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: 98482

Calculation Name: 2OTP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2OTP

Chain ID: A

ChEMBL ID:

UniProt ID: Q8N149

Base Structure: X-ray

Registration Date: 2023-09-21

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1833685.748352
FMO2-HF: Nuclear repulsion 1757594.207562
FMO2-HF: Total energy -76091.54079
FMO2-MP2: Total energy -76313.557297


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:3:LEU)


Summations of interaction energy for fragment #1(A:3:LEU)
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.
-3.1061.290.52-1.394-3.5180
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.025
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].
3A5LYS10.9241.0013.810-1.486-0.232-0.011-0.526-0.7170.003
4A6PRO0-0.037-0.0256.4810.4330.4330.0000.0000.0000.000
5A7THR0-0.030-0.0159.0360.1490.1490.0000.0000.0000.000
6A8LEU0-0.010-0.01312.432-0.018-0.0180.0000.0000.0000.000
7A9TRP00.0350.02115.4510.0170.0170.0000.0000.0000.000
8A10ALA00.0230.00319.090-0.017-0.0170.0000.0000.0000.000
9A11GLU-1-0.866-0.91421.746-0.099-0.0990.0000.0000.0000.000
10A12PRO0-0.023-0.00323.5940.0080.0080.0000.0000.0000.000
11A13GLY00.0980.04126.2100.0100.0100.0000.0000.0000.000
12A14SER0-0.034-0.02724.615-0.013-0.0130.0000.0000.0000.000
13A15VAL0-0.019-0.01326.405-0.005-0.0050.0000.0000.0000.000
14A16ILE00.0120.01528.6680.0050.0050.0000.0000.0000.000
15A17ILE00.0440.02831.5910.0010.0010.0000.0000.0000.000
16A18GLN00.0240.01834.293-0.006-0.0060.0000.0000.0000.000
17A19GLY0-0.0100.00834.4550.0040.0040.0000.0000.0000.000
18A20SER0-0.015-0.02232.8840.0050.0050.0000.0000.0000.000
19A21PRO0-0.021-0.01230.905-0.005-0.0050.0000.0000.0000.000
20A22VAL0-0.0070.00726.3250.0030.0030.0000.0000.0000.000
21A23THR00.001-0.01021.919-0.008-0.0080.0000.0000.0000.000
22A24LEU00.0070.01919.3800.0070.0070.0000.0000.0000.000
23A25ARG10.8230.90217.0570.0860.0860.0000.0000.0000.000
24A26CYS00.0710.04312.279-0.036-0.0360.0000.0000.0000.000
25A27GLN0-0.001-0.00112.2890.0090.0090.0000.0000.0000.000
26A28GLY00.0740.0188.207-0.058-0.0580.0000.0000.0000.000
27A29SER0-0.0320.0094.6970.1220.206-0.001-0.005-0.0770.000
28A30LEU00.031-0.0076.835-0.042-0.0420.0000.0000.0000.000
29A31GLN0-0.055-0.0034.435-0.183-0.032-0.001-0.007-0.1430.000
30A32ALA0-0.037-0.0177.671-0.090-0.0900.0000.0000.0000.000
31A33GLU-1-0.774-0.8878.999-0.275-0.2750.0000.0000.0000.000
32A34GLU-1-0.895-0.95410.101-0.396-0.3960.0000.0000.0000.000
33A35TYR0-0.063-0.04110.974-0.044-0.0440.0000.0000.0000.000
34A36HIS00.0200.00312.1970.0370.0370.0000.0000.0000.000
35A37LEU0-0.0140.02613.8200.0070.0070.0000.0000.0000.000
36A38TYR0-0.045-0.04316.746-0.018-0.0180.0000.0000.0000.000
37A39ARG10.9561.01117.8710.1600.1600.0000.0000.0000.000
38A40GLU-1-0.884-0.94120.084-0.105-0.1050.0000.0000.0000.000
39A41ASN0-0.018-0.02223.0030.0080.0080.0000.0000.0000.000
40A42LYS10.9620.97720.4190.1480.1480.0000.0000.0000.000
41A43SER00.0920.09720.044-0.016-0.0160.0000.0000.0000.000
42A44ALA00.1210.07720.5620.0010.0010.0000.0000.0000.000
43A45SER0-0.094-0.11717.357-0.015-0.0150.0000.0000.0000.000
44A46TRP0-0.100-0.02019.0900.0100.0100.0000.0000.0000.000
45A47VAL00.0410.01615.190-0.022-0.0220.0000.0000.0000.000
46A48ARG10.9070.97116.6640.2520.2520.0000.0000.0000.000
47A49ARG10.7750.86213.7820.3330.3330.0000.0000.0000.000
48A50ILE0-0.077-0.03513.9940.0380.0380.0000.0000.0000.000
49A51GLN00.0450.01015.398-0.016-0.0160.0000.0000.0000.000
50A52GLU-1-0.881-0.92314.759-0.221-0.2210.0000.0000.0000.000
51A53PRO0-0.054-0.01615.9400.0270.0270.0000.0000.0000.000
52A54GLY00.0530.01715.403-0.011-0.0110.0000.0000.0000.000
53A55LYS10.8740.93416.7020.1340.1340.0000.0000.0000.000
54A56ASN00.014-0.00613.711-0.038-0.0380.0000.0000.0000.000
55A57GLY00.0550.02615.0140.0150.0150.0000.0000.0000.000
56A58GLN0-0.116-0.06716.483-0.009-0.0090.0000.0000.0000.000
57A59PHE00.0160.00215.736-0.010-0.0100.0000.0000.0000.000
58A60PRO0-0.017-0.01621.2030.0060.0060.0000.0000.0000.000
59A61ILE00.0180.00524.904-0.007-0.0070.0000.0000.0000.000
60A62PRO0-0.0140.00227.7540.0060.0060.0000.0000.0000.000
61A63SER00.0420.02131.3630.0050.0050.0000.0000.0000.000
62A64ILE0-0.0260.00527.625-0.006-0.0060.0000.0000.0000.000
63A65THR00.010-0.03530.8280.0070.0070.0000.0000.0000.000
64A66TRP00.056-0.01031.286-0.002-0.0020.0000.0000.0000.000
65A67GLU-1-0.932-0.94729.479-0.097-0.0970.0000.0000.0000.000
66A68HIS00.0030.03226.4330.0000.0000.0000.0000.0000.000
67A69ALA00.0130.03026.106-0.009-0.0090.0000.0000.0000.000
68A70GLY00.0650.02824.7770.0020.0020.0000.0000.0000.000
69A71ARG10.8570.92916.8680.1680.1680.0000.0000.0000.000
70A72TYR0-0.054-0.05218.814-0.024-0.0240.0000.0000.0000.000
71A73HIS00.0880.04613.3050.0610.0610.0000.0000.0000.000
72A75GLN0-0.032-0.0547.8520.2070.2070.0000.0000.0000.000
73A76TYR0-0.024-0.0203.452-0.1780.4730.038-0.204-0.484-0.001
74A77TYR0-0.0320.0086.593-0.390-0.3900.0000.0000.0000.000
75A78SER00.0210.0035.0690.1860.1860.0000.0000.0000.000
76A79HIS00.0160.0166.983-0.018-0.0180.0000.0000.0000.000
77A80ASN0-0.044-0.0247.5400.0590.0590.0000.0000.0000.000
78A81HIS00.0060.0152.614-1.555-0.4610.439-0.362-1.172-0.002
79A82SER00.0040.0014.7420.0870.167-0.001-0.005-0.0730.000
80A83SER0-0.017-0.0193.069-1.160-0.4690.056-0.217-0.5290.000
81A84GLU-1-0.930-0.9613.5040.7921.1970.002-0.066-0.3410.000
82A85TYR0-0.035-0.0355.2780.0590.045-0.001-0.0020.0180.000
83A86SER00.0280.0097.935-0.058-0.0580.0000.0000.0000.000
84A87ASP-1-0.869-0.92910.374-0.063-0.0630.0000.0000.0000.000
85A88PRO0-0.070-0.04113.696-0.027-0.0270.0000.0000.0000.000
86A89LEU0-0.0200.00316.5830.0270.0270.0000.0000.0000.000
87A90GLU-1-0.921-0.97019.345-0.048-0.0480.0000.0000.0000.000
88A91LEU0-0.044-0.00422.9540.0090.0090.0000.0000.0000.000
89A92VAL00.007-0.00425.2100.0030.0030.0000.0000.0000.000
90A93VAL00.0100.02628.8380.0020.0020.0000.0000.0000.000
91A94THR0-0.032-0.03431.9920.0050.0050.0000.0000.0000.000
92A95GLY0-0.003-0.01135.294-0.002-0.0020.0000.0000.0000.000
93A96ALA0-0.0080.00737.152-0.001-0.0010.0000.0000.0000.000
94A97TYR00.006-0.00936.9100.0010.0010.0000.0000.0000.000
95A98SER0-0.003-0.00541.5940.0000.0000.0000.0000.0000.000
96A99LYS10.8680.94543.0110.0150.0150.0000.0000.0000.000
97A100PRO00.0830.02640.9830.0010.0010.0000.0000.0000.000
98A101THR0-0.066-0.03844.3330.0000.0000.0000.0000.0000.000
99A102LEU00.0370.03842.2500.0010.0010.0000.0000.0000.000
100A103SER0-0.008-0.01245.6950.0000.0000.0000.0000.0000.000
101A104ALA0-0.0090.00148.0200.0010.0010.0000.0000.0000.000
102A105LEU0-0.0220.04148.7930.0000.0000.0000.0000.0000.000
103A106PRO0-0.004-0.02149.8330.0010.0010.0000.0000.0000.000
104A107SER00.028-0.02953.100-0.001-0.0010.0000.0000.0000.000
105A108PRO00.022-0.00350.5100.0010.0010.0000.0000.0000.000
106A109VAL0-0.0150.01350.6390.0010.0010.0000.0000.0000.000
107A110VAL00.0290.01948.1860.0000.0000.0000.0000.0000.000
108A111THR00.0070.00551.3230.0000.0000.0000.0000.0000.000
109A112LEU00.003-0.01549.6170.0000.0000.0000.0000.0000.000
110A113GLY0-0.0090.00546.5680.0010.0010.0000.0000.0000.000
111A114GLY0-0.0030.01947.6100.0010.0010.0000.0000.0000.000
112A115ASN0-0.011-0.01446.5170.0010.0010.0000.0000.0000.000
113A116VAL0-0.013-0.01045.669-0.001-0.0010.0000.0000.0000.000
114A117THR0-0.023-0.01845.6370.0010.0010.0000.0000.0000.000
115A118LEU00.0200.01642.691-0.001-0.0010.0000.0000.0000.000
116A119GLN00.0140.00744.0120.0000.0000.0000.0000.0000.000
117A120CYS0-0.0010.00441.918-0.002-0.0020.0000.0000.0000.000
118A121VAL00.009-0.00144.0770.0000.0000.0000.0000.0000.000
119A122SER00.0440.00344.319-0.001-0.0010.0000.0000.0000.000
120A123GLN0-0.0090.00346.5190.0000.0000.0000.0000.0000.000
121A124VAL0-0.031-0.00544.6980.0000.0000.0000.0000.0000.000
122A125ALA0-0.0040.00444.9420.0010.0010.0000.0000.0000.000
123A126PHE00.001-0.01739.636-0.002-0.0020.0000.0000.0000.000
124A127ASP-1-0.934-0.95937.848-0.014-0.0140.0000.0000.0000.000
125A128GLY00.0320.01235.7700.0000.0000.0000.0000.0000.000
126A129PHE0-0.062-0.02736.012-0.002-0.0020.0000.0000.0000.000
127A130ILE0-0.013-0.00932.1480.0010.0010.0000.0000.0000.000
128A131LEU00.0010.01935.2510.0000.0000.0000.0000.0000.000
129A132CYS0-0.078-0.07131.1290.0010.0010.0000.0000.0000.000
130A133LYS10.9360.96535.440-0.013-0.0130.0000.0000.0000.000
131A134GLU-1-0.837-0.92735.944-0.013-0.0130.0000.0000.0000.000
132A135GLY0-0.053-0.02836.1960.0030.0030.0000.0000.0000.000
133A136GLU-1-0.973-0.99136.6430.0110.0110.0000.0000.0000.000
134A137ASP-1-0.920-0.95334.4020.0020.0020.0000.0000.0000.000
135A138GLU-1-0.940-0.94329.2760.0000.0000.0000.0000.0000.000
136A139HIS0-0.016-0.01232.163-0.003-0.0030.0000.0000.0000.000
137A140PRO0-0.0200.00432.5470.0010.0010.0000.0000.0000.000
138A141GLN00.0000.03030.319-0.002-0.0020.0000.0000.0000.000
139A143LEU0-0.034-0.02330.5390.0020.0020.0000.0000.0000.000
140A144ASN0-0.003-0.02628.7590.0010.0010.0000.0000.0000.000
141A145SER0-0.017-0.00130.2280.0060.0060.0000.0000.0000.000
142A146HIS00.0360.02727.736-0.010-0.0100.0000.0000.0000.000
143A147SER00.0360.00430.4440.0080.0080.0000.0000.0000.000
144A148HIS0-0.083-0.04525.131-0.001-0.0010.0000.0000.0000.000
145A149ALA00.0610.03529.3360.0040.0040.0000.0000.0000.000
146A150ARG10.9370.97229.346-0.001-0.0010.0000.0000.0000.000
147A151GLY0-0.011-0.00229.7280.0040.0040.0000.0000.0000.000
148A152TRP0-0.004-0.01630.1780.0010.0010.0000.0000.0000.000
149A153SER00.0070.02830.513-0.001-0.0010.0000.0000.0000.000
150A154TRP00.0500.00025.8630.0060.0060.0000.0000.0000.000
151A155ALA0-0.0260.00430.292-0.003-0.0030.0000.0000.0000.000
152A156ILE00.0010.01025.9930.0070.0070.0000.0000.0000.000
153A157PHE00.008-0.01027.946-0.006-0.0060.0000.0000.0000.000
154A158SER00.0250.01625.6040.0080.0080.0000.0000.0000.000
155A159VAL0-0.014-0.00126.332-0.005-0.0050.0000.0000.0000.000
156A160GLY00.0250.02325.535-0.003-0.0030.0000.0000.0000.000
157A161PRO00.000-0.02525.9290.0070.0070.0000.0000.0000.000
158A162VAL0-0.0230.00225.2100.0020.0020.0000.0000.0000.000
159A163SER00.010-0.02227.881-0.001-0.0010.0000.0000.0000.000
160A164PRO0-0.048-0.00628.1950.0010.0010.0000.0000.0000.000
161A165SER00.0520.01531.327-0.001-0.0010.0000.0000.0000.000
162A166ARG10.9360.95834.158-0.029-0.0290.0000.0000.0000.000
163A167ARG10.8710.92231.123-0.070-0.0700.0000.0000.0000.000
164A168TRP00.0390.01727.399-0.005-0.0050.0000.0000.0000.000
165A169SER0-0.021-0.00629.0690.0070.0070.0000.0000.0000.000
166A170TYR00.0130.01328.603-0.009-0.0090.0000.0000.0000.000
167A171ARG10.9170.94630.380-0.071-0.0710.0000.0000.0000.000
168A172CYS00.0010.00231.117-0.004-0.0040.0000.0000.0000.000
169A173TYR00.022-0.00233.5520.0040.0040.0000.0000.0000.000
170A174ALA00.0190.00735.432-0.001-0.0010.0000.0000.0000.000
171A175TYR0-0.026-0.01337.3440.0000.0000.0000.0000.0000.000
172A176ASP-1-0.773-0.86839.7630.0250.0250.0000.0000.0000.000
173A177SER00.011-0.00642.365-0.001-0.0010.0000.0000.0000.000
174A178ASN0-0.107-0.06344.721-0.002-0.0020.0000.0000.0000.000
175A179SER0-0.035-0.02646.200-0.001-0.0010.0000.0000.0000.000
176A180PRO00.0130.01844.6860.0020.0020.0000.0000.0000.000
177A181TYR00.0040.00445.1590.0000.0000.0000.0000.0000.000
178A182VAL0-0.032-0.00446.2870.0010.0010.0000.0000.0000.000
179A183TRP0-0.049-0.02840.9580.0010.0010.0000.0000.0000.000
180A184SER00.003-0.00137.6460.0000.0000.0000.0000.0000.000
181A185LEU0-0.011-0.01238.121-0.002-0.0020.0000.0000.0000.000
182A186PRO0-0.0100.00435.8940.0020.0020.0000.0000.0000.000
183A187SER00.0000.00530.8290.0040.0040.0000.0000.0000.000
184A188ASP-1-0.914-0.96228.7940.1160.1160.0000.0000.0000.000
185A189LEU0-0.077-0.03029.0740.0000.0000.0000.0000.0000.000
186A190LEU00.0650.04423.3160.0100.0100.0000.0000.0000.000
187A191GLU-1-0.911-0.95725.7640.0860.0860.0000.0000.0000.000
188A192LEU0-0.0120.00223.3670.0130.0130.0000.0000.0000.000
189A193LEU0-0.012-0.00419.0730.0000.0000.0000.0000.0000.000
190A194VAL00.002-0.00721.222-0.006-0.0060.0000.0000.0000.000
191A195PRO0-0.0190.00919.3270.0080.0080.0000.0000.0000.000
192A196GLY00.0300.01121.735-0.013-0.0130.0000.0000.0000.000