FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: 4LG4N

Calculation Name: 1IM3-D-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1IM3

Chain ID: D

ChEMBL ID:

UniProt ID: P61769

Base Structure: X-ray

Registration Date: 2025-07-08

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 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 176
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -702652.755621
FMO2-HF: Nuclear repulsion 664394.872156
FMO2-HF: Total energy -38257.883465
FMO2-MP2: Total energy -38368.685142


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:43:PRO)


Summations of interaction energy for fragment #1(D:43:PRO)
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.
-8.462-2.6150.588-2.8-3.636-0.005
Interaction energy analysis for fragmet #1(D:43:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.044 / q_NPA : -0.031
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].
3D44TRP0-0.0530.0954.094-0.6080.0130.002-0.215-0.4080.000
4D45PHE00.102-0.0883.806-1.9450.230-0.031-1.108-1.0360.005
5D45PHE0-0.0490.0834.8670.0910.0910.0000.0000.0000.000
6D46GLN00.006-0.1116.869-0.013-0.0130.0000.0000.0000.000
7D46GLN0-0.0820.09410.5190.0570.0570.0000.0000.0000.000
8D47ILE00.125-0.12510.5810.0090.0090.0000.0000.0000.000
9D47ILE0-0.0880.11212.374-0.008-0.0080.0000.0000.0000.000
10D48GLU00.018-0.11013.6190.0250.0250.0000.0000.0000.000
11D48GLU-1-0.963-0.83514.235-0.077-0.0770.0000.0000.0000.000
12D49ASP00.082-0.11216.2330.0190.0190.0000.0000.0000.000
13D49ASP-1-0.966-0.84219.566-0.106-0.1060.0000.0000.0000.000
14D50ASN00.122-0.11418.007-0.028-0.0280.0000.0000.0000.000
15D50ASN0-0.1390.06818.348-0.004-0.0040.0000.0000.0000.000
16D51ARG00.043-0.07120.3120.0000.0000.0000.0000.0000.000
17D51ARG10.8521.06023.6650.0860.0860.0000.0000.0000.000
18D52CYS00.112-0.11723.883-0.007-0.0070.0000.0000.0000.000
19D52CYS0-0.1850.21822.0880.0020.0020.0000.0000.0000.000
20D53TYR00.045-0.08026.3610.0020.0020.0000.0000.0000.000
21D53TYR0-0.0630.09429.5500.0010.0010.0000.0000.0000.000
22D54ILE00.177-0.13630.121-0.004-0.0040.0000.0000.0000.000
23D54ILE0-0.1040.13331.0110.0000.0000.0000.0000.0000.000
24D55ASP00.043-0.12432.6520.0030.0030.0000.0000.0000.000
25D55ASP-1-1.027-0.84234.855-0.054-0.0540.0000.0000.0000.000
26D56ASN00.020-0.11735.683-0.001-0.0010.0000.0000.0000.000
27D56ASN0-0.1500.06538.9220.0000.0000.0000.0000.0000.000
28D57GLY00.100-0.07836.2060.0010.0010.0000.0000.0000.000
29D58LYS00.1030.01933.167-0.002-0.0020.0000.0000.0000.000
30D58LYS10.8071.09033.0680.0630.0630.0000.0000.0000.000
31D59LEU00.097-0.09828.9410.0040.0040.0000.0000.0000.000
32D59LEU0-0.0900.10325.776-0.002-0.0020.0000.0000.0000.000
33D60PHE00.058-0.12428.138-0.002-0.0020.0000.0000.0000.000
34D60PHE0-0.1060.09328.8850.0020.0020.0000.0000.0000.000
35D61ALA00.129-0.10424.0800.0050.0050.0000.0000.0000.000
36D61ALA0-0.0780.12123.251-0.003-0.0030.0000.0000.0000.000
37D62ARG00.071-0.10522.405-0.004-0.0040.0000.0000.0000.000
38D62ARG10.8001.04822.0960.0860.0860.0000.0000.0000.000
39D63GLY00.014-0.11218.8750.0010.0010.0000.0000.0000.000
40D64SER00.0250.00716.0430.0050.0050.0000.0000.0000.000
41D64SER0-0.0760.04015.9620.0010.0010.0000.0000.0000.000
42D65ILE00.062-0.08611.8850.0220.0220.0000.0000.0000.000
43D65ILE0-0.0630.0989.811-0.020-0.0200.0000.0000.0000.000
44D66VAL00.029-0.08210.695-0.019-0.0190.0000.0000.0000.000
45D66VAL0-0.0110.12210.5820.0110.0110.0000.0000.0000.000
46D67GLY00.027-0.1286.583-0.129-0.1290.0000.0000.0000.000
47D68ASN00.0990.0594.6770.0180.071-0.002-0.007-0.0450.000
48D68ASN0-0.1070.0542.656-2.577-0.7090.579-1.120-1.328-0.009
49D69MET00.056-0.1855.010-0.021-0.0210.0000.0000.0000.000
50D69MET0-0.0310.1805.466-0.010-0.0100.0000.0000.0000.000
51D70SER00.094-0.0195.8360.1530.1530.0000.0000.0000.000
52D70SER0-0.0310.0607.574-0.031-0.0310.0000.0000.0000.000
53D71ARG00.037-0.0838.1120.0840.0840.0000.0000.0000.000
54D71ARG10.8781.0547.3840.5370.5370.0000.0000.0000.000
55D72PHE00.026-0.1298.635-0.145-0.1450.0000.0000.0000.000
56D72PHE0-0.0150.11310.6560.0070.0070.0000.0000.0000.000
57D73VAL00.055-0.10310.9440.0630.0630.0000.0000.0000.000
58D73VAL0-0.0550.09712.3060.0000.0000.0000.0000.0000.000
59D74PHE00.126-0.07713.393-0.057-0.0570.0000.0000.0000.000
60D74PHE0-0.0650.10815.7990.0030.0030.0000.0000.0000.000
61D75ASP00.055-0.10015.9550.0320.0320.0000.0000.0000.000
62D75ASP-1-0.964-0.82416.702-0.258-0.2580.0000.0000.0000.000
63D76PRO00.020-0.09817.976-0.008-0.0080.0000.0000.0000.000
64D77LYS00.063-0.02420.6590.0110.0110.0000.0000.0000.000
65D77LYS10.7580.99919.2680.2220.2220.0000.0000.0000.000
66D78ALA00.160-0.08823.294-0.006-0.0060.0000.0000.0000.000
67D78ALA0-0.0520.12227.8350.0020.0020.0000.0000.0000.000
68D79ASP00.101-0.11826.655-0.002-0.0020.0000.0000.0000.000
69D79ASP-1-0.984-0.82925.750-0.135-0.1350.0000.0000.0000.000
70D80TYR0-0.003-0.09927.5930.0040.0040.0000.0000.0000.000
71D80TYR0-0.1640.00731.5140.0010.0010.0000.0000.0000.000
72D81GLY00.081-0.05529.9140.0070.0070.0000.0000.0000.000
73D82GLY0-0.096-0.05229.3560.0060.0060.0000.0000.0000.000
74D83VAL00.002-0.02129.137-0.008-0.0080.0000.0000.0000.000
75D83VAL0-0.0380.09630.4910.0010.0010.0000.0000.0000.000
76D84GLY00.024-0.09627.7970.0030.0030.0000.0000.0000.000
77D85GLU0-0.004-0.06327.4400.0010.0010.0000.0000.0000.000
78D85GLU-1-0.888-0.75228.846-0.102-0.1020.0000.0000.0000.000
79D86ASN00.091-0.06524.315-0.005-0.0050.0000.0000.0000.000
80D86ASN0-0.0940.07723.176-0.009-0.0090.0000.0000.0000.000
81D87LEU00.108-0.12324.0010.0130.0130.0000.0000.0000.000
82D87LEU0-0.0640.13324.1960.0010.0010.0000.0000.0000.000
83D88TYR00.090-0.14623.814-0.015-0.0150.0000.0000.0000.000
84D88TYR0-0.1210.12924.773-0.002-0.0020.0000.0000.0000.000
85D89VAL00.006-0.11923.7710.0120.0120.0000.0000.0000.000
86D89VAL0-0.0270.12221.708-0.002-0.0020.0000.0000.0000.000
87D90HIS00.167-0.05824.171-0.007-0.0070.0000.0000.0000.000
88D90HIS0-0.0710.10827.078-0.003-0.0030.0000.0000.0000.000
89D91ALA00.089-0.08322.577-0.009-0.0090.0000.0000.0000.000
90D91ALA0-0.0720.07522.8260.0010.0010.0000.0000.0000.000
91D92ASP00.127-0.11222.619-0.009-0.0090.0000.0000.0000.000
92D92ASP-1-1.019-0.85726.538-0.077-0.0770.0000.0000.0000.000
93D93ASP00.016-0.11623.6920.0060.0060.0000.0000.0000.000
94D93ASP-1-0.919-0.80023.902-0.100-0.1000.0000.0000.0000.000
95D94VAL00.074-0.11319.440-0.007-0.0070.0000.0000.0000.000
96D94VAL0-0.0850.09117.517-0.005-0.0050.0000.0000.0000.000
97D95GLU00.064-0.12718.3480.0040.0040.0000.0000.0000.000
98D95GLU-1-1.040-0.83918.702-0.086-0.0860.0000.0000.0000.000
99D96PHE00.109-0.09614.403-0.017-0.0170.0000.0000.0000.000
100D96PHE0-0.0930.0749.947-0.005-0.0050.0000.0000.0000.000
101D97VAL00.001-0.14013.4270.0170.0170.0000.0000.0000.000
102D97VAL0-0.0670.14013.7200.0020.0020.0000.0000.0000.000
103D98PRO0-0.006-0.11310.914-0.019-0.0190.0000.0000.0000.000
104D99GLY0-0.032-0.0287.8290.0530.0530.0000.0000.0000.000
105D100GLU00.075-0.0228.7910.0740.0740.0000.0000.0000.000
106D100GLU-1-1.037-0.86011.9910.0240.0240.0000.0000.0000.000
107D101SER00.077-0.10710.372-0.024-0.0240.0000.0000.0000.000
108D101SER0-0.0230.09212.7290.0120.0120.0000.0000.0000.000
109D102LEU00.163-0.06211.7000.0220.0220.0000.0000.0000.000
110D102LEU0-0.1530.09711.755-0.014-0.0140.0000.0000.0000.000
111D103LYS00.000-0.13313.345-0.020-0.0200.0000.0000.0000.000
112D103LYS10.8911.10015.7800.0950.0950.0000.0000.0000.000
113D104TRP00.090-0.08216.8480.0030.0030.0000.0000.0000.000
114D104TRP0-0.0790.12514.841-0.011-0.0110.0000.0000.0000.000
115D105ASN00.137-0.08919.8140.0050.0050.0000.0000.0000.000
116D105ASN0-0.1390.06023.1600.0030.0030.0000.0000.0000.000
117D106VAL00.187-0.08223.5040.0100.0100.0000.0000.0000.000
118D106VAL0-0.1350.10122.549-0.002-0.0020.0000.0000.0000.000
119D107ARG00.076-0.08425.1180.0020.0020.0000.0000.0000.000
120D107ARG10.7120.98526.5220.0850.0850.0000.0000.0000.000
121D108ASN00.058-0.07228.867-0.001-0.0010.0000.0000.0000.000
122D108ASN0-0.1400.01932.3250.0030.0030.0000.0000.0000.000
123D109LEU00.266-0.06428.7830.0060.0060.0000.0000.0000.000
124D109LEU0-0.1350.11026.396-0.002-0.0020.0000.0000.0000.000
125D110ASP00.143-0.09330.247-0.002-0.0020.0000.0000.0000.000
126D110ASP-1-0.982-0.84433.623-0.071-0.0710.0000.0000.0000.000
127D111VAL0-0.002-0.13731.380-0.005-0.0050.0000.0000.0000.000
128D111VAL0-0.0460.13529.356-0.001-0.0010.0000.0000.0000.000
129D112MET00.071-0.12932.2890.0060.0060.0000.0000.0000.000
130D112MET0-0.0720.13134.0080.0000.0000.0000.0000.0000.000
131D113PRO0-0.007-0.12034.328-0.002-0.0020.0000.0000.0000.000
132D114ILE00.086-0.04635.4940.0010.0010.0000.0000.0000.000
133D114ILE0-0.0820.12634.5840.0010.0010.0000.0000.0000.000
134D115PHE00.114-0.06631.509-0.003-0.0030.0000.0000.0000.000
135D115PHE0-0.1030.09826.569-0.002-0.0020.0000.0000.0000.000
136D116GLU00.093-0.11430.5300.0060.0060.0000.0000.0000.000
137D116GLU-1-1.073-0.85230.386-0.096-0.0960.0000.0000.0000.000
138D117THR0-0.045-0.09626.6260.0050.0050.0000.0000.0000.000
139D117THR0-0.0520.03225.799-0.005-0.0050.0000.0000.0000.000
140D118LEU00.165-0.05323.8770.0010.0010.0000.0000.0000.000
141D118LEU0-0.1180.08621.7390.0010.0010.0000.0000.0000.000
142D119ALA00.098-0.10521.301-0.007-0.0070.0000.0000.0000.000
143D119ALA0-0.0970.11921.292-0.001-0.0010.0000.0000.0000.000
144D120LEU00.111-0.12018.2520.0080.0080.0000.0000.0000.000
145D120LEU0-0.1350.11416.4410.0020.0020.0000.0000.0000.000
146D121ARG00.118-0.07115.516-0.029-0.0290.0000.0000.0000.000
147D121ARG10.7931.02914.4560.3660.3660.0000.0000.0000.000
148D122LEU00.013-0.13212.3540.0480.0480.0000.0000.0000.000
149D122LEU0-0.0410.12511.654-0.007-0.0070.0000.0000.0000.000
150D123VAL00.080-0.0539.554-0.058-0.0580.0000.0000.0000.000
151D123VAL0-0.1280.0718.9770.0160.0160.0000.0000.0000.000
152D124LEU00.136-0.1466.8580.1990.1990.0000.0000.0000.000
153D124LEU0-0.0700.1256.2890.0090.0090.0000.0000.0000.000
154D125GLN0-0.008-0.1484.060-0.365-0.2480.001-0.026-0.0920.000
155D125GLN0-0.0550.1473.434-0.386-0.0100.013-0.094-0.2940.000
156D126GLY0-0.054-0.1415.012-0.155-0.069-0.001-0.002-0.0830.000
157D127ASP00.115-0.0025.5830.3100.3100.0000.0000.0000.000
158D127ASP-1-0.983-0.8193.601-3.673-3.1220.027-0.228-0.350-0.001
159D128VAL00.077-0.0976.6700.0550.0550.0000.0000.0000.000
160D128VAL0-0.1000.06110.6300.0300.0300.0000.0000.0000.000
161D129ILE0-0.041-0.12510.185-0.027-0.0270.0000.0000.0000.000
162D129ILE0-0.0220.1268.9540.0100.0100.0000.0000.0000.000
163D130TRP00.104-0.10111.7510.0140.0140.0000.0000.0000.000
164D130TRP0-0.0790.09415.0780.0130.0130.0000.0000.0000.000
165D131LEU00.027-0.10815.415-0.007-0.0070.0000.0000.0000.000
166D131LEU0-0.0510.11113.6600.0020.0020.0000.0000.0000.000
167D132ARG00.142-0.07617.2580.0040.0040.0000.0000.0000.000
168D132ARG10.8561.07520.9920.1450.1450.0000.0000.0000.000
169D133CYS00.047-0.11721.0460.0000.0000.0000.0000.0000.000
170D134VAL00.102-0.12123.430-0.002-0.0020.0000.0000.0000.000
171D134VAL0-0.0830.11426.1320.0000.0000.0000.0000.0000.000
172D135PRO0-0.028-0.10227.1830.0030.0030.0000.0000.0000.000
173D136GLU00.0970.00329.4540.0020.0020.0000.0000.0000.000
174D136GLU-1-1.088-0.98528.733-0.075-0.0750.0000.0000.0000.000
175D137LEU0-0.0010.00431.4710.0020.0020.0000.0000.0000.000
176D137LEU00.0090.00533.2960.0010.0010.0000.0000.0000.000