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: 5G2NZ

Calculation Name: 7DC5-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion

Ligand 3-letter code: SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7DC5

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2025-10-06

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 223
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2269049.287814
FMO2-HF: Nuclear repulsion 2192806.703571
FMO2-HF: Total energy -76242.584243
FMO2-MP2: Total energy -76469.110115


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:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-117.093-118.73818.032-9.17-7.214-0.096
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.789 / q_NPA : 0.876
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].
3A3PRO0-0.0090.0163.626-4.392-3.0670.010-0.679-0.655-0.001
117A117PRO0-0.0250.0012.6931.5122.2210.387-0.286-0.810-0.002
118A118GLY00.0190.0074.792-0.740-0.564-0.001-0.012-0.1620.000
137A137THR0-0.004-0.0214.1955.0845.167-0.001-0.007-0.0750.000
139A139THR0-0.022-0.0194.4585.2365.317-0.001-0.005-0.0740.000
140A140ASP-1-0.813-0.8561.673-126.515-130.99617.635-8.001-5.153-0.092
141A141THR0-0.024-0.0413.51911.70212.1640.003-0.180-0.285-0.001
4A4THR00.0250.0186.091-3.306-3.3060.0000.0000.0000.000
5A5ALA00.0690.0327.9142.0322.0320.0000.0000.0000.000
6A6VAL00.0160.0149.4751.6521.6520.0000.0000.0000.000
7A7PRO0-0.042-0.01113.2100.3480.3480.0000.0000.0000.000
8A8LEU00.0550.01015.3380.9680.9680.0000.0000.0000.000
9A9GLY00.0120.01918.2510.9130.9130.0000.0000.0000.000
10A10THR0-0.052-0.06420.739-0.061-0.0610.0000.0000.0000.000
11A11ALA00.0410.01121.8210.4120.4120.0000.0000.0000.000
12A12GLY0-0.034-0.01820.011-0.099-0.0990.0000.0000.0000.000
13A13ASN0-0.064-0.02520.684-0.300-0.3000.0000.0000.0000.000
14A14TYR0-0.040-0.01323.5570.5130.5130.0000.0000.0000.000
15A15ALA00.0000.01323.161-0.742-0.7420.0000.0000.0000.000
16A16ILE0-0.031-0.01624.691-0.261-0.2610.0000.0000.0000.000
17A17LEU0-0.008-0.00125.2180.3070.3070.0000.0000.0000.000
18A18ALA0-0.0020.01227.278-0.259-0.2590.0000.0000.0000.000
19A19SER00.025-0.01130.0130.0130.0130.0000.0000.0000.000
20A20THR0-0.057-0.04232.4770.2280.2280.0000.0000.0000.000
21A21ALA00.018-0.00534.3460.3050.3050.0000.0000.0000.000
22A22VAL00.0120.01331.973-0.363-0.3630.0000.0000.0000.000
23A23SER0-0.0080.00334.3780.2280.2280.0000.0000.0000.000
24A24THR0-0.0070.00434.580-0.387-0.3870.0000.0000.0000.000
25A25VAL00.0100.01136.4180.2910.2910.0000.0000.0000.000
26A26PRO0-0.0280.00537.330-0.222-0.2220.0000.0000.0000.000
27A27GLN0-0.027-0.01436.7280.2570.2570.0000.0000.0000.000
28A28SER0-0.014-0.03332.561-0.196-0.1960.0000.0000.0000.000
29A29ALA0-0.022-0.01731.0650.2270.2270.0000.0000.0000.000
30A30ILE00.0140.01627.926-0.437-0.4370.0000.0000.0000.000
31A31THR0-0.033-0.01826.1970.3800.3800.0000.0000.0000.000
32A32GLY00.0360.01425.687-0.670-0.6700.0000.0000.0000.000
33A33ALA0-0.024-0.00426.9800.3980.3980.0000.0000.0000.000
34A34VAL00.0400.01127.919-0.395-0.3950.0000.0000.0000.000
35A35GLY00.0230.00729.7840.3110.3110.0000.0000.0000.000
36A36ILE0-0.064-0.01430.834-0.231-0.2310.0000.0000.0000.000
37A37SER00.0220.01532.3380.3140.3140.0000.0000.0000.000
38A38PRO00.0230.01232.503-0.333-0.3330.0000.0000.0000.000
39A39ALA0-0.009-0.00135.8750.2770.2770.0000.0000.0000.000
40A40ALA00.0360.01837.233-0.131-0.1310.0000.0000.0000.000
41A41GLY00.0620.00239.031-0.125-0.1250.0000.0000.0000.000
42A42THR0-0.030-0.01640.059-0.018-0.0180.0000.0000.0000.000
43A43PHE0-0.045-0.02338.4140.1020.1020.0000.0000.0000.000
44A44LEU0-0.0110.01634.675-0.295-0.2950.0000.0000.0000.000
45A45THR0-0.013-0.02137.9910.2290.2290.0000.0000.0000.000
46A46GLY00.0310.00438.519-0.186-0.1860.0000.0000.0000.000
47A47PHE00.032-0.00233.5480.0360.0360.0000.0000.0000.000
48A48SER0-0.0380.00639.0930.0390.0390.0000.0000.0000.000
49A49LEU00.0110.01338.501-0.048-0.0480.0000.0000.0000.000
50A50THR00.0160.01741.5810.2790.2790.0000.0000.0000.000
51A51MET0-0.0150.00541.537-0.275-0.2750.0000.0000.0000.000
52A52SER0-0.022-0.01440.7780.1720.1720.0000.0000.0000.000
53A53GLY00.033-0.00442.8920.0670.0670.0000.0000.0000.000
54A54THR0-0.0130.01441.5530.0610.0610.0000.0000.0000.000
55A55GLY00.0250.01143.6750.0430.0430.0000.0000.0000.000
56A56THR0-0.022-0.01538.764-0.147-0.1470.0000.0000.0000.000
57A57PHE00.0390.03136.336-0.255-0.2550.0000.0000.0000.000
58A58SER00.0140.02037.5250.2880.2880.0000.0000.0000.000
59A59THR0-0.001-0.00937.059-0.250-0.2500.0000.0000.0000.000
60A60SER00.055-0.00736.6920.1220.1220.0000.0000.0000.000
61A61THR00.0320.01637.084-0.222-0.2220.0000.0000.0000.000
62A62GLN00.0300.02835.028-0.231-0.2310.0000.0000.0000.000
63A63VAL0-0.021-0.00531.300-0.329-0.3290.0000.0000.0000.000
64A64THR00.0060.01830.3060.3100.3100.0000.0000.0000.000
65A65GLY00.011-0.01530.045-0.529-0.5290.0000.0000.0000.000
66A66GLN0-0.029-0.00131.6550.2710.2710.0000.0000.0000.000
67A67LEU00.0130.01432.247-0.336-0.3360.0000.0000.0000.000
68A68THR0-0.016-0.01632.5830.2350.2350.0000.0000.0000.000
69A69ALA00.0440.01834.390-0.216-0.2160.0000.0000.0000.000
70A70ALA00.0180.00136.2250.0720.0720.0000.0000.0000.000
71A71ASP-1-0.837-0.91437.510-7.831-7.8310.0000.0000.0000.000
72A72TYR0-0.089-0.04238.1310.2030.2030.0000.0000.0000.000
73A73GLY00.0400.01640.7160.0040.0040.0000.0000.0000.000
74A74THR00.004-0.00539.766-0.262-0.2620.0000.0000.0000.000
75A75PRO00.014-0.00636.0600.1390.1390.0000.0000.0000.000
76A76THR0-0.015-0.03034.896-0.236-0.2360.0000.0000.0000.000
77A77PRO00.0370.02534.622-0.319-0.3190.0000.0000.0000.000
78A78SER00.0080.02034.720-0.300-0.3000.0000.0000.0000.000
79A79ILE00.0250.01630.131-0.294-0.2940.0000.0000.0000.000
80A80LEU0-0.0100.01030.044-0.427-0.4270.0000.0000.0000.000
81A81THR0-0.059-0.03930.347-0.186-0.1860.0000.0000.0000.000
82A82THR0-0.036-0.01127.036-0.164-0.1640.0000.0000.0000.000
83A83ALA00.0330.02425.913-0.421-0.4210.0000.0000.0000.000
84A84ILE0-0.001-0.01225.647-0.546-0.5460.0000.0000.0000.000
85A85GLY00.0300.02326.678-0.242-0.2420.0000.0000.0000.000
86A86ASP-1-0.801-0.86822.335-13.704-13.7040.0000.0000.0000.000
87A87MET0-0.0060.01421.843-0.887-0.8870.0000.0000.0000.000
88A88GLY00.0070.00722.409-0.465-0.4650.0000.0000.0000.000
89A89THR0-0.038-0.02020.376-0.265-0.2650.0000.0000.0000.000
90A90ALA0-0.008-0.00618.118-0.720-0.7200.0000.0000.0000.000
91A91TYR0-0.001-0.01517.969-0.752-0.7520.0000.0000.0000.000
92A92THR00.002-0.01219.528-0.337-0.3370.0000.0000.0000.000
93A93ASN0-0.0130.01814.987-1.279-1.2790.0000.0000.0000.000
94A94GLY00.0740.03015.037-1.089-1.0890.0000.0000.0000.000
95A95ALA0-0.015-0.00916.098-0.549-0.5490.0000.0000.0000.000
96A96THR0-0.073-0.05418.8490.2330.2330.0000.0000.0000.000
97A97ARG10.7530.89110.26525.95625.9560.0000.0000.0000.000
98A98SER00.0390.01815.291-0.060-0.0600.0000.0000.0000.000
99A99GLY0-0.002-0.00413.115-1.160-1.1600.0000.0000.0000.000
100A100PRO0-0.015-0.01211.445-1.810-1.8100.0000.0000.0000.000
101A101ASP-1-0.837-0.9037.240-35.530-35.5300.0000.0000.0000.000
102A102PHE0-0.054-0.0257.5631.7241.7240.0000.0000.0000.000
103A103LEU00.0250.00612.3810.0990.0990.0000.0000.0000.000
104A104GLU-1-0.787-0.87316.119-14.108-14.1080.0000.0000.0000.000
105A105ILE00.0020.01514.0440.7070.7070.0000.0000.0000.000
106A106TYR00.0340.00114.2440.3430.3430.0000.0000.0000.000
107A107THR0-0.0110.00719.7600.6970.6970.0000.0000.0000.000
108A108GLY00.0310.02119.8540.4780.4780.0000.0000.0000.000
109A109ALA0-0.035-0.01220.8490.0350.0350.0000.0000.0000.000
110A110LEU00.0230.00216.335-0.462-0.4620.0000.0000.0000.000
111A111GLY0-0.032-0.00118.865-0.457-0.4570.0000.0000.0000.000
112A112GLY0-0.001-0.00420.6050.2320.2320.0000.0000.0000.000
113A113THR0-0.067-0.03615.761-0.715-0.7150.0000.0000.0000.000
114A114THR0-0.003-0.02011.3910.0200.0200.0000.0000.0000.000
115A115LEU0-0.031-0.00411.005-0.477-0.4770.0000.0000.0000.000
116A116LEU00.0530.0306.338-1.306-1.3060.0000.0000.0000.000
119A119LEU0-0.087-0.0406.6131.2101.2100.0000.0000.0000.000
120A120TYR0-0.034-0.0478.8522.5532.5530.0000.0000.0000.000
121A121LYS10.8250.91112.56315.98615.9860.0000.0000.0000.000
122A122TRP0-0.023-0.02814.958-0.318-0.3180.0000.0000.0000.000
123A123THR0-0.057-0.06119.4230.3090.3090.0000.0000.0000.000
124A124SER0-0.017-0.01322.3930.5280.5280.0000.0000.0000.000
125A125SER0-0.027-0.01223.219-0.328-0.3280.0000.0000.0000.000
126A126VAL00.0170.02018.855-0.196-0.1960.0000.0000.0000.000
127A127GLY00.0140.00622.1610.4160.4160.0000.0000.0000.000
128A128ALA0-0.0130.01320.884-0.299-0.2990.0000.0000.0000.000
129A129SER00.022-0.00422.9170.1900.1900.0000.0000.0000.000
130A130ALA0-0.030-0.02823.9710.5230.5230.0000.0000.0000.000
131A131ASP-1-0.787-0.90121.535-13.244-13.2440.0000.0000.0000.000
132A132PHE0-0.029-0.00515.3870.1620.1620.0000.0000.0000.000
133A133THR0-0.0020.00113.0130.0920.0920.0000.0000.0000.000
134A134ILE00.0100.0179.859-0.375-0.3750.0000.0000.0000.000
135A135SER0-0.032-0.0199.4760.3950.3950.0000.0000.0000.000
136A136GLY00.0400.0065.858-3.050-3.0500.0000.0000.0000.000
138A138SER00.0020.0056.543-2.565-2.5650.0000.0000.0000.000
142A142TRP0-0.008-0.0186.053-4.821-4.8210.0000.0000.0000.000
143A143ILE0-0.042-0.0038.9112.4112.4110.0000.0000.0000.000
144A144PHE00.0090.00611.598-0.432-0.4320.0000.0000.0000.000
145A145GLN0-0.026-0.03414.6131.2811.2810.0000.0000.0000.000
146A146ILE0-0.024-0.01417.1420.1960.1960.0000.0000.0000.000
147A147ASP-1-0.763-0.87320.390-13.932-13.9320.0000.0000.0000.000
148A148GLY00.0040.00923.6410.6540.6540.0000.0000.0000.000
149A149THR0-0.038-0.03325.117-0.257-0.2570.0000.0000.0000.000
150A150LEU00.0200.01820.111-0.337-0.3370.0000.0000.0000.000
151A151GLY0-0.0030.00123.7560.4580.4580.0000.0000.0000.000
152A152LEU0-0.028-0.00921.775-0.488-0.4880.0000.0000.0000.000
153A153ALA00.0370.01124.6270.4760.4760.0000.0000.0000.000
154A154ALA00.0310.00227.425-0.206-0.2060.0000.0000.0000.000
155A155GLY0-0.045-0.01629.0210.0530.0530.0000.0000.0000.000
156A156LYS10.8410.94424.37510.95310.9530.0000.0000.0000.000
157A157LYS10.9010.93922.23811.89911.8990.0000.0000.0000.000
158A158ILE0-0.0210.01216.117-0.209-0.2090.0000.0000.0000.000
159A159THR0-0.0010.00316.6010.4880.4880.0000.0000.0000.000
160A160LEU0-0.022-0.00412.707-1.208-1.2080.0000.0000.0000.000
161A161ALA00.0230.00212.2011.3251.3250.0000.0000.0000.000
162A162GLY00.017-0.0039.913-2.179-2.1790.0000.0000.0000.000
163A163GLY00.0030.00010.389-0.781-0.7810.0000.0000.0000.000
164A164ALA0-0.0170.0098.645-0.501-0.5010.0000.0000.0000.000
165A165GLN0-0.013-0.0269.4675.4665.4660.0000.0000.0000.000
166A166ALA00.0620.03211.118-1.492-1.4920.0000.0000.0000.000
167A167LYS10.9180.96012.02423.29523.2950.0000.0000.0000.000
168A168ASN0-0.071-0.0337.1463.6143.6140.0000.0000.0000.000
169A169ILE0-0.0190.0079.378-2.927-2.9270.0000.0000.0000.000
170A170ILE0-0.029-0.01211.6552.4692.4690.0000.0000.0000.000
171A171TRP00.010-0.00714.004-0.425-0.4250.0000.0000.0000.000
172A172VAL0-0.025-0.01115.9630.7220.7220.0000.0000.0000.000
173A173VAL00.0090.01018.5990.0610.0610.0000.0000.0000.000
174A174ALA0-0.019-0.00221.9720.3770.3770.0000.0000.0000.000
175A175GLY00.0380.01224.9930.5700.5700.0000.0000.0000.000
176A176ALA0-0.018-0.00626.362-0.280-0.2800.0000.0000.0000.000
177A177VAL00.021-0.00323.512-0.247-0.2470.0000.0000.0000.000
178A178SER0-0.069-0.03226.3640.6160.6160.0000.0000.0000.000
179A179ILE00.0110.01423.342-0.272-0.2720.0000.0000.0000.000
180A180GLU-1-0.811-0.89827.026-9.676-9.6760.0000.0000.0000.000
181A181ALA00.0340.00929.468-0.196-0.1960.0000.0000.0000.000
182A182GLY00.0070.00130.570-0.057-0.0570.0000.0000.0000.000
183A183ALA0-0.057-0.00425.626-0.206-0.2060.0000.0000.0000.000
184A184GLN0-0.008-0.01723.4340.3540.3540.0000.0000.0000.000
185A185PHE00.0540.01018.859-0.353-0.3530.0000.0000.0000.000
186A186GLU-1-0.806-0.89815.823-17.675-17.6750.0000.0000.0000.000
187A187GLY00.0210.00815.241-0.851-0.8510.0000.0000.0000.000
188A188VAL0-0.058-0.02915.6301.4351.4350.0000.0000.0000.000
189A189ILE0-0.0130.00017.346-0.642-0.6420.0000.0000.0000.000
190A190LEU0-0.0050.00317.1430.6750.6750.0000.0000.0000.000
191A191ALA00.0140.00420.642-0.199-0.1990.0000.0000.0000.000
192A192LYS10.8860.94123.88812.13412.1340.0000.0000.0000.000
193A193THR0-0.041-0.02626.2200.5480.5480.0000.0000.0000.000
194A194ALA00.0140.02128.522-0.122-0.1220.0000.0000.0000.000
195A195VAL00.0200.00125.134-0.343-0.3430.0000.0000.0000.000
196A196THR0-0.041-0.01328.1190.5090.5090.0000.0000.0000.000
197A197LEU00.0150.00925.855-0.351-0.3510.0000.0000.0000.000
198A198LYS10.8460.89729.55310.17110.1710.0000.0000.0000.000
199A199THR00.0390.00231.909-0.158-0.1580.0000.0000.0000.000
200A200GLY00.0290.02932.894-0.060-0.0600.0000.0000.0000.000
201A201SER0-0.080-0.02727.802-0.317-0.3170.0000.0000.0000.000
202A202SER0-0.014-0.02725.5800.0360.0360.0000.0000.0000.000
203A203LEU0-0.0120.00720.990-0.230-0.2300.0000.0000.0000.000
204A204ASN0-0.045-0.02718.7400.9200.9200.0000.0000.0000.000
205A205GLY00.023-0.00418.319-1.099-1.0990.0000.0000.0000.000
206A206ARG10.7900.86618.52316.68316.6830.0000.0000.0000.000
207A207ILE00.0000.00621.009-0.488-0.4880.0000.0000.0000.000
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