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: VZ521

Calculation Name: 7BRD-B-Xray547

Preferred Name:

Target Type:

Ligand Name: triethylene glycol | acetate ion | di(hydroxyethyl)ether | beta-mercaptoethanol | 1,2-ethanediol | chloride ion

Ligand 3-letter code: PGE | ACT | PEG | BME | EDO | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7BRD

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2025-10-06

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 -2121661.717822
FMO2-HF: Nuclear repulsion 2048738.815226
FMO2-HF: Total energy -72922.902596
FMO2-MP2: Total energy -73138.675632


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.
-87.931-82.68533.91-15.815-23.34-0.171
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 : 0.716 / q_NPA : 0.872
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].
3A3ILE0-0.0280.0152.31010.28511.4982.722-1.009-2.926-0.003
4A4LYS10.8830.9255.14832.49132.565-0.001-0.009-0.0630.000
57A57GLU-1-0.789-0.8941.833-118.133-117.6168.078-5.167-3.428-0.074
88A88GLU-1-0.798-0.8814.060-37.371-37.1830.000-0.038-0.1490.000
90A90LEU0-0.010-0.0044.477-1.100-0.935-0.001-0.010-0.1550.000
131A131HIS00.031-0.0032.815-3.542-2.1453.493-1.088-3.802-0.011
132A132ARG10.7680.8695.30220.92020.939-0.0010.000-0.0180.000
176A176LEU0-0.0050.0072.741-6.298-5.4852.708-0.656-2.8650.001
177A177LEU0-0.042-0.0201.660-29.463-29.16811.934-6.966-5.264-0.061
178A178LYS10.9840.9852.49612.35110.8113.895-0.002-2.354-0.027
179A179ASP-1-0.859-0.9164.668-29.513-29.384-0.001-0.012-0.1150.000
180A180GLY00.0420.0342.6861.6682.2180.206-0.261-0.4950.000
181A181LEU00.031-0.0023.1955.4526.8070.874-0.541-1.6880.004
182A182THR00.0090.0104.9501.7751.8460.004-0.056-0.0180.000
5A5LEU0-0.028-0.0128.0633.4223.4220.0000.0000.0000.000
6A6ILE00.0010.0107.285-1.482-1.4820.0000.0000.0000.000
7A7VAL0-0.018-0.0199.6322.1312.1310.0000.0000.0000.000
8A8GLY00.0460.01411.853-0.708-0.7080.0000.0000.0000.000
9A9LEU0-0.078-0.04814.4700.9890.9890.0000.0000.0000.000
10A10ALA00.0330.00216.9040.1090.1090.0000.0000.0000.000
11A11ASN0-0.045-0.01020.666-0.041-0.0410.0000.0000.0000.000
12A12PRO00.0280.02024.226-0.126-0.1260.0000.0000.0000.000
13A13GLY00.0380.01126.1210.3460.3460.0000.0000.0000.000
14A14ALA00.013-0.00829.022-0.149-0.1490.0000.0000.0000.000
15A15GLU-1-0.892-0.92631.673-8.764-8.7640.0000.0000.0000.000
16A16TYR0-0.023-0.03026.913-0.095-0.0950.0000.0000.0000.000
17A17ALA00.0290.03226.886-0.447-0.4470.0000.0000.0000.000
18A18ALA0-0.056-0.03825.8170.2450.2450.0000.0000.0000.000
19A19THR0-0.045-0.01926.143-0.015-0.0150.0000.0000.0000.000
20A20ARG10.8940.92323.4149.8079.8070.0000.0000.0000.000
21A21HIS10.7700.85620.93911.68711.6870.0000.0000.0000.000
22A22ASN00.0370.01520.639-0.330-0.3300.0000.0000.0000.000
23A23ALA00.0260.01618.722-0.443-0.4430.0000.0000.0000.000
24A24GLY0-0.0080.00114.967-0.709-0.7090.0000.0000.0000.000
25A25ALA0-0.018-0.00615.016-1.129-1.1290.0000.0000.0000.000
26A26TRP00.0450.03517.398-0.542-0.5420.0000.0000.0000.000
27A27TYR00.017-0.0228.557-0.232-0.2320.0000.0000.0000.000
28A28VAL0-0.009-0.00412.674-1.101-1.1010.0000.0000.0000.000
29A29ASP-1-0.878-0.94814.861-15.135-15.1350.0000.0000.0000.000
30A30LEU00.0020.00316.612-0.008-0.0080.0000.0000.0000.000
31A31LEU0-0.026-0.01310.412-0.486-0.4860.0000.0000.0000.000
32A32ALA00.0300.01714.787-0.610-0.6100.0000.0000.0000.000
33A33ASP-1-0.881-0.91817.319-14.225-14.2250.0000.0000.0000.000
34A34ARG10.8530.90613.52520.79320.7930.0000.0000.0000.000
35A35HIS10.7530.85912.24323.46123.4610.0000.0000.0000.000
36A36ARG10.8360.90216.29414.23414.2340.0000.0000.0000.000
37A37ALA00.0380.03317.8250.6170.6170.0000.0000.0000.000
38A38PRO00.0090.01819.281-0.636-0.6360.0000.0000.0000.000
39A39LEU00.0070.01217.151-0.122-0.1220.0000.0000.0000.000
40A40ARG10.9520.97221.07112.79712.7970.0000.0000.0000.000
41A41GLU-1-0.886-0.92022.752-11.416-11.4160.0000.0000.0000.000
42A42GLU-1-0.837-0.90521.018-14.689-14.6890.0000.0000.0000.000
43A43SER00.0510.01823.597-0.384-0.3840.0000.0000.0000.000
44A44LYS10.8670.94022.85213.39413.3940.0000.0000.0000.000
45A45PHE0-0.010-0.01019.596-0.231-0.2310.0000.0000.0000.000
46A46PHE00.045-0.00120.974-0.212-0.2120.0000.0000.0000.000
47A47GLY00.0610.03420.8910.0220.0220.0000.0000.0000.000
48A48TYR0-0.042-0.01220.9590.2950.2950.0000.0000.0000.000
49A49THR0-0.027-0.04718.046-0.646-0.6460.0000.0000.0000.000
50A50SER00.001-0.02517.1450.6110.6110.0000.0000.0000.000
51A51ARG10.7900.85414.45519.68319.6830.0000.0000.0000.000
52A52ILE00.0010.01211.8771.1391.1390.0000.0000.0000.000
53A53ASN00.0040.00711.069-2.629-2.6290.0000.0000.0000.000
54A54LEU0-0.0100.0037.1881.9341.9340.0000.0000.0000.000
55A55ALA0-0.010-0.0166.509-4.696-4.6960.0000.0000.0000.000
56A56GLY00.0070.0057.119-2.896-2.8960.0000.0000.0000.000
58A58ASP-1-0.821-0.8796.793-20.285-20.2850.0000.0000.0000.000
59A59VAL0-0.023-0.0047.490-0.435-0.4350.0000.0000.0000.000
60A60ARG10.9180.96410.18023.96123.9610.0000.0000.0000.000
61A61LEU00.0020.00611.630-1.468-1.4680.0000.0000.0000.000
62A62LEU00.010-0.01213.8881.2391.2390.0000.0000.0000.000
63A63VAL00.0460.03415.337-0.612-0.6120.0000.0000.0000.000
64A64PRO0-0.047-0.01816.8570.6470.6470.0000.0000.0000.000
65A65THR0-0.018-0.03019.9700.3940.3940.0000.0000.0000.000
66A66THR0-0.045-0.03322.0630.3520.3520.0000.0000.0000.000
67A67PHE00.0420.02124.3290.3020.3020.0000.0000.0000.000
68A68MET00.0550.05719.238-0.531-0.5310.0000.0000.0000.000
69A69ASN0-0.043-0.03220.748-0.765-0.7650.0000.0000.0000.000
70A70LEU0-0.0020.01122.6830.1950.1950.0000.0000.0000.000
71A71SER00.018-0.00617.467-0.238-0.2380.0000.0000.0000.000
72A72GLY00.004-0.00117.380-0.729-0.7290.0000.0000.0000.000
73A73LYS10.8400.94018.45611.26111.2610.0000.0000.0000.000
74A74ALA00.0020.00818.8550.1080.1080.0000.0000.0000.000
75A75VAL00.009-0.00412.966-0.393-0.3930.0000.0000.0000.000
76A76ALA00.0330.02115.445-0.710-0.7100.0000.0000.0000.000
77A77ALA0-0.0070.01717.206-0.051-0.0510.0000.0000.0000.000
78A78MET0-0.0070.00315.708-0.099-0.0990.0000.0000.0000.000
79A79ALA00.0130.00613.237-0.499-0.4990.0000.0000.0000.000
80A80THR0-0.013-0.01314.679-0.145-0.1450.0000.0000.0000.000
81A81PHE0-0.053-0.02417.9230.2330.2330.0000.0000.0000.000
82A82TYR0-0.032-0.03215.1770.2390.2390.0000.0000.0000.000
83A83ARG10.8570.93215.23714.32314.3230.0000.0000.0000.000
84A84ILE0-0.0170.0069.515-0.985-0.9850.0000.0000.0000.000
85A85ASN00.0300.0209.6792.9992.9990.0000.0000.0000.000
86A86PRO0-0.004-0.0278.811-1.886-1.8860.0000.0000.0000.000
87A87ASP-1-0.865-0.9335.859-29.495-29.4950.0000.0000.0000.000
89A89ILE0-0.036-0.0205.8560.0250.0250.0000.0000.0000.000
91A91VAL0-0.022-0.0206.3981.8361.8360.0000.0000.0000.000
92A92ALA00.0050.0159.6990.2820.2820.0000.0000.0000.000
93A93HIS0-0.044-0.04311.3900.3430.3430.0000.0000.0000.000
94A94ASP-1-0.725-0.81514.504-13.628-13.6280.0000.0000.0000.000
95A95GLU-1-0.825-0.90415.749-14.623-14.6230.0000.0000.0000.000
96A96LEU00.0240.01017.8480.3410.3410.0000.0000.0000.000
97A97ASP-1-0.912-0.95218.473-12.292-12.2920.0000.0000.0000.000
98A98LEU0-0.078-0.04114.876-0.194-0.1940.0000.0000.0000.000
99A99PRO00.0170.01219.4190.0920.0920.0000.0000.0000.000
100A100PRO00.0390.00720.619-0.550-0.5500.0000.0000.0000.000
101A101GLY00.0210.02320.8920.3380.3380.0000.0000.0000.000
102A102VAL0-0.021-0.00416.525-0.373-0.3730.0000.0000.0000.000
103A103ALA00.0400.01413.2160.0790.0790.0000.0000.0000.000
104A104LYS10.9060.95611.55015.43515.4350.0000.0000.0000.000
105A105PHE00.0540.0305.998-0.424-0.4240.0000.0000.0000.000
106A106LYS10.8640.9347.01019.57819.5780.0000.0000.0000.000
107A107LEU00.0260.0245.491-1.644-1.6440.0000.0000.0000.000
108A108GLY00.0460.0367.2771.5641.5640.0000.0000.0000.000
109A109GLY0-0.009-0.01410.5200.4150.4150.0000.0000.0000.000
110A110GLY00.0290.01014.108-0.258-0.2580.0000.0000.0000.000
111A111HIS00.0520.02314.864-0.850-0.8500.0000.0000.0000.000
112A112GLY00.0570.03816.871-0.075-0.0750.0000.0000.0000.000
113A113GLY00.0080.00918.8270.3480.3480.0000.0000.0000.000
114A114HIS0-0.016-0.02817.4710.4120.4120.0000.0000.0000.000
115A115ASN0-0.014-0.04418.862-0.414-0.4140.0000.0000.0000.000
116A116GLY00.0470.03618.5730.1210.1210.0000.0000.0000.000
117A117LEU0-0.0050.00012.712-0.459-0.4590.0000.0000.0000.000
118A118LYS10.9330.96815.92310.74010.7400.0000.0000.0000.000
119A119ASP-1-0.791-0.87818.826-12.622-12.6220.0000.0000.0000.000
120A120ILE00.0310.01712.9470.0430.0430.0000.0000.0000.000
121A121ILE0-0.0070.00514.715-0.185-0.1850.0000.0000.0000.000
122A122SER0-0.053-0.01616.3690.2520.2520.0000.0000.0000.000
123A123LYS10.8410.89318.65112.28212.2820.0000.0000.0000.000
124A124LEU0-0.0020.01111.960-0.105-0.1050.0000.0000.0000.000
125A125GLY0-0.0080.00316.078-0.335-0.3350.0000.0000.0000.000
126A126ASN0-0.053-0.03518.7680.1070.1070.0000.0000.0000.000
127A127ASN00.0710.05013.090-0.282-0.2820.0000.0000.0000.000
128A128PRO00.008-0.00413.368-0.656-0.6560.0000.0000.0000.000
129A129ASN0-0.068-0.02510.153-0.857-0.8570.0000.0000.0000.000
130A130PHE00.0550.0327.174-0.706-0.7060.0000.0000.0000.000
133A133LEU00.001-0.0027.134-1.281-1.2810.0000.0000.0000.000
134A134ARG10.8360.9089.27516.88816.8880.0000.0000.0000.000
135A135VAL00.0300.00112.698-0.095-0.0950.0000.0000.0000.000
136A136GLY00.0090.00215.2410.6270.6270.0000.0000.0000.000
137A137ILE0-0.056-0.03218.3450.2500.2500.0000.0000.0000.000
138A138GLY00.0190.01621.4900.5380.5380.0000.0000.0000.000
139A139HIS00.0200.00423.497-0.330-0.3300.0000.0000.0000.000
140A140PRO0-0.041-0.00826.0870.1870.1870.0000.0000.0000.000
141A141GLY00.0400.01329.803-0.038-0.0380.0000.0000.0000.000
142A142ASP-1-0.822-0.92432.486-8.267-8.2670.0000.0000.0000.000
143A143LYS10.9050.95234.2187.0937.0930.0000.0000.0000.000
144A144ASN0-0.046-0.01033.0190.2260.2260.0000.0000.0000.000
145A145LYS10.9570.97632.8107.9647.9640.0000.0000.0000.000
146A146VAL00.1010.04226.727-0.095-0.0950.0000.0000.0000.000
147A147VAL00.0110.00528.386-0.238-0.2380.0000.0000.0000.000
148A148GLY0-0.030-0.02429.208-0.124-0.1240.0000.0000.0000.000
149A149PHE00.0350.03324.8720.1420.1420.0000.0000.0000.000
150A150VAL00.0280.00524.016-0.203-0.2030.0000.0000.0000.000
151A151LEU0-0.041-0.02625.714-0.339-0.3390.0000.0000.0000.000
152A152GLY00.0480.03528.1010.3490.3490.0000.0000.0000.000
153A153LYS10.9370.97527.7269.5159.5150.0000.0000.0000.000
154A154PRO0-0.0080.00525.4440.2750.2750.0000.0000.0000.000
155A155PRO0-0.0020.01128.3580.1590.1590.0000.0000.0000.000
156A156ALA00.029-0.00729.338-0.309-0.3090.0000.0000.0000.000
157A157SER00.0320.02129.136-0.270-0.2700.0000.0000.0000.000
158A158GLU-1-0.789-0.89226.186-10.457-10.4570.0000.0000.0000.000
159A159GLN0-0.073-0.05423.710-0.106-0.1060.0000.0000.0000.000
160A160LYS10.8590.93524.13811.82711.8270.0000.0000.0000.000
161A161LEU00.0590.02423.623-0.521-0.5210.0000.0000.0000.000
162A162ILE0-0.033-0.02219.509-0.643-0.6430.0000.0000.0000.000
163A163ASP-1-0.863-0.93019.388-13.279-13.2790.0000.0000.0000.000
164A164ASP-1-0.814-0.89819.706-13.589-13.5890.0000.0000.0000.000
165A165ALA0-0.020-0.00716.962-0.804-0.8040.0000.0000.0000.000
166A166VAL0-0.033-0.00915.312-1.422-1.4220.0000.0000.0000.000
167A167ASP-1-0.816-0.89315.146-17.924-17.9240.0000.0000.0000.000
168A168GLU-1-0.724-0.83414.857-19.760-19.7600.0000.0000.0000.000
169A169ALA00.0280.01711.272-1.766-1.7660.0000.0000.0000.000
170A170ALA0-0.0060.00410.725-2.908-2.9080.0000.0000.0000.000
171A171ARG10.7400.84311.56816.30616.3060.0000.0000.0000.000
172A172CYS0-0.056-0.02810.106-1.903-1.9030.0000.0000.0000.000
173A173THR0-0.007-0.0076.415-3.785-3.7850.0000.0000.0000.000
174A174GLU-1-0.784-0.8746.111-31.423-31.4230.0000.0000.0000.000
175A175ILE0-0.037-0.0096.537-3.272-3.2720.0000.0000.0000.000
183A183LYS10.9000.9347.76630.46430.4640.0000.0000.0000.000
184A184ALA00.0130.0156.7502.3442.3440.0000.0000.0000.000
185A185THR0-0.031-0.0367.4092.4812.4810.0000.0000.0000.000
186A186ASN0-0.069-0.0329.8851.6291.6290.0000.0000.0000.000
187A187ARG10.8750.92212.17521.24721.2470.0000.0000.0000.000
188A188LEU00.0260.00810.1181.2001.2000.0000.0000.0000.000
189A189HIS0-0.053-0.03910.6560.4170.4170.0000.0000.0000.000
190A190ALA0-0.0110.00914.3900.9480.9480.0000.0000.0000.000
191A191PHE0-0.0180.00016.4880.6700.6700.0000.0000.0000.000
192A192LYS10.8650.91518.21611.70311.7030.0000.0000.0000.000
193A193ALA0-0.0180.02420.8840.2710.2710.0000.0000.0000.000
194A194GLN-1-0.912-0.95722.913-10.432-10.4320.0000.0000.0000.000