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: MNVNZ

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1834727.15491
FMO2-HF: Nuclear repulsion 1758633.634285
FMO2-HF: Total energy -76093.520625
FMO2-MP2: Total energy -76315.287516


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.
-3.9140.8252.003-1.814-4.929-0.005
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 : -0.010
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].
3A5LYS10.9100.9623.904-0.9560.080-0.006-0.424-0.6050.002
4A6PRO0-0.027-0.0116.5470.3140.3140.0000.0000.0000.000
5A7THR0-0.039-0.0128.8620.1300.1300.0000.0000.0000.000
6A8LEU0-0.027-0.01312.368-0.017-0.0170.0000.0000.0000.000
7A9TRP00.0040.00415.4990.0220.0220.0000.0000.0000.000
8A10ALA00.0450.01819.123-0.018-0.0180.0000.0000.0000.000
9A11GLU-1-0.838-0.91221.819-0.128-0.1280.0000.0000.0000.000
10A12PRO0-0.0080.00023.7980.0070.0070.0000.0000.0000.000
11A13GLY00.0660.03825.8990.0100.0100.0000.0000.0000.000
12A14SER0-0.036-0.05324.234-0.013-0.0130.0000.0000.0000.000
13A15VAL0-0.0140.00126.225-0.002-0.0020.0000.0000.0000.000
14A16ILE00.0050.01328.6810.0040.0040.0000.0000.0000.000
15A17ILE00.0240.03131.7290.0020.0020.0000.0000.0000.000
16A18GLN00.0410.01734.316-0.007-0.0070.0000.0000.0000.000
17A19GLY0-0.0030.00434.5100.0040.0040.0000.0000.0000.000
18A20SER0-0.038-0.02332.4940.0030.0030.0000.0000.0000.000
19A21PRO0-0.024-0.01830.937-0.006-0.0060.0000.0000.0000.000
20A22VAL0-0.0100.01026.0480.0020.0020.0000.0000.0000.000
21A23THR0-0.001-0.01521.971-0.004-0.0040.0000.0000.0000.000
22A24LEU00.0160.03719.3820.0040.0040.0000.0000.0000.000
23A25ARG10.8050.87417.0650.1370.1370.0000.0000.0000.000
24A26CYS0-0.0270.00812.115-0.030-0.0300.0000.0000.0000.000
25A27GLN00.0110.00812.1900.0320.0320.0000.0000.0000.000
26A28GLY00.0600.0128.066-0.083-0.0830.0000.0000.0000.000
27A29SER0-0.0350.0034.5460.1040.205-0.001-0.006-0.0940.000
28A30LEU00.025-0.0076.773-0.047-0.0470.0000.0000.0000.000
29A31GLN0-0.0310.0083.965-0.309-0.0250.002-0.052-0.2340.000
30A32ALA0-0.0050.0127.588-0.082-0.0820.0000.0000.0000.000
31A33GLU-1-0.818-0.8838.848-0.298-0.2980.0000.0000.0000.000
32A34GLU-1-0.883-0.94710.162-0.374-0.3740.0000.0000.0000.000
33A35TYR0-0.025-0.02110.465-0.068-0.0680.0000.0000.0000.000
34A36HIS00.0360.02812.1610.0620.0620.0000.0000.0000.000
35A37LEU0-0.026-0.02213.8290.0060.0060.0000.0000.0000.000
36A38TYR0-0.035-0.02916.708-0.012-0.0120.0000.0000.0000.000
37A39ARG10.8960.96517.7480.1630.1630.0000.0000.0000.000
38A40GLU-1-0.842-0.89220.338-0.106-0.1060.0000.0000.0000.000
39A41ASN00.008-0.02423.5710.0060.0060.0000.0000.0000.000
40A42LYS10.9280.96220.7370.1330.1330.0000.0000.0000.000
41A43SER00.0140.02220.400-0.015-0.0150.0000.0000.0000.000
42A44ALA0-0.0120.00019.8040.0160.0160.0000.0000.0000.000
43A45SER00.0850.01917.311-0.026-0.0260.0000.0000.0000.000
44A46TRP0-0.0230.01719.2950.0050.0050.0000.0000.0000.000
45A47VAL00.0320.00814.875-0.023-0.0230.0000.0000.0000.000
46A48ARG10.9070.97216.8640.2670.2670.0000.0000.0000.000
47A49ARG10.7800.85113.5530.3400.3400.0000.0000.0000.000
48A50ILE0-0.086-0.01613.3980.0410.0410.0000.0000.0000.000
49A51GLN00.0300.00415.548-0.009-0.0090.0000.0000.0000.000
50A52GLU-1-0.862-0.93114.172-0.235-0.2350.0000.0000.0000.000
51A53PRO0-0.037-0.00615.5750.0250.0250.0000.0000.0000.000
52A54GLY00.0430.01615.218-0.021-0.0210.0000.0000.0000.000
53A55LYS10.8250.89716.2960.1630.1630.0000.0000.0000.000
54A56ASN00.0530.00513.362-0.045-0.0450.0000.0000.0000.000
55A57GLY00.0260.02714.3940.0280.0280.0000.0000.0000.000
56A58GLN0-0.042-0.02415.959-0.001-0.0010.0000.0000.0000.000
57A59PHE0-0.034-0.02315.741-0.006-0.0060.0000.0000.0000.000
58A60PRO0-0.015-0.01221.2390.0070.0070.0000.0000.0000.000
59A61ILE00.0280.01125.011-0.005-0.0050.0000.0000.0000.000
60A62PRO0-0.012-0.01727.7150.0050.0050.0000.0000.0000.000
61A63SER00.0350.01931.2680.0080.0080.0000.0000.0000.000
62A64ILE0-0.0480.00627.989-0.004-0.0040.0000.0000.0000.000
63A65THR00.025-0.02330.8390.0080.0080.0000.0000.0000.000
64A66TRP00.037-0.01731.308-0.003-0.0030.0000.0000.0000.000
65A67GLU-1-0.936-0.95229.629-0.098-0.0980.0000.0000.0000.000
66A68HIS00.0040.03226.634-0.001-0.0010.0000.0000.0000.000
67A69ALA00.0140.02426.468-0.008-0.0080.0000.0000.0000.000
68A70GLY00.0500.02125.1540.0040.0040.0000.0000.0000.000
69A71ARG10.8530.93216.7500.1690.1690.0000.0000.0000.000
70A72TYR0-0.032-0.04718.876-0.023-0.0230.0000.0000.0000.000
71A73HIS00.0480.02213.6200.0570.0570.0000.0000.0000.000
72A75GLN00.0800.0307.4150.2290.2290.0000.0000.0000.000
73A76TYR0-0.051-0.0313.351-0.4220.4380.059-0.292-0.627-0.002
74A77TYR0-0.010-0.0076.291-0.428-0.4280.0000.0000.0000.000
75A78SER00.011-0.0275.2110.1520.1520.0000.0000.0000.000
76A79HIS00.0320.0137.024-0.039-0.0390.0000.0000.0000.000
77A80ASN0-0.050-0.0187.2360.1000.1000.0000.0000.0000.000
78A81HIS00.0030.0142.372-1.920-0.9031.805-0.675-2.148-0.005
79A82SER0-0.005-0.0124.4100.1670.303-0.001-0.016-0.1200.000
80A83SER0-0.051-0.0262.815-1.522-0.6460.142-0.310-0.7080.000
81A84GLU-1-0.903-0.9493.6670.7561.1730.004-0.037-0.3840.000
82A85TYR0-0.033-0.0465.377-0.0080.004-0.001-0.002-0.0090.000
83A86SER0-0.043-0.0158.9830.0340.0340.0000.0000.0000.000
84A87ASP-1-0.804-0.89711.060-0.165-0.1650.0000.0000.0000.000
85A88PRO0-0.065-0.04114.120-0.029-0.0290.0000.0000.0000.000
86A89LEU00.0080.03016.9950.0290.0290.0000.0000.0000.000
87A90GLU-1-0.885-0.95019.623-0.062-0.0620.0000.0000.0000.000
88A91LEU0-0.0390.01023.2280.0050.0050.0000.0000.0000.000
89A92VAL00.013-0.00225.1050.0030.0030.0000.0000.0000.000
90A93VAL00.0060.02128.8920.0010.0010.0000.0000.0000.000
91A94THR0-0.024-0.03831.8840.0060.0060.0000.0000.0000.000
92A95GLY00.033-0.00535.490-0.002-0.0020.0000.0000.0000.000
93A96ALA0-0.0210.00337.4000.0010.0010.0000.0000.0000.000
94A97TYR0-0.008-0.00636.9430.0010.0010.0000.0000.0000.000
95A98SER00.008-0.00241.8950.0000.0000.0000.0000.0000.000
96A99LYS10.8700.93843.5720.0210.0210.0000.0000.0000.000
97A100PRO00.0780.02641.1710.0020.0020.0000.0000.0000.000
98A101THR0-0.035-0.00944.509-0.001-0.0010.0000.0000.0000.000
99A102LEU00.0220.02042.7360.0010.0010.0000.0000.0000.000
100A103SER0-0.007-0.00646.1310.0000.0000.0000.0000.0000.000
101A104ALA0-0.0080.00148.3350.0010.0010.0000.0000.0000.000
102A105LEU0-0.0090.02549.4740.0000.0000.0000.0000.0000.000
103A106PRO00.000-0.01650.5250.0010.0010.0000.0000.0000.000
104A107SER00.003-0.02652.947-0.001-0.0010.0000.0000.0000.000
105A108PRO00.007-0.00850.7190.0010.0010.0000.0000.0000.000
106A109VAL0-0.0090.02150.8890.0000.0000.0000.0000.0000.000
107A110VAL00.0330.01948.7140.0000.0000.0000.0000.0000.000
108A111THR00.0150.00451.7650.0000.0000.0000.0000.0000.000
109A112LEU00.008-0.00949.8720.0000.0000.0000.0000.0000.000
110A113GLY00.0030.00846.9600.0010.0010.0000.0000.0000.000
111A114GLY0-0.0200.00948.0340.0010.0010.0000.0000.0000.000
112A115ASN0-0.024-0.02346.4450.0000.0000.0000.0000.0000.000
113A116VAL0-0.001-0.00246.033-0.001-0.0010.0000.0000.0000.000
114A117THR0-0.010-0.00646.0170.0010.0010.0000.0000.0000.000
115A118LEU00.0160.00442.503-0.001-0.0010.0000.0000.0000.000
116A119GLN00.0320.02644.1310.0000.0000.0000.0000.0000.000
117A120CYS0-0.003-0.00142.464-0.002-0.0020.0000.0000.0000.000
118A121VAL0-0.0050.00644.5110.0010.0010.0000.0000.0000.000
119A122SER00.014-0.00744.508-0.001-0.0010.0000.0000.0000.000
120A123GLN0-0.021-0.01146.5960.0000.0000.0000.0000.0000.000
121A124VAL0-0.016-0.00344.9190.0000.0000.0000.0000.0000.000
122A125ALA0-0.0110.00045.2720.0010.0010.0000.0000.0000.000
123A126PHE0-0.008-0.01439.949-0.002-0.0020.0000.0000.0000.000
124A127ASP-1-0.912-0.95537.637-0.020-0.0200.0000.0000.0000.000
125A128GLY00.0050.01035.7310.0020.0020.0000.0000.0000.000
126A129PHE0-0.046-0.03336.193-0.002-0.0020.0000.0000.0000.000
127A130ILE0-0.008-0.00132.2850.0000.0000.0000.0000.0000.000
128A131LEU0-0.0170.00435.3960.0010.0010.0000.0000.0000.000
129A132CYS0-0.071-0.06831.241-0.001-0.0010.0000.0000.0000.000
130A133LYS10.9260.95835.9690.0030.0030.0000.0000.0000.000
131A134GLU-1-0.835-0.91736.048-0.027-0.0270.0000.0000.0000.000
132A135GLY0-0.031-0.02035.8750.0030.0030.0000.0000.0000.000
133A136GLU-1-0.979-0.98936.406-0.003-0.0030.0000.0000.0000.000
134A137ASP-1-0.917-0.95834.474-0.016-0.0160.0000.0000.0000.000
135A138GLU-1-0.929-0.93429.455-0.025-0.0250.0000.0000.0000.000
136A139HIS0-0.027-0.01632.370-0.001-0.0010.0000.0000.0000.000
137A140PRO0-0.036-0.01332.7450.0000.0000.0000.0000.0000.000
138A141GLN00.0280.04330.554-0.003-0.0030.0000.0000.0000.000
139A143LEU0-0.025-0.00530.9090.0010.0010.0000.0000.0000.000
140A144ASN00.0410.00728.6800.0020.0020.0000.0000.0000.000
141A145SER0-0.039-0.02830.6790.0050.0050.0000.0000.0000.000
142A146HIS00.0400.03228.091-0.008-0.0080.0000.0000.0000.000
143A147SER0-0.004-0.01630.7820.0070.0070.0000.0000.0000.000
144A148HIS0-0.037-0.02525.463-0.001-0.0010.0000.0000.0000.000
145A149ALA00.0530.02529.5510.0030.0030.0000.0000.0000.000
146A150ARG10.8970.97030.079-0.003-0.0030.0000.0000.0000.000
147A151GLY00.025-0.00429.5580.0000.0000.0000.0000.0000.000
148A152TRP00.0010.00130.7090.0030.0030.0000.0000.0000.000
149A153SER0-0.0170.00331.434-0.002-0.0020.0000.0000.0000.000
150A154TRP00.0140.01026.0370.0050.0050.0000.0000.0000.000
151A155ALA00.0190.00831.381-0.004-0.0040.0000.0000.0000.000
152A156ILE0-0.011-0.00126.1840.0060.0060.0000.0000.0000.000
153A157PHE00.018-0.00328.160-0.004-0.0040.0000.0000.0000.000
154A158SER00.0410.03125.5950.0070.0070.0000.0000.0000.000
155A159VAL0-0.028-0.01127.309-0.004-0.0040.0000.0000.0000.000
156A160GLY00.0060.01226.215-0.005-0.0050.0000.0000.0000.000
157A161PRO0-0.008-0.01126.1280.0040.0040.0000.0000.0000.000
158A162VAL0-0.032-0.02725.6920.0050.0050.0000.0000.0000.000
159A163SER00.005-0.01628.2430.0000.0000.0000.0000.0000.000
160A164PRO0-0.048-0.01328.3030.0040.0040.0000.0000.0000.000
161A165SER00.0590.01531.5290.0000.0000.0000.0000.0000.000
162A166ARG10.9050.94534.580-0.014-0.0140.0000.0000.0000.000
163A167ARG10.8340.87831.281-0.047-0.0470.0000.0000.0000.000
164A168TRP00.0400.02027.643-0.003-0.0030.0000.0000.0000.000
165A169SER0-0.028-0.02829.1310.0050.0050.0000.0000.0000.000
166A170TYR0-0.0120.00629.073-0.007-0.0070.0000.0000.0000.000
167A171ARG10.8790.94830.854-0.056-0.0560.0000.0000.0000.000
168A172CYS00.004-0.00331.526-0.004-0.0040.0000.0000.0000.000
169A173TYR00.0220.01334.0930.0050.0050.0000.0000.0000.000
170A174ALA00.0210.01335.895-0.002-0.0020.0000.0000.0000.000
171A175TYR0-0.002-0.00737.7720.0010.0010.0000.0000.0000.000
172A176ASP-1-0.759-0.87540.3610.0200.0200.0000.0000.0000.000
173A177SER0-0.020-0.01742.957-0.001-0.0010.0000.0000.0000.000
174A178ASN0-0.087-0.04945.377-0.002-0.0020.0000.0000.0000.000
175A179SER0-0.038-0.01746.3810.0000.0000.0000.0000.0000.000
176A180PRO00.0080.01145.0580.0020.0020.0000.0000.0000.000
177A181TYR0-0.014-0.00245.5750.0000.0000.0000.0000.0000.000
178A182VAL0-0.020-0.00346.6060.0010.0010.0000.0000.0000.000
179A183TRP0-0.058-0.03641.1730.0010.0010.0000.0000.0000.000
180A184SER0-0.012-0.01438.1350.0000.0000.0000.0000.0000.000
181A185LEU00.0220.00338.675-0.002-0.0020.0000.0000.0000.000
182A186PRO0-0.0320.00936.3160.0000.0000.0000.0000.0000.000
183A187SER00.007-0.00331.3410.0040.0040.0000.0000.0000.000
184A188ASP-1-0.844-0.93929.6320.0850.0850.0000.0000.0000.000
185A189LEU0-0.114-0.04828.992-0.003-0.0030.0000.0000.0000.000
186A190LEU00.0330.01723.7890.0100.0100.0000.0000.0000.000
187A191GLU-1-0.762-0.84626.0630.0500.0500.0000.0000.0000.000
188A192LEU0-0.039-0.01224.0130.0080.0080.0000.0000.0000.000
189A193LEU0-0.016-0.00719.703-0.003-0.0030.0000.0000.0000.000
190A194VAL00.0140.00122.090-0.008-0.0080.0000.0000.0000.000
191A195PRO0-0.0300.00119.4370.0080.0080.0000.0000.0000.000
192A196GLY00.0190.00721.951-0.009-0.0090.0000.0000.0000.000