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

tag_button

FMODB ID: 94QG2

Calculation Name: 1NFD-E-Xray372

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 1NFD

Chain ID: E

ChEMBL ID:

UniProt ID: P01849

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 OptAll
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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2085095.381065
FMO2-HF: Nuclear repulsion 2003715.211277
FMO2-HF: Total energy -81380.169788
FMO2-MP2: Total energy -81616.06908


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(E:2:TYR)


Summations of interaction energy for fragment #1(E:2:TYR)
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.
-35.842-18.13424.85-13.482-29.077-0.032
Interaction energy analysis for fragmet #1(E:2:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : 0.005
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].
3E4LEU0-0.0150.0042.789-0.2654.8620.973-2.207-3.8930.016
4E5ILE0-0.007-0.0055.579-1.033-1.0330.0000.0000.0000.000
5E6GLN00.034-0.0089.1270.1890.1890.0000.0000.0000.000
6E7PRO0-0.0290.01511.969-0.106-0.1060.0000.0000.0000.000
7E8SER00.0520.03215.783-0.028-0.0280.0000.0000.0000.000
8E9SER0-0.031-0.02417.142-0.026-0.0260.0000.0000.0000.000
9E11ALA00.0200.00519.9220.0360.0360.0000.0000.0000.000
10E12SER0-0.0010.00121.821-0.023-0.0230.0000.0000.0000.000
11E13VAL0-0.028-0.00625.2400.0180.0180.0000.0000.0000.000
12E14THR00.008-0.00427.150-0.016-0.0160.0000.0000.0000.000
13E15VAL0-0.023-0.02630.1590.0040.0040.0000.0000.0000.000
14E16GLY0-0.047-0.01731.2910.0020.0020.0000.0000.0000.000
15E17GLU-1-0.840-0.88928.7080.0470.0470.0000.0000.0000.000
16E18THR0-0.094-0.07324.6760.0040.0040.0000.0000.0000.000
17E19VAL00.0400.02121.4890.0040.0040.0000.0000.0000.000
18E20LYS10.9190.95017.954-0.241-0.2410.0000.0000.0000.000
19E21ILE00.0100.01614.348-0.018-0.0180.0000.0000.0000.000
20E22THR00.0060.00412.5420.0000.0000.0000.0000.0000.000
21E23CYS0-0.002-0.0037.854-0.062-0.0620.0000.0000.0000.000
22E24SER0-0.0270.0027.442-0.052-0.0520.0000.0000.0000.000
23E25GLY00.0670.0143.269-1.440-0.3630.139-0.526-0.6900.004
24E26ASP-1-0.854-0.9372.404-5.189-2.4494.545-2.277-5.008-0.036
25E27GLN00.009-0.0051.729-3.439-2.4407.567-2.808-5.7590.017
26E28LEU00.0250.0253.614-3.022-2.1580.045-0.061-0.8490.001
27E29PRO0-0.073-0.0374.881-1.147-1.057-0.001-0.008-0.0820.000
28E30LYS10.8930.9496.480-1.290-1.2900.0000.0000.0000.000
29E31ASN0-0.040-0.0153.8570.0750.259-0.001-0.012-0.1710.000
30E32PHE00.0250.0035.7480.2790.2790.0000.0000.0000.000
31E33ALA00.0170.0187.000-0.398-0.3980.0000.0000.0000.000
32E34TYR0-0.041-0.0228.3990.0790.0790.0000.0000.0000.000
33E35TRP00.004-0.00410.821-0.039-0.0390.0000.0000.0000.000
34E36PHE00.009-0.00812.011-0.013-0.0130.0000.0000.0000.000
35E37GLN00.0380.02615.8610.0190.0190.0000.0000.0000.000
36E38GLN00.0050.00518.737-0.040-0.0400.0000.0000.0000.000
37E39LYS10.8950.94120.4640.1070.1070.0000.0000.0000.000
38E40SER00.0120.00223.984-0.017-0.0170.0000.0000.0000.000
39E41ASP-1-0.867-0.93726.347-0.155-0.1550.0000.0000.0000.000
40E42LYS10.8970.94022.4510.2350.2350.0000.0000.0000.000
41E43ASN0-0.0070.00122.248-0.027-0.0270.0000.0000.0000.000
42E44ILE00.0190.01017.1540.0170.0170.0000.0000.0000.000
43E45LEU0-0.0010.00619.5070.0120.0120.0000.0000.0000.000
44E46LEU00.002-0.00115.0940.0000.0000.0000.0000.0000.000
45E47LEU0-0.020-0.00617.4040.0260.0260.0000.0000.0000.000
46E48ILE0-0.011-0.01914.5660.0320.0320.0000.0000.0000.000
47E49TYR00.0060.00313.711-0.046-0.0460.0000.0000.0000.000
48E50MET0-0.0140.00011.9230.0580.0580.0000.0000.0000.000
49E51ASP-1-0.748-0.88010.0300.6020.6020.0000.0000.0000.000
50E52ASN0-0.055-0.02012.495-0.007-0.0070.0000.0000.0000.000
51E53LYS10.8440.94415.624-0.093-0.0930.0000.0000.0000.000
52E54ARG10.9220.97618.025-0.058-0.0580.0000.0000.0000.000
53E55PRO0-0.0140.00819.5950.0040.0040.0000.0000.0000.000
54E56SER00.020-0.00922.3470.0120.0120.0000.0000.0000.000
55E57GLY00.0050.00225.749-0.012-0.0120.0000.0000.0000.000
56E58ILE0-0.0260.00621.467-0.003-0.0030.0000.0000.0000.000
57E59PRO00.000-0.01125.3770.0120.0120.0000.0000.0000.000
58E60GLU-1-0.909-0.97224.9660.0280.0280.0000.0000.0000.000
59E61ARG10.8040.88124.6740.0340.0340.0000.0000.0000.000
60E62PHE00.0150.02020.4680.0160.0160.0000.0000.0000.000
61E63SER00.0280.01220.304-0.010-0.0100.0000.0000.0000.000
62E64GLY00.0040.00416.2220.0070.0070.0000.0000.0000.000
63E65SER0-0.056-0.03215.225-0.013-0.0130.0000.0000.0000.000
64E66THR00.032-0.00610.0790.1110.1110.0000.0000.0000.000
65E67SER0-0.030-0.02611.621-0.163-0.1630.0000.0000.0000.000
66E68GLY00.0180.01810.8330.0830.0830.0000.0000.0000.000
67E69THR00.0180.0216.234-0.018-0.0180.0000.0000.0000.000
68E70THR0-0.013-0.0177.1170.5030.5030.0000.0000.0000.000
69E71ALA00.0810.0678.600-0.311-0.3110.0000.0000.0000.000
70E72THR0-0.065-0.06810.256-0.047-0.0470.0000.0000.0000.000
71E73LEU00.0060.04213.657-0.049-0.0490.0000.0000.0000.000
72E74THR0-0.016-0.02316.0830.0180.0180.0000.0000.0000.000
73E75ILE00.0000.01419.735-0.018-0.0180.0000.0000.0000.000
74E76SER0-0.016-0.00922.8070.0130.0130.0000.0000.0000.000
75E77GLY00.0440.03025.939-0.008-0.0080.0000.0000.0000.000
76E78ALA0-0.043-0.01326.032-0.011-0.0110.0000.0000.0000.000
77E79GLN00.019-0.00527.631-0.005-0.0050.0000.0000.0000.000
78E80PRO00.0220.00128.921-0.007-0.0070.0000.0000.0000.000
79E81GLU-1-0.833-0.89828.250-0.063-0.0630.0000.0000.0000.000
80E82ASP-1-0.787-0.87024.706-0.037-0.0370.0000.0000.0000.000
81E83GLU-1-0.824-0.88024.111-0.074-0.0740.0000.0000.0000.000
82E84ALA0-0.045-0.02322.136-0.013-0.0130.0000.0000.0000.000
83E85ALA00.0290.03018.1510.0140.0140.0000.0000.0000.000
84E86TYR0-0.041-0.04216.3150.0030.0030.0000.0000.0000.000
85E87TYR00.0040.00411.9430.0230.0230.0000.0000.0000.000
86E89LEU0-0.017-0.0087.217-0.135-0.1350.0000.0000.0000.000
87E90SER00.018-0.0113.776-0.2120.0050.000-0.034-0.1820.000
88E91SER0-0.0030.0023.6230.2810.6160.000-0.086-0.2480.000
89E92TYR0-0.0110.0012.213-17.325-11.5888.997-4.766-9.969-0.036
90E93GLY00.0560.0244.245-0.363-0.0510.008-0.122-0.1970.001
91E94ASP-1-0.916-0.9576.9420.2540.2540.0000.0000.0000.000
92E95ASN0-0.101-0.0628.845-0.106-0.1060.0000.0000.0000.000
93E95ASN0-0.089-0.0387.384-0.211-0.2110.0000.0000.0000.000
94E95ASP-1-0.837-0.8985.527-0.596-0.5960.0000.0000.0000.000
95E96LEU0-0.029-0.0255.389-0.904-0.9040.0000.0000.0000.000
96E97VAL0-0.011-0.0052.186-0.593-0.6522.579-0.574-1.9470.001
97E98PHE00.002-0.0095.3040.4770.562-0.001-0.001-0.0820.000
98E99GLY00.0340.0136.744-0.209-0.2090.0000.0000.0000.000
99E100SER0-0.052-0.0398.246-0.205-0.2050.0000.0000.0000.000
100E101GLY0-0.035-0.01011.3140.0040.0040.0000.0000.0000.000
101E102THR0-0.053-0.03613.6670.0670.0670.0000.0000.0000.000
102E103GLN0-0.018-0.01016.6220.0010.0010.0000.0000.0000.000
103E104LEU0-0.023-0.00520.2050.0260.0260.0000.0000.0000.000
104E105THR00.0080.00022.399-0.014-0.0140.0000.0000.0000.000
105E106VAL0-0.030-0.03026.2330.0150.0150.0000.0000.0000.000
106E106LEU0-0.009-0.00628.772-0.007-0.0070.0000.0000.0000.000
107E107ARG10.8730.90631.7970.0550.0550.0000.0000.0000.000
108E108GLY00.0350.02435.0100.0040.0040.0000.0000.0000.000
109E109PRO0-0.049-0.02437.7150.0000.0000.0000.0000.0000.000
110E110LYS10.8620.91539.7720.0190.0190.0000.0000.0000.000
111E111SER0-0.033-0.01240.1250.0020.0020.0000.0000.0000.000
112E112SER00.013-0.00340.740-0.002-0.0020.0000.0000.0000.000
113E113PRO0-0.029-0.00541.104-0.001-0.0010.0000.0000.0000.000
114E114LYS10.8270.91442.6880.0510.0510.0000.0000.0000.000
115E115VAL00.0190.00343.744-0.004-0.0040.0000.0000.0000.000
116E116THR0-0.037-0.02545.2000.0040.0040.0000.0000.0000.000
117E117VAL0-0.0010.00445.590-0.004-0.0040.0000.0000.0000.000
118E118PHE0-0.011-0.01245.2620.0020.0020.0000.0000.0000.000
119E119PRO00.0080.01147.832-0.003-0.0030.0000.0000.0000.000
120E120PRO00.0080.01548.959-0.002-0.0020.0000.0000.0000.000
121E121SER0-0.014-0.02549.5850.0020.0020.0000.0000.0000.000
122E122PRO00.0530.01251.4350.0000.0000.0000.0000.0000.000
123E123GLU-1-0.877-0.91851.014-0.064-0.0640.0000.0000.0000.000
124E124GLU-1-0.789-0.86146.087-0.084-0.0840.0000.0000.0000.000
125E125LEU00.0460.02749.7560.0000.0000.0000.0000.0000.000
126E126ARG10.9360.98552.5420.0630.0630.0000.0000.0000.000
127E127THR0-0.082-0.04448.274-0.001-0.0010.0000.0000.0000.000
128E128ASN0-0.013-0.02049.841-0.001-0.0010.0000.0000.0000.000
129E129LYS10.7850.88245.3400.0770.0770.0000.0000.0000.000
130E130ALA00.0730.01746.9330.0030.0030.0000.0000.0000.000
131E131THR0-0.045-0.04941.860-0.003-0.0030.0000.0000.0000.000
132E132LEU0-0.0260.00344.6330.0010.0010.0000.0000.0000.000
133E133VAL00.0220.01941.572-0.004-0.0040.0000.0000.0000.000
134E134CYS0-0.039-0.02842.3530.0020.0020.0000.0000.0000.000
135E135LEU0-0.0080.00740.116-0.006-0.0060.0000.0000.0000.000
136E136VAL00.0150.00539.1470.0060.0060.0000.0000.0000.000
137E137ASN00.0220.00739.370-0.011-0.0110.0000.0000.0000.000
138E138ASP-1-0.808-0.89139.521-0.048-0.0480.0000.0000.0000.000
139E139PHE00.0030.01335.1090.0040.0040.0000.0000.0000.000
140E140TYR00.0020.02232.407-0.002-0.0020.0000.0000.0000.000
141E141PRO0-0.005-0.00533.1300.0040.0040.0000.0000.0000.000
142E142GLY00.0430.00532.718-0.008-0.0080.0000.0000.0000.000
143E143SER0-0.019-0.02731.128-0.003-0.0030.0000.0000.0000.000
144E144ALA00.0180.00833.273-0.002-0.0020.0000.0000.0000.000
145E145THR0-0.0030.01434.672-0.007-0.0070.0000.0000.0000.000
146E146VAL0-0.021-0.02936.9120.0050.0050.0000.0000.0000.000
147E147THR0-0.020-0.00238.682-0.005-0.0050.0000.0000.0000.000
148E148TRP00.0230.00840.3050.0060.0060.0000.0000.0000.000
149E149LYS10.8480.91843.6300.0510.0510.0000.0000.0000.000
150E150ALA00.0590.04046.8570.0010.0010.0000.0000.0000.000
151E151ASN0-0.047-0.03049.6640.0020.0020.0000.0000.0000.000
152E152GLY00.0060.01151.3110.0020.0020.0000.0000.0000.000
153E153ALA00.0220.02147.8810.0000.0000.0000.0000.0000.000
154E154THR0-0.002-0.02241.5950.0010.0010.0000.0000.0000.000
155E155ILE0-0.0370.00343.2260.0000.0000.0000.0000.0000.000
156E156ASN0-0.033-0.02438.856-0.004-0.0040.0000.0000.0000.000
157E157ASP-1-0.857-0.92738.595-0.086-0.0860.0000.0000.0000.000
158E158GLY00.0100.00439.3480.0020.0020.0000.0000.0000.000
159E159VAL0-0.0100.01436.886-0.003-0.0030.0000.0000.0000.000
160E160LYS10.8990.94732.3270.1340.1340.0000.0000.0000.000
161E161THR0-0.0140.00233.9730.0070.0070.0000.0000.0000.000
162E162THR0-0.016-0.01831.764-0.010-0.0100.0000.0000.0000.000
163E163LYS10.8410.90829.9610.1140.1140.0000.0000.0000.000
164E164PRO00.0380.03529.935-0.003-0.0030.0000.0000.0000.000
165E165SER00.0200.00430.1930.0110.0110.0000.0000.0000.000
166E166LYS10.8790.92529.8660.1310.1310.0000.0000.0000.000
167E167GLN00.0240.01732.7940.0040.0040.0000.0000.0000.000
168E170GLY00.0350.02734.6150.0060.0060.0000.0000.0000.000
169E171GLN0-0.021-0.01134.9350.0070.0070.0000.0000.0000.000
170E172ASN00.002-0.00535.3350.0080.0080.0000.0000.0000.000
171E173TYR00.0180.00829.850-0.008-0.0080.0000.0000.0000.000
172E174MET0-0.030-0.01633.9570.0050.0050.0000.0000.0000.000
173E175THR0-0.048-0.02534.755-0.006-0.0060.0000.0000.0000.000
174E176SER00.0340.03935.9760.0070.0070.0000.0000.0000.000
175E177SER0-0.002-0.00336.460-0.009-0.0090.0000.0000.0000.000
176E178TYR00.018-0.00136.8690.0020.0020.0000.0000.0000.000
177E179LEU00.0210.01139.804-0.002-0.0020.0000.0000.0000.000
178E180SER0-0.002-0.02239.5750.0020.0020.0000.0000.0000.000
179E181LEU0-0.0230.01442.3190.0000.0000.0000.0000.0000.000
180E182THR0-0.007-0.03845.5640.0010.0010.0000.0000.0000.000
181E183ALA00.0280.00748.2510.0020.0020.0000.0000.0000.000
182E184ASP-1-0.784-0.86751.383-0.055-0.0550.0000.0000.0000.000
183E185GLN00.0630.06346.2510.0000.0000.0000.0000.0000.000
184E186TRP00.0500.02550.3250.0010.0010.0000.0000.0000.000
185E187LYS10.8140.88451.8640.0580.0580.0000.0000.0000.000
186E188SER0-0.030-0.00854.2380.0030.0030.0000.0000.0000.000
187E189HIS0-0.073-0.05049.648-0.001-0.0010.0000.0000.0000.000
188E190ASN00.0170.01053.8930.0000.0000.0000.0000.0000.000
189E191ARG10.9060.94052.7910.0410.0410.0000.0000.0000.000
190E192VAL00.0340.01947.376-0.001-0.0010.0000.0000.0000.000
191E193SER0-0.039-0.01448.167-0.002-0.0020.0000.0000.0000.000
192E195GLN00.0260.01444.4850.0010.0010.0000.0000.0000.000
193E196VAL00.0150.00640.131-0.004-0.0040.0000.0000.0000.000
194E197THR0-0.027-0.02540.2040.0040.0040.0000.0000.0000.000
195E198HIS0-0.003-0.01936.860-0.008-0.0080.0000.0000.0000.000
196E199GLU-1-0.792-0.89134.528-0.037-0.0370.0000.0000.0000.000
197E200GLY0-0.0120.00337.9810.0010.0010.0000.0000.0000.000
198E203GLU-1-0.841-0.91640.049-0.023-0.0230.0000.0000.0000.000
199E204THR00.0020.01742.255-0.003-0.0030.0000.0000.0000.000
200E205VAL0-0.059-0.03142.8880.0000.0000.0000.0000.0000.000
201E206GLU-1-0.759-0.85844.161-0.041-0.0410.0000.0000.0000.000
202E207LYS10.8590.94445.0030.0420.0420.0000.0000.0000.000
203E208SER0-0.024-0.04346.642-0.005-0.0050.0000.0000.0000.000
204E209LEU0-0.006-0.00446.5810.0020.0020.0000.0000.0000.000
205E210SER00.0170.00148.832-0.002-0.0020.0000.0000.0000.000
206E211PRO0-0.0130.00349.2900.0030.0030.0000.0000.0000.000
207E212ALA0-0.021-0.02152.461-0.001-0.0010.0000.0000.0000.000
208E213GLU-1-0.826-0.87255.426-0.048-0.0480.0000.0000.0000.000
209E214CYS0-0.111-0.04756.4520.0020.0020.0000.0000.0000.000
210E215LEU0-0.029-0.04457.673-0.002-0.0020.0000.0000.0000.000