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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: 39GQL

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2090669.857948
FMO2-HF: Nuclear repulsion 2009295.801668
FMO2-HF: Total energy -81374.056279
FMO2-MP2: Total energy -81610.727428


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.
-15.37-9.9230.589-10.776-25.258-0.007
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 : -0.044 / 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].
3E4LEU0-0.0250.0033.1922.2896.5370.347-1.520-3.0740.006
4E5ILE0-0.018-0.0015.453-1.707-1.604-0.001-0.006-0.0950.000
5E6GLN0-0.029-0.0168.6890.2900.2900.0000.0000.0000.000
6E7PRO0-0.0540.00511.480-0.189-0.1890.0000.0000.0000.000
7E8SER00.0480.01215.265-0.047-0.0470.0000.0000.0000.000
8E9SER0-0.031-0.01917.474-0.035-0.0350.0000.0000.0000.000
9E11ALA00.0350.00219.4090.0600.0600.0000.0000.0000.000
10E12SER00.0030.01321.605-0.032-0.0320.0000.0000.0000.000
11E13VAL0-0.020-0.00224.5970.0270.0270.0000.0000.0000.000
12E14THR00.0320.02326.539-0.021-0.0210.0000.0000.0000.000
13E15VAL0-0.005-0.01130.0190.0090.0090.0000.0000.0000.000
14E16GLY0-0.034-0.00130.636-0.002-0.0020.0000.0000.0000.000
15E17GLU-1-0.903-0.95128.4990.1770.1770.0000.0000.0000.000
16E18THR0-0.063-0.02624.8500.0110.0110.0000.0000.0000.000
17E19VAL00.0240.02320.7960.0060.0060.0000.0000.0000.000
18E20LYS10.9340.94318.301-0.525-0.5250.0000.0000.0000.000
19E21ILE00.0160.03213.770-0.016-0.0160.0000.0000.0000.000
20E22THR0-0.001-0.01412.4110.0040.0040.0000.0000.0000.000
21E23CYS0-0.0170.0097.424-0.090-0.0900.0000.0000.0000.000
22E24SER0-0.024-0.0196.6630.0000.0000.0000.0000.0000.000
23E25GLY00.040-0.0253.486-0.7620.0370.040-0.338-0.5020.002
24E26ASP-1-0.854-0.9422.0870.3480.1945.461-1.605-3.702-0.014
25E27GLN00.0490.0001.707-3.255-3.5866.390-1.525-4.5340.007
26E28LEU0-0.0030.0703.710-2.490-1.8260.010-0.052-0.6220.001
27E29PRO0-0.074-0.0345.200-1.405-1.332-0.001-0.004-0.0660.000
28E30LYS10.8790.9266.961-2.445-2.4450.0000.0000.0000.000
29E31ASN0-0.046-0.0154.634-0.0640.041-0.001-0.001-0.1020.000
30E32PHE00.0180.0066.5290.1700.1700.0000.0000.0000.000
31E33ALA00.0350.0256.635-0.063-0.0630.0000.0000.0000.000
32E34TYR0-0.062-0.0398.348-0.041-0.0410.0000.0000.0000.000
33E35TRP00.0120.02410.760-0.098-0.0980.0000.0000.0000.000
34E36PHE00.0480.01712.022-0.046-0.0460.0000.0000.0000.000
35E37GLN00.017-0.00815.5290.0190.0190.0000.0000.0000.000
36E38GLN0-0.0010.01518.473-0.042-0.0420.0000.0000.0000.000
37E39LYS10.9830.99420.418-0.032-0.0320.0000.0000.0000.000
38E40SER0-0.002-0.01723.924-0.028-0.0280.0000.0000.0000.000
39E41ASP-1-0.948-0.97226.209-0.100-0.1000.0000.0000.0000.000
40E42LYS10.8740.93422.6980.1970.1970.0000.0000.0000.000
41E43ASN00.0280.01822.572-0.020-0.0200.0000.0000.0000.000
42E44ILE0-0.027-0.00717.2410.0240.0240.0000.0000.0000.000
43E45LEU00.0020.00619.3510.0070.0070.0000.0000.0000.000
44E46LEU00.0000.00514.8540.0150.0150.0000.0000.0000.000
45E47LEU0-0.042-0.03816.1950.0140.0140.0000.0000.0000.000
46E48ILE00.0320.01814.0040.0140.0140.0000.0000.0000.000
47E49TYR0-0.002-0.01213.419-0.020-0.0200.0000.0000.0000.000
48E50MET0-0.026-0.01712.450-0.021-0.0210.0000.0000.0000.000
49E51ASP-1-0.781-0.9069.8781.4001.4000.0000.0000.0000.000
50E52ASN0-0.051-0.02212.498-0.026-0.0260.0000.0000.0000.000
51E53LYS10.8930.97316.177-0.455-0.4550.0000.0000.0000.000
52E54ARG10.8890.92317.800-0.283-0.2830.0000.0000.0000.000
53E55PRO0-0.0350.00318.879-0.010-0.0100.0000.0000.0000.000
54E56SER00.016-0.00321.8580.0020.0020.0000.0000.0000.000
55E57GLY00.0230.01125.437-0.012-0.0120.0000.0000.0000.000
56E58ILE0-0.041-0.00120.762-0.011-0.0110.0000.0000.0000.000
57E59PRO0-0.017-0.01424.7280.0150.0150.0000.0000.0000.000
58E60GLU-1-0.879-0.95124.3370.2000.2000.0000.0000.0000.000
59E61ARG10.8320.94124.496-0.125-0.1250.0000.0000.0000.000
60E62PHE00.0580.03119.8340.0240.0240.0000.0000.0000.000
61E63SER00.0220.02919.8820.0020.0020.0000.0000.0000.000
62E64GLY00.010-0.03815.920-0.011-0.0110.0000.0000.0000.000
63E65SER0-0.0110.02615.8810.0160.0160.0000.0000.0000.000
64E66THR0-0.016-0.00610.2730.1100.1100.0000.0000.0000.000
65E67SER00.0010.00312.586-0.131-0.1310.0000.0000.0000.000
66E68GLY00.0330.02411.1520.1800.1800.0000.0000.0000.000
67E69THR00.0350.0196.123-0.230-0.2300.0000.0000.0000.000
68E70THR0-0.044-0.0267.0160.6240.6240.0000.0000.0000.000
69E71ALA00.0870.0558.968-0.399-0.3990.0000.0000.0000.000
70E72THR0-0.084-0.07010.657-0.021-0.0210.0000.0000.0000.000
71E73LEU0-0.0020.03013.703-0.059-0.0590.0000.0000.0000.000
72E74THR0-0.030-0.04115.9140.0010.0010.0000.0000.0000.000
73E75ILE00.0020.01819.570-0.021-0.0210.0000.0000.0000.000
74E76SER0-0.038-0.04122.372-0.002-0.0020.0000.0000.0000.000
75E77GLY00.0340.00225.518-0.014-0.0140.0000.0000.0000.000
76E78ALA0-0.040-0.01525.685-0.014-0.0140.0000.0000.0000.000
77E79GLN00.1110.05326.954-0.008-0.0080.0000.0000.0000.000
78E80PRO0-0.011-0.01427.979-0.002-0.0020.0000.0000.0000.000
79E81GLU-1-0.985-0.98928.8430.0680.0680.0000.0000.0000.000
80E82ASP-1-0.809-0.91524.2920.1280.1280.0000.0000.0000.000
81E83GLU-1-0.935-0.95223.6530.0360.0360.0000.0000.0000.000
82E84ALA0-0.047-0.02121.857-0.027-0.0270.0000.0000.0000.000
83E85ALA0-0.0020.01718.0870.0210.0210.0000.0000.0000.000
84E86TYR00.003-0.02015.6390.0120.0120.0000.0000.0000.000
85E87TYR00.0300.02711.9770.0280.0280.0000.0000.0000.000
86E89LEU0-0.029-0.0186.949-0.095-0.0950.0000.0000.0000.000
87E90SER00.006-0.0122.9450.3700.7600.023-0.106-0.3060.000
88E91SER00.0360.0124.048-0.433-0.229-0.001-0.037-0.1660.000
89E92TYR0-0.0120.0022.087-3.042-3.69715.383-4.693-10.035-0.011
90E93GLY00.0640.0484.434-1.423-1.2380.001-0.053-0.1330.000
91E94ASP-1-0.913-0.9656.7360.4200.4200.0000.0000.0000.000
92E95ASN0-0.093-0.0489.4460.0720.0720.0000.0000.0000.000
93E95ASN0-0.076-0.0327.6290.0890.0890.0000.0000.0000.000
94E95ASP-1-0.882-0.9336.023-1.417-1.4170.0000.0000.0000.000
95E96LEU0-0.039-0.0235.325-0.122-0.1220.0000.0000.0000.000
96E97VAL0-0.010-0.0062.000-1.027-1.2772.939-0.834-1.8550.002
97E98PHE0-0.010-0.0105.1850.4290.498-0.001-0.002-0.0660.000
98E99GLY00.0590.0336.912-0.104-0.1040.0000.0000.0000.000
99E100SER00.003-0.0258.404-0.425-0.4250.0000.0000.0000.000
100E101GLY0-0.048-0.06611.593-0.037-0.0370.0000.0000.0000.000
101E102THR0-0.062-0.02014.0080.0650.0650.0000.0000.0000.000
102E103GLN0-0.025-0.02216.4480.0190.0190.0000.0000.0000.000
103E104LEU00.0070.02620.1750.0200.0200.0000.0000.0000.000
104E105THR00.000-0.02322.055-0.020-0.0200.0000.0000.0000.000
105E106VAL0-0.020-0.01425.8320.0210.0210.0000.0000.0000.000
106E106LEU0-0.030-0.02928.259-0.018-0.0180.0000.0000.0000.000
107E107ARG10.9960.98931.356-0.038-0.0380.0000.0000.0000.000
108E108GLY00.0810.02434.6060.0060.0060.0000.0000.0000.000
109E109PRO0-0.046-0.02137.205-0.003-0.0030.0000.0000.0000.000
110E110LYS10.9760.98739.950-0.040-0.0400.0000.0000.0000.000
111E111SER00.0110.00940.147-0.002-0.0020.0000.0000.0000.000
112E112SER0-0.016-0.00540.838-0.001-0.0010.0000.0000.0000.000
113E113PRO0-0.046-0.01441.272-0.001-0.0010.0000.0000.0000.000
114E114LYS10.8900.95042.7510.0170.0170.0000.0000.0000.000
115E115VAL0-0.008-0.01344.367-0.004-0.0040.0000.0000.0000.000
116E116THR0-0.005-0.00345.3430.0040.0040.0000.0000.0000.000
117E117VAL0-0.0140.01145.785-0.005-0.0050.0000.0000.0000.000
118E118PHE0-0.027-0.00845.4280.0030.0030.0000.0000.0000.000
119E119PRO0-0.0070.00647.736-0.005-0.0050.0000.0000.0000.000
120E120PRO00.0190.02748.646-0.001-0.0010.0000.0000.0000.000
121E121SER00.0310.02649.1700.0030.0030.0000.0000.0000.000
122E122PRO00.0590.01151.061-0.002-0.0020.0000.0000.0000.000
123E123GLU-1-0.901-0.96751.243-0.071-0.0710.0000.0000.0000.000
124E124GLU-1-0.796-0.89045.896-0.101-0.1010.0000.0000.0000.000
125E125LEU00.0350.07049.764-0.003-0.0030.0000.0000.0000.000
126E126ARG10.9471.01152.1040.0750.0750.0000.0000.0000.000
127E127THR0-0.139-0.11448.190-0.002-0.0020.0000.0000.0000.000
128E128ASN00.000-0.02749.603-0.002-0.0020.0000.0000.0000.000
129E129LYS10.8080.90145.3910.1010.1010.0000.0000.0000.000
130E130ALA00.0490.00947.1430.0040.0040.0000.0000.0000.000
131E131THR0-0.029-0.01841.639-0.003-0.0030.0000.0000.0000.000
132E132LEU0-0.0220.00344.4670.0040.0040.0000.0000.0000.000
133E133VAL00.0210.00841.303-0.003-0.0030.0000.0000.0000.000
134E134CYS0-0.090-0.01342.1350.0020.0020.0000.0000.0000.000
135E135LEU0-0.009-0.01340.485-0.005-0.0050.0000.0000.0000.000
136E136VAL00.0420.03839.3100.0060.0060.0000.0000.0000.000
137E137ASN00.017-0.02439.581-0.005-0.0050.0000.0000.0000.000
138E138ASP-1-0.821-0.92639.794-0.013-0.0130.0000.0000.0000.000
139E139PHE0-0.0220.00135.5630.0010.0010.0000.0000.0000.000
140E140TYR0-0.0730.07631.8270.0040.0040.0000.0000.0000.000
141E141PRO0-0.048-0.05632.7950.0010.0010.0000.0000.0000.000
142E142GLY00.068-0.01732.871-0.009-0.0090.0000.0000.0000.000
143E143SER00.003-0.01531.894-0.007-0.0070.0000.0000.0000.000
144E144ALA00.0510.04233.8500.0020.0020.0000.0000.0000.000
145E145THR0-0.047-0.03034.676-0.007-0.0070.0000.0000.0000.000
146E146VAL00.0140.00337.0630.0050.0050.0000.0000.0000.000
147E147THR0-0.027-0.00438.996-0.009-0.0090.0000.0000.0000.000
148E148TRP00.0580.01240.0270.0060.0060.0000.0000.0000.000
149E149LYS10.8610.96643.9780.0480.0480.0000.0000.0000.000
150E150ALA00.0970.02547.312-0.001-0.0010.0000.0000.0000.000
151E151ASN0-0.065-0.00749.9780.0020.0020.0000.0000.0000.000
152E152GLY00.0300.02351.9360.0010.0010.0000.0000.0000.000
153E153ALA0-0.003-0.00448.2260.0010.0010.0000.0000.0000.000
154E154THR00.021-0.02242.2530.0020.0020.0000.0000.0000.000
155E155ILE0-0.052-0.01943.902-0.002-0.0020.0000.0000.0000.000
156E156ASN0-0.041-0.03239.248-0.002-0.0020.0000.0000.0000.000
157E157ASP-1-0.872-0.93439.145-0.117-0.1170.0000.0000.0000.000
158E158GLY0-0.0160.00238.7790.0030.0030.0000.0000.0000.000
159E159VAL00.0310.02537.1160.0030.0030.0000.0000.0000.000
160E160LYS10.9020.94131.5210.1750.1750.0000.0000.0000.000
161E161THR0-0.0150.00134.0360.0110.0110.0000.0000.0000.000
162E162THR00.0110.00331.374-0.009-0.0090.0000.0000.0000.000
163E163LYS10.8510.92030.3890.0890.0890.0000.0000.0000.000
164E164PRO00.0310.03030.0630.0050.0050.0000.0000.0000.000
165E165SER00.0370.02930.2860.0130.0130.0000.0000.0000.000
166E166LYS10.9700.98430.7260.0590.0590.0000.0000.0000.000
167E167GLN0-0.031-0.00933.0230.0080.0080.0000.0000.0000.000
168E170GLY00.0730.03133.6270.0040.0040.0000.0000.0000.000
169E171GLN0-0.091-0.03034.0630.0110.0110.0000.0000.0000.000
170E172ASN00.1180.03935.1380.0000.0000.0000.0000.0000.000
171E173TYR00.002-0.00230.388-0.003-0.0030.0000.0000.0000.000
172E174MET00.012-0.01534.0300.0000.0000.0000.0000.0000.000
173E175THR0-0.085-0.02234.982-0.008-0.0080.0000.0000.0000.000
174E176SER00.004-0.00136.0060.0040.0040.0000.0000.0000.000
175E177SER0-0.016-0.02236.465-0.013-0.0130.0000.0000.0000.000
176E178TYR00.008-0.00136.9140.0020.0020.0000.0000.0000.000
177E179LEU00.0270.00440.016-0.001-0.0010.0000.0000.0000.000
178E180SER00.002-0.01039.8300.0030.0030.0000.0000.0000.000
179E181LEU0-0.0150.05042.517-0.002-0.0020.0000.0000.0000.000
180E182THR0-0.010-0.01145.7070.0010.0010.0000.0000.0000.000
181E183ALA00.0450.01348.2340.0040.0040.0000.0000.0000.000
182E184ASP-1-0.843-0.92151.358-0.075-0.0750.0000.0000.0000.000
183E185GLN00.0480.04746.6730.0020.0020.0000.0000.0000.000
184E186TRP0-0.002-0.01350.3200.0020.0020.0000.0000.0000.000
185E187LYS11.0170.99551.7100.0690.0690.0000.0000.0000.000
186E188SER0-0.087-0.05254.4910.0040.0040.0000.0000.0000.000
187E189HIS0-0.101-0.07849.3970.0000.0000.0000.0000.0000.000
188E190ASN00.0200.02654.0900.0020.0020.0000.0000.0000.000
189E191ARG10.9240.93853.0770.0410.0410.0000.0000.0000.000
190E192VAL00.0720.06747.640-0.002-0.0020.0000.0000.0000.000
191E193SER00.004-0.05048.0650.0030.0030.0000.0000.0000.000
192E195GLN00.030-0.00244.1670.0020.0020.0000.0000.0000.000
193E196VAL00.0080.00239.990-0.004-0.0040.0000.0000.0000.000
194E197THR00.0380.00739.9970.0040.0040.0000.0000.0000.000
195E198HIS0-0.045-0.05337.688-0.009-0.0090.0000.0000.0000.000
196E199GLU-1-0.797-0.87234.3150.0290.0290.0000.0000.0000.000
197E200GLY0-0.037-0.00437.9270.0020.0020.0000.0000.0000.000
198E203GLU-1-0.867-0.91539.6710.0140.0140.0000.0000.0000.000
199E204THR0-0.0330.02042.063-0.003-0.0030.0000.0000.0000.000
200E205VAL0-0.158-0.13442.498-0.004-0.0040.0000.0000.0000.000
201E206GLU-1-0.824-0.91044.091-0.026-0.0260.0000.0000.0000.000
202E207LYS10.8850.95044.6680.0170.0170.0000.0000.0000.000
203E208SER00.0370.00847.037-0.005-0.0050.0000.0000.0000.000
204E209LEU0-0.0410.00546.3120.0020.0020.0000.0000.0000.000
205E210SER00.007-0.04949.095-0.004-0.0040.0000.0000.0000.000
206E211PRO0-0.074-0.00348.7950.0030.0030.0000.0000.0000.000
207E212ALA0-0.063-0.03152.020-0.002-0.0020.0000.0000.0000.000
208E213GLU-1-0.840-0.90754.689-0.057-0.0570.0000.0000.0000.000
209E214CYS0-0.110-0.04256.5860.0020.0020.0000.0000.0000.000
210E215LEU00.0320.01456.946-0.003-0.0030.0000.0000.0000.000