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: RLL28

Calculation Name: 2QTQ-B-Xray547

Preferred Name:

Target Type:

Ligand Name: nitrate ion | 1,2-ethanediol

Ligand 3-letter code: NO3 | EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2QTQ

Chain ID: B

ChEMBL ID:

UniProt ID: Q2G9F6

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 197
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2218924.109648
FMO2-HF: Nuclear repulsion 2140116.998016
FMO2-HF: Total energy -78807.111632
FMO2-MP2: Total energy -79036.946986


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:15:GLY)


Summations of interaction energy for fragment #1(A:15:GLY)
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.
-39.168-37.47213.314-8.808-6.204-0.1
Interaction energy analysis for fragmet #1(A:15:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.830 / q_NPA : 0.897
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].
3A17ARG11.0071.0083.84345.37846.281-0.005-0.349-0.5500.000
4A18ASP-1-0.797-0.9001.818-110.430-109.86213.320-8.405-5.483-0.100
5A19LEU00.0270.0254.2879.3749.599-0.001-0.054-0.1710.000
6A20LEU0-0.0130.0076.2747.3167.3160.0000.0000.0000.000
7A21LEU00.0120.0067.4373.8973.8970.0000.0000.0000.000
8A22GLN00.0210.0158.1042.2462.2460.0000.0000.0000.000
9A23THR0-0.038-0.0289.8823.3153.3150.0000.0000.0000.000
10A24ALA0-0.002-0.01611.8542.2682.2680.0000.0000.0000.000
11A25SER0-0.027-0.01412.6771.6621.6620.0000.0000.0000.000
12A26ASN00.0260.01413.8890.9760.9760.0000.0000.0000.000
13A27ILE00.0460.01915.8131.1901.1900.0000.0000.0000.000
14A28MET0-0.068-0.02817.4410.7590.7590.0000.0000.0000.000
15A29ARG10.7980.90018.16616.97616.9760.0000.0000.0000.000
16A30GLU-1-0.959-0.97818.395-16.229-16.2290.0000.0000.0000.000
17A31GLY0-0.002-0.01421.6770.7740.7740.0000.0000.0000.000
18A32ASP-1-0.847-0.90123.517-11.724-11.7240.0000.0000.0000.000
19A33VAL00.000-0.00323.1870.4320.4320.0000.0000.0000.000
20A34VAL00.0550.01120.756-0.693-0.6930.0000.0000.0000.000
21A35ASP-1-0.832-0.86720.624-14.019-14.0190.0000.0000.0000.000
22A36ILE00.0490.04215.8870.3480.3480.0000.0000.0000.000
23A37SER00.0210.01020.481-0.038-0.0380.0000.0000.0000.000
24A38LEU00.003-0.00816.164-0.900-0.9000.0000.0000.0000.000
25A39SER00.004-0.00617.123-1.023-1.0230.0000.0000.0000.000
26A40GLU-1-0.796-0.88018.217-16.011-16.0110.0000.0000.0000.000
27A41LEU00.0060.00511.968-0.708-0.7080.0000.0000.0000.000
28A42SER0-0.079-0.04813.315-1.303-1.3030.0000.0000.0000.000
29A43LEU0-0.006-0.01314.101-0.843-0.8430.0000.0000.0000.000
30A44ARG10.8790.91414.91816.59816.5980.0000.0000.0000.000
31A45SER0-0.029-0.0199.535-1.187-1.1870.0000.0000.0000.000
32A46GLY00.0170.02010.183-1.808-1.8080.0000.0000.0000.000
33A47LEU0-0.044-0.0076.447-0.860-0.8600.0000.0000.0000.000
34A48ASN00.0660.04510.9191.5791.5790.0000.0000.0000.000
35A49SER00.0740.02612.736-1.529-1.5290.0000.0000.0000.000
36A50ALA00.0190.00714.778-0.242-0.2420.0000.0000.0000.000
37A51LEU00.017-0.0037.737-0.439-0.4390.0000.0000.0000.000
38A52VAL0-0.0010.00310.774-1.589-1.5890.0000.0000.0000.000
39A53LYS10.9050.95312.53017.54217.5420.0000.0000.0000.000
40A54TYR00.0050.0109.6051.2601.2600.0000.0000.0000.000
41A55TYR0-0.007-0.0145.922-2.985-2.9850.0000.0000.0000.000
42A56PHE0-0.003-0.0038.367-0.292-0.2920.0000.0000.0000.000
43A57GLY00.0570.05913.1521.5781.5780.0000.0000.0000.000
44A58ASN0-0.090-0.07016.4670.4320.4320.0000.0000.0000.000
45A59LYS10.9300.93716.95813.33713.3370.0000.0000.0000.000
46A60ALA00.0460.03018.200-0.442-0.4420.0000.0000.0000.000
47A61GLY00.0450.02516.236-0.161-0.1610.0000.0000.0000.000
48A62LEU0-0.027-0.01312.225-1.054-1.0540.0000.0000.0000.000
49A63LEU00.003-0.00214.321-0.850-0.8500.0000.0000.0000.000
50A64LYS10.8810.93916.64416.16916.1690.0000.0000.0000.000
51A65ALA0-0.037-0.02411.129-0.335-0.3350.0000.0000.0000.000
52A66LEU0-0.037-0.01212.090-1.739-1.7390.0000.0000.0000.000
53A67LEU00.0050.00313.4310.1640.1640.0000.0000.0000.000
54A68ASP-1-0.865-0.89613.750-20.212-20.2120.0000.0000.0000.000
55A69ARG10.8350.8878.94628.08928.0890.0000.0000.0000.000
56A70ASP-1-0.755-0.84412.410-22.038-22.0380.0000.0000.0000.000
57A71MET0-0.0100.00015.1241.3061.3060.0000.0000.0000.000
58A72GLU-1-0.863-0.91511.347-25.480-25.4800.0000.0000.0000.000
59A73ASN0-0.038-0.03314.7381.3681.3680.0000.0000.0000.000
60A74ILE00.0320.04017.6650.8300.8300.0000.0000.0000.000
61A75VAL00.0220.01519.6130.7910.7910.0000.0000.0000.000
62A76LYS10.9040.94513.64122.39322.3930.0000.0000.0000.000
63A77SER0-0.052-0.02720.4680.7250.7250.0000.0000.0000.000
64A78VAL0-0.017-0.01223.2400.7070.7070.0000.0000.0000.000
65A79ASP-1-0.875-0.94022.447-13.293-13.2930.0000.0000.0000.000
66A80ALA0-0.007-0.01025.0060.5010.5010.0000.0000.0000.000
67A81LEU0-0.038-0.00326.7940.4440.4440.0000.0000.0000.000
68A82LEU0-0.025-0.02629.1790.5130.5130.0000.0000.0000.000
69A83ALA0-0.0010.01628.9010.3560.3560.0000.0000.0000.000
70A84LYS10.8920.92730.9288.8688.8680.0000.0000.0000.000
71A85ASP-1-0.757-0.86430.916-10.112-10.1120.0000.0000.0000.000
72A86ASP-1-0.901-0.94433.594-8.320-8.3200.0000.0000.0000.000
73A87MET0-0.042-0.00232.1060.0130.0130.0000.0000.0000.000
74A88SER00.0430.01835.874-0.019-0.0190.0000.0000.0000.000
75A89PRO00.023-0.00636.087-0.268-0.2680.0000.0000.0000.000
76A90GLU-1-0.855-0.92935.578-8.385-8.3850.0000.0000.0000.000
77A91ALA00.0320.01634.571-0.260-0.2600.0000.0000.0000.000
78A92LYS10.7680.88431.3219.6659.6650.0000.0000.0000.000
79A93LEU0-0.0040.00430.579-0.471-0.4710.0000.0000.0000.000
80A94ARG10.8940.91330.6939.1879.1870.0000.0000.0000.000
81A95ARG10.8140.92126.94810.70910.7090.0000.0000.0000.000
82A96HIS00.0230.01825.646-0.157-0.1570.0000.0000.0000.000
83A97ILE00.0230.00626.054-0.479-0.4790.0000.0000.0000.000
84A98SER00.021-0.01027.091-0.151-0.1510.0000.0000.0000.000
85A99LYS10.9190.97618.06716.08516.0850.0000.0000.0000.000
86A100CYS0-0.065-0.01322.091-0.880-0.8800.0000.0000.0000.000
87A101ILE0-0.014-0.01223.216-0.402-0.4020.0000.0000.0000.000
88A102ASP-1-0.831-0.91221.702-13.269-13.2690.0000.0000.0000.000
89A103THR0-0.050-0.05017.683-0.849-0.8490.0000.0000.0000.000
90A104TYR00.009-0.00919.545-0.462-0.4620.0000.0000.0000.000
91A105TYR0-0.006-0.01022.2750.2120.2120.0000.0000.0000.000
92A106ASP-1-0.928-0.94417.141-16.953-16.9530.0000.0000.0000.000
93A107TYR0-0.033-0.02913.121-0.533-0.5330.0000.0000.0000.000
94A108PRO00.0340.02419.0440.5270.5270.0000.0000.0000.000
95A109TYR0-0.044-0.04415.4590.6500.6500.0000.0000.0000.000
96A110LEU00.0010.00618.1370.2030.2030.0000.0000.0000.000
97A111ASN00.004-0.01621.067-0.165-0.1650.0000.0000.0000.000
98A112ARG10.9170.94924.52311.51311.5130.0000.0000.0000.000
99A113LEU0-0.054-0.01417.3300.2390.2390.0000.0000.0000.000
100A114LEU00.0130.00822.023-0.034-0.0340.0000.0000.0000.000
101A115MET0-0.015-0.01723.3840.4780.4780.0000.0000.0000.000
102A116ARG10.7880.87723.42713.15113.1510.0000.0000.0000.000
103A117LEU0-0.005-0.01319.5170.1520.1520.0000.0000.0000.000
104A118VAL00.0090.00824.1060.1740.1740.0000.0000.0000.000
105A119ARG10.9060.97027.16910.34910.3490.0000.0000.0000.000
106A120ASP-1-0.921-0.96926.231-11.384-11.3840.0000.0000.0000.000
107A121SER0-0.097-0.04726.054-0.101-0.1010.0000.0000.0000.000
108A122ASP-1-0.836-0.91227.258-11.430-11.4300.0000.0000.0000.000
109A123GLU-1-0.910-0.97628.671-9.729-9.7290.0000.0000.0000.000
110A124ALA0-0.0060.00426.855-0.053-0.0530.0000.0000.0000.000
111A125GLU-1-0.759-0.85821.206-15.629-15.6290.0000.0000.0000.000
112A126ALA00.0160.01725.028-0.316-0.3160.0000.0000.0000.000
113A127LYS10.8630.91127.62410.67610.6760.0000.0000.0000.000
114A128ARG10.7830.86818.65315.94815.9480.0000.0000.0000.000
115A129ILE00.0230.00622.642-0.326-0.3260.0000.0000.0000.000
116A130ALA00.0170.00224.363-0.033-0.0330.0000.0000.0000.000
117A131ASP-1-0.856-0.92726.049-11.092-11.0920.0000.0000.0000.000
118A132GLN0-0.047-0.01919.494-0.381-0.3810.0000.0000.0000.000
119A133TYR0-0.052-0.06817.543-0.169-0.1690.0000.0000.0000.000
120A134LEU0-0.0110.01223.3760.2550.2550.0000.0000.0000.000
121A135LEU0-0.003-0.01627.1410.3430.3430.0000.0000.0000.000
122A136PRO0-0.033-0.01024.5230.4370.4370.0000.0000.0000.000
123A137LEU00.0490.03224.2190.2760.2760.0000.0000.0000.000
124A138HIS00.0330.02128.1940.2640.2640.0000.0000.0000.000
125A139ARG10.9190.95729.52910.82810.8280.0000.0000.0000.000
126A140ALA00.0150.01929.7480.3370.3370.0000.0000.0000.000
127A141TYR00.013-0.02728.4110.3030.3030.0000.0000.0000.000
128A142ASN0-0.014-0.01533.6960.4070.4070.0000.0000.0000.000
129A143ARG10.8150.89734.2599.2269.2260.0000.0000.0000.000
130A144PHE0-0.006-0.00734.2720.2370.2370.0000.0000.0000.000
131A145ILE00.0240.01635.9250.1560.1560.0000.0000.0000.000
132A146GLY00.0240.01838.5920.2220.2220.0000.0000.0000.000
133A147GLU-1-0.907-0.94737.930-8.328-8.3280.0000.0000.0000.000
134A148GLY00.0350.00939.9420.1830.1830.0000.0000.0000.000
135A149VAL0-0.021-0.00241.2070.1460.1460.0000.0000.0000.000
136A150LYS10.9060.94843.9837.3037.3030.0000.0000.0000.000
137A151ALA0-0.056-0.02243.3330.1530.1530.0000.0000.0000.000
138A152GLY00.0000.00845.4110.0630.0630.0000.0000.0000.000
139A153VAL00.0010.00641.1940.0310.0310.0000.0000.0000.000
140A154PHE0-0.041-0.01637.131-0.189-0.1890.0000.0000.0000.000
141A155ARG10.9380.96542.3327.6057.6050.0000.0000.0000.000
142A156PRO0-0.027-0.01543.030-0.179-0.1790.0000.0000.0000.000
143A157ILE00.0070.00638.1410.0490.0490.0000.0000.0000.000
144A158ASN00.0190.00039.354-0.229-0.2290.0000.0000.0000.000
145A159PRO00.0430.01136.192-0.156-0.1560.0000.0000.0000.000
146A160GLN00.0300.02834.950-0.297-0.2970.0000.0000.0000.000
147A161LEU00.0140.00234.865-0.214-0.2140.0000.0000.0000.000
148A162PHE00.0270.03632.443-0.166-0.1660.0000.0000.0000.000
149A163TYR00.0570.01627.242-0.346-0.3460.0000.0000.0000.000
150A164PHE0-0.0080.00030.466-0.339-0.3390.0000.0000.0000.000
151A165THR0-0.032-0.01231.690-0.087-0.0870.0000.0000.0000.000
152A166VAL00.0120.01127.623-0.152-0.1520.0000.0000.0000.000
153A167THR0-0.017-0.02426.284-0.244-0.2440.0000.0000.0000.000
154A168GLY00.0150.00826.710-0.375-0.3750.0000.0000.0000.000
155A169ALA0-0.016-0.01126.9540.1710.1710.0000.0000.0000.000
156A170ALA0-0.0170.01323.725-0.044-0.0440.0000.0000.0000.000
157A171ASP-1-0.765-0.87425.347-11.565-11.5650.0000.0000.0000.000
158A172ARG10.8320.93828.17610.44610.4460.0000.0000.0000.000
159A173PHE00.0270.00525.2640.1510.1510.0000.0000.0000.000
160A174PHE0-0.045-0.01924.692-0.010-0.0100.0000.0000.0000.000
161A175SER0-0.030-0.04027.0030.1870.1870.0000.0000.0000.000
162A176ALA00.0120.01530.0990.2470.2470.0000.0000.0000.000
163A177ARG10.9250.96523.37013.55413.5540.0000.0000.0000.000
164A178LEU0-0.0110.00428.5330.0450.0450.0000.0000.0000.000
165A179VAL00.013-0.00630.2390.1910.1910.0000.0000.0000.000
166A180LEU0-0.022-0.00831.4670.1980.1980.0000.0000.0000.000
167A181LYS10.8100.91425.75212.21312.2130.0000.0000.0000.000
168A182HIS0-0.042-0.02830.1520.3410.3410.0000.0000.0000.000
169A183CYS0-0.081-0.04034.4150.2230.2230.0000.0000.0000.000
170A184PHE00.0110.01435.5590.2500.2500.0000.0000.0000.000
171A185ASP-1-0.858-0.90536.477-8.202-8.2020.0000.0000.0000.000
172A186GLN0-0.094-0.06731.698-0.548-0.5480.0000.0000.0000.000
173A187ASP-1-0.834-0.91434.042-8.840-8.8400.0000.0000.0000.000
174A188THR00.036-0.00332.982-0.155-0.1550.0000.0000.0000.000
175A189LEU0-0.0160.00633.968-0.116-0.1160.0000.0000.0000.000
176A190THR00.010-0.01332.583-0.028-0.0280.0000.0000.0000.000
177A191GLU-1-0.990-0.98727.851-11.525-11.5250.0000.0000.0000.000
178A192GLN00.004-0.01530.573-0.036-0.0360.0000.0000.0000.000
179A193LEU0-0.0190.01632.696-0.037-0.0370.0000.0000.0000.000
180A194ARG10.9170.95526.63311.60411.6040.0000.0000.0000.000
181A195ASP-1-0.851-0.90026.703-12.267-12.2670.0000.0000.0000.000
182A196SER0-0.013-0.02529.169-0.065-0.0650.0000.0000.0000.000
183A197TYR00.002-0.00130.6660.0590.0590.0000.0000.0000.000
184A198ARG10.8470.91525.05212.18712.1870.0000.0000.0000.000
185A199GLU-1-0.800-0.90329.251-10.107-10.1070.0000.0000.0000.000
186A200HIS00.0210.02831.8070.0010.0010.0000.0000.0000.000
187A201THR0-0.025-0.02530.2420.2210.2210.0000.0000.0000.000
188A202VAL0-0.023-0.01129.5280.0560.0560.0000.0000.0000.000
189A203ASP-1-0.808-0.89232.223-8.836-8.8360.0000.0000.0000.000
190A204PHE0-0.048-0.02035.7160.2630.2630.0000.0000.0000.000
191A205ILE0-0.038-0.01931.1910.1350.1350.0000.0000.0000.000
192A206MET0-0.052-0.02134.3420.0540.0540.0000.0000.0000.000
193A207ALA00.0350.01136.8370.1950.1950.0000.0000.0000.000
194A208GLY0-0.0020.01838.7950.2060.2060.0000.0000.0000.000
195A209ILE0-0.065-0.04036.7720.1520.1520.0000.0000.0000.000
196A210LEU0-0.016-0.00839.1190.0990.0990.0000.0000.0000.000
197A211ALA-1-0.948-0.95741.868-6.883-6.8830.0000.0000.0000.000