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: JV7G9

Calculation Name: 3NEY-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | unknown atom or ion

Ligand 3-letter code: SO4 | UNX

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3NEY

Chain ID: A

ChEMBL ID:

UniProt ID: Q00013

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 180
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1883371.056216
FMO2-HF: Nuclear repulsion 1812532.981964
FMO2-HF: Total energy -70838.074251
FMO2-MP2: Total energy -71047.350276


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:279:PHE)


Summations of interaction energy for fragment #1(A:279:PHE)
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.
-92.725-77.56113.798-8.134-20.827-0.034
Interaction energy analysis for fragmet #1(A:279:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.828 / q_NPA : 0.914
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].
3A281GLY00.1150.0713.0217.98011.1050.008-1.436-1.697-0.003
4A282ARG10.6950.8243.30418.56919.5820.035-0.532-0.517-0.004
5A283LYS10.8750.9322.72127.11731.1663.098-1.790-5.3560.016
6A284THR0-0.022-0.0274.023-0.2500.0500.0030.077-0.3800.000
91A369ILE0-0.0200.0174.724-0.390-0.314-0.001-0.005-0.0680.000
92A370HIS0-0.019-0.0172.180-3.827-2.4401.320-1.027-1.6800.000
93A371LYS10.8560.9232.71414.16715.6570.550-0.584-1.455-0.014
95A373ASN0-0.088-0.0512.404-10.258-9.2204.749-2.344-3.4430.001
96A374LYS10.9170.9893.01122.16221.9161.2951.453-2.503-0.007
97A375ILE0-0.010-0.0072.132-9.309-6.5542.740-1.929-3.567-0.023
98A376ALA0-0.0050.0073.8253.8313.9430.002-0.015-0.0990.000
177A455SER0-0.044-0.0284.4821.6241.689-0.001-0.002-0.0620.000
7A285LEU0-0.0050.0146.7180.1760.1760.0000.0000.0000.000
8A286VAL0-0.015-0.0129.5330.7470.7470.0000.0000.0000.000
9A287LEU0-0.0040.01412.9290.3850.3850.0000.0000.0000.000
10A288ILE00.0240.01015.8880.5940.5940.0000.0000.0000.000
11A289GLY00.0440.01519.327-0.013-0.0130.0000.0000.0000.000
12A290ALA00.0090.02222.7070.0760.0760.0000.0000.0000.000
13A291SER00.007-0.00825.530-0.275-0.2750.0000.0000.0000.000
14A292GLY00.0580.02226.1910.3590.3590.0000.0000.0000.000
15A293VAL0-0.051-0.01622.9190.0820.0820.0000.0000.0000.000
16A294GLY00.0360.02223.919-0.182-0.1820.0000.0000.0000.000
17A295ARG10.8210.89818.19313.06513.0650.0000.0000.0000.000
18A296SER00.0470.01418.751-0.716-0.7160.0000.0000.0000.000
19A297HIS00.0070.00019.242-0.555-0.5550.0000.0000.0000.000
20A298ILE00.0070.01616.054-0.257-0.2570.0000.0000.0000.000
21A299LYS10.9330.98114.23113.91013.9100.0000.0000.0000.000
22A300ASN0-0.020-0.01415.118-0.986-0.9860.0000.0000.0000.000
23A301ALA00.0240.01617.469-0.097-0.0970.0000.0000.0000.000
24A302LEU00.0100.00611.978-0.256-0.2560.0000.0000.0000.000
25A303LEU0-0.048-0.03011.616-0.671-0.6710.0000.0000.0000.000
26A304SER0-0.050-0.02213.937-0.049-0.0490.0000.0000.0000.000
27A305GLN0-0.028-0.00815.153-0.343-0.3430.0000.0000.0000.000
28A306ASN0-0.0120.00210.6850.3140.3140.0000.0000.0000.000
29A307PRO00.0450.03310.616-1.618-1.6180.0000.0000.0000.000
30A308GLU-1-0.884-0.96010.141-23.416-23.4160.0000.0000.0000.000
31A309LYS10.8240.9036.18528.05328.0530.0000.0000.0000.000
32A310PHE00.005-0.0095.662-3.919-3.9190.0000.0000.0000.000
33A311VAL0-0.002-0.0047.7341.7031.7030.0000.0000.0000.000
34A312TYR00.0280.0129.260-0.752-0.7520.0000.0000.0000.000
35A313PRO0-0.036-0.00810.8600.3520.3520.0000.0000.0000.000
36A314VAL00.0250.01512.6050.5580.5580.0000.0000.0000.000
37A315PRO0-0.0100.01016.1480.0130.0130.0000.0000.0000.000
38A316TYR00.0350.00317.0190.4980.4980.0000.0000.0000.000
39A317THR0-0.019-0.02321.4260.1990.1990.0000.0000.0000.000
40A318THR00.0330.02225.1180.0150.0150.0000.0000.0000.000
41A319ARG10.8150.93027.03810.03310.0330.0000.0000.0000.000
42A320PRO00.006-0.00429.415-0.152-0.1520.0000.0000.0000.000
43A321PRO00.0080.02928.8680.0060.0060.0000.0000.0000.000
44A322ARG10.8280.87329.0959.4779.4770.0000.0000.0000.000
45A323LYS10.9580.95432.1597.0897.0890.0000.0000.0000.000
46A324SER0-0.0150.00532.3650.0450.0450.0000.0000.0000.000
47A325GLU-1-0.794-0.86827.726-9.740-9.7400.0000.0000.0000.000
48A326GLU-1-0.870-0.92924.877-9.891-9.8910.0000.0000.0000.000
49A327ASP-1-0.855-0.94624.008-11.301-11.3010.0000.0000.0000.000
50A328GLY00.0210.01420.098-0.198-0.1980.0000.0000.0000.000
51A329LYS10.9000.96019.09010.53010.5300.0000.0000.0000.000
52A330GLU-1-0.964-0.98919.575-11.332-11.3320.0000.0000.0000.000
53A331TYR0-0.041-0.04420.567-0.178-0.1780.0000.0000.0000.000
54A332HIS0-0.0220.00916.5880.0290.0290.0000.0000.0000.000
55A333PHE0-0.055-0.04322.0170.1340.1340.0000.0000.0000.000
56A334ILE00.0050.01323.6300.0950.0950.0000.0000.0000.000
57A335SER00.007-0.02126.8190.0800.0800.0000.0000.0000.000
58A336THR0-0.011-0.03028.968-0.201-0.2010.0000.0000.0000.000
59A337GLU-1-0.791-0.86430.585-8.637-8.6370.0000.0000.0000.000
60A338GLU-1-0.940-0.97124.614-10.699-10.6990.0000.0000.0000.000
61A339MET0-0.0190.00424.005-0.405-0.4050.0000.0000.0000.000
62A340THR0-0.011-0.02226.335-0.201-0.2010.0000.0000.0000.000
63A341ARG10.9400.98126.4359.7339.7330.0000.0000.0000.000
64A342ASN00.0360.02022.437-0.113-0.1130.0000.0000.0000.000
65A343ILE0-0.029-0.01023.098-0.387-0.3870.0000.0000.0000.000
66A344SER0-0.073-0.03624.982-0.073-0.0730.0000.0000.0000.000
67A345ALA0-0.007-0.00623.3870.0090.0090.0000.0000.0000.000
68A346ASN0-0.065-0.03321.540-0.479-0.4790.0000.0000.0000.000
69A347GLU-1-0.827-0.90918.828-13.084-13.0840.0000.0000.0000.000
70A348PHE0-0.080-0.04617.552-0.707-0.7070.0000.0000.0000.000
71A349LEU0-0.0260.00713.0340.1090.1090.0000.0000.0000.000
72A350GLU-1-0.766-0.87517.000-13.298-13.2980.0000.0000.0000.000
73A351PHE0-0.002-0.01419.671-0.049-0.0490.0000.0000.0000.000
74A352GLY00.0300.02122.8280.1400.1400.0000.0000.0000.000
75A353SER0-0.009-0.01926.1260.0780.0780.0000.0000.0000.000
76A354TYR0-0.004-0.00628.2100.0140.0140.0000.0000.0000.000
77A355GLN0-0.002-0.00930.054-0.013-0.0130.0000.0000.0000.000
78A356GLY00.0130.00633.3580.0880.0880.0000.0000.0000.000
79A357ASN0-0.0240.00029.8310.0810.0810.0000.0000.0000.000
80A358MET00.0250.03126.257-0.183-0.1830.0000.0000.0000.000
81A359PHE0-0.010-0.00923.321-0.021-0.0210.0000.0000.0000.000
82A360GLY00.0640.02621.0140.1270.1270.0000.0000.0000.000
83A361THR00.0230.01814.476-0.004-0.0040.0000.0000.0000.000
84A362LYS10.8550.92815.93812.75012.7500.0000.0000.0000.000
85A363PHE00.0310.01213.220-1.126-1.1260.0000.0000.0000.000
86A364GLU-1-0.841-0.91311.565-20.847-20.8470.0000.0000.0000.000
87A365THR00.0080.00311.034-0.867-0.8670.0000.0000.0000.000
88A366VAL00.0400.0237.900-0.767-0.7670.0000.0000.0000.000
89A367HIS10.8820.9436.98819.33519.3350.0000.0000.0000.000
90A368GLN0-0.011-0.0267.029-1.835-1.8350.0000.0000.0000.000
94A372GLN0-0.050-0.0245.0801.4861.4860.0000.0000.0000.000
99A377ILE0-0.013-0.0096.974-0.093-0.0930.0000.0000.0000.000
100A378LEU0-0.015-0.02310.1840.8020.8020.0000.0000.0000.000
101A379ASP-1-0.823-0.93313.010-15.382-15.3820.0000.0000.0000.000
102A380ILE0-0.041-0.00815.6720.5100.5100.0000.0000.0000.000
103A381GLU-1-0.872-0.93418.046-11.530-11.5300.0000.0000.0000.000
104A382PRO00.002-0.00720.777-0.385-0.3850.0000.0000.0000.000
105A383GLN00.0480.02221.901-0.173-0.1730.0000.0000.0000.000
106A384THR0-0.052-0.05317.5490.0300.0300.0000.0000.0000.000
107A385LEU0-0.005-0.00317.019-0.839-0.8390.0000.0000.0000.000
108A386LYS10.8950.95418.31011.12411.1240.0000.0000.0000.000
109A387ILE0-0.021-0.00716.408-0.061-0.0610.0000.0000.0000.000
110A388VAL00.0340.00613.154-0.693-0.6930.0000.0000.0000.000
111A389ARG10.8800.96213.11414.04414.0440.0000.0000.0000.000
112A390THR00.0280.01412.4640.0250.0250.0000.0000.0000.000
113A391ALA00.1070.0539.627-1.394-1.3940.0000.0000.0000.000
114A392GLU-1-0.920-0.9488.108-26.155-26.1550.0000.0000.0000.000
115A393LEU00.0240.0127.448-2.791-2.7910.0000.0000.0000.000
116A394SER0-0.016-0.0045.712-2.358-2.3580.0000.0000.0000.000
117A395PRO00.0140.0107.245-2.428-2.4280.0000.0000.0000.000
118A396PHE00.0270.0289.3140.2150.2150.0000.0000.0000.000
119A397ILE0-0.024-0.02010.8620.5090.5090.0000.0000.0000.000
120A398VAL00.014-0.00213.7910.5690.5690.0000.0000.0000.000
121A399PHE00.0030.00716.5170.3240.3240.0000.0000.0000.000
122A400ILE0-0.028-0.02217.843-0.040-0.0400.0000.0000.0000.000
123A401ALA00.0310.01021.4720.3670.3670.0000.0000.0000.000
124A402PRO0-0.003-0.01025.257-0.146-0.1460.0000.0000.0000.000
125A403THR0-0.041-0.04328.1400.0030.0030.0000.0000.0000.000
126A404ASP-1-0.911-0.94630.065-8.439-8.4390.0000.0000.0000.000
127A405GLN0-0.058-0.02633.285-0.017-0.0170.0000.0000.0000.000
128A406GLY00.0370.00635.6530.1430.1430.0000.0000.0000.000
129A407THR0-0.054-0.02539.1950.2460.2460.0000.0000.0000.000
130A408GLN00.0400.03537.612-0.343-0.3430.0000.0000.0000.000
131A409THR00.0260.00937.4990.1500.1500.0000.0000.0000.000
132A410GLU-1-0.815-0.91838.460-7.368-7.3680.0000.0000.0000.000
133A411ALA0-0.011-0.00735.603-0.116-0.1160.0000.0000.0000.000
134A412LEU0-0.0030.00732.513-0.222-0.2220.0000.0000.0000.000
135A413GLN0-0.008-0.00734.246-0.178-0.1780.0000.0000.0000.000
136A414GLN00.0000.01434.983-0.167-0.1670.0000.0000.0000.000
137A415LEU00.0310.01828.254-0.179-0.1790.0000.0000.0000.000
138A416GLN00.019-0.01230.499-0.410-0.4100.0000.0000.0000.000
139A417LYS10.8490.91531.9148.1548.1540.0000.0000.0000.000
140A418ASP-1-0.867-0.93130.252-8.977-8.9770.0000.0000.0000.000
141A419SER00.005-0.01127.507-0.455-0.4550.0000.0000.0000.000
142A420GLU-1-0.795-0.85427.914-10.038-10.0380.0000.0000.0000.000
143A421ALA0-0.012-0.00830.188-0.099-0.0990.0000.0000.0000.000
144A422ILE0-0.0150.00224.162-0.106-0.1060.0000.0000.0000.000
145A423ARG10.8260.86725.55610.06310.0630.0000.0000.0000.000
146A424SER0-0.053-0.03226.624-0.248-0.2480.0000.0000.0000.000
147A425GLN0-0.060-0.02627.868-0.045-0.0450.0000.0000.0000.000
148A426TYR0-0.014-0.02122.710-0.250-0.2500.0000.0000.0000.000
149A427ALA00.0390.03022.599-0.581-0.5810.0000.0000.0000.000
150A428HIS0-0.019-0.00322.109-0.789-0.7890.0000.0000.0000.000
151A429TYR0-0.022-0.02818.489-0.518-0.5180.0000.0000.0000.000
152A430PHE0-0.039-0.01517.431-0.749-0.7490.0000.0000.0000.000
153A431ASP-1-0.777-0.84913.409-20.295-20.2950.0000.0000.0000.000
154A432LEU0-0.004-0.00215.8640.2860.2860.0000.0000.0000.000
155A433SER0-0.037-0.02318.0170.3820.3820.0000.0000.0000.000
156A434LEU0-0.017-0.00317.5890.0850.0850.0000.0000.0000.000
157A435VAL00.0170.02221.7020.1670.1670.0000.0000.0000.000
158A436ASN0-0.027-0.01823.502-0.329-0.3290.0000.0000.0000.000
159A437ASN00.0030.01024.4930.6600.6600.0000.0000.0000.000
160A438GLY00.0320.02425.8060.1020.1020.0000.0000.0000.000
161A439VAL00.0180.00920.271-0.356-0.3560.0000.0000.0000.000
162A440ASP-1-0.853-0.92520.677-13.245-13.2450.0000.0000.0000.000
163A441GLU-1-0.772-0.85120.643-13.471-13.4710.0000.0000.0000.000
164A442THR0-0.043-0.03719.259-0.301-0.3010.0000.0000.0000.000
165A443LEU0-0.013-0.02516.015-0.707-0.7070.0000.0000.0000.000
166A444LYS10.8230.91616.26912.85412.8540.0000.0000.0000.000
167A445LYS10.8930.92316.85612.00412.0040.0000.0000.0000.000
168A446LEU0-0.0190.00213.562-0.583-0.5830.0000.0000.0000.000
169A447GLN0-0.006-0.01611.619-2.801-2.8010.0000.0000.0000.000
170A448GLU-1-0.900-0.95112.074-17.153-17.1530.0000.0000.0000.000
171A449ALA0-0.013-0.01413.795-0.693-0.6930.0000.0000.0000.000
172A450PHE0-0.041-0.0235.405-0.563-0.5630.0000.0000.0000.000
173A451ASP-1-0.828-0.9058.492-31.923-31.9230.0000.0000.0000.000
174A452GLN0-0.056-0.0179.425-0.601-0.6010.0000.0000.0000.000
175A453ALA0-0.044-0.0049.1060.6950.6950.0000.0000.0000.000
176A454CYS00.002-0.0057.963-3.413-3.4130.0000.0000.0000.000
178A456SER00.0190.0067.723-0.331-0.3310.0000.0000.0000.000
179A457PRO0-0.062-0.0278.766-0.121-0.1210.0000.0000.0000.000
180A458GLN-1-0.903-0.94410.194-18.680-18.6800.0000.0000.0000.000