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: 769KK

Calculation Name: 2NN6-I-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NN6

Chain ID: I

ChEMBL ID:

UniProt ID: Q9Y3B2

Base Structure: X-ray

Registration Date: 2023-09-24

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1596978.521123
FMO2-HF: Nuclear repulsion 1526353.629193
FMO2-HF: Total energy -70624.891929
FMO2-MP2: Total energy -70826.621698


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(I:6:ARG)


Summations of interaction energy for fragment #1(I:6:ARG)
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.
-15.748-12.241-0.01-1.576-1.92-0.001
Interaction energy analysis for fragmet #1(I:6:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.963 / q_NPA : 0.976
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].
3I8CYS00.0080.0293.818-2.1440.252-0.035-1.287-1.074-0.001
4I9ILE00.0190.0246.9371.3461.3460.0000.0000.0000.000
5I10PRO00.0300.00010.3840.0740.0740.0000.0000.0000.000
6I11GLY0-0.109-0.06612.8001.2521.2520.0000.0000.0000.000
7I12GLU-1-0.905-0.9478.390-25.658-25.6580.0000.0000.0000.000
8I13ARG10.8880.92712.12416.34816.3480.0000.0000.0000.000
9I14LEU0-0.051-0.0267.141-0.970-0.9700.0000.0000.0000.000
10I15CYS0-0.0080.01011.3950.7810.7810.0000.0000.0000.000
11I16ASN0-0.044-0.08714.176-0.233-0.2330.0000.0000.0000.000
12I17LEU0-0.060-0.02117.486-0.201-0.2010.0000.0000.0000.000
13I18GLU-1-0.879-0.92919.752-12.934-12.9340.0000.0000.0000.000
14I19GLU-1-0.858-0.95814.108-20.882-20.8820.0000.0000.0000.000
15I20GLY00.0630.04516.519-0.049-0.0490.0000.0000.0000.000
16I21SER0-0.048-0.02717.5710.3460.3460.0000.0000.0000.000
17I22PRO00.017-0.00514.587-0.529-0.5290.0000.0000.0000.000
18I23GLY00.0330.00815.6810.8790.8790.0000.0000.0000.000
19I24SER0-0.030-0.05912.1080.8800.8800.0000.0000.0000.000
20I25GLY00.008-0.01912.548-0.509-0.5090.0000.0000.0000.000
21I26THR0-0.0300.02313.325-0.498-0.4980.0000.0000.0000.000
22I27TYR00.0280.01016.0271.0461.0460.0000.0000.0000.000
23I28THR00.0140.01317.145-0.465-0.4650.0000.0000.0000.000
24I29ARG10.9260.95719.69812.23712.2370.0000.0000.0000.000
25I30HIS00.004-0.01521.966-0.341-0.3410.0000.0000.0000.000
26I31GLY00.0820.05322.0430.1050.1050.0000.0000.0000.000
27I32TYR00.0360.03317.100-0.122-0.1220.0000.0000.0000.000
28I33ILE0-0.038-0.00312.5780.3280.3280.0000.0000.0000.000
29I34PHE0-0.0190.00714.042-0.717-0.7170.0000.0000.0000.000
30I35SER00.0300.01210.914-0.295-0.2950.0000.0000.0000.000
31I36SER0-0.023-0.00913.043-0.023-0.0230.0000.0000.0000.000
32I37LEU0-0.030-0.01813.1590.1370.1370.0000.0000.0000.000
33I38ALA00.0430.00611.552-0.417-0.4170.0000.0000.0000.000
34I39GLY00.0460.0379.7741.1681.1680.0000.0000.0000.000
35I40CYS0-0.055-0.0213.652-2.457-2.1230.004-0.146-0.1920.000
36I41LEU00.0470.0363.4852.7423.2650.022-0.116-0.4280.000
37I42MET0-0.015-0.0164.310-4.495-4.241-0.001-0.027-0.2260.000
38I43LYS10.9690.9886.86631.13431.1340.0000.0000.0000.000
39I44SER0-0.002-0.0109.063-0.056-0.0560.0000.0000.0000.000
40I45SER0-0.0150.00912.425-0.561-0.5610.0000.0000.0000.000
41I46GLU-1-0.873-0.92814.730-14.446-14.4460.0000.0000.0000.000
42I47ASN0-0.047-0.02818.383-0.366-0.3660.0000.0000.0000.000
43I48GLY0-0.012-0.03620.8440.6870.6870.0000.0000.0000.000
44I49ALA0-0.070-0.01820.2040.2840.2840.0000.0000.0000.000
45I50LEU00.0240.02717.974-0.083-0.0830.0000.0000.0000.000
46I51PRO0-0.045-0.01612.949-0.005-0.0050.0000.0000.0000.000
47I52VAL00.0260.04014.3460.4130.4130.0000.0000.0000.000
48I53VAL0-0.018-0.0179.956-1.778-1.7780.0000.0000.0000.000
49I54SER0-0.029-0.00510.3761.8931.8930.0000.0000.0000.000
50I55VAL00.0300.0288.758-2.087-2.0870.0000.0000.0000.000
51I56VAL0-0.037-0.0175.9971.2591.2590.0000.0000.0000.000
52I57ARG10.8970.9479.08315.35015.3500.0000.0000.0000.000
53I58GLU-1-0.859-0.93611.099-18.637-18.6370.0000.0000.0000.000
54I59THR0-0.097-0.02612.6620.9340.9340.0000.0000.0000.000
55I60GLU-1-0.852-0.93113.036-17.739-17.7390.0000.0000.0000.000
56I61SER0-0.078-0.02215.6450.6870.6870.0000.0000.0000.000
57I62GLN00.0360.00418.8840.4320.4320.0000.0000.0000.000
58I63LEU0-0.052-0.05221.1550.2800.2800.0000.0000.0000.000
59I64LEU00.0570.01822.067-0.130-0.1300.0000.0000.0000.000
60I65PRO0-0.095-0.02726.2180.0670.0670.0000.0000.0000.000
61I66ASP-1-0.831-0.93229.860-9.128-9.1280.0000.0000.0000.000
62I67VAL00.025-0.00531.5240.2410.2410.0000.0000.0000.000
63I68GLY0-0.0010.02334.9090.1690.1690.0000.0000.0000.000
64I69ALA00.0180.00833.026-0.059-0.0590.0000.0000.0000.000
65I70ILE00.036-0.01034.5790.2280.2280.0000.0000.0000.000
66I71VAL0-0.063-0.03833.483-0.297-0.2970.0000.0000.0000.000
67I72THR00.0180.01733.6240.2470.2470.0000.0000.0000.000
68I73CYS00.000-0.03835.136-0.177-0.1770.0000.0000.0000.000
69I74LYN0-0.0340.02637.6460.1830.1830.0000.0000.0000.000
70I75VAL00.0480.02540.040-0.096-0.0960.0000.0000.0000.000
71I76SER0-0.030-0.01041.616-0.124-0.1240.0000.0000.0000.000
72I77SER0-0.009-0.00143.8820.1320.1320.0000.0000.0000.000
73I78ILE00.0280.00247.246-0.054-0.0540.0000.0000.0000.000
74I79ASN0-0.0010.02250.0770.1930.1930.0000.0000.0000.000
75I80SER00.003-0.00852.626-0.063-0.0630.0000.0000.0000.000
76I81ARG10.9330.96054.1795.3485.3480.0000.0000.0000.000
77I82PHE00.0230.00449.379-0.036-0.0360.0000.0000.0000.000
78I83ALA00.0510.03146.9670.0490.0490.0000.0000.0000.000
79I84LYS10.9290.96442.0156.8606.8600.0000.0000.0000.000
80I85VAL0-0.010-0.00240.1630.0600.0600.0000.0000.0000.000
81I86HIS00.0210.02236.536-0.218-0.2180.0000.0000.0000.000
82I87ILE0-0.0030.02033.1710.0820.0820.0000.0000.0000.000
83I88LEU0-0.036-0.01431.441-0.084-0.0840.0000.0000.0000.000
84I89TYR0-0.0030.01228.029-0.204-0.2040.0000.0000.0000.000
85I90VAL00.0020.01229.6870.2430.2430.0000.0000.0000.000
86I91GLY00.0360.00930.051-0.208-0.2080.0000.0000.0000.000
87I92SER0-0.037-0.04028.6500.0860.0860.0000.0000.0000.000
88I93MET00.0420.02922.169-0.201-0.2010.0000.0000.0000.000
89I94PRO0-0.090-0.03424.116-0.309-0.3090.0000.0000.0000.000
90I95LEU00.1400.07322.0400.3210.3210.0000.0000.0000.000
91I96LYS10.8450.92424.32410.62710.6270.0000.0000.0000.000
92I97ASN00.1000.04126.3740.5410.5410.0000.0000.0000.000
93I98SER0-0.035-0.01327.0280.2760.2760.0000.0000.0000.000
94I99PHE00.0210.01829.0660.1630.1630.0000.0000.0000.000
95I100ARG10.9180.95731.2748.3698.3690.0000.0000.0000.000
96I101GLY00.0040.00133.0370.0320.0320.0000.0000.0000.000
97I102THR0-0.069-0.04035.6340.2670.2670.0000.0000.0000.000
98I103ILE0-0.037-0.01436.542-0.089-0.0890.0000.0000.0000.000
99I104ARG10.8340.93339.7917.2957.2950.0000.0000.0000.000
100I105LYS10.9361.00543.3856.6806.6800.0000.0000.0000.000
101I106GLU-1-0.853-0.94145.659-6.310-6.3100.0000.0000.0000.000
102I107ASP-1-0.801-0.91649.411-5.589-5.5890.0000.0000.0000.000
103I108VAL00.0150.01351.931-0.020-0.0200.0000.0000.0000.000
104I109ARG10.9190.96347.1866.2456.2450.0000.0000.0000.000
105I110ALA0-0.072-0.02847.797-0.144-0.1440.0000.0000.0000.000
106I111THR0-0.063-0.03949.4430.0050.0050.0000.0000.0000.000
107I112GLU-1-0.787-0.91350.206-5.979-5.9790.0000.0000.0000.000
108I113LYS10.8630.94452.5725.6125.6120.0000.0000.0000.000
109I114ASP-1-0.840-0.91655.685-5.492-5.4920.0000.0000.0000.000
110I115LYS10.8680.91355.9895.4295.4290.0000.0000.0000.000
111I116VAL00.0060.01456.1520.0860.0860.0000.0000.0000.000
112I117GLU-1-0.794-0.88555.405-5.245-5.2450.0000.0000.0000.000
113I118ILE00.0410.03050.192-0.038-0.0380.0000.0000.0000.000
114I119TYR0-0.018-0.01952.445-0.086-0.0860.0000.0000.0000.000
115I120LYS10.7850.88654.5985.0955.0950.0000.0000.0000.000
116I121SER00.0580.02150.5760.0020.0020.0000.0000.0000.000
117I122PHE00.0260.01846.962-0.062-0.0620.0000.0000.0000.000
118I123ARG10.8740.94249.0115.6445.6440.0000.0000.0000.000
119I124PRO00.002-0.01147.233-0.092-0.0920.0000.0000.0000.000
120I125GLY00.0330.01145.096-0.138-0.1380.0000.0000.0000.000
121I126ASP-1-0.811-0.92744.235-6.416-6.4160.0000.0000.0000.000
122I127ILE00.0210.00138.649-0.106-0.1060.0000.0000.0000.000
123I128VAL0-0.057-0.01741.1630.1050.1050.0000.0000.0000.000
124I129LEU00.0490.03139.471-0.249-0.2490.0000.0000.0000.000
125I130ALA00.045-0.00839.2490.2180.2180.0000.0000.0000.000
126I131LYS10.8400.91438.2806.9976.9970.0000.0000.0000.000
127I132VAL0-0.054-0.02435.3770.1970.1970.0000.0000.0000.000
128I133ILE0-0.050-0.01738.7070.0710.0710.0000.0000.0000.000
129I134SER00.0230.00439.393-0.178-0.1780.0000.0000.0000.000
130I135LEU00.0190.01635.0730.1210.1210.0000.0000.0000.000
131I136GLY00.0660.03639.184-0.030-0.0300.0000.0000.0000.000
132I137ASP-1-0.866-0.93535.546-8.101-8.1010.0000.0000.0000.000
133I138ALA0-0.060-0.04438.678-0.015-0.0150.0000.0000.0000.000
134I139GLN0-0.023-0.02241.4470.0240.0240.0000.0000.0000.000
135I140SER0-0.0080.01737.2030.0480.0480.0000.0000.0000.000
136I141ASN0-0.013-0.04738.358-0.056-0.0560.0000.0000.0000.000
137I142TYR00.0080.00933.039-0.112-0.1120.0000.0000.0000.000
138I143LEU00.0490.04139.2840.1220.1220.0000.0000.0000.000
139I144LEU00.0770.04538.002-0.148-0.1480.0000.0000.0000.000
140I145THR0-0.038-0.04641.8200.2450.2450.0000.0000.0000.000
141I146THR0-0.018-0.00643.404-0.156-0.1560.0000.0000.0000.000
142I147ALA0-0.068-0.01945.8430.1120.1120.0000.0000.0000.000
143I148GLU-1-0.741-0.88043.200-7.031-7.0310.0000.0000.0000.000
144I149ASN0-0.043-0.02047.0540.1150.1150.0000.0000.0000.000
145I150GLU-1-0.917-0.94541.592-7.170-7.1700.0000.0000.0000.000
146I151LEU0-0.101-0.01240.957-0.076-0.0760.0000.0000.0000.000
147I152GLY0-0.0160.00144.3670.1410.1410.0000.0000.0000.000
148I153VAL0-0.032-0.03644.120-0.173-0.1730.0000.0000.0000.000
149I154VAL0-0.002-0.01041.1700.0690.0690.0000.0000.0000.000
150I155VAL00.0250.01242.190-0.152-0.1520.0000.0000.0000.000
151I156ALA0-0.046-0.00344.9340.1230.1230.0000.0000.0000.000
152I157HIS00.0060.00944.747-0.123-0.1230.0000.0000.0000.000
153I158SER0-0.002-0.02249.7670.0960.0960.0000.0000.0000.000
154I159GLU-1-0.879-0.92353.100-5.230-5.2300.0000.0000.0000.000
155I160SER0-0.023-0.02955.7910.0090.0090.0000.0000.0000.000
156I161GLY00.0390.02851.494-0.030-0.0300.0000.0000.0000.000
157I162ILE0-0.105-0.05450.552-0.098-0.0980.0000.0000.0000.000
158I163GLN00.0480.02746.539-0.095-0.0950.0000.0000.0000.000
159I164MET0-0.054-0.04249.3550.1660.1660.0000.0000.0000.000
160I165VAL00.0320.02249.356-0.142-0.1420.0000.0000.0000.000
161I166PRO00.0300.00549.4590.1020.1020.0000.0000.0000.000
162I167ILE0-0.030-0.00752.3960.0000.0000.0000.0000.0000.000
163I168SER00.0220.00754.9860.0630.0630.0000.0000.0000.000
164I169TRP00.013-0.00153.362-0.092-0.0920.0000.0000.0000.000
165I170CYS0-0.055-0.02453.095-0.092-0.0920.0000.0000.0000.000
166I171GLU-1-0.906-0.96154.213-5.165-5.1650.0000.0000.0000.000
167I172MET00.0150.01848.191-0.080-0.0800.0000.0000.0000.000
168I173GLN0-0.001-0.02353.2960.1270.1270.0000.0000.0000.000
169I174CYS0-0.0970.01353.778-0.104-0.1040.0000.0000.0000.000
170I175PRO0-0.005-0.01153.8100.0950.0950.0000.0000.0000.000
171I176LYS10.9380.96855.9805.5595.5590.0000.0000.0000.000
172I177THR00.0250.01757.6490.1060.1060.0000.0000.0000.000
173I178HIS00.0240.00759.040-0.043-0.0430.0000.0000.0000.000
174I179THR00.018-0.00257.0810.0330.0330.0000.0000.0000.000
175I180LYS10.9961.02157.9684.8024.8020.0000.0000.0000.000
176I181GLU-1-0.817-0.91053.362-5.712-5.7120.0000.0000.0000.000
177I182PHE00.006-0.01455.969-0.004-0.0040.0000.0000.0000.000
178I183ARG10.7870.87148.0466.0776.0770.0000.0000.0000.000
179I184LYS10.8160.90649.1176.1636.1630.0000.0000.0000.000
180I185VAL0-0.0350.01247.289-0.205-0.2050.0000.0000.0000.000