FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-12-18

All entries: 87239

Number of unique PDB entries: 32030

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FMODB ID: MRZ9Z

Calculation Name: 1E6B-A-Xray547

Preferred Name:

Target Type:

Ligand Name: beta-mercaptoethanol

Ligand 3-letter code: BME

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1E6B

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ZVQ3

Base Structure: X-ray

Registration Date: 2025-09-02

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 194
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2178104.974264
FMO2-HF: Nuclear repulsion 2101859.393052
FMO2-HF: Total energy -76245.581212
FMO2-MP2: Total energy -76468.109346


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:8:LYS)


Summations of interaction energy for fragment #1(A:8:LYS)
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.
-251.335-248.26120.516-11.997-11.591-0.139
Interaction energy analysis for fragmet #1(A:8:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.700 / q_NPA : 1.832
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].
3A10LYS10.8640.9272.83495.37699.2370.568-1.563-2.866-0.010
4A11LEU00.0010.0085.0657.2707.289-0.001-0.004-0.0140.000
26A33ASP-1-0.886-0.9384.765-66.786-66.748-0.001-0.007-0.0300.000
27A34TYR0-0.079-0.0604.065-11.975-11.6150.001-0.101-0.2590.000
28A35GLU-1-0.801-0.9001.745-169.628-170.93719.945-10.267-8.368-0.129
29A36TYR0-0.018-0.0334.0216.0786.1830.004-0.055-0.0540.000
5A12TYR00.0230.0288.784-0.184-0.1840.0000.0000.0000.000
6A13SER00.018-0.02310.8953.5943.5940.0000.0000.0000.000
7A14TYR00.0380.01713.3730.7440.7440.0000.0000.0000.000
8A15TRP00.0620.03016.5101.4251.4250.0000.0000.0000.000
9A16ARG10.9400.98017.97823.46723.4670.0000.0000.0000.000
10A17SER0-0.024-0.00318.5311.7661.7660.0000.0000.0000.000
11A18SER00.0310.00719.948-1.124-1.1240.0000.0000.0000.000
12A19CYS00.0190.00320.235-0.240-0.2400.0000.0000.0000.000
13A20ALA00.0490.01015.499-1.018-1.0180.0000.0000.0000.000
14A21HIS00.0050.00416.286-0.403-0.4030.0000.0000.0000.000
15A22ARG10.8640.91918.21026.05426.0540.0000.0000.0000.000
16A23VAL00.0270.01412.770-0.193-0.1930.0000.0000.0000.000
17A24ARG10.7620.89313.24534.37934.3790.0000.0000.0000.000
18A25ILE0-0.0150.00514.433-0.817-0.8170.0000.0000.0000.000
19A26ALA00.0020.00214.662-0.043-0.0430.0000.0000.0000.000
20A27LEU0-0.007-0.0088.457-0.494-0.4940.0000.0000.0000.000
21A28ALA0-0.0160.00511.524-1.297-1.2970.0000.0000.0000.000
22A29LEU0-0.045-0.03113.7481.0891.0890.0000.0000.0000.000
23A30LYS10.7210.84511.97736.00936.0090.0000.0000.0000.000
24A31GLY00.0000.02111.831-0.941-0.9410.0000.0000.0000.000
25A32LEU0-0.044-0.0187.195-3.320-3.3200.0000.0000.0000.000
30A37ILE0-0.010-0.0055.494-1.375-1.3750.0000.0000.0000.000
31A38PRO00.009-0.0048.7663.3973.3970.0000.0000.0000.000
32A39VAL00.0210.02112.319-0.432-0.4320.0000.0000.0000.000
33A40ASN0-0.025-0.03315.1352.2072.2070.0000.0000.0000.000
34A41LEU0-0.004-0.01018.3531.1411.1410.0000.0000.0000.000
35A42LEU0-0.044-0.01720.8691.1521.1520.0000.0000.0000.000
36A43LYS10.9350.96919.98428.14328.1430.0000.0000.0000.000
37A44GLY00.0170.02722.1000.6920.6920.0000.0000.0000.000
38A45ASP-1-0.814-0.90716.669-31.914-31.9140.0000.0000.0000.000
39A46GLN0-0.020-0.02217.737-1.806-1.8060.0000.0000.0000.000
40A47PHE0-0.079-0.05218.7740.2750.2750.0000.0000.0000.000
41A48ASP-1-0.797-0.88616.722-31.992-31.9920.0000.0000.0000.000
42A49SER0-0.003-0.01818.748-0.611-0.6110.0000.0000.0000.000
43A50ASP-1-0.907-0.94414.744-34.197-34.1970.0000.0000.0000.000
44A51PHE0-0.063-0.02713.104-2.656-2.6560.0000.0000.0000.000
45A52LYS10.9050.95314.80626.85026.8500.0000.0000.0000.000
46A53LYS10.9330.98514.68438.74638.7460.0000.0000.0000.000
47A54ILE0-0.050-0.0229.733-1.492-1.4920.0000.0000.0000.000
48A55ASN0-0.0090.00113.3620.0140.0140.0000.0000.0000.000
49A56PRO00.0690.04015.0472.0262.0260.0000.0000.0000.000
50A57MET0-0.031-0.02718.3732.2472.2470.0000.0000.0000.000
51A58GLY0-0.015-0.00118.0841.4281.4280.0000.0000.0000.000
52A59THR0-0.022-0.00918.672-0.361-0.3610.0000.0000.0000.000
53A60VAL00.0290.02814.993-2.145-2.1450.0000.0000.0000.000
54A61PRO0-0.075-0.04214.3642.0562.0560.0000.0000.0000.000
55A62ALA00.001-0.00412.9231.9231.9230.0000.0000.0000.000
56A63LEU0-0.0060.0108.531-3.159-3.1590.0000.0000.0000.000
57A64VAL0-0.009-0.0106.5002.9862.9860.0000.0000.0000.000
58A65ASP-1-0.790-0.8735.369-83.686-83.6860.0000.0000.0000.000
59A66GLY00.0010.0065.1895.1835.1830.0000.0000.0000.000
60A67ASP-1-0.898-0.9586.363-48.617-48.6170.0000.0000.0000.000
61A68VAL0-0.050-0.0149.2314.2014.2010.0000.0000.0000.000
62A69VAL0-0.0060.0009.853-5.019-5.0190.0000.0000.0000.000
63A70ILE0-0.0170.00512.2013.4943.4940.0000.0000.0000.000
64A71ASN0-0.030-0.03513.751-1.800-1.8000.0000.0000.0000.000
65A72ASP-1-0.751-0.89616.513-28.049-28.0490.0000.0000.0000.000
66A73SER0-0.0380.00317.742-0.840-0.8400.0000.0000.0000.000
67A74PHE00.024-0.00518.730-0.620-0.6200.0000.0000.0000.000
68A75ALA00.0250.00818.554-0.444-0.4440.0000.0000.0000.000
69A76ILE0-0.023-0.00912.942-1.301-1.3010.0000.0000.0000.000
70A77ILE0-0.009-0.01314.299-1.581-1.5810.0000.0000.0000.000
71A78MET0-0.021-0.00116.2970.4470.4470.0000.0000.0000.000
72A79TYR0-0.006-0.0218.9661.1671.1670.0000.0000.0000.000
73A80LEU0-0.016-0.0239.770-1.844-1.8440.0000.0000.0000.000
74A81ASP-1-0.835-0.91112.722-30.776-30.7760.0000.0000.0000.000
75A82GLU-1-0.982-0.98915.754-29.444-29.4440.0000.0000.0000.000
76A83LYS10.8140.9016.80761.45761.4570.0000.0000.0000.000
77A84TYR0-0.010-0.0146.218-4.011-4.0110.0000.0000.0000.000
78A85PRO00.0500.03212.3591.1071.1070.0000.0000.0000.000
79A86GLU-1-0.989-0.97615.376-27.876-27.8760.0000.0000.0000.000
80A87PRO00.0360.01515.100-1.785-1.7850.0000.0000.0000.000
81A88PRO0-0.0010.01218.006-0.946-0.9460.0000.0000.0000.000
82A89LEU00.0280.00116.5951.0601.0600.0000.0000.0000.000
83A90LEU0-0.028-0.02220.6131.2051.2050.0000.0000.0000.000
84A91PRO00.0070.02523.705-0.019-0.0190.0000.0000.0000.000
85A92ARG10.9790.97226.71319.88519.8850.0000.0000.0000.000
86A93ASP-1-0.830-0.89628.362-17.371-17.3710.0000.0000.0000.000
87A94LEU00.0890.02030.118-0.399-0.3990.0000.0000.0000.000
88A95HIS00.0300.03331.889-0.402-0.4020.0000.0000.0000.000
89A96LYS10.9220.94530.81517.73117.7310.0000.0000.0000.000
90A97ARG10.8840.95723.37722.69522.6950.0000.0000.0000.000
91A98ALA00.0090.02028.853-0.488-0.4880.0000.0000.0000.000
92A99VAL00.0460.01331.208-0.277-0.2770.0000.0000.0000.000
93A100ASN0-0.014-0.02826.389-0.859-0.8590.0000.0000.0000.000
94A101TYR00.0330.01024.019-0.190-0.1900.0000.0000.0000.000
95A102GLN0-0.023-0.01228.158-0.104-0.1040.0000.0000.0000.000
96A103ALA00.0270.00329.4370.0870.0870.0000.0000.0000.000
97A104MET0-0.0300.01124.283-0.155-0.1550.0000.0000.0000.000
98A105SER00.0410.01427.269-0.227-0.2270.0000.0000.0000.000
99A106ILE0-0.0090.00429.4830.2010.2010.0000.0000.0000.000
100A107VAL0-0.020-0.00926.4090.1860.1860.0000.0000.0000.000
101A108LEU0-0.039-0.02023.863-0.093-0.0930.0000.0000.0000.000
102A109SER0-0.083-0.05927.3150.1480.1480.0000.0000.0000.000
103A110GLY0-0.0140.00030.5890.4700.4700.0000.0000.0000.000
104A111ILE0-0.076-0.03230.9530.5350.5350.0000.0000.0000.000
105A112GLN00.0430.03924.986-0.522-0.5220.0000.0000.0000.000
106A113PRO0-0.0180.00729.3330.0890.0890.0000.0000.0000.000
107A133THR00.0140.00244.4920.0630.0630.0000.0000.0000.000
108A134ALA00.000-0.00541.741-0.260-0.2600.0000.0000.0000.000
109A135TRP0-0.0060.00137.5660.3060.3060.0000.0000.0000.000
110A136VAL00.0400.01939.869-0.242-0.2420.0000.0000.0000.000
111A137ASN00.0080.00634.3080.3360.3360.0000.0000.0000.000
112A138ASN00.0620.01538.487-0.269-0.2690.0000.0000.0000.000
113A139ALA00.0010.01236.3310.1610.1610.0000.0000.0000.000
114A140ILE00.0260.01632.660-0.176-0.1760.0000.0000.0000.000
115A141THR00.0200.02136.011-0.169-0.1690.0000.0000.0000.000
116A142LYS10.9440.98638.92315.77915.7790.0000.0000.0000.000
117A143GLY00.0220.00235.2980.0770.0770.0000.0000.0000.000
118A144PHE00.001-0.01231.929-0.248-0.2480.0000.0000.0000.000
119A145THR00.0280.00236.5680.2320.2320.0000.0000.0000.000
120A146ALA0-0.089-0.03936.9020.3490.3490.0000.0000.0000.000
121A147LEU00.0090.00331.6280.0650.0650.0000.0000.0000.000
122A148GLU-1-0.722-0.84035.272-16.620-16.6200.0000.0000.0000.000
123A149LYS10.8650.93137.66715.21915.2190.0000.0000.0000.000
124A150LEU0-0.066-0.01933.1870.2270.2270.0000.0000.0000.000
125A151LEU00.010-0.00831.625-0.105-0.1050.0000.0000.0000.000
126A152VAL00.0130.02235.763-0.022-0.0220.0000.0000.0000.000
127A153ASN0-0.055-0.02438.9580.4270.4270.0000.0000.0000.000
128A154CYS0-0.075-0.02134.264-0.087-0.0870.0000.0000.0000.000
129A155ALA00.0060.00235.972-0.127-0.1270.0000.0000.0000.000
130A156GLY00.0380.01933.801-0.390-0.3900.0000.0000.0000.000
131A157LYS10.9280.94930.76119.59919.5990.0000.0000.0000.000
132A158HIS10.8420.93027.76221.71621.7160.0000.0000.0000.000
133A159ALA00.003-0.01028.6720.7490.7490.0000.0000.0000.000
134A160THR0-0.005-0.02229.3790.3830.3830.0000.0000.0000.000
135A161GLY00.0340.01731.000-0.006-0.0060.0000.0000.0000.000
136A162ASP-1-0.846-0.91730.652-18.466-18.4660.0000.0000.0000.000
137A163GLU-1-0.954-0.96725.552-22.957-22.9570.0000.0000.0000.000
138A164ILE0-0.059-0.02321.9710.4770.4770.0000.0000.0000.000
139A165TYR00.003-0.00323.321-0.068-0.0680.0000.0000.0000.000
140A166LEU00.0310.00421.171-0.053-0.0530.0000.0000.0000.000
141A167ALA00.008-0.00523.316-0.262-0.2620.0000.0000.0000.000
142A168ASP-1-0.730-0.84924.467-22.238-22.2380.0000.0000.0000.000
143A169LEU0-0.0030.00718.361-0.151-0.1510.0000.0000.0000.000
144A170PHE0-0.003-0.01821.214-0.662-0.6620.0000.0000.0000.000
145A171LEU00.0080.00224.5070.4150.4150.0000.0000.0000.000
146A172ALA00.0360.03123.7080.3960.3960.0000.0000.0000.000
147A173PRO00.005-0.00221.9730.5050.5050.0000.0000.0000.000
148A174GLN0-0.033-0.01024.5290.3390.3390.0000.0000.0000.000
149A175ILE0-0.001-0.00527.8360.6750.6750.0000.0000.0000.000
150A176HIS0-0.0140.00524.7670.7290.7290.0000.0000.0000.000
151A177GLY0-0.032-0.03127.3880.3160.3160.0000.0000.0000.000
152A178ALA0-0.007-0.00828.3540.5410.5410.0000.0000.0000.000
153A179ILE00.0240.01831.1680.5720.5720.0000.0000.0000.000
154A180ASN00.000-0.01327.3981.0501.0500.0000.0000.0000.000
155A181ARG10.8060.90224.66623.45923.4590.0000.0000.0000.000
156A182PHE0-0.025-0.02331.4160.3490.3490.0000.0000.0000.000
157A183GLN00.0050.02334.4490.8420.8420.0000.0000.0000.000
158A184ILE0-0.042-0.01534.9020.4570.4570.0000.0000.0000.000
159A185ASN0-0.018-0.02936.509-0.626-0.6260.0000.0000.0000.000
160A186MET00.016-0.00234.004-0.028-0.0280.0000.0000.0000.000
161A187GLU-1-0.858-0.90138.073-14.370-14.3700.0000.0000.0000.000
162A188PRO0-0.045-0.02440.7000.1880.1880.0000.0000.0000.000
163A189TYR0-0.031-0.02237.3510.1210.1210.0000.0000.0000.000
164A190PRO00.0710.04337.521-0.495-0.4950.0000.0000.0000.000
165A191THR0-0.009-0.03935.080-0.242-0.2420.0000.0000.0000.000
166A192LEU0-0.020-0.02432.764-0.612-0.6120.0000.0000.0000.000
167A193ALA0-0.013-0.00232.911-0.642-0.6420.0000.0000.0000.000
168A194LYS10.8320.92733.41717.79017.7900.0000.0000.0000.000
169A195CYS0-0.057-0.01330.057-0.299-0.2990.0000.0000.0000.000
170A196TYR00.0230.01627.634-0.958-0.9580.0000.0000.0000.000
171A197GLU-1-0.845-0.91829.391-19.855-19.8550.0000.0000.0000.000
172A198SER0-0.064-0.04129.472-0.577-0.5770.0000.0000.0000.000
173A199TYR0-0.023-0.06325.073-0.619-0.6190.0000.0000.0000.000
174A200ASN0-0.041-0.00625.380-1.633-1.6330.0000.0000.0000.000
175A201GLU-1-0.939-0.96026.674-21.234-21.2340.0000.0000.0000.000
176A202LEU0-0.0080.00322.550-0.646-0.6460.0000.0000.0000.000
177A203PRO00.0290.00219.570-0.774-0.7740.0000.0000.0000.000
178A204ALA00.0010.00217.381-1.022-1.0220.0000.0000.0000.000
179A205PHE00.017-0.00118.110-1.068-1.0680.0000.0000.0000.000
180A206GLN0-0.014-0.02120.531-1.027-1.0270.0000.0000.0000.000
181A207ASN0-0.004-0.01215.7801.1241.1240.0000.0000.0000.000
182A208ALA0-0.0020.01816.212-1.749-1.7490.0000.0000.0000.000
183A209LEU00.0230.02417.407-0.064-0.0640.0000.0000.0000.000
184A210PRO0-0.051-0.01918.864-1.300-1.3000.0000.0000.0000.000
185A211GLU-1-0.796-0.91619.206-26.775-26.7750.0000.0000.0000.000
186A212LYS10.9110.96917.54727.91127.9110.0000.0000.0000.000
187A213GLN0-0.036-0.02214.119-4.228-4.2280.0000.0000.0000.000
188A214PRO00.010-0.00610.7241.4881.4880.0000.0000.0000.000
189A215ASP-1-0.769-0.86313.700-35.929-35.9290.0000.0000.0000.000
190A216ALA0-0.029-0.00415.7561.6521.6520.0000.0000.0000.000
191A217PRO0-0.061-0.04219.0640.1170.1170.0000.0000.0000.000
192A218SER00.0000.00920.773-0.165-0.1650.0000.0000.0000.000
193A219SER0-0.038-0.02422.6840.8940.8940.0000.0000.0000.000
194A220THR-1-0.924-0.94722.984-22.449-22.4490.0000.0000.0000.000