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: LZRJ9

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2090097.253223
FMO2-HF: Nuclear repulsion 2008719.66442
FMO2-HF: Total energy -81377.588803
FMO2-MP2: Total energy -81613.847857


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.
-24.387-14.8227.918-10.878-26.6051.7347234759768E-18
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 : -0.034 / 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].
3E4LEU0-0.0260.0052.8932.4386.5920.433-1.508-3.0790.007
4E5ILE0-0.028-0.0115.177-1.506-1.411-0.001-0.007-0.0870.000
5E6GLN00.029-0.0238.8260.1710.1710.0000.0000.0000.000
6E7PRO0-0.0460.01111.587-0.172-0.1720.0000.0000.0000.000
7E8SER00.0690.03115.396-0.060-0.0600.0000.0000.0000.000
8E9SER0-0.070-0.03217.210-0.038-0.0380.0000.0000.0000.000
9E11ALA00.0280.00319.5570.0540.0540.0000.0000.0000.000
10E12SER0-0.0160.00121.815-0.034-0.0340.0000.0000.0000.000
11E13VAL00.0020.00124.9140.0260.0260.0000.0000.0000.000
12E14THR00.0160.00326.835-0.021-0.0210.0000.0000.0000.000
13E15VAL0-0.001-0.01130.2920.0100.0100.0000.0000.0000.000
14E16GLY0-0.050-0.01130.937-0.003-0.0030.0000.0000.0000.000
15E17GLU-1-0.879-0.91828.7960.1830.1830.0000.0000.0000.000
16E18THR0-0.076-0.04724.3370.0100.0100.0000.0000.0000.000
17E19VAL00.0420.02821.3220.0070.0070.0000.0000.0000.000
18E20LYS10.9120.94218.242-0.492-0.4920.0000.0000.0000.000
19E21ILE00.0010.02414.250-0.012-0.0120.0000.0000.0000.000
20E22THR0-0.005-0.00912.4230.0170.0170.0000.0000.0000.000
21E23CYS00.0080.0067.798-0.118-0.1180.0000.0000.0000.000
22E24SER0-0.027-0.0067.645-0.125-0.1250.0000.0000.0000.000
23E25GLY00.025-0.0053.544-0.819-0.1460.040-0.300-0.4130.002
24E26ASP-1-0.838-0.9272.152-5.556-1.9755.023-3.112-5.492-0.021
25E27GLN00.021-0.0171.742-3.657-7.79215.113-3.421-7.5570.021
26E28LEU00.0080.0303.339-3.040-2.9750.0490.700-0.8140.001
27E29PRO0-0.078-0.0344.820-1.426-1.331-0.001-0.009-0.0860.000
28E30LYS10.8790.9346.447-2.167-2.1670.0000.0000.0000.000
29E31ASN0-0.057-0.0174.363-0.131-0.019-0.001-0.002-0.1090.000
30E32PHE00.0220.0076.3130.1350.1350.0000.0000.0000.000
31E33ALA00.0550.0386.732-0.126-0.1260.0000.0000.0000.000
32E34TYR0-0.061-0.0428.572-0.023-0.0230.0000.0000.0000.000
33E35TRP00.0010.01211.291-0.064-0.0640.0000.0000.0000.000
34E36PHE00.0410.01912.211-0.046-0.0460.0000.0000.0000.000
35E37GLN00.0470.01716.0240.0110.0110.0000.0000.0000.000
36E38GLN00.0030.01318.803-0.039-0.0390.0000.0000.0000.000
37E39LYS10.9350.95720.446-0.068-0.0680.0000.0000.0000.000
38E40SER0-0.003-0.00923.950-0.021-0.0210.0000.0000.0000.000
39E41ASP-1-0.931-0.96926.126-0.059-0.0590.0000.0000.0000.000
40E42LYS10.8670.93222.7300.1310.1310.0000.0000.0000.000
41E43ASN00.0000.00322.671-0.011-0.0110.0000.0000.0000.000
42E44ILE0-0.009-0.00717.3520.0200.0200.0000.0000.0000.000
43E45LEU00.0050.00919.5920.0040.0040.0000.0000.0000.000
44E46LEU0-0.0010.00915.2610.0160.0160.0000.0000.0000.000
45E47LEU0-0.032-0.02417.1820.0090.0090.0000.0000.0000.000
46E48ILE0-0.008-0.01914.3310.0120.0120.0000.0000.0000.000
47E49TYR00.0150.00313.743-0.013-0.0130.0000.0000.0000.000
48E50MET0-0.011-0.00712.483-0.005-0.0050.0000.0000.0000.000
49E51ASP-1-0.795-0.9259.8891.2771.2770.0000.0000.0000.000
50E52ASN0-0.0150.00412.502-0.040-0.0400.0000.0000.0000.000
51E53LYS10.8280.94116.207-0.491-0.4910.0000.0000.0000.000
52E54ARG10.9170.95518.031-0.266-0.2660.0000.0000.0000.000
53E55PRO0-0.0290.00819.395-0.010-0.0100.0000.0000.0000.000
54E56SER00.024-0.00422.1990.0020.0020.0000.0000.0000.000
55E57GLY00.0150.00825.859-0.010-0.0100.0000.0000.0000.000
56E58ILE0-0.036-0.00821.388-0.009-0.0090.0000.0000.0000.000
57E59PRO00.008-0.00125.2070.0120.0120.0000.0000.0000.000
58E60GLU-1-0.894-0.96224.6480.1980.1980.0000.0000.0000.000
59E61ARG10.7940.89224.775-0.128-0.1280.0000.0000.0000.000
60E62PHE00.0340.01520.4120.0230.0230.0000.0000.0000.000
61E63SER00.0060.01520.153-0.011-0.0110.0000.0000.0000.000
62E64GLY00.032-0.01516.103-0.005-0.0050.0000.0000.0000.000
63E65SER0-0.0040.03115.766-0.025-0.0250.0000.0000.0000.000
64E66THR0-0.048-0.0229.9470.1120.1120.0000.0000.0000.000
65E67SER0-0.0010.00812.399-0.134-0.1340.0000.0000.0000.000
66E68GLY00.0410.02410.9130.1830.1830.0000.0000.0000.000
67E69THR00.0340.0206.525-0.151-0.1510.0000.0000.0000.000
68E70THR0-0.029-0.0237.0880.6810.6810.0000.0000.0000.000
69E71ALA00.1020.0668.934-0.392-0.3920.0000.0000.0000.000
70E72THR0-0.104-0.08410.625-0.036-0.0360.0000.0000.0000.000
71E73LEU00.0020.03313.757-0.055-0.0550.0000.0000.0000.000
72E74THR0-0.024-0.04516.1120.0010.0010.0000.0000.0000.000
73E75ILE00.0160.02419.724-0.018-0.0180.0000.0000.0000.000
74E76SER0-0.036-0.01322.623-0.002-0.0020.0000.0000.0000.000
75E77GLY00.0450.00825.701-0.013-0.0130.0000.0000.0000.000
76E78ALA0-0.045-0.02125.882-0.014-0.0140.0000.0000.0000.000
77E79GLN00.0280.01627.269-0.025-0.0250.0000.0000.0000.000
78E80PRO00.0420.01328.414-0.002-0.0020.0000.0000.0000.000
79E81GLU-1-0.916-0.93329.0240.0940.0940.0000.0000.0000.000
80E82ASP-1-0.766-0.88224.6350.1460.1460.0000.0000.0000.000
81E83GLU-1-0.891-0.92624.0460.0660.0660.0000.0000.0000.000
82E84ALA0-0.057-0.03122.220-0.024-0.0240.0000.0000.0000.000
83E85ALA00.0130.01717.9000.0200.0200.0000.0000.0000.000
84E86TYR0-0.004-0.02116.0580.0200.0200.0000.0000.0000.000
85E87TYR00.0160.02911.9320.0240.0240.0000.0000.0000.000
86E89LEU0-0.027-0.0197.493-0.078-0.0780.0000.0000.0000.000
87E90SER00.011-0.0153.585-0.237-0.0210.001-0.036-0.1800.000
88E91SER00.010-0.0084.372-0.0630.083-0.001-0.018-0.1260.000
89E92TYR0-0.0130.0082.685-5.994-1.9015.630-2.708-7.014-0.008
90E93GLY00.0680.0504.861-1.171-1.0060.000-0.035-0.1300.000
91E94ASP-1-0.918-0.9656.6940.3070.3070.0000.0000.0000.000
92E95ASN0-0.095-0.0509.4190.0550.0550.0000.0000.0000.000
93E95ASN0-0.081-0.0317.9580.0160.0160.0000.0000.0000.000
94E95ASP-1-0.866-0.9275.934-0.822-0.8220.0000.0000.0000.000
95E96LEU0-0.029-0.0185.9370.1290.1290.0000.0000.0000.000
96E97VAL00.000-0.0072.111-0.955-0.6481.633-0.422-1.518-0.002
97E98PHE0-0.008-0.0065.5470.3230.3230.0000.0000.0000.000
98E99GLY00.0500.0286.867-0.107-0.1070.0000.0000.0000.000
99E100SER0-0.011-0.0278.134-0.347-0.3470.0000.0000.0000.000
100E101GLY0-0.046-0.03111.374-0.049-0.0490.0000.0000.0000.000
101E102THR0-0.056-0.03513.7470.0570.0570.0000.0000.0000.000
102E103GLN0-0.029-0.02716.3980.0100.0100.0000.0000.0000.000
103E104LEU0-0.0060.01320.0600.0140.0140.0000.0000.0000.000
104E105THR0-0.015-0.01422.208-0.020-0.0200.0000.0000.0000.000
105E106VAL0-0.023-0.02425.9750.0200.0200.0000.0000.0000.000
106E106LEU0-0.032-0.00628.588-0.017-0.0170.0000.0000.0000.000
107E107ARG10.9520.94831.642-0.048-0.0480.0000.0000.0000.000
108E108GLY00.0910.03434.9500.0040.0040.0000.0000.0000.000
109E109PRO0-0.045-0.02137.516-0.004-0.0040.0000.0000.0000.000
110E110LYS10.8740.93339.985-0.036-0.0360.0000.0000.0000.000
111E111SER00.0110.00839.883-0.003-0.0030.0000.0000.0000.000
112E112SER00.0080.00040.723-0.001-0.0010.0000.0000.0000.000
113E113PRO0-0.065-0.01940.992-0.001-0.0010.0000.0000.0000.000
114E114LYS10.8430.90842.4680.0020.0020.0000.0000.0000.000
115E115VAL0-0.026-0.02043.576-0.003-0.0030.0000.0000.0000.000
116E116THR00.0070.00045.1930.0030.0030.0000.0000.0000.000
117E117VAL00.0150.02245.673-0.004-0.0040.0000.0000.0000.000
118E118PHE0-0.022-0.01645.4600.0030.0030.0000.0000.0000.000
119E119PRO0-0.0150.00447.758-0.004-0.0040.0000.0000.0000.000
120E120PRO00.0200.02448.651-0.001-0.0010.0000.0000.0000.000
121E121SER0-0.022-0.02949.1890.0020.0020.0000.0000.0000.000
122E122PRO00.0710.01851.080-0.002-0.0020.0000.0000.0000.000
123E123GLU-1-0.871-0.91751.042-0.057-0.0570.0000.0000.0000.000
124E124GLU-1-0.804-0.87145.844-0.081-0.0810.0000.0000.0000.000
125E125LEU00.0600.03549.779-0.003-0.0030.0000.0000.0000.000
126E126ARG10.9521.00852.1180.0600.0600.0000.0000.0000.000
127E127THR0-0.097-0.05448.231-0.002-0.0020.0000.0000.0000.000
128E128ASN0-0.042-0.04749.614-0.002-0.0020.0000.0000.0000.000
129E129LYS10.7660.87045.0580.0840.0840.0000.0000.0000.000
130E130ALA00.0400.01047.1620.0030.0030.0000.0000.0000.000
131E131THR0-0.043-0.04441.808-0.003-0.0030.0000.0000.0000.000
132E132LEU0-0.0130.00844.4610.0040.0040.0000.0000.0000.000
133E133VAL00.0020.00141.166-0.002-0.0020.0000.0000.0000.000
134E134CYS0-0.065-0.00342.1660.0020.0020.0000.0000.0000.000
135E135LEU0-0.009-0.00340.123-0.003-0.0030.0000.0000.0000.000
136E136VAL00.0300.02239.1370.0050.0050.0000.0000.0000.000
137E137ASN00.003-0.03039.516-0.003-0.0030.0000.0000.0000.000
138E138ASP-1-0.806-0.88639.5840.0050.0050.0000.0000.0000.000
139E139PHE00.0070.01635.2770.0010.0010.0000.0000.0000.000
140E140TYR0-0.0390.02332.1290.0040.0040.0000.0000.0000.000
141E141PRO0-0.020-0.01932.817-0.001-0.0010.0000.0000.0000.000
142E142GLY00.062-0.01232.641-0.008-0.0080.0000.0000.0000.000
143E143SER0-0.049-0.04431.505-0.007-0.0070.0000.0000.0000.000
144E144ALA00.0610.04433.5370.0010.0010.0000.0000.0000.000
145E145THR0-0.019-0.01134.705-0.006-0.0060.0000.0000.0000.000
146E146VAL0-0.001-0.01436.9390.0050.0050.0000.0000.0000.000
147E147THR0-0.0200.00238.995-0.008-0.0080.0000.0000.0000.000
148E148TRP00.0440.00340.2510.0060.0060.0000.0000.0000.000
149E149LYS10.7990.93643.9760.0350.0350.0000.0000.0000.000
150E150ALA00.0990.03647.3110.0000.0000.0000.0000.0000.000
151E151ASN0-0.052-0.00849.9760.0020.0020.0000.0000.0000.000
152E152GLY00.0070.00951.9380.0000.0000.0000.0000.0000.000
153E153ALA00.0080.00348.3010.0010.0010.0000.0000.0000.000
154E154THR00.040-0.01442.2620.0020.0020.0000.0000.0000.000
155E155ILE0-0.042-0.01243.347-0.002-0.0020.0000.0000.0000.000
156E156ASN0-0.050-0.03939.2380.0000.0000.0000.0000.0000.000
157E157ASP-1-0.872-0.93239.142-0.101-0.1010.0000.0000.0000.000
158E158GLY00.0010.00638.7920.0030.0030.0000.0000.0000.000
159E159VAL00.0300.03937.4800.0030.0030.0000.0000.0000.000
160E160LYS10.9050.94331.8640.1430.1430.0000.0000.0000.000
161E161THR0-0.021-0.00534.0690.0110.0110.0000.0000.0000.000
162E162THR00.0070.00031.778-0.008-0.0080.0000.0000.0000.000
163E163LYS10.8490.92530.0850.0650.0650.0000.0000.0000.000
164E164PRO00.0320.03529.9100.0050.0050.0000.0000.0000.000
165E165SER00.0290.00929.9790.0070.0070.0000.0000.0000.000
166E166LYS10.9690.97630.5380.0380.0380.0000.0000.0000.000
167E167GLN00.0090.01432.8510.0050.0050.0000.0000.0000.000
168E170GLY00.0440.01633.7110.0040.0040.0000.0000.0000.000
169E171GLN0-0.0440.00334.0770.0110.0110.0000.0000.0000.000
170E172ASN00.0910.01135.072-0.001-0.0010.0000.0000.0000.000
171E173TYR0-0.0460.00630.282-0.005-0.0050.0000.0000.0000.000
172E174MET00.009-0.00834.0910.0000.0000.0000.0000.0000.000
173E175THR0-0.068-0.01134.813-0.006-0.0060.0000.0000.0000.000
174E176SER00.0340.02235.8520.0040.0040.0000.0000.0000.000
175E177SER0-0.017-0.02436.490-0.011-0.0110.0000.0000.0000.000
176E178TYR00.014-0.00336.7220.0010.0010.0000.0000.0000.000
177E179LEU00.0300.00040.037-0.001-0.0010.0000.0000.0000.000
178E180SER0-0.021-0.01740.1240.0010.0010.0000.0000.0000.000
179E181LEU0-0.0010.02742.533-0.002-0.0020.0000.0000.0000.000
180E182THR00.007-0.02945.7220.0010.0010.0000.0000.0000.000
181E183ALA00.0400.01748.2470.0030.0030.0000.0000.0000.000
182E184ASP-1-0.813-0.90451.371-0.062-0.0620.0000.0000.0000.000
183E185GLN00.0530.05746.4730.0010.0010.0000.0000.0000.000
184E186TRP00.015-0.00250.1920.0020.0020.0000.0000.0000.000
185E187LYS10.9790.97851.7260.0610.0610.0000.0000.0000.000
186E188SER0-0.092-0.03354.4170.0030.0030.0000.0000.0000.000
187E189HIS0-0.062-0.05249.672-0.001-0.0010.0000.0000.0000.000
188E190ASN00.0160.02354.0850.0020.0020.0000.0000.0000.000
189E191ARG10.9170.93553.1710.0320.0320.0000.0000.0000.000
190E192VAL00.0790.06547.733-0.001-0.0010.0000.0000.0000.000
191E193SER0-0.042-0.06048.3980.0030.0030.0000.0000.0000.000
192E195GLN00.0220.00244.1710.0020.0020.0000.0000.0000.000
193E196VAL00.0280.00339.742-0.003-0.0030.0000.0000.0000.000
194E197THR00.007-0.01240.2680.0020.0020.0000.0000.0000.000
195E198HIS0-0.025-0.04437.067-0.007-0.0070.0000.0000.0000.000
196E199GLU-1-0.757-0.85434.1470.0390.0390.0000.0000.0000.000
197E200GLY0-0.038-0.00537.7310.0020.0020.0000.0000.0000.000
198E203GLU-1-0.854-0.93139.6470.0230.0230.0000.0000.0000.000
199E204THR0-0.0190.03541.837-0.002-0.0020.0000.0000.0000.000
200E205VAL0-0.081-0.07842.504-0.004-0.0040.0000.0000.0000.000
201E206GLU-1-0.768-0.87243.829-0.015-0.0150.0000.0000.0000.000
202E207LYS10.8640.95844.8200.0090.0090.0000.0000.0000.000
203E208SER0-0.008-0.02846.761-0.005-0.0050.0000.0000.0000.000
204E209LEU0-0.0380.01546.3230.0010.0010.0000.0000.0000.000
205E210SER0-0.033-0.06749.011-0.004-0.0040.0000.0000.0000.000
206E211PRO0-0.0300.01848.8170.0020.0020.0000.0000.0000.000
207E212ALA0-0.066-0.03552.044-0.002-0.0020.0000.0000.0000.000
208E213GLU-1-0.858-0.92254.711-0.044-0.0440.0000.0000.0000.000
209E214CYS0-0.107-0.03556.6280.0010.0010.0000.0000.0000.000
210E215LEU00.0510.02557.121-0.002-0.0020.0000.0000.0000.000