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: QY55Y

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 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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2381058.306557
FMO2-HF: Nuclear repulsion 2299311.180791
FMO2-HF: Total energy -81747.125765
FMO2-MP2: Total energy -81985.85237


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.
-0.9231.2-0.017-1.208-0.8970.004
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 : 0.038 / 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].
3F31ARG10.8400.9113.8201.6213.744-0.017-1.208-0.8970.004
4F32ASP-1-0.810-0.9207.247-0.895-0.8950.0000.0000.0000.000
5F33PRO00.0070.02010.615-0.188-0.1880.0000.0000.0000.000
6F34THR00.0510.01213.0440.0710.0710.0000.0000.0000.000
7F35ARG10.7750.9068.7281.5611.5610.0000.0000.0000.000
8F36LEU00.0090.00613.469-0.063-0.0630.0000.0000.0000.000
9F37ARG10.7250.82911.6590.6130.6130.0000.0000.0000.000
10F38PRO00.0180.01413.9990.0290.0290.0000.0000.0000.000
11F39VAL00.0580.01617.037-0.002-0.0020.0000.0000.0000.000
12F40TYR0-0.045-0.02220.2350.0340.0340.0000.0000.0000.000
13F41ALA00.0660.02222.641-0.007-0.0070.0000.0000.0000.000
14F42ARG10.9260.96125.9120.0570.0570.0000.0000.0000.000
15F43ALA00.0330.02029.2810.0000.0000.0000.0000.0000.000
16F44GLY00.0830.03631.8360.0060.0060.0000.0000.0000.000
17F45LEU0-0.127-0.08330.6700.0060.0060.0000.0000.0000.000
18F46LEU0-0.037-0.01533.1190.0060.0060.0000.0000.0000.000
19F47SER00.0830.03335.894-0.002-0.0020.0000.0000.0000.000
20F48GLN00.0190.02339.0760.0020.0020.0000.0000.0000.000
21F49ALA0-0.0040.01637.5360.0000.0000.0000.0000.0000.000
22F50LYS10.8610.90939.6570.0510.0510.0000.0000.0000.000
23F51GLY00.1120.06137.9480.0010.0010.0000.0000.0000.000
24F52SER0-0.130-0.07234.357-0.001-0.0010.0000.0000.0000.000
25F53ALA00.0070.04629.927-0.003-0.0030.0000.0000.0000.000
26F54TYR0-0.064-0.05224.0840.0070.0070.0000.0000.0000.000
27F55LEU0-0.015-0.01022.075-0.007-0.0070.0000.0000.0000.000
28F56GLU-1-0.827-0.93619.060-0.107-0.1070.0000.0000.0000.000
29F57ALA0-0.034-0.00716.717-0.022-0.0220.0000.0000.0000.000
30F58GLY0-0.0130.00514.441-0.059-0.0590.0000.0000.0000.000
31F59GLY00.006-0.00313.902-0.007-0.0070.0000.0000.0000.000
32F60THR0-0.0200.01715.9990.0000.0000.0000.0000.0000.000
33F61LYS10.7880.91218.5210.0930.0930.0000.0000.0000.000
34F62VAL00.0040.00322.6670.0050.0050.0000.0000.0000.000
35F63LEU0-0.0440.00025.2440.0030.0030.0000.0000.0000.000
36F64CYS0-0.0040.01428.976-0.008-0.0080.0000.0000.0000.000
37F65ALA00.0010.01131.8090.0050.0050.0000.0000.0000.000
38F66VAL00.0280.03335.477-0.002-0.0020.0000.0000.0000.000
39F67SER0-0.089-0.08537.8120.0070.0070.0000.0000.0000.000
40F68GLY00.019-0.00641.444-0.002-0.0020.0000.0000.0000.000
41F69PRO0-0.0030.02844.197-0.002-0.0020.0000.0000.0000.000
42F70ARG10.8860.92143.5070.0610.0610.0000.0000.0000.000
43F71GLN00.0430.02248.532-0.003-0.0030.0000.0000.0000.000
44F72ALA0-0.0100.00548.1670.0020.0020.0000.0000.0000.000
45F92LEU00.0170.00152.0060.0000.0000.0000.0000.0000.000
46F93ARG10.8980.93949.5190.0640.0640.0000.0000.0000.000
47F94GLY00.0020.01647.953-0.002-0.0020.0000.0000.0000.000
48F95ARG10.9340.96440.4050.0850.0850.0000.0000.0000.000
49F96LEU0-0.0140.00736.8810.0050.0050.0000.0000.0000.000
50F97LEU0-0.005-0.00138.8190.0000.0000.0000.0000.0000.000
51F98CYS0-0.033-0.00533.924-0.002-0.0020.0000.0000.0000.000
52F99ASP-1-0.894-0.95434.058-0.090-0.0900.0000.0000.0000.000
53F100PHE00.0140.01324.526-0.007-0.0070.0000.0000.0000.000
54F101ARG10.9480.97129.0780.0830.0830.0000.0000.0000.000
55F102ARG10.8860.94220.8690.1830.1830.0000.0000.0000.000
56F103ALA00.0070.01424.9210.0110.0110.0000.0000.0000.000
57F104PRO0-0.012-0.00525.533-0.003-0.0030.0000.0000.0000.000
58F105PHE0-0.032-0.04324.5090.0100.0100.0000.0000.0000.000
59F106ALA00.0280.03921.7690.0100.0100.0000.0000.0000.000
60F107GLY0-0.029-0.02718.371-0.030-0.0300.0000.0000.0000.000
61F108ARG10.9600.99215.3540.1280.1280.0000.0000.0000.000
62F109ARG10.9520.97719.5510.0050.0050.0000.0000.0000.000
63F110ARG10.9730.98722.3700.0030.0030.0000.0000.0000.000
64F111ARG10.8600.92623.1200.1340.1340.0000.0000.0000.000
65F112ALA00.005-0.01027.160-0.003-0.0030.0000.0000.0000.000
66F113PRO00.0150.01630.621-0.001-0.0010.0000.0000.0000.000
67F114PRO00.0270.00631.181-0.006-0.0060.0000.0000.0000.000
68F115GLY00.0510.00729.9650.0000.0000.0000.0000.0000.000
69F116GLY00.0100.01530.877-0.008-0.0080.0000.0000.0000.000
70F117CYS0-0.023-0.01329.5820.0000.0000.0000.0000.0000.000
71F118GLU-1-0.782-0.86224.130-0.174-0.1740.0000.0000.0000.000
72F119GLU-1-0.803-0.93226.964-0.144-0.1440.0000.0000.0000.000
73F120ARG10.9150.99529.6920.0970.0970.0000.0000.0000.000
74F121GLU-1-0.925-0.96727.295-0.189-0.1890.0000.0000.0000.000
75F122LEU0-0.0010.00324.328-0.003-0.0030.0000.0000.0000.000
76F123ALA0-0.009-0.02428.101-0.003-0.0030.0000.0000.0000.000
77F124LEU0-0.044-0.00531.2020.0020.0020.0000.0000.0000.000
78F125ALA00.1010.06428.9760.0020.0020.0000.0000.0000.000
79F126LEU0-0.020-0.00227.776-0.001-0.0010.0000.0000.0000.000
80F127GLN0-0.072-0.07730.3430.0090.0090.0000.0000.0000.000
81F128GLU-1-0.866-0.95533.134-0.144-0.1440.0000.0000.0000.000
82F129ALA0-0.068-0.02829.960-0.001-0.0010.0000.0000.0000.000
83F130LEU0-0.088-0.07029.8040.0030.0030.0000.0000.0000.000
84F131GLU-1-0.863-0.91433.299-0.104-0.1040.0000.0000.0000.000
85F132PRO0-0.047-0.02435.2000.0080.0080.0000.0000.0000.000
86F133ALA00.0120.01434.8290.0050.0050.0000.0000.0000.000
87F134VAL0-0.018-0.00836.9250.0050.0050.0000.0000.0000.000
88F135ARG10.8700.94939.9970.0730.0730.0000.0000.0000.000
89F136LEU00.0850.01042.6890.0010.0010.0000.0000.0000.000
90F137GLY0-0.053-0.03545.8490.0040.0040.0000.0000.0000.000
91F138ARG10.8130.90447.1180.0660.0660.0000.0000.0000.000
92F139TYR00.025-0.00344.5470.0020.0020.0000.0000.0000.000
93F140PRO00.0300.02148.939-0.001-0.0010.0000.0000.0000.000
94F141ARG10.9220.94051.3730.0490.0490.0000.0000.0000.000
95F142ALA0-0.0070.00048.5570.0020.0020.0000.0000.0000.000
96F143GLN00.0140.01643.504-0.004-0.0040.0000.0000.0000.000
97F144LEU00.0080.01639.1780.0040.0040.0000.0000.0000.000
98F145GLU-1-0.848-0.89139.113-0.067-0.0670.0000.0000.0000.000
99F146VAL00.0390.02033.6720.0020.0020.0000.0000.0000.000
100F147SER0-0.006-0.00734.212-0.001-0.0010.0000.0000.0000.000
101F148ALA00.0490.00029.003-0.001-0.0010.0000.0000.0000.000
102F149LEU0-0.051-0.01227.2430.0020.0020.0000.0000.0000.000
103F150LEU00.0230.01721.0080.0000.0000.0000.0000.0000.000
104F151LEU0-0.014-0.02524.0490.0090.0090.0000.0000.0000.000
105F152GLU-1-0.838-0.92717.909-0.062-0.0620.0000.0000.0000.000
106F153ASP-1-0.817-0.94617.064-0.334-0.3340.0000.0000.0000.000
107F154GLY00.0300.00414.582-0.009-0.0090.0000.0000.0000.000
108F155GLY0-0.004-0.00113.345-0.069-0.0690.0000.0000.0000.000
109F156SER00.1280.07014.2100.0480.0480.0000.0000.0000.000
110F157ALA0-0.085-0.05016.9110.0510.0510.0000.0000.0000.000
111F158LEU00.0640.05319.4210.0400.0400.0000.0000.0000.000
112F159ALA00.0710.02920.6160.0330.0330.0000.0000.0000.000
113F160ALA0-0.044-0.02020.3100.0300.0300.0000.0000.0000.000
114F161ALA00.0360.00822.2830.0310.0310.0000.0000.0000.000
115F162LEU00.0210.01124.4600.0150.0150.0000.0000.0000.000
116F163THR0-0.032-0.01324.4060.0090.0090.0000.0000.0000.000
117F164ALA0-0.010-0.00925.9890.0160.0160.0000.0000.0000.000
118F165ALA00.072-0.01527.5990.0150.0150.0000.0000.0000.000
119F166ALA00.0370.01530.0420.0120.0120.0000.0000.0000.000
120F167LEU0-0.033-0.01328.0120.0120.0120.0000.0000.0000.000
121F168ALA0-0.002-0.00932.2130.0080.0080.0000.0000.0000.000
122F169LEU00.0530.04734.5180.0090.0090.0000.0000.0000.000
123F170ALA00.0580.02536.0150.0070.0070.0000.0000.0000.000
124F171ASP-1-0.851-0.89834.858-0.069-0.0690.0000.0000.0000.000
125F172ALA00.011-0.01036.9190.0070.0070.0000.0000.0000.000
126F173GLY0-0.136-0.04639.4100.0050.0050.0000.0000.0000.000
127F174VAL0-0.054-0.04339.0970.0040.0040.0000.0000.0000.000
128F175GLU-1-0.783-0.87241.781-0.073-0.0730.0000.0000.0000.000
129F176MET0-0.0030.02637.227-0.002-0.0020.0000.0000.0000.000
130F177TYR0-0.099-0.04339.0400.0080.0080.0000.0000.0000.000
131F178ASP-1-0.739-0.86934.687-0.145-0.1450.0000.0000.0000.000
132F179LEU0-0.065-0.04331.7780.0020.0020.0000.0000.0000.000
133F180VAL00.0360.01729.130-0.007-0.0070.0000.0000.0000.000
134F181VAL0-0.054-0.04024.820-0.001-0.0010.0000.0000.0000.000
135F182GLY00.0480.04124.287-0.003-0.0030.0000.0000.0000.000
136F183CYS0-0.070-0.03519.4260.0100.0100.0000.0000.0000.000
137F184GLY00.1080.04116.6420.0180.0180.0000.0000.0000.000
138F185LEU0-0.059-0.00515.820-0.038-0.0380.0000.0000.0000.000
139F186SER0-0.0150.01812.106-0.012-0.0120.0000.0000.0000.000
140F187LEU00.0670.05613.728-0.066-0.0660.0000.0000.0000.000
141F188ALA00.0080.0018.665-0.042-0.0420.0000.0000.0000.000
142F189PRO00.0240.0077.7580.1180.1180.0000.0000.0000.000
143F190GLY0-0.055-0.0309.7870.1570.1570.0000.0000.0000.000
144F191PRO00.0020.01510.8670.1080.1080.0000.0000.0000.000
145F192ALA00.0130.01514.0220.0470.0470.0000.0000.0000.000
146F193PRO00.042-0.00614.584-0.088-0.0880.0000.0000.0000.000
147F194THR0-0.0400.0139.864-0.025-0.0250.0000.0000.0000.000
148F195TRP00.0210.00312.909-0.055-0.0550.0000.0000.0000.000
149F196LEU0-0.025-0.0358.047-0.134-0.1340.0000.0000.0000.000
150F197LEU0-0.0020.01712.5680.1460.1460.0000.0000.0000.000
151F198ASP-1-0.837-0.90913.577-0.685-0.6850.0000.0000.0000.000
152F199PRO00.0060.03010.674-0.154-0.1540.0000.0000.0000.000
153F200THR0-0.003-0.0478.3370.3210.3210.0000.0000.0000.000
154F201ARG10.8770.96810.3700.1880.1880.0000.0000.0000.000
155F202LEU0-0.065-0.0466.9820.0820.0820.0000.0000.0000.000
156F203GLU-1-0.776-0.8685.687-2.503-2.5030.0000.0000.0000.000
157F204GLU-1-0.885-0.9537.994-0.662-0.6620.0000.0000.0000.000
158F205GLU-1-0.853-0.9209.835-0.297-0.2970.0000.0000.0000.000
159F206ARG10.7910.8845.9740.6750.6750.0000.0000.0000.000
160F207ALA0-0.036-0.00810.525-0.115-0.1150.0000.0000.0000.000
161F208ALA00.0200.03212.5540.0910.0910.0000.0000.0000.000
162F209ALA00.027-0.01314.7620.0760.0760.0000.0000.0000.000
163F210GLY00.0000.01616.109-0.075-0.0750.0000.0000.0000.000
164F211LEU00.004-0.01018.0780.0640.0640.0000.0000.0000.000
165F212THR0-0.050-0.02218.728-0.044-0.0440.0000.0000.0000.000
166F213VAL0-0.0170.00621.1440.0390.0390.0000.0000.0000.000
167F214ALA0-0.004-0.01923.725-0.017-0.0170.0000.0000.0000.000
168F215LEU0-0.061-0.04826.3800.0090.0090.0000.0000.0000.000
169F216MET0-0.044-0.01029.060-0.003-0.0030.0000.0000.0000.000
170F217PRO0-0.0060.00929.2890.0000.0000.0000.0000.0000.000
171F218VAL00.0310.01531.0990.0040.0040.0000.0000.0000.000
172F219LEU0-0.0130.01534.5210.0060.0060.0000.0000.0000.000
173F220ASN0-0.083-0.06732.149-0.001-0.0010.0000.0000.0000.000
174F221GLN0-0.0240.00233.0230.0070.0070.0000.0000.0000.000
175F222VAL00.0350.00630.531-0.010-0.0100.0000.0000.0000.000
176F223ALA00.0140.02329.3600.0080.0080.0000.0000.0000.000
177F224GLY00.0670.02628.8340.0130.0130.0000.0000.0000.000
178F225LEU0-0.061-0.02726.198-0.022-0.0220.0000.0000.0000.000
179F226LEU00.0260.00424.9750.0160.0160.0000.0000.0000.000
180F227GLY00.0400.01322.516-0.031-0.0310.0000.0000.0000.000
181F228SER0-0.075-0.01221.4270.0290.0290.0000.0000.0000.000
182F229GLY0-0.025-0.02021.801-0.029-0.0290.0000.0000.0000.000
183F230GLU-1-0.902-0.95517.555-0.475-0.4750.0000.0000.0000.000
184F231GLY00.0280.01519.4790.0100.0100.0000.0000.0000.000
185F232GLY0-0.0020.00020.542-0.014-0.0140.0000.0000.0000.000
186F233LEU0-0.057-0.02422.8350.0200.0200.0000.0000.0000.000
187F234THR00.040-0.00226.097-0.018-0.0180.0000.0000.0000.000
188F235GLU-1-0.858-0.93527.918-0.225-0.2250.0000.0000.0000.000
189F236SER0-0.062-0.02021.791-0.015-0.0150.0000.0000.0000.000
190F237TRP00.1300.05919.662-0.039-0.0390.0000.0000.0000.000
191F238ALA0-0.082-0.04323.585-0.017-0.0170.0000.0000.0000.000
192F239GLU-1-0.873-0.96217.930-0.623-0.6230.0000.0000.0000.000
193F240ALA00.0940.03620.210-0.016-0.0160.0000.0000.0000.000
194F241VAL0-0.041-0.03021.1510.0170.0170.0000.0000.0000.000
195F242ARG10.9030.95124.2060.3030.3030.0000.0000.0000.000
196F243LEU0-0.0390.00216.7040.0180.0180.0000.0000.0000.000
197F244GLY00.0560.02720.782-0.023-0.0230.0000.0000.0000.000
198F245LEU0-0.019-0.03023.1400.0100.0100.0000.0000.0000.000
199F246GLU-1-0.810-0.88819.303-0.430-0.4300.0000.0000.0000.000
200F247GLY00.0950.03821.3130.0170.0170.0000.0000.0000.000
201F248CYS0-0.0240.01622.0230.0190.0190.0000.0000.0000.000
202F249GLN00.0270.00825.4260.0320.0320.0000.0000.0000.000
203F250ARG10.7910.87316.4430.4710.4710.0000.0000.0000.000
204F251LEU0-0.014-0.02220.4250.0190.0190.0000.0000.0000.000
205F252TYR00.013-0.02024.2690.0210.0210.0000.0000.0000.000
206F253PRO0-0.048-0.02126.7650.0180.0180.0000.0000.0000.000
207F254VAL00.0300.00123.2560.0120.0120.0000.0000.0000.000
208F255LEU0-0.0370.00625.7800.0110.0110.0000.0000.0000.000
209F256GLN00.0430.04027.8720.0180.0180.0000.0000.0000.000
210F257GLN0-0.024-0.01428.5380.0050.0050.0000.0000.0000.000
211F258SER0-0.090-0.04428.2140.0120.0120.0000.0000.0000.000
212F259LEU00.0640.03730.3530.0090.0090.0000.0000.0000.000
213F260VAL00.0600.02533.3200.0100.0100.0000.0000.0000.000
214F261ARG10.9340.97628.3050.0750.0750.0000.0000.0000.000
215F262ALA00.0200.01834.0550.0080.0080.0000.0000.0000.000
216F263ALA00.0610.02435.7610.0060.0060.0000.0000.0000.000
217F264ARG10.9400.99137.7580.0620.0620.0000.0000.0000.000
218F265ARG10.9200.94635.0390.0430.0430.0000.0000.0000.000
219F266ARG10.8450.92737.9810.0650.0650.0000.0000.0000.000
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