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: J2Q39

Calculation Name: 1P2F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1P2F

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WXY0

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2659854.683406
FMO2-HF: Nuclear repulsion 2572530.490353
FMO2-HF: Total energy -87324.193053
FMO2-MP2: Total energy -87581.743903


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-9.785-6.0796.954-3.913-6.748-0.016
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.018
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].
3A3TRP00.0550.0302.547-6.916-2.8121.908-2.702-3.310-0.019
4A4LYS10.8030.8963.1090.3851.1030.061-0.125-0.6550.001
5A5ILE0-0.014-0.0075.5670.4000.4000.0000.0000.0000.000
6A6ALA00.0450.0369.371-0.012-0.0120.0000.0000.0000.000
7A7VAL0-0.032-0.02812.044-0.009-0.0090.0000.0000.0000.000
8A8VAL00.0250.02115.6580.0110.0110.0000.0000.0000.000
9A9ASP-1-0.771-0.89818.668-0.202-0.2020.0000.0000.0000.000
10A10ASP-1-0.829-0.91122.085-0.143-0.1430.0000.0000.0000.000
11A11ASP-1-0.837-0.91524.990-0.198-0.1980.0000.0000.0000.000
12A12LYS10.9830.97023.2430.1310.1310.0000.0000.0000.000
13A13ASN0-0.066-0.02823.537-0.028-0.0280.0000.0000.0000.000
14A14ILE00.0060.00321.644-0.026-0.0260.0000.0000.0000.000
15A15LEU00.0150.02518.508-0.045-0.0450.0000.0000.0000.000
16A16LYS10.8310.91918.9020.2720.2720.0000.0000.0000.000
17A17LYS10.8890.94020.0400.2090.2090.0000.0000.0000.000
18A18VAL00.0090.00516.323-0.037-0.0370.0000.0000.0000.000
19A19SER00.029-0.00315.282-0.074-0.0740.0000.0000.0000.000
20A20GLU-1-0.865-0.91515.706-0.468-0.4680.0000.0000.0000.000
21A21LYS10.7840.90417.9030.4810.4810.0000.0000.0000.000
22A22LEU00.0490.00613.147-0.060-0.0600.0000.0000.0000.000
23A23GLN0-0.015-0.02111.941-0.181-0.1810.0000.0000.0000.000
24A24GLN0-0.091-0.03911.909-0.157-0.1570.0000.0000.0000.000
25A25LEU0-0.017-0.0059.670-0.063-0.0630.0000.0000.0000.000
26A26GLY0-0.001-0.0077.235-0.792-0.7920.0000.0000.0000.000
27A27ARG10.8470.8995.6451.9741.9740.0000.0000.0000.000
28A28VAL00.0190.0167.8500.0360.0360.0000.0000.0000.000
29A29LYS10.8190.9059.2430.5930.5930.0000.0000.0000.000
30A30THR0-0.036-0.02512.284-0.005-0.0050.0000.0000.0000.000
31A31PHE00.0070.01112.6020.0020.0020.0000.0000.0000.000
32A32LEU0-0.021-0.01818.299-0.005-0.0050.0000.0000.0000.000
33A33THR0-0.0120.00421.3170.0080.0080.0000.0000.0000.000
34A34GLY00.022-0.01420.565-0.012-0.0120.0000.0000.0000.000
35A35GLU-1-0.948-0.98420.068-0.015-0.0150.0000.0000.0000.000
36A36ASP-1-0.891-0.94619.041-0.142-0.1420.0000.0000.0000.000
37A37PHE0-0.024-0.02312.855-0.001-0.0010.0000.0000.0000.000
38A38LEU0-0.035-0.02215.4570.0170.0170.0000.0000.0000.000
39A39ASN0-0.045-0.02117.5360.0420.0420.0000.0000.0000.000
40A40ASH0-0.087-0.06410.9520.0300.0300.0000.0000.0000.000
41A41GLU-1-0.874-0.93612.4330.2030.2030.0000.0000.0000.000
42A42GLU-1-0.840-0.8447.305-0.452-0.4520.0000.0000.0000.000
43A43ALA00.0070.0055.743-0.001-0.0010.0000.0000.0000.000
44A44PHE00.008-0.0295.801-0.349-0.3490.0000.0000.0000.000
45A45HIS00.0650.0312.313-4.062-5.1784.985-1.086-2.7830.002
46A46VAL0-0.008-0.0067.687-0.059-0.0590.0000.0000.0000.000
47A47VAL00.0190.01410.780-0.059-0.0590.0000.0000.0000.000
48A48VAL0-0.012-0.01113.5670.0200.0200.0000.0000.0000.000
49A49LEU00.0240.00916.3300.0040.0040.0000.0000.0000.000
50A50ASP-1-0.797-0.87419.159-0.157-0.1570.0000.0000.0000.000
51A51VAL00.002-0.00822.8690.0170.0170.0000.0000.0000.000
52A52MET0-0.076-0.03325.5740.0220.0220.0000.0000.0000.000
53A53LEU00.0150.01221.667-0.015-0.0150.0000.0000.0000.000
54A54PRO0-0.032-0.02525.7650.0110.0110.0000.0000.0000.000
55A55ASP-1-0.767-0.87424.653-0.062-0.0620.0000.0000.0000.000
56A56TYR00.0010.00524.1710.0170.0170.0000.0000.0000.000
57A57SER00.0140.01526.270-0.015-0.0150.0000.0000.0000.000
58A58GLY00.0640.01522.8300.0080.0080.0000.0000.0000.000
59A59TYR0-0.034-0.03422.4600.0010.0010.0000.0000.0000.000
60A60GLU-1-0.853-0.92623.7130.0160.0160.0000.0000.0000.000
61A61ILE00.0150.02018.4050.0150.0150.0000.0000.0000.000
62A62CYS0-0.070-0.03218.9250.0090.0090.0000.0000.0000.000
63A63ARG10.8110.89419.342-0.026-0.0260.0000.0000.0000.000
64A64MET00.0060.00019.8360.0210.0210.0000.0000.0000.000
65A65ILE0-0.0280.00014.1620.0330.0330.0000.0000.0000.000
66A66LYS10.7940.88115.5360.0120.0120.0000.0000.0000.000
67A67GLU-1-0.867-0.91518.3550.1090.1090.0000.0000.0000.000
68A68THR0-0.073-0.04015.8830.0180.0180.0000.0000.0000.000
69A69ARG10.7970.89510.529-0.292-0.2920.0000.0000.0000.000
70A70PRO00.0340.02613.821-0.035-0.0350.0000.0000.0000.000
71A71GLU-1-0.887-0.9529.9210.5210.5210.0000.0000.0000.000
72A72THR0-0.048-0.01510.504-0.037-0.0370.0000.0000.0000.000
73A73TRP00.0050.01110.619-0.075-0.0750.0000.0000.0000.000
74A74VAL00.009-0.00613.560-0.042-0.0420.0000.0000.0000.000
75A75ILE0-0.063-0.03016.088-0.003-0.0030.0000.0000.0000.000
76A76LEU00.0370.02018.485-0.013-0.0130.0000.0000.0000.000
77A77LEU0-0.042-0.02020.413-0.015-0.0150.0000.0000.0000.000
78A78THR00.0540.01223.2260.0240.0240.0000.0000.0000.000
79A79LEU00.0250.01126.977-0.011-0.0110.0000.0000.0000.000
80A80LEU0-0.037-0.00430.2860.0020.0020.0000.0000.0000.000
81A81SER00.0200.00030.111-0.007-0.0070.0000.0000.0000.000
82A82ASP-1-0.818-0.87031.547-0.081-0.0810.0000.0000.0000.000
83A83ASP-1-0.757-0.87533.195-0.077-0.0770.0000.0000.0000.000
84A84GLU-1-0.859-0.90633.809-0.048-0.0480.0000.0000.0000.000
85A85SER0-0.048-0.06130.8960.0070.0070.0000.0000.0000.000
86A86VAL0-0.0100.00328.715-0.004-0.0040.0000.0000.0000.000
87A87LEU0-0.072-0.02729.0060.0030.0030.0000.0000.0000.000
88A88LYS10.8920.93929.5140.0670.0670.0000.0000.0000.000
89A89GLY00.0050.00525.8160.0030.0030.0000.0000.0000.000
90A90PHE0-0.064-0.05125.0170.0010.0010.0000.0000.0000.000
91A91GLU-1-0.929-0.96926.137-0.017-0.0170.0000.0000.0000.000
92A92ALA0-0.0200.00223.6690.0120.0120.0000.0000.0000.000
93A93GLY00.0100.01322.3220.0090.0090.0000.0000.0000.000
94A94ALA0-0.002-0.00420.3700.0020.0020.0000.0000.0000.000
95A95ASP-1-0.771-0.86616.874-0.057-0.0570.0000.0000.0000.000
96A96ASP-1-0.755-0.86319.370-0.283-0.2830.0000.0000.0000.000
97A97TYR0-0.027-0.03021.0250.0080.0080.0000.0000.0000.000
98A98VAL0-0.032-0.02921.429-0.022-0.0220.0000.0000.0000.000
99A99THR00.0250.02924.2860.0070.0070.0000.0000.0000.000
100A100LYS10.7540.87224.8200.1720.1720.0000.0000.0000.000
101A101PRO0-0.010-0.00527.9930.0130.0130.0000.0000.0000.000
102A102PHE00.0380.00421.779-0.001-0.0010.0000.0000.0000.000
103A103ASN00.0370.01425.328-0.023-0.0230.0000.0000.0000.000
104A104PRO00.0470.00821.044-0.009-0.0090.0000.0000.0000.000
105A105GLU-1-0.802-0.88920.554-0.515-0.5150.0000.0000.0000.000
106A106ILE0-0.046-0.02221.016-0.024-0.0240.0000.0000.0000.000
107A107LEU00.0350.02317.667-0.003-0.0030.0000.0000.0000.000
108A108LEU0-0.0030.00015.203-0.036-0.0360.0000.0000.0000.000
109A109ALA0-0.023-0.01516.395-0.065-0.0650.0000.0000.0000.000
110A110ARG10.8720.93818.0280.2590.2590.0000.0000.0000.000
111A111VAL00.0570.02812.2420.0030.0030.0000.0000.0000.000
112A112LYS10.8350.90412.9970.9170.9170.0000.0000.0000.000
113A113ARG10.7010.83614.3010.2680.2680.0000.0000.0000.000
114A114PHE00.0450.02412.7040.0410.0410.0000.0000.0000.000
115A115LEU00.001-0.0067.8040.0610.0610.0000.0000.0000.000
116A116GLU-1-0.862-0.92310.067-1.339-1.3390.0000.0000.0000.000
117A117ARG10.8390.91112.4590.6140.6140.0000.0000.0000.000
118A118GLU-1-0.920-0.92911.262-0.123-0.1230.0000.0000.0000.000
119A119LYS10.7640.87414.5850.3200.3200.0000.0000.0000.000
120A120LYS10.8320.90417.0540.0310.0310.0000.0000.0000.000
121A121GLY0-0.0040.00419.428-0.001-0.0010.0000.0000.0000.000
122A122LEU0-0.023-0.00122.3280.0140.0140.0000.0000.0000.000
123A123TYR0-0.029-0.04621.2370.0080.0080.0000.0000.0000.000
124A124ASP-1-0.774-0.87824.866-0.014-0.0140.0000.0000.0000.000
125A125PHE00.0270.00025.5660.0110.0110.0000.0000.0000.000
126A126GLY00.0340.03729.2670.0060.0060.0000.0000.0000.000
127A127ASP-1-0.831-0.90531.499-0.001-0.0010.0000.0000.0000.000
128A128LEU0-0.0150.00332.368-0.007-0.0070.0000.0000.0000.000
129A129LYS10.8350.90629.3920.0220.0220.0000.0000.0000.000
130A130ILE0-0.011-0.01628.027-0.004-0.0040.0000.0000.0000.000
131A131ASP-1-0.697-0.82126.958-0.146-0.1460.0000.0000.0000.000
132A132ALA0-0.042-0.02424.4100.0000.0000.0000.0000.0000.000
133A133THR0-0.078-0.06623.250-0.033-0.0330.0000.0000.0000.000
134A134GLY00.0130.01126.086-0.006-0.0060.0000.0000.0000.000
135A135PHE0-0.103-0.03227.7540.0110.0110.0000.0000.0000.000
136A136THR00.0150.00830.7800.0110.0110.0000.0000.0000.000
137A137VAL0-0.021-0.01231.317-0.002-0.0020.0000.0000.0000.000
138A138PHE00.0140.00131.0640.0010.0010.0000.0000.0000.000
139A139LEU00.009-0.00234.3900.0030.0030.0000.0000.0000.000
140A140LYS10.7840.87236.6210.0050.0050.0000.0000.0000.000
141A141GLY00.0460.03836.1070.0010.0010.0000.0000.0000.000
142A142LYS10.9050.95237.1300.0300.0300.0000.0000.0000.000
143A143ARG10.8570.90234.7030.0860.0860.0000.0000.0000.000
144A144ILE0-0.028-0.00836.7490.0040.0040.0000.0000.0000.000
145A145HIS0-0.005-0.00738.441-0.007-0.0070.0000.0000.0000.000
146A146LEU00.014-0.00535.3790.0040.0040.0000.0000.0000.000
147A147PRO0-0.0190.00138.197-0.006-0.0060.0000.0000.0000.000
148A148LYS10.9800.99733.8800.1350.1350.0000.0000.0000.000
149A149LYS10.8240.90835.2290.1010.1010.0000.0000.0000.000
150A150GLU-1-0.784-0.91035.683-0.068-0.0680.0000.0000.0000.000
151A151PHE00.0160.01429.5550.0020.0020.0000.0000.0000.000
152A152GLU-1-0.838-0.92431.185-0.128-0.1280.0000.0000.0000.000
153A153ILE0-0.0070.00230.620-0.003-0.0030.0000.0000.0000.000
154A154LEU0-0.0020.00231.5640.0050.0050.0000.0000.0000.000
155A155LEU00.0160.01725.5170.0060.0060.0000.0000.0000.000
156A156PHE00.0230.00825.3180.0010.0010.0000.0000.0000.000
157A157LEU0-0.017-0.01426.9570.0050.0050.0000.0000.0000.000
158A158ALA0-0.011-0.00327.2960.0100.0100.0000.0000.0000.000
159A159GLU-1-0.771-0.85622.767-0.180-0.1800.0000.0000.0000.000
160A160ASN0-0.081-0.04722.645-0.002-0.0020.0000.0000.0000.000
161A161ALA00.0200.01824.9500.0130.0130.0000.0000.0000.000
162A162GLY0-0.027-0.01024.8540.0080.0080.0000.0000.0000.000
163A163LYS10.8770.93721.1740.0780.0780.0000.0000.0000.000
164A164VAL0-0.036-0.01527.147-0.006-0.0060.0000.0000.0000.000
165A165VAL00.0090.00828.471-0.007-0.0070.0000.0000.0000.000
166A166THR00.001-0.02431.0080.0030.0030.0000.0000.0000.000
167A167ARG10.7910.83434.1100.0220.0220.0000.0000.0000.000
168A168GLU-1-0.838-0.91134.411-0.051-0.0510.0000.0000.0000.000
169A169LYS10.9150.96628.3110.1090.1090.0000.0000.0000.000
170A170LEU0-0.012-0.00531.865-0.011-0.0110.0000.0000.0000.000
171A171LEU0-0.044-0.02633.980-0.004-0.0040.0000.0000.0000.000
172A172GLU-1-0.858-0.92431.998-0.098-0.0980.0000.0000.0000.000
173A173THR0-0.074-0.04328.730-0.011-0.0110.0000.0000.0000.000
174A174PHE0-0.032-0.01329.214-0.008-0.0080.0000.0000.0000.000
175A175TRP0-0.016-0.01734.2590.0050.0050.0000.0000.0000.000
176A176GLU-1-0.908-0.93636.008-0.123-0.1230.0000.0000.0000.000
177A177ASP-1-0.900-0.93237.889-0.082-0.0820.0000.0000.0000.000
178A178PRO0-0.015-0.02840.9900.0020.0020.0000.0000.0000.000
179A179VAL0-0.0060.00540.9090.0040.0040.0000.0000.0000.000
180A180SER0-0.026-0.01343.2170.0030.0030.0000.0000.0000.000
181A181PRO00.0920.01941.981-0.001-0.0010.0000.0000.0000.000
182A182ARG10.9860.99742.1710.0350.0350.0000.0000.0000.000
183A183VAL0-0.0150.00941.6790.0020.0020.0000.0000.0000.000
184A184VAL00.0690.04737.467-0.001-0.0010.0000.0000.0000.000
185A185ASP-1-0.773-0.84239.958-0.032-0.0320.0000.0000.0000.000
186A186THR0-0.081-0.05141.9760.0030.0030.0000.0000.0000.000
187A187VAL00.0110.01037.7210.0010.0010.0000.0000.0000.000
188A188ILE00.0150.01535.8770.0000.0000.0000.0000.0000.000
189A189LYS10.9230.96139.3210.0280.0280.0000.0000.0000.000
190A190ARG10.8260.90341.5390.0570.0570.0000.0000.0000.000
191A191ILE00.0520.02835.3630.0020.0020.0000.0000.0000.000
192A192ARG10.8440.89838.4620.0200.0200.0000.0000.0000.000
193A193LYS10.9190.94440.3410.0300.0300.0000.0000.0000.000
194A194ALA0-0.0110.01539.7620.0010.0010.0000.0000.0000.000
195A195ILE0-0.004-0.00534.947-0.001-0.0010.0000.0000.0000.000
196A196GLU-1-0.816-0.89537.741-0.007-0.0070.0000.0000.0000.000
197A197ASP-1-0.826-0.90540.460-0.007-0.0070.0000.0000.0000.000
198A198ASP-1-0.772-0.87043.014-0.003-0.0030.0000.0000.0000.000
199A199PRO0-0.044-0.02542.8840.0020.0020.0000.0000.0000.000
200A200ASN0-0.081-0.03643.938-0.002-0.0020.0000.0000.0000.000
201A201ARG10.8200.89443.238-0.003-0.0030.0000.0000.0000.000
202A202PRO0-0.0240.00038.7270.0020.0020.0000.0000.0000.000
203A203ARG10.8990.95534.134-0.004-0.0040.0000.0000.0000.000
204A204TYR0-0.031-0.04732.0670.0040.0040.0000.0000.0000.000
205A205ILE00.0110.01333.205-0.002-0.0020.0000.0000.0000.000
206A206LYS10.8890.94734.657-0.012-0.0120.0000.0000.0000.000
207A207THR00.0260.00335.906-0.006-0.0060.0000.0000.0000.000
208A208ILE0-0.015-0.00433.7800.0060.0060.0000.0000.0000.000
209A209TRP00.0430.00233.205-0.006-0.0060.0000.0000.0000.000
210A210GLY00.0230.03039.733-0.001-0.0010.0000.0000.0000.000
211A211VAL00.0310.01336.590-0.005-0.0050.0000.0000.0000.000
212A212GLY00.0280.01535.253-0.007-0.0070.0000.0000.0000.000
213A213TYR0-0.103-0.05634.2950.0070.0070.0000.0000.0000.000
214A214MET00.0260.02829.701-0.001-0.0010.0000.0000.0000.000
215A215PHE00.0200.02328.5500.0030.0030.0000.0000.0000.000
216A216THR0-0.036-0.02729.5200.0070.0070.0000.0000.0000.000
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