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: Y1682

Calculation Name: 2OS0-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | nickel (ii) ion

Ligand 3-letter code: SO4 | NI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2OS0

Chain ID: A

ChEMBL ID:

UniProt ID: Q82ZJ0

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 188
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2086536.813675
FMO2-HF: Nuclear repulsion 2011936.589101
FMO2-HF: Total energy -74600.224574
FMO2-MP2: Total energy -74815.761939


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.
-255.085-248.3423.708-4.39-6.06-0.045
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 : 0.810 / q_NPA : 0.905
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].
3A3THR0-0.018-0.0043.2490.6312.9600.117-1.193-1.254-0.006
4A4MET00.0890.0445.0332.0622.155-0.001-0.009-0.0830.000
36A36ASP-1-0.876-0.9442.667-80.312-76.4470.642-2.598-1.909-0.030
37A37MET0-0.057-0.0274.878-1.674-1.635-0.001-0.004-0.0340.000
39A39THR0-0.033-0.0214.2050.9981.142-0.001-0.017-0.1260.000
43A43ASN0-0.020-0.0283.0553.8844.4790.088-0.203-0.480-0.002
53A53LEU0-0.063-0.0372.282-2.249-2.6362.865-0.363-2.114-0.007
55A55LEU0-0.055-0.0254.622-0.805-0.740-0.001-0.003-0.0600.000
5A5LYS10.8720.9378.00627.91727.9170.0000.0000.0000.000
6A6ASP-1-0.812-0.8995.727-49.643-49.6430.0000.0000.0000.000
7A7ILE0-0.0170.0099.1291.9351.9350.0000.0000.0000.000
8A8ILE0-0.058-0.00411.3151.8691.8690.0000.0000.0000.000
9A9ARG10.8190.86712.09421.94921.9490.0000.0000.0000.000
10A10GLU-1-0.735-0.82817.566-12.599-12.5990.0000.0000.0000.000
11A11GLY0-0.028-0.00621.3100.1440.1440.0000.0000.0000.000
12A12ASN0-0.016-0.00117.3160.9910.9910.0000.0000.0000.000
13A13PRO00.005-0.00820.8910.0920.0920.0000.0000.0000.000
14A14THR0-0.023-0.02617.0640.8850.8850.0000.0000.0000.000
15A15LEU0-0.004-0.00117.0530.0360.0360.0000.0000.0000.000
16A16ARG10.6930.80320.28813.15913.1590.0000.0000.0000.000
17A17ALA0-0.0210.00821.6440.6880.6880.0000.0000.0000.000
18A18VAL0-0.052-0.02422.600-0.254-0.2540.0000.0000.0000.000
19A19ALA0-0.0160.00519.163-0.087-0.0870.0000.0000.0000.000
20A20GLU-1-0.900-0.95920.605-12.548-12.5480.0000.0000.0000.000
21A21GLU-1-0.941-0.98220.436-13.698-13.6980.0000.0000.0000.000
22A22VAL0-0.029-0.01617.058-0.141-0.1410.0000.0000.0000.000
23A23PRO0-0.015-0.01219.4090.7180.7180.0000.0000.0000.000
24A24VAL00.0280.02420.798-0.583-0.5830.0000.0000.0000.000
25A25PRO0-0.037-0.03022.0460.6450.6450.0000.0000.0000.000
26A26ILE0-0.0150.00116.0520.0380.0380.0000.0000.0000.000
27A27THR0-0.017-0.02715.6210.1290.1290.0000.0000.0000.000
28A28GLU-1-0.787-0.88013.256-21.328-21.3280.0000.0000.0000.000
29A29GLU-1-0.862-0.91811.162-22.230-22.2300.0000.0000.0000.000
30A30ASP-1-0.772-0.87810.774-23.122-23.1220.0000.0000.0000.000
31A31ARG10.7480.86112.09218.90518.9050.0000.0000.0000.000
32A32GLN0-0.018-0.0146.0482.7362.7360.0000.0000.0000.000
33A33LEU0-0.009-0.0037.220-3.610-3.6100.0000.0000.0000.000
34A34GLY00.0320.0027.789-1.441-1.4410.0000.0000.0000.000
35A35GLU-1-0.904-0.9507.619-28.220-28.2200.0000.0000.0000.000
38A38LEU00.0010.0057.6021.6511.6510.0000.0000.0000.000
40A40PHE0-0.066-0.0334.8370.0630.0630.0000.0000.0000.000
41A41LEU0-0.0100.0065.8982.2762.2760.0000.0000.0000.000
42A42LYS10.8680.9308.35823.05323.0530.0000.0000.0000.000
44A44SER0-0.073-0.0386.6161.4921.4920.0000.0000.0000.000
45A45GLN0-0.009-0.0338.9782.0092.0090.0000.0000.0000.000
46A46ASP-1-0.833-0.9018.613-20.032-20.0320.0000.0000.0000.000
47A47PRO00.0080.00610.099-0.833-0.8330.0000.0000.0000.000
48A48VAL0-0.052-0.0219.7790.5260.5260.0000.0000.0000.000
49A49LYS10.7630.8615.13725.58025.5800.0000.0000.0000.000
50A50ALA00.0570.0346.350-2.237-2.2370.0000.0000.0000.000
51A51GLU-1-0.897-0.9358.699-17.948-17.9480.0000.0000.0000.000
52A52GLU-1-0.865-0.9286.453-25.555-25.5550.0000.0000.0000.000
54A54GLN0-0.137-0.0705.913-0.373-0.3730.0000.0000.0000.000
56A56ARG10.8420.9098.69919.79419.7940.0000.0000.0000.000
57A57GLY00.0720.03310.823-1.547-1.5470.0000.0000.0000.000
58A58ASP-1-0.816-0.93311.573-20.936-20.9360.0000.0000.0000.000
59A59VAL00.0070.02213.061-0.324-0.3240.0000.0000.0000.000
60A60GLY0-0.077-0.05015.0240.4760.4760.0000.0000.0000.000
61A61LEU00.0380.0448.946-0.722-0.7220.0000.0000.0000.000
62A62ALA00.011-0.00413.2700.0560.0560.0000.0000.0000.000
63A63ALA00.0150.00811.944-0.818-0.8180.0000.0000.0000.000
64A64PRO00.015-0.00413.013-0.853-0.8530.0000.0000.0000.000
65A65GLN00.0540.01013.1780.3930.3930.0000.0000.0000.000
66A66LEU0-0.028-0.0127.862-1.190-1.1900.0000.0000.0000.000
67A67ASP-1-0.837-0.91111.272-20.523-20.5230.0000.0000.0000.000
68A68ILE0-0.0210.0059.5761.1801.1800.0000.0000.0000.000
69A69SER00.0260.01013.9750.2540.2540.0000.0000.0000.000
70A70LYS10.8440.91114.74421.02421.0240.0000.0000.0000.000
71A71ARG10.8050.89017.01113.10213.1020.0000.0000.0000.000
72A72ILE0-0.014-0.01012.9410.6190.6190.0000.0000.0000.000
73A73ILE0-0.025-0.01014.607-0.430-0.4300.0000.0000.0000.000
74A74ALA00.0050.01411.5680.3770.3770.0000.0000.0000.000
75A75VAL0-0.016-0.02313.4970.4820.4820.0000.0000.0000.000
76A76HIS0-0.030-0.02312.6110.2890.2890.0000.0000.0000.000
77A77VAL0-0.005-0.00215.303-0.019-0.0190.0000.0000.0000.000
78A78PRO00.0410.03716.4870.8860.8860.0000.0000.0000.000
79A79SER0-0.033-0.04319.4490.3480.3480.0000.0000.0000.000
80A80ASN0-0.084-0.06121.047-0.028-0.0280.0000.0000.0000.000
81A81ASP-1-0.886-0.94715.787-16.109-16.1090.0000.0000.0000.000
82A82PRO0-0.0150.00216.114-0.472-0.4720.0000.0000.0000.000
83A83GLU-1-0.906-0.94815.125-15.852-15.8520.0000.0000.0000.000
84A84ASN0-0.028-0.01911.0120.0790.0790.0000.0000.0000.000
85A85GLU-1-0.813-0.89212.535-19.898-19.8980.0000.0000.0000.000
86A86THR0-0.024-0.02815.2570.9770.9770.0000.0000.0000.000
87A87PRO0-0.043-0.01517.9810.5250.5250.0000.0000.0000.000
88A88SER0-0.089-0.07220.7650.5500.5500.0000.0000.0000.000
89A89LEU0-0.045-0.00619.287-0.070-0.0700.0000.0000.0000.000
90A90SER00.0980.04915.348-0.889-0.8890.0000.0000.0000.000
91A91THR0-0.106-0.04716.0580.1790.1790.0000.0000.0000.000
92A92VAL00.0570.04111.979-0.695-0.6950.0000.0000.0000.000
93A93MET0-0.130-0.05415.0481.5331.5330.0000.0000.0000.000
94A94TYR00.057-0.00312.753-0.192-0.1920.0000.0000.0000.000
95A95ASN00.0070.00618.6300.3210.3210.0000.0000.0000.000
96A96PRO0-0.0220.00919.6070.8580.8580.0000.0000.0000.000
97A97LYS10.9480.96222.45911.07911.0790.0000.0000.0000.000
98A98ILE00.0390.02226.0400.2060.2060.0000.0000.0000.000
99A99LEU0-0.094-0.06028.5880.2870.2870.0000.0000.0000.000
100A100SER0-0.011-0.01431.8250.2630.2630.0000.0000.0000.000
101A101HIS00.004-0.00432.256-0.383-0.3830.0000.0000.0000.000
102A102SER0-0.070-0.03833.8710.2060.2060.0000.0000.0000.000
103A103VAL00.0280.01436.221-0.106-0.1060.0000.0000.0000.000
104A104GLN00.0210.02836.235-0.136-0.1360.0000.0000.0000.000
105A105ASP-1-0.775-0.85734.478-9.329-9.3290.0000.0000.0000.000
106A106VAL0-0.037-0.02130.0970.2520.2520.0000.0000.0000.000
107A107CYS0-0.0240.01429.997-0.064-0.0640.0000.0000.0000.000
108A108LEU00.0660.03623.7760.1900.1900.0000.0000.0000.000
109A109GLY0-0.007-0.02128.2610.1430.1430.0000.0000.0000.000
110A110GLU-1-0.925-0.96222.966-12.130-12.1300.0000.0000.0000.000
111A111GLY0-0.026-0.00126.648-0.093-0.0930.0000.0000.0000.000
112A112GLU-1-0.757-0.86622.892-13.192-13.1920.0000.0000.0000.000
113A113GLY00.0540.03320.4270.3120.3120.0000.0000.0000.000
114A114CYS-1-0.892-0.88417.850-17.705-17.7050.0000.0000.0000.000
115A115LEU00.0450.02910.7200.3930.3930.0000.0000.0000.000
116A116SER0-0.004-0.00314.598-0.794-0.7940.0000.0000.0000.000
117A117VAL0-0.059-0.03416.7400.9310.9310.0000.0000.0000.000
118A118ASP-1-0.855-0.89216.536-18.213-18.2130.0000.0000.0000.000
119A119ARG10.7830.85319.46912.72312.7230.0000.0000.0000.000
120A120ASP-1-0.840-0.92322.866-11.587-11.5870.0000.0000.0000.000
121A121VAL0-0.103-0.06224.6940.3090.3090.0000.0000.0000.000
122A122PRO00.0370.02727.000-0.008-0.0080.0000.0000.0000.000
123A123GLY00.026-0.00129.2740.2550.2550.0000.0000.0000.000
124A124TYR0-0.048-0.01629.372-0.230-0.2300.0000.0000.0000.000
125A125VAL00.0000.01026.4720.1830.1830.0000.0000.0000.000
126A126VAL0-0.055-0.02429.467-0.029-0.0290.0000.0000.0000.000
127A127ARG10.7690.85324.71212.29912.2990.0000.0000.0000.000
128A128HIS10.8540.91330.8549.8209.8200.0000.0000.0000.000
129A129ASN00.0260.00730.556-0.564-0.5640.0000.0000.0000.000
130A130LYS10.9290.95031.1568.6438.6430.0000.0000.0000.000
131A131ILE00.0350.02525.6970.2700.2700.0000.0000.0000.000
132A132THR0-0.066-0.02729.414-0.062-0.0620.0000.0000.0000.000
133A133VAL00.0430.01724.0070.1620.1620.0000.0000.0000.000
134A134SER0-0.096-0.04826.4650.3480.3480.0000.0000.0000.000
135A135TYR00.0630.02320.681-0.046-0.0460.0000.0000.0000.000
136A136PHE00.0120.01021.3800.8270.8270.0000.0000.0000.000
137A137ASP-1-0.724-0.84718.795-15.235-15.2350.0000.0000.0000.000
138A138MET00.0420.02411.5630.4940.4940.0000.0000.0000.000
139A139ALA0-0.017-0.00116.656-0.376-0.3760.0000.0000.0000.000
140A140GLY0-0.0150.00219.7620.4620.4620.0000.0000.0000.000
141A141GLU-1-0.909-0.94821.628-11.130-11.1300.0000.0000.0000.000
142A142LYS10.8880.95023.23310.56210.5620.0000.0000.0000.000
143A143HIS10.8370.90222.66213.51713.5170.0000.0000.0000.000
144A144LYS10.9040.94625.9609.8199.8190.0000.0000.0000.000
145A145VAL00.0210.01924.5150.2080.2080.0000.0000.0000.000
146A146ARG10.8850.92527.7569.6089.6080.0000.0000.0000.000
147A147LEU00.0800.06423.5740.1050.1050.0000.0000.0000.000
148A148LYS10.9480.94527.73210.16310.1630.0000.0000.0000.000
149A149ASN00.0210.00727.404-0.188-0.1880.0000.0000.0000.000
150A150TYR00.1400.06219.6790.1690.1690.0000.0000.0000.000
151A151GLU-1-0.792-0.87322.788-13.010-13.0100.0000.0000.0000.000
152A152ALA0-0.077-0.03723.644-0.331-0.3310.0000.0000.0000.000
153A153ILE00.0230.02423.837-0.060-0.0600.0000.0000.0000.000
154A154VAL00.0530.04218.608-0.083-0.0830.0000.0000.0000.000
155A155VAL00.018-0.00820.518-0.343-0.3430.0000.0000.0000.000
156A156GLN0-0.112-0.08921.9380.3290.3290.0000.0000.0000.000
157A157HIS10.8160.87318.94515.70315.7030.0000.0000.0000.000
158A158GLU-1-0.796-0.91616.679-18.360-18.3600.0000.0000.0000.000
159A159ILE0-0.058-0.04919.370-0.001-0.0010.0000.0000.0000.000
160A160ASP-1-0.826-0.89022.212-12.120-12.1200.0000.0000.0000.000
161A161HIS10.8670.92017.26417.12317.1230.0000.0000.0000.000
162A162ILE0-0.0100.01718.200-0.257-0.2570.0000.0000.0000.000
163A163ASN0-0.021-0.01220.6490.3790.3790.0000.0000.0000.000
164A164GLY00.0560.06322.6020.5650.5650.0000.0000.0000.000
165A165ILE0-0.050-0.02323.7420.4110.4110.0000.0000.0000.000
166A166MET0-0.001-0.00120.156-1.027-1.0270.0000.0000.0000.000
167A167PHE00.0610.01821.5520.5200.5200.0000.0000.0000.000
168A168TYR0-0.015-0.03923.8280.5450.5450.0000.0000.0000.000
169A169ASP-1-0.827-0.87827.187-11.455-11.4550.0000.0000.0000.000
170A170HIS0-0.067-0.04527.1190.8040.8040.0000.0000.0000.000
171A171ILE0-0.0350.01227.9950.3320.3320.0000.0000.0000.000
172A172ASN0-0.015-0.01432.0760.1220.1220.0000.0000.0000.000
173A173LYS10.9890.97032.0179.8139.8130.0000.0000.0000.000
174A174GLU-1-0.960-0.95936.006-7.555-7.5550.0000.0000.0000.000
175A175ASN0-0.059-0.03538.4990.2120.2120.0000.0000.0000.000
176A176PRO00.0210.01833.245-0.019-0.0190.0000.0000.0000.000
177A177PHE00.0290.01431.563-0.203-0.2030.0000.0000.0000.000
178A178ALA0-0.026-0.00435.9710.1980.1980.0000.0000.0000.000
179A179LEU00.0140.01235.188-0.187-0.1870.0000.0000.0000.000
180A180LYS10.9510.97038.6958.4648.4640.0000.0000.0000.000
181A181GLU-1-0.893-0.95740.718-6.992-6.9920.0000.0000.0000.000
182A182GLY0-0.047-0.02441.248-0.059-0.0590.0000.0000.0000.000
183A183VAL0-0.082-0.03035.407-0.161-0.1610.0000.0000.0000.000
184A184LEU0-0.040-0.02934.3190.1270.1270.0000.0000.0000.000
185A185VAL00.0470.00732.354-0.152-0.1520.0000.0000.0000.000
186A186ILE0-0.068-0.02127.3690.1710.1710.0000.0000.0000.000
187A187GLU-1-0.959-0.97729.181-9.411-9.4110.0000.0000.0000.000
188A188LEU-1-0.871-0.90522.754-10.999-10.9990.0000.0000.0000.000