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: RLY78

Calculation Name: 2CWA-A-Xray547

Preferred Name:

Target Type:

Ligand Name: nitrate ion

Ligand 3-letter code: NO3

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2CWA

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLP9

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 226
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2804159.73194
FMO2-HF: Nuclear repulsion 2714014.662866
FMO2-HF: Total energy -90145.069074
FMO2-MP2: Total energy -90412.35487


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:3:ARG)


Summations of interaction energy for fragment #1(A:3:ARG)
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.
-95.399-85.6338.98-7.06-11.685-0.076
Interaction energy analysis for fragmet #1(A:3:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.783 / q_NPA : 1.877
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].
3A5LEU0-0.101-0.0552.068-35.844-30.6514.692-4.286-5.600-0.047
4A6ASN00.010-0.0064.3438.4348.6070.000-0.036-0.1360.000
132A134MET0-0.058-0.0292.819-11.641-9.5003.168-1.787-3.522-0.024
133A135GLY00.0170.0043.656-6.865-6.6690.001-0.084-0.1120.000
134A136ASN0-0.044-0.0243.487-21.245-20.5760.004-0.269-0.404-0.002
224A226PRO0-0.078-0.0284.7130.6930.801-0.001-0.008-0.0990.000
226A228ARG00.0410.0332.37918.03219.3181.116-0.590-1.812-0.003
5A7ARG10.9370.9864.97164.21164.2110.0000.0000.0000.000
6A8VAL00.0000.0029.1060.0000.0000.0000.0000.0000.000
7A9PHE00.0040.0009.748-0.379-0.3790.0000.0000.0000.000
8A10LEU0-0.022-0.00714.8750.5310.5310.0000.0000.0000.000
9A11ILE00.012-0.00118.6690.2430.2430.0000.0000.0000.000
10A12GLY00.0190.00621.7710.0840.0840.0000.0000.0000.000
11A13ALA00.0100.01225.0720.2280.2280.0000.0000.0000.000
12A14LEU0-0.0200.00126.435-0.584-0.5840.0000.0000.0000.000
13A15ALA00.0510.01929.3320.7100.7100.0000.0000.0000.000
14A16THR0-0.014-0.02231.4130.5770.5770.0000.0000.0000.000
15A17ARG10.9240.97231.82216.34016.3400.0000.0000.0000.000
16A18PRO0-0.051-0.01328.923-0.100-0.1000.0000.0000.0000.000
17A19ASP-1-0.878-0.93829.995-18.336-18.3360.0000.0000.0000.000
18A20MET0-0.025-0.00528.627-0.874-0.8740.0000.0000.0000.000
19A21ARG10.9020.95528.14821.21221.2120.0000.0000.0000.000
20A22TYR00.0700.02630.178-0.703-0.7030.0000.0000.0000.000
21A23THR0-0.044-0.01728.3840.4510.4510.0000.0000.0000.000
22A24PRO00.034-0.00231.4670.1630.1630.0000.0000.0000.000
23A25ALA0-0.035-0.00830.3600.3220.3220.0000.0000.0000.000
24A26GLY00.0360.02431.063-0.257-0.2570.0000.0000.0000.000
25A27LEU0-0.057-0.02124.024-0.316-0.3160.0000.0000.0000.000
26A28ALA00.0700.04227.1330.1950.1950.0000.0000.0000.000
27A29ILE0-0.068-0.05025.024-1.225-1.2250.0000.0000.0000.000
28A30LEU00.0530.03425.3690.7620.7620.0000.0000.0000.000
29A31ASP-1-0.827-0.86924.916-24.403-24.4030.0000.0000.0000.000
30A32LEU00.0430.01723.6610.8580.8580.0000.0000.0000.000
31A33THR00.008-0.00625.684-0.826-0.8260.0000.0000.0000.000
32A34LEU00.0070.02021.8360.5980.5980.0000.0000.0000.000
33A35ALA00.003-0.00725.746-0.401-0.4010.0000.0000.0000.000
34A36GLY00.0210.00326.2390.2210.2210.0000.0000.0000.000
35A37GLN0-0.032-0.01127.2340.2290.2290.0000.0000.0000.000
36A38ASP-1-0.826-0.92324.815-23.614-23.6140.0000.0000.0000.000
37A39LEU0-0.0110.01027.5110.1160.1160.0000.0000.0000.000
38A40LEU0-0.0090.00121.761-0.212-0.2120.0000.0000.0000.000
39A41LEU00.0060.01026.413-0.283-0.2830.0000.0000.0000.000
40A42SER0-0.061-0.04023.446-0.662-0.6620.0000.0000.0000.000
41A43ASP-1-0.853-0.92324.859-23.583-23.5830.0000.0000.0000.000
42A44ASN00.0360.02727.6390.9990.9990.0000.0000.0000.000
43A45GLY00.033-0.00129.752-0.029-0.0290.0000.0000.0000.000
44A46GLY0-0.029-0.01832.2840.2570.2570.0000.0000.0000.000
45A47GLU-1-0.870-0.94333.164-18.653-18.6530.0000.0000.0000.000
46A48ARG10.8000.88125.00423.63023.6300.0000.0000.0000.000
47A49GLU-1-0.779-0.86330.345-19.605-19.6050.0000.0000.0000.000
48A50VAL0-0.071-0.03925.091-0.219-0.2190.0000.0000.0000.000
49A51SER0-0.020-0.01127.430-0.231-0.2310.0000.0000.0000.000
50A52TRP0-0.044-0.02923.008-0.762-0.7620.0000.0000.0000.000
51A53TYR00.001-0.04026.5940.3390.3390.0000.0000.0000.000
52A54HIS0-0.057-0.03221.677-0.156-0.1560.0000.0000.0000.000
53A55ARG10.8630.94724.03723.77923.7790.0000.0000.0000.000
54A56VAL0-0.013-0.01019.560-1.331-1.3310.0000.0000.0000.000
55A57ARG10.8010.87820.60426.01126.0110.0000.0000.0000.000
56A58LEU00.0180.01619.982-1.672-1.6720.0000.0000.0000.000
57A59LEU0-0.028-0.03320.0030.6060.6060.0000.0000.0000.000
58A60GLY00.0170.00722.455-0.481-0.4810.0000.0000.0000.000
59A61ARG10.9960.97718.93926.93026.9300.0000.0000.0000.000
60A62GLN00.0170.02019.4550.3040.3040.0000.0000.0000.000
61A63ALA0-0.016-0.00222.8480.0060.0060.0000.0000.0000.000
62A64GLU-1-0.918-0.98225.337-20.131-20.1310.0000.0000.0000.000
63A65MET0-0.067-0.01923.4640.3530.3530.0000.0000.0000.000
64A66TRP00.015-0.01423.4870.7410.7410.0000.0000.0000.000
65A67GLY00.0070.00228.3200.1810.1810.0000.0000.0000.000
66A68ASP-1-0.950-0.98031.072-16.755-16.7550.0000.0000.0000.000
67A69LEU0-0.018-0.00730.7530.4150.4150.0000.0000.0000.000
68A70LEU0-0.060-0.01326.837-0.100-0.1000.0000.0000.0000.000
69A71ASP-1-0.792-0.91031.474-16.362-16.3620.0000.0000.0000.000
70A72GLN0-0.051-0.03432.333-0.298-0.2980.0000.0000.0000.000
71A73GLY0-0.016-0.00732.6210.3820.3820.0000.0000.0000.000
72A74GLN0-0.030-0.00928.8450.3770.3770.0000.0000.0000.000
73A75LEU0-0.0020.00327.278-0.520-0.5200.0000.0000.0000.000
74A76VAL00.0240.00823.7610.2210.2210.0000.0000.0000.000
75A77PHE00.0120.00415.247-0.609-0.6090.0000.0000.0000.000
76A78VAL0-0.006-0.00717.1420.4700.4700.0000.0000.0000.000
77A79GLU-1-0.880-0.92910.835-43.752-43.7520.0000.0000.0000.000
78A80GLY00.0310.00013.3571.8101.8100.0000.0000.0000.000
79A81ARG10.7320.86710.53837.16937.1690.0000.0000.0000.000
80A82LEU00.0220.01412.0113.4403.4400.0000.0000.0000.000
81A83GLU-1-0.855-0.91312.954-38.498-38.4980.0000.0000.0000.000
82A84TYR00.0480.01514.7412.4902.4900.0000.0000.0000.000
83A85ARG10.9020.95516.52128.26128.2610.0000.0000.0000.000
84A86GLN00.0670.04519.3570.7450.7450.0000.0000.0000.000
85A87TRP0-0.055-0.03621.920-0.115-0.1150.0000.0000.0000.000
86A88GLU-1-0.858-0.90725.725-20.543-20.5430.0000.0000.0000.000
87A89ARG10.8230.88028.78619.20919.2090.0000.0000.0000.000
88A90GLU-1-0.944-0.97331.305-18.938-18.9380.0000.0000.0000.000
89A91GLY00.0200.01932.4380.4890.4890.0000.0000.0000.000
90A92GLU-1-0.886-0.93826.010-23.422-23.4220.0000.0000.0000.000
91A93ARG10.7880.86924.51922.58822.5880.0000.0000.0000.000
92A94ARG10.8500.91723.60423.40723.4070.0000.0000.0000.000
93A95SER00.0290.01519.659-0.038-0.0380.0000.0000.0000.000
94A96GLU-1-0.846-0.91720.420-24.361-24.3610.0000.0000.0000.000
95A97LEU0-0.049-0.01815.865-1.852-1.8520.0000.0000.0000.000
96A98GLN0-0.044-0.01718.6602.8162.8160.0000.0000.0000.000
97A99ILE00.0390.01816.637-2.368-2.3680.0000.0000.0000.000
98A100ARG10.8150.90015.46434.57834.5780.0000.0000.0000.000
99A101ALA00.0640.03215.334-2.327-2.3270.0000.0000.0000.000
100A102ASP-1-0.837-0.89113.001-37.948-37.9480.0000.0000.0000.000
101A103PHE0-0.032-0.02014.0501.3051.3050.0000.0000.0000.000
102A104LEU0-0.004-0.00817.995-0.615-0.6150.0000.0000.0000.000
103A105ASP-1-0.868-0.92120.016-25.978-25.9780.0000.0000.0000.000
104A106PRO0-0.0040.00322.935-0.193-0.1930.0000.0000.0000.000
105A107LEU0-0.048-0.03122.929-0.122-0.1220.0000.0000.0000.000
106A108ASP-1-0.829-0.92127.048-17.522-17.5220.0000.0000.0000.000
107A109ASP-1-0.835-0.90229.249-18.062-18.0620.0000.0000.0000.000
108A110ARG10.9380.97131.50818.00318.0030.0000.0000.0000.000
109A111GLY0-0.051-0.03231.954-0.456-0.4560.0000.0000.0000.000
110A112LYS10.8860.95727.56319.75819.7580.0000.0000.0000.000
111A113GLU-1-0.836-0.90431.717-16.414-16.4140.0000.0000.0000.000
112A114ARG10.7630.84331.97117.22917.2290.0000.0000.0000.000
113A115ALA0-0.0100.00833.4740.5080.5080.0000.0000.0000.000
114A116GLU-1-0.905-0.95934.885-15.759-15.7590.0000.0000.0000.000
115A117ASP-1-0.759-0.83634.806-17.668-17.6680.0000.0000.0000.000
116A118SER0-0.002-0.02037.4160.2110.2110.0000.0000.0000.000
117A119ARG10.7750.87834.07018.04518.0450.0000.0000.0000.000
118A120GLY00.0560.04839.5680.0950.0950.0000.0000.0000.000
119A121GLN0-0.045-0.01933.972-0.358-0.3580.0000.0000.0000.000
120A122PRO0-0.0100.01032.922-0.078-0.0780.0000.0000.0000.000
121A123ARG10.8090.88930.24218.81418.8140.0000.0000.0000.000
122A124LEU0-0.0210.00025.4950.5250.5250.0000.0000.0000.000
123A125ARG10.8740.91428.69717.21017.2100.0000.0000.0000.000
124A126ALA00.0060.01226.9610.0430.0430.0000.0000.0000.000
125A127ALA0-0.047-0.00824.516-0.389-0.3890.0000.0000.0000.000
126A128LEU00.0020.01216.769-0.516-0.5160.0000.0000.0000.000
127A129ASN0-0.024-0.03619.005-1.471-1.4710.0000.0000.0000.000
128A130GLN00.0230.01813.4190.9170.9170.0000.0000.0000.000
129A131VAL0-0.017-0.01211.549-0.624-0.6240.0000.0000.0000.000
130A132PHE00.0080.0057.794-0.504-0.5040.0000.0000.0000.000
131A133LEU0-0.004-0.0068.191-2.585-2.5850.0000.0000.0000.000
135A137LEU00.0240.0296.0803.8493.8490.0000.0000.0000.000
136A138THR0-0.039-0.0409.9442.2162.2160.0000.0000.0000.000
137A139ARG10.6590.76212.23433.96833.9680.0000.0000.0000.000
138A140ASP-1-0.807-0.90114.491-33.996-33.9960.0000.0000.0000.000
139A141PRO0-0.025-0.00915.5300.4500.4500.0000.0000.0000.000
140A142GLU-1-0.833-0.88017.700-27.096-27.0960.0000.0000.0000.000
141A143LEU0-0.020-0.00720.922-0.166-0.1660.0000.0000.0000.000
142A144ARG10.9140.95522.91522.41922.4190.0000.0000.0000.000
143A145TYR00.004-0.02726.213-0.459-0.4590.0000.0000.0000.000
144A146THR0-0.064-0.02729.0040.4890.4890.0000.0000.0000.000
145A147PRO00.029-0.00431.4370.0970.0970.0000.0000.0000.000
146A148GLN0-0.025-0.00633.7640.3160.3160.0000.0000.0000.000
147A149GLY00.0400.03232.3480.0050.0050.0000.0000.0000.000
148A150THR0-0.036-0.01627.453-0.352-0.3520.0000.0000.0000.000
149A151ALA00.0590.04524.6230.0060.0060.0000.0000.0000.000
150A152VAL0-0.051-0.03723.140-0.404-0.4040.0000.0000.0000.000
151A153ALA00.0160.02718.9120.3830.3830.0000.0000.0000.000
152A154ARG10.8740.93018.52526.00526.0050.0000.0000.0000.000
153A155LEU00.0660.03413.155-0.140-0.1400.0000.0000.0000.000
154A156GLY00.1060.05913.971-0.175-0.1750.0000.0000.0000.000
155A157LEU0-0.055-0.0016.956-1.495-1.4950.0000.0000.0000.000
156A158ALA00.0190.0088.0223.3163.3160.0000.0000.0000.000
157A159VAL0-0.023-0.0195.946-10.066-10.0660.0000.0000.0000.000
158A160ASN00.0010.0125.2677.9107.9100.0000.0000.0000.000
159A161GLU-1-0.807-0.8865.230-67.039-67.0390.0000.0000.0000.000
160A162ARG10.9190.9637.44350.93650.9360.0000.0000.0000.000
161A163ARG10.8920.95110.15132.61732.6170.0000.0000.0000.000
162A164GLN00.019-0.00412.801-0.199-0.1990.0000.0000.0000.000
163A165GLY0-0.005-0.01414.5132.3272.3270.0000.0000.0000.000
164A166ALA0-0.047-0.01413.8921.0341.0340.0000.0000.0000.000
165A167GLU-1-0.755-0.86214.018-36.231-36.2310.0000.0000.0000.000
166A168GLU-1-0.918-0.9537.753-62.675-62.6750.0000.0000.0000.000
167A169ARG10.7460.82710.40749.03749.0370.0000.0000.0000.000
168A170THR0-0.008-0.0208.981-3.800-3.8000.0000.0000.0000.000
169A171HIS0-0.027-0.0159.8366.8346.8340.0000.0000.0000.000
170A172PHE00.0060.00110.406-4.071-4.0710.0000.0000.0000.000
171A173VAL0-0.023-0.01611.9262.1662.1660.0000.0000.0000.000
172A174GLU-1-0.794-0.85413.419-34.775-34.7750.0000.0000.0000.000
173A175VAL0-0.035-0.02212.1520.4710.4710.0000.0000.0000.000
174A176GLN00.0200.02415.5311.1011.1010.0000.0000.0000.000
175A177ALA00.0160.00817.283-1.160-1.1600.0000.0000.0000.000
176A178TRP00.000-0.02719.2871.6051.6050.0000.0000.0000.000
177A179ARG10.8040.89922.15422.06822.0680.0000.0000.0000.000
178A180ASP-1-0.771-0.89422.861-25.133-25.1330.0000.0000.0000.000
179A181LEU0-0.041-0.00916.213-1.061-1.0610.0000.0000.0000.000
180A182ALA0-0.052-0.04018.064-1.756-1.7560.0000.0000.0000.000
181A183GLU-1-0.845-0.91519.861-23.774-23.7740.0000.0000.0000.000
182A184TRP00.0410.01911.873-1.439-1.4390.0000.0000.0000.000
183A185ALA0-0.012-0.01615.493-1.188-1.1880.0000.0000.0000.000
184A186ALA0-0.015-0.00716.214-1.038-1.0380.0000.0000.0000.000
185A187GLU-1-0.947-0.95917.612-28.035-28.0350.0000.0000.0000.000
186A188LEU0-0.068-0.01411.600-1.165-1.1650.0000.0000.0000.000
187A189ARG10.8570.90113.46332.91932.9190.0000.0000.0000.000
188A190LYS10.9320.96712.44530.79730.7970.0000.0000.0000.000
189A191GLY0-0.018-0.0099.5101.2701.2700.0000.0000.0000.000
190A192ASP-1-0.785-0.8688.214-50.868-50.8680.0000.0000.0000.000
191A193GLY0-0.019-0.0065.219-3.703-3.7030.0000.0000.0000.000
192A194LEU0-0.008-0.0165.3067.5077.5070.0000.0000.0000.000
193A195PHE0-0.027-0.0295.769-10.766-10.7660.0000.0000.0000.000
194A196VAL00.0210.0047.4946.7706.7700.0000.0000.0000.000
195A197ILE00.0000.01210.767-2.856-2.8560.0000.0000.0000.000
196A198GLY00.0360.00913.0202.3272.3270.0000.0000.0000.000
197A199ARG10.9230.97015.84926.83526.8350.0000.0000.0000.000
198A200LEU00.0320.01315.446-0.377-0.3770.0000.0000.0000.000
199A201VAL00.0120.01319.0641.8211.8210.0000.0000.0000.000
200A202ASN0-0.032-0.04521.957-0.286-0.2860.0000.0000.0000.000
201A203ASP-1-0.750-0.80024.357-24.994-24.9940.0000.0000.0000.000
202A204SER0-0.042-0.03626.7730.0060.0060.0000.0000.0000.000
203A205TRP00.0220.01126.9190.1950.1950.0000.0000.0000.000
204A206THR0-0.072-0.03732.9730.0790.0790.0000.0000.0000.000
205A207SER0-0.0010.00433.9430.0220.0220.0000.0000.0000.000
206A208SER00.0460.01935.2190.2250.2250.0000.0000.0000.000
207A209SER00.0080.01437.5070.3770.3770.0000.0000.0000.000
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