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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: YZMR2

Calculation Name: 4XHJ-H-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: NAG

PDB ID: 4XHJ

Chain ID: H

ChEMBL ID:

UniProt ID: Q775J3

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2115650.284832
FMO2-HF: Nuclear repulsion 2034605.031455
FMO2-HF: Total energy -81045.253378
FMO2-MP2: Total energy -81274.620872


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(H:1:GLN)


Summations of interaction energy for fragment #1(H:1:GLN)
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.
-5.974-2.610.266-1.318-2.3120.008
Interaction energy analysis for fragmet #1(H:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.022
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].
3H3GLN0-0.0060.0052.795-5.371-2.3710.258-1.206-2.0520.008
4H4LEU0-0.008-0.0165.736-0.151-0.1510.0000.0000.0000.000
5H5VAL00.0140.0229.4850.0640.0640.0000.0000.0000.000
6H6GLN0-0.037-0.03111.655-0.101-0.1010.0000.0000.0000.000
7H7SER0-0.068-0.01315.2890.0330.0330.0000.0000.0000.000
8H8GLY00.0470.02118.241-0.030-0.0300.0000.0000.0000.000
9H9ALA00.028-0.02719.3190.0190.0190.0000.0000.0000.000
10H10GLU-1-0.938-0.97122.2150.2910.2910.0000.0000.0000.000
11H11MET00.0230.02925.832-0.005-0.0050.0000.0000.0000.000
12H12LYS10.8970.95128.485-0.204-0.2040.0000.0000.0000.000
13H13LYS10.9680.98731.750-0.132-0.1320.0000.0000.0000.000
14H14PRO00.0530.00734.7830.0050.0050.0000.0000.0000.000
15H15GLY0-0.0110.01436.411-0.003-0.0030.0000.0000.0000.000
16H16ALA0-0.040-0.00233.4890.0000.0000.0000.0000.0000.000
17H17SER0-0.014-0.02431.276-0.002-0.0020.0000.0000.0000.000
18H18VAL0-0.051-0.01325.7950.0020.0020.0000.0000.0000.000
19H19LYS10.9430.96624.307-0.216-0.2160.0000.0000.0000.000
20H20VAL00.0110.03219.0220.0140.0140.0000.0000.0000.000
21H21SER0-0.002-0.00618.075-0.012-0.0120.0000.0000.0000.000
22H22CYS0-0.044-0.00213.6990.0310.0310.0000.0000.0000.000
23H23LYS10.8580.93010.929-0.632-0.6320.0000.0000.0000.000
24H24ALA00.0530.0379.9930.0960.0960.0000.0000.0000.000
25H25SER0-0.024-0.0345.9750.1940.1940.0000.0000.0000.000
26H26GLY00.0400.0233.542-0.641-0.4450.009-0.099-0.1070.000
27H27TYR00.002-0.0034.1121.1491.317-0.001-0.013-0.1530.000
28H28THR00.0040.0047.485-0.143-0.1430.0000.0000.0000.000
29H29PHE00.0410.01111.089-0.027-0.0270.0000.0000.0000.000
30H30ILE00.0410.00012.887-0.014-0.0140.0000.0000.0000.000
31H31GLY0-0.011-0.00114.286-0.030-0.0300.0000.0000.0000.000
32H32TYR0-0.035-0.01111.5160.0280.0280.0000.0000.0000.000
33H33HIS0-0.047-0.02115.021-0.001-0.0010.0000.0000.0000.000
34H34LEU00.0090.00513.6560.0220.0220.0000.0000.0000.000
35H35HIS00.0290.00916.745-0.037-0.0370.0000.0000.0000.000
36H36TRP00.0280.01118.0210.0320.0320.0000.0000.0000.000
37H37VAL0-0.005-0.00219.875-0.026-0.0260.0000.0000.0000.000
38H38ARG10.8640.96220.855-0.127-0.1270.0000.0000.0000.000
39H39GLN0-0.007-0.00821.9370.0090.0090.0000.0000.0000.000
40H40ALA00.0530.03424.4530.0110.0110.0000.0000.0000.000
41H41PRO00.014-0.01126.9230.0000.0000.0000.0000.0000.000
42H42GLY00.0010.00927.230-0.010-0.0100.0000.0000.0000.000
43H43GLN0-0.0190.00027.941-0.012-0.0120.0000.0000.0000.000
44H44GLY00.0270.00726.1030.0070.0070.0000.0000.0000.000
45H45LEU0-0.021-0.01720.6070.0110.0110.0000.0000.0000.000
46H46GLU-1-0.831-0.92424.4700.1140.1140.0000.0000.0000.000
47H47TRP0-0.043-0.01721.6240.0110.0110.0000.0000.0000.000
48H48MET0-0.052-0.02523.907-0.004-0.0040.0000.0000.0000.000
49H49GLY00.0890.02123.717-0.013-0.0130.0000.0000.0000.000
50H50TRP0-0.050-0.01420.5270.0160.0160.0000.0000.0000.000
51H51ILE00.0430.01419.741-0.011-0.0110.0000.0000.0000.000
52H52ASN0-0.025-0.01819.9020.0340.0340.0000.0000.0000.000
53H53PRO00.0350.03316.502-0.015-0.0150.0000.0000.0000.000
54H54ASN00.0490.01419.0550.0020.0020.0000.0000.0000.000
55H55SER0-0.078-0.02320.710-0.009-0.0090.0000.0000.0000.000
56H56GLY00.003-0.00623.151-0.008-0.0080.0000.0000.0000.000
57H57GLU-1-0.890-0.93424.5290.1320.1320.0000.0000.0000.000
58H58THR0-0.066-0.03124.6640.0160.0160.0000.0000.0000.000
59H59ASN0-0.022-0.01325.583-0.015-0.0150.0000.0000.0000.000
60H60TYR00.0850.03926.2190.0170.0170.0000.0000.0000.000
61H61ALA00.0460.02628.577-0.009-0.0090.0000.0000.0000.000
62H62GLN00.0490.00030.0960.0000.0000.0000.0000.0000.000
63H63LYS10.9210.97831.821-0.107-0.1070.0000.0000.0000.000
64H64PHE0-0.003-0.03128.3670.0010.0010.0000.0000.0000.000
65H65GLN0-0.0260.01431.4270.0050.0050.0000.0000.0000.000
66H66ASP-1-0.834-0.91533.1000.1060.1060.0000.0000.0000.000
67H67TRP0-0.084-0.05232.9410.0000.0000.0000.0000.0000.000
68H68VAL0-0.018-0.01126.8700.0090.0090.0000.0000.0000.000
69H69THR0-0.017-0.00428.144-0.009-0.0090.0000.0000.0000.000
70H70MET0-0.043-0.00223.1580.0160.0160.0000.0000.0000.000
71H71THR00.0220.00823.488-0.007-0.0070.0000.0000.0000.000
72H72ARG10.8390.91418.935-0.198-0.1980.0000.0000.0000.000
73H73ASP-1-0.836-0.92519.0230.2430.2430.0000.0000.0000.000
74H74THR0-0.039-0.04017.7780.0240.0240.0000.0000.0000.000
75H75SER00.0000.02317.0670.0040.0040.0000.0000.0000.000
76H76ILE0-0.0070.00815.8700.0190.0190.0000.0000.0000.000
77H77ASN0-0.032-0.00810.9650.0330.0330.0000.0000.0000.000
78H78THR00.0200.00513.5860.0400.0400.0000.0000.0000.000
79H79ALA00.011-0.00316.201-0.037-0.0370.0000.0000.0000.000
80H80TYR0-0.005-0.01318.4910.0250.0250.0000.0000.0000.000
81H81MET0-0.0300.01121.579-0.024-0.0240.0000.0000.0000.000
82H82GLU-1-0.839-0.94223.5450.1870.1870.0000.0000.0000.000
83H83LEU00.0020.00227.116-0.010-0.0100.0000.0000.0000.000
84H84ARG10.9400.97029.283-0.141-0.1410.0000.0000.0000.000
85H85LEU0-0.050-0.01929.576-0.003-0.0030.0000.0000.0000.000
86H86ARG10.9890.99433.274-0.118-0.1180.0000.0000.0000.000
87H87SER0-0.099-0.05834.593-0.008-0.0080.0000.0000.0000.000
88H88ASP-1-0.826-0.89634.6060.1010.1010.0000.0000.0000.000
89H89ASP-1-0.941-0.99630.1360.1400.1400.0000.0000.0000.000
90H90THR0-0.0170.01229.0410.0160.0160.0000.0000.0000.000
91H91ALA00.003-0.00225.727-0.010-0.0100.0000.0000.0000.000
92H92VAL00.0030.01120.1250.0130.0130.0000.0000.0000.000
93H93TYR0-0.015-0.03921.202-0.015-0.0150.0000.0000.0000.000
94H94TYR00.0530.02615.6020.0480.0480.0000.0000.0000.000
95H96ALA00.0510.01213.3330.0430.0430.0000.0000.0000.000
96H97ARG10.8780.9658.370-0.547-0.5470.0000.0000.0000.000
97H98GLY0-0.012-0.01012.886-0.025-0.0250.0000.0000.0000.000
98H99GLY0-0.038-0.03712.6090.0390.0390.0000.0000.0000.000
99H100MET0-0.005-0.00713.4580.0080.0080.0000.0000.0000.000
100H101THR00.000-0.00216.500-0.011-0.0110.0000.0000.0000.000
101H102MET00.0360.00618.618-0.004-0.0040.0000.0000.0000.000
102H103VAL0-0.0060.00920.361-0.015-0.0150.0000.0000.0000.000
103H104ARG10.9070.95719.855-0.142-0.1420.0000.0000.0000.000
104H105GLY00.0520.01620.024-0.012-0.0120.0000.0000.0000.000
105H106VAL00.0080.01815.219-0.003-0.0030.0000.0000.0000.000
106H107MET0-0.0200.00014.8310.0220.0220.0000.0000.0000.000
107H108MET0-0.042-0.0099.699-0.035-0.0350.0000.0000.0000.000
108H109ASP-1-0.822-0.9117.1150.3720.3720.0000.0000.0000.000
109H110TRP00.019-0.0109.869-0.007-0.0070.0000.0000.0000.000
110H111GLY00.0290.02510.1180.0960.0960.0000.0000.0000.000
111H112GLN0-0.0070.01012.0150.0450.0450.0000.0000.0000.000
112H113GLY00.003-0.00213.375-0.063-0.0630.0000.0000.0000.000
113H114THR0-0.014-0.01716.8400.0400.0400.0000.0000.0000.000
114H115LEU0-0.030-0.00719.716-0.027-0.0270.0000.0000.0000.000
115H116VAL00.0060.00423.1200.0040.0040.0000.0000.0000.000
116H117THR00.010-0.00826.081-0.015-0.0150.0000.0000.0000.000
117H118VAL00.0050.00929.5510.0010.0010.0000.0000.0000.000
118H119SER00.0390.00932.719-0.010-0.0100.0000.0000.0000.000
119H120SER00.0450.00135.8830.0050.0050.0000.0000.0000.000
120H121ALA0-0.0170.01537.325-0.002-0.0020.0000.0000.0000.000
121H122SER0-0.004-0.01137.0070.0060.0060.0000.0000.0000.000
122H123THR0-0.023-0.01032.288-0.002-0.0020.0000.0000.0000.000
123H124LYS10.9380.96334.139-0.119-0.1190.0000.0000.0000.000
124H125GLY00.0400.02432.7160.0100.0100.0000.0000.0000.000
125H126PRO0-0.002-0.00130.110-0.009-0.0090.0000.0000.0000.000
126H127SER0-0.0190.00133.218-0.003-0.0030.0000.0000.0000.000
127H128VAL0-0.003-0.01631.182-0.002-0.0020.0000.0000.0000.000
128H129PHE0-0.024-0.03034.377-0.004-0.0040.0000.0000.0000.000
129H130PRO0-0.055-0.03334.446-0.002-0.0020.0000.0000.0000.000
130H131LEU00.0200.01034.934-0.003-0.0030.0000.0000.0000.000
131H132ALA00.0040.00436.7690.0000.0000.0000.0000.0000.000
132H133PRO00.0270.02435.8040.0020.0020.0000.0000.0000.000
133H145LEU00.0450.03429.930-0.003-0.0030.0000.0000.0000.000
134H146GLY0-0.078-0.02033.0600.0030.0030.0000.0000.0000.000
135H147CYS0-0.060-0.01725.4770.0090.0090.0000.0000.0000.000
136H148LEU00.0500.01432.2320.0000.0000.0000.0000.0000.000
137H149VAL00.0010.01929.5880.0000.0000.0000.0000.0000.000
138H150LYS10.9010.94732.990-0.090-0.0900.0000.0000.0000.000
139H151ASP-1-0.862-0.93535.7030.0940.0940.0000.0000.0000.000
140H152TYR0-0.024-0.01329.644-0.001-0.0010.0000.0000.0000.000
141H153PHE00.0060.00032.840-0.003-0.0030.0000.0000.0000.000
142H154PRO0-0.037-0.01529.4210.0020.0020.0000.0000.0000.000
143H155GLU-1-0.770-0.86826.8610.1880.1880.0000.0000.0000.000
144H156PRO0-0.011-0.02422.6950.0030.0030.0000.0000.0000.000
145H157VAL00.000-0.01225.1770.0000.0000.0000.0000.0000.000
146H158THR0-0.0190.00019.7790.0090.0090.0000.0000.0000.000
147H159VAL0-0.002-0.01322.359-0.008-0.0080.0000.0000.0000.000
148H160SER0-0.0080.00419.0260.0210.0210.0000.0000.0000.000
149H161TRP00.0450.01121.013-0.011-0.0110.0000.0000.0000.000
150H162ASN00.0310.00120.7710.0060.0060.0000.0000.0000.000
151H163SER0-0.016-0.02117.9250.0050.0050.0000.0000.0000.000
152H164GLY0-0.015-0.00416.6550.0660.0660.0000.0000.0000.000
153H165ALA0-0.0200.00416.335-0.010-0.0100.0000.0000.0000.000
154H166LEU0-0.059-0.02018.162-0.044-0.0440.0000.0000.0000.000
155H167THR00.0200.01615.9910.0220.0220.0000.0000.0000.000
156H168SER00.002-0.00518.3940.0110.0110.0000.0000.0000.000
157H169GLY00.023-0.00521.2840.0070.0070.0000.0000.0000.000
158H170VAL0-0.037-0.01221.0360.0040.0040.0000.0000.0000.000
159H171HIS00.0060.00823.9090.0070.0070.0000.0000.0000.000
160H172THR0-0.023-0.01923.4090.0060.0060.0000.0000.0000.000
161H173PHE0-0.020-0.01126.1160.0000.0000.0000.0000.0000.000
162H174PRO00.0290.00428.2950.0130.0130.0000.0000.0000.000
163H175ALA00.0000.01629.277-0.007-0.0070.0000.0000.0000.000
164H176VAL0-0.0070.00131.053-0.007-0.0070.0000.0000.0000.000
165H177LEU0-0.019-0.02734.2920.0040.0040.0000.0000.0000.000
166H178GLN0-0.022-0.00236.698-0.011-0.0110.0000.0000.0000.000
167H179SER00.0260.00239.9360.0000.0000.0000.0000.0000.000
168H180SER0-0.011-0.00941.2810.0000.0000.0000.0000.0000.000
169H181GLY00.0170.01639.8360.0010.0010.0000.0000.0000.000
170H182LEU0-0.085-0.03436.8020.0080.0080.0000.0000.0000.000
171H183TYR00.0140.01031.219-0.002-0.0020.0000.0000.0000.000
172H184SER0-0.041-0.02033.919-0.003-0.0030.0000.0000.0000.000
173H185LEU00.0490.03628.125-0.004-0.0040.0000.0000.0000.000
174H186SER00.0240.00231.8030.0020.0020.0000.0000.0000.000
175H187SER0-0.008-0.01426.1800.0060.0060.0000.0000.0000.000
176H188VAL00.0290.03228.481-0.005-0.0050.0000.0000.0000.000
177H189VAL00.0330.01524.8410.0060.0060.0000.0000.0000.000
178H190THR0-0.012-0.00825.925-0.008-0.0080.0000.0000.0000.000
179H191VAL0-0.001-0.00228.6680.0010.0010.0000.0000.0000.000
180H192PRO0-0.0020.01630.0790.0000.0000.0000.0000.0000.000
181H200THR00.0090.00530.2410.0020.0020.0000.0000.0000.000
182H201TYR00.000-0.00325.2370.0070.0070.0000.0000.0000.000
183H202ILE00.000-0.00925.057-0.003-0.0030.0000.0000.0000.000
184H204ASN00.0380.00922.0850.0100.0100.0000.0000.0000.000
185H205VAL00.0370.02523.6160.0180.0180.0000.0000.0000.000
186H206ASN0-0.018-0.01720.840-0.011-0.0110.0000.0000.0000.000
187H207HIS00.0290.01524.339-0.002-0.0020.0000.0000.0000.000
188H208LYS10.9240.95421.264-0.324-0.3240.0000.0000.0000.000
189H209PRO0-0.040-0.01424.8800.0000.0000.0000.0000.0000.000
190H210SER00.0130.00128.027-0.002-0.0020.0000.0000.0000.000
191H211ASN0-0.081-0.02126.2150.0130.0130.0000.0000.0000.000
192H212THR00.0210.01927.378-0.015-0.0150.0000.0000.0000.000
193H213LYS10.9500.96322.114-0.301-0.3010.0000.0000.0000.000
194H214VAL0-0.0140.00226.969-0.014-0.0140.0000.0000.0000.000
195H215ASP-1-0.865-0.92426.1990.1990.1990.0000.0000.0000.000
196H216LYS10.8970.94228.606-0.120-0.1200.0000.0000.0000.000
197H217ARG10.8690.91629.988-0.054-0.0540.0000.0000.0000.000
198H218VAL0-0.037-0.01630.738-0.002-0.0020.0000.0000.0000.000
199H219GLU-1-0.805-0.89133.5550.0420.0420.0000.0000.0000.000
200H220PRO00.0030.00636.9210.0030.0030.0000.0000.0000.000
201H221LYS10.9580.96939.776-0.056-0.0560.0000.0000.0000.000
202H222SER00.0050.00842.846-0.002-0.0020.0000.0000.0000.000
203H223CYS0-0.053-0.02444.8400.0030.0030.0000.0000.0000.000
204H224ASP-1-0.920-0.95147.7190.0250.0250.0000.0000.0000.000