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: VYVY1

Calculation Name: 2FCK-A-Xray547

Preferred Name:

Target Type:

Ligand Name: nitrate ion

Ligand 3-letter code: NO3

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2FCK

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

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 178
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1996328.286981
FMO2-HF: Nuclear repulsion 1923990.189943
FMO2-HF: Total energy -72338.097038
FMO2-MP2: Total energy -72547.606293


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.
-112.281-103.2029.561-5.139-13.503-0.057
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 : 0.818 / q_NPA : 0.920
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].
3A3PRO00.0470.0203.862-0.4801.044-0.018-0.634-0.8720.001
5A5PHE0-0.100-0.0402.545-1.4610.9991.736-0.962-3.234-0.011
6A6GLN00.0510.0205.1254.2904.317-0.001-0.004-0.0220.000
7A7ILE0-0.0280.0084.765-0.840-0.722-0.001-0.003-0.1140.000
62A62TRP0-0.0090.0074.006-3.252-2.6860.001-0.094-0.4740.000
63A63VAL0-0.106-0.0704.958-6.236-6.171-0.001-0.002-0.0620.000
65A65ALA0-0.049-0.0194.5380.3910.490-0.001-0.008-0.0900.000
68A68TYR0-0.030-0.0172.438-14.690-11.3904.510-2.428-5.383-0.036
70A70PHE0-0.045-0.0333.155-1.283-0.9800.022-0.047-0.2780.000
86A86ILE00.0270.0194.5001.0201.095-0.001-0.003-0.0710.000
89A89PHE0-0.033-0.0164.571-1.060-0.979-0.001-0.002-0.0780.000
122A122PHE0-0.013-0.0182.250-2.384-2.6443.299-0.806-2.234-0.011
126A126ARG10.8700.9354.19741.16441.4690.006-0.066-0.2440.000
127A127LEU0-0.079-0.0403.667-3.737-3.3210.011-0.080-0.3470.000
4A4ASP-1-0.883-0.9316.780-29.476-29.4760.0000.0000.0000.000
8A8VAL0-0.031-0.0137.9901.5071.5070.0000.0000.0000.000
9A9THR0-0.012-0.03111.8310.1120.1120.0000.0000.0000.000
10A10GLN0-0.009-0.00714.7700.1270.1270.0000.0000.0000.000
11A11ARG10.7860.86518.14012.90712.9070.0000.0000.0000.000
12A12LEU0-0.0160.00914.7020.2880.2880.0000.0000.0000.000
13A13GLN00.0140.00212.1240.4090.4090.0000.0000.0000.000
14A14LEU0-0.0150.0128.4620.7610.7610.0000.0000.0000.000
15A15ARG10.7860.8478.08117.16617.1660.0000.0000.0000.000
16A16LEU00.0450.0277.4211.4291.4290.0000.0000.0000.000
17A17ILE0-0.0140.0089.6731.1371.1370.0000.0000.0000.000
18A18THR0-0.052-0.05213.160-0.701-0.7010.0000.0000.0000.000
19A19ALA0-0.007-0.02614.9300.6610.6610.0000.0000.0000.000
20A20ASP-1-0.892-0.93917.727-14.306-14.3060.0000.0000.0000.000
21A21GLU-1-0.771-0.82015.904-17.856-17.8560.0000.0000.0000.000
22A22ALA00.022-0.00219.566-0.040-0.0400.0000.0000.0000.000
23A23GLU-1-0.942-0.95921.229-10.722-10.7220.0000.0000.0000.000
24A24GLU-1-0.846-0.93620.290-13.254-13.2540.0000.0000.0000.000
25A25LEU0-0.022-0.00817.4250.1190.1190.0000.0000.0000.000
26A26VAL00.008-0.00120.5890.3380.3380.0000.0000.0000.000
27A27GLN0-0.046-0.02324.2460.4450.4450.0000.0000.0000.000
28A28CYS0-0.082-0.04720.8500.3090.3090.0000.0000.0000.000
29A29ILE0-0.0140.00921.2100.2430.2430.0000.0000.0000.000
30A30ARG10.8340.90424.61710.67010.6700.0000.0000.0000.000
31A31GLN0-0.035-0.00826.5400.5250.5250.0000.0000.0000.000
32A32SER0-0.061-0.04425.4510.1500.1500.0000.0000.0000.000
33A33GLN0-0.002-0.00327.5920.1370.1370.0000.0000.0000.000
34A34THR0-0.039-0.03727.2140.0800.0800.0000.0000.0000.000
35A35LEU00.004-0.00321.560-0.099-0.0990.0000.0000.0000.000
36A36HIS0-0.013-0.01324.436-0.341-0.3410.0000.0000.0000.000
37A37GLN0-0.0040.00126.537-0.011-0.0110.0000.0000.0000.000
38A38TRP0-0.009-0.01023.282-0.038-0.0380.0000.0000.0000.000
39A39VAL0-0.034-0.01519.344-0.493-0.4930.0000.0000.0000.000
40A40ASP-1-0.818-0.90321.053-11.959-11.9590.0000.0000.0000.000
41A41TRP00.0280.01518.2110.0010.0010.0000.0000.0000.000
42A42CYS0-0.068-0.02418.7520.2560.2560.0000.0000.0000.000
43A43HIS00.0400.01822.4740.2930.2930.0000.0000.0000.000
44A44ALA00.0430.01026.0800.1000.1000.0000.0000.0000.000
45A45LEU0-0.0030.00629.684-0.043-0.0430.0000.0000.0000.000
46A46PHE0-0.038-0.00321.2490.0750.0750.0000.0000.0000.000
47A47SER00.0570.02027.104-0.023-0.0230.0000.0000.0000.000
48A48GLN00.029-0.00724.779-0.056-0.0560.0000.0000.0000.000
49A49GLN00.0180.01123.790-0.234-0.2340.0000.0000.0000.000
50A50GLU-1-0.887-0.94523.311-12.789-12.7890.0000.0000.0000.000
51A51ALA0-0.020-0.00120.633-0.675-0.6750.0000.0000.0000.000
52A52GLU-1-0.863-0.93619.167-13.443-13.4430.0000.0000.0000.000
53A53GLN0-0.019-0.00318.771-0.991-0.9910.0000.0000.0000.000
54A54PHE00.0440.01114.872-0.941-0.9410.0000.0000.0000.000
55A55ILE0-0.0200.00514.762-1.346-1.3460.0000.0000.0000.000
56A56GLN0-0.034-0.02213.912-1.566-1.5660.0000.0000.0000.000
57A57ALA00.0190.00813.872-1.373-1.3730.0000.0000.0000.000
58A58THR0-0.026-0.01510.139-1.462-1.4620.0000.0000.0000.000
59A59ARG10.9580.9749.44422.19122.1910.0000.0000.0000.000
60A60LEU0-0.037-0.0189.054-2.742-2.7420.0000.0000.0000.000
61A61ASN00.0480.00510.002-1.131-1.1310.0000.0000.0000.000
64A64LYS10.7970.8996.77521.36521.3650.0000.0000.0000.000
66A66GLU-1-0.841-0.8985.897-22.028-22.0280.0000.0000.0000.000
67A67ALA00.0080.0037.9841.3281.3280.0000.0000.0000.000
69A69GLY00.0490.0175.7702.1302.1300.0000.0000.0000.000
71A71GLY00.0480.0239.0831.9581.9580.0000.0000.0000.000
72A72VAL0-0.053-0.02911.779-1.052-1.0520.0000.0000.0000.000
73A73PHE00.0570.02213.0841.0871.0870.0000.0000.0000.000
74A74GLU-1-0.777-0.84616.046-12.568-12.5680.0000.0000.0000.000
75A75ARG10.8550.91215.98116.21616.2160.0000.0000.0000.000
76A76GLN0-0.055-0.02918.8510.2060.2060.0000.0000.0000.000
77A77THR0-0.039-0.05021.9530.1100.1100.0000.0000.0000.000
78A78GLN00.0000.01116.560-0.343-0.3430.0000.0000.0000.000
79A79THR00.0090.01620.089-0.202-0.2020.0000.0000.0000.000
80A80LEU00.0400.03115.714-0.547-0.5470.0000.0000.0000.000
81A81VAL0-0.015-0.01917.3570.6660.6660.0000.0000.0000.000
82A82GLY00.012-0.01117.4920.6630.6630.0000.0000.0000.000
83A83MET0-0.0240.00111.903-0.394-0.3940.0000.0000.0000.000
84A84VAL0-0.019-0.0209.6021.1581.1580.0000.0000.0000.000
85A85ALA0-0.004-0.0019.012-1.618-1.6180.0000.0000.0000.000
87A87ASN0-0.053-0.0458.446-1.544-1.5440.0000.0000.0000.000
88A88GLU-1-0.847-0.92610.591-19.572-19.5720.0000.0000.0000.000
90A90TYR00.0150.00110.7921.0231.0230.0000.0000.0000.000
91A91HIS00.0670.0238.4562.4222.4220.0000.0000.0000.000
92A92THR0-0.043-0.01713.4990.1220.1220.0000.0000.0000.000
93A93PHE0-0.030-0.02416.2270.9140.9140.0000.0000.0000.000
94A94ASN0-0.043-0.02812.915-0.856-0.8560.0000.0000.0000.000
95A95MET0-0.0010.01813.2320.2580.2580.0000.0000.0000.000
96A96ALA00.0200.0109.558-1.077-1.0770.0000.0000.0000.000
97A97SER0-0.0110.01111.4971.4551.4550.0000.0000.0000.000
98A98LEU00.017-0.0089.933-1.596-1.5960.0000.0000.0000.000
99A99GLY0-0.0050.00212.4631.3451.3450.0000.0000.0000.000
100A100TYR0-0.056-0.05613.057-0.979-0.9790.0000.0000.0000.000
101A101TRP00.0340.01915.3611.0691.0690.0000.0000.0000.000
102A102ILE0-0.0070.00415.643-0.366-0.3660.0000.0000.0000.000
103A103GLY00.0910.05519.5100.5570.5570.0000.0000.0000.000
104A104ASP-1-0.784-0.86322.764-10.626-10.6260.0000.0000.0000.000
105A105ARG10.8260.91325.43110.54210.5420.0000.0000.0000.000
106A106TYR00.0690.03521.2200.1690.1690.0000.0000.0000.000
107A107GLN0-0.048-0.03221.529-0.018-0.0180.0000.0000.0000.000
108A108ARG10.9290.97523.0899.6819.6810.0000.0000.0000.000
109A109GLN00.0150.02423.5690.2930.2930.0000.0000.0000.000
110A110GLY00.0310.01222.349-0.172-0.1720.0000.0000.0000.000
111A111TYR0-0.053-0.06118.601-0.432-0.4320.0000.0000.0000.000
112A112GLY00.0360.01517.168-0.679-0.6790.0000.0000.0000.000
113A113LYS10.9330.96116.65111.81011.8100.0000.0000.0000.000
114A114GLU-1-0.757-0.81815.912-14.912-14.9120.0000.0000.0000.000
115A115ALA00.0470.01612.854-0.745-0.7450.0000.0000.0000.000
116A116LEU00.0320.01011.796-1.210-1.2100.0000.0000.0000.000
117A117THR0-0.020-0.03312.550-0.375-0.3750.0000.0000.0000.000
118A118ALA0-0.0020.00510.720-0.449-0.4490.0000.0000.0000.000
119A119LEU0-0.0060.0036.448-1.562-1.5620.0000.0000.0000.000
120A120ILE00.0300.0198.472-1.434-1.4340.0000.0000.0000.000
121A121LEU00.0170.00910.957-0.299-0.2990.0000.0000.0000.000
123A123CYS0-0.042-0.0387.384-2.065-2.0650.0000.0000.0000.000
124A124PHE00.0160.0088.356-0.036-0.0360.0000.0000.0000.000
125A125GLU-1-0.919-0.96310.960-18.237-18.2370.0000.0000.0000.000
128A128GLU-1-0.918-0.9377.771-21.116-21.1160.0000.0000.0000.000
129A129LEU0-0.0340.0048.0681.2411.2410.0000.0000.0000.000
130A130THR00.0240.00511.8780.6240.6240.0000.0000.0000.000
131A131ARG10.7210.81214.56414.28014.2800.0000.0000.0000.000
132A132LEU0-0.0240.00010.450-1.181-1.1810.0000.0000.0000.000
133A133GLU-1-0.808-0.88714.314-12.734-12.7340.0000.0000.0000.000
134A134ILE00.0050.01015.331-0.770-0.7700.0000.0000.0000.000
135A135VAL0-0.006-0.00417.3150.7010.7010.0000.0000.0000.000
136A136CYS0-0.057-0.00619.843-0.256-0.2560.0000.0000.0000.000
137A137ASP-1-0.748-0.88122.459-10.173-10.1730.0000.0000.0000.000
138A138PRO0-0.018-0.02825.2600.0410.0410.0000.0000.0000.000
139A139GLU-1-0.901-0.93828.497-8.700-8.7000.0000.0000.0000.000
140A140ASN0-0.0120.01623.2990.2580.2580.0000.0000.0000.000
141A141VAL00.0500.02125.579-0.368-0.3680.0000.0000.0000.000
142A142PRO0-0.014-0.01525.250-0.151-0.1510.0000.0000.0000.000
143A143SER0-0.011-0.01221.106-0.351-0.3510.0000.0000.0000.000
144A144GLN0-0.004-0.00721.778-0.218-0.2180.0000.0000.0000.000
145A145ALA0-0.001-0.00723.939-0.073-0.0730.0000.0000.0000.000
146A146LEU0-0.077-0.03718.4540.0610.0610.0000.0000.0000.000
147A147ALA00.0750.04419.447-0.361-0.3610.0000.0000.0000.000
148A148LEU0-0.0010.01120.519-0.089-0.0890.0000.0000.0000.000
149A149ARG10.9020.96422.52011.32311.3230.0000.0000.0000.000
150A150CYS0-0.088-0.04617.403-0.078-0.0780.0000.0000.0000.000
151A151GLY00.0180.02218.844-0.424-0.4240.0000.0000.0000.000
152A152ALA0-0.0010.00819.007-0.056-0.0560.0000.0000.0000.000
153A153ASN0-0.005-0.00420.7250.9150.9150.0000.0000.0000.000
154A154ARG10.9190.96123.1599.5119.5110.0000.0000.0000.000
155A155GLU-1-0.764-0.82523.228-11.712-11.7120.0000.0000.0000.000
156A156GLN00.0020.00126.0890.2750.2750.0000.0000.0000.000
157A157LEU0-0.024-0.00726.347-0.289-0.2890.0000.0000.0000.000
158A158ALA00.0130.00625.4390.2830.2830.0000.0000.0000.000
159A159PRO00.021-0.00727.247-0.157-0.1570.0000.0000.0000.000
160A160ASN0-0.008-0.01927.249-0.094-0.0940.0000.0000.0000.000
161A161ARG10.8680.94118.08513.39813.3980.0000.0000.0000.000
162A162PHE0-0.014-0.00620.876-0.633-0.6330.0000.0000.0000.000
163A163LEU00.0070.00521.7100.4960.4960.0000.0000.0000.000
164A164TYR0-0.026-0.01722.551-0.211-0.2110.0000.0000.0000.000
165A165ALA00.0180.00524.6140.4310.4310.0000.0000.0000.000
166A166GLY0-0.032-0.00924.7470.2340.2340.0000.0000.0000.000
167A167GLU-1-0.946-0.96325.798-9.233-9.2330.0000.0000.0000.000
168A168PRO0-0.048-0.03926.306-0.297-0.2970.0000.0000.0000.000
169A169LYS10.9180.96626.20210.93610.9360.0000.0000.0000.000
170A170ALA0-0.022-0.01726.345-0.259-0.2590.0000.0000.0000.000
171A171GLY00.0270.01124.533-0.018-0.0180.0000.0000.0000.000
172A172ILE0-0.076-0.03125.0240.2140.2140.0000.0000.0000.000
173A173VAL00.0120.01320.743-0.449-0.4490.0000.0000.0000.000
174A174PHE0-0.007-0.02520.4970.6350.6350.0000.0000.0000.000
175A175SER0-0.028-0.03318.811-0.645-0.6450.0000.0000.0000.000
176A176LEU0-0.017-0.00815.2140.4260.4260.0000.0000.0000.000
177A177ILE0-0.029-0.02317.059-0.385-0.3850.0000.0000.0000.000
178A178PRO-1-0.898-0.92715.377-13.404-13.4040.0000.0000.0000.000