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: LJ9V9

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 OptHSide
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 -1923001.346843
FMO2-HF: Nuclear repulsion 1851363.227724
FMO2-HF: Total energy -71638.119119
FMO2-MP2: Total energy -71847.071766


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.
-142.345-135.7991.537-3.711-4.371-0.017
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 : 0.973 / q_NPA : 0.993
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].
3A9ARG10.8790.9042.60414.71918.9121.432-2.675-2.949-0.010
4A10GLY0-0.002-0.0104.8001.4331.520-0.001-0.005-0.0820.000
5A11ASN0-0.055-0.0325.7770.2320.2320.0000.0000.0000.000
6A12VAL00.0090.0137.4683.2093.2090.0000.0000.0000.000
7A13GLY00.0030.0048.538-1.603-1.6030.0000.0000.0000.000
8A14PHE0-0.027-0.0098.3240.4920.4920.0000.0000.0000.000
9A15VAL00.005-0.00312.8750.5840.5840.0000.0000.0000.000
10A16ALA0-0.0120.00016.5790.1410.1410.0000.0000.0000.000
11A17GLY00.0560.02019.4090.2450.2450.0000.0000.0000.000
12A18SER0-0.120-0.05222.9590.3320.3320.0000.0000.0000.000
13A19SER00.0000.00521.4690.1650.1650.0000.0000.0000.000
14A20TYR0-0.012-0.00916.920-0.255-0.2550.0000.0000.0000.000
15A21GLY00.0230.00415.6850.2240.2240.0000.0000.0000.000
16A22THR0-0.031-0.01210.830-1.306-1.3060.0000.0000.0000.000
17A23GLY00.0260.01412.8491.4871.4870.0000.0000.0000.000
18A24SER0-0.0290.00412.421-1.714-1.7140.0000.0000.0000.000
19A25VAL00.0080.00512.5261.7121.7120.0000.0000.0000.000
20A26TRP00.015-0.01413.240-1.827-1.8270.0000.0000.0000.000
21A27THR00.0040.00616.0600.9060.9060.0000.0000.0000.000
22A28ARG10.7570.83318.79412.85712.8570.0000.0000.0000.000
23A29ASN0-0.002-0.00522.3280.0730.0730.0000.0000.0000.000
24A30ASN0-0.042-0.02224.1910.2730.2730.0000.0000.0000.000
25A31GLU-1-0.841-0.88823.342-12.000-12.0000.0000.0000.0000.000
26A32VAL0-0.022-0.01317.564-0.519-0.5190.0000.0000.0000.000
27A33VAL0-0.013-0.01518.9880.5890.5890.0000.0000.0000.000
28A34VAL00.001-0.00716.719-1.147-1.1470.0000.0000.0000.000
29A35LEU0-0.016-0.00117.1861.0051.0050.0000.0000.0000.000
30A36THR00.014-0.01617.046-0.788-0.7880.0000.0000.0000.000
31A37ALA00.0490.04318.7210.5220.5220.0000.0000.0000.000
32A38SER0-0.052-0.06520.8950.0290.0290.0000.0000.0000.000
33A39HIS0-0.076-0.06120.5960.1040.1040.0000.0000.0000.000
34A40VAL00.0150.03018.3430.2320.2320.0000.0000.0000.000
35A41VAL0-0.0210.00521.6180.2210.2210.0000.0000.0000.000
36A42GLY00.0800.04223.6480.2980.2980.0000.0000.0000.000
37A43ARG10.9470.95026.9708.4668.4660.0000.0000.0000.000
38A44ALA0-0.028-0.01629.3500.1640.1640.0000.0000.0000.000
39A45ASN0-0.023-0.01527.887-0.142-0.1420.0000.0000.0000.000
40A46MET00.0200.01926.223-0.143-0.1430.0000.0000.0000.000
41A47ALA00.0160.00721.3100.0410.0410.0000.0000.0000.000
42A48THR0-0.0090.00319.0540.1360.1360.0000.0000.0000.000
43A49LEU00.0150.02414.121-0.340-0.3400.0000.0000.0000.000
44A50LYS10.9600.97112.13820.93120.9310.0000.0000.0000.000
45A51ILE00.004-0.0059.696-1.130-1.1300.0000.0000.0000.000
46A52GLY00.0100.0209.8090.8210.8210.0000.0000.0000.000
47A53ASP-1-0.930-0.96810.890-21.234-21.2340.0000.0000.0000.000
48A54ALA0-0.051-0.01514.1181.5371.5370.0000.0000.0000.000
49A55MET0-0.017-0.02115.419-0.642-0.6420.0000.0000.0000.000
50A56LEU00.0060.01018.1060.7340.7340.0000.0000.0000.000
51A57THR0-0.021-0.01520.320-0.229-0.2290.0000.0000.0000.000
52A58LEU0-0.009-0.00519.6690.2130.2130.0000.0000.0000.000
53A59THR00.002-0.00923.8600.3760.3760.0000.0000.0000.000
54A60PHE0-0.010-0.01020.334-0.100-0.1000.0000.0000.0000.000
55A61LYS10.9340.97126.15511.18611.1860.0000.0000.0000.000
56A62LYS10.8370.92326.01910.64710.6470.0000.0000.0000.000
57A63ASN0-0.0310.00227.5230.6550.6550.0000.0000.0000.000
58A64GLY00.0630.03827.681-0.266-0.2660.0000.0000.0000.000
59A65ASP-1-0.781-0.86822.621-12.614-12.6140.0000.0000.0000.000
60A66PHE00.0480.05920.890-0.575-0.5750.0000.0000.0000.000
61A67ALA0-0.003-0.00722.4830.6250.6250.0000.0000.0000.000
62A68GLU-1-0.793-0.87821.783-13.425-13.4250.0000.0000.0000.000
63A69ALA0-0.016-0.00521.7200.7060.7060.0000.0000.0000.000
64A70VAL0-0.014-0.00221.970-0.512-0.5120.0000.0000.0000.000
65A71THR00.0210.00420.3710.4970.4970.0000.0000.0000.000
66A72THR00.0460.02023.117-0.133-0.1330.0000.0000.0000.000
67A73GLN00.053-0.00717.318-0.456-0.4560.0000.0000.0000.000
68A74SER0-0.081-0.05720.641-0.412-0.4120.0000.0000.0000.000
69A75GLU-1-0.916-0.92022.123-12.225-12.2250.0000.0000.0000.000
70A76LEU0-0.045-0.02415.147-0.453-0.4530.0000.0000.0000.000
71A77PRO00.0340.03417.254-0.424-0.4240.0000.0000.0000.000
72A78GLY00.0330.00713.882-1.250-1.2500.0000.0000.0000.000
73A79ASN0-0.061-0.01812.8412.3132.3130.0000.0000.0000.000
74A80TRP0-0.033-0.02210.270-2.504-2.5040.0000.0000.0000.000
75A81PRO00.0180.02611.5621.1841.1840.0000.0000.0000.000
76A82GLN00.0290.00214.2900.3580.3580.0000.0000.0000.000
77A83LEU0-0.027-0.01017.342-0.528-0.5280.0000.0000.0000.000
78A84HIS00.0030.01518.7941.3771.3770.0000.0000.0000.000
79A85PHE0-0.014-0.00819.891-0.466-0.4660.0000.0000.0000.000
80A86ALA00.0090.00121.8570.4180.4180.0000.0000.0000.000
81A87GLN0-0.069-0.03123.3880.1670.1670.0000.0000.0000.000
82A88PRO00.0320.01323.387-0.317-0.3170.0000.0000.0000.000
83A89THR0-0.013-0.00123.3420.7780.7780.0000.0000.0000.000
84A90THR0-0.030-0.02023.322-0.484-0.4840.0000.0000.0000.000
85A91GLY00.0210.01222.0900.2560.2560.0000.0000.0000.000
86A92PRO00.0180.02216.6840.1030.1030.0000.0000.0000.000
87A93ALA0-0.020-0.00416.3360.2500.2500.0000.0000.0000.000
88A94SER00.0030.00910.923-0.222-0.2220.0000.0000.0000.000
89A95TRP0-0.004-0.00311.8130.5230.5230.0000.0000.0000.000
90A96CYS0-0.069-0.0449.028-1.340-1.3400.0000.0000.0000.000
91A97THR00.001-0.0046.7070.8040.8040.0000.0000.0000.000
92A98ALA00.026-0.0076.735-3.696-3.6960.0000.0000.0000.000
93A99THR0-0.081-0.0513.772-2.404-2.1230.001-0.047-0.2340.000
94A100GLY00.0390.0343.130-5.595-4.0580.098-0.879-0.756-0.007
95A101ASP-1-0.791-0.8683.766-28.145-27.8470.007-0.066-0.2390.000
96A102GLU-1-0.764-0.8677.193-21.782-21.7820.0000.0000.0000.000
97A103GLU-1-0.996-1.0069.681-18.608-18.6080.0000.0000.0000.000
98A104GLY00.0560.02012.4240.7310.7310.0000.0000.0000.000
99A105LEU0-0.044-0.02315.8520.0610.0610.0000.0000.0000.000
100A106LEU00.008-0.01219.3210.0660.0660.0000.0000.0000.000
101A107SER00.003-0.02421.1150.4200.4200.0000.0000.0000.000
102A108GLY00.016-0.00324.837-0.174-0.1740.0000.0000.0000.000
103A109GLU-1-0.906-0.95927.338-10.115-10.1150.0000.0000.0000.000
104A110VAL0-0.001-0.00324.2390.0600.0600.0000.0000.0000.000
105A111CYS0-0.0460.01620.181-0.397-0.3970.0000.0000.0000.000
106A112LEU0-0.0080.00319.5140.3380.3380.0000.0000.0000.000
107A113ALA00.0610.02414.247-0.685-0.6850.0000.0000.0000.000
108A114TRP0-0.0170.01510.0460.6500.6500.0000.0000.0000.000
109A115THR00.003-0.01112.297-0.983-0.9830.0000.0000.0000.000
110A116THR0-0.025-0.01412.3971.1191.1190.0000.0000.0000.000
111A117SER00.0560.01214.762-0.027-0.0270.0000.0000.0000.000
112A118GLY0-0.0140.00113.8040.1190.1190.0000.0000.0000.000
113A119ASP-1-0.758-0.84410.465-21.700-21.7000.0000.0000.0000.000
114A120SER00.0150.01313.045-0.328-0.3280.0000.0000.0000.000
115A121GLY0-0.046-0.03515.922-0.341-0.3410.0000.0000.0000.000
116A122SER0-0.012-0.02912.017-0.921-0.9210.0000.0000.0000.000
117A123ALA0-0.0290.00113.1321.2031.2030.0000.0000.0000.000
118A124VAL00.0290.01313.660-1.132-1.1320.0000.0000.0000.000
119A125VAL0-0.028-0.03312.3830.7960.7960.0000.0000.0000.000
120A126GLN00.043-0.00215.5330.1820.1820.0000.0000.0000.000
121A127GLY0-0.0080.00616.2940.6530.6530.0000.0000.0000.000
122A128ASP-1-0.957-0.98714.869-17.954-17.9540.0000.0000.0000.000
123A129ALA00.0070.00216.3090.2120.2120.0000.0000.0000.000
124A130VAL0-0.026-0.01015.901-0.483-0.4830.0000.0000.0000.000
125A131VAL00.005-0.00218.1010.9200.9200.0000.0000.0000.000
126A132GLY0-0.007-0.02719.1180.9600.9600.0000.0000.0000.000
127A133VAL0-0.061-0.00317.748-0.959-0.9590.0000.0000.0000.000
128A134HIS00.0200.01315.5440.7690.7690.0000.0000.0000.000
129A135THR0-0.008-0.02017.605-0.012-0.0120.0000.0000.0000.000
130A136GLY00.0170.00319.8320.2960.2960.0000.0000.0000.000
131A137SER0-0.028-0.00718.311-0.064-0.0640.0000.0000.0000.000
132A138ASN00.004-0.00420.5080.5900.5900.0000.0000.0000.000
133A139THR0-0.006-0.01921.607-0.442-0.4420.0000.0000.0000.000
134A140SER0-0.033-0.03921.9260.1840.1840.0000.0000.0000.000
135A141GLY00.0280.02518.500-0.086-0.0860.0000.0000.0000.000
136A142VAL0-0.0020.02019.354-0.325-0.3250.0000.0000.0000.000
137A143ALA0-0.010-0.01018.080-0.313-0.3130.0000.0000.0000.000
138A144TYR0-0.0080.00420.0580.5060.5060.0000.0000.0000.000
139A145VAL00.0240.01118.853-0.547-0.5470.0000.0000.0000.000
140A146THR0-0.018-0.00821.4050.8610.8610.0000.0000.0000.000
141A147THR00.0290.01522.619-0.498-0.4980.0000.0000.0000.000
142A148PRO00.0530.01822.8160.3470.3470.0000.0000.0000.000
143A149SER0-0.063-0.03725.2470.2190.2190.0000.0000.0000.000
144A150GLY00.0000.00027.4800.3960.3960.0000.0000.0000.000
145A151LYS10.8660.94528.29810.44110.4410.0000.0000.0000.000
146A152LEU00.0070.00324.831-0.385-0.3850.0000.0000.0000.000
147A153LEU0-0.031-0.02422.9300.4740.4740.0000.0000.0000.000
148A154GLY00.0250.01124.316-0.361-0.3610.0000.0000.0000.000
149A155ALA0-0.033-0.01625.2830.0660.0660.0000.0000.0000.000
150A156ASP-1-0.937-0.94628.493-9.149-9.1490.0000.0000.0000.000
151A157THR0-0.021-0.01229.872-0.066-0.0660.0000.0000.0000.000
152A158VAL00.0120.00428.5230.0830.0830.0000.0000.0000.000
153A159THR0-0.0240.00931.451-0.105-0.1050.0000.0000.0000.000
154A160LEU00.0850.04128.387-0.262-0.2620.0000.0000.0000.000
155A161SER0-0.057-0.04931.005-0.253-0.2530.0000.0000.0000.000
156A162SER0-0.074-0.04432.966-0.087-0.0870.0000.0000.0000.000
157A163LEU00.0630.02425.640-0.121-0.1210.0000.0000.0000.000
158A164SER00.014-0.03228.487-0.360-0.3600.0000.0000.0000.000
159A165LYS10.8400.93829.8978.8528.8520.0000.0000.0000.000
160A166HIS0-0.046-0.01427.083-0.055-0.0550.0000.0000.0000.000
161A167PHE00.0270.02921.993-0.477-0.4770.0000.0000.0000.000
162A168THR00.0230.02125.4540.3420.3420.0000.0000.0000.000
163A169GLY00.0100.00926.275-0.326-0.3260.0000.0000.0000.000
164A170PRO0-0.025-0.01527.7890.2410.2410.0000.0000.0000.000
165A171LEU00.0320.00829.195-0.297-0.2970.0000.0000.0000.000
166A172THR0-0.056-0.02826.014-0.060-0.0600.0000.0000.0000.000
167A173SER00.0140.00328.8720.0800.0800.0000.0000.0000.000
168A174ILE0-0.0040.01427.502-0.351-0.3510.0000.0000.0000.000
169A175PRO00.0180.02223.4590.2980.2980.0000.0000.0000.000
170A176LYS10.9080.94325.49310.20610.2060.0000.0000.0000.000
171A177ASP-1-0.879-0.92122.788-11.409-11.4090.0000.0000.0000.000
172A178ILE00.0070.01723.853-0.426-0.4260.0000.0000.0000.000
173A179PRO00.0350.00024.1410.3370.3370.0000.0000.0000.000
174A180ASP-1-0.888-0.93826.961-8.978-8.9780.0000.0000.0000.000
175A181ASN0-0.101-0.05828.2980.3450.3450.0000.0000.0000.000
176A182ILE0-0.0090.00025.000-0.050-0.0500.0000.0000.0000.000
177A183ILE0-0.007-0.01129.5900.1460.1460.0000.0000.0000.000
178A184ALA00.024-0.00532.043-0.048-0.0480.0000.0000.0000.000
179A185ASP-1-0.768-0.85533.442-8.284-8.2840.0000.0000.0000.000
180A186VAL0-0.044-0.02032.9510.1790.1790.0000.0000.0000.000
181A187ASP-1-0.914-0.95934.330-8.233-8.2330.0000.0000.0000.000
182A188ALA0-0.039-0.02831.591-0.138-0.1380.0000.0000.0000.000
183A189VAL00.0250.00927.0480.0940.0940.0000.0000.0000.000
184A190PRO00.0140.01027.285-0.034-0.0340.0000.0000.0000.000
185A191ARG10.9520.97123.74510.89310.8930.0000.0000.0000.000
186A192SER0-0.025-0.03122.043-0.368-0.3680.0000.0000.0000.000
187A193LEU00.0350.02821.490-0.488-0.4880.0000.0000.0000.000
188A194ALA0-0.012-0.01522.471-0.265-0.2650.0000.0000.0000.000
189A195MET00.000-0.01118.5090.0700.0700.0000.0000.0000.000
190A196LEU0-0.0020.01316.798-0.526-0.5260.0000.0000.0000.000
191A197ILE0-0.026-0.01617.647-0.473-0.4730.0000.0000.0000.000
192A198ASP-1-0.907-0.97019.094-12.525-12.5250.0000.0000.0000.000
193A199GLY0-0.056-0.01015.616-0.206-0.2060.0000.0000.0000.000
194A200LEU0-0.059-0.01513.940-1.178-1.1780.0000.0000.0000.000
195A201SER0-0.034-0.02711.3940.1310.1310.0000.0000.0000.000
196A202ASN0-0.036-0.0139.767-1.372-1.3720.0000.0000.0000.000
197A203ARG10.7340.8595.30422.78922.7890.0000.0000.0000.000
198A204GLU-1-0.998-0.9984.166-29.263-29.1130.000-0.039-0.1110.000