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: N9MLQ

Calculation Name: 3DMB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DMB

Chain ID: A

ChEMBL ID:

UniProt ID: Q8P8H7

Base Structure: X-ray

Registration Date: 2023-09-20

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 146
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1202313.344901
FMO2-HF: Nuclear repulsion 1146944.585132
FMO2-HF: Total energy -55368.759769
FMO2-MP2: Total energy -55530.838949


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:0:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
-15.114-13.5498.784-5.557-4.792-0.05
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.003
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].
3A2ALA00.011-0.0073.016-1.2550.8280.029-1.063-1.0490.003
4A3ASP-1-0.848-0.9101.919-15.999-16.7508.757-4.444-3.562-0.053
5A4PRO00.019-0.0034.4820.8290.864-0.001-0.014-0.0200.000
6A5LYS10.8040.8827.4691.2151.2150.0000.0000.0000.000
7A6GLU-1-0.782-0.8904.609-1.083-0.885-0.001-0.036-0.1610.000
8A7LEU0-0.032-0.0147.1110.5110.5110.0000.0000.0000.000
9A8GLN00.0440.0279.3630.3190.3190.0000.0000.0000.000
10A9ASP-1-0.796-0.87310.457-0.758-0.7580.0000.0000.0000.000
11A10LYS10.8240.9177.0270.9790.9790.0000.0000.0000.000
12A11PHE00.0140.01212.7860.1110.1110.0000.0000.0000.000
13A12TRP00.006-0.00415.1660.0870.0870.0000.0000.0000.000
14A13LYS10.9510.97615.1340.2640.2640.0000.0000.0000.000
15A14ALA00.0330.01916.9210.0410.0410.0000.0000.0000.000
16A15LEU0-0.0020.00018.7410.0340.0340.0000.0000.0000.000
17A16LYS10.8560.92720.7060.2040.2040.0000.0000.0000.000
18A17SER0-0.031-0.02921.3740.0120.0120.0000.0000.0000.000
19A18ASP-1-0.799-0.88321.011-0.069-0.0690.0000.0000.0000.000
20A19ARG10.8630.95723.6410.1240.1240.0000.0000.0000.000
21A20THR0-0.032-0.01325.326-0.001-0.0010.0000.0000.0000.000
22A21VAL0-0.0150.00823.988-0.001-0.0010.0000.0000.0000.000
23A22MET0-0.0110.00426.3580.0070.0070.0000.0000.0000.000
24A23LEU0-0.008-0.00727.419-0.006-0.0060.0000.0000.0000.000
25A24GLY00.0260.00829.3400.0110.0110.0000.0000.0000.000
26A25LEU0-0.036-0.02130.301-0.010-0.0100.0000.0000.0000.000
27A26ASP-1-0.812-0.89629.485-0.088-0.0880.0000.0000.0000.000
28A27GLY0-0.016-0.00531.5150.0010.0010.0000.0000.0000.000
29A28VAL0-0.078-0.05134.0760.0010.0010.0000.0000.0000.000
30A29GLU-1-0.912-0.94136.239-0.029-0.0290.0000.0000.0000.000
31A30ASP-1-0.828-0.90537.882-0.036-0.0360.0000.0000.0000.000
32A31GLY00.0190.00934.044-0.003-0.0030.0000.0000.0000.000
33A32HIS0-0.065-0.05034.494-0.005-0.0050.0000.0000.0000.000
34A33ALA0-0.0170.00032.015-0.003-0.0030.0000.0000.0000.000
35A34ARG10.8890.92832.5140.0570.0570.0000.0000.0000.000
36A35PRO0-0.0090.00430.348-0.007-0.0070.0000.0000.0000.000
37A36MET0-0.034-0.00929.9880.0030.0030.0000.0000.0000.000
38A37THR00.002-0.00428.998-0.005-0.0050.0000.0000.0000.000
39A38ALA00.0220.01325.496-0.001-0.0010.0000.0000.0000.000
40A39GLN0-0.045-0.03026.8160.0110.0110.0000.0000.0000.000
41A40ILE00.0270.01621.137-0.003-0.0030.0000.0000.0000.000
42A41GLU-1-0.800-0.85925.420-0.131-0.1310.0000.0000.0000.000
43A42GLY00.0340.02323.626-0.016-0.0160.0000.0000.0000.000
44A43ASP-1-0.914-0.97319.964-0.193-0.1930.0000.0000.0000.000
45A44SER0-0.048-0.03216.916-0.040-0.0400.0000.0000.0000.000
46A45GLY00.0280.02318.5230.0180.0180.0000.0000.0000.000
47A46GLY00.0100.00220.1870.0150.0150.0000.0000.0000.000
48A47PRO0-0.029-0.02023.523-0.003-0.0030.0000.0000.0000.000
49A48ILE0-0.0150.00421.872-0.004-0.0040.0000.0000.0000.000
50A49TRP00.0370.01425.9430.0140.0140.0000.0000.0000.000
51A50PHE00.019-0.00526.525-0.002-0.0020.0000.0000.0000.000
52A51PHE00.0310.02031.6710.0030.0030.0000.0000.0000.000
53A52THR0-0.024-0.00435.1140.0030.0030.0000.0000.0000.000
54A53SER00.0550.02937.6590.0000.0000.0000.0000.0000.000
55A54LYS10.7670.86041.1090.0600.0600.0000.0000.0000.000
56A55ASP-1-0.828-0.89143.385-0.043-0.0430.0000.0000.0000.000
57A56ASN0-0.027-0.02336.1990.0040.0040.0000.0000.0000.000
58A57ALA00.0280.00040.569-0.003-0.0030.0000.0000.0000.000
59A58LEU00.0000.00633.994-0.001-0.0010.0000.0000.0000.000
60A59ILE00.0200.01237.988-0.003-0.0030.0000.0000.0000.000
61A60ALA0-0.038-0.02039.587-0.002-0.0020.0000.0000.0000.000
62A61MET0-0.034-0.00738.6560.0020.0020.0000.0000.0000.000
63A62LEU0-0.058-0.01134.757-0.003-0.0030.0000.0000.0000.000
64A63GLY00.0300.00937.726-0.002-0.0020.0000.0000.0000.000
65A64GLN0-0.039-0.02736.697-0.001-0.0010.0000.0000.0000.000
66A65GLY0-0.0040.00334.218-0.008-0.0080.0000.0000.0000.000
67A66ARG10.8600.94533.6430.0760.0760.0000.0000.0000.000
68A67ARG10.8720.93726.6310.1130.1130.0000.0000.0000.000
69A68VAL00.005-0.00227.4310.0110.0110.0000.0000.0000.000
70A69ILE00.0000.00524.389-0.013-0.0130.0000.0000.0000.000
71A70GLY00.0380.00024.4930.0110.0110.0000.0000.0000.000
72A71ALA0-0.0210.00822.928-0.016-0.0160.0000.0000.0000.000
73A72PHE00.001-0.01618.6920.0020.0020.0000.0000.0000.000
74A73SER00.0070.00020.2060.0080.0080.0000.0000.0000.000
75A74SER0-0.014-0.03117.9670.0010.0010.0000.0000.0000.000
76A75LYS10.8090.87320.1380.0840.0840.0000.0000.0000.000
77A76GLY00.0000.00520.7790.0110.0110.0000.0000.0000.000
78A77HIS0-0.070-0.03720.0320.0300.0300.0000.0000.0000.000
79A78ASP-1-0.823-0.87215.022-0.019-0.0190.0000.0000.0000.000
80A79LEU0-0.023-0.00512.8210.0150.0150.0000.0000.0000.000
81A80PHE00.0050.00415.7550.0050.0050.0000.0000.0000.000
82A81ALA0-0.009-0.01316.099-0.036-0.0360.0000.0000.0000.000
83A82SER0-0.020-0.00318.0250.0320.0320.0000.0000.0000.000
84A83ILE0-0.008-0.00319.803-0.029-0.0290.0000.0000.0000.000
85A84SER00.0310.02221.3290.0340.0340.0000.0000.0000.000
86A85GLY00.0580.02022.931-0.026-0.0260.0000.0000.0000.000
87A86SER0-0.042-0.01625.6610.0190.0190.0000.0000.0000.000
88A87LEU00.0090.00629.369-0.007-0.0070.0000.0000.0000.000
89A88ARG10.8810.91431.4940.1290.1290.0000.0000.0000.000
90A89GLU-1-0.759-0.85334.429-0.073-0.0730.0000.0000.0000.000
91A90ASP-1-0.856-0.93234.701-0.112-0.1120.0000.0000.0000.000
92A91THR0-0.007-0.01436.358-0.005-0.0050.0000.0000.0000.000
93A92ASP-1-0.805-0.90936.901-0.091-0.0910.0000.0000.0000.000
94A93PRO00.0090.00338.310-0.002-0.0020.0000.0000.0000.000
95A94ALA00.0460.02138.1320.0000.0000.0000.0000.0000.000
96A95VAL0-0.023-0.02432.716-0.004-0.0040.0000.0000.0000.000
97A96VAL0-0.011-0.00634.990-0.001-0.0010.0000.0000.0000.000
98A97ASP-1-0.848-0.91937.330-0.071-0.0710.0000.0000.0000.000
99A98ARG10.7440.84131.7280.1230.1230.0000.0000.0000.000
100A99LEU0-0.0180.00029.967-0.003-0.0030.0000.0000.0000.000
101A100TRP00.0170.02033.2300.0020.0020.0000.0000.0000.000
102A101ASN0-0.031-0.02932.8200.0040.0040.0000.0000.0000.000
103A102PRO00.032-0.00135.9560.0020.0020.0000.0000.0000.000
104A103TYR0-0.014-0.00432.7390.0020.0020.0000.0000.0000.000
105A104VAL0-0.0060.00734.2280.0020.0020.0000.0000.0000.000
106A105ALA0-0.014-0.01736.8560.0030.0030.0000.0000.0000.000
107A106ALA0-0.016-0.00739.5510.0030.0030.0000.0000.0000.000
108A107TRP0-0.070-0.01736.5820.0040.0040.0000.0000.0000.000
109A108TYR0-0.060-0.04738.628-0.002-0.0020.0000.0000.0000.000
110A109GLU-1-0.886-0.93243.873-0.033-0.0330.0000.0000.0000.000
111A110GLY0-0.056-0.03247.2100.0010.0010.0000.0000.0000.000
112A111GLY0-0.015-0.01444.397-0.001-0.0010.0000.0000.0000.000
113A112LYS10.7890.86339.7270.0680.0680.0000.0000.0000.000
114A113ASP-1-0.908-0.94643.453-0.053-0.0530.0000.0000.0000.000
115A114ASP-1-0.846-0.90244.933-0.042-0.0420.0000.0000.0000.000
116A115PRO0-0.003-0.00845.734-0.002-0.0020.0000.0000.0000.000
117A116LYS10.8230.90445.6890.0390.0390.0000.0000.0000.000
118A117LEU00.0130.02539.702-0.002-0.0020.0000.0000.0000.000
119A118ALA0-0.026-0.01439.4730.0010.0010.0000.0000.0000.000
120A119LEU0-0.0070.00233.268-0.001-0.0010.0000.0000.0000.000
121A120LEU00.0120.00233.048-0.001-0.0010.0000.0000.0000.000
122A121ARG10.7660.85929.7240.1370.1370.0000.0000.0000.000
123A122LEU00.0120.01224.9610.0060.0060.0000.0000.0000.000
124A123ASP-1-0.786-0.87226.492-0.173-0.1730.0000.0000.0000.000
125A124ALA0-0.052-0.03721.9080.0050.0050.0000.0000.0000.000
126A125ASP-1-0.886-0.92522.469-0.247-0.2470.0000.0000.0000.000
127A126HIS0-0.070-0.05717.904-0.023-0.0230.0000.0000.0000.000
128A127ALA00.0310.00216.6590.0370.0370.0000.0000.0000.000
129A128GLN0-0.0260.01515.307-0.055-0.0550.0000.0000.0000.000
130A129ILE0-0.017-0.02312.2570.0190.0190.0000.0000.0000.000
131A130TRP0-0.018-0.00712.806-0.004-0.0040.0000.0000.0000.000
132A131LEU0-0.004-0.0028.566-0.044-0.0440.0000.0000.0000.000
133A132ASN0-0.064-0.03212.7600.1050.1050.0000.0000.0000.000
134A133GLY00.0080.01213.6860.0360.0360.0000.0000.0000.000
135A134SER0-0.023-0.01714.278-0.066-0.0660.0000.0000.0000.000
136A135SER00.005-0.00715.7810.0680.0680.0000.0000.0000.000
137A136LEU0-0.022-0.00218.373-0.047-0.0470.0000.0000.0000.000
138A137LEU00.0280.01720.442-0.004-0.0040.0000.0000.0000.000
139A138ALA00.0190.00423.9680.0090.0090.0000.0000.0000.000
140A139GLY00.0330.01226.330-0.010-0.0100.0000.0000.0000.000
141A140ILE0-0.027-0.01628.096-0.011-0.0110.0000.0000.0000.000
142A141LYS10.9250.96731.559-0.157-0.1570.0000.0000.0000.000
143A142VAL00.0130.01033.558-0.006-0.0060.0000.0000.0000.000
144A143LEU0-0.0050.00436.5500.0020.0020.0000.0000.0000.000
145A144LEU00.015-0.00335.3640.0000.0000.0000.0000.0000.000
146A145GLY00.0110.01740.000-0.004-0.0040.0000.0000.0000.000