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: K9423

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 OptH
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 -3035568.688852
FMO2-HF: Nuclear repulsion 2939965.956461
FMO2-HF: Total energy -95602.732391
FMO2-MP2: Total energy -95876.320272


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.
-0.392.3830.431-1.15-2.055-0.001
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 : -0.017 / q_NPA : -0.023
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].
3C48ARG10.9490.9493.2700.1852.1000.058-0.886-1.086-0.001
4C49ASN0-0.0110.0015.8220.1230.1230.0000.0000.0000.000
5C50ALA00.0240.0132.767-0.847-0.2240.374-0.235-0.7640.000
6C51PRO00.0370.0124.3190.0650.2180.000-0.024-0.1290.000
7C52TYR00.0230.0175.6840.0780.0780.0000.0000.0000.000
8C53TYR0-0.033-0.0826.0790.0190.0190.0000.0000.0000.000
9C54ASN0-0.023-0.0175.469-0.060-0.0600.0000.0000.0000.000
10C55MET0-0.0260.0006.9160.0610.0610.0000.0000.0000.000
11C56ASN00.007-0.0108.819-0.039-0.0390.0000.0000.0000.000
12C57HIS0-0.093-0.0169.2210.0210.0210.0000.0000.0000.000
13C58LYS10.9000.93912.897-0.026-0.0260.0000.0000.0000.000
14C59HIS0-0.020-0.00116.564-0.001-0.0010.0000.0000.0000.000
15C60ARG10.9240.99213.7840.1170.1170.0000.0000.0000.000
16C61GLY00.0650.01716.656-0.005-0.0050.0000.0000.0000.000
17C62MET0-0.063-0.02019.2840.0010.0010.0000.0000.0000.000
18C63ALA00.0360.02522.513-0.005-0.0050.0000.0000.0000.000
19C64ILE0-0.045-0.02224.4940.0050.0050.0000.0000.0000.000
20C65ILE00.0200.00227.831-0.003-0.0030.0000.0000.0000.000
21C66PHE00.0090.00129.9510.0030.0030.0000.0000.0000.000
22C67ASN00.0540.01333.452-0.003-0.0030.0000.0000.0000.000
23C68HIS00.0270.01536.1760.0010.0010.0000.0000.0000.000
24C69GLU-1-0.947-0.97539.534-0.025-0.0250.0000.0000.0000.000
25C70HIS0-0.0030.00542.5740.0010.0010.0000.0000.0000.000
26C71PHE0-0.007-0.01141.593-0.001-0.0010.0000.0000.0000.000
27C72ASP-1-0.916-0.92746.361-0.017-0.0170.0000.0000.0000.000
28C73ILE0-0.051-0.03245.2330.0000.0000.0000.0000.0000.000
29C74HIS00.0630.02349.501-0.001-0.0010.0000.0000.0000.000
30C75SER0-0.098-0.05951.714-0.001-0.0010.0000.0000.0000.000
31C76LEU00.0350.03344.649-0.001-0.0010.0000.0000.0000.000
32C77LYS10.9210.94848.4850.0210.0210.0000.0000.0000.000
33C78SER0-0.0180.00346.709-0.001-0.0010.0000.0000.0000.000
34C79ARG10.9090.94937.2660.0340.0340.0000.0000.0000.000
35C80THR00.018-0.00343.2680.0000.0000.0000.0000.0000.000
36C81GLY00.0040.00442.011-0.001-0.0010.0000.0000.0000.000
37C82THR00.0810.03337.890-0.003-0.0030.0000.0000.0000.000
38C83ASN00.008-0.01237.350-0.002-0.0020.0000.0000.0000.000
39C84VAL0-0.0180.01637.4310.0000.0000.0000.0000.0000.000
40C85ASP-1-0.826-0.88734.306-0.044-0.0440.0000.0000.0000.000
41C86SER0-0.0050.00333.217-0.002-0.0020.0000.0000.0000.000
42C87ASP-1-0.884-0.93832.587-0.033-0.0330.0000.0000.0000.000
43C88ASN0-0.080-0.07331.708-0.002-0.0020.0000.0000.0000.000
44C89LEU00.1010.03426.790-0.002-0.0020.0000.0000.0000.000
45C90SER00.017-0.00728.316-0.002-0.0020.0000.0000.0000.000
46C91LYS10.8320.92928.4820.0420.0420.0000.0000.0000.000
47C92VAL00.0260.01424.9600.0000.0000.0000.0000.0000.000
48C93LEU00.0650.02322.808-0.004-0.0040.0000.0000.0000.000
49C94LYS10.8820.94623.4270.0390.0390.0000.0000.0000.000
50C95THR0-0.084-0.01324.013-0.002-0.0020.0000.0000.0000.000
51C96LEU00.0630.02919.144-0.003-0.0030.0000.0000.0000.000
52C97GLY00.0000.00019.364-0.009-0.0090.0000.0000.0000.000
53C98PHE0-0.006-0.00319.1170.0030.0030.0000.0000.0000.000
54C99LYS10.9190.94822.0670.0360.0360.0000.0000.0000.000
55C100VAL0-0.069-0.02824.8330.0010.0010.0000.0000.0000.000
56C101THR0-0.013-0.00527.2560.0050.0050.0000.0000.0000.000
57C102VAL00.0050.01030.288-0.002-0.0020.0000.0000.0000.000
58C103PHE00.0160.00630.9190.0030.0030.0000.0000.0000.000
59C104PRO0-0.007-0.01435.391-0.002-0.0020.0000.0000.0000.000
60C105ASN00.0360.01338.5370.0010.0010.0000.0000.0000.000
61C106LEU0-0.0040.00536.0790.0010.0010.0000.0000.0000.000
62C107LYS10.8970.94339.8700.0140.0140.0000.0000.0000.000
63C108SER00.035-0.00539.090-0.001-0.0010.0000.0000.0000.000
64C109GLU-1-0.951-0.97638.123-0.016-0.0160.0000.0000.0000.000
65C110GLU-1-0.838-0.93238.072-0.017-0.0170.0000.0000.0000.000
66C111ILE00.0180.01433.3610.0000.0000.0000.0000.0000.000
67C112ASN00.0340.02433.385-0.004-0.0040.0000.0000.0000.000
68C113LYS10.9390.97033.3500.0130.0130.0000.0000.0000.000
69C114PHE00.008-0.00131.9970.0010.0010.0000.0000.0000.000
70C115ILE00.0210.01728.1960.0000.0000.0000.0000.0000.000
71C116GLN0-0.0080.00528.323-0.003-0.0030.0000.0000.0000.000
72C117GLN00.021-0.00528.9300.0000.0000.0000.0000.0000.000
73C118THR0-0.085-0.05024.8470.0010.0010.0000.0000.0000.000
74C119ALA0-0.032-0.03824.5680.0010.0010.0000.0000.0000.000
75C120GLU-1-0.945-0.94224.726-0.010-0.0100.0000.0000.0000.000
76C121MET0-0.029-0.01423.7410.0010.0010.0000.0000.0000.000
77C122ASP-1-0.844-0.90620.1400.0140.0140.0000.0000.0000.000
78C123HIS10.8370.91218.2020.0330.0330.0000.0000.0000.000
79C124SER00.034-0.01415.559-0.015-0.0150.0000.0000.0000.000
80C125ASP-1-0.884-0.93814.4930.0120.0120.0000.0000.0000.000
81C126ALA0-0.092-0.05216.051-0.008-0.0080.0000.0000.0000.000
82C127ASP-1-0.705-0.86911.785-0.137-0.1370.0000.0000.0000.000
83C128CYS0-0.090-0.05413.262-0.013-0.0130.0000.0000.0000.000
84C129LEU0-0.0150.00015.9330.0130.0130.0000.0000.0000.000
85C130LEU0-0.0290.01119.646-0.007-0.0070.0000.0000.0000.000
86C131VAL00.0250.01722.3330.0070.0070.0000.0000.0000.000
87C132ALA0-0.018-0.00825.842-0.004-0.0040.0000.0000.0000.000
88C133VAL0-0.010-0.00528.4760.0040.0040.0000.0000.0000.000
89C134LEU0-0.043-0.02231.964-0.002-0.0020.0000.0000.0000.000
90C135THR0-0.004-0.03034.8990.0030.0030.0000.0000.0000.000
91C136ALA00.0280.02838.053-0.001-0.0010.0000.0000.0000.000
92C137GLY0-0.002-0.01339.6200.0000.0000.0000.0000.0000.000
93C138GLU-1-0.860-0.91639.368-0.036-0.0360.0000.0000.0000.000
94C139LEU00.006-0.02333.473-0.001-0.0010.0000.0000.0000.000
95C140GLY0-0.029-0.01834.538-0.002-0.0020.0000.0000.0000.000
96C141MET0-0.053-0.02236.6590.0020.0020.0000.0000.0000.000
97C142LEU0-0.0120.01132.954-0.001-0.0010.0000.0000.0000.000
98C143TYR00.0450.02137.6630.0020.0020.0000.0000.0000.000
99C144ALA0-0.0190.02038.887-0.001-0.0010.0000.0000.0000.000
100C145LYS10.8600.93440.4050.0190.0190.0000.0000.0000.000
101C146ASP-1-0.778-0.87842.925-0.020-0.0200.0000.0000.0000.000
102C147THR00.0250.00342.3550.0000.0000.0000.0000.0000.000
103C148HIS00.013-0.00440.967-0.002-0.0020.0000.0000.0000.000
104C149TYR0-0.006-0.00833.8120.0010.0010.0000.0000.0000.000
105C150LYS10.9990.98935.1580.0310.0310.0000.0000.0000.000
106C151PRO00.0310.02231.6400.0000.0000.0000.0000.0000.000
107C152ASP-1-0.761-0.89029.786-0.040-0.0400.0000.0000.0000.000
108C153ASN0-0.072-0.04829.6260.0010.0010.0000.0000.0000.000
109C154LEU0-0.0220.00028.8030.0020.0020.0000.0000.0000.000
110C155TRP00.0380.02824.650-0.001-0.0010.0000.0000.0000.000
111C156TYR0-0.046-0.01225.330-0.001-0.0010.0000.0000.0000.000
112C157TYR0-0.018-0.02026.6490.0000.0000.0000.0000.0000.000
113C158PHE00.0370.00021.7530.0020.0020.0000.0000.0000.000
114C159THR0-0.062-0.02520.987-0.004-0.0040.0000.0000.0000.000
115C160ALA00.0430.01718.0010.0050.0050.0000.0000.0000.000
116C161ASP-1-0.854-0.92819.725-0.028-0.0280.0000.0000.0000.000
117C162LYS10.8920.95622.8790.0360.0360.0000.0000.0000.000
118C163CYS0-0.060-0.01820.8670.0030.0030.0000.0000.0000.000
119C164PRO00.0220.01518.759-0.007-0.0070.0000.0000.0000.000
120C165THR0-0.025-0.00716.923-0.005-0.0050.0000.0000.0000.000
121C166LEU0-0.014-0.03616.000-0.004-0.0040.0000.0000.0000.000
122C167ALA00.0080.01514.761-0.016-0.0160.0000.0000.0000.000
123C168GLY0-0.049-0.01811.3460.0000.0000.0000.0000.0000.000
124C169LYS10.8870.97611.2230.0320.0320.0000.0000.0000.000
125C170PRO0-0.0060.00812.1480.0090.0090.0000.0000.0000.000
126C171LYS10.8560.93515.1190.1040.1040.0000.0000.0000.000
127C172LEU0-0.032-0.01617.254-0.002-0.0020.0000.0000.0000.000
128C173PHE00.009-0.00821.0380.0080.0080.0000.0000.0000.000
129C174PHE00.007-0.00422.061-0.003-0.0030.0000.0000.0000.000
130C175ILE00.0150.01727.0600.0040.0040.0000.0000.0000.000
131C176GLN00.0400.02130.618-0.003-0.0030.0000.0000.0000.000
132C177ALA0-0.024-0.02933.5990.0020.0020.0000.0000.0000.000
133C178CYM-1-0.880-0.89536.655-0.040-0.0400.0000.0000.0000.000
134C179GLN00.026-0.01339.3390.0020.0020.0000.0000.0000.000
135C180GLY0-0.013-0.00240.556-0.002-0.0020.0000.0000.0000.000
136C181ASP-1-0.901-0.92842.193-0.031-0.0310.0000.0000.0000.000
137C182ARG10.8660.92038.6230.0410.0410.0000.0000.0000.000
138C183LEU00.0150.00644.6140.0010.0010.0000.0000.0000.000
139C184ASP-1-0.929-0.95544.536-0.033-0.0330.0000.0000.0000.000
140C185GLY0-0.0250.00046.6530.0010.0010.0000.0000.0000.000
141C186GLY00.019-0.01050.1230.0000.0000.0000.0000.0000.000
142C187ILE0-0.041-0.00353.0980.0010.0010.0000.0000.0000.000
143C201SER00.0510.01433.760-0.001-0.0010.0000.0000.0000.000
144C202TYR00.0030.01027.7240.0010.0010.0000.0000.0000.000
145C203ARG10.8690.91830.1700.0380.0380.0000.0000.0000.000
146C204ILE00.026-0.00125.477-0.001-0.0010.0000.0000.0000.000
147C205PRO0-0.0350.00523.7710.0020.0020.0000.0000.0000.000
148C206VAL00.0360.00622.809-0.007-0.0070.0000.0000.0000.000
149C207HIS0-0.001-0.01019.0540.0020.0020.0000.0000.0000.000
150C208ALA00.0260.01914.799-0.001-0.0010.0000.0000.0000.000
151C209ASP-1-0.826-0.87213.012-0.164-0.1640.0000.0000.0000.000
152C210PHE00.0090.01115.8020.0090.0090.0000.0000.0000.000
153C211LEU0-0.012-0.01118.997-0.010-0.0100.0000.0000.0000.000
154C212ILE0-0.007-0.00420.6930.0070.0070.0000.0000.0000.000
155C213ALA0-0.0100.01224.417-0.003-0.0030.0000.0000.0000.000
156C214PHE00.0320.00926.3830.0030.0030.0000.0000.0000.000
157C215SER0-0.012-0.01230.0340.0000.0000.0000.0000.0000.000
158C216THR0-0.072-0.03133.0890.0000.0000.0000.0000.0000.000
159C217VAL00.0680.02535.3250.0020.0020.0000.0000.0000.000
160C218PRO0-0.030-0.00537.9100.0000.0000.0000.0000.0000.000
161C219GLY00.0270.01539.9400.0020.0020.0000.0000.0000.000
162C220TYR0-0.066-0.07139.337-0.001-0.0010.0000.0000.0000.000
163C221PHE00.0410.04036.8720.0010.0010.0000.0000.0000.000
164C222SER00.015-0.02342.0640.0010.0010.0000.0000.0000.000
165C223TRP0-0.062-0.01045.2820.0000.0000.0000.0000.0000.000
166C224ARG10.9580.98346.8940.0210.0210.0000.0000.0000.000
167C225ASN00.0410.00650.633-0.001-0.0010.0000.0000.0000.000
168C226THR0-0.0190.00748.145-0.001-0.0010.0000.0000.0000.000
169C227THR00.026-0.00244.065-0.001-0.0010.0000.0000.0000.000
170C228ARG10.8840.92841.9400.0300.0300.0000.0000.0000.000
171C229GLY00.0640.03838.0040.0000.0000.0000.0000.0000.000
172C230SER00.043-0.01135.7710.0000.0000.0000.0000.0000.000
173C231TRP00.0740.04235.767-0.003-0.0030.0000.0000.0000.000
174C232PHE0-0.011-0.00828.452-0.003-0.0030.0000.0000.0000.000
175C233MET00.0180.00829.399-0.004-0.0040.0000.0000.0000.000
176C234GLN0-0.0150.00931.2220.0000.0000.0000.0000.0000.000
177C235ALA00.0210.01130.627-0.003-0.0030.0000.0000.0000.000
178C236LEU00.0250.00124.720-0.004-0.0040.0000.0000.0000.000
179C237CYS0-0.085-0.02026.484-0.003-0.0030.0000.0000.0000.000
180C238GLU-1-0.917-0.97827.254-0.058-0.0580.0000.0000.0000.000
181C239GLU-1-0.892-0.95325.002-0.088-0.0880.0000.0000.0000.000
182C240LEU0-0.012-0.01821.202-0.006-0.0060.0000.0000.0000.000
183C241ARG10.8570.96223.1640.0560.0560.0000.0000.0000.000
184C242TYR0-0.019-0.01924.480-0.002-0.0020.0000.0000.0000.000
185C243ALA00.018-0.02522.880-0.001-0.0010.0000.0000.0000.000
186C244GLY0-0.0190.00520.112-0.010-0.0100.0000.0000.0000.000
187C245THR0-0.034-0.01116.352-0.003-0.0030.0000.0000.0000.000
188C246GLU-1-0.866-0.92916.438-0.166-0.1660.0000.0000.0000.000
189C247ARG10.8630.94516.7960.1030.1030.0000.0000.0000.000
190C248ASP-1-0.797-0.88514.850-0.183-0.1830.0000.0000.0000.000
191C249ILE00.011-0.01115.9950.0180.0180.0000.0000.0000.000
192C250LEU00.006-0.00117.6130.0150.0150.0000.0000.0000.000
193C251THR00.0120.00418.5350.0150.0150.0000.0000.0000.000
194C252LEU0-0.019-0.01219.8230.0120.0120.0000.0000.0000.000
195C253LEU0-0.023-0.01121.8590.0110.0110.0000.0000.0000.000
196C254THR0-0.019-0.00323.2020.0090.0090.0000.0000.0000.000
197C255PHE0-0.003-0.00923.3880.0060.0060.0000.0000.0000.000
198C256VAL0-0.037-0.01726.1590.0070.0070.0000.0000.0000.000
199C257CYS0-0.0120.00527.9330.0060.0060.0000.0000.0000.000
200C258GLN00.0010.01229.7090.0010.0010.0000.0000.0000.000
201C259LYS10.9100.96029.5020.0720.0720.0000.0000.0000.000
202C260VAL00.0200.01532.6440.0030.0030.0000.0000.0000.000
203C261ALA0-0.079-0.06733.9270.0030.0030.0000.0000.0000.000
204C262LEU0-0.089-0.05534.7860.0020.0020.0000.0000.0000.000
205C263ASP-1-0.810-0.87937.397-0.046-0.0460.0000.0000.0000.000
206C264PHE0-0.081-0.04539.0220.0030.0030.0000.0000.0000.000
207C265GLU-1-0.972-0.99940.844-0.040-0.0400.0000.0000.0000.000
208C266SER00.0230.04143.1450.0020.0020.0000.0000.0000.000
209C267ASN0-0.113-0.07442.5910.0010.0010.0000.0000.0000.000
210C268ALA00.0040.00645.3030.0000.0000.0000.0000.0000.000
211C269PRO0-0.040-0.00746.5800.0010.0010.0000.0000.0000.000
212C270ASP-1-0.786-0.90849.238-0.031-0.0310.0000.0000.0000.000
213C271SER0-0.098-0.05451.3690.0010.0010.0000.0000.0000.000
214C272ALA0-0.051-0.00551.4950.0010.0010.0000.0000.0000.000
215C273MET00.0290.01150.7350.0010.0010.0000.0000.0000.000
216C274MET00.000-0.00949.419-0.001-0.0010.0000.0000.0000.000
217C275HIS0-0.043-0.00944.000-0.001-0.0010.0000.0000.0000.000
218C276GLN00.019-0.01743.9760.0000.0000.0000.0000.0000.000
219C277GLN0-0.058-0.01937.030-0.001-0.0010.0000.0000.0000.000
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