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

tag_button

FMODB ID: JRLZ9

Calculation Name: 3PJY-A-Xray549

Preferred Name:

Target Type:

Ligand Name: sulfate ion | chloride ion

Ligand 3-letter code: SO4 | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3PJY

Chain ID: A

ChEMBL ID:

UniProt ID: Q92PM3

Base Structure: X-ray

Registration Date: 2025-10-12

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 129
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1137364.042315
FMO2-HF: Nuclear repulsion 1086037.882786
FMO2-HF: Total energy -51326.159529
FMO2-MP2: Total energy -51472.803252


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:0:GLY)


Summations of interaction energy for fragment #1(A:0: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.
-48.15-47.3660-0.319-0.465-0.001
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.834 / q_NPA : 0.901
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].
3A30VAL0-0.0050.0033.819-4.043-3.2590.000-0.319-0.465-0.001
4A31SER0-0.030-0.0156.2925.2475.2470.0000.0000.0000.000
5A32TYR00.0380.0148.353-0.154-0.1540.0000.0000.0000.000
6A33ALA00.0150.01811.843-0.145-0.1450.0000.0000.0000.000
7A34LYS10.8540.91513.66121.75321.7530.0000.0000.0000.000
8A35GLU-1-0.797-0.90116.276-13.664-13.6640.0000.0000.0000.000
9A36ARG10.8270.90320.03912.62612.6260.0000.0000.0000.000
10A37VAL00.0560.04223.4020.2090.2090.0000.0000.0000.000
11A38ARG10.8170.87125.83810.17910.1790.0000.0000.0000.000
12A39LEU00.0220.01929.4890.0800.0800.0000.0000.0000.000
13A40ILE0-0.034-0.02231.6750.1930.1930.0000.0000.0000.000
14A41THR00.0120.01535.3110.1410.1410.0000.0000.0000.000
15A42ALA00.0440.01038.0910.1230.1230.0000.0000.0000.000
16A43SER0-0.099-0.05341.0430.2000.2000.0000.0000.0000.000
17A44GLY00.0210.01140.5750.1440.1440.0000.0000.0000.000
18A45ARG10.8740.94637.5018.1548.1540.0000.0000.0000.000
19A46THR00.0580.03234.220-0.040-0.0400.0000.0000.0000.000
20A47HIS0-0.075-0.04831.9400.0160.0160.0000.0000.0000.000
21A48ASP-1-0.817-0.86628.123-10.579-10.5790.0000.0000.0000.000
22A49LEU0-0.010-0.00525.0480.0060.0060.0000.0000.0000.000
23A50THR0-0.041-0.01419.1960.1320.1320.0000.0000.0000.000
24A51VAL0-0.0110.00820.114-0.112-0.1120.0000.0000.0000.000
25A52GLU-1-0.855-0.92813.852-22.786-22.7860.0000.0000.0000.000
26A53LEU00.0070.00415.9920.5120.5120.0000.0000.0000.000
27A54ALA0-0.013-0.01115.231-1.593-1.5930.0000.0000.0000.000
28A55VAL00.0460.01415.6481.0951.0950.0000.0000.0000.000
29A56ASP-1-0.870-0.92312.625-22.897-22.8970.0000.0000.0000.000
30A57PRO00.011-0.02616.1520.0880.0880.0000.0000.0000.000
31A58SER00.0200.02711.3540.3380.3380.0000.0000.0000.000
32A59GLN00.0090.00411.0831.2041.2040.0000.0000.0000.000
33A60ARG10.8740.93413.80216.33216.3320.0000.0000.0000.000
34A61GLU-1-0.958-0.98216.995-16.224-16.2240.0000.0000.0000.000
35A62GLN0-0.081-0.06411.530-0.132-0.1320.0000.0000.0000.000
36A63GLY00.0400.02215.313-0.804-0.8040.0000.0000.0000.000
37A64LEU0-0.022-0.03916.4510.6660.6660.0000.0000.0000.000
38A65MET0-0.0020.05115.6950.1210.1210.0000.0000.0000.000
39A66TYR0-0.027-0.02713.869-0.607-0.6070.0000.0000.0000.000
40A67ARG10.8030.90814.95219.74119.7410.0000.0000.0000.000
41A68ARG10.9380.96117.86015.77415.7740.0000.0000.0000.000
42A69GLN00.0020.00419.2680.9920.9920.0000.0000.0000.000
43A70MET00.0210.02819.364-1.495-1.4950.0000.0000.0000.000
44A71ALA00.0410.04721.3150.6710.6710.0000.0000.0000.000
45A72PRO00.015-0.01423.688-0.033-0.0330.0000.0000.0000.000
46A73ASP-1-0.863-0.91624.735-12.478-12.4780.0000.0000.0000.000
47A74HIS0-0.083-0.05619.098-0.976-0.9760.0000.0000.0000.000
48A75GLY00.0510.00921.3340.5230.5230.0000.0000.0000.000
49A76MET0-0.092-0.00814.990-0.988-0.9880.0000.0000.0000.000
50A77LEU00.0230.01619.7530.8340.8340.0000.0000.0000.000
51A78PHE0-0.011-0.00919.330-1.050-1.0500.0000.0000.0000.000
52A79ASP-1-0.812-0.91120.137-13.280-13.2800.0000.0000.0000.000
53A80PHE0-0.008-0.02620.775-0.758-0.7580.0000.0000.0000.000
54A81GLY00.0000.01323.251-0.045-0.0450.0000.0000.0000.000
55A82GLU-1-0.919-0.94223.941-11.411-11.4110.0000.0000.0000.000
56A83THR0-0.041-0.03227.5690.0290.0290.0000.0000.0000.000
57A84ARG10.8510.91324.77412.36412.3640.0000.0000.0000.000
58A85PRO0-0.0190.00030.664-0.151-0.1510.0000.0000.0000.000
59A86VAL00.0050.01426.637-0.282-0.2820.0000.0000.0000.000
60A87MET0-0.021-0.01527.0550.2700.2700.0000.0000.0000.000
61A88MET00.0220.03122.297-0.433-0.4330.0000.0000.0000.000
62A89TRP00.027-0.00222.2520.7810.7810.0000.0000.0000.000
63A90MET00.0050.01423.921-0.619-0.6190.0000.0000.0000.000
64A91LYS10.8700.94022.17412.50812.5080.0000.0000.0000.000
65A92ASN00.005-0.00917.6650.2130.2130.0000.0000.0000.000
66A93THR00.0130.02019.725-1.080-1.0800.0000.0000.0000.000
67A94TYR0-0.043-0.03719.5110.6360.6360.0000.0000.0000.000
68A95LEU0-0.0030.01420.9070.5330.5330.0000.0000.0000.000
69A96PRO00.0180.01324.3560.0400.0400.0000.0000.0000.000
70A97LEU00.004-0.00422.504-0.175-0.1750.0000.0000.0000.000
71A98ASP-1-0.776-0.86927.090-9.888-9.8880.0000.0000.0000.000
72A99MET0-0.023-0.00825.591-0.223-0.2230.0000.0000.0000.000
73A100LEU00.0100.00228.1070.5520.5520.0000.0000.0000.000
74A101PHE00.0250.01028.408-0.455-0.4550.0000.0000.0000.000
75A102ILE0-0.006-0.00127.9910.4440.4440.0000.0000.0000.000
76A103ALA00.0420.02129.914-0.237-0.2370.0000.0000.0000.000
77A104SER00.031-0.00430.044-0.123-0.1230.0000.0000.0000.000
78A105ASP-1-0.836-0.88531.056-9.269-9.2690.0000.0000.0000.000
79A106GLY00.1130.05530.8430.1670.1670.0000.0000.0000.000
80A107THR0-0.133-0.08531.8130.1020.1020.0000.0000.0000.000
81A108ILE0-0.009-0.00631.832-0.173-0.1730.0000.0000.0000.000
82A109ARG10.8700.94933.6789.1629.1620.0000.0000.0000.000
83A110THR00.001-0.00734.0740.1740.1740.0000.0000.0000.000
84A111ILE00.013-0.00232.388-0.318-0.3180.0000.0000.0000.000
85A112HIS0-0.048-0.01031.4090.4570.4570.0000.0000.0000.000
86A113GLU-1-0.875-0.95531.302-9.397-9.3970.0000.0000.0000.000
87A114ASN0-0.075-0.05231.6500.0330.0330.0000.0000.0000.000
88A115ALA00.0340.03328.2390.2150.2150.0000.0000.0000.000
89A116VAL00.006-0.01429.018-0.235-0.2350.0000.0000.0000.000
90A117PRO00.017-0.00726.087-0.149-0.1490.0000.0000.0000.000
91A118HIS0-0.037-0.02522.3860.3550.3550.0000.0000.0000.000
92A119SER0-0.0160.01426.0470.1790.1790.0000.0000.0000.000
93A120GLU-1-0.834-0.92527.026-12.203-12.2030.0000.0000.0000.000
94A121ALA0-0.045-0.01928.4970.1310.1310.0000.0000.0000.000
95A122ILE00.0090.00528.700-0.323-0.3230.0000.0000.0000.000
96A123ILE0-0.045-0.01729.4310.4530.4530.0000.0000.0000.000
97A124ASP-1-0.896-0.95729.815-10.126-10.1260.0000.0000.0000.000
98A125SER0-0.009-0.00830.9440.1440.1440.0000.0000.0000.000
99A126ARG10.9080.96132.7139.1879.1870.0000.0000.0000.000
100A127GLU-1-0.859-0.94135.283-8.599-8.5990.0000.0000.0000.000
101A128PRO0-0.043-0.03133.202-0.305-0.3050.0000.0000.0000.000
102A129VAL0-0.025-0.00829.1650.2160.2160.0000.0000.0000.000
103A130ALA0-0.005-0.00328.066-0.065-0.0650.0000.0000.0000.000
104A131TYR00.0300.01423.945-0.637-0.6370.0000.0000.0000.000
105A132VAL0-0.012-0.00224.4580.5300.5300.0000.0000.0000.000
106A133LEU0-0.0190.00723.820-0.684-0.6840.0000.0000.0000.000
107A134GLU-1-0.846-0.93422.326-13.606-13.6060.0000.0000.0000.000
108A135LEU00.007-0.00523.614-0.494-0.4940.0000.0000.0000.000
109A136ASN00.003-0.01524.321-0.125-0.1250.0000.0000.0000.000
110A137ALA0-0.0130.00326.7720.3570.3570.0000.0000.0000.000
111A138GLY0-0.011-0.00330.0390.1200.1200.0000.0000.0000.000
112A139THR0-0.063-0.04728.8240.2890.2890.0000.0000.0000.000
113A140VAL00.0280.00831.5640.1390.1390.0000.0000.0000.000
114A141LYS10.9780.99233.6448.3968.3960.0000.0000.0000.000
115A142ARG10.8300.92229.62010.57210.5720.0000.0000.0000.000
116A143LEU0-0.041-0.01830.6290.1050.1050.0000.0000.0000.000
117A144GLY0-0.032-0.00135.3150.1690.1690.0000.0000.0000.000
118A145VAL0-0.050-0.02333.1630.1180.1180.0000.0000.0000.000
119A146SER0-0.014-0.01136.3670.1170.1170.0000.0000.0000.000
120A147PRO0-0.025-0.02536.955-0.174-0.1740.0000.0000.0000.000
121A148GLY0-0.029-0.01037.6070.2480.2480.0000.0000.0000.000
122A149ASP-1-0.792-0.88235.765-8.496-8.4960.0000.0000.0000.000
123A150ARG10.8570.91934.2438.8678.8670.0000.0000.0000.000
124A151LEU0-0.018-0.01226.201-0.056-0.0560.0000.0000.0000.000
125A152GLU-1-0.903-0.95330.198-9.334-9.3340.0000.0000.0000.000
126A153GLY0-0.002-0.02626.248-0.297-0.2970.0000.0000.0000.000
127A154ALA0-0.068-0.02923.1870.3820.3820.0000.0000.0000.000
128A155GLY0-0.036-0.02024.138-0.511-0.5110.0000.0000.0000.000
129A156LEU-1-0.918-0.93625.506-10.462-10.4620.0000.0000.0000.000