FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: GYG81

Calculation Name: 4M1A-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4M1A

Chain ID: A

ChEMBL ID:

UniProt ID: D1AJN4

Base Structure: X-ray

Registration Date: 2025-07-09

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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 207
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -869245.550798
FMO2-HF: Nuclear repulsion 825073.885921
FMO2-HF: Total energy -44171.664877
FMO2-MP2: Total energy -44301.180448


3D Structure Molmil
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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
1.872-2.08210.0692.486-8.602-0.017
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.187 / q_NPA : 0.029
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].
4A3HIS00.0920.0182.6445.6620.3450.5005.568-0.751-0.006
5A3HIS0-0.0790.0932.6375.6344.9686.763-2.320-3.7760.003
6A4ILE00.054-0.1234.305-0.603-0.5970.000-0.0240.0190.000
7A4ILE0-0.0390.1226.118-0.077-0.0770.0000.0000.0000.000
8A5ARG00.038-0.1437.9150.1450.1450.0000.0000.0000.000
9A5ARG10.8871.0908.230-1.992-1.9920.0000.0000.0000.000
10A6VAL00.029-0.07910.868-0.106-0.1060.0000.0000.0000.000
11A6VAL0-0.0200.10613.074-0.015-0.0150.0000.0000.0000.000
12A7ARG00.055-0.11214.4210.0420.0420.0000.0000.0000.000
13A7ARG10.8191.05114.366-0.579-0.5790.0000.0000.0000.000
14A8GLY00.066-0.07017.604-0.034-0.0340.0000.0000.0000.000
15A9ALA00.0620.03320.014-0.040-0.0400.0000.0000.0000.000
16A9ALA0-0.0170.08719.312-0.001-0.0010.0000.0000.0000.000
17A10GLU00.060-0.10020.8940.0440.0440.0000.0000.0000.000
18A10GLU-1-0.968-0.85023.8080.1760.1760.0000.0000.0000.000
19A11LYS00.198-0.08519.6410.0040.0040.0000.0000.0000.000
20A11LYS10.8181.08319.236-0.406-0.4060.0000.0000.0000.000
21A12GLU00.044-0.14619.6520.0320.0320.0000.0000.0000.000
22A12GLU-1-1.002-0.85323.4740.1630.1630.0000.0000.0000.000
23A13LYS00.040-0.09921.135-0.010-0.0100.0000.0000.0000.000
24A13LYS10.9131.10421.648-0.140-0.1400.0000.0000.0000.000
25A14VAL00.125-0.08616.994-0.049-0.0490.0000.0000.0000.000
26A14VAL0-0.0660.10615.0850.0050.0050.0000.0000.0000.000
27A15ARG00.147-0.08216.3870.0120.0120.0000.0000.0000.000
28A15ARG10.7220.99217.995-0.196-0.1960.0000.0000.0000.000
29A16ASP00.108-0.14517.222-0.011-0.0110.0000.0000.0000.000
30A16ASP-1-0.956-0.78521.0270.1460.1460.0000.0000.0000.000
31A17PHE0-0.011-0.05617.042-0.050-0.0500.0000.0000.0000.000
32A17PHE0-0.0710.06013.122-0.002-0.0020.0000.0000.0000.000
33A18THR00.020-0.09813.915-0.065-0.0650.0000.0000.0000.000
34A18THR0-0.0750.03012.6330.0250.0250.0000.0000.0000.000
35A19ALA00.057-0.05414.492-0.042-0.0420.0000.0000.0000.000
36A19ALA0-0.0730.09918.6980.0000.0000.0000.0000.0000.000
37A20GLY0-0.022-0.11816.134-0.008-0.0080.0000.0000.0000.000
38A21LEU00.091-0.02113.562-0.086-0.0860.0000.0000.0000.000
39A21LEU0-0.0980.11212.2540.0080.0080.0000.0000.0000.000
40A22ALA00.133-0.14410.030-0.059-0.0590.0000.0000.0000.000
41A22ALA0-0.0820.1459.2390.0190.0190.0000.0000.0000.000
42A23ASP00.026-0.10410.781-0.217-0.2170.0000.0000.0000.000
43A23ASP-1-0.973-0.86314.316-0.326-0.3260.0000.0000.0000.000
44A24GLU00.083-0.10013.551-0.095-0.0950.0000.0000.0000.000
45A24GLU-1-1.007-0.86315.010-0.323-0.3230.0000.0000.0000.000
46A25LEU0-0.020-0.11110.638-0.016-0.0160.0000.0000.0000.000
47A25LEU0-0.0820.0769.4160.0240.0240.0000.0000.0000.000
48A26GLY00.061-0.08610.112-0.172-0.1720.0000.0000.0000.000
49A27ILE00.0200.00310.964-0.121-0.1210.0000.0000.0000.000
50A27ILE0-0.0540.08615.1970.0220.0220.0000.0000.0000.000
51A28ILE00.091-0.09713.985-0.005-0.0050.0000.0000.0000.000
52A28ILE0-0.1440.07113.3420.0130.0130.0000.0000.0000.000
53A29ALA00.027-0.0749.7080.1390.1390.0000.0000.0000.000
54A29ALA0-0.0720.0579.122-0.078-0.0780.0000.0000.0000.000
55A30GLU00.031-0.11810.793-0.261-0.2610.0000.0000.0000.000
56A30GLU-1-1.028-0.85012.854-0.768-0.7680.0000.0000.0000.000
57A31CYS00.023-0.1418.474-0.019-0.0190.0000.0000.0000.000
58A31CYS0-0.1630.0877.494-0.300-0.3000.0000.0000.0000.000
59A32PRO00.034-0.0978.1690.2560.2560.0000.0000.0000.000
60A33ALA00.1770.0237.580-0.543-0.5430.0000.0000.0000.000
61A33ALA0-0.0510.12310.7140.0540.0540.0000.0000.0000.000
62A34ASP00.095-0.1277.571-0.040-0.0400.0000.0000.0000.000
63A34ASP-1-1.032-0.8747.776-0.444-0.4440.0000.0000.0000.000
64A35TRP00.087-0.1343.7960.7000.8640.000-0.038-0.1260.000
65A35TRP0-0.1200.1273.598-0.2170.0080.001-0.085-0.1410.000
66A36PHE00.030-0.0552.503-5.493-3.9340.724-1.218-1.064-0.018
67A36PHE0-0.0880.0596.371-0.093-0.0930.0000.0000.0000.000
68A37THR00.021-0.0694.764-0.0030.057-0.002-0.003-0.0560.000
69A37THR00.0180.0923.9410.8971.005-0.001-0.014-0.0930.000
70A38PHE00.031-0.1236.1120.0490.0490.0000.0000.0000.000
71A38PHE0-0.0270.1239.250-0.034-0.0340.0000.0000.0000.000
72A39GLU00.051-0.1849.580-0.054-0.0540.0000.0000.0000.000
73A39GLU-1-0.941-0.7929.0672.0672.0670.0000.0000.0000.000
74A40TYR00.102-0.07011.875-0.065-0.0650.0000.0000.0000.000
75A40TYR0-0.1770.02116.527-0.013-0.0130.0000.0000.0000.000
76A41VAL00.027-0.11015.3370.0730.0730.0000.0000.0000.000
77A41VAL0-0.0730.09813.5870.0040.0040.0000.0000.0000.000
78A42GLU00.132-0.12216.103-0.058-0.0580.0000.0000.0000.000
79A42GLU-1-1.018-0.78020.0700.3880.3880.0000.0000.0000.000
80A43THR0-0.088-0.09319.7870.0220.0220.0000.0000.0000.000
81A43THR0-0.0240.01118.812-0.001-0.0010.0000.0000.0000.000
82A44THR00.031-0.06821.590-0.004-0.0040.0000.0000.0000.000
83A44THR00.0110.09425.6380.0010.0010.0000.0000.0000.000
84A45PHE00.073-0.07125.0140.0100.0100.0000.0000.0000.000
85A45PHE0-0.0540.10520.7500.0020.0020.0000.0000.0000.000
86A46PHE00.123-0.13526.055-0.008-0.0080.0000.0000.0000.000
87A46PHE0-0.1060.11528.2910.0000.0000.0000.0000.0000.000
88A47PHE00.086-0.11429.1170.0060.0060.0000.0000.0000.000
89A47PHE0-0.0650.12630.038-0.003-0.0030.0000.0000.0000.000
90A48ASP0-0.030-0.11731.684-0.001-0.0010.0000.0000.0000.000
91A48ASP-1-0.994-0.87035.4360.0970.0970.0000.0000.0000.000
92A49GLY0-0.005-0.12734.279-0.007-0.0070.0000.0000.0000.000
93A50LYS00.006-0.04934.4700.0000.0000.0000.0000.0000.000
94A50LYS10.9411.08234.916-0.106-0.1060.0000.0000.0000.000
95A51GLU00.048-0.06331.1470.0050.0050.0000.0000.0000.000
96A51GLU-1-1.020-0.86129.4340.1920.1920.0000.0000.0000.000
97A52ASP00.100-0.14229.741-0.016-0.0160.0000.0000.0000.000
98A52ASP-1-0.979-0.82928.8450.1440.1440.0000.0000.0000.000
99A53ASP00.069-0.08728.1460.0180.0180.0000.0000.0000.000
100A53ASP-1-0.924-0.82627.3450.1460.1460.0000.0000.0000.000
101A54GLY00.005-0.10625.0820.0180.0180.0000.0000.0000.000
102A55LEU00.064-0.00823.413-0.021-0.0210.0000.0000.0000.000
103A55LEU0-0.1710.08421.492-0.001-0.0010.0000.0000.0000.000
104A56VAL00.164-0.12820.2340.0290.0290.0000.0000.0000.000
105A56VAL0-0.1130.13918.184-0.001-0.0010.0000.0000.0000.000
106A57PHE00.109-0.07017.719-0.044-0.0440.0000.0000.0000.000
107A57PHE0-0.1340.03815.243-0.011-0.0110.0000.0000.0000.000
108A58ILE00.101-0.11413.8570.0850.0850.0000.0000.0000.000
109A58ILE0-0.1170.09812.009-0.011-0.0110.0000.0000.0000.000
110A59GLU00.099-0.07111.336-0.149-0.1490.0000.0000.0000.000
111A59GLU-1-0.961-0.85410.7380.7790.7790.0000.0000.0000.000
112A60VAL00.097-0.1247.8200.2710.2710.0000.0000.0000.000
113A60VAL0-0.0850.1297.164-0.041-0.0410.0000.0000.0000.000
114A61LEU0-0.012-0.1125.859-0.579-0.5790.0000.0000.0000.000
115A61LEU0-0.0670.0955.2140.1160.1160.0000.0000.0000.000
116A62TRP00.096-0.0883.8860.6651.0830.003-0.138-0.2830.000
117A62TRP0-0.0340.0805.300-0.125-0.1250.0000.0000.0000.000
118A63PHE00.127-0.0884.5800.7160.779-0.002-0.033-0.0290.000
119A63PHE0-0.0540.1023.710-0.408-0.1450.081-0.135-0.209-0.001
120A64ASP00.074-0.1406.352-0.168-0.1680.0000.0000.0000.000
121A64ASP-1-0.902-0.82010.721-0.530-0.5300.0000.0000.0000.000
122A65ARG0-0.016-0.1099.753-0.147-0.1470.0000.0000.0000.000
123A65ARG10.8301.0715.7112.7682.7680.0000.0000.0000.000
124A66ASP00.092-0.11811.8180.0970.0970.0000.0000.0000.000
125A66ASP-1-0.918-0.80816.243-0.580-0.5800.0000.0000.0000.000
126A67SER00.099-0.12814.853-0.041-0.0410.0000.0000.0000.000
127A67SER0-0.0340.10118.7050.0050.0050.0000.0000.0000.000
128A68GLU00.073-0.09217.4280.0430.0430.0000.0000.0000.000
129A68GLU-1-0.971-0.83118.373-0.399-0.3990.0000.0000.0000.000
130A69ALA00.126-0.12313.8920.0840.0840.0000.0000.0000.000
131A69ALA0-0.0560.15013.123-0.035-0.0350.0000.0000.0000.000
132A70ARG00.050-0.07613.4810.0050.0050.0000.0000.0000.000
133A70ARG10.7751.02613.0020.3870.3870.0000.0000.0000.000
134A71ASP00.135-0.14214.4380.0550.0550.0000.0000.0000.000
135A71ASP-1-1.008-0.85019.064-0.219-0.2190.0000.0000.0000.000
136A72LYS00.003-0.12417.1300.0670.0670.0000.0000.0000.000
137A72LYS10.8531.08216.4970.3760.3760.0000.0000.0000.000
138A73ILE00.050-0.08312.9660.0490.0490.0000.0000.0000.000
139A73ILE0-0.0590.10910.389-0.010-0.0100.0000.0000.0000.000
140A74ALA00.154-0.14614.4610.0650.0650.0000.0000.0000.000
141A74ALA0-0.0790.14016.2860.0050.0050.0000.0000.0000.000
142A75ALA00.054-0.08216.4680.0590.0590.0000.0000.0000.000
143A75ALA0-0.0410.10419.746-0.003-0.0030.0000.0000.0000.000
144A76LEU00.180-0.14617.0690.0410.0410.0000.0000.0000.000
145A76LEU0-0.1450.15914.8770.0020.0020.0000.0000.0000.000
146A77PHE0-0.008-0.12215.7690.0230.0230.0000.0000.0000.000
147A77PHE0-0.0150.10710.6450.0110.0110.0000.0000.0000.000
148A78THR00.065-0.10616.8780.0430.0430.0000.0000.0000.000
149A78THR0-0.0980.06019.1690.0120.0120.0000.0000.0000.000
150A79GLU00.063-0.11620.1820.0290.0290.0000.0000.0000.000
151A79GLU-1-1.024-0.85021.369-0.111-0.1110.0000.0000.0000.000
152A80ARG00.003-0.15419.5980.0080.0080.0000.0000.0000.000
153A80ARG10.8711.10117.7910.0910.0910.0000.0000.0000.000
154A81TRP00.095-0.06620.1980.0060.0060.0000.0000.0000.000
155A81TRP0-0.0790.06916.3940.0090.0090.0000.0000.0000.000
156A82LYS00.058-0.08521.4470.0160.0160.0000.0000.0000.000
157A82LYS10.8031.02523.698-0.056-0.0560.0000.0000.0000.000
158A83LYS00.082-0.15724.279-0.002-0.0020.0000.0000.0000.000
159A83LYS10.8411.07723.7430.0270.0270.0000.0000.0000.000
160A84ILE00.040-0.08324.799-0.008-0.0080.0000.0000.0000.000
161A84ILE0-0.0920.07022.0710.0030.0030.0000.0000.0000.000
162A85THR0-0.001-0.04625.6040.0040.0040.0000.0000.0000.000
163A85THR0-0.0540.07023.7150.0050.0050.0000.0000.0000.000
164A86ASP00.012-0.12626.611-0.009-0.0090.0000.0000.0000.000
165A86ASP-1-0.912-0.83229.9980.0750.0750.0000.0000.0000.000
166A87LYS00.076-0.15125.521-0.011-0.0110.0000.0000.0000.000
167A87LYS10.7701.04524.086-0.182-0.1820.0000.0000.0000.000
168A88ILE00.037-0.10824.815-0.013-0.0130.0000.0000.0000.000
169A88ILE0-0.0510.11623.162-0.001-0.0010.0000.0000.0000.000
170A89VAL00.050-0.10420.8040.0270.0270.0000.0000.0000.000
171A89VAL0-0.0610.12018.8250.0000.0000.0000.0000.0000.000
172A90THR00.030-0.07219.305-0.036-0.0360.0000.0000.0000.000
173A90THR0-0.0270.06118.417-0.003-0.0030.0000.0000.0000.000
174A91ILE00.060-0.14415.3140.0590.0590.0000.0000.0000.000
175A91ILE0-0.1000.13913.619-0.001-0.0010.0000.0000.0000.000
176A92VAL00.033-0.11914.030-0.072-0.0720.0000.0000.0000.000
177A92VAL0-0.0810.12214.0100.0050.0050.0000.0000.0000.000
178A93PHE00.104-0.11610.7860.1330.1330.0000.0000.0000.000
179A93PHE0-0.0720.11310.063-0.009-0.0090.0000.0000.0000.000
180A94ASN00.036-0.0819.628-0.087-0.0870.0000.0000.0000.000
181A94ASN0-0.1280.0569.337-0.078-0.0780.0000.0000.0000.000
182A95PRO00.033-0.0968.4410.0480.0480.0000.0000.0000.000
183A96LEU00.046-0.0476.3120.3400.3400.0000.0000.0000.000
184A96LEU0-0.0380.1363.896-0.0550.0260.0110.035-0.1280.000
185A97ILE00.119-0.0667.778-0.310-0.3100.0000.0000.0000.000
186A97ILE0-0.1060.08711.2310.0150.0150.0000.0000.0000.000
187A98GLU00.037-0.1288.0110.1900.1900.0000.0000.0000.000
188A98GLU-1-0.955-0.8487.765-1.281-1.2810.0000.0000.0000.000
189A99ASN00.085-0.0449.0650.0750.0750.0000.0000.0000.000
190A99ASN0-0.0940.04513.5170.0200.0200.0000.0000.0000.000
191A100MET00.045-0.11410.5540.0520.0520.0000.0000.0000.000
192A100MET0-0.1340.07410.7410.0230.0230.0000.0000.0000.000
193A101TYR00.106-0.0996.7650.3700.3700.0000.0000.0000.000
194A101TYR0-0.1010.0672.722-3.997-5.2241.9881.000-1.7610.006
195A102TYR00.019-0.0938.111-0.427-0.4270.0000.0000.0000.000
196A102TYR0-0.1080.06910.430-0.043-0.0430.0000.0000.0000.000
197A103GLU00.153-0.1536.4830.7330.7330.0000.0000.0000.000
198A103GLU-1-0.989-0.7904.1820.2430.328-0.001-0.026-0.0590.000
199A104ASP00.013-0.1497.639-0.329-0.3290.0000.0000.0000.000
200A104ASP-1-1.009-0.81810.5280.7290.7290.0000.0000.0000.000
201A105GLY0-0.021-0.13910.911-0.163-0.1630.0000.0000.0000.000
202A106VAL0-0.018-0.01211.238-0.022-0.0220.0000.0000.0000.000
203A106VAL0-0.0470.09410.703-0.019-0.0190.0000.0000.0000.000
204A107HIS00.115-0.1309.6470.1410.1410.0000.0000.0000.000
205A107HIS0-0.1950.08910.158-0.018-0.0180.0000.0000.0000.000
206A108PHE0-0.011-0.0836.0690.2780.2780.0000.0000.0000.000
207A108PHE00.0400.0163.811-0.863-0.6390.004-0.083-0.145-0.001