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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: ZVG6N

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 OptAll
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 -1794517.950335
FMO2-HF: Nuclear repulsion 1724785.26921
FMO2-HF: Total energy -69732.681125
FMO2-MP2: Total energy -69932.836812


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.
0.4112.32-0.002-0.908-0.9990.004
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 : 0.030 / q_NPA : 0.010
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].
3G3GLN0-0.019-0.0053.855-1.1280.781-0.002-0.908-0.9990.004
4G4ASN00.000-0.0045.7550.7360.7360.0000.0000.0000.000
5G5PHE00.002-0.0108.234-0.099-0.0990.0000.0000.0000.000
6G6VAL00.0420.03711.7510.1120.1120.0000.0000.0000.000
7G7THR0-0.044-0.05012.989-0.017-0.0170.0000.0000.0000.000
8G8LYS10.8800.93515.3810.1200.1200.0000.0000.0000.000
9G9HIS00.0400.04217.8640.0380.0380.0000.0000.0000.000
10G10ASP-1-0.791-0.86718.174-0.490-0.4900.0000.0000.0000.000
11G11THR0-0.010-0.00520.2470.0500.0500.0000.0000.0000.000
12G12ALA00.0750.04822.391-0.025-0.0250.0000.0000.0000.000
13G13ILE00.0590.03520.961-0.001-0.0010.0000.0000.0000.000
14G14GLN0-0.048-0.02524.9610.0170.0170.0000.0000.0000.000
15G15THR0-0.0020.00027.9780.0230.0230.0000.0000.0000.000
16G16SER0-0.004-0.00629.524-0.005-0.0050.0000.0000.0000.000
17G17ARG10.8630.92324.9690.2730.2730.0000.0000.0000.000
18G18PHE00.0630.03231.7450.0090.0090.0000.0000.0000.000
19G19SER0-0.035-0.02732.558-0.011-0.0110.0000.0000.0000.000
20G20VAL00.0320.03234.4620.0070.0070.0000.0000.0000.000
21G21THR0-0.016-0.01835.7440.0000.0000.0000.0000.0000.000
22G22GLY00.0470.02938.4870.0030.0030.0000.0000.0000.000
23G23ASN0-0.034-0.03040.5200.0010.0010.0000.0000.0000.000
24G24VAL00.0270.01736.944-0.002-0.0020.0000.0000.0000.000
25G25ILE00.0030.00140.4320.0020.0020.0000.0000.0000.000
26G26PRO0-0.041-0.00239.104-0.002-0.0020.0000.0000.0000.000
27G27ALA00.0360.00740.9900.0030.0030.0000.0000.0000.000
28G28ALA00.0640.03341.803-0.001-0.0010.0000.0000.0000.000
29G29PRO00.002-0.01241.432-0.002-0.0020.0000.0000.0000.000
30G30THR0-0.010-0.00643.341-0.001-0.0010.0000.0000.0000.000
31G31GLY00.0330.02246.0490.0010.0010.0000.0000.0000.000
32G32ASN0-0.040-0.03045.5170.0010.0010.0000.0000.0000.000
33G33ILE00.0100.03838.8270.0000.0000.0000.0000.0000.000
34G34PRO0-0.015-0.01140.725-0.003-0.0030.0000.0000.0000.000
35G35VAL00.0310.01137.786-0.003-0.0030.0000.0000.0000.000
36G36ILE0-0.054-0.02134.4800.0000.0000.0000.0000.0000.000
37G37ASN0-0.044-0.05134.895-0.006-0.0060.0000.0000.0000.000
38G38GLY00.0500.03038.9560.0050.0050.0000.0000.0000.000
39G39GLY00.0070.00139.5700.0020.0020.0000.0000.0000.000
40G40SER0-0.076-0.04436.695-0.007-0.0070.0000.0000.0000.000
41G41ILE0-0.039-0.02032.5090.0010.0010.0000.0000.0000.000
42G42THR00.0890.01835.2950.0030.0030.0000.0000.0000.000
43G43ALA0-0.0470.00732.2300.0030.0030.0000.0000.0000.000
44G44GLH00.028-0.02530.783-0.009-0.0090.0000.0000.0000.000
45G45ARG10.8760.92523.0570.2860.2860.0000.0000.0000.000
46G46ALA00.005-0.00328.2340.0090.0090.0000.0000.0000.000
47G47VAL0-0.055-0.03125.804-0.016-0.0160.0000.0000.0000.000
48G48VAL00.0300.02028.4200.0080.0080.0000.0000.0000.000
49G49ASN0-0.053-0.02727.4140.0000.0000.0000.0000.0000.000
50G50LEU00.0340.00630.2480.0110.0110.0000.0000.0000.000
51G51TYR00.0220.00531.5490.0000.0000.0000.0000.0000.000
52G52ALA00.0250.02634.2600.0050.0050.0000.0000.0000.000
53G53ASN0-0.046-0.02836.7400.0020.0020.0000.0000.0000.000
54G54MET00.0270.04136.394-0.002-0.0020.0000.0000.0000.000
55G55ASN0-0.005-0.00438.5330.0070.0070.0000.0000.0000.000
56G56VAL00.0290.00941.231-0.001-0.0010.0000.0000.0000.000
57G57SER0-0.024-0.02943.6800.0030.0030.0000.0000.0000.000
58G58THR0-0.043-0.00845.7920.0020.0020.0000.0000.0000.000
59G59SER00.007-0.02144.6550.0030.0030.0000.0000.0000.000
60G60SER0-0.016-0.00743.583-0.002-0.0020.0000.0000.0000.000
61G61ASP-1-0.895-0.93040.488-0.027-0.0270.0000.0000.0000.000
62G62GLY00.0650.03639.686-0.002-0.0020.0000.0000.0000.000
63G63SER0-0.052-0.03436.555-0.001-0.0010.0000.0000.0000.000
64G64PHE00.0540.01633.1490.0010.0010.0000.0000.0000.000
65G65ILE00.0250.01334.950-0.002-0.0020.0000.0000.0000.000
66G66VAL0-0.037-0.00331.572-0.001-0.0010.0000.0000.0000.000
67G67ALA00.019-0.00533.227-0.001-0.0010.0000.0000.0000.000
68G68MET0-0.0660.02529.807-0.006-0.0060.0000.0000.0000.000
69G69LYS10.8770.93534.9890.1050.1050.0000.0000.0000.000
70G70VAL0-0.025-0.01234.123-0.012-0.0120.0000.0000.0000.000
71G71ASP-1-0.846-0.89434.214-0.136-0.1360.0000.0000.0000.000
72G72THR00.017-0.00835.676-0.001-0.0010.0000.0000.0000.000
73G73SER0-0.063-0.04437.3400.0080.0080.0000.0000.0000.000
74G74PRO0-0.051-0.01833.9910.0020.0020.0000.0000.0000.000
75G75THR00.018-0.00136.4830.0050.0050.0000.0000.0000.000
76G76ASP-1-0.935-0.95633.188-0.115-0.1150.0000.0000.0000.000
77G77PRO00.0080.00835.4290.0000.0000.0000.0000.0000.000
78G78ASN0-0.010-0.03432.5070.0090.0090.0000.0000.0000.000
79G79CYS0-0.0110.01829.525-0.004-0.0040.0000.0000.0000.000
80G80VAL00.0190.01824.2940.0070.0070.0000.0000.0000.000
81G81ILE00.0140.00127.171-0.016-0.0160.0000.0000.0000.000
82G82SER00.000-0.01722.4200.0070.0070.0000.0000.0000.000
83G83ALA00.0310.00423.662-0.003-0.0030.0000.0000.0000.000
84G84GLY0-0.021-0.01321.350-0.008-0.0080.0000.0000.0000.000
85G85VAL0-0.048-0.01421.988-0.001-0.0010.0000.0000.0000.000
86G86ASN00.0020.01119.9620.0120.0120.0000.0000.0000.000
87G87LEU0-0.0030.01023.924-0.004-0.0040.0000.0000.0000.000
88G88SER0-0.029-0.01326.7290.0090.0090.0000.0000.0000.000
89G89PHE00.036-0.01928.454-0.004-0.0040.0000.0000.0000.000
90G90ALA0-0.007-0.00532.0600.0050.0050.0000.0000.0000.000
91G91GLY00.0280.02534.1860.0060.0060.0000.0000.0000.000
92G92THR0-0.034-0.02132.585-0.001-0.0010.0000.0000.0000.000
93G93SER0-0.010-0.00833.2630.0030.0030.0000.0000.0000.000
94G94TYR0-0.0440.01629.4820.0020.0020.0000.0000.0000.000
95G95PRO0-0.0150.01728.9930.0020.0020.0000.0000.0000.000
96G96ILE00.023-0.00928.7640.0010.0010.0000.0000.0000.000
97G97VAL0-0.014-0.02926.160-0.004-0.0040.0000.0000.0000.000
98G98GLY00.0170.01328.4190.0080.0080.0000.0000.0000.000
99G99ILE00.0210.02026.219-0.006-0.0060.0000.0000.0000.000
100G100VAL0-0.028-0.01629.9450.0110.0110.0000.0000.0000.000
101G101ARG10.8250.90733.7350.0640.0640.0000.0000.0000.000
102G102PHE00.0330.00736.2640.0060.0060.0000.0000.0000.000
103G103GLU-1-0.697-0.83239.842-0.069-0.0690.0000.0000.0000.000
104G104SER0-0.028-0.01142.6050.0030.0030.0000.0000.0000.000
105G105ALA00.0830.05245.205-0.004-0.0040.0000.0000.0000.000
106G106SER0-0.030-0.00245.825-0.002-0.0020.0000.0000.0000.000
107G107GLU-1-0.759-0.86343.530-0.097-0.0970.0000.0000.0000.000
108G108GLN0-0.056-0.03240.145-0.008-0.0080.0000.0000.0000.000
109G109PRO00.0000.00941.5480.0040.0040.0000.0000.0000.000
110G110THR00.0510.02741.936-0.003-0.0030.0000.0000.0000.000
111G111SER0-0.062-0.02542.6870.0020.0020.0000.0000.0000.000
112G112ILE00.0070.01540.505-0.001-0.0010.0000.0000.0000.000
113G113ALA00.0320.02643.6470.0010.0010.0000.0000.0000.000
114G114GLY00.027-0.00942.620-0.002-0.0020.0000.0000.0000.000
115G115SER0-0.091-0.06942.8280.0010.0010.0000.0000.0000.000
116G116GLU-1-0.911-0.91744.187-0.042-0.0420.0000.0000.0000.000
117G117VAL0-0.077-0.04437.804-0.006-0.0060.0000.0000.0000.000
118G118GLU-1-0.780-0.81736.770-0.052-0.0520.0000.0000.0000.000
119G119HIS00.014-0.01134.027-0.010-0.0100.0000.0000.0000.000
120G120TYR0-0.032-0.04430.1210.0040.0040.0000.0000.0000.000
121G121PRO0-0.028-0.02729.087-0.009-0.0090.0000.0000.0000.000
122G122ILE0-0.0130.00423.935-0.004-0.0040.0000.0000.0000.000
123G123GLU-1-0.880-0.94119.3220.0020.0020.0000.0000.0000.000
124G124MET0-0.089-0.01721.217-0.026-0.0260.0000.0000.0000.000
125G125SER0-0.029-0.01317.6490.0230.0230.0000.0000.0000.000
126G126VAL00.0030.00219.4390.0180.0180.0000.0000.0000.000
127G127GLY00.0610.02221.860-0.013-0.0130.0000.0000.0000.000
128G128SER0-0.037-0.01924.9420.0120.0120.0000.0000.0000.000
129G129GLY00.0640.01126.762-0.006-0.0060.0000.0000.0000.000
130G130GLY00.0600.01928.746-0.001-0.0010.0000.0000.0000.000
131G131VAL0-0.036-0.00623.820-0.010-0.0100.0000.0000.0000.000
132G132CYS00.0090.03124.7820.0130.0130.0000.0000.0000.000
133G133SER0-0.021-0.03020.110-0.020-0.0200.0000.0000.0000.000
134G134ALA00.0400.01220.7920.0220.0220.0000.0000.0000.000
135G135ARG10.8490.91215.1540.4420.4420.0000.0000.0000.000
136G136ASP-1-0.780-0.87318.582-0.110-0.1100.0000.0000.0000.000
137G137CYS0-0.052-0.02721.132-0.015-0.0150.0000.0000.0000.000
138G138ALA00.0640.03724.0030.0180.0180.0000.0000.0000.000
139G139THR0-0.031-0.01527.200-0.017-0.0170.0000.0000.0000.000
140G140VAL00.0060.01029.5400.0100.0100.0000.0000.0000.000
141G141ASP-1-0.784-0.86432.845-0.077-0.0770.0000.0000.0000.000
142G142ILE0-0.002-0.01533.516-0.001-0.0010.0000.0000.0000.000
143G143HIS0-0.0190.00636.5110.0020.0020.0000.0000.0000.000
144G144PRO0-0.054-0.02740.3230.0030.0030.0000.0000.0000.000
145G145ARG10.7360.78938.3490.0610.0610.0000.0000.0000.000
146G146THR0-0.040-0.02444.6330.0050.0050.0000.0000.0000.000
147G147SER0-0.019-0.02347.378-0.004-0.0040.0000.0000.0000.000
148G148GLY00.0080.00347.9820.0030.0030.0000.0000.0000.000
149G149ASN0-0.097-0.04244.737-0.001-0.0010.0000.0000.0000.000
150G150ASN00.000-0.01041.820-0.004-0.0040.0000.0000.0000.000
151G151VAL00.0440.01837.4040.0040.0040.0000.0000.0000.000
152G152PHE0-0.065-0.03037.414-0.008-0.0080.0000.0000.0000.000
153G153VAL00.0480.02431.4550.0060.0060.0000.0000.0000.000
154G154GLY00.005-0.00231.691-0.006-0.0060.0000.0000.0000.000
155G155VAL0-0.030-0.00827.9290.0010.0010.0000.0000.0000.000
156G156ILE0-0.0120.01230.9390.0000.0000.0000.0000.0000.000
157G157CYS0-0.052-0.02830.532-0.002-0.0020.0000.0000.0000.000
158G158SER00.032-0.00432.7060.0030.0030.0000.0000.0000.000
159G159SER00.012-0.02133.4620.0010.0010.0000.0000.0000.000
160G160ALA00.0170.01235.7450.0000.0000.0000.0000.0000.000
161G161LYS10.8560.92937.5600.0220.0220.0000.0000.0000.000
162G162TRP00.001-0.00233.832-0.002-0.0020.0000.0000.0000.000
163G163THR0-0.043-0.04937.5990.0060.0060.0000.0000.0000.000
164G164SER00.0050.00638.339-0.004-0.0040.0000.0000.0000.000
165G165GLY00.0250.01438.2090.0030.0030.0000.0000.0000.000
166G166ARG10.8500.94134.3250.0880.0880.0000.0000.0000.000
167G167VAL00.0060.01631.8070.0020.0020.0000.0000.0000.000
168G168ILE0-0.038-0.02829.027-0.003-0.0030.0000.0000.0000.000
169G169GLY00.0530.02427.0440.0020.0020.0000.0000.0000.000
170G170THR0-0.088-0.04725.057-0.009-0.0090.0000.0000.0000.000
171G171ILE00.0360.02925.829-0.002-0.0020.0000.0000.0000.000
172G172ALA00.0070.00723.562-0.001-0.0010.0000.0000.0000.000
173G173THR0-0.016-0.03325.2900.0060.0060.0000.0000.0000.000
174G174THR0-0.064-0.03124.623-0.011-0.0110.0000.0000.0000.000
175G175GLN00.1020.05126.5480.0040.0040.0000.0000.0000.000
176G176VAL0-0.048-0.02423.305-0.013-0.0130.0000.0000.0000.000
177G177ILE00.0200.00826.3450.0120.0120.0000.0000.0000.000
178G178HIS0-0.036-0.01826.337-0.013-0.0130.0000.0000.0000.000
179G179GLU-1-0.922-0.95320.432-0.341-0.3410.0000.0000.0000.000
180G180TYR0-0.057-0.03320.5190.0110.0110.0000.0000.0000.000
181G181GLN00.0090.01519.346-0.065-0.0650.0000.0000.0000.000
182G182VAL00.0230.00214.235-0.017-0.0170.0000.0000.0000.000
183G183LEU00.0160.01013.212-0.004-0.0040.0000.0000.0000.000
184G184GLN00.0380.02312.206-0.138-0.1380.0000.0000.0000.000
185G185PRO0-0.011-0.0129.0160.1370.1370.0000.0000.0000.000
186G186LEU0-0.012-0.0027.6560.0050.0050.0000.0000.0000.000
187G187LYS10.9050.96212.0260.8710.8710.0000.0000.0000.000