FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: QM7GY

Calculation Name: 2OFI-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 1',2'-dideoxyribofuranose-5'-phosphate | 3-methyl-3h-purin-6-ylamine | zinc ion

Ligand 3-letter code: 3DR | ADK | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2OFI

Chain ID: A

ChEMBL ID:

UniProt ID: Q8Z2A5

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 184
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2040510.033181
FMO2-HF: Nuclear repulsion 1965708.764274
FMO2-HF: Total energy -74801.268906
FMO2-MP2: Total energy -75013.8573


3D Structure Molmil
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(A:1:MET)


Summations of interaction energy for fragment #1(A: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.
-57.412-50.7915.729-3.695-8.653-0.04
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.844 / q_NPA : 0.917
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].
3A3ARG10.8410.8732.89546.81149.6330.249-1.017-2.054-0.003
4A4CYS00.0510.0445.3741.3761.413-0.001-0.002-0.0330.000
18A18ASP-1-0.748-0.8434.935-44.823-44.729-0.001-0.004-0.0890.000
180A180PHE0-0.015-0.0352.527-8.206-4.7465.483-2.641-6.302-0.037
181A181CYS0-0.003-0.0134.4370.6530.861-0.001-0.031-0.1750.000
5A5ASP-1-0.799-0.9049.108-25.200-25.2000.0000.0000.0000.000
6A6TRP0-0.018-0.00211.3710.0370.0370.0000.0000.0000.000
7A7VAL0-0.070-0.0187.1541.0151.0150.0000.0000.0000.000
8A8SER00.0130.0059.626-1.275-1.2750.0000.0000.0000.000
9A9GLN00.027-0.0118.882-3.648-3.6480.0000.0000.0000.000
10A10ASP-1-0.877-0.93510.952-18.817-18.8170.0000.0000.0000.000
11A11PRO00.0320.00010.553-1.116-1.1160.0000.0000.0000.000
12A12LEU00.0150.02411.494-0.536-0.5360.0000.0000.0000.000
13A13TYR00.015-0.01211.6950.2940.2940.0000.0000.0000.000
14A14ILE0-0.0070.0026.173-0.980-0.9800.0000.0000.0000.000
15A15ALA0-0.0060.0038.470-1.079-1.0790.0000.0000.0000.000
16A16TYR00.0520.01810.2210.0280.0280.0000.0000.0000.000
17A17HIS10.7470.8496.25434.15534.1550.0000.0000.0000.000
19A19ASN0-0.075-0.0327.6270.2420.2420.0000.0000.0000.000
20A20GLU-1-0.782-0.84710.824-15.496-15.4960.0000.0000.0000.000
21A21TRP00.003-0.00212.4080.1970.1970.0000.0000.0000.000
22A22GLY00.0190.01812.498-1.661-1.6610.0000.0000.0000.000
23A23VAL0-0.044-0.01813.1470.0080.0080.0000.0000.0000.000
24A24PRO0-0.032-0.02315.5180.6150.6150.0000.0000.0000.000
25A25GLU-1-0.844-0.89919.247-12.962-12.9620.0000.0000.0000.000
26A26THR0-0.004-0.02721.2550.4870.4870.0000.0000.0000.000
27A27ASP-1-0.848-0.92524.462-10.278-10.2780.0000.0000.0000.000
28A28SER00.014-0.02026.429-0.255-0.2550.0000.0000.0000.000
29A29ARG10.8370.92328.4139.5179.5170.0000.0000.0000.000
30A30LYS10.9430.97521.71712.24412.2440.0000.0000.0000.000
31A31LEU00.0220.02623.782-0.244-0.2440.0000.0000.0000.000
32A32PHE00.013-0.00325.7620.0670.0670.0000.0000.0000.000
33A33GLU-1-0.817-0.90223.171-12.390-12.3900.0000.0000.0000.000
34A34MET00.0080.00520.046-0.104-0.1040.0000.0000.0000.000
35A35ILE00.0090.01523.932-0.021-0.0210.0000.0000.0000.000
36A36CYS0-0.062-0.01926.7230.3920.3920.0000.0000.0000.000
37A37LEU0-0.041-0.02622.4480.1180.1180.0000.0000.0000.000
38A38GLU-1-0.856-0.94320.678-14.089-14.0890.0000.0000.0000.000
39A39GLY0-0.014-0.00624.5260.1810.1810.0000.0000.0000.000
40A40GLN0-0.060-0.04426.1350.4500.4500.0000.0000.0000.000
41A41GLN00.0200.02021.8950.3850.3850.0000.0000.0000.000
42A42ALA00.0000.00924.9350.0090.0090.0000.0000.0000.000
43A43GLY00.0130.01026.9910.3530.3530.0000.0000.0000.000
44A44LEU0-0.0300.00024.9050.1240.1240.0000.0000.0000.000
45A45SER00.0500.02719.721-0.245-0.2450.0000.0000.0000.000
46A46TRP00.1000.04216.1670.6050.6050.0000.0000.0000.000
47A47ILE00.0100.01215.4360.4050.4050.0000.0000.0000.000
48A48THR0-0.060-0.03918.1920.2790.2790.0000.0000.0000.000
49A49VAL0-0.009-0.00121.5790.5160.5160.0000.0000.0000.000
50A50LEU0-0.0090.01014.9620.3240.3240.0000.0000.0000.000
51A51LYS10.9290.95718.75615.04515.0450.0000.0000.0000.000
52A52LYS10.8050.91820.72511.57811.5780.0000.0000.0000.000
53A53ARG10.7850.87517.08515.94215.9420.0000.0000.0000.000
54A54GLU-1-0.808-0.91321.610-12.727-12.7270.0000.0000.0000.000
55A55ASN0-0.017-0.00824.8420.5160.5160.0000.0000.0000.000
56A56TYR00.003-0.01326.1870.4190.4190.0000.0000.0000.000
57A57ARG10.8270.88920.73813.52513.5250.0000.0000.0000.000
58A58ALA0-0.0090.01228.0410.3230.3230.0000.0000.0000.000
59A59CYS0-0.112-0.05930.7440.3940.3940.0000.0000.0000.000
60A60PHE0-0.002-0.01231.1020.3240.3240.0000.0000.0000.000
61A61HIS00.0430.00632.186-0.142-0.1420.0000.0000.0000.000
62A62GLN0-0.011-0.01928.8980.2530.2530.0000.0000.0000.000
63A63PHE00.0120.00126.848-0.162-0.1620.0000.0000.0000.000
64A64ASP-1-0.782-0.88530.245-8.534-8.5340.0000.0000.0000.000
65A65PRO00.0150.00532.7610.2030.2030.0000.0000.0000.000
66A66ILE00.0390.02835.3240.2100.2100.0000.0000.0000.000
67A67ARG10.8810.93536.3758.2098.2090.0000.0000.0000.000
68A68ILE0-0.003-0.00132.3860.1140.1140.0000.0000.0000.000
69A69ALA0-0.0110.00937.0500.1310.1310.0000.0000.0000.000
70A70ALA00.0240.01939.9700.2060.2060.0000.0000.0000.000
71A71MET0-0.0680.00336.3600.0500.0500.0000.0000.0000.000
72A72GLN0-0.018-0.02741.3190.1560.1560.0000.0000.0000.000
73A73GLU-1-0.922-0.96742.752-6.705-6.7050.0000.0000.0000.000
74A74GLU-1-0.897-0.95243.756-6.802-6.8020.0000.0000.0000.000
75A75ASP-1-0.803-0.88339.787-7.620-7.6200.0000.0000.0000.000
76A76VAL0-0.031-0.01739.161-0.241-0.2410.0000.0000.0000.000
77A77GLU-1-0.757-0.85339.537-7.481-7.4810.0000.0000.0000.000
78A78ARG10.8740.92737.5287.7987.7980.0000.0000.0000.000
79A79LEU0-0.061-0.03434.690-0.190-0.1900.0000.0000.0000.000
80A80LEU0-0.014-0.01435.983-0.287-0.2870.0000.0000.0000.000
81A81GLN00.0030.00637.789-0.104-0.1040.0000.0000.0000.000
82A82ASN0-0.019-0.00333.281-0.255-0.2550.0000.0000.0000.000
83A83THR00.008-0.01132.165-0.200-0.2000.0000.0000.0000.000
84A84GLY00.0290.02729.356-0.356-0.3560.0000.0000.0000.000
85A85ILE00.0160.00828.078-0.525-0.5250.0000.0000.0000.000
86A86ILE0-0.0060.00126.074-0.021-0.0210.0000.0000.0000.000
87A87ARG10.9230.98030.2908.9828.9820.0000.0000.0000.000
88A88HIS00.0370.01433.1710.2060.2060.0000.0000.0000.000
89A89ARG10.8630.90335.0477.2587.2580.0000.0000.0000.000
90A90GLY00.0360.01537.0930.0300.0300.0000.0000.0000.000
91A91LYS10.7950.88128.55510.44910.4490.0000.0000.0000.000
92A92ILE00.0370.02333.134-0.152-0.1520.0000.0000.0000.000
93A93GLN00.0420.00134.991-0.026-0.0260.0000.0000.0000.000
94A94ALA0-0.039-0.00133.2930.1090.1090.0000.0000.0000.000
95A95ILE00.0240.02230.0470.0140.0140.0000.0000.0000.000
96A96ILE00.0290.00533.5800.0450.0450.0000.0000.0000.000
97A97SER0-0.076-0.04837.2000.2330.2330.0000.0000.0000.000
98A98ASN00.0280.00831.7220.3280.3280.0000.0000.0000.000
99A99ALA00.0150.02435.045-0.030-0.0300.0000.0000.0000.000
100A100ARG10.8240.89935.8867.5017.5010.0000.0000.0000.000
101A101ALA0-0.0040.00336.9440.1450.1450.0000.0000.0000.000
102A102TRP00.0080.00031.2680.1890.1890.0000.0000.0000.000
103A103LEU0-0.025-0.01236.1160.0690.0690.0000.0000.0000.000
104A104ALA0-0.041-0.01239.0600.1510.1510.0000.0000.0000.000
105A105MET0-0.070-0.00434.5880.0630.0630.0000.0000.0000.000
106A106GLU-1-0.729-0.85233.719-8.763-8.7630.0000.0000.0000.000
107A107GLN0-0.058-0.04338.248-0.038-0.0380.0000.0000.0000.000
108A108ASN0-0.093-0.04741.3010.3300.3300.0000.0000.0000.000
109A109GLY00.0020.01841.1280.0860.0860.0000.0000.0000.000
110A110GLU-1-0.824-0.87437.194-8.207-8.2070.0000.0000.0000.000
111A111SER00.0300.01633.180-0.149-0.1490.0000.0000.0000.000
112A112PHE0-0.034-0.05128.649-0.060-0.0600.0000.0000.0000.000
113A113ALA00.0200.00628.644-0.227-0.2270.0000.0000.0000.000
114A114ASP-1-0.821-0.91029.509-9.467-9.4670.0000.0000.0000.000
115A115PHE0-0.032-0.01631.939-0.015-0.0150.0000.0000.0000.000
116A116VAL0-0.046-0.02527.140-0.040-0.0400.0000.0000.0000.000
117A117TRP0-0.003-0.01621.684-0.222-0.2220.0000.0000.0000.000
118A118SER0-0.084-0.03628.4120.0500.0500.0000.0000.0000.000
119A119PHE0-0.078-0.04929.0310.2970.2970.0000.0000.0000.000
120A120VAL00.007-0.00124.190-0.264-0.2640.0000.0000.0000.000
121A121ASP-1-0.924-0.94427.472-9.997-9.9970.0000.0000.0000.000
122A122GLY0-0.040-0.01927.285-0.091-0.0910.0000.0000.0000.000
123A123GLN0-0.039-0.02520.5510.0600.0600.0000.0000.0000.000
124A124PRO00.0200.01219.3650.1290.1290.0000.0000.0000.000
125A125GLN0-0.024-0.00120.4470.0540.0540.0000.0000.0000.000
126A126ILE00.0120.01115.360-0.526-0.5260.0000.0000.0000.000
127A127THR0-0.043-0.01014.8060.8150.8150.0000.0000.0000.000
128A128GLN00.006-0.01416.562-0.112-0.1120.0000.0000.0000.000
129A129ALA0-0.0320.00316.4770.0350.0350.0000.0000.0000.000
130A130ALA00.0270.00714.206-1.146-1.1460.0000.0000.0000.000
131A131SER0-0.028-0.04613.441-1.617-1.6170.0000.0000.0000.000
132A132LEU00.023-0.00614.6121.0711.0710.0000.0000.0000.000
133A133ASP-1-0.870-0.89516.159-15.560-15.5600.0000.0000.0000.000
134A134LYS10.8260.89818.55515.55715.5570.0000.0000.0000.000
135A135ILE0-0.0060.01514.9440.1340.1340.0000.0000.0000.000
136A136PRO0-0.0110.01119.4950.4140.4140.0000.0000.0000.000
137A137THR00.024-0.00521.854-0.221-0.2210.0000.0000.0000.000
138A138SER0-0.031-0.02523.8000.3820.3820.0000.0000.0000.000
139A139THR00.0510.03125.088-0.082-0.0820.0000.0000.0000.000
140A140PRO00.0600.02328.0450.1270.1270.0000.0000.0000.000
141A141ALA00.0560.04327.5900.3000.3000.0000.0000.0000.000
142A142SER00.0430.00626.6100.0400.0400.0000.0000.0000.000
143A143ASP-1-0.879-0.91128.729-9.703-9.7030.0000.0000.0000.000
144A144ALA0-0.039-0.01732.1570.3020.3020.0000.0000.0000.000
145A145LEU00.0580.04427.7770.2730.2730.0000.0000.0000.000
146A146ALA00.030-0.00331.0910.2020.2020.0000.0000.0000.000
147A147LYS10.8680.93632.6128.0858.0850.0000.0000.0000.000
148A148ALA0-0.021-0.00434.7860.3020.3020.0000.0000.0000.000
149A149LEU00.0620.03930.4390.2070.2070.0000.0000.0000.000
150A150LYS10.8850.93934.4309.1049.1040.0000.0000.0000.000
151A151LYS10.8970.95537.5407.4397.4390.0000.0000.0000.000
152A152ARG10.7740.83536.8528.3978.3970.0000.0000.0000.000
153A153GLY00.0000.00939.5390.0260.0260.0000.0000.0000.000
154A154PHE00.0110.00333.072-0.027-0.0270.0000.0000.0000.000
155A155LYS10.8640.92634.9247.8787.8780.0000.0000.0000.000
156A156PHE0-0.023-0.02130.716-0.176-0.1760.0000.0000.0000.000
157A157VAL00.0810.06230.202-0.314-0.3140.0000.0000.0000.000
158A158GLY0-0.012-0.02030.3760.3240.3240.0000.0000.0000.000
159A159THR00.046-0.00629.092-0.421-0.4210.0000.0000.0000.000
160A160THR00.0480.01524.470-0.069-0.0690.0000.0000.0000.000
161A161ILE0-0.073-0.00624.440-0.402-0.4020.0000.0000.0000.000
162A162CYS0-0.035-0.01124.801-0.184-0.1840.0000.0000.0000.000
163A163TYR00.005-0.02420.5770.2180.2180.0000.0000.0000.000
164A164SER0-0.021-0.00320.460-0.600-0.6000.0000.0000.0000.000
165A165PHE00.001-0.00920.219-0.554-0.5540.0000.0000.0000.000
166A166MET00.0190.00721.703-0.071-0.0710.0000.0000.0000.000
167A167GLN0-0.034-0.02917.197-0.430-0.4300.0000.0000.0000.000
168A168ALA0-0.045-0.02116.848-0.743-0.7430.0000.0000.0000.000
169A169CYS0-0.032-0.02317.301-0.398-0.3980.0000.0000.0000.000
170A170GLY00.0680.04217.7160.3940.3940.0000.0000.0000.000
171A171LEU0-0.015-0.00518.4600.2470.2470.0000.0000.0000.000
172A172VAL0-0.034-0.01519.2610.3750.3750.0000.0000.0000.000
173A173ASN00.0280.00312.879-1.398-1.3980.0000.0000.0000.000
174A174ASP-1-0.720-0.85015.481-16.243-16.2430.0000.0000.0000.000
175A175HIS00.0530.0019.678-2.950-2.9500.0000.0000.0000.000
176A176ILE0-0.0110.0089.5570.3500.3500.0000.0000.0000.000
177A177THR00.0390.00810.278-2.639-2.6390.0000.0000.0000.000
178A178GLY00.0230.0278.822-0.466-0.4660.0000.0000.0000.000
179A179CYS0-0.166-0.0566.223-8.023-8.0230.0000.0000.0000.000
182A182HIS0-0.059-0.0267.2053.8663.8660.0000.0000.0000.000
183A183PRO0-0.056-0.0259.298-0.823-0.8230.0000.0000.0000.000
184A184GLY-1-0.924-0.95310.658-18.914-18.9140.0000.0000.0000.000