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: Z7ZLN

Calculation Name: 1B25-A-Xray547

Preferred Name:

Target Type:

Ligand Name: tungstopterin | iron/sulfur cluster

Ligand 3-letter code: PTT | SF4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1B25

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U1K3

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 619
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -15069117.359883
FMO2-HF: Nuclear repulsion 14827876.884224
FMO2-HF: Total energy -241240.475659
FMO2-MP2: Total energy -241945.57466


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.
-134.648-128.11417.789-5.744-18.582-0.081
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 : 0.809 / q_NPA : 0.919
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].
3A3GLY00.0560.0193.2581.1143.1550.044-0.968-1.117-0.003
4A4TRP0-0.070-0.0412.5041.9002.7323.078-0.957-2.9530.002
5A5TRP0-0.041-0.0412.913-11.944-9.9640.469-1.119-1.330-0.012
6A6GLY00.0220.0112.471-3.220-3.5694.466-1.588-2.529-0.002
7A7ARG10.8590.9413.17329.68626.3750.1903.577-0.456-0.001
23A23TYR0-0.125-0.0894.5531.8352.130-0.001-0.040-0.2550.000
24A24PRO00.0490.0232.926-7.413-6.0670.151-0.644-0.854-0.008
25A25GLU-1-0.808-0.9182.084-101.249-97.4059.222-4.861-8.206-0.057
26A26GLU-1-0.886-0.9553.002-28.116-28.9150.1230.980-0.3040.000
28A28ALA00.0270.0114.2171.6242.0030.049-0.100-0.3280.000
29A29LYS10.8720.9374.67048.08948.193-0.001-0.006-0.0970.000
107A107ASP-1-0.718-0.8435.287-30.312-30.140-0.001-0.018-0.1530.000
8A8ILE0-0.014-0.0056.8310.7490.7490.0000.0000.0000.000
9A9LEU0-0.0020.0149.8020.3750.3750.0000.0000.0000.000
10A10ARG10.7260.81713.26116.05116.0510.0000.0000.0000.000
11A11VAL00.0600.02015.8140.2330.2330.0000.0000.0000.000
12A12ASN00.0640.03219.6250.5930.5930.0000.0000.0000.000
13A13LEU00.0370.00322.2690.2690.2690.0000.0000.0000.000
14A14THR0-0.067-0.01225.6130.4090.4090.0000.0000.0000.000
15A15THR0-0.034-0.03823.8800.3320.3320.0000.0000.0000.000
16A16GLY00.0160.01925.5930.2020.2020.0000.0000.0000.000
17A17GLU-1-0.879-0.91419.842-13.432-13.4320.0000.0000.0000.000
18A18VAL00.0210.00118.264-0.127-0.1270.0000.0000.0000.000
19A19LYS10.8470.91315.01814.28314.2830.0000.0000.0000.000
20A20VAL00.0190.0019.605-0.041-0.0410.0000.0000.0000.000
21A21GLN00.0110.0229.1400.7920.7920.0000.0000.0000.000
22A22GLU-1-0.914-0.9595.734-30.719-30.7190.0000.0000.0000.000
27A27VAL0-0.011-0.0036.3592.6262.6260.0000.0000.0000.000
30A30LYS10.8350.9377.57620.40520.4050.0000.0000.0000.000
31A31PHE00.020-0.00610.0792.0482.0480.0000.0000.0000.000
32A32ILE0-0.0070.0199.1021.3761.3760.0000.0000.0000.000
33A33GLY00.0680.0199.136-1.758-1.7580.0000.0000.0000.000
34A34GLY0-0.023-0.01110.8091.0571.0570.0000.0000.0000.000
35A35ARG10.7600.82914.17512.42512.4250.0000.0000.0000.000
36A36GLY00.0210.00914.3880.4200.4200.0000.0000.0000.000
37A37LEU0-0.025-0.0138.8440.0310.0310.0000.0000.0000.000
38A38ALA00.0200.00212.3660.2650.2650.0000.0000.0000.000
39A39ALA00.0150.01015.5640.4990.4990.0000.0000.0000.000
40A40TRP00.0210.0159.3810.1200.1200.0000.0000.0000.000
41A41ILE00.0100.00911.7050.3450.3450.0000.0000.0000.000
42A42LEU0-0.026-0.00714.9060.5580.5580.0000.0000.0000.000
43A43TRP00.0350.01517.5090.6290.6290.0000.0000.0000.000
44A44ASN0-0.051-0.03114.8600.8700.8700.0000.0000.0000.000
45A45GLU-1-0.799-0.87114.838-14.741-14.7410.0000.0000.0000.000
46A46ALA0-0.0190.00319.0650.3780.3780.0000.0000.0000.000
47A47ARG10.8050.88320.05012.22812.2280.0000.0000.0000.000
48A48GLY00.012-0.00123.9770.1260.1260.0000.0000.0000.000
49A49VAL0-0.063-0.01024.6390.2840.2840.0000.0000.0000.000
50A50GLU-1-0.811-0.91327.648-8.325-8.3250.0000.0000.0000.000
51A51PRO0-0.0180.01627.778-0.242-0.2420.0000.0000.0000.000
52A52LEU00.0090.00728.425-0.174-0.1740.0000.0000.0000.000
53A53SER0-0.040-0.03128.6740.1010.1010.0000.0000.0000.000
54A54PRO0-0.054-0.04427.486-0.269-0.2690.0000.0000.0000.000
55A55GLU-1-0.849-0.93624.900-10.006-10.0060.0000.0000.0000.000
56A56ASN0-0.039-0.01023.413-0.836-0.8360.0000.0000.0000.000
57A57LYS10.8210.90918.72012.23112.2310.0000.0000.0000.000
58A58LEU00.0200.01620.9260.0750.0750.0000.0000.0000.000
59A59ILE0-0.034-0.01715.365-0.514-0.5140.0000.0000.0000.000
60A60PHE00.0310.00717.1070.4990.4990.0000.0000.0000.000
61A61ALA0-0.007-0.00313.492-0.881-0.8810.0000.0000.0000.000
62A62ALA00.0190.00312.1070.8270.8270.0000.0000.0000.000
63A63GLY00.0460.0199.619-0.403-0.4030.0000.0000.0000.000
64A64PRO0-0.023-0.0026.7870.1680.1680.0000.0000.0000.000
65A65PHE00.029-0.0068.481-0.109-0.1090.0000.0000.0000.000
66A66ASN00.0010.01411.7870.2390.2390.0000.0000.0000.000
67A67GLY00.0210.00511.530-1.440-1.4400.0000.0000.0000.000
68A68LEU0-0.032-0.0089.690-0.173-0.1730.0000.0000.0000.000
69A69PRO0-0.035-0.02014.0030.6250.6250.0000.0000.0000.000
70A70THR00.0180.01713.7650.5980.5980.0000.0000.0000.000
71A71PRO00.0290.00116.9730.5340.5340.0000.0000.0000.000
72A72SER0-0.034-0.02219.9540.1670.1670.0000.0000.0000.000
73A73GLY00.0450.02516.9230.1170.1170.0000.0000.0000.000
74A74GLY0-0.017-0.00516.737-0.712-0.7120.0000.0000.0000.000
75A75LYS10.8050.84618.20212.58412.5840.0000.0000.0000.000
76A76LEU00.0060.02015.985-0.926-0.9260.0000.0000.0000.000
77A77VAL0-0.0090.00516.8800.7680.7680.0000.0000.0000.000
78A78VAL0-0.010-0.00618.161-0.362-0.3620.0000.0000.0000.000
79A79ALA00.026-0.00919.0370.3850.3850.0000.0000.0000.000
80A80ALA00.0280.01120.734-0.218-0.2180.0000.0000.0000.000
81A81LYS10.8430.92522.5189.7319.7310.0000.0000.0000.000
82A82SER0-0.044-0.04025.0410.2200.2200.0000.0000.0000.000
83A83PRO0-0.008-0.01628.0100.2080.2080.0000.0000.0000.000
84A84LEU0-0.048-0.00731.2460.2320.2320.0000.0000.0000.000
85A85THR0-0.018-0.02030.0040.1290.1290.0000.0000.0000.000
86A86GLY00.0080.01330.6300.1240.1240.0000.0000.0000.000
87A87GLY00.0400.01027.995-0.125-0.1250.0000.0000.0000.000
88A88TYR0-0.048-0.05319.325-0.318-0.3180.0000.0000.0000.000
89A89GLY00.0200.00124.1020.3320.3320.0000.0000.0000.000
90A90ASP-1-0.762-0.83821.044-12.788-12.7880.0000.0000.0000.000
91A91GLY0-0.034-0.03222.6150.5790.5790.0000.0000.0000.000
92A92ASN0-0.065-0.04719.320-0.326-0.3260.0000.0000.0000.000
93A93LEU00.0270.03321.6860.4590.4590.0000.0000.0000.000
94A94GLY00.036-0.01721.717-0.604-0.6040.0000.0000.0000.000
95A95THR0-0.023-0.02420.5810.2620.2620.0000.0000.0000.000
96A96MET00.0360.00320.583-0.695-0.6950.0000.0000.0000.000
97A97ALA00.0020.00419.809-0.549-0.5490.0000.0000.0000.000
98A98SER0-0.043-0.03016.604-0.936-0.9360.0000.0000.0000.000
99A99VAL0-0.017-0.01915.210-1.044-1.0440.0000.0000.0000.000
100A100HIS00.0620.02515.479-1.408-1.4080.0000.0000.0000.000
101A101LEU00.0070.01513.204-0.429-0.4290.0000.0000.0000.000
102A102ARG10.8230.8986.67126.08426.0840.0000.0000.0000.000
103A103ARG10.8670.91411.34915.89215.8920.0000.0000.0000.000
104A104ALA00.0060.02013.810-0.155-0.1550.0000.0000.0000.000
105A105GLY0-0.0170.00210.338-0.120-0.1200.0000.0000.0000.000
106A106TYR0-0.048-0.0399.132-1.566-1.5660.0000.0000.0000.000
108A108ALA0-0.005-0.0138.9021.1621.1620.0000.0000.0000.000
109A109LEU0-0.0070.01412.061-0.535-0.5350.0000.0000.0000.000
110A110VAL0-0.010-0.00313.9530.4860.4860.0000.0000.0000.000
111A111VAL00.000-0.00316.5280.0480.0480.0000.0000.0000.000
112A112GLU-1-0.848-0.92618.932-12.747-12.7470.0000.0000.0000.000
113A113GLY00.0340.02221.9370.1320.1320.0000.0000.0000.000
114A114LYS10.9260.93525.3978.6398.6390.0000.0000.0000.000
115A115ALA00.0160.03328.4340.1290.1290.0000.0000.0000.000
116A116LYS10.8870.93830.0689.1789.1780.0000.0000.0000.000
117A117LYS10.9270.96133.5437.8827.8820.0000.0000.0000.000
118A118PRO00.0280.01232.558-0.213-0.2130.0000.0000.0000.000
119A119VAL0-0.0130.00627.9090.0690.0690.0000.0000.0000.000
120A120TYR0-0.034-0.03927.0710.0630.0630.0000.0000.0000.000
121A121ILE00.0020.01020.954-0.021-0.0210.0000.0000.0000.000
122A122TYR0-0.056-0.04423.7980.1650.1650.0000.0000.0000.000
123A123ILE0-0.002-0.00617.130-0.306-0.3060.0000.0000.0000.000
124A124GLU-1-0.834-0.90920.166-12.102-12.1020.0000.0000.0000.000
125A125ASP-1-0.768-0.84916.345-16.967-16.9670.0000.0000.0000.000
126A126ASP-1-0.810-0.88614.312-20.159-20.1590.0000.0000.0000.000
127A127ASN0-0.0410.00217.2440.5230.5230.0000.0000.0000.000
128A128VAL00.018-0.00117.533-0.053-0.0530.0000.0000.0000.000
129A129SER0-0.036-0.01920.9540.4960.4960.0000.0000.0000.000
130A130ILE0-0.0070.00623.816-0.101-0.1010.0000.0000.0000.000
131A131LEU0-0.0010.00926.0440.2460.2460.0000.0000.0000.000
132A132SER0-0.028-0.03929.4330.0060.0060.0000.0000.0000.000
133A133ALA00.0410.00631.436-0.042-0.0420.0000.0000.0000.000
134A134GLU-1-0.887-0.93933.468-7.756-7.7560.0000.0000.0000.000
135A135GLY0-0.0020.00536.9800.1680.1680.0000.0000.0000.000
136A136LEU0-0.017-0.01432.2910.0610.0610.0000.0000.0000.000
137A137TRP0-0.019-0.01232.171-0.105-0.1050.0000.0000.0000.000
138A138GLY00.0010.00336.8670.1990.1990.0000.0000.0000.000
139A139LYS10.7730.88336.9217.7947.7940.0000.0000.0000.000
140A140THR00.0650.02836.612-0.222-0.2220.0000.0000.0000.000
141A141THR0-0.017-0.02132.127-0.069-0.0690.0000.0000.0000.000
142A142PHE00.0510.02132.834-0.211-0.2110.0000.0000.0000.000
143A143GLU-1-0.762-0.83934.563-7.802-7.8020.0000.0000.0000.000
144A144THR0-0.046-0.03531.123-0.058-0.0580.0000.0000.0000.000
145A145GLU-1-0.790-0.89228.846-10.419-10.4190.0000.0000.0000.000
146A146ARG10.8090.87431.3237.6547.6540.0000.0000.0000.000
147A147GLU-1-0.792-0.88934.389-7.883-7.8830.0000.0000.0000.000
148A148LEU0-0.012-0.00828.720-0.108-0.1080.0000.0000.0000.000
149A149LYS10.8170.90527.28710.23210.2320.0000.0000.0000.000
150A150GLU-1-0.990-0.99131.472-8.256-8.2560.0000.0000.0000.000
151A151ILE0-0.054-0.00831.9910.0990.0990.0000.0000.0000.000
152A152HIS00.0150.01227.962-0.004-0.0040.0000.0000.0000.000
153A153GLY00.0110.02428.988-0.295-0.2950.0000.0000.0000.000
154A154LYS10.9860.96329.3188.5178.5170.0000.0000.0000.000
155A155ASN0-0.066-0.02225.399-0.026-0.0260.0000.0000.0000.000
156A156VAL00.0090.00323.614-0.493-0.4930.0000.0000.0000.000
157A157GLY0-0.012-0.00522.0920.2850.2850.0000.0000.0000.000
158A158VAL0-0.002-0.00523.134-0.044-0.0440.0000.0000.0000.000
159A159LEU0-0.0140.01920.566-0.019-0.0190.0000.0000.0000.000
160A160THR0-0.027-0.02325.1680.1940.1940.0000.0000.0000.000
161A161ILE00.0310.02728.599-0.074-0.0740.0000.0000.0000.000
162A162GLY00.0450.03431.0030.0770.0770.0000.0000.0000.000
163A163PRO00.0280.00534.806-0.119-0.1190.0000.0000.0000.000
164A164ALA00.0340.02435.8670.0650.0650.0000.0000.0000.000
165A165GLY00.0220.00732.587-0.056-0.0560.0000.0000.0000.000
166A166GLU-1-0.819-0.90333.443-8.102-8.1020.0000.0000.0000.000
167A167ASN0-0.064-0.02835.1610.0880.0880.0000.0000.0000.000
168A168LEU0-0.047-0.02533.0630.1080.1080.0000.0000.0000.000
169A169VAL00.0190.03235.4830.1170.1170.0000.0000.0000.000
170A170LYS10.8590.91634.4557.5137.5130.0000.0000.0000.000
171A171TYR0-0.007-0.01432.927-0.282-0.2820.0000.0000.0000.000
172A172ALA00.0200.01132.447-0.036-0.0360.0000.0000.0000.000
173A173VAL0-0.095-0.03828.998-0.283-0.2830.0000.0000.0000.000
174A174VAL0-0.003-0.00724.5090.0990.0990.0000.0000.0000.000
175A175ILE00.0110.00727.486-0.127-0.1270.0000.0000.0000.000
176A176SER0-0.023-0.01425.465-0.265-0.2650.0000.0000.0000.000
177A177GLN0-0.017-0.03425.157-0.297-0.2970.0000.0000.0000.000
178A178GLU-1-0.916-0.95629.474-8.229-8.2290.0000.0000.0000.000
179A179GLY00.0980.05731.2380.2270.2270.0000.0000.0000.000
180A180ARG10.7720.86326.6799.9289.9280.0000.0000.0000.000
181A181ALA00.0760.03127.938-0.126-0.1260.0000.0000.0000.000
182A182ALA0-0.047-0.02423.837-0.228-0.2280.0000.0000.0000.000
183A183GLY00.0290.00125.6850.1060.1060.0000.0000.0000.000
184A184ARG10.8210.87726.3558.9128.9120.0000.0000.0000.000
185A185PRO00.0100.02427.1570.2320.2320.0000.0000.0000.000
186A186GLY00.1350.08429.5640.0030.0030.0000.0000.0000.000
187A187MET0-0.067-0.01024.479-0.139-0.1390.0000.0000.0000.000
188A188GLY00.0160.00927.005-0.137-0.1370.0000.0000.0000.000
189A189ALA00.0430.02629.3040.1230.1230.0000.0000.0000.000
190A190VAL0-0.0140.00424.9890.0780.0780.0000.0000.0000.000
191A191MET0-0.0260.01226.039-0.129-0.1290.0000.0000.0000.000
192A192GLY00.0500.02427.4240.0430.0430.0000.0000.0000.000
193A193SER0-0.056-0.03928.9710.1420.1420.0000.0000.0000.000
194A194LYS10.7630.88523.43210.88710.8870.0000.0000.0000.000
195A195LYS10.8810.94528.6638.1318.1310.0000.0000.0000.000
196A196LEU0-0.0150.01023.7840.0440.0440.0000.0000.0000.000
197A197LYS10.7840.87128.2168.4568.4560.0000.0000.0000.000
198A198ALA00.021-0.01627.3460.0500.0500.0000.0000.0000.000
199A199VAL0-0.020-0.00520.642-0.144-0.1440.0000.0000.0000.000
200A200VAL0-0.0060.00424.0240.0660.0660.0000.0000.0000.000
201A201ILE00.003-0.00717.691-0.355-0.3550.0000.0000.0000.000
202A202ARG10.9420.96420.43212.75912.7590.0000.0000.0000.000
203A203GLY00.0350.01316.773-0.429-0.4290.0000.0000.0000.000
204A204THR0-0.136-0.10517.2670.3090.3090.0000.0000.0000.000
205A205LYS10.8490.92211.98721.02321.0230.0000.0000.0000.000
206A206GLU-1-0.894-0.92912.105-21.933-21.9330.0000.0000.0000.000
207A207ILE0-0.0010.0007.608-1.076-1.0760.0000.0000.0000.000
208A208PRO0-0.0070.0015.5000.8920.8920.0000.0000.0000.000
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