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: 2L2KR

Calculation Name: 2NN6-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NN6

Chain ID: B

ChEMBL ID:

UniProt ID: Q9Y3B2

Base Structure: X-ray

Registration Date: 2023-09-26

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
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2720886.360056
FMO2-HF: Nuclear repulsion 2631124.796121
FMO2-HF: Total energy -89761.563935
FMO2-MP2: Total energy -90021.99277


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(B:6:LEU)


Summations of interaction energy for fragment #1(B:6:LEU)
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.
-8.26-2.0780.341-2.716-3.809-0.005
Interaction energy analysis for fragmet #1(B:6:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.004
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].
3B8ASP-1-0.857-0.9523.789-3.778-0.865-0.025-1.503-1.3850.005
4B9GLN00.0290.0336.4670.3050.3050.0000.0000.0000.000
5B10GLY00.0010.0149.5080.1830.1830.0000.0000.0000.000
6B11TYR0-0.138-0.0829.1380.3120.3120.0000.0000.0000.000
7B12ARG10.8540.9166.2460.3390.3390.0000.0000.0000.000
8B13VAL00.0510.0162.846-0.8180.0880.303-0.126-1.084-0.002
9B14ASP-1-0.846-0.9085.052-0.713-0.555-0.001-0.015-0.1420.000
10B15GLY0-0.0130.0208.4640.2030.2030.0000.0000.0000.000
11B16ARG10.7310.8419.7700.9430.9430.0000.0000.0000.000
12B17ARG10.8590.92010.6570.5560.5560.0000.0000.0000.000
13B18ALA00.0250.0159.7350.0550.0550.0000.0000.0000.000
14B19GLY00.0610.02611.5950.0850.0850.0000.0000.0000.000
15B20GLU-1-0.925-0.95614.740-0.519-0.5190.0000.0000.0000.000
16B21LEU00.0400.01814.868-0.059-0.0590.0000.0000.0000.000
17B22ARG10.7670.84713.8620.2090.2090.0000.0000.0000.000
18B23LYS10.8650.92116.6610.4630.4630.0000.0000.0000.000
19B24ILE00.0610.05720.0630.0060.0060.0000.0000.0000.000
20B25GLN0-0.039-0.01222.4530.0090.0090.0000.0000.0000.000
21B26ALA00.027-0.01425.8590.0030.0030.0000.0000.0000.000
22B27ARG10.8530.93828.4040.0720.0720.0000.0000.0000.000
23B28MET00.0350.01431.7440.0020.0020.0000.0000.0000.000
24B29GLY00.0380.00633.919-0.001-0.0010.0000.0000.0000.000
25B30VAL0-0.118-0.05333.4420.0010.0010.0000.0000.0000.000
26B31PHE00.000-0.01234.4880.0020.0020.0000.0000.0000.000
27B32ALA00.0720.03939.319-0.001-0.0010.0000.0000.0000.000
28B33GLN0-0.092-0.04542.1830.0000.0000.0000.0000.0000.000
29B34ALA0-0.027-0.02940.3030.0030.0030.0000.0000.0000.000
30B35ASP-1-0.870-0.95341.196-0.034-0.0340.0000.0000.0000.000
31B36GLY00.0700.04838.600-0.003-0.0030.0000.0000.0000.000
32B37SER0-0.077-0.04135.9650.0030.0030.0000.0000.0000.000
33B38ALA00.0310.03031.407-0.006-0.0060.0000.0000.0000.000
34B39TYR0-0.063-0.05925.9450.0090.0090.0000.0000.0000.000
35B40ILE0-0.0140.00524.328-0.009-0.0090.0000.0000.0000.000
36B41GLU-1-0.769-0.89122.143-0.099-0.0990.0000.0000.0000.000
37B42GLN00.013-0.01618.283-0.008-0.0080.0000.0000.0000.000
38B43GLY00.0170.01317.277-0.015-0.0150.0000.0000.0000.000
39B44ASN0-0.092-0.05816.4470.0100.0100.0000.0000.0000.000
40B45THR00.0250.04017.7590.0300.0300.0000.0000.0000.000
41B46LYS10.7580.91919.6760.0900.0900.0000.0000.0000.000
42B47ALA00.0550.03723.4720.0160.0160.0000.0000.0000.000
43B48LEU0-0.074-0.03726.266-0.010-0.0100.0000.0000.0000.000
44B49ALA00.0190.02229.9540.0070.0070.0000.0000.0000.000
45B50VAL0-0.036-0.02731.739-0.004-0.0040.0000.0000.0000.000
46B51VAL0-0.0060.02135.5250.0030.0030.0000.0000.0000.000
47B52TYR0-0.047-0.00438.0460.0000.0000.0000.0000.0000.000
48B53GLY00.1120.05241.8290.0000.0000.0000.0000.0000.000
49B54PRO0-0.034-0.01544.1090.0030.0030.0000.0000.0000.000
50B55HIS0-0.071-0.04443.7590.0020.0020.0000.0000.0000.000
51B56GLU-1-0.794-0.89447.828-0.011-0.0110.0000.0000.0000.000
52B57ILE0-0.016-0.02247.9520.0010.0010.0000.0000.0000.000
53B58ARG10.9060.96147.1810.0120.0120.0000.0000.0000.000
54B59GLY0-0.006-0.01248.0590.0010.0010.0000.0000.0000.000
55B60SER0-0.042-0.02147.8320.0000.0000.0000.0000.0000.000
56B61ARG10.8660.92749.8380.0080.0080.0000.0000.0000.000
57B62ALA00.0130.00950.752-0.001-0.0010.0000.0000.0000.000
58B63ARG10.9670.98943.095-0.001-0.0010.0000.0000.0000.000
59B64ALA00.0280.00048.6230.0000.0000.0000.0000.0000.000
60B65LEU00.0280.01943.9710.0000.0000.0000.0000.0000.000
61B66PRO0-0.0020.00048.210-0.001-0.0010.0000.0000.0000.000
62B67ASP-1-0.838-0.91447.825-0.022-0.0220.0000.0000.0000.000
63B68ARG10.8750.94241.1990.0260.0260.0000.0000.0000.000
64B69ALA0-0.026-0.00843.8630.0010.0010.0000.0000.0000.000
65B70LEU0-0.047-0.03442.3920.0020.0020.0000.0000.0000.000
66B71VAL0-0.002-0.00736.935-0.002-0.0020.0000.0000.0000.000
67B72ASN0-0.042-0.01737.8610.0040.0040.0000.0000.0000.000
68B73CYS00.0460.01433.192-0.005-0.0050.0000.0000.0000.000
69B74GLN0-0.036-0.02633.3480.0030.0030.0000.0000.0000.000
70B75TYR-1-0.847-0.93023.382-0.007-0.0070.0000.0000.0000.000
71B76SER-1-0.764-0.86828.8610.0140.0140.0000.0000.0000.000
72B77SER-1-0.825-0.91224.0330.0230.0230.0000.0000.0000.000
73B78ALA00.008-0.01326.0740.0090.0090.0000.0000.0000.000
74B79THR0-0.079-0.05424.9700.0090.0090.0000.0000.0000.000
75B80PHE00.0350.00524.1380.0140.0140.0000.0000.0000.000
76B81SER0-0.0130.01822.542-0.001-0.0010.0000.0000.0000.000
77B82THR0-0.029-0.00319.4140.0020.0020.0000.0000.0000.000
78B83GLY00.0650.04417.744-0.002-0.0020.0000.0000.0000.000
79B84GLU-1-0.917-0.97118.5430.2160.2160.0000.0000.0000.000
80B85ARG10.9920.96921.590-0.094-0.0940.0000.0000.0000.000
81B86LYS10.7890.92021.093-0.169-0.1690.0000.0000.0000.000
82B87ARG10.8810.92726.311-0.086-0.0860.0000.0000.0000.000
83B88ARG00.0860.02923.5130.0180.0180.0000.0000.0000.000
84B89PRO00.0300.03729.650-0.001-0.0010.0000.0000.0000.000
85B90HIS0-0.0050.00631.4060.0020.0020.0000.0000.0000.000
86B91GLY0-0.053-0.02827.9100.0020.0020.0000.0000.0000.000
87B92ASP-1-0.801-0.90827.7380.0390.0390.0000.0000.0000.000
88B93ARG10.9250.94827.727-0.070-0.0700.0000.0000.0000.000
89B94LYS11.0331.02720.017-0.115-0.1150.0000.0000.0000.000
90B95SER00.0440.04325.996-0.007-0.0070.0000.0000.0000.000
91B96CYS0-0.0270.00627.550-0.007-0.0070.0000.0000.0000.000
92B97GLU-1-0.899-0.94925.6960.0280.0280.0000.0000.0000.000
93B98MET00.019-0.00622.238-0.012-0.0120.0000.0000.0000.000
94B99GLY0-0.015-0.01226.872-0.008-0.0080.0000.0000.0000.000
95B100LEU0-0.076-0.04430.157-0.007-0.0070.0000.0000.0000.000
96B101GLN00.0280.00124.053-0.004-0.0040.0000.0000.0000.000
97B102LEU0-0.039-0.01726.925-0.008-0.0080.0000.0000.0000.000
98B103ARG10.8530.91029.9690.0100.0100.0000.0000.0000.000
99B104GLN0-0.027-0.00530.607-0.008-0.0080.0000.0000.0000.000
100B105THR0-0.001-0.02728.201-0.005-0.0050.0000.0000.0000.000
101B106PHE00.0140.00029.977-0.003-0.0030.0000.0000.0000.000
102B107GLU-1-0.867-0.91534.217-0.019-0.0190.0000.0000.0000.000
103B108ALA0-0.089-0.01534.0980.0010.0010.0000.0000.0000.000
104B109ALA0-0.112-0.06234.3690.0010.0010.0000.0000.0000.000
105B110ILE00.1070.03435.869-0.001-0.0010.0000.0000.0000.000
106B111LEU00.0070.01338.5350.0000.0000.0000.0000.0000.000
107B112THR00.0000.01440.8290.0010.0010.0000.0000.0000.000
108B113GLN0-0.022-0.00843.5690.0010.0010.0000.0000.0000.000
109B114LEU0-0.011-0.00146.1820.0010.0010.0000.0000.0000.000
110B115HIS00.0410.00144.3160.0000.0000.0000.0000.0000.000
111B116PRO00.1250.09147.8590.0010.0010.0000.0000.0000.000
112B117ARG10.8790.93049.0740.0130.0130.0000.0000.0000.000
113B118SER0-0.119-0.05146.9050.0010.0010.0000.0000.0000.000
114B119GLN0-0.078-0.07642.4490.0010.0010.0000.0000.0000.000
115B120ILE00.0010.03239.5960.0000.0000.0000.0000.0000.000
116B121ASP-1-0.795-0.86039.080-0.017-0.0170.0000.0000.0000.000
117B122ILE00.039-0.02433.567-0.002-0.0020.0000.0000.0000.000
118B123TYR0-0.161-0.07233.8540.0040.0040.0000.0000.0000.000
119B124VAL0-0.036-0.02527.927-0.005-0.0050.0000.0000.0000.000
120B125GLN0-0.042-0.02228.8770.0070.0070.0000.0000.0000.000
121B126VAL00.0030.01922.227-0.013-0.0130.0000.0000.0000.000
122B127LEU0-0.056-0.04525.4330.0090.0090.0000.0000.0000.000
123B128GLN0-0.049-0.05720.159-0.005-0.0050.0000.0000.0000.000
124B129ALA00.0550.03419.088-0.024-0.0240.0000.0000.0000.000
125B130ASP-1-0.862-0.96313.888-0.118-0.1180.0000.0000.0000.000
126B131GLY00.0660.06213.970-0.048-0.0480.0000.0000.0000.000
127B132GLY00.0250.01614.893-0.030-0.0300.0000.0000.0000.000
128B133THR00.003-0.00617.134-0.007-0.0070.0000.0000.0000.000
129B134TYR00.1040.03919.765-0.009-0.0090.0000.0000.0000.000
130B135ALA00.0390.00319.8260.0000.0000.0000.0000.0000.000
131B136ALA00.0160.01921.196-0.007-0.0070.0000.0000.0000.000
132B137CYS0-0.019-0.01122.846-0.002-0.0020.0000.0000.0000.000
133B138VAL00.0650.05724.9040.0030.0030.0000.0000.0000.000
134B139ASN00.0960.06223.5890.0040.0040.0000.0000.0000.000
135B140ALA0-0.0160.00326.4130.0060.0060.0000.0000.0000.000
136B141ALA0-0.014-0.00928.2050.0060.0060.0000.0000.0000.000
137B142THR0-0.037-0.04829.8130.0010.0010.0000.0000.0000.000
138B143LEU0-0.090-0.05828.4860.0010.0010.0000.0000.0000.000
139B144ALA00.0250.01232.4690.0030.0030.0000.0000.0000.000
140B145VAL0-0.010-0.02134.4130.0040.0040.0000.0000.0000.000
141B146LEU0-0.041-0.03833.3830.0000.0000.0000.0000.0000.000
142B147ASP-1-0.811-0.88636.718-0.052-0.0520.0000.0000.0000.000
143B148ALA00.0160.05438.4200.0020.0020.0000.0000.0000.000
144B149GLY0-0.029-0.03340.3950.0030.0030.0000.0000.0000.000
145B150ILE0-0.102-0.05040.2300.0000.0000.0000.0000.0000.000
146B151PRO0-0.050-0.01240.541-0.003-0.0030.0000.0000.0000.000
147B152MET00.0290.00034.5420.0010.0010.0000.0000.0000.000
148B153ARG10.8740.94037.3170.0470.0470.0000.0000.0000.000
149B154ASP-1-0.766-0.88933.091-0.095-0.0950.0000.0000.0000.000
150B155PHE0-0.036-0.01230.2310.0020.0020.0000.0000.0000.000
151B156VAL0-0.010-0.01328.644-0.007-0.0070.0000.0000.0000.000
152B157CYS0-0.031-0.01425.5890.0010.0010.0000.0000.0000.000
153B158ALA00.0160.02822.691-0.001-0.0010.0000.0000.0000.000
154B159CYS0-0.083-0.00618.880-0.016-0.0160.0000.0000.0000.000
155B160SER00.0530.02314.9380.0270.0270.0000.0000.0000.000
156B161ALA0-0.017-0.01014.133-0.041-0.0410.0000.0000.0000.000
157B162GLY00.0100.01010.2830.0620.0620.0000.0000.0000.000
158B163PHE0-0.023-0.01810.228-0.116-0.1160.0000.0000.0000.000
159B164VAL00.013-0.0103.697-0.0160.1840.002-0.025-0.1780.000
160B165ASP-1-0.855-0.9103.353-5.283-3.2780.062-1.047-1.020-0.008
161B166GLY0-0.051-0.0316.1680.0890.0890.0000.0000.0000.000
162B167THR0-0.075-0.0518.2820.0240.0240.0000.0000.0000.000
163B168ALA0-0.0020.0059.901-0.009-0.0090.0000.0000.0000.000
164B169LEU0-0.017-0.0026.579-0.040-0.0400.0000.0000.0000.000
165B170ALA00.0270.01511.2280.1080.1080.0000.0000.0000.000
166B171ASP-1-0.905-0.94613.599-0.374-0.3740.0000.0000.0000.000
167B172LEU0-0.027-0.0098.900-0.068-0.0680.0000.0000.0000.000
168B173SER0-0.039-0.0349.9520.0890.0890.0000.0000.0000.000
169B174HIS00.0420.01711.4960.0540.0540.0000.0000.0000.000
170B175VAL00.004-0.0055.6260.1090.1090.0000.0000.0000.000
171B176GLU-1-0.760-0.8425.779-0.292-0.2920.0000.0000.0000.000
172B177GLU-1-0.808-0.8806.7500.0870.0870.0000.0000.0000.000
173B178ALA0-0.080-0.0457.6210.0260.0260.0000.0000.0000.000
174B179ALA0-0.058-0.0225.3660.1700.1700.0000.0000.0000.000
175B180GLY0-0.062-0.0236.4260.0460.0460.0000.0000.0000.000
176B181GLY00.0440.0218.457-0.036-0.0360.0000.0000.0000.000
177B182PRO0-0.048-0.0398.245-0.023-0.0230.0000.0000.0000.000
178B183GLN00.014-0.01610.737-0.065-0.0650.0000.0000.0000.000
179B184LEU00.0460.02313.3040.0360.0360.0000.0000.0000.000
180B185ALA0-0.001-0.01016.639-0.034-0.0340.0000.0000.0000.000
181B186LEU00.0000.00419.3050.0140.0140.0000.0000.0000.000
182B187ALA0-0.0170.00722.823-0.010-0.0100.0000.0000.0000.000
183B188LEU0-0.054-0.02425.2000.0030.0030.0000.0000.0000.000
184B189LEU00.0380.01727.569-0.002-0.0020.0000.0000.0000.000
185B190PRO00.024-0.00628.9290.0010.0010.0000.0000.0000.000
186B191ALA0-0.0250.00430.9280.0020.0020.0000.0000.0000.000
187B192SER0-0.076-0.04533.7480.0010.0010.0000.0000.0000.000
188B193GLY0-0.069-0.02730.161-0.003-0.0030.0000.0000.0000.000
189B194GLN0-0.015-0.00629.7290.0010.0010.0000.0000.0000.000
190B195ILE00.0260.00425.677-0.005-0.0050.0000.0000.0000.000
191B196ALA0-0.034-0.01228.5820.0070.0070.0000.0000.0000.000
192B197LEU00.0130.02524.7470.0060.0060.0000.0000.0000.000
193B198LEU0-0.037-0.05522.062-0.013-0.0130.0000.0000.0000.000
194B199GLU-1-0.830-0.89021.978-0.013-0.0130.0000.0000.0000.000
195B200MET0-0.055-0.00716.870-0.010-0.0100.0000.0000.0000.000
196B201ASP-1-0.905-0.94417.0590.0200.0200.0000.0000.0000.000
197B202ALA0-0.0180.01213.6690.0150.0150.0000.0000.0000.000
198B203ARG10.9150.94313.285-0.131-0.1310.0000.0000.0000.000
199B204LEU0-0.053-0.02313.4990.0040.0040.0000.0000.0000.000
200B205HIS0-0.038-0.04015.3770.0290.0290.0000.0000.0000.000
201B206GLU-1-0.921-0.95417.963-0.069-0.0690.0000.0000.0000.000
202B207ASP-1-0.808-0.88318.799-0.131-0.1310.0000.0000.0000.000
203B208HIS0-0.021-0.00914.885-0.043-0.0430.0000.0000.0000.000
204B209LEU00.0620.03116.966-0.026-0.0260.0000.0000.0000.000
205B210GLU-1-0.807-0.89219.327-0.157-0.1570.0000.0000.0000.000
206B211ARG10.8350.90215.9600.2020.2020.0000.0000.0000.000
207B212VAL0-0.0190.00013.749-0.028-0.0280.0000.0000.0000.000
208B213LEU0-0.038-0.03916.342-0.001-0.0010.0000.0000.0000.000
209B214GLU-1-0.917-0.97019.800-0.181-0.1810.0000.0000.0000.000
210B215ALA0-0.050-0.01915.688-0.009-0.0090.0000.0000.0000.000
211B216ALA00.0230.00617.7190.0010.0010.0000.0000.0000.000
212B217ALA00.0380.02818.8310.0100.0100.0000.0000.0000.000
213B218GLN0-0.035-0.03920.9770.0260.0260.0000.0000.0000.000
214B219ALA00.0180.00018.4090.0070.0070.0000.0000.0000.000
215B220ALA00.0360.00320.5050.0060.0060.0000.0000.0000.000
216B221ARG10.9640.98023.3010.1600.1600.0000.0000.0000.000
217B222ASP-1-0.860-0.91121.667-0.251-0.2510.0000.0000.0000.000
218B223VAL00.0550.02221.6000.0140.0140.0000.0000.0000.000
219B224HIS10.8520.93424.2130.1470.1470.0000.0000.0000.000
220B225THR0-0.075-0.04726.8840.0080.0080.0000.0000.0000.000
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222B227LEU00.0780.01026.3170.0110.0110.0000.0000.0000.000
223B228ASP-1-0.805-0.87429.090-0.101-0.1010.0000.0000.0000.000
224B229ARG10.9070.95530.0850.1650.1650.0000.0000.0000.000
225B230VAL0-0.028-0.01028.2600.0080.0080.0000.0000.0000.000
226B231VAL00.0350.02131.5960.0080.0080.0000.0000.0000.000
227B232ARG10.8090.87534.3760.1090.1090.0000.0000.0000.000
228B233GLN0-0.089-0.04134.4340.0070.0070.0000.0000.0000.000
229B234HIS10.9180.96135.5470.0750.0750.0000.0000.0000.000
230B235VAL00.0350.02837.8130.0050.0050.0000.0000.0000.000
231B236ARG10.9410.96540.5300.0870.0870.0000.0000.0000.000
232B237GLU-1-0.901-0.96539.069-0.064-0.0640.0000.0000.0000.000
233B238ALA00.0580.04541.7110.0040.0040.0000.0000.0000.000
234B239SER0-0.060-0.02843.3750.0030.0030.0000.0000.0000.000
235B240ILE0-0.120-0.03744.8100.0050.0050.0000.0000.0000.000