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: 97RJ2

Calculation Name: 4JRR-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | glycerol

Ligand 3-letter code: SO4 | GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4JRR

Chain ID: A

ChEMBL ID:

UniProt ID: Q5ZZ88

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 -2101697.175901
FMO2-HF: Nuclear repulsion 2025548.952328
FMO2-HF: Total energy -76148.223572
FMO2-MP2: Total energy -76366.031101


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:29:GLY)


Summations of interaction energy for fragment #1(A:29:GLY)
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.
-19.615-15.9092.998-3.547-3.158-0.048
Interaction energy analysis for fragmet #1(A:29:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.832 / q_NPA : 0.904
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].
3A31HIS00.0200.0072.123-34.077-30.4522.999-3.535-3.090-0.048
4A32MET0-0.0020.0074.7855.1025.183-0.001-0.012-0.0680.000
5A33GLN00.0430.0228.2960.1090.1090.0000.0000.0000.000
6A34PHE00.0050.01210.9021.9551.9550.0000.0000.0000.000
7A35ILE0-0.029-0.02011.955-0.656-0.6560.0000.0000.0000.000
8A36GLU-1-0.868-0.93514.960-15.776-15.7760.0000.0000.0000.000
9A37GLY0-0.024-0.01817.415-0.274-0.2740.0000.0000.0000.000
10A38LYS10.8570.92517.37517.54317.5430.0000.0000.0000.000
11A39ASP-1-0.750-0.86116.507-18.264-18.2640.0000.0000.0000.000
12A40TYR00.0150.00015.0551.0251.0250.0000.0000.0000.000
13A41GLN0-0.0030.00220.534-0.070-0.0700.0000.0000.0000.000
14A42THR00.0330.02020.8850.3480.3480.0000.0000.0000.000
15A43VAL0-0.026-0.00723.4840.4050.4050.0000.0000.0000.000
16A44ALA00.0380.02327.288-0.169-0.1690.0000.0000.0000.000
17A45SER0-0.013-0.01828.904-0.019-0.0190.0000.0000.0000.000
18A46ALA0-0.0020.00830.9870.2520.2520.0000.0000.0000.000
19A47GLN00.0260.01334.406-0.326-0.3260.0000.0000.0000.000
20A48LEU0-0.013-0.00433.3520.1750.1750.0000.0000.0000.000
21A49SER0-0.007-0.00537.1180.0370.0370.0000.0000.0000.000
22A50THR0-0.022-0.01433.4520.2400.2400.0000.0000.0000.000
23A51ASN0-0.012-0.01336.370-0.144-0.1440.0000.0000.0000.000
24A52LYS10.9890.99231.8139.6409.6400.0000.0000.0000.000
25A53ASP-1-0.856-0.92033.863-8.772-8.7720.0000.0000.0000.000
26A54LYS10.8060.90134.4098.3338.3330.0000.0000.0000.000
27A55THR0-0.040-0.01828.869-0.205-0.2050.0000.0000.0000.000
28A56PRO00.0150.01425.7860.1360.1360.0000.0000.0000.000
29A57LEU0-0.0070.00528.1600.2000.2000.0000.0000.0000.000
30A58ILE00.0220.00826.439-0.417-0.4170.0000.0000.0000.000
31A59THR0-0.043-0.01929.7740.4960.4960.0000.0000.0000.000
32A60GLU-1-0.829-0.92031.515-9.687-9.6870.0000.0000.0000.000
33A61PHE00.000-0.00732.5540.3750.3750.0000.0000.0000.000
34A62PHE00.056-0.00234.928-0.146-0.1460.0000.0000.0000.000
35A63SER00.0580.00637.5040.2600.2600.0000.0000.0000.000
36A64TYR00.025-0.00540.818-0.050-0.0500.0000.0000.0000.000
37A65GLY00.0300.02443.2200.0630.0630.0000.0000.0000.000
38A66CYS0-0.090-0.02637.400-0.004-0.0040.0000.0000.0000.000
39A67PRO00.0430.02339.646-0.106-0.1060.0000.0000.0000.000
40A68TRP00.020-0.01533.8800.0210.0210.0000.0000.0000.000
41A69CYS0-0.037-0.00134.927-0.246-0.2460.0000.0000.0000.000
42A70TYR00.0130.00836.532-0.116-0.1160.0000.0000.0000.000
43A71LYS10.9050.95834.9778.8498.8490.0000.0000.0000.000
44A72ILE00.0800.04531.103-0.078-0.0780.0000.0000.0000.000
45A73ASP-1-0.844-0.90133.471-8.709-8.7090.0000.0000.0000.000
46A74ALA00.0200.00735.597-0.045-0.0450.0000.0000.0000.000
47A75PRO00.0460.02231.284-0.086-0.0860.0000.0000.0000.000
48A76LEU0-0.0010.00330.197-0.346-0.3460.0000.0000.0000.000
49A77ASN0-0.011-0.00132.063-0.186-0.1860.0000.0000.0000.000
50A78ASP-1-0.884-0.92632.755-9.297-9.2970.0000.0000.0000.000
51A79TRP0-0.093-0.06124.7120.0210.0210.0000.0000.0000.000
52A80ALA00.013-0.00129.570-0.219-0.2190.0000.0000.0000.000
53A81THR0-0.044-0.03531.4280.0610.0610.0000.0000.0000.000
54A82ARG10.9000.95327.72610.97010.9700.0000.0000.0000.000
55A83MET0-0.0400.00224.133-0.445-0.4450.0000.0000.0000.000
56A84GLY00.0170.01628.649-0.083-0.0830.0000.0000.0000.000
57A85LYS10.9060.94030.9019.1949.1940.0000.0000.0000.000
58A86GLY0-0.015-0.00426.852-0.112-0.1120.0000.0000.0000.000
59A87ALA0-0.004-0.01726.448-0.464-0.4640.0000.0000.0000.000
60A88HIS0-0.0070.02628.8800.3530.3530.0000.0000.0000.000
61A89LEU00.0050.00331.562-0.230-0.2300.0000.0000.0000.000
62A90GLU-1-0.916-0.95033.242-8.143-8.1430.0000.0000.0000.000
63A91ARG10.8320.90034.7078.6398.6390.0000.0000.0000.000
64A92VAL0-0.0140.00637.0730.2800.2800.0000.0000.0000.000
65A93PRO0-0.0430.00238.331-0.145-0.1450.0000.0000.0000.000
66A94VAL00.000-0.00837.9110.0320.0320.0000.0000.0000.000
67A95VAL0-0.042-0.05941.2320.1290.1290.0000.0000.0000.000
68A96PHE00.0180.00837.7220.0240.0240.0000.0000.0000.000
69A97LYS10.9350.97543.6887.3327.3320.0000.0000.0000.000
70A98PRO00.0640.01846.8020.0130.0130.0000.0000.0000.000
71A99ASN00.0210.00549.159-0.014-0.0140.0000.0000.0000.000
72A100TRP0-0.012-0.00440.903-0.062-0.0620.0000.0000.0000.000
73A101ASP-1-0.786-0.88246.842-6.488-6.4880.0000.0000.0000.000
74A102LEU00.0000.01248.977-0.011-0.0110.0000.0000.0000.000
75A103TYR0-0.035-0.04645.833-0.070-0.0700.0000.0000.0000.000
76A104ALA00.0220.00944.996-0.091-0.0910.0000.0000.0000.000
77A105LYS10.8200.90245.9596.1786.1780.0000.0000.0000.000
78A106ALA00.0200.02648.3710.0340.0340.0000.0000.0000.000
79A107TYR00.0110.00840.2570.0080.0080.0000.0000.0000.000
80A108TYR0-0.001-0.02342.549-0.095-0.0950.0000.0000.0000.000
81A109THR00.0170.00946.4810.0660.0660.0000.0000.0000.000
82A110ALA00.0240.00646.7170.0500.0500.0000.0000.0000.000
83A111LYS10.9190.96641.1127.6107.6100.0000.0000.0000.000
84A112THR0-0.086-0.05745.427-0.065-0.0650.0000.0000.0000.000
85A113LEU0-0.032-0.01848.2480.0530.0530.0000.0000.0000.000
86A114ALA0-0.028-0.00345.9740.0310.0310.0000.0000.0000.000
87A115MET00.0240.01146.5870.0070.0070.0000.0000.0000.000
88A116SER0-0.022-0.01441.9810.0250.0250.0000.0000.0000.000
89A117ASP-1-0.870-0.93240.804-8.011-8.0110.0000.0000.0000.000
90A118LYS10.8750.94242.4906.3106.3100.0000.0000.0000.000
91A119MET0-0.010-0.01945.8450.0600.0600.0000.0000.0000.000
92A120ASN00.0450.04039.8060.2130.2130.0000.0000.0000.000
93A121PRO00.0400.02242.0160.0130.0130.0000.0000.0000.000
94A122ILE0-0.0070.00843.4920.0720.0720.0000.0000.0000.000
95A123LEU0-0.002-0.00746.0020.1260.1260.0000.0000.0000.000
96A124PHE0-0.005-0.00339.1010.0400.0400.0000.0000.0000.000
97A125LYS10.8270.92344.4176.7626.7620.0000.0000.0000.000
98A126ALA00.0300.01946.5280.0740.0740.0000.0000.0000.000
99A127ILE0-0.024-0.00646.5180.0840.0840.0000.0000.0000.000
100A128GLN0-0.070-0.05042.650-0.012-0.0120.0000.0000.0000.000
101A129GLU-1-0.903-0.93245.799-6.948-6.9480.0000.0000.0000.000
102A130ASP-1-0.863-0.94647.476-6.372-6.3720.0000.0000.0000.000
103A131LYS10.7910.90347.3146.9706.9700.0000.0000.0000.000
104A132ASN00.0620.03551.3280.1540.1540.0000.0000.0000.000
105A133PRO0-0.005-0.00451.389-0.113-0.1130.0000.0000.0000.000
106A134LEU00.0120.01150.581-0.074-0.0740.0000.0000.0000.000
107A135ALA00.0220.01553.463-0.034-0.0340.0000.0000.0000.000
108A136THR00.0050.00754.7860.0290.0290.0000.0000.0000.000
109A137LYS10.9600.96756.3975.6765.6760.0000.0000.0000.000
110A138GLN0-0.005-0.00857.734-0.029-0.0290.0000.0000.0000.000
111A139SER0-0.015-0.01756.721-0.039-0.0390.0000.0000.0000.000
112A140MET00.0160.02550.671-0.070-0.0700.0000.0000.0000.000
113A141VAL00.0010.00355.311-0.045-0.0450.0000.0000.0000.000
114A142ASP-1-0.789-0.86757.911-5.272-5.2720.0000.0000.0000.000
115A143PHE00.0130.00750.5320.0050.0050.0000.0000.0000.000
116A144PHE00.004-0.00749.606-0.095-0.0950.0000.0000.0000.000
117A145VAL0-0.0140.00154.993-0.002-0.0020.0000.0000.0000.000
118A146ALA0-0.030-0.00856.9260.0290.0290.0000.0000.0000.000
119A147HIS0-0.055-0.03052.667-0.078-0.0780.0000.0000.0000.000
120A148GLY0-0.014-0.00954.255-0.105-0.1050.0000.0000.0000.000
121A149VAL0-0.056-0.02053.463-0.024-0.0240.0000.0000.0000.000
122A150ASP-1-0.785-0.90456.453-5.240-5.2400.0000.0000.0000.000
123A151ARG10.8650.90158.6695.1375.1370.0000.0000.0000.000
124A152GLU-1-0.865-0.93660.725-5.208-5.2080.0000.0000.0000.000
125A153ILE0-0.0140.00955.354-0.065-0.0650.0000.0000.0000.000
126A154ALA00.002-0.00255.740-0.091-0.0910.0000.0000.0000.000
127A155LYS10.8500.90856.7805.0625.0620.0000.0000.0000.000
128A156SER0-0.015-0.02458.798-0.065-0.0650.0000.0000.0000.000
129A157ALA0-0.0050.00053.383-0.041-0.0410.0000.0000.0000.000
130A158PHE0-0.013-0.01651.790-0.099-0.0990.0000.0000.0000.000
131A159GLU-1-0.932-0.94655.718-5.232-5.2320.0000.0000.0000.000
132A160ASN0-0.042-0.01858.345-0.003-0.0030.0000.0000.0000.000
133A161SER00.0690.03854.1040.0040.0040.0000.0000.0000.000
134A162PRO00.0780.03853.667-0.144-0.1440.0000.0000.0000.000
135A163THR0-0.009-0.00750.236-0.102-0.1020.0000.0000.0000.000
136A164ILE0-0.0090.00048.928-0.187-0.1870.0000.0000.0000.000
137A165ASP-1-0.813-0.91148.821-6.247-6.2470.0000.0000.0000.000
138A166MET0-0.004-0.00148.799-0.173-0.1730.0000.0000.0000.000
139A167ARG10.9290.98841.6237.2957.2950.0000.0000.0000.000
140A168VAL00.0090.00644.200-0.239-0.2390.0000.0000.0000.000
141A169ASN00.011-0.00144.291-0.208-0.2080.0000.0000.0000.000
142A170SER0-0.017-0.01442.693-0.146-0.1460.0000.0000.0000.000
143A171GLY0-0.002-0.00840.147-0.217-0.2170.0000.0000.0000.000
144A172MET00.0570.04839.328-0.299-0.2990.0000.0000.0000.000
145A173SER0-0.015-0.01740.003-0.108-0.1080.0000.0000.0000.000
146A174LEU0-0.025-0.00535.192-0.154-0.1540.0000.0000.0000.000
147A175MET0-0.028-0.00535.361-0.245-0.2450.0000.0000.0000.000
148A176ALA00.0120.00235.153-0.240-0.2400.0000.0000.0000.000
149A177HIS0-0.027-0.01032.8190.0600.0600.0000.0000.0000.000
150A178TYR0-0.022-0.03631.012-0.191-0.1910.0000.0000.0000.000
151A179GLN0-0.049-0.02430.912-0.369-0.3690.0000.0000.0000.000
152A180ILE0-0.043-0.01430.421-0.322-0.3220.0000.0000.0000.000
153A181ASN00.010-0.00833.4570.1140.1140.0000.0000.0000.000
154A182ALA00.0140.01033.1510.2150.2150.0000.0000.0000.000
155A183VAL0-0.0200.00134.113-0.100-0.1000.0000.0000.0000.000
156A184PRO00.006-0.01232.0120.1880.1880.0000.0000.0000.000
157A185ALA00.001-0.00330.171-0.296-0.2960.0000.0000.0000.000
158A186PHE00.0060.00027.3800.2790.2790.0000.0000.0000.000
159A187VAL0-0.004-0.00427.728-0.337-0.3370.0000.0000.0000.000
160A188VAL00.0060.00324.2730.2830.2830.0000.0000.0000.000
161A189ASN00.020-0.01123.6870.3090.3090.0000.0000.0000.000
162A190ASN0-0.0110.01527.0190.0030.0030.0000.0000.0000.000
163A191LYS10.8480.94323.20012.24512.2450.0000.0000.0000.000
164A192TYR00.051-0.00219.971-0.731-0.7310.0000.0000.0000.000
165A193LYS10.8660.94824.03411.73911.7390.0000.0000.0000.000
166A194THR00.020-0.01222.791-0.536-0.5360.0000.0000.0000.000
167A195ASP-1-0.805-0.90125.024-11.034-11.0340.0000.0000.0000.000
168A196LEU00.0300.00626.076-0.395-0.3950.0000.0000.0000.000
169A197GLN0-0.058-0.01527.544-0.158-0.1580.0000.0000.0000.000
170A198MET0-0.068-0.02622.243-0.231-0.2310.0000.0000.0000.000
171A199ALA0-0.0080.00222.242-0.695-0.6950.0000.0000.0000.000
172A200GLY0-0.0080.00523.010-0.417-0.4170.0000.0000.0000.000
173A201SER0-0.025-0.02723.8440.2960.2960.0000.0000.0000.000
174A202GLU-1-0.856-0.95625.541-10.562-10.5620.0000.0000.0000.000
175A203GLU-1-0.947-0.95922.623-13.795-13.7950.0000.0000.0000.000
176A204ARG10.8230.90315.01918.61818.6180.0000.0000.0000.000
177A205LEU00.0180.00421.510-0.455-0.4550.0000.0000.0000.000
178A206PHE00.0140.00023.683-0.134-0.1340.0000.0000.0000.000
179A207GLU-1-0.897-0.93118.514-17.610-17.6100.0000.0000.0000.000
180A208ILE0-0.047-0.02818.957-0.732-0.7320.0000.0000.0000.000
181A209LEU0-0.009-0.00120.248-0.172-0.1720.0000.0000.0000.000
182A210ASN00.0120.00020.4000.5850.5850.0000.0000.0000.000
183A211TYR0-0.018-0.00713.459-0.046-0.0460.0000.0000.0000.000
184A212LEU0-0.015-0.02118.428-0.121-0.1210.0000.0000.0000.000
185A213VAL00.0080.00720.7410.2060.2060.0000.0000.0000.000
186A214ARG10.9120.95718.84915.54215.5420.0000.0000.0000.000
187A215LYS10.8310.94415.77918.12218.1220.0000.0000.0000.000
188A216SER-1-0.869-0.91119.974-12.685-12.6850.0000.0000.0000.000