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: 521NZ

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 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 235
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3042777.388438
FMO2-HF: Nuclear repulsion 2947171.512994
FMO2-HF: Total energy -95605.875444
FMO2-MP2: Total energy -95879.145352


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.
0.6063.5560.557-1.374-2.1340.003
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 : 0.028 / q_NPA : 0.017
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].
3C48ARG10.9660.9623.4320.5302.7460.016-1.082-1.1500.003
4C49ASN0-0.049-0.0255.8620.3450.3450.0000.0000.0000.000
5C50ALA00.0390.0262.520-0.623-0.0400.540-0.263-0.8610.000
6C51PRO00.0360.0094.083-0.1230.0280.001-0.029-0.1230.000
7C52TYR00.0260.0216.217-0.026-0.0260.0000.0000.0000.000
8C53TYR0-0.026-0.0536.2600.0810.0810.0000.0000.0000.000
9C54ASN0-0.010-0.0105.9180.1720.1720.0000.0000.0000.000
10C55MET0-0.058-0.0167.179-0.061-0.0610.0000.0000.0000.000
11C56ASN0-0.010-0.0177.608-0.018-0.0180.0000.0000.0000.000
12C57HIS0-0.073-0.02410.3120.0600.0600.0000.0000.0000.000
13C58LYS10.8050.88312.721-0.220-0.2200.0000.0000.0000.000
14C59HIS0-0.011-0.00716.302-0.020-0.0200.0000.0000.0000.000
15C60ARG10.8540.93813.847-0.197-0.1970.0000.0000.0000.000
16C61GLY00.0710.02316.703-0.006-0.0060.0000.0000.0000.000
17C62MET0-0.067-0.02319.2440.0000.0000.0000.0000.0000.000
18C63ALA00.0290.01822.312-0.002-0.0020.0000.0000.0000.000
19C64ILE0-0.050-0.02024.6970.0010.0010.0000.0000.0000.000
20C65ILE00.0300.01528.084-0.003-0.0030.0000.0000.0000.000
21C66PHE00.0250.01029.9880.0000.0000.0000.0000.0000.000
22C67ASN00.0190.00733.735-0.002-0.0020.0000.0000.0000.000
23C68HIS0-0.006-0.00336.5000.0010.0010.0000.0000.0000.000
24C69GLU-1-0.808-0.90340.0060.0180.0180.0000.0000.0000.000
25C70HIS0-0.007-0.00242.934-0.002-0.0020.0000.0000.0000.000
26C71PHE0-0.003-0.01141.9450.0000.0000.0000.0000.0000.000
27C72ASP-1-0.851-0.90046.7510.0070.0070.0000.0000.0000.000
28C73ILE0-0.019-0.00845.482-0.001-0.0010.0000.0000.0000.000
29C74HIS00.0540.02749.9240.0010.0010.0000.0000.0000.000
30C75SER0-0.067-0.03852.440-0.001-0.0010.0000.0000.0000.000
31C76LEU00.0530.03345.2030.0000.0000.0000.0000.0000.000
32C77LYS10.8670.93248.420-0.001-0.0010.0000.0000.0000.000
33C78SER0-0.006-0.00246.6860.0000.0000.0000.0000.0000.000
34C79ARG10.8330.85638.125-0.011-0.0110.0000.0000.0000.000
35C80THR00.006-0.00742.8030.0010.0010.0000.0000.0000.000
36C81GLY00.0240.01442.5290.0000.0000.0000.0000.0000.000
37C82THR00.0250.00838.0690.0010.0010.0000.0000.0000.000
38C83ASN00.008-0.01737.4000.0010.0010.0000.0000.0000.000
39C84VAL0-0.027-0.00337.1780.0030.0030.0000.0000.0000.000
40C85ASP-1-0.799-0.87434.1580.0260.0260.0000.0000.0000.000
41C86SER0-0.034-0.02132.9800.0030.0030.0000.0000.0000.000
42C87ASP-1-0.858-0.92232.3580.0390.0390.0000.0000.0000.000
43C88ASN0-0.016-0.00532.8250.0090.0090.0000.0000.0000.000
44C89LEU00.0830.03426.6230.0050.0050.0000.0000.0000.000
45C90SER00.0310.00628.0860.0080.0080.0000.0000.0000.000
46C91LYS10.8270.90728.626-0.042-0.0420.0000.0000.0000.000
47C92VAL00.0020.01324.8000.0060.0060.0000.0000.0000.000
48C93LEU00.0460.02222.9460.0090.0090.0000.0000.0000.000
49C94LYS10.8640.93423.517-0.060-0.0600.0000.0000.0000.000
50C95THR0-0.039-0.02024.2620.0070.0070.0000.0000.0000.000
51C96LEU00.0040.01919.4760.0090.0090.0000.0000.0000.000
52C97GLY00.0330.01919.3030.0150.0150.0000.0000.0000.000
53C98PHE00.006-0.00519.0680.0040.0040.0000.0000.0000.000
54C99LYS10.8990.95822.182-0.074-0.0740.0000.0000.0000.000
55C100VAL0-0.041-0.03124.774-0.007-0.0070.0000.0000.0000.000
56C101THR0-0.052-0.02327.0920.0020.0020.0000.0000.0000.000
57C102VAL00.0180.00730.173-0.001-0.0010.0000.0000.0000.000
58C103PHE00.0130.00130.7340.0000.0000.0000.0000.0000.000
59C104PRO00.021-0.00235.450-0.002-0.0020.0000.0000.0000.000
60C105ASN0-0.009-0.01238.642-0.002-0.0020.0000.0000.0000.000
61C106LEU00.0200.03036.129-0.001-0.0010.0000.0000.0000.000
62C107LYS10.9020.93740.138-0.006-0.0060.0000.0000.0000.000
63C108SER00.008-0.01738.9010.0010.0010.0000.0000.0000.000
64C109GLU-1-0.919-0.96137.862-0.002-0.0020.0000.0000.0000.000
65C110GLU-1-0.825-0.89938.0040.0100.0100.0000.0000.0000.000
66C111ILE00.0050.00233.7100.0020.0020.0000.0000.0000.000
67C112ASN00.0180.01033.5710.0000.0000.0000.0000.0000.000
68C113LYS10.8820.93233.213-0.012-0.0120.0000.0000.0000.000
69C114PHE0-0.015-0.00732.3010.0020.0020.0000.0000.0000.000
70C115ILE0-0.0220.00028.5280.0030.0030.0000.0000.0000.000
71C116GLN00.0020.00828.4040.0000.0000.0000.0000.0000.000
72C117GLN00.0150.01128.901-0.002-0.0020.0000.0000.0000.000
73C118THR0-0.017-0.02024.8240.0060.0060.0000.0000.0000.000
74C119ALA0-0.008-0.00424.3930.0050.0050.0000.0000.0000.000
75C120GLU-1-0.882-0.92324.445-0.007-0.0070.0000.0000.0000.000
76C121MET0-0.044-0.02224.5180.0050.0050.0000.0000.0000.000
77C122ASP-1-0.797-0.86619.4010.0540.0540.0000.0000.0000.000
78C123HIS10.8020.88318.406-0.034-0.0340.0000.0000.0000.000
79C124SER00.0420.00515.2840.0040.0040.0000.0000.0000.000
80C125ASP-1-0.799-0.89514.1280.2270.2270.0000.0000.0000.000
81C126ALA0-0.037-0.01315.9800.0190.0190.0000.0000.0000.000
82C127ASP-1-0.691-0.82412.4030.2560.2560.0000.0000.0000.000
83C128CYS0-0.099-0.03813.387-0.021-0.0210.0000.0000.0000.000
84C129LEU0-0.0040.00616.1130.0030.0030.0000.0000.0000.000
85C130LEU0-0.0230.00219.842-0.005-0.0050.0000.0000.0000.000
86C131VAL00.0120.00322.5020.0020.0020.0000.0000.0000.000
87C132ALA0-0.010-0.00626.062-0.001-0.0010.0000.0000.0000.000
88C133VAL0-0.008-0.00928.7370.0000.0000.0000.0000.0000.000
89C134LEU0-0.0170.00532.181-0.001-0.0010.0000.0000.0000.000
90C135THR00.001-0.02135.2880.0010.0010.0000.0000.0000.000
91C136ALA00.0350.01938.3070.0000.0000.0000.0000.0000.000
92C137GLY0-0.009-0.02639.3610.0000.0000.0000.0000.0000.000
93C138GLU-1-0.810-0.90339.417-0.014-0.0140.0000.0000.0000.000
94C139LEU00.0360.01633.1760.0000.0000.0000.0000.0000.000
95C140GLY00.024-0.00134.848-0.002-0.0020.0000.0000.0000.000
96C141MET0-0.058-0.01136.949-0.002-0.0020.0000.0000.0000.000
97C142LEU0-0.0220.00233.5410.0020.0020.0000.0000.0000.000
98C143TYR00.0430.01438.120-0.001-0.0010.0000.0000.0000.000
99C144ALA0-0.0270.01838.9670.0020.0020.0000.0000.0000.000
100C145LYS10.8000.88640.587-0.009-0.0090.0000.0000.0000.000
101C146ASP-1-0.747-0.87543.1540.0020.0020.0000.0000.0000.000
102C147THR00.000-0.00342.471-0.001-0.0010.0000.0000.0000.000
103C148HIS0-0.0080.00041.2590.0010.0010.0000.0000.0000.000
104C149TYR00.006-0.00334.2340.0000.0000.0000.0000.0000.000
105C150LYS10.9400.94735.3860.0210.0210.0000.0000.0000.000
106C151PRO00.0050.01032.0140.0000.0000.0000.0000.0000.000
107C152ASP-1-0.766-0.88129.874-0.026-0.0260.0000.0000.0000.000
108C153ASN0-0.043-0.03030.110-0.001-0.0010.0000.0000.0000.000
109C154LEU0-0.0040.00429.0770.0010.0010.0000.0000.0000.000
110C155TRP00.0400.01025.0380.0040.0040.0000.0000.0000.000
111C156TYR0-0.048-0.01425.478-0.006-0.0060.0000.0000.0000.000
112C157TYR00.014-0.02126.826-0.006-0.0060.0000.0000.0000.000
113C158PHE0-0.012-0.00221.9670.0010.0010.0000.0000.0000.000
114C159THR0-0.055-0.04921.0830.0010.0010.0000.0000.0000.000
115C160ALA00.0320.00417.9880.0050.0050.0000.0000.0000.000
116C161ASP-1-0.818-0.86819.808-0.070-0.0700.0000.0000.0000.000
117C162LYS10.8000.90023.0390.0550.0550.0000.0000.0000.000
118C163CYS0-0.033-0.01021.1430.0130.0130.0000.0000.0000.000
119C164PRO00.0500.02218.6150.0000.0000.0000.0000.0000.000
120C165THR0-0.014-0.01316.710-0.006-0.0060.0000.0000.0000.000
121C166LEU00.004-0.00515.9140.0220.0220.0000.0000.0000.000
122C167ALA0-0.007-0.00414.839-0.008-0.0080.0000.0000.0000.000
123C168GLY0-0.040-0.01411.0740.0000.0000.0000.0000.0000.000
124C169LYS10.8020.91410.816-0.083-0.0830.0000.0000.0000.000
125C170PRO0-0.0220.00812.433-0.023-0.0230.0000.0000.0000.000
126C171LYS10.8430.93215.3610.0600.0600.0000.0000.0000.000
127C172LEU0-0.018-0.01017.611-0.009-0.0090.0000.0000.0000.000
128C173PHE0-0.001-0.00521.4770.0040.0040.0000.0000.0000.000
129C174PHE00.0200.00322.259-0.004-0.0040.0000.0000.0000.000
130C175ILE0-0.009-0.00227.4770.0020.0020.0000.0000.0000.000
131C176GLN00.044-0.04431.123-0.001-0.0010.0000.0000.0000.000
132C177ALA00.002-0.01634.0970.0010.0010.0000.0000.0000.000
133C178CYM-1-0.857-0.72637.0200.0060.0060.0000.0000.0000.000
134C179GLN0-0.050-0.02739.689-0.001-0.0010.0000.0000.0000.000
135C180GLY00.0260.02140.833-0.001-0.0010.0000.0000.0000.000
136C181ASP-1-0.830-0.88542.152-0.006-0.0060.0000.0000.0000.000
137C182ARG10.8120.88139.0740.0100.0100.0000.0000.0000.000
138C183LEU00.0070.00845.357-0.001-0.0010.0000.0000.0000.000
139C184ASP-1-0.932-0.95744.674-0.018-0.0180.0000.0000.0000.000
140C185GLY00.004-0.00247.206-0.001-0.0010.0000.0000.0000.000
141C186GLY00.000-0.00650.7400.0010.0010.0000.0000.0000.000
142C187ILE0-0.0340.00253.8530.0000.0000.0000.0000.0000.000
143C201SER00.018-0.00234.1560.0010.0010.0000.0000.0000.000
144C202TYR0-0.026-0.01728.1990.0000.0000.0000.0000.0000.000
145C203ARG10.8450.91330.5280.0340.0340.0000.0000.0000.000
146C204ILE00.0480.01125.9140.0010.0010.0000.0000.0000.000
147C205PRO0-0.0230.00923.703-0.005-0.0050.0000.0000.0000.000
148C206VAL00.0280.00923.391-0.003-0.0030.0000.0000.0000.000
149C207HIS0-0.005-0.01419.310-0.010-0.0100.0000.0000.0000.000
150C208ALA00.0360.02515.1990.0090.0090.0000.0000.0000.000
151C209ASP-1-0.785-0.86713.161-0.106-0.1060.0000.0000.0000.000
152C210PHE00.0020.00515.8750.0200.0200.0000.0000.0000.000
153C211LEU0-0.014-0.01119.315-0.006-0.0060.0000.0000.0000.000
154C212ILE0-0.012-0.00521.0940.0070.0070.0000.0000.0000.000
155C213ALA0-0.0080.00124.912-0.003-0.0030.0000.0000.0000.000
156C214PHE00.0370.00926.9450.0040.0040.0000.0000.0000.000
157C215SER00.000-0.01130.652-0.003-0.0030.0000.0000.0000.000
158C216THR0-0.055-0.03033.247-0.003-0.0030.0000.0000.0000.000
159C217VAL00.0760.02735.3810.0000.0000.0000.0000.0000.000
160C218PRO0-0.035-0.00438.0580.0020.0020.0000.0000.0000.000
161C219GLY00.0180.01839.5630.0000.0000.0000.0000.0000.000
162C220TYR0-0.059-0.10439.2660.0020.0020.0000.0000.0000.000
163C221PHE00.0660.04837.0530.0000.0000.0000.0000.0000.000
164C222SER00.025-0.01442.4140.0000.0000.0000.0000.0000.000
165C223TRP0-0.072-0.01745.7610.0000.0000.0000.0000.0000.000
166C224ARG10.9510.96847.287-0.017-0.0170.0000.0000.0000.000
167C225ASN00.0500.02050.8130.0000.0000.0000.0000.0000.000
168C226THR0-0.042-0.01047.7780.0000.0000.0000.0000.0000.000
169C227THR00.0590.01443.9970.0010.0010.0000.0000.0000.000
170C228ARG10.8650.91341.905-0.023-0.0230.0000.0000.0000.000
171C229GLY00.0140.03737.8590.0010.0010.0000.0000.0000.000
172C230SER00.004-0.03636.044-0.002-0.0020.0000.0000.0000.000
173C231TRP00.0060.00735.5870.0020.0020.0000.0000.0000.000
174C232PHE00.0360.01528.3660.0020.0020.0000.0000.0000.000
175C233MET00.0130.01330.0480.0040.0040.0000.0000.0000.000
176C234GLN0-0.032-0.01731.1520.0040.0040.0000.0000.0000.000
177C235ALA00.0640.03930.8890.0040.0040.0000.0000.0000.000
178C236LEU00.009-0.00524.9360.0040.0040.0000.0000.0000.000
179C237CYS0-0.087-0.05426.7080.0070.0070.0000.0000.0000.000
180C238GLU-1-0.858-0.91128.2040.0390.0390.0000.0000.0000.000
181C239GLU-1-0.827-0.89924.6660.0480.0480.0000.0000.0000.000
182C240LEU0-0.022-0.03121.8090.0080.0080.0000.0000.0000.000
183C241ARG10.8610.92923.091-0.049-0.0490.0000.0000.0000.000
184C242TYR0-0.020-0.01925.0450.0060.0060.0000.0000.0000.000
185C243ALA00.0370.01922.476-0.001-0.0010.0000.0000.0000.000
186C244GLY0-0.0010.01420.0610.0040.0040.0000.0000.0000.000
187C245THR0-0.103-0.05216.4360.0140.0140.0000.0000.0000.000
188C246GLU-1-0.853-0.92816.0930.1640.1640.0000.0000.0000.000
189C247ARG10.8350.91417.303-0.062-0.0620.0000.0000.0000.000
190C248ASP-1-0.789-0.86314.8640.0290.0290.0000.0000.0000.000
191C249ILE00.019-0.01116.498-0.009-0.0090.0000.0000.0000.000
192C250LEU0-0.0030.00417.641-0.006-0.0060.0000.0000.0000.000
193C251THR0-0.007-0.02018.408-0.007-0.0070.0000.0000.0000.000
194C252LEU0-0.039-0.01619.817-0.001-0.0010.0000.0000.0000.000
195C253LEU0-0.001-0.01022.131-0.003-0.0030.0000.0000.0000.000
196C254THR00.0010.00623.362-0.006-0.0060.0000.0000.0000.000
197C255PHE00.003-0.00223.215-0.001-0.0010.0000.0000.0000.000
198C256VAL0-0.074-0.02926.2400.0000.0000.0000.0000.0000.000
199C257CYS0-0.036-0.02527.891-0.002-0.0020.0000.0000.0000.000
200C258GLN0-0.016-0.01329.526-0.001-0.0010.0000.0000.0000.000
201C259LYS10.8280.91229.078-0.033-0.0330.0000.0000.0000.000
202C260VAL00.0750.04232.931-0.001-0.0010.0000.0000.0000.000
203C261ALA0-0.092-0.04834.148-0.001-0.0010.0000.0000.0000.000
204C262LEU0-0.058-0.04334.671-0.002-0.0020.0000.0000.0000.000
205C263ASP-1-0.817-0.90236.9540.0150.0150.0000.0000.0000.000
206C264PHE0-0.084-0.04938.974-0.001-0.0010.0000.0000.0000.000
207C265GLU-1-0.927-0.96040.8280.0060.0060.0000.0000.0000.000
208C266SER00.0080.01343.6850.0000.0000.0000.0000.0000.000
209C267ASN0-0.106-0.07242.6770.0000.0000.0000.0000.0000.000
210C268ALA00.0080.01245.7730.0000.0000.0000.0000.0000.000
211C269PRO0-0.062-0.01646.8330.0000.0000.0000.0000.0000.000
212C270ASP-1-0.773-0.89348.6820.0000.0000.0000.0000.0000.000
213C271SER0-0.075-0.05351.185-0.001-0.0010.0000.0000.0000.000
214C272ALA0-0.044-0.01751.362-0.001-0.0010.0000.0000.0000.000
215C273MET0-0.0020.00551.144-0.001-0.0010.0000.0000.0000.000
216C274MET0-0.028-0.02049.9010.0000.0000.0000.0000.0000.000
217C275HIS0-0.010-0.00544.4260.0000.0000.0000.0000.0000.000
218C276GLN0-0.006-0.01344.1750.0000.0000.0000.0000.0000.000
219C277GLN0-0.0100.01037.9420.0030.0030.0000.0000.0000.000
220C278LYS10.9530.98936.4720.0060.0060.0000.0000.0000.000
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