FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 7G83K

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:

Apendix: None


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 180
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1805086.895054
FMO2-HF: Nuclear repulsion 1736226.166704
FMO2-HF: Total energy -68860.72835
FMO2-MP2: Total energy -69058.55643


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.
-3.3153.2855.088-3.647-8.04-0.008
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 : 0.016 / q_NPA : 0.013
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].
3D385THR0-0.055-0.0372.657-3.2820.6510.701-2.158-2.476-0.006
4D386VAL0-0.062-0.0254.3380.3990.492-0.001-0.013-0.0790.000
5D387ARG10.9740.9597.4490.8630.8630.0000.0000.0000.000
6D388TYR00.1070.0278.9640.0140.0140.0000.0000.0000.000
7D389ASP-1-0.931-0.93410.693-0.191-0.1910.0000.0000.0000.000
8D390TYR00.0740.02913.766-0.002-0.0020.0000.0000.0000.000
9D391GLY00.0090.01016.350-0.018-0.0180.0000.0000.0000.000
10D392HIS10.7330.8659.8510.2370.2370.0000.0000.0000.000
11D393TYR00.0650.02112.2930.0020.0020.0000.0000.0000.000
12D394LEU00.0070.01411.0330.0140.0140.0000.0000.0000.000
13D395ILE0-0.036-0.0298.219-0.015-0.0150.0000.0000.0000.000
14D396MET0-0.0130.00710.5130.0410.0410.0000.0000.0000.000
15D397LEU0-0.015-0.0108.232-0.023-0.0230.0000.0000.0000.000
16D398GLY00.0660.00811.8410.0530.0530.0000.0000.0000.000
17D399PRO0-0.0080.00914.534-0.034-0.0340.0000.0000.0000.000
18D400PHE0-0.0040.01417.9380.0070.0070.0000.0000.0000.000
19D413TYR00.0600.02318.9950.0020.0020.0000.0000.0000.000
20D414ALA0-0.026-0.03120.6940.0020.0020.0000.0000.0000.000
21D415GLU-1-0.851-0.91421.1910.3250.3250.0000.0000.0000.000
22D416SER0-0.048-0.03116.9800.0380.0380.0000.0000.0000.000
23D417SER0-0.027-0.02216.2930.0580.0580.0000.0000.0000.000
24D418TRP0-0.006-0.00317.0430.0470.0470.0000.0000.0000.000
25D419ALA00.0310.01615.9180.0460.0460.0000.0000.0000.000
26D420GLN00.0040.00611.5040.1310.1310.0000.0000.0000.000
27D421ALA00.0170.00912.0120.1380.1380.0000.0000.0000.000
28D422ALA00.0400.04613.3400.0710.0710.0000.0000.0000.000
29D423VAL00.002-0.0029.5220.0920.0920.0000.0000.0000.000
30D424GLN0-0.042-0.0367.3280.0620.0620.0000.0000.0000.000
31D425THR00.0490.0318.3480.2410.2410.0000.0000.0000.000
32D426ALA00.010-0.00810.0990.0430.0430.0000.0000.0000.000
33D427LEU0-0.045-0.0224.418-0.248-0.086-0.001-0.010-0.1500.000
34D428GLU-1-0.905-0.9426.6121.7781.7780.0000.0000.0000.000
35D429LEU0-0.034-0.0147.593-0.349-0.3490.0000.0000.0000.000
36D430PHE00.001-0.0176.434-0.278-0.2780.0000.0000.0000.000
37D431SER0-0.044-0.0234.768-0.175-0.089-0.001-0.004-0.0800.000
38D432ALA0-0.009-0.0016.933-0.296-0.2960.0000.0000.0000.000
39D433LEU0-0.108-0.04310.328-0.140-0.1400.0000.0000.0000.000
40D434TYR0-0.045-0.0599.997-0.087-0.0870.0000.0000.0000.000
41D435PRO0-0.0030.0408.822-0.047-0.0470.0000.0000.0000.000
42D436ALA00.022-0.0059.539-0.128-0.1280.0000.0000.0000.000
43D437PRO00.005-0.0016.7090.1220.1220.0000.0000.0000.000
44D438CYS0-0.051-0.0227.3180.0620.0620.0000.0000.0000.000
45D439ILE00.0510.0222.567-0.8080.0581.117-0.307-1.6750.001
46D440SER0-0.063-0.0183.743-1.003-0.7410.006-0.118-0.150-0.001
47D441GLY00.0730.0314.7890.1190.185-0.001-0.006-0.0590.000
48D442TYR00.0220.0062.298-1.278-0.3993.269-1.005-3.144-0.002
49D443ALA00.005-0.0094.112-0.450-0.3370.000-0.017-0.0960.000
50D444ARG10.8640.9276.678-0.601-0.6010.0000.0000.0000.000
51D445PRO0-0.0220.0127.691-0.048-0.0480.0000.0000.0000.000
52D446PRO00.0440.01610.666-0.023-0.0230.0000.0000.0000.000
53D447GLY0-0.0540.00113.1110.0630.0630.0000.0000.0000.000
54D448PRO0-0.038-0.03114.845-0.010-0.0100.0000.0000.0000.000
55D449SER00.040-0.01815.693-0.025-0.0250.0000.0000.0000.000
56D450ALA00.0050.00617.1900.0260.0260.0000.0000.0000.000
57D451VAL00.0620.02816.7310.0040.0040.0000.0000.0000.000
58D452ILE00.000-0.00116.5480.0100.0100.0000.0000.0000.000
59D453GLU-1-0.894-0.94116.6610.1270.1270.0000.0000.0000.000
60D454HIS0-0.057-0.02011.210-0.050-0.0500.0000.0000.0000.000
61D455LEU0-0.003-0.01512.3930.0120.0120.0000.0000.0000.000
62D456GLY00.0080.01814.036-0.031-0.0310.0000.0000.0000.000
63D457SER0-0.078-0.03011.334-0.025-0.0250.0000.0000.0000.000
64D458LEU0-0.032-0.0187.815-0.031-0.0310.0000.0000.0000.000
65D459VAL0-0.025-0.0049.888-0.051-0.0510.0000.0000.0000.000
66D460PRO0-0.054-0.01810.821-0.019-0.0190.0000.0000.0000.000
67D461LYS10.8240.90113.7640.2230.2230.0000.0000.0000.000
68D462GLY0-0.035-0.00316.3350.0040.0040.0000.0000.0000.000
69D463GLY00.0830.03617.5450.0060.0060.0000.0000.0000.000
70D464LEU0-0.065-0.02913.467-0.005-0.0050.0000.0000.0000.000
71D465LEU0-0.0150.01017.811-0.001-0.0010.0000.0000.0000.000
72D466LEU0-0.021-0.00917.7600.0070.0070.0000.0000.0000.000
73D467PHE00.0240.00720.160-0.011-0.0110.0000.0000.0000.000
74D468LEU00.0190.00222.3580.0130.0130.0000.0000.0000.000
75D469SER0-0.075-0.06324.9500.0100.0100.0000.0000.0000.000
76D470HIS0-0.028-0.02119.7480.0230.0230.0000.0000.0000.000
77D471LEU0-0.036-0.00720.0200.0240.0240.0000.0000.0000.000
78D472PRO00.0220.00219.596-0.004-0.0040.0000.0000.0000.000
79D473ASP-1-0.837-0.92821.9240.1760.1760.0000.0000.0000.000
80D474ASP-1-0.827-0.89924.4630.1710.1710.0000.0000.0000.000
81D475VAL0-0.004-0.00123.291-0.011-0.0110.0000.0000.0000.000
82D476LYS10.7700.88424.383-0.167-0.1670.0000.0000.0000.000
83D477ASP-1-0.865-0.94327.0120.1130.1130.0000.0000.0000.000
84D478GLY0-0.104-0.03229.503-0.008-0.0080.0000.0000.0000.000
85D479LEU0-0.088-0.04027.482-0.007-0.0070.0000.0000.0000.000
86D480GLY0-0.016-0.00431.957-0.009-0.0090.0000.0000.0000.000
87D488THR00.0310.00135.819-0.001-0.0010.0000.0000.0000.000
88D489GLY00.0370.02135.626-0.001-0.0010.0000.0000.0000.000
89D490PRO00.053-0.00132.8300.0050.0050.0000.0000.0000.000
90D491GLY00.0160.01833.5890.0020.0020.0000.0000.0000.000
91D492MET00.0010.00130.4240.0020.0020.0000.0000.0000.000
92D493GLN00.0470.03428.7670.0030.0030.0000.0000.0000.000
93D494GLN0-0.043-0.00729.0900.0060.0060.0000.0000.0000.000
94D495PHE00.0330.02828.9930.0040.0040.0000.0000.0000.000
95D496VAL00.0470.04024.7590.0090.0090.0000.0000.0000.000
96D497SER0-0.049-0.03125.2240.0090.0090.0000.0000.0000.000
97D498SER0-0.098-0.06825.9450.0090.0090.0000.0000.0000.000
98D499TYR0-0.009-0.02324.6700.0020.0020.0000.0000.0000.000
99D500PHE0-0.015-0.02418.3900.0210.0210.0000.0000.0000.000
100D501LEU0-0.0300.00921.1870.0030.0030.0000.0000.0000.000
101D502ASN0-0.040-0.03722.0140.0160.0160.0000.0000.0000.000
102D503PRO00.0460.03621.8880.0070.0070.0000.0000.0000.000
103D504ALA00.0210.01219.1710.0110.0110.0000.0000.0000.000
104D505CYS00.0220.03214.8070.0180.0180.0000.0000.0000.000
105D506SER0-0.023-0.01414.8760.0060.0060.0000.0000.0000.000
106D507ASN0-0.024-0.02812.9300.0900.0900.0000.0000.0000.000
107D508VAL0-0.018-0.0026.3650.0250.0250.0000.0000.0000.000
108D509PHE00.0490.0279.046-0.038-0.0380.0000.0000.0000.000
109D510ILE00.007-0.0034.3380.0120.152-0.001-0.009-0.1310.000
110D511THR00.0360.0276.320-0.157-0.1570.0000.0000.0000.000
111D512VAL00.0050.0217.109-0.108-0.1080.0000.0000.0000.000
112D513ARG10.9500.9798.6480.4450.4450.0000.0000.0000.000
113D514GLN00.0990.03010.796-0.001-0.0010.0000.0000.0000.000
114D515ARG10.8670.92413.6920.1730.1730.0000.0000.0000.000
115D516GLY00.0330.02015.570-0.017-0.0170.0000.0000.0000.000
116D517GLU-1-0.934-0.96615.722-0.273-0.2730.0000.0000.0000.000
117D518LYS10.8650.92816.879-0.023-0.0230.0000.0000.0000.000
118D519ILE00.0590.04013.487-0.006-0.0060.0000.0000.0000.000
119D520ASN00.011-0.00116.1040.0540.0540.0000.0000.0000.000
120D521GLY00.0080.01519.862-0.011-0.0110.0000.0000.0000.000
121D522ARG10.9280.97716.370-0.153-0.1530.0000.0000.0000.000
122D523THR00.010-0.00916.821-0.031-0.0310.0000.0000.0000.000
123D524VAL00.0830.04510.7320.0290.0290.0000.0000.0000.000
124D525LEU00.0680.02312.8670.0660.0660.0000.0000.0000.000
125D526GLN0-0.030-0.01114.4950.0280.0280.0000.0000.0000.000
126D527ALA0-0.0280.00012.9730.0170.0170.0000.0000.0000.000
127D528LEU00.0210.0128.9310.0620.0620.0000.0000.0000.000
128D529GLY00.0750.04012.4020.0470.0470.0000.0000.0000.000
129D530ARG10.8640.90215.949-0.219-0.2190.0000.0000.0000.000
130D531ALA00.0090.00111.948-0.001-0.0010.0000.0000.0000.000
131D532CYS0-0.022-0.00612.4130.1020.1020.0000.0000.0000.000
132D533ASP-1-0.895-0.94414.2720.3030.3030.0000.0000.0000.000
133D534MET0-0.063-0.01816.645-0.023-0.0230.0000.0000.0000.000
134D535ALA0-0.0130.00413.636-0.007-0.0070.0000.0000.0000.000
135D536GLY0-0.041-0.00215.6110.0140.0140.0000.0000.0000.000
136D537CYS0-0.046-0.03113.6520.0560.0560.0000.0000.0000.000
137D538GLN0-0.0030.00716.078-0.022-0.0220.0000.0000.0000.000
138D539HIS00.014-0.01313.2920.0400.0400.0000.0000.0000.000
139D540TYR00.0330.03314.852-0.033-0.0330.0000.0000.0000.000
140D541VAL0-0.023-0.02514.2910.0310.0310.0000.0000.0000.000
141D542LEU00.0180.01714.661-0.029-0.0290.0000.0000.0000.000
142D543GLY00.0900.02815.992-0.021-0.0210.0000.0000.0000.000
143D544SER0-0.0180.00215.6140.0120.0120.0000.0000.0000.000
144D545THR0-0.069-0.02412.880-0.005-0.0050.0000.0000.0000.000
145D546VAL00.0510.01015.751-0.022-0.0220.0000.0000.0000.000
146D547PRO0-0.010-0.01918.828-0.003-0.0030.0000.0000.0000.000
147D548LEU0-0.029-0.00321.023-0.004-0.0040.0000.0000.0000.000
148D549GLY00.0310.01421.7380.0050.0050.0000.0000.0000.000
149D550GLY00.0720.04020.494-0.006-0.0060.0000.0000.0000.000
150D551LEU00.0210.01118.4260.0080.0080.0000.0000.0000.000
151D552ASN0-0.048-0.02521.281-0.008-0.0080.0000.0000.0000.000
152D553PHE00.0740.04422.3720.0080.0080.0000.0000.0000.000
153D554VAL00.0540.02124.276-0.009-0.0090.0000.0000.0000.000
154D555ASN0-0.044-0.04326.5480.0140.0140.0000.0000.0000.000
155D556ASP-1-0.732-0.86624.6810.0880.0880.0000.0000.0000.000
156D557LEU0-0.0230.00327.8620.0010.0010.0000.0000.0000.000
157D558ALA0-0.055-0.01130.0050.0010.0010.0000.0000.0000.000
158D559SER0-0.023-0.01430.480-0.001-0.0010.0000.0000.0000.000
159D560PRO00.0210.01826.3870.0000.0000.0000.0000.0000.000
160D561VAL00.0320.02623.065-0.007-0.0070.0000.0000.0000.000
161D562SER0-0.052-0.02424.2380.0140.0140.0000.0000.0000.000
162D563THR0-0.007-0.02318.888-0.003-0.0030.0000.0000.0000.000
163D564ALA0-0.054-0.04319.2870.0030.0030.0000.0000.0000.000
164D565GLU-1-0.859-0.92121.1890.0300.0300.0000.0000.0000.000
165D566MET00.0020.00118.679-0.003-0.0030.0000.0000.0000.000
166D567MET0-0.147-0.06417.4710.0020.0020.0000.0000.0000.000
167D568ASP-1-0.859-0.92121.569-0.012-0.0120.0000.0000.0000.000
168D569ASP-1-0.932-0.96324.197-0.026-0.0260.0000.0000.0000.000
169D570PHE0-0.059-0.05123.7220.0050.0050.0000.0000.0000.000
170D571SER0-0.074-0.01827.9070.0030.0030.0000.0000.0000.000
171D572PRO00.0230.02426.1160.0030.0030.0000.0000.0000.000
172D573PHE0-0.035-0.02128.392-0.006-0.0060.0000.0000.0000.000
173D574PHE00.008-0.00625.8030.0030.0030.0000.0000.0000.000
174D575THR00.0190.00725.3470.0050.0050.0000.0000.0000.000
175D576VAL0-0.088-0.05723.728-0.001-0.0010.0000.0000.0000.000
176D577GLU-1-0.908-0.95423.2660.0100.0100.0000.0000.0000.000
177D578PHE00.0220.00716.4150.0110.0110.0000.0000.0000.000
178D579PRO00.0080.01118.966-0.004-0.0040.0000.0000.0000.000
179D580PRO0-0.013-0.02021.003-0.011-0.0110.0000.0000.0000.000
180D581ILE0-0.0110.00618.1380.0080.0080.0000.0000.0000.000