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: 2N5JR

Calculation Name: 1M06-G-Xray372

Preferred Name:

Target Type:

Ligand Name: 1',2'-dideoxyribofuranose-5'-phosphate

ligand 3-letter code: 3DR

PDB ID: 1M06

Chain ID: G

ChEMBL ID:

UniProt ID: P08767

Base Structure: X-ray

Registration Date: 2023-09-23

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1798589.269286
FMO2-HF: Nuclear repulsion 1728859.474847
FMO2-HF: Total energy -69729.794438
FMO2-MP2: Total energy -69930.369375


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(G:1:MET)


Summations of interaction energy for fragment #1(G:1:MET)
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.
-0.7091.760.014-1.251-1.2310.005
Interaction energy analysis for fragmet #1(G:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.007
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].
3G3GLN00.0190.0203.474-1.8370.6320.014-1.251-1.2310.005
4G4ASN0-0.001-0.0076.0450.4560.4560.0000.0000.0000.000
5G5PHE00.010-0.0228.095-0.085-0.0850.0000.0000.0000.000
6G6VAL00.0290.04611.5470.0430.0430.0000.0000.0000.000
7G7THR0-0.023-0.02913.0150.0440.0440.0000.0000.0000.000
8G8LYS10.9900.99515.638-0.084-0.0840.0000.0000.0000.000
9G9HIS00.0600.05318.6150.0160.0160.0000.0000.0000.000
10G10ASP-1-0.862-0.92718.805-0.370-0.3700.0000.0000.0000.000
11G11THR0-0.060-0.03120.6090.0290.0290.0000.0000.0000.000
12G12ALA00.0770.03922.753-0.022-0.0220.0000.0000.0000.000
13G13ILE00.0510.03121.337-0.008-0.0080.0000.0000.0000.000
14G14GLN0-0.047-0.01125.3660.0050.0050.0000.0000.0000.000
15G15THR0-0.003-0.01128.2620.0170.0170.0000.0000.0000.000
16G16SER00.017-0.00229.850-0.001-0.0010.0000.0000.0000.000
17G17ARG10.8870.93925.3250.2020.2020.0000.0000.0000.000
18G18PHE00.0610.03132.3040.0050.0050.0000.0000.0000.000
19G19SER0-0.016-0.00233.530-0.005-0.0050.0000.0000.0000.000
20G20VAL00.0310.02535.0420.0040.0040.0000.0000.0000.000
21G21THR0-0.022-0.02436.4560.0000.0000.0000.0000.0000.000
22G22GLY00.0260.01639.0620.0030.0030.0000.0000.0000.000
23G23ASN0-0.032-0.03040.5800.0030.0030.0000.0000.0000.000
24G24VAL00.0340.03137.674-0.002-0.0020.0000.0000.0000.000
25G25ILE00.003-0.00940.8830.0020.0020.0000.0000.0000.000
26G26PRO0-0.0230.01439.3020.0000.0000.0000.0000.0000.000
27G27ALA00.0350.00941.2960.0020.0020.0000.0000.0000.000
28G28ALA00.0780.03642.0640.0010.0010.0000.0000.0000.000
29G29PRO00.0180.00241.844-0.002-0.0020.0000.0000.0000.000
30G30THR0-0.020-0.01043.770-0.001-0.0010.0000.0000.0000.000
31G31GLY00.0150.02146.5720.0000.0000.0000.0000.0000.000
32G32ASN0-0.010-0.01446.1910.0020.0020.0000.0000.0000.000
33G33ILE00.0250.02839.470-0.001-0.0010.0000.0000.0000.000
34G34PRO0-0.012-0.00241.168-0.003-0.0030.0000.0000.0000.000
35G35VAL00.0180.02839.037-0.001-0.0010.0000.0000.0000.000
36G36ILE0-0.0260.00435.708-0.002-0.0020.0000.0000.0000.000
37G37ASN0-0.063-0.06536.161-0.004-0.0040.0000.0000.0000.000
38G38GLY00.0600.04539.9990.0040.0040.0000.0000.0000.000
39G39GLY0-0.027-0.00540.4400.0000.0000.0000.0000.0000.000
40G40SER0-0.035-0.02937.992-0.008-0.0080.0000.0000.0000.000
41G41ILE00.007-0.00633.222-0.001-0.0010.0000.0000.0000.000
42G42THR00.058-0.03035.2810.0070.0070.0000.0000.0000.000
43G43ALA0-0.0250.03532.0930.0010.0010.0000.0000.0000.000
44G44GLH00.1480.07931.080-0.004-0.0040.0000.0000.0000.000
45G45ARG10.9110.97523.8870.1810.1810.0000.0000.0000.000
46G46ALA0-0.215-0.06929.0940.0050.0050.0000.0000.0000.000
47G47VAL0-0.069-0.06726.750-0.007-0.0070.0000.0000.0000.000
48G48VAL00.0300.02429.1960.0000.0000.0000.0000.0000.000
49G49ASN0-0.061-0.03428.085-0.004-0.0040.0000.0000.0000.000
50G50LEU00.0540.02030.7460.0070.0070.0000.0000.0000.000
51G51TYR00.0200.00131.949-0.002-0.0020.0000.0000.0000.000
52G52ALA00.0130.01034.6300.0010.0010.0000.0000.0000.000
53G53ASN0-0.091-0.05036.8690.0020.0020.0000.0000.0000.000
54G54MET00.0290.02536.741-0.001-0.0010.0000.0000.0000.000
55G55ASN00.0260.02239.0100.0030.0030.0000.0000.0000.000
56G56VAL00.0310.00442.0350.0000.0000.0000.0000.0000.000
57G57SER0-0.066-0.02244.3550.0020.0020.0000.0000.0000.000
58G58THR00.007-0.00346.4650.0010.0010.0000.0000.0000.000
59G59SER00.0050.01844.8190.0020.0020.0000.0000.0000.000
60G60SER00.016-0.00743.906-0.002-0.0020.0000.0000.0000.000
61G61ASP-1-0.977-0.96940.7830.0010.0010.0000.0000.0000.000
62G62GLY00.0530.01239.763-0.001-0.0010.0000.0000.0000.000
63G63SER0-0.061-0.03336.9780.0020.0020.0000.0000.0000.000
64G64PHE00.0080.00033.335-0.001-0.0010.0000.0000.0000.000
65G65ILE00.0250.00435.6520.0010.0010.0000.0000.0000.000
66G66VAL0-0.035-0.00432.400-0.003-0.0030.0000.0000.0000.000
67G67ALA0-0.012-0.01733.9730.0010.0010.0000.0000.0000.000
68G68MET00.0370.08630.905-0.014-0.0140.0000.0000.0000.000
69G69LYS10.9200.97235.3940.0700.0700.0000.0000.0000.000
70G70VAL00.014-0.00934.401-0.007-0.0070.0000.0000.0000.000
71G71ASP-1-0.892-0.92134.690-0.083-0.0830.0000.0000.0000.000
72G72THR00.023-0.02236.0160.0010.0010.0000.0000.0000.000
73G73SER0-0.085-0.04837.0520.0040.0040.0000.0000.0000.000
74G74PRO0-0.045-0.02333.9260.0020.0020.0000.0000.0000.000
75G75THR00.0600.01936.3070.0030.0030.0000.0000.0000.000
76G76ASP-1-0.982-0.97533.215-0.053-0.0530.0000.0000.0000.000
77G77PRO0-0.0180.00934.752-0.001-0.0010.0000.0000.0000.000
78G78ASN00.0600.00732.6990.0040.0040.0000.0000.0000.000
79G79CYS0-0.0020.02729.491-0.002-0.0020.0000.0000.0000.000
80G80VAL00.0190.01024.3160.0060.0060.0000.0000.0000.000
81G81ILE00.0130.00727.653-0.015-0.0150.0000.0000.0000.000
82G82SER0-0.005-0.02323.1220.0090.0090.0000.0000.0000.000
83G83ALA00.0260.00424.597-0.010-0.0100.0000.0000.0000.000
84G84GLY0-0.023-0.02222.6090.0040.0040.0000.0000.0000.000
85G85VAL0-0.045-0.01623.227-0.009-0.0090.0000.0000.0000.000
86G86ASN00.001-0.00120.2500.0200.0200.0000.0000.0000.000
87G87LEU0-0.0150.00824.302-0.008-0.0080.0000.0000.0000.000
88G88SER00.0030.01226.9100.0120.0120.0000.0000.0000.000
89G89PHE00.002-0.04028.421-0.005-0.0050.0000.0000.0000.000
90G90ALA0-0.030-0.01531.8400.0030.0030.0000.0000.0000.000
91G91GLY00.0240.01134.1540.0040.0040.0000.0000.0000.000
92G92THR0-0.047-0.03432.8620.0000.0000.0000.0000.0000.000
93G93SER00.0110.01533.4120.0010.0010.0000.0000.0000.000
94G94TYR0-0.0660.00430.1840.0020.0020.0000.0000.0000.000
95G95PRO0-0.0200.01628.9100.0020.0020.0000.0000.0000.000
96G96ILE00.068-0.01529.4780.0060.0060.0000.0000.0000.000
97G97VAL0-0.021-0.02226.561-0.008-0.0080.0000.0000.0000.000
98G98GLY00.0580.03029.0630.0100.0100.0000.0000.0000.000
99G99ILE0-0.0100.01327.192-0.009-0.0090.0000.0000.0000.000
100G100VAL0-0.019-0.01231.0700.0070.0070.0000.0000.0000.000
101G101ARG10.8660.93334.7920.0190.0190.0000.0000.0000.000
102G102PHE00.0110.00637.3200.0040.0040.0000.0000.0000.000
103G103GLU-1-0.712-0.85540.925-0.031-0.0310.0000.0000.0000.000
104G104SER00.012-0.01143.4310.0020.0020.0000.0000.0000.000
105G105ALA00.0660.03945.934-0.003-0.0030.0000.0000.0000.000
106G106SER0-0.067-0.02647.249-0.003-0.0030.0000.0000.0000.000
107G107GLU-1-0.825-0.93044.076-0.059-0.0590.0000.0000.0000.000
108G108GLN0-0.044-0.01841.136-0.004-0.0040.0000.0000.0000.000
109G109PRO0-0.0160.00042.5750.0020.0020.0000.0000.0000.000
110G110THR00.0590.02743.173-0.001-0.0010.0000.0000.0000.000
111G111SER0-0.086-0.05043.7300.0010.0010.0000.0000.0000.000
112G112ILE00.0140.01241.3230.0000.0000.0000.0000.0000.000
113G113ALA00.0370.02244.1850.0010.0010.0000.0000.0000.000
114G114GLY00.0670.00043.0770.0000.0000.0000.0000.0000.000
115G115SER0-0.075-0.03843.3000.0010.0010.0000.0000.0000.000
116G116GLU-1-0.947-0.96744.869-0.013-0.0130.0000.0000.0000.000
117G117VAL0-0.098-0.04038.532-0.003-0.0030.0000.0000.0000.000
118G118GLU-1-0.788-0.83937.488-0.002-0.0020.0000.0000.0000.000
119G119HIS0-0.003-0.02934.849-0.005-0.0050.0000.0000.0000.000
120G120TYR0-0.052-0.05430.9810.0040.0040.0000.0000.0000.000
121G121PRO0-0.022-0.01929.701-0.005-0.0050.0000.0000.0000.000
122G122ILE0-0.006-0.00524.8000.0000.0000.0000.0000.0000.000
123G123GLU-1-0.943-0.96019.1890.1410.1410.0000.0000.0000.000
124G124MET0-0.093-0.00122.387-0.018-0.0180.0000.0000.0000.000
125G125SER0-0.019-0.01117.8280.0230.0230.0000.0000.0000.000
126G126VAL0-0.026-0.00919.8040.0140.0140.0000.0000.0000.000
127G127GLY00.0830.02522.179-0.012-0.0120.0000.0000.0000.000
128G128SER0-0.0410.00125.1270.0050.0050.0000.0000.0000.000
129G129GLY00.0800.01026.855-0.004-0.0040.0000.0000.0000.000
130G130GLY00.0580.01428.898-0.003-0.0030.0000.0000.0000.000
131G131VAL0-0.026-0.00323.923-0.009-0.0090.0000.0000.0000.000
132G132CYS0-0.0050.01025.3700.0100.0100.0000.0000.0000.000
133G133SER0-0.031-0.01520.531-0.013-0.0130.0000.0000.0000.000
134G134ALA00.0360.01421.1940.0220.0220.0000.0000.0000.000
135G135ARG10.8690.93715.6780.2180.2180.0000.0000.0000.000
136G136ASP-1-0.844-0.89319.6560.0500.0500.0000.0000.0000.000
137G137CYS0-0.082-0.05722.027-0.024-0.0240.0000.0000.0000.000
138G138ALA00.0640.03624.7740.0160.0160.0000.0000.0000.000
139G139THR0-0.018-0.02027.658-0.013-0.0130.0000.0000.0000.000
140G140VAL00.0160.01829.8190.0050.0050.0000.0000.0000.000
141G141ASP-1-0.810-0.88733.134-0.026-0.0260.0000.0000.0000.000
142G142ILE0-0.017-0.02333.782-0.002-0.0020.0000.0000.0000.000
143G143HIS0-0.0220.00936.690-0.002-0.0020.0000.0000.0000.000
144G144PRO0-0.054-0.02940.2960.0030.0030.0000.0000.0000.000
145G145ARG10.7530.82338.8210.0150.0150.0000.0000.0000.000
146G146THR0-0.052-0.01044.8420.0030.0030.0000.0000.0000.000
147G147SER0-0.056-0.04548.070-0.003-0.0030.0000.0000.0000.000
148G148GLY00.0350.01548.3080.0010.0010.0000.0000.0000.000
149G149ASN0-0.062-0.00745.878-0.002-0.0020.0000.0000.0000.000
150G150ASN0-0.0230.00142.667-0.004-0.0040.0000.0000.0000.000
151G151VAL00.0420.01037.7930.0030.0030.0000.0000.0000.000
152G152PHE0-0.050-0.01837.962-0.007-0.0070.0000.0000.0000.000
153G153VAL00.0570.01632.2410.0060.0060.0000.0000.0000.000
154G154GLY00.0050.00632.432-0.008-0.0080.0000.0000.0000.000
155G155VAL00.0140.01429.0450.0060.0060.0000.0000.0000.000
156G156ILE0-0.022-0.00531.519-0.004-0.0040.0000.0000.0000.000
157G157CYS0-0.049-0.02230.9970.0030.0030.0000.0000.0000.000
158G158SER00.013-0.01933.121-0.001-0.0010.0000.0000.0000.000
159G159SER0-0.013-0.03733.8970.0010.0010.0000.0000.0000.000
160G160ALA00.0280.01736.111-0.001-0.0010.0000.0000.0000.000
161G161LYS10.9340.96037.832-0.008-0.0080.0000.0000.0000.000
162G162TRP0-0.019-0.01834.109-0.001-0.0010.0000.0000.0000.000
163G163THR0-0.029-0.02537.8150.0030.0030.0000.0000.0000.000
164G164SER0-0.034-0.01438.657-0.003-0.0030.0000.0000.0000.000
165G165GLY00.0370.01738.1710.0020.0020.0000.0000.0000.000
166G166ARG10.8980.97734.3800.0620.0620.0000.0000.0000.000
167G167VAL00.0120.01532.0030.0020.0020.0000.0000.0000.000
168G168ILE0-0.041-0.03429.046-0.004-0.0040.0000.0000.0000.000
169G169GLY00.0490.01127.2870.0030.0030.0000.0000.0000.000
170G170THR0-0.094-0.04925.339-0.011-0.0110.0000.0000.0000.000
171G171ILE00.0310.02626.4060.0030.0030.0000.0000.0000.000
172G172ALA0-0.002-0.00824.687-0.005-0.0050.0000.0000.0000.000
173G173THR00.007-0.03226.5410.0120.0120.0000.0000.0000.000
174G174THR0-0.050-0.05125.362-0.017-0.0170.0000.0000.0000.000
175G175GLN00.0890.05127.3520.0080.0080.0000.0000.0000.000
176G176VAL0-0.040-0.02623.745-0.011-0.0110.0000.0000.0000.000
177G177ILE00.0270.01026.6550.0110.0110.0000.0000.0000.000
178G178HIS0-0.018-0.02226.247-0.010-0.0100.0000.0000.0000.000
179G179GLU-1-0.955-0.95420.223-0.190-0.1900.0000.0000.0000.000
180G180TYR0-0.041-0.02920.6390.0040.0040.0000.0000.0000.000
181G181GLN0-0.0040.01219.592-0.045-0.0450.0000.0000.0000.000
182G182VAL00.0350.00114.642-0.016-0.0160.0000.0000.0000.000
183G183LEU0-0.0030.00313.136-0.001-0.0010.0000.0000.0000.000
184G184GLN00.0300.01712.343-0.133-0.1330.0000.0000.0000.000
185G185PRO0-0.013-0.0178.8230.1280.1280.0000.0000.0000.000
186G186LEU00.004-0.0018.1420.0530.0530.0000.0000.0000.000
187G187LYS10.9110.98311.9840.6220.6220.0000.0000.0000.000