Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 7M6VK

Calculation Name: 2PL2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PL2

Chain ID: A

ChEMBL ID:

UniProt ID: Q72L02

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2093714.368211
FMO2-HF: Nuclear repulsion 2018781.710515
FMO2-HF: Total energy -74932.657696
FMO2-MP2: Total energy -75156.576577


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:28:ALA)


Summations of interaction energy for fragment #1(A:28:ALA)
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.
-15.91-9.7160.561-3.146-3.607-0.003
Interaction energy analysis for fragmet #1(A:28:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.004
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].
3A30GLN00.0200.0053.034-5.303-2.0290.131-1.735-1.6700.010
4A31ASN0-0.015-0.0154.424-1.961-1.705-0.001-0.024-0.2300.000
5A32PRO0-0.0240.0004.289-0.412-0.240-0.001-0.045-0.1260.000
6A33LEU00.0920.0587.002-0.127-0.1270.0000.0000.0000.000
7A34ARG10.9500.9708.613-1.456-1.4560.0000.0000.0000.000
8A35LEU0-0.028-0.0169.959-0.162-0.1620.0000.0000.0000.000
9A36GLY00.0510.02111.332-0.101-0.1010.0000.0000.0000.000
10A37VAL00.0140.00413.176-0.060-0.0600.0000.0000.0000.000
11A38GLN0-0.033-0.01614.319-0.038-0.0380.0000.0000.0000.000
12A39LEU00.0450.00714.760-0.045-0.0450.0000.0000.0000.000
13A40TYR0-0.0070.01017.341-0.043-0.0430.0000.0000.0000.000
14A41ALA0-0.011-0.00219.247-0.023-0.0230.0000.0000.0000.000
15A42LEU0-0.053-0.01919.704-0.015-0.0150.0000.0000.0000.000
16A43GLY00.0200.01622.280-0.018-0.0180.0000.0000.0000.000
17A44ARG10.8660.93020.023-0.070-0.0700.0000.0000.0000.000
18A45TYR00.0680.01319.6360.0060.0060.0000.0000.0000.000
19A46ASP-1-0.839-0.91319.444-0.047-0.0470.0000.0000.0000.000
20A47ALA0-0.049-0.02217.163-0.024-0.0240.0000.0000.0000.000
21A48ALA0-0.010-0.00815.655-0.014-0.0140.0000.0000.0000.000
22A49LEU00.0110.00314.925-0.007-0.0070.0000.0000.0000.000
23A50THR00.0090.01214.535-0.038-0.0380.0000.0000.0000.000
24A51LEU0-0.077-0.03210.224-0.115-0.1150.0000.0000.0000.000
25A52PHE00.0270.00210.195-0.079-0.0790.0000.0000.0000.000
26A53GLU-1-0.883-0.93911.537-0.310-0.3100.0000.0000.0000.000
27A54ARG10.8780.9306.8200.5610.5610.0000.0000.0000.000
28A55ALA0-0.0190.0016.659-0.470-0.4700.0000.0000.0000.000
29A56LEU00.0770.0337.329-0.115-0.1150.0000.0000.0000.000
30A57LYS10.8600.9327.8910.7880.7880.0000.0000.0000.000
31A58GLU-1-0.948-0.9712.947-7.032-4.6330.433-1.341-1.491-0.013
32A59ASN0-0.016-0.0025.360-0.110-0.017-0.001-0.001-0.0900.000
33A60PRO0-0.021-0.0167.4620.2280.2280.0000.0000.0000.000
34A61GLN0-0.085-0.02910.9760.0150.0150.0000.0000.0000.000
35A62ASP-1-0.805-0.9179.8480.3310.3310.0000.0000.0000.000
36A63PRO00.007-0.00411.994-0.009-0.0090.0000.0000.0000.000
37A64GLU-1-0.896-0.95112.1980.5700.5700.0000.0000.0000.000
38A65ALA00.0570.02310.6440.0010.0010.0000.0000.0000.000
39A66LEU00.0120.01112.798-0.018-0.0180.0000.0000.0000.000
40A67TYR0-0.032-0.00315.712-0.002-0.0020.0000.0000.0000.000
41A68TRP00.013-0.00514.522-0.038-0.0380.0000.0000.0000.000
42A69LEU0-0.0150.01415.291-0.007-0.0070.0000.0000.0000.000
43A70ALA00.0240.00617.055-0.006-0.0060.0000.0000.0000.000
44A71ARG10.9210.96920.019-0.136-0.1360.0000.0000.0000.000
45A72THR0-0.040-0.04718.2600.0100.0100.0000.0000.0000.000
46A73GLN00.0300.01020.0520.0030.0030.0000.0000.0000.000
47A74LEU0-0.0340.00422.577-0.003-0.0030.0000.0000.0000.000
48A75LYS10.8640.93623.730-0.072-0.0720.0000.0000.0000.000
49A76LEU0-0.040-0.01021.3480.0010.0010.0000.0000.0000.000
50A77GLY00.0250.01325.553-0.009-0.0090.0000.0000.0000.000
51A78LEU0-0.042-0.01422.259-0.007-0.0070.0000.0000.0000.000
52A79VAL00.0510.00525.479-0.003-0.0030.0000.0000.0000.000
53A80ASN00.0050.00526.7710.0030.0030.0000.0000.0000.000
54A81PRO00.012-0.00622.565-0.001-0.0010.0000.0000.0000.000
55A82ALA00.0750.04822.630-0.006-0.0060.0000.0000.0000.000
56A83LEU0-0.053-0.02523.7940.0090.0090.0000.0000.0000.000
57A84GLU-1-0.967-0.99023.373-0.069-0.0690.0000.0000.0000.000
58A85ASN00.0880.01518.746-0.017-0.0170.0000.0000.0000.000
59A86GLY00.0020.00421.1270.0110.0110.0000.0000.0000.000
60A87LYS10.9500.97523.4970.0490.0490.0000.0000.0000.000
61A88THR0-0.0190.00019.793-0.003-0.0030.0000.0000.0000.000
62A89LEU0-0.0640.00317.7740.0040.0040.0000.0000.0000.000
63A90VAL0-0.019-0.00521.1570.0120.0120.0000.0000.0000.000
64A91ALA0-0.018-0.00323.9420.0030.0030.0000.0000.0000.000
65A92ARG10.9280.96318.2170.0980.0980.0000.0000.0000.000
66A93THR0-0.020-0.01018.6940.0050.0050.0000.0000.0000.000
67A94PRO00.0880.06621.5860.0150.0150.0000.0000.0000.000
68A95ARG10.9561.01023.153-0.069-0.0690.0000.0000.0000.000
69A96TYR00.0250.01717.4480.0240.0240.0000.0000.0000.000
70A97LEU00.0420.00322.031-0.014-0.0140.0000.0000.0000.000
71A98GLY00.0180.01320.977-0.009-0.0090.0000.0000.0000.000
72A99GLY00.0460.01722.056-0.012-0.0120.0000.0000.0000.000
73A100TYR0-0.030-0.07623.383-0.013-0.0130.0000.0000.0000.000
74A101MET0-0.0270.00524.680-0.007-0.0070.0000.0000.0000.000
75A102VAL00.0350.01721.471-0.006-0.0060.0000.0000.0000.000
76A103LEU0-0.031-0.01924.906-0.009-0.0090.0000.0000.0000.000
77A104SER0-0.001-0.00427.308-0.006-0.0060.0000.0000.0000.000
78A105GLU-1-0.945-0.98526.4760.0620.0620.0000.0000.0000.000
79A106ALA0-0.007-0.01027.349-0.005-0.0050.0000.0000.0000.000
80A107TYR0-0.009-0.01029.338-0.008-0.0080.0000.0000.0000.000
81A108VAL00.0280.02332.633-0.002-0.0020.0000.0000.0000.000
82A109ALA0-0.049-0.02131.136-0.001-0.0010.0000.0000.0000.000
83A110LEU0-0.033-0.03431.903-0.003-0.0030.0000.0000.0000.000
84A111TYR00.0200.02534.776-0.001-0.0010.0000.0000.0000.000
85A112ARG10.9190.96335.030-0.021-0.0210.0000.0000.0000.000
86A113GLN0-0.072-0.02734.4450.0000.0000.0000.0000.0000.000
87A114ALA0-0.014-0.00337.983-0.003-0.0030.0000.0000.0000.000
88A115GLU-1-0.994-0.98740.443-0.014-0.0140.0000.0000.0000.000
89A116ASP-1-0.762-0.86042.730-0.007-0.0070.0000.0000.0000.000
90A117ARG10.9390.94744.071-0.002-0.0020.0000.0000.0000.000
91A118GLU-1-0.972-0.99845.148-0.004-0.0040.0000.0000.0000.000
92A119ARG10.9090.95037.6660.0200.0200.0000.0000.0000.000
93A120GLY00.022-0.00940.3790.0000.0000.0000.0000.0000.000
94A121LYS10.9660.98940.287-0.006-0.0060.0000.0000.0000.000
95A122GLY00.0500.03640.9300.0020.0020.0000.0000.0000.000
96A123TYR00.0560.03035.5580.0000.0000.0000.0000.0000.000
97A124LEU00.0240.00436.3130.0030.0030.0000.0000.0000.000
98A125GLU-1-0.928-0.96737.9770.0150.0150.0000.0000.0000.000
99A126GLN0-0.066-0.03634.5910.0010.0010.0000.0000.0000.000
100A127ALA00.0130.00833.4870.0020.0020.0000.0000.0000.000
101A128LEU00.0070.00334.2740.0060.0060.0000.0000.0000.000
102A129SER0-0.029-0.00835.9120.0030.0030.0000.0000.0000.000
103A130VAL00.0120.00929.5980.0030.0030.0000.0000.0000.000
104A131LEU0-0.0080.00430.9330.0070.0070.0000.0000.0000.000
105A132LYS10.8070.89232.801-0.034-0.0340.0000.0000.0000.000
106A133ASP-1-0.896-0.95731.7010.0260.0260.0000.0000.0000.000
107A134ALA00.014-0.00328.7180.0050.0050.0000.0000.0000.000
108A135GLU-1-0.820-0.89430.2170.0590.0590.0000.0000.0000.000
109A136ARG10.8610.92732.679-0.037-0.0370.0000.0000.0000.000
110A137VAL0-0.043-0.00726.2650.0010.0010.0000.0000.0000.000
111A138ASN0-0.045-0.03526.8990.0060.0060.0000.0000.0000.000
112A139PRO00.0550.03030.167-0.001-0.0010.0000.0000.0000.000
113A140ARG10.9390.97731.589-0.117-0.1170.0000.0000.0000.000
114A141TYR00.0620.03424.6530.0120.0120.0000.0000.0000.000
115A142ALA00.0910.04329.997-0.008-0.0080.0000.0000.0000.000
116A143PRO00.0170.00126.820-0.010-0.0100.0000.0000.0000.000
117A144LEU00.0290.02428.436-0.009-0.0090.0000.0000.0000.000
118A145HIS0-0.047-0.01831.325-0.012-0.0120.0000.0000.0000.000
119A146LEU00.0270.02331.491-0.006-0.0060.0000.0000.0000.000
120A147GLN00.015-0.01230.390-0.012-0.0120.0000.0000.0000.000
121A148ARG10.8990.95433.443-0.057-0.0570.0000.0000.0000.000
122A149GLY00.010-0.00436.196-0.005-0.0050.0000.0000.0000.000
123A150LEU0-0.020-0.01033.890-0.004-0.0040.0000.0000.0000.000
124A151VAL00.014-0.00635.312-0.005-0.0050.0000.0000.0000.000
125A152TYR00.002-0.00838.120-0.002-0.0020.0000.0000.0000.000
126A153ALA00.0180.02040.837-0.003-0.0030.0000.0000.0000.000
127A154LEU0-0.063-0.00237.178-0.003-0.0030.0000.0000.0000.000
128A155LEU0-0.015-0.00341.279-0.003-0.0030.0000.0000.0000.000
129A156GLY0-0.053-0.02443.815-0.001-0.0010.0000.0000.0000.000
130A157GLU-1-0.877-0.93944.3900.0220.0220.0000.0000.0000.000
131A158ARG10.9570.96945.366-0.020-0.0200.0000.0000.0000.000
132A159ASP-1-0.839-0.93846.1060.0280.0280.0000.0000.0000.000
133A160LYS10.8640.92143.563-0.022-0.0220.0000.0000.0000.000
134A161ALA00.0020.02541.6420.0040.0040.0000.0000.0000.000
135A162GLU-1-0.774-0.90441.5610.0440.0440.0000.0000.0000.000
136A163ALA0-0.0020.00842.8640.0040.0040.0000.0000.0000.000
137A164SER0-0.044-0.04238.4650.0030.0030.0000.0000.0000.000
138A165LEU00.0420.03337.4970.0050.0050.0000.0000.0000.000
139A166LYS10.8850.95338.817-0.041-0.0410.0000.0000.0000.000
140A167GLN0-0.027-0.01837.2630.0040.0040.0000.0000.0000.000
141A168ALA0-0.017-0.02234.7900.0050.0050.0000.0000.0000.000
142A169LEU0-0.035-0.01435.3870.0060.0060.0000.0000.0000.000
143A170ALA0-0.055-0.02337.4300.0040.0040.0000.0000.0000.000
144A171LEU0-0.134-0.05033.3490.0030.0030.0000.0000.0000.000
145A172GLU-1-0.924-0.97030.0530.1530.1530.0000.0000.0000.000
146A173ASP-1-0.851-0.90133.7820.0790.0790.0000.0000.0000.000
147A174THR00.019-0.00231.3720.0040.0040.0000.0000.0000.000
148A175PRO00.0750.02032.922-0.006-0.0060.0000.0000.0000.000
149A176GLU-1-0.912-0.91729.8930.0980.0980.0000.0000.0000.000
150A177ILE00.0130.00132.602-0.008-0.0080.0000.0000.0000.000
151A178ARG10.7970.87035.685-0.078-0.0780.0000.0000.0000.000
152A179SER00.017-0.03736.549-0.006-0.0060.0000.0000.0000.000
153A180ALA0-0.0100.01836.312-0.005-0.0050.0000.0000.0000.000
154A181LEU0-0.013-0.01938.289-0.005-0.0050.0000.0000.0000.000
155A182ALA0-0.0050.00141.258-0.004-0.0040.0000.0000.0000.000
156A183GLU-1-0.901-0.96539.2530.0350.0350.0000.0000.0000.000
157A184LEU0-0.046-0.01142.139-0.004-0.0040.0000.0000.0000.000
158A185TYR0-0.037-0.00243.721-0.002-0.0020.0000.0000.0000.000
159A186LEU00.0120.01544.550-0.002-0.0020.0000.0000.0000.000
160A187SER0-0.110-0.05645.101-0.003-0.0030.0000.0000.0000.000
161A188MET0-0.073-0.05546.124-0.003-0.0030.0000.0000.0000.000
162A189GLY00.0350.02949.699-0.001-0.0010.0000.0000.0000.000
163A190ARG10.7970.92749.564-0.035-0.0350.0000.0000.0000.000
164A191LEU00.0800.01649.8380.0020.0020.0000.0000.0000.000
165A192ASP-1-0.881-0.93350.0390.0340.0340.0000.0000.0000.000
166A193GLU-1-0.900-0.97048.7490.0390.0390.0000.0000.0000.000
167A194ALA0-0.009-0.00845.9800.0030.0030.0000.0000.0000.000
168A195LEU0-0.012-0.00745.5270.0040.0040.0000.0000.0000.000
169A196ALA0-0.0050.00446.5620.0030.0030.0000.0000.0000.000
170A197GLN00.0230.03842.4970.0070.0070.0000.0000.0000.000
171A198TYR00.0450.02240.1870.0050.0050.0000.0000.0000.000
172A199ALA00.0120.01742.1530.0040.0040.0000.0000.0000.000
173A200LYS10.9450.98141.195-0.071-0.0710.0000.0000.0000.000
174A201ALA00.0030.00038.0850.0050.0050.0000.0000.0000.000
175A202LEU0-0.044-0.04438.2490.0050.0050.0000.0000.0000.000
176A203GLU-1-0.936-0.95340.1750.0680.0680.0000.0000.0000.000
177A204GLN0-0.125-0.07935.9120.0030.0030.0000.0000.0000.000
178A205ALA0-0.0010.00034.2550.0080.0080.0000.0000.0000.000
179A206PRO00.0820.06236.115-0.004-0.0040.0000.0000.0000.000
180A207LYS10.8580.90735.454-0.096-0.0960.0000.0000.0000.000
181A208ASP-1-0.794-0.87734.1440.0860.0860.0000.0000.0000.000
182A209LEU00.007-0.02435.445-0.006-0.0060.0000.0000.0000.000
183A210ASP-1-0.881-0.92133.8700.0590.0590.0000.0000.0000.000
184A211LEU00.024-0.00835.982-0.006-0.0060.0000.0000.0000.000
185A212ARG10.8380.91138.176-0.069-0.0690.0000.0000.0000.000
186A213VAL00.0060.01239.163-0.004-0.0040.0000.0000.0000.000
187A214ARG10.9350.97935.209-0.057-0.0570.0000.0000.0000.000
188A215TYR00.0190.01641.696-0.002-0.0020.0000.0000.0000.000
189A216ALA00.000-0.00444.187-0.003-0.0030.0000.0000.0000.000
190A217SER0-0.015-0.02544.319-0.003-0.0030.0000.0000.0000.000
191A218ALA00.0150.01545.529-0.002-0.0020.0000.0000.0000.000
192A219LEU00.0140.00147.235-0.002-0.0020.0000.0000.0000.000
193A220LEU0-0.139-0.04448.444-0.002-0.0020.0000.0000.0000.000
194A221LEU0-0.074-0.03450.995-0.002-0.0020.0000.0000.0000.000