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: QNV1Y

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 OptH
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 -1959728.674499
FMO2-HF: Nuclear repulsion 1883365.984199
FMO2-HF: Total energy -76362.6903
FMO2-MP2: Total energy -76585.357862


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.
80.69382.909-0.012-1.03-1.1750.004
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 : -0.919 / q_NPA : -0.973
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].
3A7ILE00.0010.0013.787-0.7761.205-0.012-1.008-0.9610.004
4A8PRO00.0150.0215.417-3.405-3.4050.0000.0000.0000.000
5A9TYR0-0.010-0.0148.075-2.141-2.1410.0000.0000.0000.000
6A10LYS10.9690.96910.734-22.588-22.5880.0000.0000.0000.000
7A11ALA00.0050.01113.390-0.913-0.9130.0000.0000.0000.000
8A12VAL0-0.0200.00416.369-0.353-0.3530.0000.0000.0000.000
9A13VAL0-0.014-0.00819.712-0.304-0.3040.0000.0000.0000.000
10A14ASN0-0.028-0.02322.939-0.151-0.1510.0000.0000.0000.000
11A15ILE0-0.0080.00026.302-0.188-0.1880.0000.0000.0000.000
12A16GLU-1-0.841-0.87628.65810.16510.1650.0000.0000.0000.000
13A17ASN0-0.032-0.03031.766-0.412-0.4120.0000.0000.0000.000
14A18ILE0-0.0080.02534.3000.1600.1600.0000.0000.0000.000
15A19VAL0-0.027-0.00136.596-0.234-0.2340.0000.0000.0000.000
16A20ALA00.001-0.00839.5960.1060.1060.0000.0000.0000.000
17A21THR00.001-0.00241.889-0.194-0.1940.0000.0000.0000.000
18A22VAL0-0.029-0.01345.3990.0740.0740.0000.0000.0000.000
19A23THR0-0.007-0.00948.067-0.074-0.0740.0000.0000.0000.000
20A24LEU0-0.046-0.03151.1540.0030.0030.0000.0000.0000.000
21A25ASP-1-0.964-0.98654.2895.4685.4680.0000.0000.0000.000
22A26GLN0-0.009-0.00656.308-0.153-0.1530.0000.0000.0000.000
23A27THR0-0.027-0.01058.4130.0650.0650.0000.0000.0000.000
24A28LEU0-0.035-0.02356.585-0.030-0.0300.0000.0000.0000.000
25A29ASP-1-0.841-0.90560.7894.8734.8730.0000.0000.0000.000
26A30LEU0-0.001-0.02657.3440.0030.0030.0000.0000.0000.000
27A31TYR00.0590.03860.8810.0340.0340.0000.0000.0000.000
28A32ALA0-0.016-0.01063.870-0.014-0.0140.0000.0000.0000.000
29A33MET0-0.039-0.02257.3040.0420.0420.0000.0000.0000.000
30A34GLU-1-0.947-0.99360.0455.1205.1200.0000.0000.0000.000
31A35ARG10.9700.99761.099-4.680-4.6800.0000.0000.0000.000
32A36SER0-0.075-0.02462.990-0.049-0.0490.0000.0000.0000.000
33A37VAL0-0.090-0.05056.9070.0230.0230.0000.0000.0000.000
34A38PRO0-0.0070.00458.609-0.001-0.0010.0000.0000.0000.000
35A39ASN0-0.033-0.03556.3960.0590.0590.0000.0000.0000.000
36A40VAL0-0.0220.02154.9740.1430.1430.0000.0000.0000.000
37A41GLU-1-0.882-0.94954.6295.6305.6300.0000.0000.0000.000
38A42TYR0-0.032-0.03556.1540.1030.1030.0000.0000.0000.000
39A43ASP-1-0.732-0.85657.9295.1415.1410.0000.0000.0000.000
40A44PRO0-0.097-0.04458.4570.0800.0800.0000.0000.0000.000
41A45ASP-1-0.897-0.93659.6305.0005.0000.0000.0000.0000.000
42A46GLN0-0.137-0.06455.8700.1090.1090.0000.0000.0000.000
43A47PHE0-0.030-0.03449.7390.1690.1690.0000.0000.0000.000
44A48PRO0-0.015-0.00153.375-0.065-0.0650.0000.0000.0000.000
45A49GLY0-0.056-0.02253.486-0.056-0.0560.0000.0000.0000.000
46A50LEU00.0310.01754.5290.0000.0000.0000.0000.0000.000
47A51ILE0-0.037-0.02750.2050.1630.1630.0000.0000.0000.000
48A52PHE00.0250.00150.412-0.074-0.0740.0000.0000.0000.000
49A53ARG10.9640.97548.635-6.081-6.0810.0000.0000.0000.000
50A54LEU0-0.034-0.01746.969-0.106-0.1060.0000.0000.0000.000
51A55GLU-1-0.856-0.93345.8316.9096.9090.0000.0000.0000.000
52A56SER0-0.102-0.03743.373-0.039-0.0390.0000.0000.0000.000
53A57PRO00.0370.01240.712-0.121-0.1210.0000.0000.0000.000
54A58LYS10.9970.98941.238-7.525-7.5250.0000.0000.0000.000
55A59ILE0-0.037-0.00441.1400.1390.1390.0000.0000.0000.000
56A60THR0-0.021-0.01044.020-0.204-0.2040.0000.0000.0000.000
57A61SER0-0.021-0.01845.6050.1450.1450.0000.0000.0000.000
58A62LEU00.0100.01747.039-0.107-0.1070.0000.0000.0000.000
59A63ILE00.006-0.01350.0870.0700.0700.0000.0000.0000.000
60A64PHE00.0470.02149.648-0.089-0.0890.0000.0000.0000.000
61A65LYS11.0511.02654.797-5.205-5.2050.0000.0000.0000.000
62A66SER0-0.018-0.00354.091-0.049-0.0490.0000.0000.0000.000
63A67GLY00.0770.05055.6170.0000.0000.0000.0000.0000.000
64A68LYS10.9030.95648.414-6.263-6.2630.0000.0000.0000.000
65A69MET00.0120.01948.834-0.088-0.0880.0000.0000.0000.000
66A70VAL0-0.020-0.01144.4460.1240.1240.0000.0000.0000.000
67A71VAL0-0.011-0.00543.201-0.085-0.0850.0000.0000.0000.000
68A72THR00.003-0.01240.9470.2500.2500.0000.0000.0000.000
69A73GLY00.0560.01439.308-0.191-0.1910.0000.0000.0000.000
70A74ALA0-0.0250.00338.2840.1100.1100.0000.0000.0000.000
71A75LYS10.9620.97133.084-8.846-8.8460.0000.0000.0000.000
72A76SER00.0860.04232.9710.2240.2240.0000.0000.0000.000
73A77THR00.1000.03234.651-0.214-0.2140.0000.0000.0000.000
74A78ASP-1-0.902-0.94636.6298.1168.1160.0000.0000.0000.000
75A79GLU-1-0.902-0.96337.1957.9267.9260.0000.0000.0000.000
76A80LEU00.0270.01838.937-0.262-0.2620.0000.0000.0000.000
77A81ILE00.002-0.00640.748-0.294-0.2940.0000.0000.0000.000
78A82LYS10.9130.95140.552-7.935-7.9350.0000.0000.0000.000
79A83ALA00.0550.03843.413-0.212-0.2120.0000.0000.0000.000
80A84VAL00.0440.02644.621-0.205-0.2050.0000.0000.0000.000
81A85LYS10.9130.95746.264-6.973-6.9730.0000.0000.0000.000
82A86ARG10.9040.96747.344-6.667-6.6670.0000.0000.0000.000
83A87ILE00.0160.00047.401-0.154-0.1540.0000.0000.0000.000
84A88ILE00.0210.00450.283-0.155-0.1550.0000.0000.0000.000
85A89LYS10.8960.95052.618-5.996-5.9960.0000.0000.0000.000
86A90THR00.0000.00553.529-0.135-0.1350.0000.0000.0000.000
87A91LEU00.0670.02853.820-0.108-0.1080.0000.0000.0000.000
88A92LYS10.8980.96555.876-5.719-5.7190.0000.0000.0000.000
89A93LYS10.8550.93458.444-5.323-5.3230.0000.0000.0000.000
90A94TYR0-0.022-0.03758.737-0.038-0.0380.0000.0000.0000.000
91A95GLY00.0760.04761.947-0.042-0.0420.0000.0000.0000.000
92A96MET0-0.0610.01256.620-0.017-0.0170.0000.0000.0000.000
93A97GLN00.0590.01860.6520.0950.0950.0000.0000.0000.000
94A98LEU0-0.035-0.02754.5120.0620.0620.0000.0000.0000.000
95A99THR00.0490.03258.770-0.046-0.0460.0000.0000.0000.000
96A100GLY00.0420.01556.531-0.018-0.0180.0000.0000.0000.000
97A101LYS10.8700.93051.260-5.842-5.8420.0000.0000.0000.000
98A102PRO00.0540.04650.3050.0230.0230.0000.0000.0000.000
99A103LYS10.9710.97647.044-6.342-6.3420.0000.0000.0000.000
100A104ILE00.0230.00442.363-0.057-0.0570.0000.0000.0000.000
101A105GLN0-0.050-0.02242.265-0.044-0.0440.0000.0000.0000.000
102A106ILE00.0460.02936.145-0.115-0.1150.0000.0000.0000.000
103A107GLN0-0.087-0.05639.456-0.067-0.0670.0000.0000.0000.000
104A108ASN00.0310.00334.6360.1910.1910.0000.0000.0000.000
105A109ILE0-0.0060.02431.071-0.190-0.1900.0000.0000.0000.000
106A110VAL0-0.027-0.00631.1460.0840.0840.0000.0000.0000.000
107A111ALA0-0.005-0.00526.933-0.103-0.1030.0000.0000.0000.000
108A112SER0-0.033-0.05125.5560.0830.0830.0000.0000.0000.000
109A113ALA00.010-0.00920.6290.0760.0760.0000.0000.0000.000
110A114ASN0-0.019-0.00418.401-0.940-0.9400.0000.0000.0000.000
111A115LEU0-0.005-0.02314.9700.3850.3850.0000.0000.0000.000
112A116HIS0-0.101-0.06413.4970.0280.0280.0000.0000.0000.000
113A117VAL00.0280.03010.5131.4691.4690.0000.0000.0000.000
114A118ILE0-0.022-0.01112.909-1.396-1.3960.0000.0000.0000.000
115A119VAL0-0.017-0.01914.0810.8120.8120.0000.0000.0000.000
116A120ASN00.004-0.00715.715-1.400-1.4000.0000.0000.0000.000
117A121LEU00.009-0.01817.397-0.017-0.0170.0000.0000.0000.000
118A122ASP-1-0.852-0.91920.80711.80611.8060.0000.0000.0000.000
119A123LYS10.8390.92113.157-18.470-18.4700.0000.0000.0000.000
120A124ALA00.0460.00218.202-0.111-0.1110.0000.0000.0000.000
121A125ALA0-0.019-0.02219.417-0.299-0.2990.0000.0000.0000.000
122A126PHE0-0.037-0.01122.148-0.468-0.4680.0000.0000.0000.000
123A127LEU0-0.0190.00117.0560.0410.0410.0000.0000.0000.000
124A128LEU0-0.087-0.02419.2830.1730.1730.0000.0000.0000.000
125A129GLU-1-0.881-0.93621.92110.27110.2710.0000.0000.0000.000
126A130ASN0-0.066-0.06325.482-0.030-0.0300.0000.0000.0000.000
127A131ASN0-0.080-0.04325.008-0.093-0.0930.0000.0000.0000.000
128A132MET00.0260.02627.716-0.372-0.3720.0000.0000.0000.000
129A133TYR0-0.005-0.02024.7370.2750.2750.0000.0000.0000.000
130A134GLU-1-0.870-0.92727.6569.0029.0020.0000.0000.0000.000
131A135PRO00.001-0.00127.855-0.242-0.2420.0000.0000.0000.000
132A136GLU-1-0.942-0.96429.8508.4938.4930.0000.0000.0000.000
133A137GLN0-0.079-0.03732.930-0.372-0.3720.0000.0000.0000.000
134A138PHE0-0.056-0.03728.201-0.111-0.1110.0000.0000.0000.000
135A139PRO0-0.0050.00328.0470.1770.1770.0000.0000.0000.000
136A140GLY00.0040.00125.5410.4290.4290.0000.0000.0000.000
137A141LEU00.0050.01922.055-0.274-0.2740.0000.0000.0000.000
138A142ILE0-0.052-0.03325.6610.0950.0950.0000.0000.0000.000
139A143TYR00.0480.02124.283-0.018-0.0180.0000.0000.0000.000
140A144ARG10.9440.97426.885-8.892-8.8920.0000.0000.0000.000
141A145MET0-0.0230.00222.7510.0880.0880.0000.0000.0000.000
142A146ASP-1-0.888-0.94328.1779.3889.3880.0000.0000.0000.000
143A147GLU-1-0.992-0.97628.2539.9889.9880.0000.0000.0000.000
144A148PRO0-0.032-0.03425.9510.4840.4840.0000.0000.0000.000
145A149ARG10.9910.99029.037-8.381-8.3810.0000.0000.0000.000
146A150VAL0-0.038-0.01126.948-0.222-0.2220.0000.0000.0000.000
147A151VAL0-0.013-0.01129.4830.0170.0170.0000.0000.0000.000
148A152LEU0-0.019-0.01722.8900.0110.0110.0000.0000.0000.000
149A153LEU0-0.0130.01126.354-0.189-0.1890.0000.0000.0000.000
150A154ILE00.0320.01220.1900.2320.2320.0000.0000.0000.000
151A155PHE00.029-0.00422.233-0.357-0.3570.0000.0000.0000.000
152A156SER00.0760.04319.8170.5290.5290.0000.0000.0000.000
153A157SER00.0150.01418.3430.6380.6380.0000.0000.0000.000
154A158GLY00.0830.05117.2830.5640.5640.0000.0000.0000.000
155A159LYS10.9000.96818.105-11.536-11.5360.0000.0000.0000.000
156A160MET00.000-0.00120.5400.0940.0940.0000.0000.0000.000
157A161VAL0-0.032-0.01323.230-0.200-0.2000.0000.0000.0000.000
158A162ILE00.0040.00723.4550.0520.0520.0000.0000.0000.000
159A163THR0-0.008-0.00627.426-0.350-0.3500.0000.0000.0000.000
160A164GLY00.0240.00231.0790.1190.1190.0000.0000.0000.000
161A165ALA00.0160.02929.931-0.138-0.1380.0000.0000.0000.000
162A166LYS10.9010.93832.068-8.216-8.2160.0000.0000.0000.000
163A167ARG10.9050.95231.758-9.759-9.7590.0000.0000.0000.000
164A168GLU-1-0.827-0.92727.81610.87710.8770.0000.0000.0000.000
165A169ASP-1-0.874-0.95226.94010.62510.6250.0000.0000.0000.000
166A170GLU-1-0.840-0.93126.2529.9339.9330.0000.0000.0000.000
167A171VAL00.0130.00925.0670.2800.2800.0000.0000.0000.000
168A172HIS0-0.020-0.02222.6640.8560.8560.0000.0000.0000.000
169A173LYS10.9190.97621.703-10.988-10.9880.0000.0000.0000.000
170A174ALA0-0.008-0.02421.9870.4380.4380.0000.0000.0000.000
171A175VAL00.0000.01018.6160.2910.2910.0000.0000.0000.000
172A176LYS10.9100.95414.891-18.239-18.2390.0000.0000.0000.000
173A177LYS10.8810.93717.141-11.617-11.6170.0000.0000.0000.000
174A178ILE0-0.003-0.00618.4650.3010.3010.0000.0000.0000.000
175A179PHE00.0180.01310.028-0.122-0.1220.0000.0000.0000.000
176A180ASP-1-0.786-0.90713.68320.06420.0640.0000.0000.0000.000
177A181LYS10.9100.97014.139-14.232-14.2320.0000.0000.0000.000
178A182LEU0-0.020-0.01914.9700.0720.0720.0000.0000.0000.000
179A183VAL00.0060.0088.8020.3650.3650.0000.0000.0000.000
180A184GLU-1-0.947-0.96610.55917.44817.4480.0000.0000.0000.000
181A185LEU0-0.059-0.04112.483-0.071-0.0710.0000.0000.0000.000
182A186ASP-1-0.905-0.9469.34022.74122.7410.0000.0000.0000.000
183A187CYS0-0.094-0.03511.209-1.219-1.2190.0000.0000.0000.000
184A188VAL00.000-0.0019.960-1.135-1.1350.0000.0000.0000.000
185A189LYS10.9961.0049.898-20.385-20.3850.0000.0000.0000.000
186A190PRO00.0270.0076.008-2.696-2.6960.0000.0000.0000.000
187A191VAL0-0.004-0.0178.8381.3781.3780.0000.0000.0000.000
188A192GLU-1-0.913-0.93411.15818.55018.5500.0000.0000.0000.000
189A193GLU-1-0.953-0.9626.65132.53432.5340.0000.0000.0000.000
190A194GLU-1-0.980-0.9867.39028.49128.4910.0000.0000.0000.000
191A195GLU-1-0.997-0.9896.86627.97427.9740.0000.0000.0000.000
192A196LEU0-0.030-0.0253.9610.0160.2510.000-0.022-0.2140.000
193A197GLU-1-0.995-0.9927.40023.12323.1230.0000.0000.0000.000