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: 4LJ3N

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1960302.76136
FMO2-HF: Nuclear repulsion 1883937.947684
FMO2-HF: Total energy -76364.813676
FMO2-MP2: Total energy -76587.342604


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.
64.46567.4340.094-1.321-1.7420.01
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 : -0.940 / q_NPA : -0.978
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].
3A7ILE00.0080.0023.876-1.3990.254-0.006-0.754-0.8930.004
4A8PRO00.0090.0205.226-3.110-3.1100.0000.0000.0000.000
5A9TYR0-0.023-0.0297.874-2.064-2.0640.0000.0000.0000.000
6A10LYS10.8480.90710.382-25.061-25.0610.0000.0000.0000.000
7A11ALA0-0.0230.01012.972-1.010-1.0100.0000.0000.0000.000
8A12VAL0-0.0130.00616.161-0.419-0.4190.0000.0000.0000.000
9A13VAL0-0.009-0.01819.581-0.227-0.2270.0000.0000.0000.000
10A14ASN0-0.039-0.03023.017-0.195-0.1950.0000.0000.0000.000
11A15ILE0-0.0060.00226.623-0.141-0.1410.0000.0000.0000.000
12A16GLU-1-0.816-0.87629.0029.9459.9450.0000.0000.0000.000
13A17ASN0-0.019-0.02932.242-0.371-0.3710.0000.0000.0000.000
14A18ILE0-0.0320.01434.4610.1300.1300.0000.0000.0000.000
15A19VAL00.0040.02036.804-0.251-0.2510.0000.0000.0000.000
16A20ALA00.019-0.00139.5640.1050.1050.0000.0000.0000.000
17A21THR0-0.049-0.03641.973-0.174-0.1740.0000.0000.0000.000
18A22VAL0-0.0090.00345.4910.0920.0920.0000.0000.0000.000
19A23THR0-0.004-0.00548.160-0.077-0.0770.0000.0000.0000.000
20A24LEU0-0.026-0.02951.298-0.009-0.0090.0000.0000.0000.000
21A25ASP-1-0.960-0.97254.4585.4175.4170.0000.0000.0000.000
22A26GLN0-0.023-0.02056.606-0.152-0.1520.0000.0000.0000.000
23A27THR0-0.011-0.00558.7360.0590.0590.0000.0000.0000.000
24A28LEU0-0.044-0.02056.818-0.027-0.0270.0000.0000.0000.000
25A29ASP-1-0.790-0.90660.9584.8694.8690.0000.0000.0000.000
26A30LEU0-0.026-0.02357.4770.0120.0120.0000.0000.0000.000
27A31TYR00.0370.02161.0880.0430.0430.0000.0000.0000.000
28A32ALA00.0290.01464.269-0.004-0.0040.0000.0000.0000.000
29A33MET0-0.0410.00257.8140.0470.0470.0000.0000.0000.000
30A34GLU-1-0.816-0.92360.7904.9574.9570.0000.0000.0000.000
31A35ARG10.8060.90961.710-4.752-4.7520.0000.0000.0000.000
32A36SER0-0.043-0.01963.293-0.082-0.0820.0000.0000.0000.000
33A37VAL0-0.067-0.04057.0960.0300.0300.0000.0000.0000.000
34A38PRO00.0000.00459.0290.0160.0160.0000.0000.0000.000
35A39ASN0-0.039-0.03556.3540.0320.0320.0000.0000.0000.000
36A40VAL0-0.0440.00555.3960.1280.1280.0000.0000.0000.000
37A41GLU-1-0.790-0.87654.4715.6765.6760.0000.0000.0000.000
38A42TYR0-0.037-0.04056.1540.1030.1030.0000.0000.0000.000
39A43ASP-1-0.754-0.85958.1295.0965.0960.0000.0000.0000.000
40A44PRO0-0.087-0.03458.6910.0860.0860.0000.0000.0000.000
41A45ASP-1-0.894-0.93459.9004.9814.9810.0000.0000.0000.000
42A46GLN0-0.116-0.06456.4580.1130.1130.0000.0000.0000.000
43A47PHE0-0.032-0.03850.2640.1700.1700.0000.0000.0000.000
44A48PRO0-0.0050.00654.092-0.068-0.0680.0000.0000.0000.000
45A49GLY0-0.054-0.03554.269-0.043-0.0430.0000.0000.0000.000
46A50LEU0-0.012-0.00555.1490.0010.0010.0000.0000.0000.000
47A51ILE00.0050.00050.4480.1310.1310.0000.0000.0000.000
48A52PHE00.0170.00450.547-0.082-0.0820.0000.0000.0000.000
49A53ARG10.8610.89249.114-5.884-5.8840.0000.0000.0000.000
50A54LEU0-0.038-0.02046.958-0.107-0.1070.0000.0000.0000.000
51A55GLU-1-0.726-0.84645.2126.9696.9690.0000.0000.0000.000
52A56SER0-0.0060.01343.458-0.100-0.1000.0000.0000.0000.000
53A57PRO00.0230.00640.695-0.122-0.1220.0000.0000.0000.000
54A58LYS10.8630.90241.822-7.162-7.1620.0000.0000.0000.000
55A59ILE0-0.053-0.01341.1630.1460.1460.0000.0000.0000.000
56A60THR0-0.011-0.00744.194-0.206-0.2060.0000.0000.0000.000
57A61SER0-0.031-0.02945.6540.1370.1370.0000.0000.0000.000
58A62LEU00.0240.02547.592-0.089-0.0890.0000.0000.0000.000
59A63ILE00.0190.00550.5140.0610.0610.0000.0000.0000.000
60A64PHE00.0290.01150.100-0.075-0.0750.0000.0000.0000.000
61A65LYS11.0131.00355.312-5.184-5.1840.0000.0000.0000.000
62A66SER0-0.0070.00455.121-0.060-0.0600.0000.0000.0000.000
63A67GLY00.0530.04155.9340.0270.0270.0000.0000.0000.000
64A68LYS10.9220.96048.907-6.176-6.1760.0000.0000.0000.000
65A69MET00.0270.02349.108-0.095-0.0950.0000.0000.0000.000
66A70VAL0-0.019-0.00144.9960.1190.1190.0000.0000.0000.000
67A71VAL0-0.023-0.01843.612-0.091-0.0910.0000.0000.0000.000
68A72THR00.0190.01141.2340.2410.2410.0000.0000.0000.000
69A73GLY00.0410.01339.827-0.197-0.1970.0000.0000.0000.000
70A74ALA0-0.0220.00238.3840.1160.1160.0000.0000.0000.000
71A75LYS10.8990.93132.466-9.080-9.0800.0000.0000.0000.000
72A76SER00.0700.03832.9470.2120.2120.0000.0000.0000.000
73A77THR00.0690.01134.820-0.263-0.2630.0000.0000.0000.000
74A78ASP-1-0.811-0.89036.6117.6397.6390.0000.0000.0000.000
75A79GLU-1-0.811-0.90537.0217.8917.8910.0000.0000.0000.000
76A80LEU00.0360.01839.036-0.261-0.2610.0000.0000.0000.000
77A81ILE0-0.018-0.01540.203-0.283-0.2830.0000.0000.0000.000
78A82LYS10.7930.88139.780-7.900-7.9000.0000.0000.0000.000
79A83ALA00.0350.02343.340-0.199-0.1990.0000.0000.0000.000
80A84VAL00.0260.00744.696-0.197-0.1970.0000.0000.0000.000
81A85LYS10.9130.96245.409-6.921-6.9210.0000.0000.0000.000
82A86ARG10.8530.93346.575-6.669-6.6690.0000.0000.0000.000
83A87ILE00.0200.02147.348-0.145-0.1450.0000.0000.0000.000
84A88ILE00.0250.00850.165-0.150-0.1500.0000.0000.0000.000
85A89LYS10.9050.95252.653-5.933-5.9330.0000.0000.0000.000
86A90THR0-0.026-0.02053.215-0.132-0.1320.0000.0000.0000.000
87A91LEU00.0500.01253.739-0.104-0.1040.0000.0000.0000.000
88A92LYS10.9180.96956.263-5.570-5.5700.0000.0000.0000.000
89A93LYS10.8400.94258.449-5.276-5.2760.0000.0000.0000.000
90A94TYR00.009-0.01259.028-0.039-0.0390.0000.0000.0000.000
91A95GLY00.0720.04961.894-0.038-0.0380.0000.0000.0000.000
92A96MET0-0.0400.00456.739-0.011-0.0110.0000.0000.0000.000
93A97GLN0-0.001-0.01460.7860.0460.0460.0000.0000.0000.000
94A98LEU0-0.009-0.01554.6530.0680.0680.0000.0000.0000.000
95A99THR00.0580.03358.767-0.028-0.0280.0000.0000.0000.000
96A100GLY00.0270.01656.494-0.026-0.0260.0000.0000.0000.000
97A101LYS10.8930.94351.246-5.745-5.7450.0000.0000.0000.000
98A102PRO00.0420.04350.7070.0300.0300.0000.0000.0000.000
99A103LYS10.9740.97847.454-6.160-6.1600.0000.0000.0000.000
100A104ILE00.0270.00842.852-0.055-0.0550.0000.0000.0000.000
101A105GLN0-0.041-0.02442.409-0.031-0.0310.0000.0000.0000.000
102A106ILE00.0590.03736.210-0.118-0.1180.0000.0000.0000.000
103A107GLN0-0.049-0.02639.7370.0350.0350.0000.0000.0000.000
104A108ASN00.020-0.00334.8950.1870.1870.0000.0000.0000.000
105A109ILE0-0.0310.00931.310-0.177-0.1770.0000.0000.0000.000
106A110VAL00.0050.01332.0750.1750.1750.0000.0000.0000.000
107A111ALA0-0.004-0.00827.550-0.101-0.1010.0000.0000.0000.000
108A112SER0-0.027-0.03226.2790.1150.1150.0000.0000.0000.000
109A113ALA00.0280.00021.0870.0540.0540.0000.0000.0000.000
110A114ASN0-0.034-0.01918.194-0.653-0.6530.0000.0000.0000.000
111A115LEU00.024-0.01215.4370.3180.3180.0000.0000.0000.000
112A116HIS0-0.074-0.04313.7870.1430.1430.0000.0000.0000.000
113A117VAL00.0010.01110.5771.4491.4490.0000.0000.0000.000
114A118ILE0-0.0120.00513.011-1.402-1.4020.0000.0000.0000.000
115A119VAL0-0.016-0.01213.9080.9470.9470.0000.0000.0000.000
116A120ASN0-0.007-0.01115.174-1.612-1.6120.0000.0000.0000.000
117A121LEU00.005-0.00716.996-0.074-0.0740.0000.0000.0000.000
118A122ASP-1-0.802-0.88420.45112.09612.0960.0000.0000.0000.000
119A123LYS10.7940.89413.371-19.133-19.1330.0000.0000.0000.000
120A124ALA00.0410.00218.085-0.162-0.1620.0000.0000.0000.000
121A125ALA00.004-0.00119.435-0.318-0.3180.0000.0000.0000.000
122A126PHE0-0.058-0.01022.089-0.576-0.5760.0000.0000.0000.000
123A127LEU0-0.021-0.01017.1580.1340.1340.0000.0000.0000.000
124A128LEU0-0.055-0.01519.3260.1890.1890.0000.0000.0000.000
125A129GLU-1-0.838-0.92522.12110.01710.0170.0000.0000.0000.000
126A130ASN0-0.092-0.04825.5550.0910.0910.0000.0000.0000.000
127A131ASN0-0.075-0.06025.105-0.065-0.0650.0000.0000.0000.000
128A132MET0-0.0110.00527.290-0.432-0.4320.0000.0000.0000.000
129A133TYR0-0.053-0.05423.9650.0710.0710.0000.0000.0000.000
130A134GLU-1-0.866-0.93627.3959.1569.1560.0000.0000.0000.000
131A135PRO00.0310.02227.658-0.219-0.2190.0000.0000.0000.000
132A136GLU-1-0.914-0.94329.6688.7078.7070.0000.0000.0000.000
133A137GLN0-0.137-0.07532.762-0.492-0.4920.0000.0000.0000.000
134A138PHE0-0.033-0.03328.233-0.139-0.1390.0000.0000.0000.000
135A139PRO0-0.0010.01928.3250.2240.2240.0000.0000.0000.000
136A140GLY0-0.010-0.02125.2640.4200.4200.0000.0000.0000.000
137A141LEU0-0.0220.00721.724-0.281-0.2810.0000.0000.0000.000
138A142ILE0-0.020-0.01025.1460.1380.1380.0000.0000.0000.000
139A143TYR00.0280.00424.5510.1810.1810.0000.0000.0000.000
140A144ARG10.8360.91426.635-9.111-9.1110.0000.0000.0000.000
141A145MET0-0.0090.02323.0480.1210.1210.0000.0000.0000.000
142A146ASP-1-0.816-0.91728.0259.1419.1410.0000.0000.0000.000
143A147GLU-1-0.873-0.91127.02910.77710.7770.0000.0000.0000.000
144A148PRO00.0350.00926.2200.4160.4160.0000.0000.0000.000
145A149ARG10.9490.97429.197-8.294-8.2940.0000.0000.0000.000
146A150VAL0-0.051-0.02227.555-0.298-0.2980.0000.0000.0000.000
147A151VAL00.000-0.00329.5050.0360.0360.0000.0000.0000.000
148A152LEU0-0.012-0.00923.344-0.016-0.0160.0000.0000.0000.000
149A153LEU0-0.016-0.00326.788-0.224-0.2240.0000.0000.0000.000
150A154ILE00.0310.01120.2450.2170.2170.0000.0000.0000.000
151A155PHE00.018-0.00322.213-0.374-0.3740.0000.0000.0000.000
152A156SER00.0840.04219.5260.4510.4510.0000.0000.0000.000
153A157SER0-0.010-0.00618.2720.5720.5720.0000.0000.0000.000
154A158GLY00.0820.05917.3760.3910.3910.0000.0000.0000.000
155A159LYS10.8980.97118.111-11.434-11.4340.0000.0000.0000.000
156A160MET00.009-0.00121.1500.1610.1610.0000.0000.0000.000
157A161VAL0-0.045-0.01723.471-0.285-0.2850.0000.0000.0000.000
158A162ILE00.0140.01724.1550.1080.1080.0000.0000.0000.000
159A163THR00.0050.00628.107-0.388-0.3880.0000.0000.0000.000
160A164GLY00.0250.00431.6580.1180.1180.0000.0000.0000.000
161A165ALA00.0160.02830.367-0.144-0.1440.0000.0000.0000.000
162A166LYS10.7930.86632.524-8.058-8.0580.0000.0000.0000.000
163A167ARG10.7880.87031.044-9.674-9.6740.0000.0000.0000.000
164A168GLU-1-0.805-0.90027.94710.52910.5290.0000.0000.0000.000
165A169ASP-1-0.798-0.88626.64910.38410.3840.0000.0000.0000.000
166A170GLU-1-0.846-0.92626.1899.7569.7560.0000.0000.0000.000
167A171VAL00.0260.01225.3230.2450.2450.0000.0000.0000.000
168A172HIS0-0.016-0.02322.6260.7830.7830.0000.0000.0000.000
169A173LYS10.8500.92321.589-10.636-10.6360.0000.0000.0000.000
170A174ALA00.003-0.00722.1010.4240.4240.0000.0000.0000.000
171A175VAL00.0160.00318.9390.2990.2990.0000.0000.0000.000
172A176LYS10.8600.91414.612-17.811-17.8110.0000.0000.0000.000
173A177LYS10.8460.91217.467-11.361-11.3610.0000.0000.0000.000
174A178ILE0-0.007-0.01118.9260.1830.1830.0000.0000.0000.000
175A179PHE00.0180.01410.6590.0120.0120.0000.0000.0000.000
176A180ASP-1-0.801-0.88813.55219.56819.5680.0000.0000.0000.000
177A181LYS10.7790.88113.931-14.592-14.5920.0000.0000.0000.000
178A182LEU00.013-0.00214.6940.0220.0220.0000.0000.0000.000
179A183VAL00.0100.0128.5960.6070.6070.0000.0000.0000.000
180A184GLU-1-0.845-0.89810.52317.21517.2150.0000.0000.0000.000
181A185LEU0-0.012-0.01012.681-0.025-0.0250.0000.0000.0000.000
182A186ASP-1-0.865-0.9269.64822.36022.3600.0000.0000.0000.000
183A187CYS0-0.079-0.02511.288-1.267-1.2670.0000.0000.0000.000
184A188VAL0-0.005-0.0139.891-1.174-1.1740.0000.0000.0000.000
185A189LYS10.8890.9309.382-22.950-22.9500.0000.0000.0000.000
186A190PRO00.0230.0106.165-2.446-2.4460.0000.0000.0000.000
187A191VAL0-0.031-0.0338.8111.3231.3230.0000.0000.0000.000
188A192GLU-1-0.881-0.92311.26117.65617.6560.0000.0000.0000.000
189A193GLU-1-0.852-0.9066.73627.07427.0740.0000.0000.0000.000
190A194GLU-1-0.963-0.9728.27827.61727.6170.0000.0000.0000.000
191A195GLU-1-0.884-0.9326.59729.09029.0900.0000.0000.0000.000
192A196LEU0-0.027-0.0123.073-3.521-2.2050.100-0.567-0.8490.006
193A197GLU-1-0.987-0.9807.09522.54022.5400.0000.0000.0000.000