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

tag_button

FMODB ID: 22Z7R

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 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 180
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1808464.557598
FMO2-HF: Nuclear repulsion 1739602.690539
FMO2-HF: Total energy -68861.867059
FMO2-MP2: Total energy -69059.589314


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.
-2.5453.9754.379-3.189-7.709-0.006
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 : 0.035 / q_NPA : 0.020
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].
3D385THR0-0.063-0.0332.837-2.8260.8630.400-1.925-2.165-0.005
4D386VAL0-0.092-0.0424.4100.5110.596-0.001-0.012-0.0710.000
5D387ARG10.9730.9547.6880.8970.8970.0000.0000.0000.000
6D388TYR00.0740.0319.5390.0290.0290.0000.0000.0000.000
7D389ASP-1-0.879-0.92510.675-0.264-0.2640.0000.0000.0000.000
8D390TYR00.0570.03113.949-0.006-0.0060.0000.0000.0000.000
9D391GLY00.0030.00916.478-0.016-0.0160.0000.0000.0000.000
10D392HIS10.7540.87610.5940.3570.3570.0000.0000.0000.000
11D393TYR00.0480.00712.7320.0080.0080.0000.0000.0000.000
12D394LEU0-0.0110.00011.527-0.021-0.0210.0000.0000.0000.000
13D395ILE0-0.045-0.0357.9500.0020.0020.0000.0000.0000.000
14D396MET0-0.0110.01810.8060.0090.0090.0000.0000.0000.000
15D397LEU0-0.018-0.0107.945-0.014-0.0140.0000.0000.0000.000
16D398GLY00.0780.01411.9180.0560.0560.0000.0000.0000.000
17D399PRO00.0020.01114.606-0.030-0.0300.0000.0000.0000.000
18D400PHE0-0.069-0.03417.9140.0100.0100.0000.0000.0000.000
19D413TYR00.0670.03218.5880.0050.0050.0000.0000.0000.000
20D414ALA0-0.016-0.01620.208-0.004-0.0040.0000.0000.0000.000
21D415GLU-1-0.852-0.92020.6710.2860.2860.0000.0000.0000.000
22D416SER0-0.053-0.04116.7190.0360.0360.0000.0000.0000.000
23D417SER0-0.014-0.01715.8810.0570.0570.0000.0000.0000.000
24D418TRP0-0.0070.00216.3770.0510.0510.0000.0000.0000.000
25D419ALA00.0240.01215.4490.0360.0360.0000.0000.0000.000
26D420GLN0-0.010-0.00611.0270.1060.1060.0000.0000.0000.000
27D421ALA00.0390.02211.3400.1310.1310.0000.0000.0000.000
28D422ALA00.0280.03512.7070.0830.0830.0000.0000.0000.000
29D423VAL00.008-0.0159.1510.0470.0470.0000.0000.0000.000
30D424GLN0-0.044-0.0217.3180.0680.0680.0000.0000.0000.000
31D425THR00.0380.0108.2000.1940.1940.0000.0000.0000.000
32D426ALA00.000-0.00810.393-0.016-0.0160.0000.0000.0000.000
33D427LEU0-0.024-0.0104.194-0.295-0.110-0.001-0.013-0.1720.000
34D428GLU-1-0.927-0.9416.4291.6901.6900.0000.0000.0000.000
35D429LEU0-0.025-0.0137.660-0.260-0.2600.0000.0000.0000.000
36D430PHE0-0.008-0.0236.579-0.198-0.1980.0000.0000.0000.000
37D431SER0-0.033-0.0315.301-0.110-0.1100.0000.0000.0000.000
38D432ALA0-0.022-0.0047.443-0.205-0.2050.0000.0000.0000.000
39D433LEU0-0.087-0.03410.692-0.111-0.1110.0000.0000.0000.000
40D434TYR0-0.071-0.0769.854-0.066-0.0660.0000.0000.0000.000
41D435PRO00.0270.0439.010-0.074-0.0740.0000.0000.0000.000
42D436ALA00.019-0.0019.210-0.079-0.0790.0000.0000.0000.000
43D437PRO00.008-0.0036.6110.0370.0370.0000.0000.0000.000
44D438CYS0-0.048-0.0206.5790.1850.1850.0000.0000.0000.000
45D439ILE00.0640.0462.397-0.719-0.2182.172-0.422-2.2510.002
46D440SER0-0.025-0.0194.604-0.600-0.564-0.001-0.008-0.0270.000
47D441GLY00.0500.0464.6060.0230.078-0.001-0.007-0.0460.000
48D442TYR00.0180.0032.461-1.761-0.0041.812-0.774-2.795-0.003
49D443ALA00.0020.0114.304-0.314-0.2340.000-0.022-0.0570.000
50D444ARG10.8500.8977.206-0.390-0.3900.0000.0000.0000.000
51D445PRO0-0.0140.0077.887-0.006-0.0060.0000.0000.0000.000
52D446PRO00.0350.00810.945-0.027-0.0270.0000.0000.0000.000
53D447GLY0-0.035-0.00913.2860.0570.0570.0000.0000.0000.000
54D448PRO0-0.058-0.03714.631-0.010-0.0100.0000.0000.0000.000
55D449SER00.040-0.01615.156-0.007-0.0070.0000.0000.0000.000
56D450ALA00.0430.02917.1290.0230.0230.0000.0000.0000.000
57D451VAL00.0360.01916.608-0.002-0.0020.0000.0000.0000.000
58D452ILE00.0150.00416.544-0.005-0.0050.0000.0000.0000.000
59D453GLU-1-0.882-0.91616.2580.0670.0670.0000.0000.0000.000
60D454HIS0-0.049-0.01811.556-0.025-0.0250.0000.0000.0000.000
61D455LEU00.006-0.00412.463-0.020-0.0200.0000.0000.0000.000
62D456GLY00.0290.02014.036-0.031-0.0310.0000.0000.0000.000
63D457SER0-0.087-0.05211.471-0.025-0.0250.0000.0000.0000.000
64D458LEU0-0.057-0.0237.840-0.053-0.0530.0000.0000.0000.000
65D459VAL0-0.041-0.01210.400-0.060-0.0600.0000.0000.0000.000
66D460PRO0-0.028-0.01111.045-0.002-0.0020.0000.0000.0000.000
67D461LYS10.8030.89313.9190.2910.2910.0000.0000.0000.000
68D462GLY0-0.040-0.01616.406-0.004-0.0040.0000.0000.0000.000
69D463GLY00.0970.04817.9810.0040.0040.0000.0000.0000.000
70D464LEU0-0.067-0.02813.790-0.013-0.0130.0000.0000.0000.000
71D465LEU0-0.0010.00917.8930.0070.0070.0000.0000.0000.000
72D466LEU0-0.009-0.00518.1930.0010.0010.0000.0000.0000.000
73D467PHE00.020-0.00320.427-0.004-0.0040.0000.0000.0000.000
74D468LEU00.0160.00122.4240.0110.0110.0000.0000.0000.000
75D469SER0-0.047-0.05325.0450.0090.0090.0000.0000.0000.000
76D470HIS0-0.022-0.02919.5470.0180.0180.0000.0000.0000.000
77D471LEU0-0.033-0.00419.6280.0150.0150.0000.0000.0000.000
78D472PRO00.0160.00119.269-0.001-0.0010.0000.0000.0000.000
79D473ASP-1-0.812-0.90321.5880.1090.1090.0000.0000.0000.000
80D474ASP-1-0.792-0.87024.3100.1330.1330.0000.0000.0000.000
81D475VAL0-0.029-0.01523.161-0.010-0.0100.0000.0000.0000.000
82D476LYS10.8010.90523.198-0.106-0.1060.0000.0000.0000.000
83D477ASP-1-0.858-0.92327.3320.0720.0720.0000.0000.0000.000
84D478GLY0-0.061-0.02229.911-0.007-0.0070.0000.0000.0000.000
85D479LEU0-0.075-0.03827.288-0.006-0.0060.0000.0000.0000.000
86D480GLY0-0.098-0.04731.744-0.009-0.0090.0000.0000.0000.000
87D488THR00.0400.00435.996-0.001-0.0010.0000.0000.0000.000
88D489GLY00.0530.02935.108-0.001-0.0010.0000.0000.0000.000
89D490PRO00.038-0.01033.1450.0030.0030.0000.0000.0000.000
90D491GLY00.0000.01633.8390.0020.0020.0000.0000.0000.000
91D492MET00.0110.00530.6060.0020.0020.0000.0000.0000.000
92D493GLN00.0250.03428.7840.0030.0030.0000.0000.0000.000
93D494GLN0-0.0220.00729.1540.0030.0030.0000.0000.0000.000
94D495PHE00.0150.02129.0860.0040.0040.0000.0000.0000.000
95D496VAL00.0540.03524.8920.0070.0070.0000.0000.0000.000
96D497SER0-0.038-0.03625.6320.0060.0060.0000.0000.0000.000
97D498SER0-0.098-0.07126.1310.0070.0070.0000.0000.0000.000
98D499TYR0-0.001-0.00424.5450.0030.0030.0000.0000.0000.000
99D500PHE00.010-0.02018.4250.0160.0160.0000.0000.0000.000
100D501LEU0-0.0610.00021.150-0.002-0.0020.0000.0000.0000.000
101D502ASN0-0.022-0.03122.0620.0100.0100.0000.0000.0000.000
102D503PRO00.0390.02721.6450.0060.0060.0000.0000.0000.000
103D504ALA00.0190.02019.3710.0040.0040.0000.0000.0000.000
104D505CYS00.0010.01915.5150.0180.0180.0000.0000.0000.000
105D506SER0-0.013-0.00914.4770.0070.0070.0000.0000.0000.000
106D507ASN0-0.003-0.01112.7720.0650.0650.0000.0000.0000.000
107D508VAL0-0.0300.0076.0710.0310.0310.0000.0000.0000.000
108D509PHE00.0570.0258.998-0.048-0.0480.0000.0000.0000.000
109D510ILE00.004-0.0044.541-0.0670.065-0.001-0.006-0.1250.000
110D511THR00.0410.0146.904-0.032-0.0320.0000.0000.0000.000
111D512VAL0-0.019-0.0056.994-0.078-0.0780.0000.0000.0000.000
112D513ARG10.9320.9698.9360.5390.5390.0000.0000.0000.000
113D514GLN00.0600.02910.951-0.023-0.0230.0000.0000.0000.000
114D515ARG10.8800.92413.5670.2420.2420.0000.0000.0000.000
115D516GLY00.0330.02315.945-0.016-0.0160.0000.0000.0000.000
116D517GLU-1-0.928-0.96615.126-0.339-0.3390.0000.0000.0000.000
117D518LYS10.8760.93416.3670.0260.0260.0000.0000.0000.000
118D519ILE00.0510.04013.2910.0010.0010.0000.0000.0000.000
119D520ASN00.0170.00516.2260.0410.0410.0000.0000.0000.000
120D521GLY00.0260.01819.751-0.009-0.0090.0000.0000.0000.000
121D522ARG10.8920.95916.308-0.084-0.0840.0000.0000.0000.000
122D523THR00.0110.00916.581-0.024-0.0240.0000.0000.0000.000
123D524VAL00.0670.03210.5140.0350.0350.0000.0000.0000.000
124D525LEU00.0690.03012.6060.0510.0510.0000.0000.0000.000
125D526GLN0-0.011-0.00514.2280.0260.0260.0000.0000.0000.000
126D527ALA0-0.021-0.00512.8200.0220.0220.0000.0000.0000.000
127D528LEU00.0330.0208.3480.0470.0470.0000.0000.0000.000
128D529GLY00.0790.04211.8870.0560.0560.0000.0000.0000.000
129D530ARG10.8540.91315.211-0.153-0.1530.0000.0000.0000.000
130D531ALA00.0110.00311.8760.0060.0060.0000.0000.0000.000
131D532CYS0-0.021-0.01111.9000.0800.0800.0000.0000.0000.000
132D533ASP-1-0.893-0.95114.0820.2180.2180.0000.0000.0000.000
133D534MET0-0.064-0.03016.446-0.020-0.0200.0000.0000.0000.000
134D535ALA0-0.0080.01713.5310.0050.0050.0000.0000.0000.000
135D536GLY0-0.0290.00215.5160.0210.0210.0000.0000.0000.000
136D537CYS0-0.059-0.02613.0460.0280.0280.0000.0000.0000.000
137D538GLN00.0180.00615.568-0.019-0.0190.0000.0000.0000.000
138D539HIS0-0.018-0.01713.2210.0230.0230.0000.0000.0000.000
139D540TYR00.0090.00114.439-0.022-0.0220.0000.0000.0000.000
140D541VAL0-0.025-0.02614.1800.0120.0120.0000.0000.0000.000
141D542LEU00.0440.01814.721-0.020-0.0200.0000.0000.0000.000
142D543GLY00.0690.03716.251-0.009-0.0090.0000.0000.0000.000
143D544SER0-0.052-0.02815.637-0.006-0.0060.0000.0000.0000.000
144D545THR0-0.038-0.01113.1090.0080.0080.0000.0000.0000.000
145D546VAL00.0440.00315.815-0.018-0.0180.0000.0000.0000.000
146D547PRO0-0.034-0.02819.227-0.002-0.0020.0000.0000.0000.000
147D548LEU0-0.0230.00521.301-0.002-0.0020.0000.0000.0000.000
148D549GLY00.0470.02622.3350.0050.0050.0000.0000.0000.000
149D550GLY00.0350.02020.411-0.012-0.0120.0000.0000.0000.000
150D551LEU0-0.021-0.01318.460-0.002-0.0020.0000.0000.0000.000
151D552ASN0-0.020-0.01921.1610.0040.0040.0000.0000.0000.000
152D553PHE00.0690.03922.4680.0050.0050.0000.0000.0000.000
153D554VAL00.0650.02124.793-0.006-0.0060.0000.0000.0000.000
154D555ASN0-0.027-0.01727.0900.0110.0110.0000.0000.0000.000
155D556ASP-1-0.736-0.86624.8240.0310.0310.0000.0000.0000.000
156D557LEU0-0.019-0.00227.9630.0030.0030.0000.0000.0000.000
157D558ALA0-0.042-0.00630.1250.0020.0020.0000.0000.0000.000
158D559SER0-0.040-0.03830.856-0.001-0.0010.0000.0000.0000.000
159D560PRO0-0.0140.02726.238-0.003-0.0030.0000.0000.0000.000
160D561VAL00.0200.01323.044-0.004-0.0040.0000.0000.0000.000
161D562SER0-0.020-0.01224.0160.0110.0110.0000.0000.0000.000
162D563THR0-0.001-0.02118.592-0.006-0.0060.0000.0000.0000.000
163D564ALA0-0.055-0.02519.243-0.007-0.0070.0000.0000.0000.000
164D565GLU-1-0.833-0.91020.891-0.025-0.0250.0000.0000.0000.000
165D566MET00.0000.00818.558-0.005-0.0050.0000.0000.0000.000
166D567MET0-0.119-0.05017.774-0.005-0.0050.0000.0000.0000.000
167D568ASP-1-0.856-0.91821.387-0.056-0.0560.0000.0000.0000.000
168D569ASP-1-0.908-0.95724.459-0.071-0.0710.0000.0000.0000.000
169D570PHE0-0.076-0.04323.4740.0040.0040.0000.0000.0000.000
170D571SER0-0.078-0.03227.8890.0050.0050.0000.0000.0000.000
171D572PRO00.0060.01625.9790.0050.0050.0000.0000.0000.000
172D573PHE0-0.034-0.02128.270-0.001-0.0010.0000.0000.0000.000
173D574PHE0-0.012-0.01825.9260.0010.0010.0000.0000.0000.000
174D575THR00.0090.00425.2430.0040.0040.0000.0000.0000.000
175D576VAL0-0.080-0.04624.0440.0050.0050.0000.0000.0000.000
176D577GLU-1-0.851-0.92823.448-0.048-0.0480.0000.0000.0000.000
177D578PHE00.0100.01116.8590.0100.0100.0000.0000.0000.000
178D579PRO0-0.0110.00219.396-0.002-0.0020.0000.0000.0000.000
179D580PRO0-0.002-0.01221.159-0.012-0.0120.0000.0000.0000.000
180D581ILE0-0.0060.01018.1980.0070.0070.0000.0000.0000.000