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: R9448

Calculation Name: 2NN6-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NN6

Chain ID: F

ChEMBL ID:

UniProt ID: Q9Y3B2

Base Structure: X-ray

Registration Date: 2023-06-26

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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2383536.733023
FMO2-HF: Nuclear repulsion 2301793.363461
FMO2-HF: Total energy -81743.369562
FMO2-MP2: Total energy -81982.688464


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(F:29:GLY)


Summations of interaction energy for fragment #1(F:29:GLY)
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.
0.5241.733-0.018-0.605-0.586-0.001
Interaction energy analysis for fragmet #1(F:29:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.010
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].
3F31ARG10.8800.9363.8201.9483.157-0.018-0.605-0.586-0.001
4F32ASP-1-0.806-0.9107.247-0.555-0.5550.0000.0000.0000.000
5F33PRO0-0.0100.01210.615-0.153-0.1530.0000.0000.0000.000
6F34THR00.0780.01213.0440.0350.0350.0000.0000.0000.000
7F35ARG10.7930.9278.5691.3261.3260.0000.0000.0000.000
8F36LEU0-0.004-0.00113.459-0.053-0.0530.0000.0000.0000.000
9F37ARG10.8330.92011.7650.6260.6260.0000.0000.0000.000
10F38PRO00.0140.00713.9890.0460.0460.0000.0000.0000.000
11F39VAL00.0620.02117.028-0.008-0.0080.0000.0000.0000.000
12F40TYR0-0.041-0.01320.2250.0360.0360.0000.0000.0000.000
13F41ALA00.0560.01222.632-0.007-0.0070.0000.0000.0000.000
14F42ARG10.9320.96325.9030.1320.1320.0000.0000.0000.000
15F43ALA00.0390.02629.272-0.003-0.0030.0000.0000.0000.000
16F44GLY00.0810.01231.8260.0060.0060.0000.0000.0000.000
17F45LEU0-0.117-0.08630.7650.0060.0060.0000.0000.0000.000
18F46LEU0-0.041-0.01432.8480.0050.0050.0000.0000.0000.000
19F47SER00.0730.04235.8850.0000.0000.0000.0000.0000.000
20F48GLN00.0160.00739.0680.0030.0030.0000.0000.0000.000
21F49ALA0-0.026-0.00737.5310.0040.0040.0000.0000.0000.000
22F50LYS10.8610.92539.6470.0790.0790.0000.0000.0000.000
23F51GLY00.0810.03937.8060.0020.0020.0000.0000.0000.000
24F52SER0-0.188-0.05134.075-0.002-0.0020.0000.0000.0000.000
25F53ALA00.0380.01829.9800.0000.0000.0000.0000.0000.000
26F54TYR0-0.052-0.03123.8340.0040.0040.0000.0000.0000.000
27F55LEU0-0.014-0.00322.693-0.002-0.0020.0000.0000.0000.000
28F56GLU-1-0.876-0.94920.248-0.252-0.2520.0000.0000.0000.000
29F57ALA00.003-0.00916.800-0.004-0.0040.0000.0000.0000.000
30F58GLY0-0.031-0.01114.430-0.065-0.0650.0000.0000.0000.000
31F59GLY00.0250.00213.894-0.059-0.0590.0000.0000.0000.000
32F60THR0-0.0450.03815.9900.0120.0120.0000.0000.0000.000
33F61LYS10.8000.92018.4900.3080.3080.0000.0000.0000.000
34F62VAL00.0380.03122.6580.0070.0070.0000.0000.0000.000
35F63LEU0-0.043-0.01825.2840.0060.0060.0000.0000.0000.000
36F64CYS0-0.0210.07828.966-0.004-0.0040.0000.0000.0000.000
37F65ALA00.0090.00631.8490.0050.0050.0000.0000.0000.000
38F66VAL00.0330.04335.5090.0000.0000.0000.0000.0000.000
39F67SER0-0.061-0.05437.8850.0050.0050.0000.0000.0000.000
40F68GLY00.025-0.00341.5410.0000.0000.0000.0000.0000.000
41F69PRO00.0160.03244.263-0.001-0.0010.0000.0000.0000.000
42F70ARG10.9590.97144.7680.0700.0700.0000.0000.0000.000
43F71GLN00.0530.02948.572-0.002-0.0020.0000.0000.0000.000
44F72ALA0-0.0120.00448.2150.0010.0010.0000.0000.0000.000
45F92LEU00.0370.00751.9910.0000.0000.0000.0000.0000.000
46F93ARG10.8920.93749.3500.0530.0530.0000.0000.0000.000
47F94GLY00.0070.01547.931-0.001-0.0010.0000.0000.0000.000
48F95ARG10.9730.97841.0590.0790.0790.0000.0000.0000.000
49F96LEU0-0.0520.00137.2350.0030.0030.0000.0000.0000.000
50F97LEU00.0010.02738.6850.0010.0010.0000.0000.0000.000
51F98CYS0-0.036-0.01034.103-0.003-0.0030.0000.0000.0000.000
52F99ASP-1-0.910-0.96333.593-0.112-0.1120.0000.0000.0000.000
53F100PHE00.0290.02524.748-0.011-0.0110.0000.0000.0000.000
54F101ARG10.9840.98129.2070.1250.1250.0000.0000.0000.000
55F102ARG10.9590.98921.4220.2170.2170.0000.0000.0000.000
56F103ALA0-0.0130.00025.1360.0120.0120.0000.0000.0000.000
57F104PRO0-0.021-0.00625.719-0.007-0.0070.0000.0000.0000.000
58F105PHE0-0.012-0.03224.8660.0100.0100.0000.0000.0000.000
59F106ALA00.0280.03321.909-0.008-0.0080.0000.0000.0000.000
60F107GLY0-0.031-0.02418.602-0.021-0.0210.0000.0000.0000.000
61F108ARG10.9460.98616.0280.2820.2820.0000.0000.0000.000
62F109ARG10.9500.97619.8070.1230.1230.0000.0000.0000.000
63F110ARG10.9650.98122.5820.0860.0860.0000.0000.0000.000
64F111ARG10.9831.00623.0880.1820.1820.0000.0000.0000.000
65F112ALA00.018-0.00927.324-0.003-0.0030.0000.0000.0000.000
66F113PRO0-0.0110.01130.804-0.001-0.0010.0000.0000.0000.000
67F114PRO00.0250.00631.306-0.007-0.0070.0000.0000.0000.000
68F115GLY00.0580.01230.0400.0050.0050.0000.0000.0000.000
69F116GLY00.0090.01330.931-0.005-0.0050.0000.0000.0000.000
70F117CYS0-0.022-0.01329.2450.0010.0010.0000.0000.0000.000
71F118GLU-1-0.908-0.96025.285-0.168-0.1680.0000.0000.0000.000
72F119GLU-1-0.869-0.95927.730-0.156-0.1560.0000.0000.0000.000
73F120ARG10.8730.97829.7240.0930.0930.0000.0000.0000.000
74F121GLU-1-0.907-0.95227.190-0.150-0.1500.0000.0000.0000.000
75F122LEU0-0.0020.00424.422-0.006-0.0060.0000.0000.0000.000
76F123ALA0-0.010-0.02928.087-0.004-0.0040.0000.0000.0000.000
77F124LEU0-0.053-0.00431.2090.0030.0030.0000.0000.0000.000
78F125ALA00.0990.06128.8830.0020.0020.0000.0000.0000.000
79F126LEU0-0.024-0.00628.141-0.001-0.0010.0000.0000.0000.000
80F127GLN00.029-0.03130.3080.0060.0060.0000.0000.0000.000
81F128GLU-1-0.819-0.95233.025-0.111-0.1110.0000.0000.0000.000
82F129ALA0-0.116-0.04329.9140.0010.0010.0000.0000.0000.000
83F130LEU0-0.071-0.07129.7150.0020.0020.0000.0000.0000.000
84F131GLU-1-0.910-0.95133.254-0.092-0.0920.0000.0000.0000.000
85F132PRO0-0.059-0.01335.0740.0070.0070.0000.0000.0000.000
86F133ALA00.0140.00834.8210.0040.0040.0000.0000.0000.000
87F134VAL00.044-0.00536.8660.0030.0030.0000.0000.0000.000
88F135ARG10.8980.99339.9630.0670.0670.0000.0000.0000.000
89F136LEU00.0810.01942.8280.0000.0000.0000.0000.0000.000
90F137GLY0-0.061-0.03845.8080.0030.0030.0000.0000.0000.000
91F138ARG10.8930.96447.2500.0640.0640.0000.0000.0000.000
92F139TYR00.0380.00644.9740.0010.0010.0000.0000.0000.000
93F140PRO00.0230.02648.929-0.001-0.0010.0000.0000.0000.000
94F141ARG10.9120.93351.3540.0460.0460.0000.0000.0000.000
95F142ALA0-0.0130.00148.5090.0010.0010.0000.0000.0000.000
96F143GLN00.0010.00143.559-0.001-0.0010.0000.0000.0000.000
97F144LEU0-0.0090.01139.0330.0020.0020.0000.0000.0000.000
98F145GLU-1-0.937-0.98238.564-0.090-0.0900.0000.0000.0000.000
99F146VAL0-0.0020.01033.7100.0000.0000.0000.0000.0000.000
100F147SER00.008-0.00934.343-0.002-0.0020.0000.0000.0000.000
101F148ALA00.0490.00829.064-0.003-0.0030.0000.0000.0000.000
102F149LEU0-0.0380.00427.0820.0020.0020.0000.0000.0000.000
103F150LEU0-0.0100.00620.761-0.004-0.0040.0000.0000.0000.000
104F151LEU0-0.011-0.03624.0500.0070.0070.0000.0000.0000.000
105F152GLU-1-0.850-0.93117.423-0.322-0.3220.0000.0000.0000.000
106F153ASP-1-0.810-0.95417.114-0.397-0.3970.0000.0000.0000.000
107F154GLY0-0.011-0.03214.747-0.040-0.0400.0000.0000.0000.000
108F155GLY0-0.006-0.01213.389-0.052-0.0520.0000.0000.0000.000
109F156SER00.1500.09114.2610.0690.0690.0000.0000.0000.000
110F157ALA0-0.095-0.05516.9150.0540.0540.0000.0000.0000.000
111F158LEU00.0920.05619.4870.0380.0380.0000.0000.0000.000
112F159ALA00.0710.02020.6350.0330.0330.0000.0000.0000.000
113F160ALA0-0.044-0.00820.4440.0230.0230.0000.0000.0000.000
114F161ALA00.0780.00722.3390.0300.0300.0000.0000.0000.000
115F162LEU0-0.062-0.02824.4310.0140.0140.0000.0000.0000.000
116F163THR0-0.0350.00124.1770.0120.0120.0000.0000.0000.000
117F164ALA0-0.043-0.02425.9790.0150.0150.0000.0000.0000.000
118F165ALA00.130-0.05127.5880.0140.0140.0000.0000.0000.000
119F166ALA00.034-0.00330.0250.0120.0120.0000.0000.0000.000
120F167LEU0-0.072-0.01428.3800.0110.0110.0000.0000.0000.000
121F168ALA00.007-0.00632.2020.0090.0090.0000.0000.0000.000
122F169LEU00.0470.05133.8140.0100.0100.0000.0000.0000.000
123F170ALA00.0580.00535.9930.0070.0070.0000.0000.0000.000
124F171ASP-1-0.899-0.92134.858-0.105-0.1050.0000.0000.0000.000
125F172ALA0-0.018-0.02636.9080.0060.0060.0000.0000.0000.000
126F173GLY0-0.118-0.03539.3930.0050.0050.0000.0000.0000.000
127F174VAL0-0.061-0.04839.0350.0050.0050.0000.0000.0000.000
128F175GLU-1-0.907-0.97541.769-0.073-0.0730.0000.0000.0000.000
129F176MET0-0.0340.03937.456-0.002-0.0020.0000.0000.0000.000
130F177TYR0-0.083-0.03539.0290.0060.0060.0000.0000.0000.000
131F178ASP-1-0.724-0.86133.967-0.122-0.1220.0000.0000.0000.000
132F179LEU0-0.091-0.06131.756-0.001-0.0010.0000.0000.0000.000
133F180VAL00.0860.03729.124-0.002-0.0020.0000.0000.0000.000
134F181VAL0-0.060-0.02924.848-0.007-0.0070.0000.0000.0000.000
135F182GLY00.0450.02724.2160.0060.0060.0000.0000.0000.000
136F183CYS0-0.095-0.04819.381-0.005-0.0050.0000.0000.0000.000
137F184GLY00.1090.04416.5540.0200.0200.0000.0000.0000.000
138F185LEU0-0.0780.00415.586-0.033-0.0330.0000.0000.0000.000
139F186SER0-0.0040.02311.6160.0350.0350.0000.0000.0000.000
140F187LEU00.0600.05313.455-0.033-0.0330.0000.0000.0000.000
141F188ALA00.0130.0038.802-0.018-0.0180.0000.0000.0000.000
142F189PRO00.0110.0077.5030.1020.1020.0000.0000.0000.000
143F190GLY0-0.050-0.03510.0360.1210.1210.0000.0000.0000.000
144F191PRO00.0020.02411.319-0.013-0.0130.0000.0000.0000.000
145F192ALA00.0190.00514.644-0.031-0.0310.0000.0000.0000.000
146F193PRO00.024-0.00715.014-0.017-0.0170.0000.0000.0000.000
147F194THR0-0.0180.02210.1040.0220.0220.0000.0000.0000.000
148F195TRP00.0350.00012.939-0.045-0.0450.0000.0000.0000.000
149F196LEU0-0.016-0.0267.820-0.064-0.0640.0000.0000.0000.000
150F197LEU0-0.0050.01612.4170.0820.0820.0000.0000.0000.000
151F198ASP-1-0.899-0.97213.577-0.664-0.6640.0000.0000.0000.000
152F199PRO0-0.0250.00510.568-0.151-0.1510.0000.0000.0000.000
153F200THR0-0.017-0.0457.9140.2820.2820.0000.0000.0000.000
154F201ARG10.9030.96710.4350.5240.5240.0000.0000.0000.000
155F202LEU0-0.042-0.0447.2420.0800.0800.0000.0000.0000.000
156F203GLU-1-0.905-0.9335.648-2.736-2.7360.0000.0000.0000.000
157F204GLU-1-0.908-0.9717.961-0.436-0.4360.0000.0000.0000.000
158F205GLU-1-0.938-0.9609.805-0.513-0.5130.0000.0000.0000.000
159F206ARG10.8800.9364.8730.6090.6090.0000.0000.0000.000
160F207ALA0-0.043-0.01010.3540.0200.0200.0000.0000.0000.000
161F208ALA00.0100.03112.3140.0630.0630.0000.0000.0000.000
162F209ALA00.044-0.01614.4850.0440.0440.0000.0000.0000.000
163F210GLY0-0.0020.01815.869-0.063-0.0630.0000.0000.0000.000
164F211LEU00.0200.00217.8880.0450.0450.0000.0000.0000.000
165F212THR0-0.065-0.03318.567-0.044-0.0440.0000.0000.0000.000
166F213VAL0-0.0050.02921.0050.0310.0310.0000.0000.0000.000
167F214ALA00.001-0.01423.592-0.018-0.0180.0000.0000.0000.000
168F215LEU0-0.047-0.04026.2600.0140.0140.0000.0000.0000.000
169F216MET0-0.081-0.02129.048-0.011-0.0110.0000.0000.0000.000
170F217PRO0-0.0230.00829.3560.0020.0020.0000.0000.0000.000
171F218VAL00.014-0.00431.0870.0060.0060.0000.0000.0000.000
172F219LEU00.0020.02634.5090.0070.0070.0000.0000.0000.000
173F220ASN0-0.099-0.08232.2070.0030.0030.0000.0000.0000.000
174F221GLN00.0010.01032.9810.0060.0060.0000.0000.0000.000
175F222VAL00.0450.01130.331-0.010-0.0100.0000.0000.0000.000
176F223ALA0-0.0140.02829.0020.0050.0050.0000.0000.0000.000
177F224GLY00.0620.02328.7070.0100.0100.0000.0000.0000.000
178F225LEU0-0.039-0.04226.055-0.019-0.0190.0000.0000.0000.000
179F226LEU00.009-0.00224.8750.0140.0140.0000.0000.0000.000
180F227GLY00.0510.01622.328-0.027-0.0270.0000.0000.0000.000
181F228SER0-0.081-0.03621.3390.0190.0190.0000.0000.0000.000
182F229GLY0-0.017-0.00821.560-0.013-0.0130.0000.0000.0000.000
183F230GLU-1-0.906-0.94917.037-0.206-0.2060.0000.0000.0000.000
184F231GLY00.0350.01819.3440.0200.0200.0000.0000.0000.000
185F232GLY00.0270.01220.391-0.014-0.0140.0000.0000.0000.000
186F233LEU0-0.087-0.03222.7900.0050.0050.0000.0000.0000.000
187F234THR00.0590.00425.956-0.011-0.0110.0000.0000.0000.000
188F235GLU-1-0.846-0.93327.813-0.097-0.0970.0000.0000.0000.000
189F236SER0-0.068-0.03721.881-0.008-0.0080.0000.0000.0000.000
190F237TRP00.1040.07919.615-0.020-0.0200.0000.0000.0000.000
191F238ALA0-0.081-0.05223.276-0.018-0.0180.0000.0000.0000.000
192F239GLU-1-0.862-0.95118.573-0.301-0.3010.0000.0000.0000.000
193F240ALA00.0780.00819.638-0.017-0.0170.0000.0000.0000.000
194F241VAL0-0.031-0.01720.8770.0000.0000.0000.0000.0000.000
195F242ARG10.8810.93624.0810.1440.1440.0000.0000.0000.000
196F243LEU0-0.0490.01316.8220.0050.0050.0000.0000.0000.000
197F244GLY00.0680.02820.782-0.027-0.0270.0000.0000.0000.000
198F245LEU0-0.029-0.03823.098-0.002-0.0020.0000.0000.0000.000
199F246GLU-1-0.855-0.93219.494-0.316-0.3160.0000.0000.0000.000
200F247GLY00.0470.01221.2960.0030.0030.0000.0000.0000.000
201F248CYS00.0030.02522.0110.0050.0050.0000.0000.0000.000
202F249GLN00.0750.02725.4140.0130.0130.0000.0000.0000.000
203F250ARG10.9050.96316.5840.3810.3810.0000.0000.0000.000
204F251LEU0-0.009-0.03020.3260.0060.0060.0000.0000.0000.000
205F252TYR00.033-0.01124.2580.0120.0120.0000.0000.0000.000
206F253PRO0-0.023-0.00926.5210.0120.0120.0000.0000.0000.000
207F254VAL00.050-0.00723.3030.0060.0060.0000.0000.0000.000
208F255LEU0-0.0790.02126.3940.0020.0020.0000.0000.0000.000
209F256GLN00.0360.02027.8610.0120.0120.0000.0000.0000.000
210F257GLN0-0.056-0.02228.1280.0020.0020.0000.0000.0000.000
211F258SER0-0.076-0.03628.2230.0080.0080.0000.0000.0000.000
212F259LEU00.0780.04830.3430.0050.0050.0000.0000.0000.000
213F260VAL00.0550.01933.3090.0080.0080.0000.0000.0000.000
214F261ARG10.9370.97928.7370.1290.1290.0000.0000.0000.000
215F262ALA00.0230.01634.0960.0070.0070.0000.0000.0000.000
216F263ALA00.0600.02735.7520.0070.0070.0000.0000.0000.000
217F264ARG10.9410.99037.4570.0880.0880.0000.0000.0000.000
218F265ARG10.8970.93434.7480.0920.0920.0000.0000.0000.000
219F266ARG10.9640.99038.6320.0910.0910.0000.0000.0000.000
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