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: 3GL2L

Calculation Name: 1E4C-P-Xray549

Preferred Name:

Target Type:

Ligand Name: sulfate ion | beta-mercaptoethanol | zinc ion

Ligand 3-letter code: SO4 | BME | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1E4C

Chain ID: P

ChEMBL ID:

UniProt ID: P0AB87

Base Structure: X-ray

Registration Date: 2025-10-11

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 206
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230712
Total energy (hartree)
FMO2-HF: Electronic energy -2346938.108283
FMO2-HF: Nuclear repulsion 2266661.45525
FMO2-HF: Total energy -80276.653033
FMO2-MP2: Total energy -80508.922795


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(P:1:MET)


Summations of interaction energy for fragment #1(P: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.
12.29714.758-0.011-0.963-1.4850.001
Interaction energy analysis for fragmet #1(P:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.872 / q_NPA : 0.926
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].
3P3ARG10.9200.9183.84724.70226.469-0.021-0.832-0.9140.001
5P5LYS10.7580.8813.95341.70141.8760.000-0.025-0.1490.000
6P6LEU00.0680.0333.5712.0312.5500.010-0.106-0.4220.000
4P4ASN0-0.037-0.0346.6734.6784.6780.0000.0000.0000.000
7P7ALA00.0120.0116.1043.7723.7720.0000.0000.0000.000
8P8ARG10.9860.9929.09429.45829.4580.0000.0000.0000.000
9P9GLN00.0500.0305.595-2.884-2.8840.0000.0000.0000.000
10P10ILE00.0170.0299.8501.9871.9870.0000.0000.0000.000
11P11ILE00.0200.01811.9681.7191.7190.0000.0000.0000.000
12P12ASP-1-0.901-0.95112.723-20.562-20.5620.0000.0000.0000.000
13P13THR0-0.034-0.03612.6901.1391.1390.0000.0000.0000.000
14P14CYS0-0.039-0.02415.2961.2861.2860.0000.0000.0000.000
15P15LEU0-0.029-0.00217.7021.1241.1240.0000.0000.0000.000
16P16GLU-1-0.866-0.94618.090-13.927-13.9270.0000.0000.0000.000
17P17MET0-0.019-0.00219.2080.7640.7640.0000.0000.0000.000
18P18THR0-0.041-0.02421.0110.7890.7890.0000.0000.0000.000
19P19ARG10.8740.94421.30614.36514.3650.0000.0000.0000.000
20P20LEU0-0.020-0.00321.3610.4660.4660.0000.0000.0000.000
21P21GLY0-0.0110.00425.0760.3500.3500.0000.0000.0000.000
22P22LEU0-0.028-0.00722.6470.2430.2430.0000.0000.0000.000
23P23ASN0-0.035-0.03623.0540.1960.1960.0000.0000.0000.000
24P24GLN00.0080.00725.1030.2540.2540.0000.0000.0000.000
25P25GLY00.0230.00927.7320.0370.0370.0000.0000.0000.000
26P26THR0-0.055-0.03725.032-0.371-0.3710.0000.0000.0000.000
27P27ALA00.0020.01525.462-0.153-0.1530.0000.0000.0000.000
28P28GLY00.0080.01822.396-0.067-0.0670.0000.0000.0000.000
29P29ASN0-0.080-0.05619.315-0.363-0.3630.0000.0000.0000.000
30P30VAL00.0240.01113.6550.0570.0570.0000.0000.0000.000
31P31SER0-0.005-0.01313.004-0.502-0.5020.0000.0000.0000.000
32P32VAL0-0.008-0.0117.130-0.587-0.5870.0000.0000.0000.000
33P33ARG10.8610.9438.99721.35321.3530.0000.0000.0000.000
34P34TYR0-0.068-0.0544.930-3.012-3.0120.0000.0000.0000.000
35P35GLN0-0.039-0.0247.1950.8250.8250.0000.0000.0000.000
36P36ASP-1-0.819-0.9119.111-19.866-19.8660.0000.0000.0000.000
37P37GLY00.0240.02111.6581.5461.5460.0000.0000.0000.000
38P38MET0-0.062-0.02210.828-1.104-1.1040.0000.0000.0000.000
39P39LEU0-0.045-0.0097.5840.1860.1860.0000.0000.0000.000
40P40ILE00.000-0.00911.459-0.015-0.0150.0000.0000.0000.000
41P41THR00.0490.03314.6240.0280.0280.0000.0000.0000.000
42P42PRO0-0.0080.00617.0990.4690.4690.0000.0000.0000.000
43P43THR00.017-0.01320.4510.1410.1410.0000.0000.0000.000
44P44GLY00.0010.00523.8970.0690.0690.0000.0000.0000.000
45P45ILE0-0.0140.00120.8530.3750.3750.0000.0000.0000.000
46P46PRO00.0010.01323.129-0.315-0.3150.0000.0000.0000.000
47P47TYR00.0840.02620.616-0.421-0.4210.0000.0000.0000.000
48P48GLU-1-0.848-0.92020.619-12.623-12.6230.0000.0000.0000.000
49P49LYS10.7930.87823.02212.81312.8130.0000.0000.0000.000
50P50LEU00.0170.01917.144-0.137-0.1370.0000.0000.0000.000
51P51THR0-0.004-0.01516.975-0.119-0.1190.0000.0000.0000.000
52P52GLU-1-0.861-0.95811.711-21.503-21.5030.0000.0000.0000.000
53P53SER0-0.030-0.01313.842-0.523-0.5230.0000.0000.0000.000
54P54HIS0-0.0010.01016.348-0.107-0.1070.0000.0000.0000.000
55P55ILE0-0.046-0.00411.5880.4030.4030.0000.0000.0000.000
56P56VAL00.0180.01114.585-0.650-0.6500.0000.0000.0000.000
57P57PHE0-0.047-0.02211.192-1.316-1.3160.0000.0000.0000.000
58P58ILE0-0.012-0.01114.1651.4451.4450.0000.0000.0000.000
59P59ASP-1-0.790-0.89414.579-16.295-16.2950.0000.0000.0000.000
60P60GLY00.0730.02415.9540.5230.5230.0000.0000.0000.000
61P61ASN0-0.131-0.06017.0121.0831.0830.0000.0000.0000.000
62P62GLY0-0.022-0.02319.1550.7670.7670.0000.0000.0000.000
63P63LYS10.8700.94319.89114.09614.0960.0000.0000.0000.000
64P64HIS0-0.007-0.00818.801-0.958-0.9580.0000.0000.0000.000
65P65GLU-1-0.778-0.84715.672-19.644-19.6440.0000.0000.0000.000
66P66GLU-1-0.938-0.97019.042-12.929-12.9290.0000.0000.0000.000
67P67GLY00.0150.00220.815-0.547-0.5470.0000.0000.0000.000
68P68LYS10.8010.92015.78918.35318.3530.0000.0000.0000.000
69P69LEU00.0260.01221.4600.6190.6190.0000.0000.0000.000
70P70PRO00.0410.02121.656-0.592-0.5920.0000.0000.0000.000
71P71GLN00.0270.01619.7610.6740.6740.0000.0000.0000.000
72P72SER0-0.023-0.03022.1470.0830.0830.0000.0000.0000.000
73P73GLU-1-0.747-0.88223.156-11.770-11.7700.0000.0000.0000.000
74P74TRP0-0.038-0.01319.616-0.284-0.2840.0000.0000.0000.000
75P75ARG10.9050.96119.91010.98610.9860.0000.0000.0000.000
76P76PHE00.0820.03621.436-0.189-0.1890.0000.0000.0000.000
77P77HIS00.0050.02716.528-0.898-0.8980.0000.0000.0000.000
78P78MET00.0210.01317.059-0.548-0.5480.0000.0000.0000.000
79P79ALA0-0.012-0.00918.106-0.092-0.0920.0000.0000.0000.000
80P80ALA00.0390.02318.2050.2190.2190.0000.0000.0000.000
81P81TYR0-0.034-0.04012.396-0.513-0.5130.0000.0000.0000.000
82P82GLN0-0.015-0.01016.133-0.526-0.5260.0000.0000.0000.000
83P83SER0-0.095-0.04918.9560.4820.4820.0000.0000.0000.000
84P84ARG10.8350.90817.30214.65714.6570.0000.0000.0000.000
85P85PRO0-0.002-0.01714.959-0.892-0.8920.0000.0000.0000.000
86P86ASP-1-0.826-0.89712.874-17.111-17.1110.0000.0000.0000.000
87P87ALA0-0.0140.01712.664-0.897-0.8970.0000.0000.0000.000
88P88ASN0-0.033-0.0448.472-0.351-0.3510.0000.0000.0000.000
89P89ALA0-0.031-0.0089.672-1.912-1.9120.0000.0000.0000.000
90P90VAL0-0.0020.00511.9941.3181.3180.0000.0000.0000.000
91P91VAL00.004-0.00115.541-0.510-0.5100.0000.0000.0000.000
92P92HIS10.7980.89618.01813.07813.0780.0000.0000.0000.000
93P93ASN00.038-0.00621.3770.1320.1320.0000.0000.0000.000
94P94HIS00.0370.01224.3320.0630.0630.0000.0000.0000.000
95P95ALA00.0580.04926.6530.3000.3000.0000.0000.0000.000
96P96VAL00.0290.02728.5640.1970.1970.0000.0000.0000.000
97P97HIS0-0.044-0.03631.9540.5570.5570.0000.0000.0000.000
98P98CYS0-0.035-0.02228.5390.1130.1130.0000.0000.0000.000
99P99THR0-0.003-0.02230.6560.1120.1120.0000.0000.0000.000
100P100ALA00.0110.02332.3820.2230.2230.0000.0000.0000.000
101P101VAL00.008-0.00533.7130.2460.2460.0000.0000.0000.000
102P102SER0-0.021-0.02732.1280.1310.1310.0000.0000.0000.000
103P103ILE0-0.028-0.01634.2120.1340.1340.0000.0000.0000.000
104P104LEU0-0.062-0.02637.4080.2260.2260.0000.0000.0000.000
105P105ASN0-0.023-0.01736.369-0.067-0.0670.0000.0000.0000.000
106P106ARG10.7830.87736.8537.5287.5280.0000.0000.0000.000
107P107SER00.0020.00333.683-0.182-0.1820.0000.0000.0000.000
108P108ILE00.0050.00430.7250.2290.2290.0000.0000.0000.000
109P109PRO00.0220.01532.994-0.235-0.2350.0000.0000.0000.000
110P110ALA00.0820.03833.712-0.154-0.1540.0000.0000.0000.000
111P111ILE0-0.041-0.02134.7520.1600.1600.0000.0000.0000.000
112P112HIS00.0160.00731.5240.0030.0030.0000.0000.0000.000
113P113TYR00.0840.03328.943-0.017-0.0170.0000.0000.0000.000
114P114MET00.0140.00225.022-0.186-0.1860.0000.0000.0000.000
115P115ILE0-0.077-0.01327.044-0.422-0.4220.0000.0000.0000.000
116P116ALA00.0400.02727.092-0.255-0.2550.0000.0000.0000.000
117P117ALA00.0030.00822.733-0.380-0.3800.0000.0000.0000.000
118P118ALA0-0.038-0.02022.096-0.646-0.6460.0000.0000.0000.000
119P119GLY0-0.008-0.01223.927-0.169-0.1690.0000.0000.0000.000
120P120GLY0-0.016-0.02024.4690.2050.2050.0000.0000.0000.000
121P121ASN0-0.009-0.01428.307-0.336-0.3360.0000.0000.0000.000
122P122SER00.0220.00130.1870.1620.1620.0000.0000.0000.000
123P123ILE00.0000.02726.847-0.410-0.4100.0000.0000.0000.000
124P124PRO00.0000.00227.8260.4240.4240.0000.0000.0000.000
125P125CYS00.0030.00330.049-0.270-0.2700.0000.0000.0000.000
126P126ALA0-0.0140.00328.9490.2010.2010.0000.0000.0000.000
127P127PRO00.011-0.00831.0380.0290.0290.0000.0000.0000.000
128P128TYR0-0.0130.00332.527-0.274-0.2740.0000.0000.0000.000
129P129ALA00.0270.01832.2510.2060.2060.0000.0000.0000.000
130P130THR00.0100.00132.200-0.176-0.1760.0000.0000.0000.000
131P131PHE00.0670.04428.039-0.222-0.2220.0000.0000.0000.000
132P132GLY00.0360.01726.4560.1690.1690.0000.0000.0000.000
133P133THR0-0.052-0.03727.541-0.085-0.0850.0000.0000.0000.000
134P134ARG10.9540.96325.47910.66810.6680.0000.0000.0000.000
135P135GLU-1-0.798-0.89528.748-8.916-8.9160.0000.0000.0000.000
136P136LEU00.0170.02027.758-0.131-0.1310.0000.0000.0000.000
137P137SER0-0.036-0.04024.668-0.461-0.4610.0000.0000.0000.000
138P138GLU-1-0.970-0.98125.678-10.120-10.1200.0000.0000.0000.000
139P139HIS0-0.012-0.00528.273-0.174-0.1740.0000.0000.0000.000
140P140VAL00.004-0.00123.328-0.061-0.0610.0000.0000.0000.000
141P141ALA0-0.022-0.01223.816-0.264-0.2640.0000.0000.0000.000
142P142LEU00.0100.01424.837-0.193-0.1930.0000.0000.0000.000
143P143ALA00.0160.01027.0410.0110.0110.0000.0000.0000.000
144P144LEU0-0.030-0.01520.753-0.124-0.1240.0000.0000.0000.000
145P145LYS10.8500.94722.34211.86611.8660.0000.0000.0000.000
146P146ASN00.002-0.00823.419-0.514-0.5140.0000.0000.0000.000
147P147ARG10.8400.91724.18210.64210.6420.0000.0000.0000.000
148P148LYS10.9080.94617.80514.79814.7980.0000.0000.0000.000
149P149ALA0-0.009-0.01220.609-0.586-0.5860.0000.0000.0000.000
150P150THR0-0.024-0.02823.3030.5060.5060.0000.0000.0000.000
151P151LEU00.0080.01726.097-0.328-0.3280.0000.0000.0000.000
152P152LEU0-0.0190.00325.540-0.026-0.0260.0000.0000.0000.000
153P153GLN00.0940.02929.7090.0130.0130.0000.0000.0000.000
154P154HIS0-0.071-0.04433.339-0.126-0.1260.0000.0000.0000.000
155P155HIS0-0.057-0.01627.6660.1060.1060.0000.0000.0000.000
156P156GLY00.0130.00328.458-0.123-0.1230.0000.0000.0000.000
157P157LEU0-0.0290.00623.0800.1310.1310.0000.0000.0000.000
158P158ILE00.0100.00620.702-0.424-0.4240.0000.0000.0000.000
159P159ALA00.0290.01220.1900.4410.4410.0000.0000.0000.000
160P160CYS0-0.008-0.00116.618-0.748-0.7480.0000.0000.0000.000
161P161GLU-1-0.755-0.86714.455-16.928-16.9280.0000.0000.0000.000
162P162VAL00.0080.00610.553-1.300-1.3000.0000.0000.0000.000
163P163ASN0-0.020-0.0238.927-1.253-1.2530.0000.0000.0000.000
164P164LEU00.0460.0168.9601.4601.4600.0000.0000.0000.000
165P165GLU-1-0.939-0.95511.568-22.720-22.7200.0000.0000.0000.000
166P166LYS10.9680.98412.90420.84720.8470.0000.0000.0000.000
167P167ALA0-0.0180.00614.8141.0831.0830.0000.0000.0000.000
168P168LEU00.012-0.00116.4240.9330.9330.0000.0000.0000.000
169P169TRP0-0.022-0.00618.0650.5240.5240.0000.0000.0000.000
170P170LEU00.0190.00919.2370.7720.7720.0000.0000.0000.000
171P171ALA0-0.018-0.02120.7640.7000.7000.0000.0000.0000.000
172P172HIS00.0280.01322.4960.3820.3820.0000.0000.0000.000
173P173GLU-1-0.873-0.94423.514-11.341-11.3410.0000.0000.0000.000
174P174VAL0-0.026-0.01724.8170.5460.5460.0000.0000.0000.000
175P175GLU-1-0.682-0.83426.855-9.817-9.8170.0000.0000.0000.000
176P176VAL00.0110.00928.4750.4930.4930.0000.0000.0000.000
177P177LEU0-0.024-0.01127.9820.4570.4570.0000.0000.0000.000
178P178ALA00.0140.00331.0330.3800.3800.0000.0000.0000.000
179P179GLN0-0.009-0.00432.7830.1460.1460.0000.0000.0000.000
180P180LEU0-0.0080.01032.9450.3710.3710.0000.0000.0000.000
181P181TYR00.0410.02635.4440.3030.3030.0000.0000.0000.000
182P182LEU0-0.005-0.00636.0420.2520.2520.0000.0000.0000.000
183P183THR0-0.064-0.04738.2420.2500.2500.0000.0000.0000.000
184P184THR0-0.036-0.03839.4590.2160.2160.0000.0000.0000.000
185P185LEU00.0040.00039.7830.1960.1960.0000.0000.0000.000
186P186ALA0-0.068-0.01743.1180.1640.1640.0000.0000.0000.000
187P187ILE0-0.076-0.03145.0140.1770.1770.0000.0000.0000.000
188P188THR0-0.044-0.03545.1430.2250.2250.0000.0000.0000.000
189P189ASP-1-0.782-0.84544.395-7.265-7.2650.0000.0000.0000.000
190P190PRO0-0.020-0.01044.1730.1440.1440.0000.0000.0000.000
191P191VAL0-0.0050.00140.1530.1090.1090.0000.0000.0000.000
192P192PRO0-0.031-0.02342.085-0.046-0.0460.0000.0000.0000.000
193P193VAL0-0.026-0.01438.195-0.178-0.1780.0000.0000.0000.000
194P194LEU0-0.0150.00034.4790.1680.1680.0000.0000.0000.000
195P195SER0-0.036-0.04038.037-0.071-0.0710.0000.0000.0000.000
196P196ASP-1-0.809-0.90435.439-8.517-8.5170.0000.0000.0000.000
197P197GLU-1-0.877-0.92734.927-7.747-7.7470.0000.0000.0000.000
198P198GLU-1-0.927-0.95435.321-8.548-8.5480.0000.0000.0000.000
199P199ILE0-0.015-0.02130.777-0.284-0.2840.0000.0000.0000.000
200P200ALA00.0040.00430.844-0.345-0.3450.0000.0000.0000.000
201P201VAL0-0.009-0.00130.725-0.237-0.2370.0000.0000.0000.000
202P202VAL0-0.072-0.04028.601-0.216-0.2160.0000.0000.0000.000
203P203LEU0-0.056-0.03326.049-0.351-0.3510.0000.0000.0000.000
204P204GLU-1-0.954-0.96425.823-10.320-10.3200.0000.0000.0000.000
205P205LYS10.8490.91826.6159.2359.2350.0000.0000.0000.000
206P206PHE-1-0.983-0.96721.735-13.003-13.0030.0000.0000.0000.000