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: RLM88

Calculation Name: 2IOC-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 2'-deoxyadenosine-5'-monophosphate | manganese (ii) ion

Ligand 3-letter code: D5M | MN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2IOC

Chain ID: B

ChEMBL ID:

UniProt ID: Q91XB0

Base Structure: X-ray

Registration Date: 2025-10-05

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 227
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2714398.522389
FMO2-HF: Nuclear repulsion 2626710.370987
FMO2-HF: Total energy -87688.151401
FMO2-MP2: Total energy -87942.280447


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:8:HIS)


Summations of interaction energy for fragment #1(A:8:HIS)
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.
-173.191-162.76518.495-12.842-16.079-0.158
Interaction energy analysis for fragmet #1(A:8:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.695 / q_NPA : 1.841
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].
3A10HIS0-0.029-0.0181.877-39.132-37.2046.259-4.460-3.728-0.054
4A11MET0-0.0300.0032.5954.9976.1741.467-0.514-2.130-0.003
111A118PRO0-0.025-0.0203.5130.5920.8840.004-0.051-0.2440.000
144A151PHE0-0.038-0.0282.431-11.288-9.1021.585-1.107-2.663-0.010
213A220ASP-1-0.771-0.8623.087-95.992-95.0500.031-0.353-0.620-0.003
214A221GLU-1-0.918-0.9492.210-94.822-93.0493.473-2.727-2.519-0.039
215A222HIS10.8190.9074.31156.47356.661-0.001-0.031-0.1570.000
216A223ALA0-0.0020.0282.7186.2126.9110.223-0.301-0.621-0.001
217A224ARG10.8320.8911.93610.20611.2505.455-3.277-3.223-0.048
218A225PRO00.0480.0154.1764.2554.452-0.001-0.021-0.1740.000
5A12GLN0-0.036-0.0125.67212.14512.1450.0000.0000.0000.000
6A13THR0-0.015-0.0219.1766.1476.1470.0000.0000.0000.000
7A14LEU0-0.011-0.0038.351-5.608-5.6080.0000.0000.0000.000
8A15ILE00.014-0.00511.2583.4073.4070.0000.0000.0000.000
9A16PHE0-0.012-0.01413.695-1.797-1.7970.0000.0000.0000.000
10A17LEU0-0.035-0.01715.7210.9790.9790.0000.0000.0000.000
11A18ASP-1-0.895-0.95617.443-27.440-27.4400.0000.0000.0000.000
12A19LEU0-0.032-0.01719.7850.3660.3660.0000.0000.0000.000
13A20GLU-1-0.758-0.86422.792-22.128-22.1280.0000.0000.0000.000
14A21ALA0-0.010-0.01125.698-0.011-0.0110.0000.0000.0000.000
15A22THR00.0370.02427.7110.3020.3020.0000.0000.0000.000
16A23GLY00.0510.02529.1060.8700.8700.0000.0000.0000.000
17A24LEU00.0430.04227.379-0.911-0.9110.0000.0000.0000.000
18A25PRO00.0670.01923.9800.5400.5400.0000.0000.0000.000
19A26SER0-0.019-0.00126.379-0.011-0.0110.0000.0000.0000.000
20A27SER0-0.042-0.03029.6780.5050.5050.0000.0000.0000.000
21A28ARG10.8430.90527.92120.89920.8990.0000.0000.0000.000
22A29PRO0-0.0300.01825.7330.4080.4080.0000.0000.0000.000
23A30GLU-1-0.726-0.84927.061-20.132-20.1320.0000.0000.0000.000
24A31VAL00.012-0.00823.5920.3300.3300.0000.0000.0000.000
25A32THR0-0.105-0.06126.8230.8510.8510.0000.0000.0000.000
26A33GLU-1-0.816-0.92226.887-20.756-20.7560.0000.0000.0000.000
27A34LEU0-0.0040.01120.928-0.900-0.9000.0000.0000.0000.000
28A35CYS0-0.0440.01122.4850.5550.5550.0000.0000.0000.000
29A36LEU00.0190.00117.390-1.743-1.7430.0000.0000.0000.000
30A37LEU00.0010.00318.3661.2471.2470.0000.0000.0000.000
31A38ALA0-0.0100.00215.837-2.102-2.1020.0000.0000.0000.000
32A39VAL00.022-0.00615.0232.2292.2290.0000.0000.0000.000
33A40HIS00.0550.03112.541-1.441-1.4410.0000.0000.0000.000
34A41ARG10.8430.8837.29361.47461.4740.0000.0000.0000.000
35A42ARG10.9440.97512.47735.29835.2980.0000.0000.0000.000
36A43ALA0-0.030-0.01415.5701.8751.8750.0000.0000.0000.000
37A44LEU00.0210.00813.0061.5071.5070.0000.0000.0000.000
38A45GLU-1-0.853-0.93112.852-41.514-41.5140.0000.0000.0000.000
39A46ASN0-0.047-0.02316.4000.2290.2290.0000.0000.0000.000
40A47THR0-0.085-0.03918.7071.7851.7850.0000.0000.0000.000
41A48SER0-0.007-0.01221.090-0.321-0.3210.0000.0000.0000.000
42A49ILE0-0.0010.00520.895-0.281-0.2810.0000.0000.0000.000
43A50SER00.0200.01022.3871.2051.2050.0000.0000.0000.000
44A51GLN0-0.011-0.00224.324-0.669-0.6690.0000.0000.0000.000
45A52GLY00.011-0.00127.5740.5080.5080.0000.0000.0000.000
46A53HIS0-0.042-0.01026.942-0.745-0.7450.0000.0000.0000.000
47A54PRO00.0290.02129.4330.5670.5670.0000.0000.0000.000
48A55PRO0-0.035-0.00925.4150.3180.3180.0000.0000.0000.000
49A56PRO00.011-0.01528.3370.1260.1260.0000.0000.0000.000
50A57VAL00.0210.02225.483-0.776-0.7760.0000.0000.0000.000
51A58PRO0-0.040-0.01221.8110.4620.4620.0000.0000.0000.000
52A59ARG10.9610.98624.37721.01821.0180.0000.0000.0000.000
53A60PRO00.0640.05322.494-0.961-0.9610.0000.0000.0000.000
54A61PRO00.001-0.01119.2120.9720.9720.0000.0000.0000.000
55A62ARG10.9100.95022.52321.94321.9430.0000.0000.0000.000
56A63VAL0-0.038-0.01721.0350.8640.8640.0000.0000.0000.000
57A64VAL00.0000.00219.667-1.342-1.3420.0000.0000.0000.000
58A65ASP-1-0.838-0.88819.300-27.592-27.5920.0000.0000.0000.000
59A66LYS10.8170.88120.47422.21922.2190.0000.0000.0000.000
60A67LEU0-0.016-0.00122.1280.7590.7590.0000.0000.0000.000
61A68SER00.002-0.02023.397-0.847-0.8470.0000.0000.0000.000
62A69LEU0-0.021-0.00625.2330.7440.7440.0000.0000.0000.000
63A70CYS00.0200.02427.666-0.164-0.1640.0000.0000.0000.000
64A71ILE0-0.056-0.03425.9720.1190.1190.0000.0000.0000.000
65A72ALA00.0460.01430.3590.2970.2970.0000.0000.0000.000
66A73PRO0-0.025-0.00131.241-0.330-0.3300.0000.0000.0000.000
67A74GLY0-0.004-0.03532.3300.6000.6000.0000.0000.0000.000
68A75LYS10.8010.89131.21719.69419.6940.0000.0000.0000.000
69A76ALA00.0290.00334.957-0.299-0.2990.0000.0000.0000.000
70A77CYS0-0.030-0.00233.994-0.430-0.4300.0000.0000.0000.000
71A78SER0-0.046-0.02833.1210.5060.5060.0000.0000.0000.000
72A79PRO00.031-0.00435.579-0.243-0.2430.0000.0000.0000.000
73A80GLY00.0440.03234.836-0.039-0.0390.0000.0000.0000.000
74A81ALA0-0.015-0.00531.450-0.348-0.3480.0000.0000.0000.000
75A82SER0-0.055-0.03732.759-0.043-0.0430.0000.0000.0000.000
76A83GLU-1-0.936-0.97135.566-16.103-16.1030.0000.0000.0000.000
77A84ILE0-0.077-0.03530.122-0.013-0.0130.0000.0000.0000.000
78A85THR00.006-0.01529.950-0.098-0.0980.0000.0000.0000.000
79A86GLY0-0.0140.01632.633-0.026-0.0260.0000.0000.0000.000
80A87LEU00.0100.02030.6130.3570.3570.0000.0000.0000.000
81A88SER00.027-0.00234.8520.1780.1780.0000.0000.0000.000
82A89LYS10.7950.88836.15116.19916.1990.0000.0000.0000.000
83A90ALA00.0320.01737.039-0.011-0.0110.0000.0000.0000.000
84A91GLU-1-0.844-0.90038.416-14.972-14.9720.0000.0000.0000.000
85A92LEU0-0.014-0.01633.137-0.033-0.0330.0000.0000.0000.000
86A93GLU-1-0.814-0.90236.778-16.054-16.0540.0000.0000.0000.000
87A94VAL0-0.0300.00039.0910.1690.1690.0000.0000.0000.000
88A95GLN0-0.060-0.03538.382-0.050-0.0500.0000.0000.0000.000
89A96GLY0-0.0030.00338.457-0.361-0.3610.0000.0000.0000.000
90A97ARG10.8140.91133.38317.48917.4890.0000.0000.0000.000
91A98GLN00.0040.00332.7350.3180.3180.0000.0000.0000.000
92A99ARG10.8810.94731.02618.80318.8030.0000.0000.0000.000
93A100PHE00.0500.02021.745-0.370-0.3700.0000.0000.0000.000
94A101ASP-1-0.840-0.92327.628-20.816-20.8160.0000.0000.0000.000
95A102ASP-1-0.734-0.88225.995-23.398-23.3980.0000.0000.0000.000
96A103ASN0-0.073-0.02525.995-0.656-0.6560.0000.0000.0000.000
97A104LEU00.0540.02424.225-0.666-0.6660.0000.0000.0000.000
98A105ALA00.0270.01722.049-1.224-1.2240.0000.0000.0000.000
99A106ILE0-0.017-0.01621.416-1.413-1.4130.0000.0000.0000.000
100A107LEU0-0.0120.00122.572-0.790-0.7900.0000.0000.0000.000
101A108LEU00.011-0.00419.288-0.926-0.9260.0000.0000.0000.000
102A109ARG10.9310.97816.48130.80130.8010.0000.0000.0000.000
103A110ALA0-0.033-0.01618.184-1.210-1.2100.0000.0000.0000.000
104A111PHE0-0.005-0.00217.888-0.553-0.5530.0000.0000.0000.000
105A112LEU00.015-0.00413.634-1.170-1.1700.0000.0000.0000.000
106A113GLN0-0.025-0.02714.642-2.223-2.2230.0000.0000.0000.000
107A114ARG10.9260.98316.34627.97727.9770.0000.0000.0000.000
108A115GLN0-0.069-0.03913.401-0.550-0.5500.0000.0000.0000.000
109A116PRO0-0.016-0.00612.398-1.922-1.9220.0000.0000.0000.000
110A117GLN00.0270.0318.349-6.656-6.6560.0000.0000.0000.000
112A119CYS00.0180.0176.1841.1451.1450.0000.0000.0000.000
113A120CYS0-0.046-0.0256.373-6.808-6.8080.0000.0000.0000.000
114A121LEU00.0300.0278.4354.3024.3020.0000.0000.0000.000
115A122VAL0-0.015-0.0169.919-4.150-4.1500.0000.0000.0000.000
116A123ALA00.1050.05712.2092.4742.4740.0000.0000.0000.000
117A124HIS00.0240.01315.028-2.326-2.3260.0000.0000.0000.000
118A125ASN0-0.019-0.02217.0041.6671.6670.0000.0000.0000.000
119A126GLY00.0620.04315.0720.8160.8160.0000.0000.0000.000
120A127ASP-1-0.832-0.91311.458-47.122-47.1220.0000.0000.0000.000
121A128ARG10.8370.91414.36929.19229.1920.0000.0000.0000.000
122A129TYR0-0.051-0.03518.0791.3961.3960.0000.0000.0000.000
123A130ASP-1-0.768-0.89516.924-30.146-30.1460.0000.0000.0000.000
124A131PHE00.016-0.00311.665-0.367-0.3670.0000.0000.0000.000
125A132PRO00.0090.00115.5970.4130.4130.0000.0000.0000.000
126A133LEU0-0.0140.00617.8950.9550.9550.0000.0000.0000.000
127A134LEU00.0310.01016.4380.6980.6980.0000.0000.0000.000
128A135GLN0-0.030-0.02014.4561.1951.1950.0000.0000.0000.000
129A136THR0-0.035-0.03318.4830.3540.3540.0000.0000.0000.000
130A137GLU-1-0.818-0.90422.109-22.123-22.1230.0000.0000.0000.000
131A138LEU0-0.045-0.02817.8490.5510.5510.0000.0000.0000.000
132A139ALA0-0.025-0.01121.1230.4880.4880.0000.0000.0000.000
133A140ARG10.7880.89722.54622.54522.5450.0000.0000.0000.000
134A141LEU0-0.056-0.00623.3681.0091.0090.0000.0000.0000.000
135A142SER0-0.045-0.01825.700-0.117-0.1170.0000.0000.0000.000
136A143THR0-0.067-0.04123.085-0.725-0.7250.0000.0000.0000.000
137A144PRO0-0.001-0.00819.088-0.619-0.6190.0000.0000.0000.000
138A145SER00.0430.02615.2540.2030.2030.0000.0000.0000.000
139A146PRO0-0.042-0.03016.357-1.268-1.2680.0000.0000.0000.000
140A147LEU00.006-0.00213.105-1.664-1.6640.0000.0000.0000.000
141A148ASP-1-0.851-0.91511.534-42.842-42.8420.0000.0000.0000.000
142A149GLY0-0.035-0.0168.640-2.820-2.8200.0000.0000.0000.000
143A150THR0-0.080-0.0287.815-3.718-3.7180.0000.0000.0000.000
145A152CYS0-0.0340.0006.7398.1888.1880.0000.0000.0000.000
146A153VAL00.0510.0046.972-6.356-6.3560.0000.0000.0000.000
147A154ASP-1-0.729-0.8538.979-32.373-32.3730.0000.0000.0000.000
148A155SER00.037-0.00712.412-1.559-1.5590.0000.0000.0000.000
149A156ILE0-0.058-0.02414.0811.4881.4880.0000.0000.0000.000
150A157ALA0-0.056-0.03612.3311.3351.3350.0000.0000.0000.000
151A158ALA00.0500.03111.2210.6020.6020.0000.0000.0000.000
152A159LEU00.032-0.00112.8061.1081.1080.0000.0000.0000.000
153A160LYS10.8920.96616.43632.12332.1230.0000.0000.0000.000
154A161ALA0-0.0120.00313.8381.5251.5250.0000.0000.0000.000
155A162LEU00.0220.00613.8731.3461.3460.0000.0000.0000.000
156A163GLU-1-0.742-0.83016.919-23.444-23.4440.0000.0000.0000.000
157A164GLN0-0.141-0.07417.8681.7071.7070.0000.0000.0000.000
158A165ALA00.0620.05217.8890.5670.5670.0000.0000.0000.000
159A166SER00.0360.00820.0320.9120.9120.0000.0000.0000.000
160A167SER0-0.043-0.03721.9990.1280.1280.0000.0000.0000.000
161A168PRO0-0.0230.00422.4370.7560.7560.0000.0000.0000.000
162A169SER0-0.033-0.00823.9020.7740.7740.0000.0000.0000.000
163A170GLY00.0710.04624.4930.4760.4760.0000.0000.0000.000
164A171ASN0-0.066-0.03923.545-0.228-0.2280.0000.0000.0000.000
165A172GLY00.0900.05225.8330.3360.3360.0000.0000.0000.000
166A173SER0-0.0010.00127.882-0.779-0.7790.0000.0000.0000.000
167A174ARG10.8880.92823.37622.68122.6810.0000.0000.0000.000
168A175LYS10.8770.93924.04424.43124.4310.0000.0000.0000.000
169A176SER00.0410.02625.391-0.848-0.8480.0000.0000.0000.000
170A177TYR00.013-0.01720.1870.1100.1100.0000.0000.0000.000
171A178SER00.0460.02021.787-1.069-1.0690.0000.0000.0000.000
172A179LEU00.0720.03621.0410.0930.0930.0000.0000.0000.000
173A180GLY00.1210.05523.022-0.037-0.0370.0000.0000.0000.000
174A181SER0-0.053-0.00625.9580.5060.5060.0000.0000.0000.000
175A182ILE0-0.046-0.01319.8730.2130.2130.0000.0000.0000.000
176A183TYR00.0630.02923.833-0.185-0.1850.0000.0000.0000.000
177A184THR0-0.013-0.01325.0320.6020.6020.0000.0000.0000.000
178A185ARG10.7240.81923.11724.26024.2600.0000.0000.0000.000
179A186LEU0-0.060-0.02320.9570.2050.2050.0000.0000.0000.000
180A187TYR00.004-0.02921.833-0.028-0.0280.0000.0000.0000.000
181A188TRP0-0.057-0.01928.1240.9450.9450.0000.0000.0000.000
182A189GLN0-0.0030.00330.1010.5870.5870.0000.0000.0000.000
183A190ALA00.0190.00730.125-0.494-0.4940.0000.0000.0000.000
184A191PRO0-0.026-0.01027.173-0.079-0.0790.0000.0000.0000.000
185A192THR0-0.028-0.03329.0730.5160.5160.0000.0000.0000.000
186A193ASP-1-0.870-0.92728.936-19.827-19.8270.0000.0000.0000.000
187A194SER0-0.056-0.00927.757-0.348-0.3480.0000.0000.0000.000
188A195HIS10.8290.90827.40921.71221.7120.0000.0000.0000.000
189A196THR00.0900.04828.0210.5700.5700.0000.0000.0000.000
190A197ALA00.0630.04023.811-0.557-0.5570.0000.0000.0000.000
191A198GLU-1-0.793-0.91223.475-23.563-23.5630.0000.0000.0000.000
192A199GLY00.0300.02124.671-0.513-0.5130.0000.0000.0000.000
193A200ASP-1-0.808-0.89523.087-23.508-23.5080.0000.0000.0000.000
194A201VAL0-0.012-0.01319.343-1.234-1.2340.0000.0000.0000.000
195A202LEU0-0.013-0.00920.354-1.251-1.2510.0000.0000.0000.000
196A203THR0-0.009-0.00422.5770.0100.0100.0000.0000.0000.000
197A204LEU0-0.039-0.02715.939-0.578-0.5780.0000.0000.0000.000
198A205LEU0-0.002-0.00117.308-1.384-1.3840.0000.0000.0000.000
199A206SER00.007-0.00118.711-0.429-0.4290.0000.0000.0000.000
200A207ILE0-0.039-0.00618.1600.2260.2260.0000.0000.0000.000
201A208CYS0-0.080-0.03014.758-1.593-1.5930.0000.0000.0000.000
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