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: 9RQ22

Calculation Name: 2YY6-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion

Ligand 3-letter code: SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2YY6

Chain ID: A

ChEMBL ID:

UniProt ID: O67359

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 208
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2427432.095899
FMO2-HF: Nuclear repulsion 2347551.594322
FMO2-HF: Total energy -79880.501577
FMO2-MP2: Total energy -80119.248121


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.
-232.36-224.83719.912-13.565-13.872-0.148
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 : 0.750 / q_NPA : 0.871
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].
3A3VAL00.0210.0163.764-4.865-3.084-0.017-0.895-0.8690.000
96A96LYS10.8020.9012.62830.83531.4730.244-0.162-0.720-0.001
97A97GLY00.006-0.0012.698-8.343-6.8430.717-0.895-1.323-0.010
98A98PHE0-0.086-0.0482.512-17.529-14.6573.385-1.857-4.401-0.018
99A99LYS10.8880.9553.25073.41274.0890.016-0.132-0.561-0.001
152A152GLU-1-0.863-0.9221.846-146.254-146.34215.568-9.596-5.884-0.118
156A156LYS10.7780.8934.59637.79537.938-0.001-0.028-0.1140.000
4A4ILE00.0000.0005.9824.4914.4910.0000.0000.0000.000
5A5LEU0-0.013-0.0039.4550.6940.6940.0000.0000.0000.000
6A6PHE00.0400.00911.6421.5461.5460.0000.0000.0000.000
7A7ASP0-0.021-0.04615.3870.1270.1270.0000.0000.0000.000
8A8LEU00.0540.01819.005-0.186-0.1860.0000.0000.0000.000
9A9ASP-1-0.784-0.86921.148-12.171-12.1710.0000.0000.0000.000
10A10GLY0-0.059-0.02624.608-0.009-0.0090.0000.0000.0000.000
11A11THR0-0.019-0.01618.7050.0560.0560.0000.0000.0000.000
12A12LEU00.0200.01816.091-0.135-0.1350.0000.0000.0000.000
13A13ILE0-0.016-0.01520.0730.2920.2920.0000.0000.0000.000
14A14ASP-1-0.845-0.91223.753-10.418-10.4180.0000.0000.0000.000
15A15SER0-0.024-0.05127.1420.3870.3870.0000.0000.0000.000
16A16ALA0-0.014-0.01029.1670.3310.3310.0000.0000.0000.000
17A17LYS10.9020.94831.7099.9219.9210.0000.0000.0000.000
18A18ASP-1-0.621-0.76232.323-9.521-9.5210.0000.0000.0000.000
19A19ILE0-0.051-0.01830.4270.1590.1590.0000.0000.0000.000
20A20ALA00.0120.00334.0930.2030.2030.0000.0000.0000.000
21A21LEU00.0470.03037.3130.2210.2210.0000.0000.0000.000
22A22ALA00.0080.00336.1020.2010.2010.0000.0000.0000.000
23A23LEU0-0.0280.00037.9310.1100.1100.0000.0000.0000.000
24A24GLU-1-0.921-0.95339.428-7.262-7.2620.0000.0000.0000.000
25A25LYS10.8180.89041.1227.8867.8860.0000.0000.0000.000
26A26THR0-0.004-0.02139.7700.0920.0920.0000.0000.0000.000
27A27LEU0-0.017-0.01642.4030.1230.1230.0000.0000.0000.000
28A28LYS10.9420.98844.8997.0147.0140.0000.0000.0000.000
29A29GLU-1-0.990-1.00244.960-7.130-7.1300.0000.0000.0000.000
30A30LEU0-0.034-0.01743.2190.0870.0870.0000.0000.0000.000
31A31GLY0-0.0170.02447.6870.1090.1090.0000.0000.0000.000
32A32LEU0-0.024-0.01745.9300.0230.0230.0000.0000.0000.000
33A33GLU-1-0.860-0.95647.108-6.637-6.6370.0000.0000.0000.000
34A34GLU-1-0.882-0.94247.875-6.488-6.4880.0000.0000.0000.000
35A35TYR0-0.080-0.03845.443-0.011-0.0110.0000.0000.0000.000
36A36TYR0-0.025-0.02340.594-0.267-0.2670.0000.0000.0000.000
37A37PRO0-0.067-0.02340.6400.0860.0860.0000.0000.0000.000
38A38ASP-1-0.875-0.94042.928-7.064-7.0640.0000.0000.0000.000
39A39ASN0-0.061-0.03639.049-0.105-0.1050.0000.0000.0000.000
40A40VAL00.0520.01937.243-0.189-0.1890.0000.0000.0000.000
41A41THR00.018-0.00633.466-0.097-0.0970.0000.0000.0000.000
42A42LYS10.9010.96433.7217.8507.8500.0000.0000.0000.000
43A43TYR0-0.012-0.00635.5530.0680.0680.0000.0000.0000.000
44A44ILE0-0.026-0.00229.756-0.123-0.1230.0000.0000.0000.000
45A45GLY00.0530.01328.908-0.212-0.2120.0000.0000.0000.000
46A46GLY0-0.0210.00027.744-0.429-0.4290.0000.0000.0000.000
47A47GLY0-0.002-0.00228.7880.0030.0030.0000.0000.0000.000
48A48VAL00.000-0.00829.3830.2050.2050.0000.0000.0000.000
49A49ARG10.9661.00032.5029.6089.6080.0000.0000.0000.000
50A50ALA00.0570.03031.8600.2400.2400.0000.0000.0000.000
51A51LEU0-0.0160.00333.5220.1890.1890.0000.0000.0000.000
52A52LEU00.0440.00535.1550.2430.2430.0000.0000.0000.000
53A53GLU-1-0.916-0.95836.238-8.807-8.8070.0000.0000.0000.000
54A54LYS10.8820.93434.7519.2579.2570.0000.0000.0000.000
55A55VAL0-0.029-0.00538.8380.1430.1430.0000.0000.0000.000
56A56LEU00.0410.02841.1600.1880.1880.0000.0000.0000.000
57A57LYS10.9290.97742.0997.2627.2620.0000.0000.0000.000
58A58ASP-1-0.862-0.92843.482-6.834-6.8340.0000.0000.0000.000
59A59LYS10.8890.93346.2036.6726.6720.0000.0000.0000.000
60A60PHE0-0.030-0.00238.144-0.042-0.0420.0000.0000.0000.000
61A61ARG10.8620.93042.9397.0727.0720.0000.0000.0000.000
62A62GLU-1-0.951-0.97139.301-8.292-8.2920.0000.0000.0000.000
63A63GLU-1-0.768-0.89839.408-7.561-7.5610.0000.0000.0000.000
64A64TYR00.0170.00041.054-0.048-0.0480.0000.0000.0000.000
65A65VAL0-0.058-0.04134.639-0.188-0.1880.0000.0000.0000.000
66A66GLU-1-0.924-0.95536.331-8.148-8.1480.0000.0000.0000.000
67A67VAL00.0570.03438.150-0.093-0.0930.0000.0000.0000.000
68A68PHE00.0280.01133.861-0.132-0.1320.0000.0000.0000.000
69A69ARG10.8430.92530.6239.8599.8590.0000.0000.0000.000
70A70LYS10.8840.93035.2938.1978.1970.0000.0000.0000.000
71A71HIS00.0590.03837.484-0.169-0.1690.0000.0000.0000.000
72A72TYR0-0.026-0.02729.550-0.311-0.3110.0000.0000.0000.000
73A73LEU0-0.058-0.04531.058-0.432-0.4320.0000.0000.0000.000
74A74GLU-1-0.877-0.90834.185-8.055-8.0550.0000.0000.0000.000
75A75ASN0-0.008-0.01235.7680.1370.1370.0000.0000.0000.000
76A76PRO0-0.034-0.01130.202-0.063-0.0630.0000.0000.0000.000
77A77VAL0-0.008-0.01828.293-0.367-0.3670.0000.0000.0000.000
78A78VAL0-0.061-0.01531.4370.1970.1970.0000.0000.0000.000
79A79TYR0-0.038-0.04633.1350.0210.0210.0000.0000.0000.000
80A80THR0-0.097-0.07127.059-0.226-0.2260.0000.0000.0000.000
81A81LYS10.9350.97026.39610.24610.2460.0000.0000.0000.000
82A82PRO00.0400.01720.926-0.094-0.0940.0000.0000.0000.000
83A83TYR00.0190.01921.3170.5250.5250.0000.0000.0000.000
84A84PRO00.032-0.00721.378-0.415-0.4150.0000.0000.0000.000
85A85GLU-1-0.762-0.85417.768-14.682-14.6820.0000.0000.0000.000
86A86ILE0-0.0110.02616.751-0.956-0.9560.0000.0000.0000.000
87A87PRO00.022-0.00415.798-0.946-0.9460.0000.0000.0000.000
88A88TYR00.0050.01113.412-0.626-0.6260.0000.0000.0000.000
89A89THR0-0.006-0.01712.248-0.855-0.8550.0000.0000.0000.000
90A90LEU0-0.030-0.01711.051-1.748-1.7480.0000.0000.0000.000
91A91GLU-1-0.849-0.91410.946-22.363-22.3630.0000.0000.0000.000
92A92ALA00.0060.00810.246-1.527-1.5270.0000.0000.0000.000
93A93LEU0-0.040-0.0216.707-2.034-2.0340.0000.0000.0000.000
94A94LYS10.8690.9425.75223.84523.8450.0000.0000.0000.000
95A95SER0-0.045-0.0377.355-2.561-2.5610.0000.0000.0000.000
100A100LEU0-0.025-0.0025.5021.6941.6940.0000.0000.0000.000
101A101ALA00.0220.0049.1491.2291.2290.0000.0000.0000.000
102A102VAL0-0.0250.00411.7980.4960.4960.0000.0000.0000.000
103A103VAL00.0420.02114.1260.2600.2600.0000.0000.0000.000
104A104SER0-0.002-0.00716.9070.7240.7240.0000.0000.0000.000
105A105ASN00.003-0.00820.603-0.311-0.3110.0000.0000.0000.000
106A106LYS10.8230.90223.73312.53812.5380.0000.0000.0000.000
107A107LEU00.0430.02023.923-0.446-0.4460.0000.0000.0000.000
108A108GLU-1-0.859-0.89420.713-14.981-14.9810.0000.0000.0000.000
109A109GLU-1-0.886-0.94523.004-11.150-11.1500.0000.0000.0000.000
110A110LEU0-0.039-0.03025.5390.0780.0780.0000.0000.0000.000
111A111SER0-0.036-0.03521.183-0.013-0.0130.0000.0000.0000.000
112A112LYS10.8850.93519.42714.89614.8960.0000.0000.0000.000
113A113LYS10.9741.00522.17610.63410.6340.0000.0000.0000.000
114A114ILE0-0.010-0.02124.8450.2000.2000.0000.0000.0000.000
115A115LEU0-0.015-0.00618.3500.0030.0030.0000.0000.0000.000
116A116ASP-1-0.843-0.88222.179-14.166-14.1660.0000.0000.0000.000
117A117ILE0-0.058-0.02623.7640.1800.1800.0000.0000.0000.000
118A118LEU0-0.051-0.02323.3930.3140.3140.0000.0000.0000.000
119A119ASN0-0.057-0.02522.059-0.302-0.3020.0000.0000.0000.000
120A120LEU0-0.011-0.01418.272-0.570-0.5700.0000.0000.0000.000
121A121SER0-0.011-0.05417.255-1.236-1.2360.0000.0000.0000.000
122A122GLY00.0050.01016.252-0.900-0.9000.0000.0000.0000.000
123A123TYR00.0040.00212.860-0.860-0.8600.0000.0000.0000.000
124A124PHE0-0.052-0.02511.836-2.331-2.3310.0000.0000.0000.000
125A125ASP-1-0.839-0.9247.588-34.462-34.4620.0000.0000.0000.000
126A126LEU0-0.022-0.01611.0231.0591.0590.0000.0000.0000.000
127A127ILE0-0.017-0.01213.329-0.144-0.1440.0000.0000.0000.000
128A128VAL00.0110.01315.3600.9220.9220.0000.0000.0000.000
129A129GLY00.014-0.00517.8860.0800.0800.0000.0000.0000.000
130A130GLY0-0.057-0.04321.430-0.111-0.1110.0000.0000.0000.000
131A131ASP-1-0.864-0.93123.806-12.120-12.1200.0000.0000.0000.000
132A132THR00.030-0.00319.046-0.183-0.1830.0000.0000.0000.000
133A133PHE00.0360.01816.3150.4030.4030.0000.0000.0000.000
134A134GLY00.0010.00522.430-0.183-0.1830.0000.0000.0000.000
135A135GLU-1-0.880-0.90223.026-12.852-12.8520.0000.0000.0000.000
136A136LYS10.8990.96422.91411.30011.3000.0000.0000.0000.000
137A137LYS10.8190.91918.36616.63716.6370.0000.0000.0000.000
138A138PRO0-0.0040.02122.8300.4140.4140.0000.0000.0000.000
139A139SER0-0.020-0.01020.3300.1070.1070.0000.0000.0000.000
140A140PRO00.0600.03518.6570.6120.6120.0000.0000.0000.000
141A141THR0-0.005-0.05017.675-1.305-1.3050.0000.0000.0000.000
142A142PRO00.0060.01017.747-0.843-0.8430.0000.0000.0000.000
143A143VAL00.0310.02913.225-0.900-0.9000.0000.0000.0000.000
144A144LEU0-0.006-0.00413.060-1.692-1.6920.0000.0000.0000.000
145A145LYS10.9440.98313.22213.94113.9410.0000.0000.0000.000
146A146THR0-0.025-0.03611.145-0.279-0.2790.0000.0000.0000.000
147A147LEU0-0.025-0.0097.978-1.718-1.7180.0000.0000.0000.000
148A148GLU-1-0.934-0.9638.963-22.310-22.3100.0000.0000.0000.000
149A149ILE0-0.042-0.02411.012-0.909-0.9090.0000.0000.0000.000
150A150LEU0-0.030-0.0106.801-0.886-0.8860.0000.0000.0000.000
151A151GLY0-0.0110.0066.419-6.130-6.1300.0000.0000.0000.000
153A153GLU-1-0.838-0.9125.554-26.729-26.7290.0000.0000.0000.000
154A154PRO00.022-0.0047.650-3.203-3.2030.0000.0000.0000.000
155A155GLU-1-0.845-0.9349.190-27.644-27.6440.0000.0000.0000.000
157A157ALA00.0010.0066.307-5.560-5.5600.0000.0000.0000.000
158A158LEU0-0.031-0.0138.4863.3663.3660.0000.0000.0000.000
159A159ILE0-0.014-0.00211.511-0.308-0.3080.0000.0000.0000.000
160A160VAL00.002-0.00213.3220.6980.6980.0000.0000.0000.000
161A161GLY00.013-0.00616.1570.1200.1200.0000.0000.0000.000
162A162ASP-1-0.774-0.87019.852-13.752-13.7520.0000.0000.0000.000
163A163THR0-0.034-0.03223.2790.7740.7740.0000.0000.0000.000
164A164ASP-1-0.671-0.82723.734-11.989-11.9890.0000.0000.0000.000
165A165ALA00.0260.00424.237-0.394-0.3940.0000.0000.0000.000
166A166ASP-1-0.748-0.83319.584-15.570-15.5700.0000.0000.0000.000
167A167ILE00.0140.01119.321-0.991-0.9910.0000.0000.0000.000
168A168GLU-1-0.880-0.94720.429-12.734-12.7340.0000.0000.0000.000
169A169ALA0-0.003-0.01518.594-0.282-0.2820.0000.0000.0000.000
170A170GLY00.0530.02615.921-0.596-0.5960.0000.0000.0000.000
171A171LYS10.9420.97516.76113.42313.4230.0000.0000.0000.000
172A172ARG10.8110.87919.43813.33113.3310.0000.0000.0000.000
173A173ALA0-0.025-0.00615.0010.2470.2470.0000.0000.0000.000
174A174GLY00.0090.01214.971-0.759-0.7590.0000.0000.0000.000
175A175THR0-0.059-0.02111.643-0.816-0.8160.0000.0000.0000.000
176A176LYS10.8450.93012.14722.13222.1320.0000.0000.0000.000
177A177THR0-0.023-0.02314.105-0.056-0.0560.0000.0000.0000.000
178A178ALA00.010-0.01015.2940.2900.2900.0000.0000.0000.000
179A179LEU0-0.0020.01017.2840.0580.0580.0000.0000.0000.000
180A180ALA00.0220.00818.821-0.322-0.3220.0000.0000.0000.000
181A181LEU0-0.019-0.01120.0180.6300.6300.0000.0000.0000.000
182A182TRP0-0.053-0.03016.1670.3290.3290.0000.0000.0000.000
183A183GLY00.0260.01923.1120.2990.2990.0000.0000.0000.000
184A184TYR0-0.084-0.03824.0480.6220.6220.0000.0000.0000.000
185A185VAL00.0470.00725.098-0.118-0.1180.0000.0000.0000.000
186A186LYS10.8000.91025.79112.78312.7830.0000.0000.0000.000
187A187LEU0-0.030-0.00524.4250.0230.0230.0000.0000.0000.000
188A188ASN0-0.127-0.06328.4080.4760.4760.0000.0000.0000.000
189A189SER0-0.004-0.02629.9770.1320.1320.0000.0000.0000.000
190A190GLN0-0.095-0.04024.820-0.447-0.4470.0000.0000.0000.000
191A191ILE00.0150.00223.7230.1440.1440.0000.0000.0000.000
192A192PRO0-0.033-0.00319.451-0.242-0.2420.0000.0000.0000.000
193A193ASP-1-0.812-0.88516.388-18.304-18.3040.0000.0000.0000.000
194A194PHE0-0.001-0.01012.7580.0510.0510.0000.0000.0000.000
195A195THR00.002-0.00817.7010.5110.5110.0000.0000.0000.000
196A196LEU0-0.0180.00213.977-0.169-0.1690.0000.0000.0000.000
197A197SER0-0.042-0.03418.0240.6170.6170.0000.0000.0000.000
198A198ARG10.9060.93318.90113.07913.0790.0000.0000.0000.000
199A199PRO00.0060.00915.972-0.722-0.7220.0000.0000.0000.000
200A200SER0-0.004-0.03214.204-1.137-1.1370.0000.0000.0000.000
201A201ASP-1-0.825-0.90313.962-15.484-15.4840.0000.0000.0000.000
202A202LEU0-0.011-0.0039.764-0.561-0.5610.0000.0000.0000.000
203A203VAL0-0.005-0.0079.146-1.680-1.6800.0000.0000.0000.000
204A204LYS10.8850.9449.21714.28314.2830.0000.0000.0000.000
205A205LEU0-0.0220.0049.594-0.284-0.2840.0000.0000.0000.000
206A206MET0-0.087-0.0355.348-0.451-0.4510.0000.0000.0000.000
207A207ASP-1-0.868-0.9295.642-26.338-26.3380.0000.0000.0000.000
208A208ASN-1-1.009-0.9866.242-21.772-21.7720.0000.0000.0000.000