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: 9GKR2

Calculation Name: 1MBM-A-Xray372

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: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1926533.324137
FMO2-HF: Nuclear repulsion 1854894.905725
FMO2-HF: Total energy -71638.418412
FMO2-MP2: Total energy -71847.411006


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.
-153.969-147.96.099-5.934-6.234-0.054
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 : 0.958 / q_NPA : 0.984
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].
3A9ARG10.8810.9112.44214.75418.4991.474-2.511-2.708-0.015
4A10GLY0-0.006-0.0114.9161.7961.876-0.001-0.003-0.0750.000
5A11ASN0-0.050-0.0295.9920.6610.6610.0000.0000.0000.000
6A12VAL00.0050.0087.2233.1563.1560.0000.0000.0000.000
7A13GLY00.0060.0008.649-1.800-1.8000.0000.0000.0000.000
8A14PHE0-0.023-0.0097.9890.4170.4170.0000.0000.0000.000
9A15VAL0-0.001-0.00812.6020.5750.5750.0000.0000.0000.000
10A16ALA0-0.0020.00416.3620.0680.0680.0000.0000.0000.000
11A17GLY00.0500.01319.3170.2220.2220.0000.0000.0000.000
12A18SER0-0.115-0.05122.8660.3050.3050.0000.0000.0000.000
13A19SER00.0110.01721.1780.1670.1670.0000.0000.0000.000
14A20TYR00.004-0.01016.726-0.167-0.1670.0000.0000.0000.000
15A21GLY00.0030.01014.8630.3370.3370.0000.0000.0000.000
16A22THR0-0.0140.00210.398-1.321-1.3210.0000.0000.0000.000
17A23GLY00.0230.01412.3821.6861.6860.0000.0000.0000.000
18A24SER0-0.0350.00012.159-1.817-1.8170.0000.0000.0000.000
19A25VAL00.0180.00812.6291.7431.7430.0000.0000.0000.000
20A26TRP00.018-0.00813.536-1.720-1.7200.0000.0000.0000.000
21A27THR00.006-0.00716.2530.8720.8720.0000.0000.0000.000
22A28ARG10.7660.83719.23612.81212.8120.0000.0000.0000.000
23A29ASN0-0.001-0.00522.6960.0720.0720.0000.0000.0000.000
24A30ASN0-0.033-0.01824.4900.4650.4650.0000.0000.0000.000
25A31GLU-1-0.839-0.88723.562-12.060-12.0600.0000.0000.0000.000
26A32VAL0-0.019-0.00617.907-0.502-0.5020.0000.0000.0000.000
27A33VAL0-0.027-0.01819.3040.5730.5730.0000.0000.0000.000
28A34VAL00.002-0.00816.767-1.081-1.0810.0000.0000.0000.000
29A35LEU0-0.025-0.00316.9051.0191.0190.0000.0000.0000.000
30A36THR00.010-0.01716.536-0.870-0.8700.0000.0000.0000.000
31A37ALA00.0480.04018.2510.5150.5150.0000.0000.0000.000
32A38SER0-0.069-0.06320.4640.0680.0680.0000.0000.0000.000
33A39HIS0-0.045-0.04219.9960.1370.1370.0000.0000.0000.000
34A40VAL00.0090.02517.9150.2870.2870.0000.0000.0000.000
35A41VAL0-0.0200.00121.1620.2680.2680.0000.0000.0000.000
36A42GLY00.0670.03823.3180.3570.3570.0000.0000.0000.000
37A43ARG10.9310.93726.5768.4878.4870.0000.0000.0000.000
38A44ALA00.0100.00428.4040.2140.2140.0000.0000.0000.000
39A45ASN0-0.031-0.01627.373-0.115-0.1150.0000.0000.0000.000
40A46MET00.0310.02526.086-0.150-0.1500.0000.0000.0000.000
41A47ALA00.0010.00221.1710.1060.1060.0000.0000.0000.000
42A48THR0-0.018-0.00819.1790.1960.1960.0000.0000.0000.000
43A49LEU00.0310.03114.387-0.345-0.3450.0000.0000.0000.000
44A50LYS10.9600.97012.16120.76520.7650.0000.0000.0000.000
45A51ILE00.0030.0049.743-1.082-1.0820.0000.0000.0000.000
46A52GLY00.0200.0179.6200.5210.5210.0000.0000.0000.000
47A53ASP-1-0.940-0.97810.602-20.623-20.6230.0000.0000.0000.000
48A54ALA0-0.0350.00613.8551.4761.4760.0000.0000.0000.000
49A55MET0-0.026-0.02915.103-0.759-0.7590.0000.0000.0000.000
50A56LEU0-0.0010.00317.7880.7230.7230.0000.0000.0000.000
51A57THR0-0.025-0.01720.366-0.226-0.2260.0000.0000.0000.000
52A58LEU00.0010.00719.7870.1760.1760.0000.0000.0000.000
53A59THR0-0.004-0.02023.9260.3450.3450.0000.0000.0000.000
54A60PHE0-0.028-0.01820.248-0.064-0.0640.0000.0000.0000.000
55A61LYS10.8850.94125.83511.80711.8070.0000.0000.0000.000
56A62LYS10.8320.92125.45810.71210.7120.0000.0000.0000.000
57A63ASN0-0.045-0.01627.0730.6700.6700.0000.0000.0000.000
58A64GLY00.0710.04227.066-0.289-0.2890.0000.0000.0000.000
59A65ASP-1-0.779-0.87122.105-12.691-12.6910.0000.0000.0000.000
60A66PHE00.0480.05320.616-0.570-0.5700.0000.0000.0000.000
61A67ALA0-0.001-0.00722.1060.6610.6610.0000.0000.0000.000
62A68GLU-1-0.761-0.85721.395-13.203-13.2030.0000.0000.0000.000
63A69ALA0-0.0190.00421.7240.7020.7020.0000.0000.0000.000
64A70VAL0-0.029-0.01822.077-0.482-0.4820.0000.0000.0000.000
65A71THR00.0120.00520.6110.4800.4800.0000.0000.0000.000
66A72THR00.0300.01623.137-0.119-0.1190.0000.0000.0000.000
67A73GLN00.039-0.00417.529-0.575-0.5750.0000.0000.0000.000
68A74SER0-0.070-0.05221.062-0.249-0.2490.0000.0000.0000.000
69A75GLU-1-0.866-0.90722.337-12.109-12.1090.0000.0000.0000.000
70A76LEU0-0.036-0.01815.424-0.465-0.4650.0000.0000.0000.000
71A77PRO00.0220.03117.537-0.458-0.4580.0000.0000.0000.000
72A78GLY00.031-0.00214.121-1.124-1.1240.0000.0000.0000.000
73A79ASN0-0.064-0.01513.0611.8811.8810.0000.0000.0000.000
74A80TRP0-0.022-0.01710.480-2.274-2.2740.0000.0000.0000.000
75A81PRO00.0050.02311.9191.2361.2360.0000.0000.0000.000
76A82GLN00.0450.01414.7110.3800.3800.0000.0000.0000.000
77A83LEU0-0.029-0.01417.646-0.460-0.4600.0000.0000.0000.000
78A84HIS0-0.0250.00718.6741.4861.4860.0000.0000.0000.000
79A85PHE0-0.018-0.02019.807-0.519-0.5190.0000.0000.0000.000
80A86ALA00.0080.00521.9070.4200.4200.0000.0000.0000.000
81A87GLN0-0.061-0.03223.6310.2690.2690.0000.0000.0000.000
82A88PRO00.0280.01523.278-0.387-0.3870.0000.0000.0000.000
83A89THR0-0.021-0.00823.1860.8220.8220.0000.0000.0000.000
84A90THR0-0.021-0.01522.988-0.567-0.5670.0000.0000.0000.000
85A91GLY00.0250.01522.0230.2870.2870.0000.0000.0000.000
86A92PRO00.0250.02516.6370.1040.1040.0000.0000.0000.000
87A93ALA0-0.029-0.00816.2170.3250.3250.0000.0000.0000.000
88A94SER00.0150.01110.849-0.222-0.2220.0000.0000.0000.000
89A95TRP00.007-0.00611.5660.6100.6100.0000.0000.0000.000
90A96CYS0-0.069-0.0438.828-1.479-1.4790.0000.0000.0000.000
91A97THR00.0240.0026.3261.0311.0310.0000.0000.0000.000
92A98ALA0-0.010-0.0216.404-4.027-4.0270.0000.0000.0000.000
93A99THR0-0.085-0.0483.916-0.873-0.3820.000-0.196-0.296-0.001
94A100GLY00.0210.0212.029-14.472-13.3414.607-3.053-2.686-0.038
95A101ASP-1-0.771-0.8473.574-27.739-27.3970.017-0.087-0.2710.000
96A102GLU-1-0.752-0.8646.996-22.762-22.7620.0000.0000.0000.000
97A103GLU-1-0.986-0.9949.171-18.967-18.9670.0000.0000.0000.000
98A104GLY00.0530.02412.0130.5750.5750.0000.0000.0000.000
99A105LEU0-0.0070.00015.4460.0740.0740.0000.0000.0000.000
100A106LEU00.006-0.01419.0670.0480.0480.0000.0000.0000.000
101A107SER0-0.008-0.03020.8540.4500.4500.0000.0000.0000.000
102A108GLY00.0190.00624.370-0.240-0.2400.0000.0000.0000.000
103A109GLU-1-0.900-0.95827.040-10.375-10.3750.0000.0000.0000.000
104A110VAL0-0.016-0.01724.1380.0630.0630.0000.0000.0000.000
105A111CYS0-0.0420.01919.727-0.305-0.3050.0000.0000.0000.000
106A112LEU0-0.010-0.00419.0140.4260.4260.0000.0000.0000.000
107A113ALA00.0730.03613.609-0.656-0.6560.0000.0000.0000.000
108A114TRP0-0.0200.0159.4530.5650.5650.0000.0000.0000.000
109A115THR0-0.013-0.01111.832-1.125-1.1250.0000.0000.0000.000
110A116THR0-0.003-0.01712.0771.2541.2540.0000.0000.0000.000
111A117SER00.024-0.00814.5910.0190.0190.0000.0000.0000.000
112A118GLY0-0.0120.00512.9300.2120.2120.0000.0000.0000.000
113A119ASP-1-0.739-0.8239.905-22.258-22.2580.0000.0000.0000.000
114A120SER00.0230.01912.423-0.173-0.1730.0000.0000.0000.000
115A121GLY0-0.049-0.02615.155-0.444-0.4440.0000.0000.0000.000
116A122SER0-0.007-0.03511.553-1.108-1.1080.0000.0000.0000.000
117A123ALA0-0.026-0.00212.9211.2671.2670.0000.0000.0000.000
118A124VAL00.0120.01113.339-1.155-1.1550.0000.0000.0000.000
119A125VAL0-0.014-0.01512.5080.9670.9670.0000.0000.0000.000
120A126GLN00.031-0.01515.7470.2970.2970.0000.0000.0000.000
121A127GLY0-0.0010.00815.9330.6570.6570.0000.0000.0000.000
122A128ASP-1-0.938-0.98114.503-18.405-18.4050.0000.0000.0000.000
123A129ALA0-0.0020.00415.7850.1610.1610.0000.0000.0000.000
124A130VAL0-0.020-0.00716.004-0.491-0.4910.0000.0000.0000.000
125A131VAL0-0.012-0.01118.1850.9000.9000.0000.0000.0000.000
126A132GLY00.003-0.01819.2000.9330.9330.0000.0000.0000.000
127A133VAL0-0.059-0.00917.323-0.975-0.9750.0000.0000.0000.000
128A134HIS00.0370.02115.1960.7040.7040.0000.0000.0000.000
129A135THR0-0.002-0.03417.2230.0250.0250.0000.0000.0000.000
130A136GLY00.0080.00219.2020.4380.4380.0000.0000.0000.000
131A137SER0-0.040-0.00517.383-0.128-0.1280.0000.0000.0000.000
132A138ASN0-0.015-0.01219.7730.6240.6240.0000.0000.0000.000
133A139THR00.011-0.01521.158-0.429-0.4290.0000.0000.0000.000
134A140SER0-0.024-0.04321.8560.1370.1370.0000.0000.0000.000
135A141GLY00.0170.01918.383-0.127-0.1270.0000.0000.0000.000
136A142VAL0-0.0080.00618.671-0.461-0.4610.0000.0000.0000.000
137A143ALA0-0.025-0.00617.285-0.356-0.3560.0000.0000.0000.000
138A144TYR0-0.0100.00019.2280.5100.5100.0000.0000.0000.000
139A145VAL00.0300.01618.245-0.583-0.5830.0000.0000.0000.000
140A146THR0-0.031-0.00820.8200.8390.8390.0000.0000.0000.000
141A147THR00.0220.00022.246-0.539-0.5390.0000.0000.0000.000
142A148PRO00.0280.01522.6330.2990.2990.0000.0000.0000.000
143A149SER0-0.041-0.02125.0100.2590.2590.0000.0000.0000.000
144A150GLY00.0320.02127.2880.4220.4220.0000.0000.0000.000
145A151LYS10.7970.89427.86710.44810.4480.0000.0000.0000.000
146A152LEU00.0140.01424.225-0.416-0.4160.0000.0000.0000.000
147A153LEU00.0140.00222.3340.4960.4960.0000.0000.0000.000
148A154GLY00.008-0.00123.523-0.304-0.3040.0000.0000.0000.000
149A155ALA0-0.027-0.01624.4550.0600.0600.0000.0000.0000.000
150A156ASP-1-0.886-0.90427.707-9.374-9.3740.0000.0000.0000.000
151A157THR0-0.036-0.02529.734-0.009-0.0090.0000.0000.0000.000
152A158VAL00.0000.00228.1470.1110.1110.0000.0000.0000.000
153A159THR0-0.039-0.02231.347-0.048-0.0480.0000.0000.0000.000
154A160LEU00.0850.04228.008-0.248-0.2480.0000.0000.0000.000
155A161SER0-0.049-0.04430.726-0.233-0.2330.0000.0000.0000.000
156A162SER0-0.057-0.03932.844-0.064-0.0640.0000.0000.0000.000
157A163LEU00.0490.02025.390-0.114-0.1140.0000.0000.0000.000
158A164SER00.016-0.03528.224-0.366-0.3660.0000.0000.0000.000
159A165LYS10.8150.92029.5268.9008.9000.0000.0000.0000.000
160A166HIS0-0.0260.00526.668-0.012-0.0120.0000.0000.0000.000
161A167PHE00.0110.02521.873-0.482-0.4820.0000.0000.0000.000
162A168THR00.0110.00825.3460.3600.3600.0000.0000.0000.000
163A169GLY00.0240.02325.884-0.375-0.3750.0000.0000.0000.000
164A170PRO0-0.023-0.02227.6750.2200.2200.0000.0000.0000.000
165A171LEU00.0270.00928.959-0.309-0.3090.0000.0000.0000.000
166A172THR0-0.050-0.03025.750-0.027-0.0270.0000.0000.0000.000
167A173SER00.0210.00428.8850.0180.0180.0000.0000.0000.000
168A174ILE0-0.0060.01327.247-0.377-0.3770.0000.0000.0000.000
169A175PRO0-0.0040.00922.8970.2640.2640.0000.0000.0000.000
170A176LYS10.9140.94824.68710.70110.7010.0000.0000.0000.000
171A177ASP-1-0.889-0.90022.995-11.383-11.3830.0000.0000.0000.000
172A178ILE00.0160.00623.826-0.441-0.4410.0000.0000.0000.000
173A179PRO00.0220.00623.7360.3610.3610.0000.0000.0000.000
174A180ASP-1-0.886-0.93626.635-9.137-9.1370.0000.0000.0000.000
175A181ASN0-0.107-0.06327.7330.2310.2310.0000.0000.0000.000
176A182ILE0-0.012-0.00724.562-0.005-0.0050.0000.0000.0000.000
177A183ILE00.0200.00729.2200.1100.1100.0000.0000.0000.000
178A184ALA00.0330.00131.896-0.043-0.0430.0000.0000.0000.000
179A185ASP-1-0.770-0.83633.247-8.425-8.4250.0000.0000.0000.000
180A186VAL0-0.055-0.02532.5510.1850.1850.0000.0000.0000.000
181A187ASP-1-0.894-0.95134.007-8.416-8.4160.0000.0000.0000.000
182A188ALA0-0.042-0.02831.008-0.215-0.2150.0000.0000.0000.000
183A189VAL00.0400.01726.6960.1380.1380.0000.0000.0000.000
184A190PRO00.0090.00227.299-0.061-0.0610.0000.0000.0000.000
185A191ARG10.9190.96623.60310.93610.9360.0000.0000.0000.000
186A192SER00.002-0.02221.778-0.313-0.3130.0000.0000.0000.000
187A193LEU00.0230.02121.242-0.512-0.5120.0000.0000.0000.000
188A194ALA00.0020.00022.494-0.163-0.1630.0000.0000.0000.000
189A195MET0-0.017-0.02818.3400.0210.0210.0000.0000.0000.000
190A196LEU0-0.011-0.00116.560-0.542-0.5420.0000.0000.0000.000
191A197ILE0-0.039-0.00317.697-0.341-0.3410.0000.0000.0000.000
192A198ASP-1-0.890-0.97218.845-12.557-12.5570.0000.0000.0000.000
193A199GLY0-0.056-0.00815.678-0.178-0.1780.0000.0000.0000.000
194A200LEU0-0.029-0.00313.912-1.265-1.2650.0000.0000.0000.000
195A201SER0-0.059-0.03711.3000.2420.2420.0000.0000.0000.000
196A202ASN0-0.041-0.0279.639-1.590-1.5900.0000.0000.0000.000
197A203ARG10.7270.8375.20323.20723.2070.0000.0000.0000.000
198A204GLU-1-0.990-0.9953.917-33.865-33.5850.002-0.084-0.1980.000