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: 6YRNZ

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 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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1798380.585196
FMO2-HF: Nuclear repulsion 1728648.792783
FMO2-HF: Total energy -69731.792413
FMO2-MP2: Total energy -69932.085677


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.
-0.3331.983-0.002-1.169-1.1450.006
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 : 0.018 / q_NPA : 0.006
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].
3G3GLN0-0.0050.0053.695-1.9040.412-0.002-1.169-1.1450.006
4G4ASN0-0.001-0.0126.0540.6920.6920.0000.0000.0000.000
5G5PHE00.011-0.0168.301-0.033-0.0330.0000.0000.0000.000
6G6VAL00.0380.05111.7620.0840.0840.0000.0000.0000.000
7G7THR0-0.036-0.03813.202-0.007-0.0070.0000.0000.0000.000
8G8LYS10.8820.93515.5890.0870.0870.0000.0000.0000.000
9G9HIS00.0370.03318.1340.0330.0330.0000.0000.0000.000
10G10ASP-1-0.830-0.89718.701-0.472-0.4720.0000.0000.0000.000
11G11THR0-0.014-0.00620.4440.0420.0420.0000.0000.0000.000
12G12ALA00.0980.05522.566-0.023-0.0230.0000.0000.0000.000
13G13ILE00.0390.01321.163-0.009-0.0090.0000.0000.0000.000
14G14GLN0-0.053-0.02425.3760.0110.0110.0000.0000.0000.000
15G15THR00.0100.00528.2780.0210.0210.0000.0000.0000.000
16G16SER00.011-0.00229.746-0.003-0.0030.0000.0000.0000.000
17G17ARG10.8820.93724.9850.2700.2700.0000.0000.0000.000
18G18PHE00.0560.03131.9520.0090.0090.0000.0000.0000.000
19G19SER0-0.0060.00533.162-0.007-0.0070.0000.0000.0000.000
20G20VAL00.0320.02134.7010.0070.0070.0000.0000.0000.000
21G21THR0-0.028-0.02836.1420.0000.0000.0000.0000.0000.000
22G22GLY00.0310.02338.7680.0030.0030.0000.0000.0000.000
23G23ASN0-0.029-0.02840.3940.0010.0010.0000.0000.0000.000
24G24VAL00.0360.01837.277-0.002-0.0020.0000.0000.0000.000
25G25ILE0-0.017-0.01140.7090.0020.0020.0000.0000.0000.000
26G26PRO0-0.0270.01539.1410.0000.0000.0000.0000.0000.000
27G27ALA00.0290.00641.1330.0030.0030.0000.0000.0000.000
28G28ALA00.0800.03541.862-0.001-0.0010.0000.0000.0000.000
29G29PRO00.0230.00141.645-0.002-0.0020.0000.0000.0000.000
30G30THR0-0.011-0.00443.533-0.001-0.0010.0000.0000.0000.000
31G31GLY00.0050.01446.3480.0010.0010.0000.0000.0000.000
32G32ASN0-0.001-0.01145.8790.0020.0020.0000.0000.0000.000
33G33ILE0-0.0240.01139.121-0.001-0.0010.0000.0000.0000.000
34G34PRO00.0200.01340.721-0.003-0.0030.0000.0000.0000.000
35G35VAL00.0090.01338.384-0.003-0.0030.0000.0000.0000.000
36G36ILE0-0.0240.00535.182-0.001-0.0010.0000.0000.0000.000
37G37ASN0-0.051-0.05835.406-0.006-0.0060.0000.0000.0000.000
38G38GLY00.0640.04439.4860.0050.0050.0000.0000.0000.000
39G39GLY0-0.035-0.00939.9870.0010.0010.0000.0000.0000.000
40G40SER0-0.037-0.02437.025-0.007-0.0070.0000.0000.0000.000
41G41ILE0-0.035-0.01332.787-0.001-0.0010.0000.0000.0000.000
42G42THR00.0950.00535.1020.0080.0080.0000.0000.0000.000
43G43ALA0-0.0450.01132.2170.0010.0010.0000.0000.0000.000
44G44GLH00.034-0.01131.014-0.003-0.0030.0000.0000.0000.000
45G45ARG10.8750.93823.1620.2710.2710.0000.0000.0000.000
46G46ALA00.0260.00528.7150.0080.0080.0000.0000.0000.000
47G47VAL0-0.067-0.03026.293-0.012-0.0120.0000.0000.0000.000
48G48VAL00.0390.02728.7290.0040.0040.0000.0000.0000.000
49G49ASN0-0.075-0.03727.758-0.005-0.0050.0000.0000.0000.000
50G50LEU00.0490.02130.4200.0110.0110.0000.0000.0000.000
51G51TYR00.0380.00331.689-0.002-0.0020.0000.0000.0000.000
52G52ALA00.0020.00734.3970.0030.0030.0000.0000.0000.000
53G53ASN0-0.073-0.04236.8130.0020.0020.0000.0000.0000.000
54G54MET00.0310.03836.662-0.002-0.0020.0000.0000.0000.000
55G55ASN00.0220.00838.9150.0050.0050.0000.0000.0000.000
56G56VAL00.0190.00641.7250.0000.0000.0000.0000.0000.000
57G57SER0-0.035-0.01344.2330.0030.0030.0000.0000.0000.000
58G58THR0-0.002-0.01046.3990.0020.0020.0000.0000.0000.000
59G59SER0-0.0100.00844.6470.0030.0030.0000.0000.0000.000
60G60SER00.002-0.01143.786-0.002-0.0020.0000.0000.0000.000
61G61ASP-1-0.931-0.94940.600-0.024-0.0240.0000.0000.0000.000
62G62GLY00.0430.00939.5650.0000.0000.0000.0000.0000.000
63G63SER0-0.108-0.05036.725-0.001-0.0010.0000.0000.0000.000
64G64PHE00.0440.01433.1760.0010.0010.0000.0000.0000.000
65G65ILE00.0280.01235.278-0.002-0.0020.0000.0000.0000.000
66G66VAL0-0.043-0.01431.844-0.002-0.0020.0000.0000.0000.000
67G67ALA00.006-0.00833.386-0.001-0.0010.0000.0000.0000.000
68G68MET0-0.1240.01730.053-0.009-0.0090.0000.0000.0000.000
69G69LYS10.8970.94434.8930.0980.0980.0000.0000.0000.000
70G70VAL00.0080.01134.177-0.011-0.0110.0000.0000.0000.000
71G71ASP-1-0.878-0.90034.757-0.122-0.1220.0000.0000.0000.000
72G72THR00.017-0.01836.2170.0000.0000.0000.0000.0000.000
73G73SER0-0.076-0.05037.3950.0070.0070.0000.0000.0000.000
74G74PRO0-0.040-0.02234.0440.0040.0040.0000.0000.0000.000
75G75THR00.0410.01736.5040.0040.0040.0000.0000.0000.000
76G76ASP-1-0.965-0.97133.296-0.096-0.0960.0000.0000.0000.000
77G77PRO00.0110.01135.203-0.001-0.0010.0000.0000.0000.000
78G78ASN00.002-0.02132.1810.0070.0070.0000.0000.0000.000
79G79CYS0-0.0130.01929.684-0.002-0.0020.0000.0000.0000.000
80G80VAL00.0180.01024.6860.0060.0060.0000.0000.0000.000
81G81ILE00.0080.00227.659-0.015-0.0150.0000.0000.0000.000
82G82SER00.005-0.00922.6080.0060.0060.0000.0000.0000.000
83G83ALA00.0400.01223.924-0.004-0.0040.0000.0000.0000.000
84G84GLY0-0.028-0.02422.012-0.007-0.0070.0000.0000.0000.000
85G85VAL0-0.049-0.01922.673-0.002-0.0020.0000.0000.0000.000
86G86ASN0-0.0090.00720.0830.0120.0120.0000.0000.0000.000
87G87LEU0-0.0030.01424.158-0.004-0.0040.0000.0000.0000.000
88G88SER0-0.0120.00626.8200.0090.0090.0000.0000.0000.000
89G89PHE00.028-0.03528.357-0.003-0.0030.0000.0000.0000.000
90G90ALA0-0.030-0.01531.7840.0040.0040.0000.0000.0000.000
91G91GLY00.0330.01534.1140.0050.0050.0000.0000.0000.000
92G92THR0-0.044-0.02432.578-0.001-0.0010.0000.0000.0000.000
93G93SER00.0080.00333.2980.0020.0020.0000.0000.0000.000
94G94TYR0-0.0710.00629.8420.0040.0040.0000.0000.0000.000
95G95PRO0-0.0150.00728.8280.0020.0020.0000.0000.0000.000
96G96ILE00.0510.01229.1340.0050.0050.0000.0000.0000.000
97G97VAL0-0.028-0.02826.164-0.006-0.0060.0000.0000.0000.000
98G98GLY00.0440.02528.8070.0090.0090.0000.0000.0000.000
99G99ILE0-0.0030.01226.641-0.008-0.0080.0000.0000.0000.000
100G100VAL0-0.011-0.01230.6050.0100.0100.0000.0000.0000.000
101G101ARG10.8410.91034.2850.0530.0530.0000.0000.0000.000
102G102PHE00.0290.01136.7120.0060.0060.0000.0000.0000.000
103G103GLU-1-0.694-0.82940.287-0.061-0.0610.0000.0000.0000.000
104G104SER0-0.010-0.01942.9500.0030.0030.0000.0000.0000.000
105G105ALA00.0650.03845.479-0.003-0.0030.0000.0000.0000.000
106G106SER0-0.055-0.01646.524-0.002-0.0020.0000.0000.0000.000
107G107GLU-1-0.766-0.87943.797-0.089-0.0890.0000.0000.0000.000
108G108GLN0-0.040-0.01840.697-0.006-0.0060.0000.0000.0000.000
109G109PRO00.0020.01041.9590.0030.0030.0000.0000.0000.000
110G110THR00.0460.02342.575-0.002-0.0020.0000.0000.0000.000
111G111SER0-0.072-0.04043.2340.0010.0010.0000.0000.0000.000
112G112ILE00.0080.00840.7890.0000.0000.0000.0000.0000.000
113G113ALA00.0280.02543.8010.0010.0010.0000.0000.0000.000
114G114GLY00.051-0.00242.778-0.001-0.0010.0000.0000.0000.000
115G115SER0-0.103-0.06742.9990.0000.0000.0000.0000.0000.000
116G116GLU-1-0.907-0.93544.410-0.036-0.0360.0000.0000.0000.000
117G117VAL0-0.099-0.04038.052-0.005-0.0050.0000.0000.0000.000
118G118GLU-1-0.780-0.81537.266-0.040-0.0400.0000.0000.0000.000
119G119HIS00.011-0.02234.605-0.007-0.0070.0000.0000.0000.000
120G120TYR0-0.029-0.03330.5510.0040.0040.0000.0000.0000.000
121G121PRO0-0.025-0.01929.311-0.008-0.0080.0000.0000.0000.000
122G122ILE0-0.007-0.00224.499-0.003-0.0030.0000.0000.0000.000
123G123GLU-1-0.872-0.92319.1570.0280.0280.0000.0000.0000.000
124G124MET0-0.084-0.01922.121-0.023-0.0230.0000.0000.0000.000
125G125SER0-0.027-0.01317.6320.0240.0240.0000.0000.0000.000
126G126VAL0-0.019-0.01919.5260.0170.0170.0000.0000.0000.000
127G127GLY00.0900.02722.006-0.011-0.0110.0000.0000.0000.000
128G128SER0-0.045-0.00124.9940.0110.0110.0000.0000.0000.000
129G129GLY00.0840.01426.731-0.004-0.0040.0000.0000.0000.000
130G130GLY00.0520.01328.824-0.002-0.0020.0000.0000.0000.000
131G131VAL0-0.023-0.00223.804-0.010-0.0100.0000.0000.0000.000
132G132CYS00.0060.02525.1930.0110.0110.0000.0000.0000.000
133G133SER0-0.043-0.03520.463-0.019-0.0190.0000.0000.0000.000
134G134ALA00.0350.01220.9840.0230.0230.0000.0000.0000.000
135G135ARG10.8610.93115.1840.4010.4010.0000.0000.0000.000
136G136ASP-1-0.790-0.88419.244-0.072-0.0720.0000.0000.0000.000
137G137CYS0-0.067-0.02521.521-0.020-0.0200.0000.0000.0000.000
138G138ALA00.0550.03424.2870.0170.0170.0000.0000.0000.000
139G139THR0-0.017-0.01827.370-0.015-0.0150.0000.0000.0000.000
140G140VAL00.0150.01229.8770.0080.0080.0000.0000.0000.000
141G141ASP-1-0.800-0.87133.121-0.063-0.0630.0000.0000.0000.000
142G142ILE00.015-0.01533.931-0.002-0.0020.0000.0000.0000.000
143G143HIS0-0.0260.01236.8720.0010.0010.0000.0000.0000.000
144G144PRO0-0.043-0.02940.4780.0030.0030.0000.0000.0000.000
145G145ARG10.7370.79138.7250.0500.0500.0000.0000.0000.000
146G146THR0-0.065-0.02544.8750.0050.0050.0000.0000.0000.000
147G147SER0-0.026-0.03148.004-0.003-0.0030.0000.0000.0000.000
148G148GLY00.0030.00048.3780.0020.0020.0000.0000.0000.000
149G149ASN0-0.062-0.01045.314-0.001-0.0010.0000.0000.0000.000
150G150ASN0-0.013-0.00442.340-0.005-0.0050.0000.0000.0000.000
151G151VAL00.0390.00837.7040.0040.0040.0000.0000.0000.000
152G152PHE0-0.057-0.02137.479-0.009-0.0090.0000.0000.0000.000
153G153VAL00.0450.01631.6980.0060.0060.0000.0000.0000.000
154G154GLY00.0170.01331.752-0.008-0.0080.0000.0000.0000.000
155G155VAL0-0.0020.00328.2180.0050.0050.0000.0000.0000.000
156G156ILE0-0.026-0.00131.057-0.001-0.0010.0000.0000.0000.000
157G157CYS0-0.056-0.02830.8430.0000.0000.0000.0000.0000.000
158G158SER00.041-0.01132.9270.0020.0020.0000.0000.0000.000
159G159SER0-0.004-0.02833.7090.0000.0000.0000.0000.0000.000
160G160ALA00.0190.01235.9260.0010.0010.0000.0000.0000.000
161G161LYS10.9250.95437.6610.0160.0160.0000.0000.0000.000
162G162TRP00.000-0.00733.959-0.002-0.0020.0000.0000.0000.000
163G163THR0-0.041-0.03437.6980.0050.0050.0000.0000.0000.000
164G164SER0-0.021-0.00638.568-0.005-0.0050.0000.0000.0000.000
165G165GLY00.0340.01738.1150.0020.0020.0000.0000.0000.000
166G166ARG10.8780.96834.5010.0900.0900.0000.0000.0000.000
167G167VAL00.0150.01531.8580.0020.0020.0000.0000.0000.000
168G168ILE0-0.042-0.02829.198-0.003-0.0030.0000.0000.0000.000
169G169GLY00.0570.01527.0870.0010.0010.0000.0000.0000.000
170G170THR0-0.107-0.05424.960-0.010-0.0100.0000.0000.0000.000
171G171ILE00.0280.02526.003-0.001-0.0010.0000.0000.0000.000
172G172ALA00.004-0.00324.133-0.001-0.0010.0000.0000.0000.000
173G173THR0-0.019-0.05625.9290.0080.0080.0000.0000.0000.000
174G174THR0-0.073-0.06525.116-0.014-0.0140.0000.0000.0000.000
175G175GLN00.1100.05527.0820.0050.0050.0000.0000.0000.000
176G176VAL0-0.053-0.03623.845-0.011-0.0110.0000.0000.0000.000
177G177ILE00.0260.01226.8560.0130.0130.0000.0000.0000.000
178G178HIS0-0.024-0.02126.385-0.011-0.0110.0000.0000.0000.000
179G179GLU-1-0.948-0.95120.394-0.297-0.2970.0000.0000.0000.000
180G180TYR0-0.043-0.03420.7160.0100.0100.0000.0000.0000.000
181G181GLN00.0020.01519.622-0.056-0.0560.0000.0000.0000.000
182G182VAL00.027-0.00114.746-0.024-0.0240.0000.0000.0000.000
183G183LEU00.0100.00913.516-0.003-0.0030.0000.0000.0000.000
184G184GLN00.0250.02412.315-0.115-0.1150.0000.0000.0000.000
185G185PRO00.000-0.0219.0380.1250.1250.0000.0000.0000.000
186G186LEU0-0.0170.0007.7820.0660.0660.0000.0000.0000.000
187G187LYS10.9100.97011.9600.7610.7610.0000.0000.0000.000