.000
72D466LEU0-0.009-0.00717.5610.0050.0050.0000.0000.0000.000
73D467PHE00.0280.00520.164-0.009-0.0090.0000.0000.0000.000
74D468LEU00.010-0.00522.2850.0130.0130.0000.0000.0000.000
75D469SER0-0.069-0.01724.5690.0120.0120.0000.0000.0000.000
76D470HIS0-0.018-0.01819.6250.0220.0220.0000.0000.0000.000
77D471LEU0-0.038-0.01119.8800.0210.0210.0000.0000.0000.000
78D472PRO00.0040.00619.343-0.001-0.0010.0000.0000.0000.000
79D473ASP-1-0.877-0.95921.7110.1650.1650.0000.0000.0000.000
80D474ASP-1-0.859-0.90624.2250.1520.1520.0000.0000.0000.000
81D475VAL00.0020.00023.307-0.011-0.0110.0000.0000.0000.000
82D476LYS10.7950.90324.390-0.144-0.1440.0000.0000.0000.000
83D477ASP-1-0.875-0.94426.8360.1020.1020.0000.0000.0000.000
84D478GLY0-0.097-0.03329.306-0.007-0.0070.0000.0000.0000.000
85D479LEU0-0.076-0.03527.557-0.008-0.0080.0000.0000.0000.000
86D480GLY0-0.024-0.01031.805-0.008-0.0080.0000.0000.0000.000
87D488THR00.0380.00635.780-0.001-0.0010.0000.0000.0000.000
88D489GLY00.0390.01635.595-0.001-0.0010.0000.0000.0000.000
89D490PRO00.039-0.00732.7440.0040.0040.0000.0000.0000.000
90D491GLY00.0260.02633.5120.0020.0020.0000.0000.0000.000
91D492MET0-0.003-0.00329.9250.0020.0020.0000.0000.0000.000
92D493GLN00.0290.02328.9270.0030.0030.0000.0000.0000.000
93D494GLN0-0.047-0.02429.0080.0070.0070.0000.0000.0000.000
94D495PHE00.0180.01928.6680.0030.0030.0000.0000.0000.000
95D496VAL00.0490.02224.6790.0080.0080.0000.0000.0000.000
96D497SER0-0.032-0.01325.0980.0070.0070.0000.0000.0000.000
97D498SER0-0.057-0.02525.8070.0070.0070.0000.0000.0000.000
98D499TYR0-0.044-0.03024.3950.0000.0000.0000.0000.0000.000
99D500PHE00.009-0.01718.7740.0200.0200.0000.0000.0000.000
100D501LEU0-0.0220.00921.0590.0000.0000.0000.0000.0000.000
101D502ASN0-0.038-0.03722.0410.0130.0130.0000.0000.0000.000
102D503PRO00.0360.03721.9120.0060.0060.0000.0000.0000.000
103D504ALA00.0170.00719.3910.0080.0080.0000.0000.0000.000
104D505CYS00.0060.02115.0370.0210.0210.0000.0000.0000.000
105D506SER0-0.050-0.03015.1670.0090.0090.0000.0000.0000.000
106D507ASN0-0.023-0.03113.1270.0890.0890.0000.0000.0000.000
107D508VAL0-0.0210.0016.5310.0020.0020.0000.0000.0000.000
108D509PHE00.0430.0248.950-0.023-0.0230.0000.0000.0000.000
109D510ILE00.010-0.0064.464-0.0400.101-0.001-0.008-0.1320.000
110D511THR00.0420.0336.281-0.122-0.1220.0000.0000.0000.000
111D512VAL00.0150.0166.588-0.135-0.1350.0000.0000.0000.000
112D513ARG10.9200.9598.2420.5330.5330.0000.0000.0000.000
113D514GLN00.0990.02910.5230.0030.0030.0000.0000.0000.000
114D515ARG10.8680.92313.3520.2170.2170.0000.0000.0000.000
115D516GLY00.0360.02115.346-0.014-0.0140.0000.0000.0000.000
116D517GLU-1-0.941-0.97115.172-0.280-0.2800.0000.0000.0000.000
117D518LYS10.8870.95116.868-0.022-0.0220.0000.0000.0000.000
118D519ILE00.0840.04813.519-0.008-0.0080.0000.0000.0000.000
119D520ASN00.000-0.00116.7570.0560.0560.0000.0000.0000.000
120D521GLY00.0090.01019.849-0.013-0.0130.0000.0000.0000.000
121D522ARG10.9250.97116.256-0.177-0.1770.0000.0000.0000.000
122D523THR00.012-0.01016.375-0.036-0.0360.0000.0000.0000.000
123D524VAL00.0740.03910.3390.0350.0350.0000.0000.0000.000
124D525LEU00.0810.03412.7100.0700.0700.0000.0000.0000.000
125D526GLN0-0.040-0.00914.2430.0320.0320.0000.0000.0000.000
126D527ALA0-0.025-0.00112.9910.0190.0190.0000.0000.0000.000
127D528LEU00.0110.0098.6470.0650.0650.0000.0000.0000.000
128D529GLY00.0620.03212.3130.0450.0450.0000.0000.0000.000
129D530ARG10.9110.94015.778-0.236-0.2360.0000.0000.0000.000
130D531ALA00.010-0.00111.966-0.001-0.0010.0000.0000.0000.000
131D532CYS00.0050.01311.8830.0940.0940.0000.0000.0000.000
132D533ASP-1-0.898-0.94314.3740.3170.3170.0000.0000.0000.000
133D534MET0-0.118-0.06216.828-0.024-0.0240.0000.0000.0000.000
134D535ALA0-0.0100.00313.742-0.003-0.0030.0000.0000.0000.000
135D536GLY0-0.049-0.00315.7150.0130.0130.0000.0000.0000.000
136D537CYS0-0.050-0.03013.5130.0510.0510.0000.0000.0000.000
137D538GLN0-0.0020.00816.077-0.034-0.0340.0000.0000.0000.000
138D539HIS00.009-0.02013.0060.0410.0410.0000.0000.0000.000
139D540TYR00.0710.04114.631-0.033-0.0330.0000.0000.0000.000
140D541VAL0-0.012-0.01914.2610.0230.0230.0000.0000.0000.000
141D542LEU00.0080.01814.298-0.027-0.0270.0000.0000.0000.000
142D543GLY00.0880.02115.980-0.016-0.0160.0000.0000.0000.000
143D544SER0-0.0150.01015.6560.0050.0050.0000.0000.0000.000
144D545THR0-0.0290.04812.921-0.007-0.0070.0000.0000.0000.000
145D546VAL00.0400.00615.475-0.020-0.0200.0000.0000.0000.000
146D547PRO00.002-0.03018.642-0.008-0.0080.0000.0000.0000.000
147D548LEU0-0.0340.00320.854-0.004-0.0040.0000.0000.0000.000
148D549GLY00.0310.00721.5600.0030.0030.0000.0000.0000.000
149D550GLY00.0750.04020.375-0.009-0.0090.0000.0000.0000.000
150D551LEU00.0340.01918.4270.0030.0030.0000.0000.0000.000
151D552ASN0-0.043-0.03121.090-0.002-0.0020.0000.0000.0000.000
152D553PHE00.0560.04122.0390.0050.0050.0000.0000.0000.000
153D554VAL00.0640.02624.112-0.007-0.0070.0000.0000.0000.000
154D555ASN0-0.052-0.04326.5610.0140.0140.0000.0000.0000.000
155D556ASP-1-0.745-0.91324.8270.0610.0610.0000.0000.0000.000
156D557LEU0-0.043-0.01027.8210.0020.0020.0000.0000.0000.000
157D558ALA0-0.052-0.00729.9210.0020.0020.0000.0000.0000.000
158D559SER0-0.023-0.01530.7820.0000.0000.0000.0000.0000.000
159D560PRO00.0170.01726.333-0.001-0.0010.0000.0000.0000.000
160D561VAL00.0580.03323.296-0.007-0.0070.0000.0000.0000.000
161D562SER0-0.025-0.00824.1540.0140.0140.0000.0000.0000.000
162D563THR0-0.032-0.03818.860-0.003-0.0030.0000.0000.0000.000
163D564ALA0-0.036-0.03319.1530.0000.0000.0000.0000.0000.000
164D565GLU-1-0.909-0.94520.8950.0100.0100.0000.0000.0000.000
165D566MET0-0.0170.00618.708-0.007-0.0070.0000.0000.0000.000
166D567MET0-0.156-0.06516.187-0.003-0.0030.0000.0000.0000.000
167D568ASP-1-0.843-0.90621.245-0.029-0.0290.0000.0000.0000.000
168D569ASP-1-0.920-0.96723.961-0.056-0.0560.0000.0000.0000.000
169D570PHE0-0.037-0.04423.6970.0020.0020.0000.0000.0000.000
170D571SER0-0.090-0.02927.7920.0040.0040.0000.0000.0000.000
171D572PRO00.0140.02625.8820.0040.0040.0000.0000.0000.000
172D573PHE0-0.017-0.01728.194-0.004-0.0040.0000.0000.0000.000
173D574PHE00.0110.00426.2080.0030.0030.0000.0000.0000.000
174D575THR00.0100.00325.0950.0050.0050.0000.0000.0000.000
175D576VAL0-0.077-0.04723.3700.0010.0010.0000.0000.0000.000
176D577GLU-1-0.919-0.95523.126-0.031-0.0310.0000.0000.0000.000
177D578PHE00.021-0.00216.4230.0100.0100.0000.0000.0000.000
178D579PRO00.0000.00418.956-0.001-0.0010.0000.0000.0000.000
179D580PRO0-0.017-0.01921.045-0.013-0.0130.0000.0000.0000.000
180D581ILE0-0.0060.01218.0970.0060.0060.0000.0000.0000.000