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: 7MGJK

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 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
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2722612.166528
FMO2-HF: Nuclear repulsion 2632855.301509
FMO2-HF: Total energy -89756.865019
FMO2-MP2: Total energy -90018.131576


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.
-8.633-1.6380.976-3.115-4.854-0.02
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 : -0.004 / q_NPA : -0.016
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-1-0.829-0.9153.559-0.2891.845-0.013-0.945-1.175-0.001
4B9GLN00.0500.0436.090-0.136-0.1360.0000.0000.0000.000
5B10GLY0-0.0080.0119.1600.0280.0280.0000.0000.0000.000
6B11TYR0-0.124-0.0738.8270.0910.0910.0000.0000.0000.000
7B12ARG10.8740.9486.3140.6160.6160.0000.0000.0000.000
8B13VAL00.0760.0212.613-1.306-0.0810.756-0.352-1.628-0.003
9B14ASP-1-0.851-0.9095.077-0.757-0.594-0.001-0.014-0.1480.000
10B15GLY0-0.0220.0108.4170.2120.2120.0000.0000.0000.000
11B16ARG10.7240.8439.6970.8720.8720.0000.0000.0000.000
12B17ARG10.8240.88810.6570.2630.2630.0000.0000.0000.000
13B18ALA00.017-0.0029.7930.0030.0030.0000.0000.0000.000
14B19GLY00.0570.02311.3480.0460.0460.0000.0000.0000.000
15B20GLU-1-0.947-0.92714.584-0.409-0.4090.0000.0000.0000.000
16B21LEU00.0810.01314.850-0.059-0.0590.0000.0000.0000.000
17B22ARG10.7400.90114.1940.3520.3520.0000.0000.0000.000
18B23LYS10.9270.94416.6680.3390.3390.0000.0000.0000.000
19B24ILE00.0400.06520.077-0.006-0.0060.0000.0000.0000.000
20B25GLN0-0.032-0.00822.4640.0230.0230.0000.0000.0000.000
21B26ALA00.037-0.00925.874-0.004-0.0040.0000.0000.0000.000
22B27ARG10.8580.93928.4160.1110.1110.0000.0000.0000.000
23B28MET00.0340.02331.759-0.001-0.0010.0000.0000.0000.000
24B29GLY00.059-0.01633.9290.0020.0020.0000.0000.0000.000
25B30VAL0-0.104-0.04133.5820.0020.0020.0000.0000.0000.000
26B31PHE0-0.009-0.02234.6050.0030.0030.0000.0000.0000.000
27B32ALA00.0740.03939.335-0.001-0.0010.0000.0000.0000.000
28B33GLN0-0.098-0.04942.1150.0020.0020.0000.0000.0000.000
29B34ALA0-0.031-0.02640.1570.0010.0010.0000.0000.0000.000
30B35ASP-1-0.898-0.97240.968-0.054-0.0540.0000.0000.0000.000
31B36GLY00.1100.02638.337-0.001-0.0010.0000.0000.0000.000
32B37SER0-0.088-0.02935.779-0.001-0.0010.0000.0000.0000.000
33B38ALA0-0.0080.02031.315-0.002-0.0020.0000.0000.0000.000
34B39TYR0-0.075-0.05525.8650.0040.0040.0000.0000.0000.000
35B40ILE0-0.0290.00024.401-0.002-0.0020.0000.0000.0000.000
36B41GLU-1-0.814-0.92721.957-0.174-0.1740.0000.0000.0000.000
37B42GLN00.052-0.01318.2630.0000.0000.0000.0000.0000.000
38B43GLY00.0050.00717.296-0.031-0.0310.0000.0000.0000.000
39B44ASN0-0.051-0.04816.5590.0360.0360.0000.0000.0000.000
40B45THR00.0470.03717.5810.0060.0060.0000.0000.0000.000
41B46LYS10.7790.96219.6550.1950.1950.0000.0000.0000.000
42B47ALA00.0680.01823.4550.0070.0070.0000.0000.0000.000
43B48LEU0-0.079-0.03326.132-0.002-0.0020.0000.0000.0000.000
44B49ALA00.0200.02829.7910.0040.0040.0000.0000.0000.000
45B50VAL0-0.036-0.02531.5400.0000.0000.0000.0000.0000.000
46B51VAL0-0.0400.04335.3240.0010.0010.0000.0000.0000.000
47B52TYR0-0.045-0.01137.8130.0010.0010.0000.0000.0000.000
48B53GLY00.1160.05241.6020.0000.0000.0000.0000.0000.000
49B54PRO0-0.031-0.02843.8410.0010.0010.0000.0000.0000.000
50B55HIS0-0.064-0.02043.6230.0050.0050.0000.0000.0000.000
51B56GLU-1-0.940-0.98747.589-0.033-0.0330.0000.0000.0000.000
52B57ILE0-0.024-0.01048.0350.0000.0000.0000.0000.0000.000
53B58ARG10.9951.00547.0860.0370.0370.0000.0000.0000.000
54B59GLY0-0.030-0.02847.9510.0010.0010.0000.0000.0000.000
55B60SER0-0.039-0.01047.833-0.001-0.0010.0000.0000.0000.000
56B61ARG10.9900.98849.6980.0300.0300.0000.0000.0000.000
57B62ALA0-0.0030.00150.5040.0000.0000.0000.0000.0000.000
58B63ARG10.9590.98243.0620.0380.0380.0000.0000.0000.000
59B64ALA00.027-0.00348.424-0.001-0.0010.0000.0000.0000.000
60B65LEU00.0320.02244.0360.0010.0010.0000.0000.0000.000
61B66PRO00.0010.00548.116-0.001-0.0010.0000.0000.0000.000
62B67ASP-1-0.909-0.94547.461-0.041-0.0410.0000.0000.0000.000
63B68ARG10.9460.97640.6850.0500.0500.0000.0000.0000.000
64B69ALA0-0.055-0.00943.6640.0010.0010.0000.0000.0000.000
65B70LEU0-0.071-0.03242.1130.0010.0010.0000.0000.0000.000
66B71VAL00.018-0.00436.795-0.001-0.0010.0000.0000.0000.000
67B72ASN0-0.063-0.02137.7040.0000.0000.0000.0000.0000.000
68B73CYS00.0360.01232.744-0.004-0.0040.0000.0000.0000.000
69B74GLN0-0.023-0.02233.2750.0010.0010.0000.0000.0000.000
70B75TYR-1-0.850-0.93023.764-0.116-0.1160.0000.0000.0000.000
71B76SER-1-0.569-0.62728.870-0.071-0.0710.0000.0000.0000.000
72B77SER-1-0.782-0.95424.105-0.115-0.1150.0000.0000.0000.000
73B78ALA00.048-0.01226.0080.0100.0100.0000.0000.0000.000
74B79THR0-0.093-0.10025.070-0.002-0.0020.0000.0000.0000.000
75B80PHE00.042-0.00124.3450.0060.0060.0000.0000.0000.000
76B81SER0-0.0370.00722.613-0.012-0.0120.0000.0000.0000.000
77B82THR0-0.0300.00619.531-0.012-0.0120.0000.0000.0000.000
78B83GLY00.0630.04218.006-0.007-0.0070.0000.0000.0000.000
79B84GLU-1-0.960-0.98318.785-0.023-0.0230.0000.0000.0000.000
80B85ARG10.9940.96421.8880.0440.0440.0000.0000.0000.000
81B86LYS10.8670.94822.6790.0440.0440.0000.0000.0000.000
82B87ARG10.9000.94426.5450.0220.0220.0000.0000.0000.000
83B88ARG00.0660.06723.9310.0060.0060.0000.0000.0000.000
84B89PRO00.0350.03729.7660.0000.0000.0000.0000.0000.000
85B90HIS0-0.008-0.00131.5630.0030.0030.0000.0000.0000.000
86B91GLY0-0.086-0.04328.0510.0030.0030.0000.0000.0000.000
87B92ASP-1-0.794-0.90027.821-0.051-0.0510.0000.0000.0000.000
88B93ARG10.9620.94827.7100.0260.0260.0000.0000.0000.000
89B94LYS11.0291.02220.2690.0750.0750.0000.0000.0000.000
90B95SER00.0700.03425.990-0.001-0.0010.0000.0000.0000.000
91B96CYS0-0.0250.04727.510-0.001-0.0010.0000.0000.0000.000
92B97GLU-1-0.918-0.97925.287-0.073-0.0730.0000.0000.0000.000
93B98MET00.015-0.01222.186-0.006-0.0060.0000.0000.0000.000
94B99GLY00.028-0.02626.733-0.003-0.0030.0000.0000.0000.000
95B100LEU0-0.066-0.05830.0030.0000.0000.0000.0000.0000.000
96B101GLN00.0640.04123.7070.0020.0020.0000.0000.0000.000
97B102LEU00.0000.03527.286-0.003-0.0030.0000.0000.0000.000
98B103ARG10.9241.03629.7720.0590.0590.0000.0000.0000.000
99B104GLN00.0430.02130.357-0.003-0.0030.0000.0000.0000.000
100B105THR0-0.103-0.11628.1760.0020.0020.0000.0000.0000.000
101B106PHE00.032-0.00129.8150.0000.0000.0000.0000.0000.000
102B107GLU-1-0.969-0.97933.955-0.055-0.0550.0000.0000.0000.000
103B108ALA0-0.106-0.02633.8290.0040.0040.0000.0000.0000.000
104B109ALA0-0.111-0.06034.0410.0040.0040.0000.0000.0000.000
105B110ILE00.0990.02735.544-0.002-0.0020.0000.0000.0000.000
106B111LEU0-0.0040.02238.2010.0020.0020.0000.0000.0000.000
107B112THR00.0340.01940.8000.0020.0020.0000.0000.0000.000
108B113GLN00.0150.00543.3000.0010.0010.0000.0000.0000.000
109B114LEU0-0.027-0.01545.8790.0020.0020.0000.0000.0000.000
110B115HIS00.0380.00144.8250.0000.0000.0000.0000.0000.000
111B116PRO00.1130.08447.6420.0000.0000.0000.0000.0000.000
112B117ARG10.8970.93748.9040.0330.0330.0000.0000.0000.000
113B118SER0-0.114-0.04246.4490.0000.0000.0000.0000.0000.000
114B119GLN0-0.062-0.06042.133-0.002-0.0020.0000.0000.0000.000
115B120ILE0-0.0050.04039.2810.0000.0000.0000.0000.0000.000
116B121ASP-1-0.818-0.92338.893-0.055-0.0550.0000.0000.0000.000
117B122ILE00.032-0.03633.284-0.001-0.0010.0000.0000.0000.000
118B123TYR0-0.150-0.03933.6570.0000.0000.0000.0000.0000.000
119B124VAL0-0.050-0.02527.766-0.003-0.0030.0000.0000.0000.000
120B125GLN0-0.316-0.19827.0970.0080.0080.0000.0000.0000.000
121B126VAL00.0170.01522.391-0.008-0.0080.0000.0000.0000.000
122B127LEU0-0.104-0.04325.3610.0080.0080.0000.0000.0000.000
123B128GLN00.004-0.05620.622-0.009-0.0090.0000.0000.0000.000
124B129ALA00.0230.01919.114-0.014-0.0140.0000.0000.0000.000
125B130ASP-1-0.876-0.96313.793-0.391-0.3910.0000.0000.0000.000
126B131GLY00.1150.06613.708-0.045-0.0450.0000.0000.0000.000
127B132GLY0-0.038-0.03014.724-0.001-0.0010.0000.0000.0000.000
128B133THR00.013-0.00216.8590.0090.0090.0000.0000.0000.000
129B134TYR00.1210.04219.5790.0070.0070.0000.0000.0000.000
130B135ALA00.032-0.00919.5860.0090.0090.0000.0000.0000.000
131B136ALA00.0180.03121.0510.0050.0050.0000.0000.0000.000
132B137CYS00.018-0.02322.5610.0100.0100.0000.0000.0000.000
133B138VAL00.0510.07123.9470.0100.0100.0000.0000.0000.000
134B139ASN00.0520.05623.2130.0110.0110.0000.0000.0000.000
135B140ALA0-0.0020.00126.0190.0090.0090.0000.0000.0000.000
136B141ALA00.0060.00027.9200.0080.0080.0000.0000.0000.000
137B142THR0-0.063-0.07929.2490.0050.0050.0000.0000.0000.000
138B143LEU0-0.102-0.10928.1420.0050.0050.0000.0000.0000.000
139B144ALA00.0230.00332.1670.0050.0050.0000.0000.0000.000
140B145VAL00.006-0.00634.1240.0060.0060.0000.0000.0000.000
141B146LEU0-0.0650.01432.1490.0020.0020.0000.0000.0000.000
142B147ASP-1-0.819-0.88336.460-0.071-0.0710.0000.0000.0000.000
143B148ALA00.0200.05738.2280.0030.0030.0000.0000.0000.000
144B149GLY0-0.030-0.03040.0820.0030.0030.0000.0000.0000.000
145B150ILE0-0.095-0.04839.3380.0020.0020.0000.0000.0000.000
146B151PRO0-0.066-0.00940.132-0.003-0.0030.0000.0000.0000.000
147B152MET00.027-0.02534.3400.0000.0000.0000.0000.0000.000
148B153ARG10.8920.94736.9140.0630.0630.0000.0000.0000.000
149B154ASP-1-0.769-0.90932.158-0.099-0.0990.0000.0000.0000.000
150B155PHE0-0.095-0.02330.3340.0000.0000.0000.0000.0000.000
151B156VAL00.0080.00227.746-0.005-0.0050.0000.0000.0000.000
152B157CYS0-0.006-0.00824.9310.0010.0010.0000.0000.0000.000
153B158ALA00.0100.02922.2590.0020.0020.0000.0000.0000.000
154B159CYS0-0.1160.04418.241-0.013-0.0130.0000.0000.0000.000
155B160SER00.0480.02414.5040.0230.0230.0000.0000.0000.000
156B161ALA0-0.006-0.01413.620-0.021-0.0210.0000.0000.0000.000
157B162GLY00.0190.0049.9040.0430.0430.0000.0000.0000.000
158B163PHE0-0.034-0.0119.818-0.074-0.0740.0000.0000.0000.000
159B164VAL00.012-0.0053.446-0.1450.1490.016-0.047-0.2630.000
160B165ASP-1-0.852-0.8823.117-6.982-3.8030.218-1.757-1.640-0.016
161B166GLY0-0.047-0.0365.7030.1840.1840.0000.0000.0000.000
162B167THR0-0.089-0.0847.8300.0630.0630.0000.0000.0000.000
163B168ALA00.0090.0119.267-0.052-0.0520.0000.0000.0000.000
164B169LEU0-0.020-0.0135.788-0.008-0.0080.0000.0000.0000.000
165B170ALA00.0260.01410.4840.0710.0710.0000.0000.0000.000
166B171ASP-1-0.919-0.97712.942-0.442-0.4420.0000.0000.0000.000
167B172LEU0-0.026-0.0109.574-0.062-0.0620.0000.0000.0000.000
168B173SER0-0.033-0.0569.8980.0680.0680.0000.0000.0000.000
169B174HIS00.0780.03711.2050.0650.0650.0000.0000.0000.000
170B175VAL0-0.022-0.0155.7670.0640.0640.0000.0000.0000.000
171B176GLU-1-0.814-0.8845.573-0.664-0.6640.0000.0000.0000.000
172B177GLU-1-0.807-0.8576.554-0.140-0.1400.0000.0000.0000.000
173B178ALA0-0.071-0.0427.6020.0640.0640.0000.0000.0000.000
174B179ALA0-0.055-0.0215.3410.0990.0990.0000.0000.0000.000
175B180GLY0-0.075-0.0336.3300.0480.0480.0000.0000.0000.000
176B181GLY00.0490.0238.2940.0100.0100.0000.0000.0000.000
177B182PRO0-0.045-0.0517.9220.0100.0100.0000.0000.0000.000
178B183GLN00.0380.00410.629-0.067-0.0670.0000.0000.0000.000
179B184LEU00.0400.01413.2200.0360.0360.0000.0000.0000.000
180B185ALA00.0090.00116.356-0.032-0.0320.0000.0000.0000.000
181B186LEU00.0240.01419.0360.0160.0160.0000.0000.0000.000
182B187ALA0-0.0390.00022.495-0.011-0.0110.0000.0000.0000.000
183B188LEU0-0.028-0.02625.0790.0050.0050.0000.0000.0000.000
184B189LEU00.0370.01827.100-0.002-0.0020.0000.0000.0000.000
185B190PRO0-0.014-0.01628.4210.0040.0040.0000.0000.0000.000
186B191ALA0-0.0100.00930.3140.0040.0040.0000.0000.0000.000
187B192SER0-0.068-0.03433.1890.0020.0020.0000.0000.0000.000
188B193GLY0-0.044-0.02329.586-0.001-0.0010.0000.0000.0000.000
189B194GLN0-0.019-0.00929.200-0.001-0.0010.0000.0000.0000.000
190B195ILE00.024-0.00425.194-0.005-0.0050.0000.0000.0000.000
191B196ALA0-0.037-0.01328.1760.0050.0050.0000.0000.0000.000
192B197LEU00.0150.02724.5590.0060.0060.0000.0000.0000.000
193B198LEU0-0.053-0.05921.909-0.008-0.0080.0000.0000.0000.000
194B199GLU-1-0.901-0.94121.839-0.087-0.0870.0000.0000.0000.000
195B200MET0-0.0590.00716.682-0.019-0.0190.0000.0000.0000.000
196B201ASP-1-0.881-0.94316.909-0.102-0.1020.0000.0000.0000.000
197B202ALA0-0.0300.00313.217-0.009-0.0090.0000.0000.0000.000
198B203ARG10.9080.95313.0460.0140.0140.0000.0000.0000.000
199B204LEU0-0.064-0.01513.2910.0070.0070.0000.0000.0000.000
200B205HIS0-0.006-0.00615.1570.0260.0260.0000.0000.0000.000
201B206GLU-1-0.934-0.97617.769-0.086-0.0860.0000.0000.0000.000
202B207ASP-1-0.875-0.93018.647-0.098-0.0980.0000.0000.0000.000
203B208HIS0-0.052-0.02813.866-0.019-0.0190.0000.0000.0000.000
204B209LEU00.0950.02616.547-0.026-0.0260.0000.0000.0000.000
205B210GLU-1-0.784-0.88918.939-0.140-0.1400.0000.0000.0000.000
206B211ARG10.9390.96015.1130.1740.1740.0000.0000.0000.000
207B212VAL0-0.0360.00013.441-0.023-0.0230.0000.0000.0000.000
208B213LEU0-0.039-0.04215.848-0.006-0.0060.0000.0000.0000.000
209B214GLU-1-0.859-0.93419.335-0.165-0.1650.0000.0000.0000.000
210B215ALA0-0.141-0.05115.027-0.007-0.0070.0000.0000.0000.000
211B216ALA00.0310.00017.0660.0030.0030.0000.0000.0000.000
212B217ALA00.0430.03918.2740.0090.0090.0000.0000.0000.000
213B218GLN00.062-0.01920.1370.0200.0200.0000.0000.0000.000
214B219ALA0-0.009-0.01117.7800.0060.0060.0000.0000.0000.000
215B220ALA00.057-0.03519.8210.0040.0040.0000.0000.0000.000
216B221ARG10.9310.98222.6970.1510.1510.0000.0000.0000.000
217B222ASP-1-0.893-0.93420.978-0.210-0.2100.0000.0000.0000.000
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