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: K2G33

Calculation Name: 1MP9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1MP9

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UWN7

Base Structure: X-ray

Registration Date: 2023-09-27

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1960709.253585
FMO2-HF: Nuclear repulsion 1884345.138315
FMO2-HF: Total energy -76364.115269
FMO2-MP2: Total energy -76586.70068


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:5:ASP)


Summations of interaction energy for fragment #1(A:5:ASP)
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.
69.29572.3260.011-1.429-1.6120.006
Interaction energy analysis for fragmet #1(A:5:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.942 / q_NPA : -0.980
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].
3A7ILE0-0.003-0.0023.804-1.1391.027-0.013-1.084-1.0680.004
4A8PRO00.0100.0165.363-3.191-3.1910.0000.0000.0000.000
5A9TYR0-0.023-0.0208.090-1.927-1.9270.0000.0000.0000.000
6A10LYS10.9190.94610.371-25.232-25.2320.0000.0000.0000.000
7A11ALA0-0.0050.00813.452-0.876-0.8760.0000.0000.0000.000
8A12VAL0-0.0170.00516.483-0.379-0.3790.0000.0000.0000.000
9A13VAL0-0.015-0.01419.803-0.307-0.3070.0000.0000.0000.000
10A14ASN0-0.025-0.02223.044-0.197-0.1970.0000.0000.0000.000
11A15ILE00.0040.00726.412-0.165-0.1650.0000.0000.0000.000
12A16GLU-1-0.820-0.88828.8679.9629.9620.0000.0000.0000.000
13A17ASN0-0.020-0.02231.911-0.402-0.4020.0000.0000.0000.000
14A18ILE0-0.0100.02534.4130.1620.1620.0000.0000.0000.000
15A19VAL0-0.0190.00236.722-0.235-0.2350.0000.0000.0000.000
16A20ALA00.009-0.00439.7270.1000.1000.0000.0000.0000.000
17A21THR0-0.020-0.01442.006-0.179-0.1790.0000.0000.0000.000
18A22VAL0-0.016-0.00845.5150.0730.0730.0000.0000.0000.000
19A23THR0-0.004-0.00248.161-0.080-0.0800.0000.0000.0000.000
20A24LEU0-0.040-0.03151.2500.0040.0040.0000.0000.0000.000
21A25ASP-1-0.962-0.98154.3765.4365.4360.0000.0000.0000.000
22A26GLN00.005-0.00656.398-0.149-0.1490.0000.0000.0000.000
23A27THR0-0.035-0.01458.5250.0610.0610.0000.0000.0000.000
24A28LEU0-0.037-0.02156.856-0.030-0.0300.0000.0000.0000.000
25A29ASP-1-0.828-0.91760.9144.8534.8530.0000.0000.0000.000
26A30LEU0-0.021-0.03357.3330.0020.0020.0000.0000.0000.000
27A31TYR00.0600.03861.0280.0370.0370.0000.0000.0000.000
28A32ALA00.0000.00964.022-0.012-0.0120.0000.0000.0000.000
29A33MET0-0.035-0.00357.7500.0430.0430.0000.0000.0000.000
30A34GLU-1-0.934-0.98660.2705.0465.0460.0000.0000.0000.000
31A35ARG10.9560.99361.238-4.671-4.6710.0000.0000.0000.000
32A36SER0-0.087-0.04262.896-0.051-0.0510.0000.0000.0000.000
33A37VAL0-0.085-0.05257.0220.0220.0220.0000.0000.0000.000
34A38PRO00.0050.00858.851-0.001-0.0010.0000.0000.0000.000
35A39ASN0-0.040-0.03656.6230.0410.0410.0000.0000.0000.000
36A40VAL0-0.0200.01955.1030.1370.1370.0000.0000.0000.000
37A41GLU-1-0.786-0.88154.1695.6945.6940.0000.0000.0000.000
38A42TYR0-0.022-0.03456.3190.1010.1010.0000.0000.0000.000
39A43ASP-1-0.740-0.84958.1135.1055.1050.0000.0000.0000.000
40A44PRO0-0.087-0.04058.6590.0760.0760.0000.0000.0000.000
41A45ASP-1-0.897-0.93159.8414.9764.9760.0000.0000.0000.000
42A46GLN0-0.139-0.07756.1340.1240.1240.0000.0000.0000.000
43A47PHE0-0.026-0.03349.9320.1680.1680.0000.0000.0000.000
44A48PRO0-0.007-0.00153.762-0.061-0.0610.0000.0000.0000.000
45A49GLY0-0.058-0.02353.657-0.056-0.0560.0000.0000.0000.000
46A50LEU00.0150.01254.702-0.001-0.0010.0000.0000.0000.000
47A51ILE0-0.032-0.02150.2990.1540.1540.0000.0000.0000.000
48A52PHE00.016-0.00450.547-0.074-0.0740.0000.0000.0000.000
49A53ARG10.8610.90848.902-5.936-5.9360.0000.0000.0000.000
50A54LEU0-0.016-0.00446.906-0.109-0.1090.0000.0000.0000.000
51A55GLU-1-0.758-0.86645.3456.9656.9650.0000.0000.0000.000
52A56SER0-0.075-0.00743.456-0.052-0.0520.0000.0000.0000.000
53A57PRO00.0500.00040.741-0.128-0.1280.0000.0000.0000.000
54A58LYS10.8750.91141.547-7.173-7.1730.0000.0000.0000.000
55A59ILE0-0.037-0.01141.1640.1410.1410.0000.0000.0000.000
56A60THR0-0.018-0.00144.139-0.206-0.2060.0000.0000.0000.000
57A61SER0-0.021-0.02545.7410.1370.1370.0000.0000.0000.000
58A62LEU00.0130.02147.321-0.106-0.1060.0000.0000.0000.000
59A63ILE00.012-0.01250.2390.0680.0680.0000.0000.0000.000
60A64PHE00.0400.02349.702-0.089-0.0890.0000.0000.0000.000
61A65LYS11.0511.02554.949-5.175-5.1750.0000.0000.0000.000
62A66SER0-0.012-0.00154.441-0.047-0.0470.0000.0000.0000.000
63A67GLY00.0690.04655.7370.0010.0010.0000.0000.0000.000
64A68LYS10.8990.95548.568-6.221-6.2210.0000.0000.0000.000
65A69MET00.0190.02348.973-0.079-0.0790.0000.0000.0000.000
66A70VAL0-0.024-0.01344.6280.1250.1250.0000.0000.0000.000
67A71VAL0-0.007-0.00343.480-0.081-0.0810.0000.0000.0000.000
68A72THR00.009-0.00941.0560.2460.2460.0000.0000.0000.000
69A73GLY00.0560.02039.443-0.187-0.1870.0000.0000.0000.000
70A74ALA0-0.034-0.00338.4020.1020.1020.0000.0000.0000.000
71A75LYS10.9190.95032.556-9.087-9.0870.0000.0000.0000.000
72A76SER00.0740.03333.0470.2200.2200.0000.0000.0000.000
73A77THR00.0760.02234.820-0.258-0.2580.0000.0000.0000.000
74A78ASP-1-0.828-0.90936.6577.7947.7940.0000.0000.0000.000
75A79GLU-1-0.869-0.93237.0517.9137.9130.0000.0000.0000.000
76A80LEU00.0260.01038.991-0.257-0.2570.0000.0000.0000.000
77A81ILE0-0.012-0.01540.431-0.285-0.2850.0000.0000.0000.000
78A82LYS10.8280.90639.709-7.989-7.9890.0000.0000.0000.000
79A83ALA00.0570.03743.482-0.207-0.2070.0000.0000.0000.000
80A84VAL00.0350.02144.740-0.202-0.2020.0000.0000.0000.000
81A85LYS10.9210.96445.762-6.948-6.9480.0000.0000.0000.000
82A86ARG10.8800.95146.916-6.664-6.6640.0000.0000.0000.000
83A87ILE00.014-0.00147.339-0.152-0.1520.0000.0000.0000.000
84A88ILE00.0150.00050.224-0.152-0.1520.0000.0000.0000.000
85A89LYS10.9070.95852.668-5.941-5.9410.0000.0000.0000.000
86A90THR0-0.013-0.00453.451-0.133-0.1330.0000.0000.0000.000
87A91LEU00.0780.02753.761-0.110-0.1100.0000.0000.0000.000
88A92LYS10.9040.96955.924-5.646-5.6460.0000.0000.0000.000
89A93LYS10.8470.93258.501-5.270-5.2700.0000.0000.0000.000
90A94TYR0-0.017-0.03259.080-0.045-0.0450.0000.0000.0000.000
91A95GLY00.0810.04962.024-0.044-0.0440.0000.0000.0000.000
92A96MET0-0.0550.00756.959-0.018-0.0180.0000.0000.0000.000
93A97GLN00.004-0.00960.7160.0620.0620.0000.0000.0000.000
94A98LEU0-0.005-0.01054.5680.0610.0610.0000.0000.0000.000
95A99THR00.0460.03158.823-0.043-0.0430.0000.0000.0000.000
96A100GLY00.0400.01556.564-0.018-0.0180.0000.0000.0000.000
97A101LYS10.8780.93251.326-5.778-5.7780.0000.0000.0000.000
98A102PRO00.0540.04950.5090.0230.0230.0000.0000.0000.000
99A103LYS10.9620.97647.150-6.232-6.2320.0000.0000.0000.000
100A104ILE00.020-0.00242.684-0.055-0.0550.0000.0000.0000.000
101A105GLN0-0.043-0.01742.349-0.011-0.0110.0000.0000.0000.000
102A106ILE00.0460.02536.256-0.115-0.1150.0000.0000.0000.000
103A107GLN0-0.093-0.05439.571-0.004-0.0040.0000.0000.0000.000
104A108ASN00.023-0.00134.9400.1870.1870.0000.0000.0000.000
105A109ILE00.0000.02631.320-0.187-0.1870.0000.0000.0000.000
106A110VAL0-0.028-0.00631.4390.0960.0960.0000.0000.0000.000
107A111ALA0-0.003-0.00827.207-0.101-0.1010.0000.0000.0000.000
108A112SER0-0.028-0.02625.9420.0960.0960.0000.0000.0000.000
109A113ALA00.020-0.00320.8460.0570.0570.0000.0000.0000.000
110A114ASN0-0.040-0.02018.345-0.736-0.7360.0000.0000.0000.000
111A115LEU00.013-0.01715.2150.3740.3740.0000.0000.0000.000
112A116HIS0-0.083-0.04113.7430.0090.0090.0000.0000.0000.000
113A117VAL00.0190.01810.6121.4581.4580.0000.0000.0000.000
114A118ILE0-0.018-0.00513.188-1.374-1.3740.0000.0000.0000.000
115A119VAL0-0.012-0.01814.2560.8470.8470.0000.0000.0000.000
116A120ASN0-0.004-0.00515.712-1.447-1.4470.0000.0000.0000.000
117A121LEU00.014-0.01217.402-0.008-0.0080.0000.0000.0000.000
118A122ASP-1-0.811-0.89220.81411.89211.8920.0000.0000.0000.000
119A123LYS10.8140.90413.048-18.963-18.9630.0000.0000.0000.000
120A124ALA00.036-0.00118.175-0.112-0.1120.0000.0000.0000.000
121A125ALA0-0.020-0.01619.428-0.304-0.3040.0000.0000.0000.000
122A126PHE0-0.051-0.01722.152-0.500-0.5000.0000.0000.0000.000
123A127LEU0-0.0200.00017.0670.0410.0410.0000.0000.0000.000
124A128LEU0-0.072-0.01719.2190.1800.1800.0000.0000.0000.000
125A129GLU-1-0.857-0.93421.93610.11610.1160.0000.0000.0000.000
126A130ASN0-0.085-0.05625.4980.0470.0470.0000.0000.0000.000
127A131ASN0-0.072-0.05024.975-0.020-0.0200.0000.0000.0000.000
128A132MET0-0.0050.00927.728-0.364-0.3640.0000.0000.0000.000
129A133TYR0-0.019-0.03724.2520.2020.2020.0000.0000.0000.000
130A134GLU-1-0.873-0.92727.6659.0219.0210.0000.0000.0000.000
131A135PRO00.0140.00427.616-0.252-0.2520.0000.0000.0000.000
132A136GLU-1-0.917-0.94529.8558.6308.6300.0000.0000.0000.000
133A137GLN0-0.126-0.06732.942-0.448-0.4480.0000.0000.0000.000
134A138PHE0-0.042-0.03528.602-0.122-0.1220.0000.0000.0000.000
135A139PRO00.0060.00728.1440.1730.1730.0000.0000.0000.000
136A140GLY0-0.0080.00025.7400.4280.4280.0000.0000.0000.000
137A141LEU0-0.0080.01422.004-0.271-0.2710.0000.0000.0000.000
138A142ILE0-0.053-0.03125.6690.0810.0810.0000.0000.0000.000
139A143TYR00.0520.02124.8070.0750.0750.0000.0000.0000.000
140A144ARG10.9400.97526.897-8.891-8.8910.0000.0000.0000.000
141A145MET0-0.0210.00923.0460.0770.0770.0000.0000.0000.000
142A146ASP-1-0.913-0.95828.2289.4199.4190.0000.0000.0000.000
143A147GLU-1-0.917-0.92327.84610.45910.4590.0000.0000.0000.000
144A148PRO00.020-0.01726.1740.4670.4670.0000.0000.0000.000
145A149ARG10.9780.98529.209-8.335-8.3350.0000.0000.0000.000
146A150VAL0-0.042-0.01527.187-0.234-0.2340.0000.0000.0000.000
147A151VAL0-0.018-0.01029.7160.0200.0200.0000.0000.0000.000
148A152LEU0-0.014-0.01323.1900.0090.0090.0000.0000.0000.000
149A153LEU0-0.0170.00826.617-0.180-0.1800.0000.0000.0000.000
150A154ILE00.0320.00920.4470.2300.2300.0000.0000.0000.000
151A155PHE00.0330.00322.528-0.334-0.3340.0000.0000.0000.000
152A156SER00.0900.04920.0070.4750.4750.0000.0000.0000.000
153A157SER00.0050.00418.5660.5620.5620.0000.0000.0000.000
154A158GLY00.0740.04917.5540.5300.5300.0000.0000.0000.000
155A159LYS10.9070.97218.382-11.431-11.4310.0000.0000.0000.000
156A160MET00.0020.00020.6060.1200.1200.0000.0000.0000.000
157A161VAL0-0.037-0.01723.473-0.220-0.2200.0000.0000.0000.000
158A162ILE00.0060.00923.6180.0540.0540.0000.0000.0000.000
159A163THR00.001-0.00527.628-0.353-0.3530.0000.0000.0000.000
160A164GLY00.0270.00731.2770.1140.1140.0000.0000.0000.000
161A165ALA00.0080.02530.045-0.142-0.1420.0000.0000.0000.000
162A166LYS10.8850.92632.212-8.110-8.1100.0000.0000.0000.000
163A167ARG10.8100.88231.422-9.703-9.7030.0000.0000.0000.000
164A168GLU-1-0.808-0.90927.84010.71910.7190.0000.0000.0000.000
165A169ASP-1-0.804-0.89426.98210.41310.4130.0000.0000.0000.000
166A170GLU-1-0.844-0.92126.3189.8159.8150.0000.0000.0000.000
167A171VAL00.0090.00325.3760.2770.2770.0000.0000.0000.000
168A172HIS0-0.021-0.03322.7010.8030.8030.0000.0000.0000.000
169A173LYS10.8280.91321.793-10.712-10.7120.0000.0000.0000.000
170A174ALA00.004-0.01422.1060.4350.4350.0000.0000.0000.000
171A175VAL0-0.0050.00418.7910.3060.3060.0000.0000.0000.000
172A176LYS10.8880.92114.726-18.026-18.0260.0000.0000.0000.000
173A177LYS10.8970.94717.280-11.548-11.5480.0000.0000.0000.000
174A178ILE00.004-0.00518.5100.3290.3290.0000.0000.0000.000
175A179PHE00.0180.01510.357-0.018-0.0180.0000.0000.0000.000
176A180ASP-1-0.792-0.88313.68619.72919.7290.0000.0000.0000.000
177A181LYS10.7840.88414.155-14.626-14.6260.0000.0000.0000.000
178A182LEU00.005-0.00814.8440.1310.1310.0000.0000.0000.000
179A183VAL00.0060.0058.7710.4640.4640.0000.0000.0000.000
180A184GLU-1-0.843-0.88810.57517.05717.0570.0000.0000.0000.000
181A185LEU0-0.034-0.02612.5000.0280.0280.0000.0000.0000.000
182A186ASP-1-0.877-0.9439.32022.48222.4820.0000.0000.0000.000
183A187CYS0-0.085-0.02411.223-1.127-1.1270.0000.0000.0000.000
184A188VAL0-0.002-0.00210.268-1.099-1.0990.0000.0000.0000.000
185A189LYS10.9310.9639.575-22.635-22.6350.0000.0000.0000.000
186A190PRO00.0090.0036.343-2.539-2.5390.0000.0000.0000.000
187A191VAL0-0.012-0.0239.0541.3801.3800.0000.0000.0000.000
188A192GLU-1-0.903-0.92911.40318.03918.0390.0000.0000.0000.000
189A193GLU-1-0.919-0.9506.82929.44029.4400.0000.0000.0000.000
190A194GLU-1-0.967-0.9748.08527.52227.5220.0000.0000.0000.000
191A195GLU-1-0.904-0.9546.86627.67427.6740.0000.0000.0000.000
192A196LEU0-0.023-0.0093.475-1.261-0.3960.024-0.345-0.5440.002
193A197GLU-1-0.998-0.9917.10622.87222.8720.0000.0000.0000.000