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

tag_button

FMODB ID: 491LN

Calculation Name: 2NN3-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NN3

Chain ID: C

ChEMBL ID:

UniProt ID: P89116

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 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 235
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3035001.639755
FMO2-HF: Nuclear repulsion 2939397.130309
FMO2-HF: Total energy -95604.509445
FMO2-MP2: Total energy -95877.89438


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(C:46:VAL)


Summations of interaction energy for fragment #1(C:46:VAL)
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.
0.0123.7630.278-1.908-2.1220.004
Interaction energy analysis for fragmet #1(C:46:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : 0.013
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].
3C48ARG10.9530.9603.366-0.2412.7570.027-1.682-1.3440.004
4C49ASN0-0.043-0.0175.8910.5050.5050.0000.0000.0000.000
5C50ALA00.0250.0152.855-0.780-0.1650.251-0.203-0.6630.000
6C51PRO00.0380.0104.2630.0310.1690.000-0.023-0.1150.000
7C52TYR00.0210.0175.8140.0210.0210.0000.0000.0000.000
8C53TYR0-0.020-0.0476.1910.0910.0910.0000.0000.0000.000
9C54ASN0-0.018-0.0175.6330.1320.1320.0000.0000.0000.000
10C55MET0-0.043-0.0106.956-0.077-0.0770.0000.0000.0000.000
11C56ASN0-0.002-0.0198.108-0.041-0.0410.0000.0000.0000.000
12C57HIS0-0.062-0.01510.1690.1170.1170.0000.0000.0000.000
13C58LYS10.7940.86912.916-0.339-0.3390.0000.0000.0000.000
14C59HIS0-0.0100.00116.516-0.027-0.0270.0000.0000.0000.000
15C60ARG10.8880.95913.581-0.259-0.2590.0000.0000.0000.000
16C61GLY00.0680.01416.7210.0000.0000.0000.0000.0000.000
17C62MET0-0.072-0.02419.361-0.003-0.0030.0000.0000.0000.000
18C63ALA00.0420.03222.585-0.003-0.0030.0000.0000.0000.000
19C64ILE0-0.054-0.02824.5440.0010.0010.0000.0000.0000.000
20C65ILE00.0280.00227.896-0.004-0.0040.0000.0000.0000.000
21C66PHE00.0120.00129.8590.0000.0000.0000.0000.0000.000
22C67ASN00.0330.01333.510-0.004-0.0040.0000.0000.0000.000
23C68HIS00.0010.00936.2130.0010.0010.0000.0000.0000.000
24C69GLU-1-0.882-0.93239.5720.0260.0260.0000.0000.0000.000
25C70HIS00.0250.01642.598-0.003-0.0030.0000.0000.0000.000
26C71PHE0-0.004-0.01341.5610.0010.0010.0000.0000.0000.000
27C72ASP-1-0.898-0.92546.4160.0150.0150.0000.0000.0000.000
28C73ILE0-0.041-0.02345.106-0.001-0.0010.0000.0000.0000.000
29C74HIS00.0660.02249.5370.0010.0010.0000.0000.0000.000
30C75SER0-0.102-0.06151.772-0.001-0.0010.0000.0000.0000.000
31C76LEU00.0290.03044.693-0.001-0.0010.0000.0000.0000.000
32C77LYS10.9190.95248.606-0.005-0.0050.0000.0000.0000.000
33C78SER0-0.013-0.00346.7380.0000.0000.0000.0000.0000.000
34C79ARG10.8740.90537.604-0.019-0.0190.0000.0000.0000.000
35C80THR00.0130.00743.2690.0020.0020.0000.0000.0000.000
36C81GLY00.000-0.00741.9840.0000.0000.0000.0000.0000.000
37C82THR00.0610.02538.0020.0000.0000.0000.0000.0000.000
38C83ASN0-0.008-0.03237.3410.0030.0030.0000.0000.0000.000
39C84VAL0-0.0230.00637.5010.0030.0030.0000.0000.0000.000
40C85ASP-1-0.781-0.86634.3190.0330.0330.0000.0000.0000.000
41C86SER0-0.0120.00433.2260.0040.0040.0000.0000.0000.000
42C87ASP-1-0.885-0.94232.5740.0530.0530.0000.0000.0000.000
43C88ASN0-0.055-0.02932.5960.0090.0090.0000.0000.0000.000
44C89LEU00.0900.02826.6260.0060.0060.0000.0000.0000.000
45C90SER00.0210.00028.2860.0100.0100.0000.0000.0000.000
46C91LYS10.8220.90328.461-0.050-0.0500.0000.0000.0000.000
47C92VAL00.0260.02124.8160.0070.0070.0000.0000.0000.000
48C93LEU00.0700.03622.9610.0110.0110.0000.0000.0000.000
49C94LYS10.8880.95123.407-0.077-0.0770.0000.0000.0000.000
50C95THR0-0.095-0.03723.9810.0100.0100.0000.0000.0000.000
51C96LEU00.0300.01919.4620.0100.0100.0000.0000.0000.000
52C97GLY00.0110.00019.3250.0210.0210.0000.0000.0000.000
53C98PHE0-0.017-0.01118.9190.0090.0090.0000.0000.0000.000
54C99LYS10.9130.96022.086-0.109-0.1090.0000.0000.0000.000
55C100VAL0-0.037-0.02724.879-0.006-0.0060.0000.0000.0000.000
56C101THR0-0.032-0.01427.2930.0010.0010.0000.0000.0000.000
57C102VAL00.0200.01530.344-0.002-0.0020.0000.0000.0000.000
58C103PHE00.0150.00630.8710.0000.0000.0000.0000.0000.000
59C104PRO0-0.005-0.01435.456-0.003-0.0030.0000.0000.0000.000
60C105ASN00.0310.02038.590-0.002-0.0020.0000.0000.0000.000
61C106LEU00.0010.02336.012-0.001-0.0010.0000.0000.0000.000
62C107LYS10.8820.91439.956-0.020-0.0200.0000.0000.0000.000
63C108SER00.035-0.01739.0870.0020.0020.0000.0000.0000.000
64C109GLU-1-0.944-0.97138.1090.0110.0110.0000.0000.0000.000
65C110GLU-1-0.819-0.89938.0300.0240.0240.0000.0000.0000.000
66C111ILE0-0.0020.00433.4170.0030.0030.0000.0000.0000.000
67C112ASN00.0270.01033.3500.0010.0010.0000.0000.0000.000
68C113LYS10.9650.98533.299-0.028-0.0280.0000.0000.0000.000
69C114PHE00.0070.00032.1800.0020.0020.0000.0000.0000.000
70C115ILE00.0090.01328.3610.0050.0050.0000.0000.0000.000
71C116GLN0-0.030-0.01228.2610.0000.0000.0000.0000.0000.000
72C117GLN00.0090.00128.9470.0000.0000.0000.0000.0000.000
73C118THR0-0.072-0.05224.9010.0090.0090.0000.0000.0000.000
74C119ALA0-0.028-0.03124.5340.0080.0080.0000.0000.0000.000
75C120GLU-1-0.889-0.90924.7840.0230.0230.0000.0000.0000.000
76C121MET0-0.029-0.01623.9120.0050.0050.0000.0000.0000.000
77C122ASP-1-0.799-0.87319.8260.1310.1310.0000.0000.0000.000
78C123HIS10.8140.90518.316-0.079-0.0790.0000.0000.0000.000
79C124SER00.045-0.01115.5400.0170.0170.0000.0000.0000.000
80C125ASP-1-0.797-0.88314.4020.3360.3360.0000.0000.0000.000
81C126ALA0-0.080-0.03715.9850.0160.0160.0000.0000.0000.000
82C127ASP-1-0.675-0.81212.3050.3930.3930.0000.0000.0000.000
83C128CYS0-0.091-0.04313.345-0.023-0.0230.0000.0000.0000.000
84C129LEU0-0.0070.00616.0180.0010.0010.0000.0000.0000.000
85C130LEU0-0.0260.00719.730-0.008-0.0080.0000.0000.0000.000
86C131VAL00.0190.01122.3850.0020.0020.0000.0000.0000.000
87C132ALA0-0.017-0.00425.903-0.004-0.0040.0000.0000.0000.000
88C133VAL0-0.005-0.00628.5120.0010.0010.0000.0000.0000.000
89C134LEU0-0.026-0.01232.005-0.001-0.0010.0000.0000.0000.000
90C135THR0-0.007-0.03734.9200.0000.0000.0000.0000.0000.000
91C136ALA00.0300.02738.083-0.001-0.0010.0000.0000.0000.000
92C137GLY00.011-0.00939.6960.0000.0000.0000.0000.0000.000
93C138GLU-1-0.852-0.90339.457-0.010-0.0100.0000.0000.0000.000
94C139LEU00.016-0.00932.9970.0010.0010.0000.0000.0000.000
95C140GLY00.000-0.01234.664-0.001-0.0010.0000.0000.0000.000
96C141MET0-0.046-0.01236.779-0.002-0.0020.0000.0000.0000.000
97C142LEU00.0030.02233.0750.0010.0010.0000.0000.0000.000
98C143TYR00.0430.01737.734-0.001-0.0010.0000.0000.0000.000
99C144ALA0-0.0220.01838.9250.0020.0020.0000.0000.0000.000
100C145LYS10.8290.91440.424-0.021-0.0210.0000.0000.0000.000
101C146ASP-1-0.768-0.87542.9990.0120.0120.0000.0000.0000.000
102C147THR00.0170.00142.449-0.002-0.0020.0000.0000.0000.000
103C148HIS0-0.004-0.00741.0130.0010.0010.0000.0000.0000.000
104C149TYR00.008-0.00133.8390.0000.0000.0000.0000.0000.000
105C150LYS10.9460.95535.2960.0130.0130.0000.0000.0000.000
106C151PRO00.0210.01631.7830.0010.0010.0000.0000.0000.000
107C152ASP-1-0.760-0.87929.844-0.014-0.0140.0000.0000.0000.000
108C153ASN0-0.061-0.04129.6750.0010.0010.0000.0000.0000.000
109C154LEU0-0.0160.00228.7560.0040.0040.0000.0000.0000.000
110C155TRP00.0380.01324.7220.0060.0060.0000.0000.0000.000
111C156TYR0-0.050-0.01125.355-0.005-0.0050.0000.0000.0000.000
112C157TYR0-0.015-0.01726.658-0.006-0.0060.0000.0000.0000.000
113C158PHE00.023-0.00421.7640.0070.0070.0000.0000.0000.000
114C159THR0-0.068-0.04520.9720.0040.0040.0000.0000.0000.000
115C160ALA00.0530.02318.0120.0070.0070.0000.0000.0000.000
116C161ASP-1-0.804-0.86919.704-0.036-0.0360.0000.0000.0000.000
117C162LYS10.8340.91022.8430.0310.0310.0000.0000.0000.000
118C163CYS0-0.069-0.03220.9240.0170.0170.0000.0000.0000.000
119C164PRO00.0200.01518.7730.0060.0060.0000.0000.0000.000
120C165THR0-0.035-0.01917.0920.0020.0020.0000.0000.0000.000
121C166LEU0-0.004-0.01816.0920.0300.0300.0000.0000.0000.000
122C167ALA00.0010.01314.835-0.009-0.0090.0000.0000.0000.000
123C168GLY0-0.047-0.01811.3340.0180.0180.0000.0000.0000.000
124C169LYS10.8270.93111.240-0.214-0.2140.0000.0000.0000.000
125C170PRO0-0.0160.00812.218-0.037-0.0370.0000.0000.0000.000
126C171LYS10.8510.92815.1600.0130.0130.0000.0000.0000.000
127C172LEU0-0.025-0.01317.228-0.014-0.0140.0000.0000.0000.000
128C173PHE00.002-0.01021.0960.0050.0050.0000.0000.0000.000
129C174PHE00.007-0.00221.943-0.006-0.0060.0000.0000.0000.000
130C175ILE00.0130.01327.0750.0030.0030.0000.0000.0000.000
131C176GLN00.010-0.04930.672-0.002-0.0020.0000.0000.0000.000
132C177ALA0-0.003-0.02233.6010.0020.0020.0000.0000.0000.000
133C178CYM-1-0.828-0.77636.7310.0110.0110.0000.0000.0000.000
134C179GLN0-0.011-0.03139.374-0.001-0.0010.0000.0000.0000.000
135C180GLY0-0.0030.00640.700-0.001-0.0010.0000.0000.0000.000
136C181ASP-1-0.876-0.92242.347-0.005-0.0050.0000.0000.0000.000
137C182ARG10.8660.92438.9100.0100.0100.0000.0000.0000.000
138C183LEU00.0130.00244.805-0.001-0.0010.0000.0000.0000.000
139C184ASP-1-0.926-0.94944.708-0.016-0.0160.0000.0000.0000.000
140C185GLY0-0.0250.00146.840-0.001-0.0010.0000.0000.0000.000
141C186GLY00.014-0.01250.3180.0010.0010.0000.0000.0000.000
142C187ILE0-0.039-0.00253.3050.0010.0010.0000.0000.0000.000
143C201SER00.0520.02033.9740.0000.0000.0000.0000.0000.000
144C202TYR0-0.046-0.03227.8530.0020.0020.0000.0000.0000.000
145C203ARG10.8530.91530.3960.0220.0220.0000.0000.0000.000
146C204ILE00.0240.00125.5970.0030.0030.0000.0000.0000.000
147C205PRO0-0.0260.00823.792-0.006-0.0060.0000.0000.0000.000
148C206VAL00.0260.00023.052-0.002-0.0020.0000.0000.0000.000
149C207HIS00.006-0.00719.102-0.004-0.0040.0000.0000.0000.000
150C208ALA00.0250.02314.9220.0100.0100.0000.0000.0000.000
151C209ASP-1-0.814-0.88913.169-0.066-0.0660.0000.0000.0000.000
152C210PHE00.0050.01015.9090.0260.0260.0000.0000.0000.000
153C211LEU0-0.028-0.01419.009-0.009-0.0090.0000.0000.0000.000
154C212ILE00.002-0.00620.8180.0090.0090.0000.0000.0000.000
155C213ALA0-0.0110.01524.542-0.006-0.0060.0000.0000.0000.000
156C214PHE00.0490.01126.5170.0050.0050.0000.0000.0000.000
157C215SER0-0.027-0.03130.166-0.003-0.0030.0000.0000.0000.000
158C216THR0-0.079-0.03433.180-0.004-0.0040.0000.0000.0000.000
159C217VAL00.0780.03235.290-0.001-0.0010.0000.0000.0000.000
160C218PRO0-0.035-0.01237.9170.0020.0020.0000.0000.0000.000
161C219GLY00.0300.02739.9130.0010.0010.0000.0000.0000.000
162C220TYR0-0.091-0.10339.2790.0020.0020.0000.0000.0000.000
163C221PHE00.0560.04836.711-0.001-0.0010.0000.0000.0000.000
164C222SER00.015-0.01241.9840.0000.0000.0000.0000.0000.000
165C223TRP0-0.065-0.02145.2100.0000.0000.0000.0000.0000.000
166C224ARG10.9710.98446.816-0.021-0.0210.0000.0000.0000.000
167C225ASN00.0500.01850.5580.0000.0000.0000.0000.0000.000
168C226THR0-0.045-0.00448.0420.0000.0000.0000.0000.0000.000
169C227THR00.0720.01044.2780.0000.0000.0000.0000.0000.000
170C228ARG10.8360.90941.871-0.028-0.0280.0000.0000.0000.000
171C229GLY00.0490.04737.8230.0010.0010.0000.0000.0000.000
172C230SER00.021-0.01835.893-0.002-0.0020.0000.0000.0000.000
173C231TRP00.0590.02735.7010.0020.0020.0000.0000.0000.000
174C232PHE00.0140.00428.4340.0030.0030.0000.0000.0000.000
175C233MET0-0.002-0.00429.5630.0050.0050.0000.0000.0000.000
176C234GLN0-0.040-0.01631.1590.0050.0050.0000.0000.0000.000
177C235ALA00.0270.01830.6470.0040.0040.0000.0000.0000.000
178C236LEU00.0260.00124.8210.0030.0030.0000.0000.0000.000
179C237CYS0-0.063-0.02626.4020.0090.0090.0000.0000.0000.000
180C238GLU-1-0.850-0.92227.1530.0410.0410.0000.0000.0000.000
181C239GLU-1-0.858-0.92224.8100.0430.0430.0000.0000.0000.000
182C240LEU0-0.016-0.01721.4070.0070.0070.0000.0000.0000.000
183C241ARG10.8710.95323.056-0.054-0.0540.0000.0000.0000.000
184C242TYR0-0.038-0.01624.3440.0080.0080.0000.0000.0000.000
185C243ALA00.027-0.01422.715-0.007-0.0070.0000.0000.0000.000
186C244GLY0-0.0160.00519.9870.0040.0040.0000.0000.0000.000
187C245THR0-0.057-0.01916.5640.0100.0100.0000.0000.0000.000
188C246GLU-1-0.870-0.93616.2590.1650.1650.0000.0000.0000.000
189C247ARG10.8310.91416.806-0.059-0.0590.0000.0000.0000.000
190C248ASP-1-0.792-0.86714.6950.0120.0120.0000.0000.0000.000
191C249ILE00.008-0.01516.065-0.007-0.0070.0000.0000.0000.000
192C250LEU0-0.006-0.00317.661-0.004-0.0040.0000.0000.0000.000
193C251THR0-0.009-0.01718.479-0.007-0.0070.0000.0000.0000.000
194C252LEU0-0.0010.00219.9640.0000.0000.0000.0000.0000.000
195C253LEU0-0.019-0.00921.651-0.002-0.0020.0000.0000.0000.000
196C254THR0-0.012-0.01023.224-0.005-0.0050.0000.0000.0000.000
197C255PHE0-0.003-0.00723.251-0.001-0.0010.0000.0000.0000.000
198C256VAL0-0.042-0.01526.1650.0010.0010.0000.0000.0000.000
199C257CYS0-0.031-0.01327.682-0.002-0.0020.0000.0000.0000.000
200C258GLN00.0050.00929.8040.0000.0000.0000.0000.0000.000
201C259LYS10.8700.93029.357-0.033-0.0330.0000.0000.0000.000
202C260VAL00.0290.01532.4850.0000.0000.0000.0000.0000.000
203C261ALA0-0.090-0.06033.931-0.001-0.0010.0000.0000.0000.000
204C262LEU0-0.071-0.05034.519-0.002-0.0020.0000.0000.0000.000
205C263ASP-1-0.828-0.89437.2120.0140.0140.0000.0000.0000.000
206C264PHE0-0.077-0.04739.1000.0000.0000.0000.0000.0000.000
207C265GLU-1-0.976-0.99440.9310.0030.0030.0000.0000.0000.000
208C266SER00.0210.02643.2230.0010.0010.0000.0000.0000.000
209C267ASN0-0.110-0.07142.2820.0000.0000.0000.0000.0000.000
210C268ALA0-0.0010.00945.270-0.001-0.0010.0000.0000.0000.000
211C269PRO0-0.030-0.00646.6830.0000.0000.0000.0000.0000.000
212C270ASP-1-0.792-0.89749.344-0.001-0.0010.0000.0000.0000.000
213C271SER0-0.088-0.06351.478-0.001-0.0010.0000.0000.0000.000
214C272ALA0-0.065-0.00951.589-0.001-0.0010.0000.0000.0000.000
215C273MET00.0360.01750.937-0.001-0.0010.0000.0000.0000.000
216C274MET0-0.001-0.00749.5490.0000.0000.0000.0000.0000.000
217C275HIS0-0.025-0.00244.3370.0010.0010.0000.0000.0000.000
218C276GLN00.000-0.02844.1940.0000.0000.0000.0000.0000.000
219C277GLN0-0.0240.00437.6600.0030.0030.0000.0000.0000.000
220C278LYS10.9550.97836.3430.0110.0110.0000.0000.0000.000
221C279GLN0-0.0400.01537.600-0.004-0.0040.0000.0000.0000.000
222C280VAL00.004-0.00632.5570.0020.0020.0000.0000.0000.000
223C281PRO00.0240.00129.687-0.001-0.0010.0000.0000.0000.000
224C282CYS0-0.036-0.00529.795-0.005-0.0050.0000.0000.0000.000
225C283ILE00.0240.00023.3650.0040.0040.0000.0000.0000.000
226C284THR0-0.0090.00824.384-0.009-0.0090.0000.0000.0000.000
227C285SER00.048-0.00318.6740.0120.0120.0000.0000.0000.000
228C286MET0-0.034-0.00519.060-0.008-0.0080.0000.0000.0000.000
229C287LEU0-0.036-0.00114.617-0.011-0.0110.0000.0000.0000.000
230C288THR0-0.042-0.03711.727-0.025-0.0250.0000.0000.0000.000
231C289ARG10.8270.9204.9960.1530.1530.0000.0000.0000.000
232C290LEU00.0390.02410.5170.0230.0230.0000.0000.0000.000
233C291LEU0-0.011-0.01710.6490.0450.0450.0000.0000.0000.000
234C292VAL00.0420.01911.726-0.021-0.0210.0000.0000.0000.000
235C293PHE00.0240.01912.4810.0540.0540.0000.0000.0000.000