Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: R1J48

Calculation Name: 1MBM-A-Xray309

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1MBM

Chain ID: A

ChEMBL ID:

UniProt ID: P19811

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 198
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1921099.811154
FMO2-HF: Nuclear repulsion 1849463.221253
FMO2-HF: Total energy -71636.589901
FMO2-MP2: Total energy -71845.510223


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(A:7:LYS )


Summations of interaction energy for fragment #1(A:7:LYS )
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.
-167.317-161.9030.769-2.605-3.574-0.017
Interaction energy analysis for fragmet #1(A:7:LYS )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.992 / q_NPA : 0.977
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].
3A9ARG 10.8860.9062.75614.65618.4640.702-2.153-2.357-0.016
4A10GLY 0-0.008-0.0124.8411.3681.4560.000-0.005-0.0820.000
5A11ASN 0-0.053-0.0275.9760.4520.4520.0000.0000.0000.000
6A12VAL 00.0080.0147.2003.4533.4530.0000.0000.0000.000
7A13GLY 00.0020.0038.373-1.627-1.6270.0000.0000.0000.000
8A14PHE 0-0.029-0.0098.5620.6590.6590.0000.0000.0000.000
9A15VAL 00.0170.00312.8600.5500.5500.0000.0000.0000.000
10A16ALA 0-0.012-0.00316.5630.2340.2340.0000.0000.0000.000
11A17GLY 00.0460.01519.3960.2370.2370.0000.0000.0000.000
12A18SER 0-0.125-0.05322.9470.3430.3430.0000.0000.0000.000
13A19SER 0-0.0040.00821.3740.1580.1580.0000.0000.0000.000
14A20TYR 0-0.022-0.01616.887-0.241-0.2410.0000.0000.0000.000
15A21GLY 00.0350.01015.8040.2290.2290.0000.0000.0000.000
16A22THR 0-0.030-0.01210.896-1.205-1.2050.0000.0000.0000.000
17A23GLY 00.0260.00612.8251.4231.4230.0000.0000.0000.000
18A24SER 0-0.0190.01312.142-1.749-1.7490.0000.0000.0000.000
19A25VAL 00.0150.00812.6141.7521.7520.0000.0000.0000.000
20A26TRP 00.003-0.02513.338-1.814-1.8140.0000.0000.0000.000
21A27THR 00.0030.00916.0620.9930.9930.0000.0000.0000.000
22A28ARG 10.7920.88418.80112.81512.8150.0000.0000.0000.000
23A29ASN 00.004-0.00122.2740.2030.2030.0000.0000.0000.000
24A30ASN 0-0.039-0.02024.2300.1380.1380.0000.0000.0000.000
25A31GLU -1-0.860-0.90223.522-11.935-11.9350.0000.0000.0000.000
26A32VAL 0-0.020-0.01417.878-0.545-0.5450.0000.0000.0000.000
27A33VAL 0-0.011-0.01319.0940.6280.6280.0000.0000.0000.000
28A34VAL 00.006-0.00416.758-1.179-1.1790.0000.0000.0000.000
29A35LEU 0-0.015-0.00317.1971.0081.0080.0000.0000.0000.000
30A36THR 00.018-0.00816.872-0.764-0.7640.0000.0000.0000.000
31A37ALA 00.0500.04218.6940.5290.5290.0000.0000.0000.000
32A38SER 0-0.052-0.06121.0020.0280.0280.0000.0000.0000.000
33A39HIS 0-0.082-0.06921.2110.1600.1600.0000.0000.0000.000
34A40VAL 00.0160.02918.4100.2260.2260.0000.0000.0000.000
35A41VAL 0-0.0130.01221.6070.2050.2050.0000.0000.0000.000
36A42GLY 00.0920.04723.6330.3240.3240.0000.0000.0000.000
37A43ARG 10.9510.95526.9578.4408.4400.0000.0000.0000.000
38A44ALA 0-0.038-0.02129.3980.1700.1700.0000.0000.0000.000
39A45ASN 0-0.035-0.03627.892-0.244-0.2440.0000.0000.0000.000
40A46MET 00.0170.02626.283-0.131-0.1310.0000.0000.0000.000
41A47ALA 00.0090.00021.3470.0390.0390.0000.0000.0000.000
42A48THR 0-0.0120.00219.2040.0690.0690.0000.0000.0000.000
43A49LEU 00.0100.02213.781-0.327-0.3270.0000.0000.0000.000
44A50LYS 10.9510.96912.01620.89820.8980.0000.0000.0000.000
45A51ILE 00.009-0.0059.736-1.074-1.0740.0000.0000.0000.000
46A52GLY 00.0030.0189.9190.7510.7510.0000.0000.0000.000
47A53ASP -1-0.920-0.96411.030-21.624-21.6240.0000.0000.0000.000
48A54ALA 0-0.058-0.01914.2341.6421.6420.0000.0000.0000.000
49A55MET 0-0.014-0.01815.525-0.534-0.5340.0000.0000.0000.000
50A56LEU 00.0110.01418.2230.7430.7430.0000.0000.0000.000
51A57THR 0-0.029-0.01520.310-0.181-0.1810.0000.0000.0000.000
52A58LEU 0-0.003-0.00419.3880.2200.2200.0000.0000.0000.000
53A59THR 0-0.002-0.01023.7490.4080.4080.0000.0000.0000.000
54A60PHE 0-0.010-0.01020.233-0.133-0.1330.0000.0000.0000.000
55A61LYS 10.9390.97225.92210.72710.7270.0000.0000.0000.000
56A62LYS 10.8450.92726.49410.42110.4210.0000.0000.0000.000
57A63ASN 0-0.0140.00427.5430.6150.6150.0000.0000.0000.000
58A64GLY 00.0610.03527.763-0.254-0.2540.0000.0000.0000.000
59A65ASP -1-0.791-0.89322.861-12.403-12.4030.0000.0000.0000.000
60A66PHE 00.0470.06121.221-0.568-0.5680.0000.0000.0000.000
61A67ALA 0-0.010-0.01122.4250.6120.6120.0000.0000.0000.000
62A68GLU -1-0.822-0.92321.702-13.317-13.3170.0000.0000.0000.000
63A69ALA 0-0.016-0.00121.6420.7060.7060.0000.0000.0000.000
64A70VAL 0-0.009-0.00122.120-0.527-0.5270.0000.0000.0000.000
65A71THR 00.0170.00620.6880.4510.4510.0000.0000.0000.000
66A72THR 00.0470.01623.445-0.070-0.0700.0000.0000.0000.000
67A73GLN 00.0710.00917.723-0.581-0.5810.0000.0000.0000.000
68A74SER 0-0.045-0.02220.666-0.385-0.3850.0000.0000.0000.000
69A75GLU -1-0.963-0.96522.477-12.453-12.4530.0000.0000.0000.000
70A76LEU 0-0.037-0.01815.684-0.467-0.4670.0000.0000.0000.000
71A77PRO 00.0240.03116.977-0.428-0.4280.0000.0000.0000.000
72A78GLY 00.0360.00413.818-1.339-1.3390.0000.0000.0000.000
73A79ASN 0-0.067-0.02612.3362.2802.2800.0000.0000.0000.000
74A80TRP 0-0.042-0.02410.640-2.556-2.5560.0000.0000.0000.000
75A81PRO 00.0260.02211.4211.2751.2750.0000.0000.0000.000
76A82GLN 00.026-0.00114.1290.3580.3580.0000.0000.0000.000
77A83LEU 0-0.028-0.00917.067-0.494-0.4940.0000.0000.0000.000
78A84HIS 00.0230.02018.6921.3761.3760.0000.0000.0000.000
79A85PHE 0-0.013-0.00519.925-0.412-0.4120.0000.0000.0000.000
80A86ALA 00.008-0.00222.1510.4200.4200.0000.0000.0000.000
81A87GLN 0-0.062-0.02223.6870.1130.1130.0000.0000.0000.000
82A88PRO 00.0240.01123.291-0.314-0.3140.0000.0000.0000.000
83A89THR 0-0.011-0.00523.1700.7830.7830.0000.0000.0000.000
84A90THR 0-0.037-0.02022.992-0.457-0.4570.0000.0000.0000.000
85A91GLY 00.0220.01521.8210.2310.2310.0000.0000.0000.000
86A92PRO 00.0220.02116.5780.0630.0630.0000.0000.0000.000
87A93ALA 0-0.015-0.00316.0000.2020.2020.0000.0000.0000.000
88A94SER 00.0110.01310.653-0.331-0.3310.0000.0000.0000.000
89A95TRP 0-0.024-0.00811.5080.5090.5090.0000.0000.0000.000
90A96CYS 0-0.053-0.0268.747-1.927-1.9270.0000.0000.0000.000
91A97THR 00.0160.0006.8900.8670.8670.0000.0000.0000.000
92A98ALA 00.017-0.0166.899-3.506-3.5060.0000.0000.0000.000
93A99THR 0-0.095-0.0504.151-2.381-2.1830.001-0.025-0.1730.000
94A100GLY 00.0590.0463.083-2.346-1.5500.057-0.286-0.566-0.001
95A101ASP -1-0.834-0.8923.615-29.193-28.9190.008-0.057-0.2240.000
96A102GLU -1-0.721-0.8446.759-21.254-21.2540.0000.0000.0000.000
97A103GLU -1-1.006-1.0159.361-18.207-18.2070.0000.0000.0000.000
98A104GLY 00.0550.01712.1000.8100.8100.0000.0000.0000.000
99A105LEU 0-0.036-0.02215.4570.0740.0740.0000.0000.0000.000
100A106LEU 0-0.009-0.00718.9490.0820.0820.0000.0000.0000.000
101A107SER 00.003-0.03020.6930.4310.4310.0000.0000.0000.000
102A108GLY 00.007-0.00924.481-0.152-0.1520.0000.0000.0000.000
103A109GLU -1-0.899-0.95127.007-9.869-9.8690.0000.0000.0000.000
104A110VAL 0-0.007-0.00323.9910.0480.0480.0000.0000.0000.000
105A111CYS 0-0.0460.00419.947-0.388-0.3880.0000.0000.0000.000
106A112LEU 0-0.0100.00119.3430.3410.3410.0000.0000.0000.000
107A113ALA 00.0660.02614.129-0.679-0.6790.0000.0000.0000.000
108A114TRP 0-0.0150.01910.4730.6940.6940.0000.0000.0000.000
109A115THR 00.013-0.00612.472-0.876-0.8760.0000.0000.0000.000
110A116THR 0-0.016-0.01112.9680.9570.9570.0000.0000.0000.000
111A117SER 00.011-0.00815.360-0.284-0.2840.0000.0000.0000.000
112A118GLY 00.0210.01514.3090.0390.0390.0000.0000.0000.000
113A119ASP -1-0.742-0.83611.115-20.663-20.6630.0000.0000.0000.000
114A120SER 0-0.0100.00313.547-0.320-0.3200.0000.0000.0000.000
115A121GLY 0-0.037-0.02916.182-0.350-0.3500.0000.0000.0000.000
116A122SER 0-0.008-0.02612.029-0.924-0.9240.0000.0000.0000.000
117A123ALA 0-0.0280.00313.4601.1961.1960.0000.0000.0000.000
118A124VAL 00.0320.01613.449-1.060-1.0600.0000.0000.0000.000
119A125VAL 0-0.031-0.03212.8050.7270.7270.0000.0000.0000.000
120A126GLN 00.030-0.01115.6160.1540.1540.0000.0000.0000.000
121A127GLY 0-0.0090.00516.2670.6220.6220.0000.0000.0000.000
122A128ASP -1-0.971-0.98814.987-17.748-17.7480.0000.0000.0000.000
123A129ALA 00.0090.00216.3070.1820.1820.0000.0000.0000.000
124A130VAL 0-0.027-0.01016.150-0.463-0.4630.0000.0000.0000.000
125A131VAL 00.000-0.00418.3220.9380.9380.0000.0000.0000.000
126A132GLY 0-0.013-0.03219.3280.9480.9480.0000.0000.0000.000
127A133VAL 0-0.0520.00117.712-0.954-0.9540.0000.0000.0000.000
128A134HIS 00.0400.02015.7510.6430.6430.0000.0000.0000.000
129A135THR 0-0.0230.00017.7060.0260.0260.0000.0000.0000.000
130A136GLY 00.0280.00520.1940.2950.2950.0000.0000.0000.000
131A137SER 0-0.030-0.00318.722-0.043-0.0430.0000.0000.0000.000
132A138ASN 00.021-0.00620.7980.5640.5640.0000.0000.0000.000
133A139THR 0-0.017-0.01721.870-0.406-0.4060.0000.0000.0000.000
134A140SER 0-0.008-0.00922.1590.1700.1700.0000.0000.0000.000
135A141GLY 00.0470.03618.621-0.091-0.0910.0000.0000.0000.000
136A142VAL 0-0.0060.02119.353-0.305-0.3050.0000.0000.0000.000
137A143ALA 0-0.005-0.00618.091-0.295-0.2950.0000.0000.0000.000
138A144TYR 0-0.0020.00020.1050.5040.5040.0000.0000.0000.000
139A145VAL 00.0300.01218.747-0.541-0.5410.0000.0000.0000.000
140A146THR 0-0.035-0.01621.3600.8480.8480.0000.0000.0000.000
141A147THR 00.0240.00722.539-0.480-0.4800.0000.0000.0000.000
142A148PRO 00.0650.02523.0680.3640.3640.0000.0000.0000.000
143A149SER 0-0.086-0.04525.5090.2600.2600.0000.0000.0000.000
144A150GLY 0-0.0030.00127.5800.4000.4000.0000.0000.0000.000
145A151LYS 10.8970.95928.17110.06310.0630.0000.0000.0000.000
146A152LEU 00.007-0.00124.921-0.383-0.3830.0000.0000.0000.000
147A153LEU 0-0.041-0.02222.6300.3880.3880.0000.0000.0000.000
148A154GLY 00.0210.00724.242-0.346-0.3460.0000.0000.0000.000
149A155ALA 0-0.042-0.02325.1740.0820.0820.0000.0000.0000.000
150A156ASP -1-0.943-0.94428.469-9.011-9.0110.0000.0000.0000.000
151A157THR 0-0.035-0.03029.749-0.121-0.1210.0000.0000.0000.000
152A158VAL 00.0100.00428.1770.0720.0720.0000.0000.0000.000
153A159THR 0-0.0020.01431.152-0.097-0.0970.0000.0000.0000.000
154A160LEU 00.0870.03827.902-0.249-0.2490.0000.0000.0000.000
155A161SER 0-0.060-0.03130.710-0.253-0.2530.0000.0000.0000.000
156A162SER 0-0.084-0.03732.780-0.133-0.1330.0000.0000.0000.000
157A163LEU 00.0630.02425.406-0.131-0.1310.0000.0000.0000.000
158A164SER 00.005-0.04628.213-0.362-0.3620.0000.0000.0000.000
159A165LYS 10.8640.94529.6568.8148.8140.0000.0000.0000.000
160A166HIS 0-0.052-0.01626.850-0.062-0.0620.0000.0000.0000.000
161A167PHE 00.0300.02821.659-0.472-0.4720.0000.0000.0000.000
162A168THR 00.0130.01625.3900.3370.3370.0000.0000.0000.000
163A169GLY 00.009-0.00226.214-0.309-0.3090.0000.0000.0000.000
164A170PRO 0-0.035-0.01827.7420.2550.2550.0000.0000.0000.000
165A171LEU 00.0370.00929.146-0.288-0.2880.0000.0000.0000.000
166A172THR 0-0.051-0.02426.026-0.065-0.0650.0000.0000.0000.000
167A173SER 00.014-0.00328.8190.1410.1410.0000.0000.0000.000
168A174ILE 0-0.0010.01627.338-0.355-0.3550.0000.0000.0000.000
169A175PRO 00.0220.02423.2030.2770.2770.0000.0000.0000.000
170A176LYS 10.9040.94025.28310.00610.0060.0000.0000.0000.000
171A177ASP -1-0.936-0.96922.670-11.302-11.3020.0000.0000.0000.000
172A178ILE 00.0090.02223.762-0.411-0.4110.0000.0000.0000.000
173A179PRO 00.033-0.00124.1050.3370.3370.0000.0000.0000.000
174A180ASP -1-0.883-0.94126.931-8.710-8.7100.0000.0000.0000.000
175A181ASN 0-0.057-0.02628.3670.4410.4410.0000.0000.0000.000
176A182ILE 0-0.018-0.00324.830-0.055-0.0550.0000.0000.0000.000
177A183ILE 0-0.014-0.01229.3720.1600.1600.0000.0000.0000.000
178A184ALA 00.027-0.00331.840-0.048-0.0480.0000.0000.0000.000
179A185ASP -1-0.797-0.88033.153-8.160-8.1600.0000.0000.0000.000
180A186VAL 0-0.044-0.01932.7010.1800.1800.0000.0000.0000.000
181A187ASP -1-0.923-0.96634.054-8.131-8.1310.0000.0000.0000.000
182A188ALA 0-0.029-0.02131.402-0.142-0.1420.0000.0000.0000.000
183A189VAL 00.0180.00726.7220.0950.0950.0000.0000.0000.000
184A190PRO 00.0110.00727.121-0.044-0.0440.0000.0000.0000.000
185A191ARG 10.9610.97423.73910.91510.9150.0000.0000.0000.000
186A192SER 0-0.028-0.02021.908-0.390-0.3900.0000.0000.0000.000
187A193LEU 00.0310.02621.344-0.465-0.4650.0000.0000.0000.000
188A194ALA 0-0.010-0.01722.244-0.251-0.2510.0000.0000.0000.000
189A195MET 00.007-0.00918.4240.0310.0310.0000.0000.0000.000
190A196LEU 0-0.0040.01116.576-0.518-0.5180.0000.0000.0000.000
191A197ILE 0-0.025-0.01317.386-0.425-0.4250.0000.0000.0000.000
192A198ASP -1-0.937-0.98418.795-12.334-12.3340.0000.0000.0000.000
193A199GLY 0-0.034-0.00115.430-0.205-0.2050.0000.0000.0000.000
194A200LEU 0-0.059-0.01713.697-1.072-1.0720.0000.0000.0000.000
195A201SER 0-0.060-0.04411.5910.1450.1450.0000.0000.0000.000
196A202ASN 0-0.046-0.0149.526-1.197-1.1970.0000.0000.0000.000
197A203ARG 10.7090.8415.27421.53721.5370.0000.0000.0000.000
198A204GLU -2-1.942-1.9613.907-57.205-56.9550.001-0.079-0.1720.000