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: 8QYYY

Calculation Name: 4WIN-A-Xray547

Preferred Name:

Target Type:

Ligand Name: nitrate ion

Ligand 3-letter code: NO3

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4WIN

Chain ID: A

ChEMBL ID:

UniProt ID: Q8IJR9

Base Structure: X-ray

Registration Date: 2025-10-05

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 228
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3086960.848886
FMO2-HF: Nuclear repulsion 2991948.96821
FMO2-HF: Total energy -95011.880676
FMO2-MP2: Total energy -95280.691311


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:6:TYR)


Summations of interaction energy for fragment #1(A:6:TYR)
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.
27.97135.0671.762-2.316-6.542-0.005
Interaction energy analysis for fragmet #1(A:6:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.833 / q_NPA : 0.902
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].
3A8LYS10.8800.9652.70557.26259.8960.487-0.964-2.157-0.002
4A9ILE00.0150.0175.3393.2343.295-0.001-0.003-0.0570.000
27A32PHE0-0.022-0.0152.667-4.294-0.8831.278-1.089-3.600-0.003
28A33SER00.0230.0114.5390.3900.426-0.001-0.014-0.0210.000
44A49ASN0-0.054-0.0343.6799.82810.3840.000-0.209-0.3470.000
228A233LYS00.1080.0734.367-25.723-25.325-0.001-0.037-0.3600.000
5A10LEU0-0.013-0.0068.460-0.009-0.0090.0000.0000.0000.000
6A11VAL0-0.012-0.00910.9781.4951.4950.0000.0000.0000.000
7A12LEU00.0230.00413.7010.0110.0110.0000.0000.0000.000
8A13ASN00.006-0.01417.0101.0541.0540.0000.0000.0000.000
9A14PHE00.013-0.00119.7090.2390.2390.0000.0000.0000.000
10A15GLY00.0390.01822.7680.6000.6000.0000.0000.0000.000
11A16SER0-0.041-0.00821.7170.6110.6110.0000.0000.0000.000
12A17GLN00.0260.00523.090-0.245-0.2450.0000.0000.0000.000
13A18TYR00.0500.02522.6880.0550.0550.0000.0000.0000.000
14A19PHE00.0030.00815.678-0.506-0.5060.0000.0000.0000.000
15A20HIS00.0370.00415.391-1.011-1.0110.0000.0000.0000.000
16A21LEU0-0.013-0.00616.848-0.628-0.6280.0000.0000.0000.000
17A22ILE00.0320.02613.993-0.362-0.3620.0000.0000.0000.000
18A23VAL00.0170.01311.713-0.937-0.9370.0000.0000.0000.000
19A24LYS10.8920.95112.67514.32214.3220.0000.0000.0000.000
20A25ARG10.8820.95414.53513.73013.7300.0000.0000.0000.000
21A26LEU00.0280.0119.622-0.469-0.4690.0000.0000.0000.000
22A27ASN00.0250.01110.038-2.934-2.9340.0000.0000.0000.000
23A28ASN0-0.092-0.04411.236-0.582-0.5820.0000.0000.0000.000
24A29ILE00.0090.01610.773-0.034-0.0340.0000.0000.0000.000
25A30LYS10.7500.8757.98819.81619.8160.0000.0000.0000.000
26A31ILE00.0460.0286.274-3.354-3.3540.0000.0000.0000.000
29A34GLU-1-0.908-0.9657.193-32.038-32.0380.0000.0000.0000.000
30A35THR0-0.034-0.0108.9561.5651.5650.0000.0000.0000.000
31A36LYS10.9410.97312.61820.51120.5110.0000.0000.0000.000
32A37ASP-1-0.829-0.91315.618-14.400-14.4000.0000.0000.0000.000
33A38TYR00.006-0.00619.025-0.422-0.4220.0000.0000.0000.000
34A39GLY00.0250.01921.4930.1090.1090.0000.0000.0000.000
35A40VAL0-0.036-0.01315.7700.0370.0370.0000.0000.0000.000
36A41GLU-1-0.873-0.95018.894-12.801-12.8010.0000.0000.0000.000
37A42LEU00.0340.01517.431-0.969-0.9690.0000.0000.0000.000
38A43LYS10.8710.92216.96213.88913.8890.0000.0000.0000.000
39A44ASP-1-0.878-0.93415.600-17.160-17.1600.0000.0000.0000.000
40A45ILE0-0.011-0.02912.252-1.532-1.5320.0000.0000.0000.000
41A46LYS10.8440.93012.38919.07919.0790.0000.0000.0000.000
42A47ASP-1-0.873-0.92211.591-21.505-21.5050.0000.0000.0000.000
43A48MET0-0.044-0.0057.987-3.184-3.1840.0000.0000.0000.000
45A50ILE0-0.031-0.0186.369-5.228-5.2280.0000.0000.0000.000
46A51LYS10.8740.9376.68235.42435.4240.0000.0000.0000.000
47A52GLY00.0630.0229.7462.0832.0830.0000.0000.0000.000
48A53VAL0-0.051-0.01711.248-1.587-1.5870.0000.0000.0000.000
49A54ILE0-0.002-0.00213.1740.8040.8040.0000.0000.0000.000
50A55LEU0-0.0220.00315.703-0.193-0.1930.0000.0000.0000.000
51A56SER0-0.010-0.01919.0230.3090.3090.0000.0000.0000.000
52A57GLY00.0610.02220.4200.3560.3560.0000.0000.0000.000
53A58GLY0-0.002-0.01923.727-0.449-0.4490.0000.0000.0000.000
54A59PRO0-0.035-0.00926.5060.1960.1960.0000.0000.0000.000
55A60TYR00.0060.01127.8810.3800.3800.0000.0000.0000.000
56A61SER00.0700.04131.299-0.161-0.1610.0000.0000.0000.000
57A62VAL00.0410.01629.2220.0230.0230.0000.0000.0000.000
58A63THR0-0.039-0.03031.635-0.127-0.1270.0000.0000.0000.000
59A64GLU-1-0.957-0.96334.571-8.131-8.1310.0000.0000.0000.000
60A65ALA00.006-0.00734.206-0.255-0.2550.0000.0000.0000.000
61A66GLY0-0.020-0.01432.9750.0720.0720.0000.0000.0000.000
62A67SER0-0.017-0.01230.794-0.215-0.2150.0000.0000.0000.000
63A68PRO0-0.0440.00625.370-0.099-0.0990.0000.0000.0000.000
64A69HIS10.8510.90926.37110.54810.5480.0000.0000.0000.000
65A70LEU00.0090.00819.683-0.278-0.2780.0000.0000.0000.000
66A71LYS10.8990.95122.53013.40213.4020.0000.0000.0000.000
67A72LYS10.8920.93923.21610.78110.7810.0000.0000.0000.000
68A73GLU-1-0.888-0.94622.711-13.262-13.2620.0000.0000.0000.000
69A74VAL0-0.028-0.01118.008-0.552-0.5520.0000.0000.0000.000
70A75PHE00.0360.00519.451-0.776-0.7760.0000.0000.0000.000
71A76GLU-1-0.828-0.91321.108-12.004-12.0040.0000.0000.0000.000
72A77TYR00.0130.00714.0690.0960.0960.0000.0000.0000.000
73A78PHE00.004-0.01014.336-0.840-0.8400.0000.0000.0000.000
74A79LEU00.0250.02518.090-0.415-0.4150.0000.0000.0000.000
75A80GLU-1-0.927-0.96321.016-13.473-13.4730.0000.0000.0000.000
76A81LYS10.8630.92615.48516.90816.9080.0000.0000.0000.000
77A82LYS10.8130.91916.45113.83513.8350.0000.0000.0000.000
78A83ILE0-0.0270.00213.102-0.610-0.6100.0000.0000.0000.000
79A84PRO00.0020.00714.1120.9610.9610.0000.0000.0000.000
80A85ILE00.0020.00115.409-1.036-1.0360.0000.0000.0000.000
81A86PHE00.0160.00216.4330.7510.7510.0000.0000.0000.000
82A87GLY00.004-0.00218.575-0.353-0.3530.0000.0000.0000.000
83A88ILE00.016-0.00418.5520.2880.2880.0000.0000.0000.000
84A89CYS-1-0.799-0.79922.344-11.218-11.2180.0000.0000.0000.000
85A90TYR0-0.031-0.07725.3030.1420.1420.0000.0000.0000.000
86A91GLY00.0170.01222.4910.1120.1120.0000.0000.0000.000
87A92MET0-0.051-0.01723.495-0.295-0.2950.0000.0000.0000.000
88A93GLN00.0230.00625.3540.4720.4720.0000.0000.0000.000
89A94GLU-1-0.766-0.85824.249-11.283-11.2830.0000.0000.0000.000
90A95ILE0-0.019-0.01221.6680.0850.0850.0000.0000.0000.000
91A96ALA0-0.004-0.00125.9230.1870.1870.0000.0000.0000.000
92A97VAL00.0030.00429.6380.2280.2280.0000.0000.0000.000
93A98GLN0-0.087-0.03724.9900.0680.0680.0000.0000.0000.000
94A99MET0-0.060-0.02226.422-0.222-0.2220.0000.0000.0000.000
95A100ASN0-0.006-0.01229.9560.2750.2750.0000.0000.0000.000
96A101GLY00.0720.04832.3860.2690.2690.0000.0000.0000.000
97A102GLU-1-0.979-0.98733.596-7.926-7.9260.0000.0000.0000.000
98A103VAL0-0.007-0.01931.600-0.138-0.1380.0000.0000.0000.000
99A104LYS10.9120.96934.9547.7487.7480.0000.0000.0000.000
100A105LYS10.8790.91036.3998.2258.2250.0000.0000.0000.000
101A106SER0-0.0140.00236.2930.0480.0480.0000.0000.0000.000
102A107LYS10.8760.94838.7317.3217.3210.0000.0000.0000.000
103A108THR0-0.031-0.05140.4940.1900.1900.0000.0000.0000.000
104A109SER0-0.0130.01236.927-0.100-0.1000.0000.0000.0000.000
105A110GLU-1-0.739-0.83534.166-8.743-8.7430.0000.0000.0000.000
106A111TYR0-0.026-0.03732.542-0.338-0.3380.0000.0000.0000.000
107A112GLY00.0330.02932.5800.2410.2410.0000.0000.0000.000
108A113CYS0-0.062-0.03531.763-0.191-0.1910.0000.0000.0000.000
109A114THR0-0.0130.00232.0620.3680.3680.0000.0000.0000.000
110A115ASP-1-0.836-0.89432.056-9.183-9.1830.0000.0000.0000.000
111A116VAL0-0.046-0.03529.7280.1500.1500.0000.0000.0000.000
112A117ASN00.0200.02531.924-0.036-0.0360.0000.0000.0000.000
113A118ILE00.013-0.00228.192-0.143-0.1430.0000.0000.0000.000
114A119LEU0-0.051-0.02031.3690.2450.2450.0000.0000.0000.000
115A120ARG10.7270.81631.9088.9808.9800.0000.0000.0000.000
116A121ASN0-0.044-0.05634.6010.3110.3110.0000.0000.0000.000
117A122ASP-1-0.872-0.91936.757-8.479-8.4790.0000.0000.0000.000
118A123ASN0-0.021-0.01734.2680.2580.2580.0000.0000.0000.000
119A124ILE00.0510.02738.2190.0870.0870.0000.0000.0000.000
120A125ASN0-0.041-0.02839.8530.1910.1910.0000.0000.0000.000
121A126ASN0-0.050-0.02338.7590.0010.0010.0000.0000.0000.000
122A127ILE0-0.037-0.00137.013-0.021-0.0210.0000.0000.0000.000
123A128THR0-0.020-0.02241.0270.1090.1090.0000.0000.0000.000
124A129TYR00.0140.00237.1890.1760.1760.0000.0000.0000.000
125A130CYS0-0.0220.00043.267-0.001-0.0010.0000.0000.0000.000
126A131ARG10.8490.89644.2966.0526.0520.0000.0000.0000.000
127A132ASN0-0.051-0.02442.2700.2250.2250.0000.0000.0000.000
128A133PHE00.005-0.01039.230-0.056-0.0560.0000.0000.0000.000
129A134GLY00.0020.00243.8630.0380.0380.0000.0000.0000.000
130A135ASP-1-0.842-0.88246.796-6.023-6.0230.0000.0000.0000.000
131A136SER00.0070.00645.4600.0770.0770.0000.0000.0000.000
132A137SER00.0070.00147.6930.0460.0460.0000.0000.0000.000
133A138SER0-0.012-0.02447.7000.0210.0210.0000.0000.0000.000
134A139ALA00.0710.03142.298-0.073-0.0730.0000.0000.0000.000
135A140MET0-0.005-0.00843.056-0.109-0.1090.0000.0000.0000.000
136A141ASP-1-0.889-0.94144.661-6.624-6.6240.0000.0000.0000.000
137A142LEU00.0030.02740.694-0.071-0.0710.0000.0000.0000.000
138A143TYR0-0.009-0.03837.111-0.076-0.0760.0000.0000.0000.000
139A144SER0-0.047-0.01540.517-0.133-0.1330.0000.0000.0000.000
140A145ASN0-0.064-0.03341.4320.0460.0460.0000.0000.0000.000
141A146TYR0-0.027-0.01936.303-0.243-0.2430.0000.0000.0000.000
142A147LYS10.8420.92832.4209.7319.7310.0000.0000.0000.000
143A148LEU00.0550.03333.839-0.304-0.3040.0000.0000.0000.000
144A149MET0-0.045-0.01427.217-0.087-0.0870.0000.0000.0000.000
145A150ASN00.0210.01132.7320.3090.3090.0000.0000.0000.000
146A151GLU-1-0.876-0.92129.255-9.846-9.8460.0000.0000.0000.000
147A152THR00.0170.00126.8820.1460.1460.0000.0000.0000.000
148A153CYS0-0.0070.00725.024-0.528-0.5280.0000.0000.0000.000
149A154CYS00.0520.01321.0520.0520.0520.0000.0000.0000.000
150A155LEU00.0090.01519.064-0.493-0.4930.0000.0000.0000.000
151A156PHE0-0.006-0.02221.367-0.287-0.2870.0000.0000.0000.000
152A157GLU-1-0.858-0.91020.819-13.876-13.8760.0000.0000.0000.000
153A158ASN0-0.036-0.03221.7450.0470.0470.0000.0000.0000.000
154A159ILE0-0.0150.01624.2540.1090.1090.0000.0000.0000.000
155A160LYS10.9330.95926.78910.64310.6430.0000.0000.0000.000
156A161SER00.0000.01230.1300.3950.3950.0000.0000.0000.000
157A162ASP-1-0.734-0.81930.919-9.581-9.5810.0000.0000.0000.000
158A163ILE0-0.027-0.03032.4850.1350.1350.0000.0000.0000.000
159A164THR0-0.054-0.04127.365-0.223-0.2230.0000.0000.0000.000
160A165THR00.005-0.01429.7830.1410.1410.0000.0000.0000.000
161A166VAL0-0.025-0.02726.650-0.467-0.4670.0000.0000.0000.000
162A167TRP0-0.0040.00026.7640.4020.4020.0000.0000.0000.000
163A168MET0-0.0030.00827.950-0.494-0.4940.0000.0000.0000.000
164A169ASN0-0.041-0.04529.2650.3380.3380.0000.0000.0000.000
165A170HIS10.8260.89830.1639.0099.0090.0000.0000.0000.000
166A171ASN00.016-0.01232.3320.4300.4300.0000.0000.0000.000
167A172ASP-1-0.837-0.88133.038-8.537-8.5370.0000.0000.0000.000
168A173GLU-1-0.815-0.91633.219-8.467-8.4670.0000.0000.0000.000
169A174VAL00.0170.00530.2390.1000.1000.0000.0000.0000.000
170A175THR0-0.011-0.01233.5850.1270.1270.0000.0000.0000.000
171A176LYS10.8630.95735.9938.6708.6700.0000.0000.0000.000
172A177ILE00.0140.00231.733-0.238-0.2380.0000.0000.0000.000
173A178PRO00.0190.00929.0470.1590.1590.0000.0000.0000.000
174A179GLU-1-0.853-0.93231.008-9.200-9.2000.0000.0000.0000.000
175A180ASN0-0.038-0.03530.408-0.035-0.0350.0000.0000.0000.000
176A181PHE0-0.015-0.01325.414-0.245-0.2450.0000.0000.0000.000
177A182TYR0-0.020-0.01329.1180.3020.3020.0000.0000.0000.000
178A183LEU0-0.017-0.00229.986-0.345-0.3450.0000.0000.0000.000
179A184VAL00.010-0.01326.9120.1180.1180.0000.0000.0000.000
180A185SER0-0.030-0.02129.280-0.236-0.2360.0000.0000.0000.000
181A186SER0-0.014-0.01331.3660.0550.0550.0000.0000.0000.000
182A187SER00.044-0.00633.885-0.171-0.1710.0000.0000.0000.000
183A188GLU-1-0.907-0.96035.609-7.399-7.3990.0000.0000.0000.000
184A189ASN0-0.0360.00037.7440.3780.3780.0000.0000.0000.000
185A190CYS0-0.042-0.00433.847-0.174-0.1740.0000.0000.0000.000
186A191LEU00.0380.04535.323-0.132-0.1320.0000.0000.0000.000
187A192ILE0-0.0020.00631.510-0.174-0.1740.0000.0000.0000.000
188A193CYS0-0.0080.01531.013-0.355-0.3550.0000.0000.0000.000
189A194SER0-0.012-0.03425.904-0.494-0.4940.0000.0000.0000.000
190A195ILE0-0.011-0.00326.4330.3970.3970.0000.0000.0000.000
191A196TYR00.029-0.00223.066-0.282-0.2820.0000.0000.0000.000
192A197ASN0-0.015-0.00624.7950.1270.1270.0000.0000.0000.000
193A198LYS10.9490.98324.03010.31610.3160.0000.0000.0000.000
194A199GLU-1-0.825-0.90123.749-11.835-11.8350.0000.0000.0000.000
195A200TYR0-0.008-0.01122.614-0.261-0.2610.0000.0000.0000.000
196A201ASN00.0030.01418.217-0.249-0.2490.0000.0000.0000.000
197A202ILE0-0.0060.00519.497-0.812-0.8120.0000.0000.0000.000
198A203TYR00.000-0.02419.3920.7950.7950.0000.0000.0000.000
199A204GLY00.0020.00821.752-0.417-0.4170.0000.0000.0000.000
200A205VAL0-0.0260.00622.5920.3160.3160.0000.0000.0000.000
201A206GLN00.024-0.00925.281-0.299-0.2990.0000.0000.0000.000
202A207TYR00.041-0.00324.2620.2130.2130.0000.0000.0000.000
203A208HIS10.8170.83823.65411.30811.3080.0000.0000.0000.000
204A209PRO00.0300.03520.2080.2020.2020.0000.0000.0000.000
205A210GLU-1-0.794-0.90719.063-13.570-13.5700.0000.0000.0000.000
206A211VAL0-0.025-0.00520.218-0.196-0.1960.0000.0000.0000.000
207A212TYR0-0.009-0.02319.485-0.256-0.2560.0000.0000.0000.000
208A213GLU-1-0.879-0.94224.372-9.914-9.9140.0000.0000.0000.000
209A214SER0-0.051-0.01723.8670.4460.4460.0000.0000.0000.000
210A215LEU00.0010.01224.024-0.618-0.6180.0000.0000.0000.000
211A216ASP-1-0.821-0.88623.955-11.611-11.6110.0000.0000.0000.000
212A217GLY00.0120.00021.610-0.508-0.5080.0000.0000.0000.000
213A218GLU-1-0.871-0.94016.842-16.504-16.5040.0000.0000.0000.000
214A219LEU0-0.0140.00817.296-1.079-1.0790.0000.0000.0000.000
215A220MET00.0210.04918.616-0.543-0.5430.0000.0000.0000.000
216A221PHE00.019-0.00914.183-0.734-0.7340.0000.0000.0000.000
217A222TYR0-0.020-0.00913.686-1.487-1.4870.0000.0000.0000.000
218A223ASN0-0.026-0.02814.542-1.499-1.4990.0000.0000.0000.000
219A224PHE00.0300.00713.326-0.571-0.5710.0000.0000.0000.000
220A225ALA00.0160.0099.846-0.829-0.8290.0000.0000.0000.000
221A226TYR0-0.041-0.0359.193-2.733-2.7330.0000.0000.0000.000
222A227ASN0-0.010-0.01912.500-1.049-1.0490.0000.0000.0000.000
223A228ILE0-0.0420.00215.5270.5280.5280.0000.0000.0000.000
224A229CYS0-0.042-0.01911.2430.2800.2800.0000.0000.0000.000
225A230LYS10.8120.91611.29617.17417.1740.0000.0000.0000.000
226A231CYS0-0.044-0.0086.790-2.610-2.6100.0000.0000.0000.000
227A232LYS10.8280.9025.23045.74945.7490.0000.0000.0000.000