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: QNZGY

Calculation Name: 2NO2-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2NO2

Chain ID: A

ChEMBL ID:

UniProt ID: O00291

Base Structure: X-ray

Registration Date: 2025-07-09

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 201
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -483619.882854
FMO2-HF: Nuclear repulsion 443116.407726
FMO2-HF: Total energy -40503.475128
FMO2-MP2: Total energy -40622.281819


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:480:GLY)


Summations of interaction energy for fragment #1(A:480: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.
-1.2240.6251.468-1.077-2.240.004
Interaction energy analysis for fragmet #1(A:480:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.061 / q_NPA : 0.009
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].
3A481SER00.0190.0954.6860.6090.824-0.001-0.085-0.1300.000
4A482HIS00.135-0.0563.326-0.2120.7980.022-0.444-0.5880.001
5A482HIS0-0.0710.0964.8950.1560.1560.0000.0000.0000.000
6A483ALA00.109-0.0983.236-0.837-1.1580.0600.695-0.4340.001
7A483ALA0-0.0640.1192.2361.1121.3361.387-0.917-0.6930.003
8A484ASP00.072-0.1243.3780.4640.8230.001-0.155-0.2050.000
9A484ASP-1-1.000-0.8504.021-6.609-6.3410.001-0.166-0.103-0.001
10A485LEU00.046-0.1065.1790.5530.647-0.002-0.005-0.0870.000
11A485LEU0-0.0720.1127.3790.0170.0170.0000.0000.0000.000
12A486LEU00.115-0.1087.5190.0650.0650.0000.0000.0000.000
13A486LEU0-0.0680.1267.6390.0390.0390.0000.0000.0000.000
14A487ARG00.112-0.1087.5720.1810.1810.0000.0000.0000.000
15A487ARG10.8331.0785.6281.6091.6090.0000.0000.0000.000
16A488LYS00.053-0.0938.8020.1280.1280.0000.0000.0000.000
17A488LYS10.8391.0458.6231.5221.5220.0000.0000.0000.000
18A489ASN00.142-0.07310.7500.0600.0600.0000.0000.0000.000
19A489ASN0-0.1090.07112.389-0.015-0.0150.0000.0000.0000.000
20A490ALA00.094-0.13512.2470.0450.0450.0000.0000.0000.000
21A490ALA0-0.0960.12112.7170.0130.0130.0000.0000.0000.000
22A491GLU00.102-0.11713.4350.0740.0740.0000.0000.0000.000
23A491GLU-1-1.018-0.83713.785-0.298-0.2980.0000.0000.0000.000
24A492VAL00.062-0.09815.1840.0400.0400.0000.0000.0000.000
25A492VAL0-0.0450.11515.298-0.003-0.0030.0000.0000.0000.000
26A493THR00.039-0.09316.9920.0190.0190.0000.0000.0000.000
27A493THR0-0.0520.07917.2010.0160.0160.0000.0000.0000.000
28A494LYS00.035-0.13418.2070.0310.0310.0000.0000.0000.000
29A494LYS10.9001.12018.2070.0730.0730.0000.0000.0000.000
30A495GLN00.121-0.08419.4270.0260.0260.0000.0000.0000.000
31A495GLN0-0.0720.09418.064-0.039-0.0390.0000.0000.0000.000
32A496VAL00.121-0.10321.2060.0090.0090.0000.0000.0000.000
33A496VAL0-0.0760.10521.3430.0030.0030.0000.0000.0000.000
34A497SER0-0.019-0.06622.8790.0090.0090.0000.0000.0000.000
35A497SER0-0.0830.03923.5970.0040.0040.0000.0000.0000.000
36A498MET00.068-0.10223.9410.0150.0150.0000.0000.0000.000
37A498MET0-0.1020.08523.093-0.008-0.0080.0000.0000.0000.000
38A499ALA00.113-0.07225.3860.0090.0090.0000.0000.0000.000
39A499ALA0-0.0730.10225.883-0.002-0.0020.0000.0000.0000.000
40A500ARG00.134-0.07627.1830.0040.0040.0000.0000.0000.000
41A500ARG10.8271.05525.5070.0760.0760.0000.0000.0000.000
42A501GLN00.094-0.11228.6180.0080.0080.0000.0000.0000.000
43A501GLN0-0.1610.08429.0080.0020.0020.0000.0000.0000.000
44A502ALA00.139-0.07629.7480.0080.0080.0000.0000.0000.000
45A502ALA0-0.0920.10029.965-0.002-0.0020.0000.0000.0000.000
46A503GLN00.046-0.08231.4330.0030.0030.0000.0000.0000.000
47A503GLN0-0.1230.07131.710-0.007-0.0070.0000.0000.0000.000
48A504VAL00.115-0.10833.3090.0020.0020.0000.0000.0000.000
49A504VAL0-0.1080.09733.5150.0010.0010.0000.0000.0000.000
50A505ASP00.047-0.10634.2740.0060.0060.0000.0000.0000.000
51A505ASP-1-0.962-0.84633.188-0.062-0.0620.0000.0000.0000.000
52A506LEU00.112-0.10535.4040.0050.0050.0000.0000.0000.000
53A506LEU0-0.1160.10433.832-0.002-0.0020.0000.0000.0000.000
54A507GLU00.077-0.13937.1580.0020.0020.0000.0000.0000.000
55A507GLU-1-0.979-0.84236.425-0.061-0.0610.0000.0000.0000.000
56A508ARG00.065-0.10538.9250.0030.0030.0000.0000.0000.000
57A508ARG10.8111.06038.7250.0420.0420.0000.0000.0000.000
58A509GLU00.106-0.14439.8080.0050.0050.0000.0000.0000.000
59A509GLU-1-0.999-0.81638.842-0.065-0.0650.0000.0000.0000.000
60A510LYS00.090-0.12141.2920.0020.0020.0000.0000.0000.000
61A510LYS10.8421.07341.5750.0550.0550.0000.0000.0000.000
62A511LYS00.111-0.08643.1200.0010.0010.0000.0000.0000.000
63A511LYS10.8441.06644.4340.0320.0320.0000.0000.0000.000
64A512GLU00.074-0.11145.0410.0020.0020.0000.0000.0000.000
65A512GLU-1-1.023-0.84044.151-0.042-0.0420.0000.0000.0000.000
66A513LEU00.045-0.10945.8610.0030.0030.0000.0000.0000.000
67A513LEU0-0.0560.11443.5510.0000.0000.0000.0000.0000.000
68A514GLU00.093-0.10347.1860.0010.0010.0000.0000.0000.000
69A514GLU-1-0.995-0.84246.864-0.047-0.0470.0000.0000.0000.000
70A515ASP00.158-0.07349.1030.0010.0010.0000.0000.0000.000
71A515ASP-1-1.042-0.87649.934-0.032-0.0320.0000.0000.0000.000
72A516SER0-0.030-0.14450.4240.0020.0020.0000.0000.0000.000
73A516SER0-0.0390.05849.6550.0000.0000.0000.0000.0000.000
74A517LEU00.042-0.13151.2240.0020.0020.0000.0000.0000.000
75A517LEU0-0.1010.11549.5570.0000.0000.0000.0000.0000.000
76A518GLU00.151-0.14352.8010.0010.0010.0000.0000.0000.000
77A518GLU-1-1.007-0.81053.888-0.030-0.0300.0000.0000.0000.000
78A519ARG00.041-0.09754.9310.0020.0020.0000.0000.0000.000
79A519ARG10.8121.05351.8440.0300.0300.0000.0000.0000.000
80A520ILE00.037-0.09955.7730.0020.0020.0000.0000.0000.000
81A520ILE0-0.0570.10054.5750.0000.0000.0000.0000.0000.000
82A521SER00.047-0.06557.1830.0000.0000.0000.0000.0000.000
83A521SER0-0.0440.06757.0150.0000.0000.0000.0000.0000.000
84A522ASP00.092-0.10958.7040.0000.0000.0000.0000.0000.000
85A522ASP-1-0.950-0.79259.622-0.025-0.0250.0000.0000.0000.000
86A523GLN00.014-0.15660.4570.0010.0010.0000.0000.0000.000
87A523GLN0-0.1380.07460.2840.0000.0000.0000.0000.0000.000
88A524GLY00.031-0.08261.1970.0010.0010.0000.0000.0000.000
89A525GLN00.117-0.00162.6980.0000.0000.0000.0000.0000.000
90A525GLN0-0.0610.12163.442-0.001-0.0010.0000.0000.0000.000
91A526ARG00.058-0.11364.8300.0010.0010.0000.0000.0000.000
92A526ARG10.7791.03563.1170.0230.0230.0000.0000.0000.000
93A527LYS00.127-0.07266.0330.0010.0010.0000.0000.0000.000
94A527LYS10.8791.05764.3600.0250.0250.0000.0000.0000.000
95A528THR00.044-0.07567.0700.0010.0010.0000.0000.0000.000
96A528THR0-0.0620.06266.0780.0000.0000.0000.0000.0000.000
97A529GLN00.032-0.11668.7310.0000.0000.0000.0000.0000.000
98A529GLN0-0.0830.11170.0920.0010.0010.0000.0000.0000.000
99A530GLU00.197-0.08270.9940.0000.0000.0000.0000.0000.000
100A530GLU-1-1.026-0.84869.371-0.021-0.0210.0000.0000.0000.000
101A531GLN00.133-0.06671.6790.0010.0010.0000.0000.0000.000
102A531GLN0-0.1200.08671.3640.0000.0000.0000.0000.0000.000
103A532LEU00.007-0.12773.1960.0000.0000.0000.0000.0000.000
104A532LEU0-0.0860.08972.0730.0000.0000.0000.0000.0000.000
105A533GLU00.069-0.14475.1250.0000.0000.0000.0000.0000.000
106A533GLU-1-1.005-0.82674.914-0.018-0.0180.0000.0000.0000.000
107A534VAL00.089-0.11076.2190.0010.0010.0000.0000.0000.000
108A534VAL0-0.0840.10674.9720.0000.0000.0000.0000.0000.000
109A535LEU00.101-0.07677.2920.0010.0010.0000.0000.0000.000
110A535LEU0-0.1520.06677.0260.0000.0000.0000.0000.0000.000
111A536GLU00.052-0.15478.9850.0000.0000.0000.0000.0000.000
112A536GLU-1-0.944-0.81580.031-0.017-0.0170.0000.0000.0000.000
113A537SER00.028-0.11380.8490.0000.0000.0000.0000.0000.000
114A537SER0-0.0290.10481.1440.0000.0000.0000.0000.0000.000
115A538LEU00.119-0.07781.6940.0010.0010.0000.0000.0000.000
116A538LEU0-0.1240.10080.3290.0000.0000.0000.0000.0000.000
117A539LYS00.050-0.11083.2600.0000.0000.0000.0000.0000.000
118A539LYS10.8501.05881.0720.0180.0180.0000.0000.0000.000
119A540GLN00.089-0.10885.2440.0000.0000.0000.0000.0000.000
120A540GLN0-0.1390.09685.4860.0000.0000.0000.0000.0000.000
121A541GLU00.056-0.15086.2920.0010.0010.0000.0000.0000.000
122A541GLU-1-0.970-0.81483.994-0.015-0.0150.0000.0000.0000.000
123A542LEU00.140-0.09587.4240.0010.0010.0000.0000.0000.000
124A542LEU0-0.1190.10687.6270.0000.0000.0000.0000.0000.000
125A543ALA00.134-0.11689.2310.0000.0000.0000.0000.0000.000
126A543ALA0-0.1150.11190.1970.0000.0000.0000.0000.0000.000
127A544THR0-0.102-0.15290.9950.0000.0000.0000.0000.0000.000
128A544THR0-0.0200.08090.7630.0000.0000.0000.0000.0000.000
129A545SER00.176-0.00291.9580.0000.0000.0000.0000.0000.000
130A545SER0-0.0500.07191.7290.0000.0000.0000.0000.0000.000
131A546GLN00.089-0.08693.4250.0000.0000.0000.0000.0000.000
132A546GLN0-0.1300.07592.8410.0000.0000.0000.0000.0000.000
133A547ARG00.063-0.09795.3300.0000.0000.0000.0000.0000.000
134A547ARG10.8231.05291.9550.0130.0130.0000.0000.0000.000
135A548GLU00.081-0.12596.6990.0000.0000.0000.0000.0000.000
136A548GLU-1-0.979-0.83594.756-0.012-0.0120.0000.0000.0000.000
137A549LEU00.069-0.15497.4960.0000.0000.0000.0000.0000.000
138A549LEU0-0.0850.13696.0120.0000.0000.0000.0000.0000.000
139A550GLN00.161-0.09199.1390.0000.0000.0000.0000.0000.000
140A550GLN0-0.1410.099100.2210.0000.0000.0000.0000.0000.000
141A551VAL00.039-0.139101.3010.0000.0000.0000.0000.0000.000
142A551VAL0-0.0950.120101.6670.0000.0000.0000.0000.0000.000
143A552LEU00.082-0.135102.2270.0000.0000.0000.0000.0000.000
144A552LEU0-0.0510.143101.0390.0000.0000.0000.0000.0000.000
145A553GLN00.031-0.107103.3890.0000.0000.0000.0000.0000.000
146A553GLN0-0.0770.107102.5240.0000.0000.0000.0000.0000.000
147A554GLY00.021-0.088105.1240.0000.0000.0000.0000.0000.000
148A555SER00.0850.020106.9090.0000.0000.0000.0000.0000.000
149A555SER0-0.0640.073106.7600.0000.0000.0000.0000.0000.000
150A556LEU00.061-0.110107.6370.0000.0000.0000.0000.0000.000
151A556LEU0-0.1120.114106.5260.0000.0000.0000.0000.0000.000
152A557GLU00.161-0.085109.1470.0000.0000.0000.0000.0000.000
153A557GLU-1-1.053-0.877109.806-0.010-0.0100.0000.0000.0000.000
154A558THR0-0.014-0.089111.2560.0000.0000.0000.0000.0000.000
155A558THR0-0.0530.051112.1410.0000.0000.0000.0000.0000.000
156A559SER00.095-0.059112.1880.0000.0000.0000.0000.0000.000
157A559SER0-0.0470.074111.8790.0000.0000.0000.0000.0000.000
158A560ALA00.097-0.124113.0400.0000.0000.0000.0000.0000.000
159A560ALA0-0.1000.132112.9860.0000.0000.0000.0000.0000.000
160A561GLN00.110-0.109114.6870.0000.0000.0000.0000.0000.000
161A561GLN0-0.1100.105116.5960.0000.0000.0000.0000.0000.000
162A562SER0-0.001-0.103116.6900.0000.0000.0000.0000.0000.000
163A562SER0-0.0840.053116.9330.0000.0000.0000.0000.0000.000
164A563GLU00.065-0.152117.3690.0000.0000.0000.0000.0000.000
165A563GLU-1-1.014-0.831114.965-0.008-0.0080.0000.0000.0000.000
166A564ALA00.079-0.102118.8920.0000.0000.0000.0000.0000.000
167A564ALA0-0.0960.108119.7430.0000.0000.0000.0000.0000.000
168A565ASN00.079-0.084121.0480.0000.0000.0000.0000.0000.000
169A565ASN0-0.1100.073121.7310.0000.0000.0000.0000.0000.000
170A566TRP00.126-0.079122.1650.0000.0000.0000.0000.0000.000
171A566TRP0-0.1190.093120.0300.0000.0000.0000.0000.0000.000
172A567ALA00.176-0.061123.1870.0000.0000.0000.0000.0000.000
173A567ALA0-0.0980.103123.1890.0000.0000.0000.0000.0000.000
174A568ALA00.115-0.105124.9070.0000.0000.0000.0000.0000.000
175A568ALA0-0.1120.100126.5170.0000.0000.0000.0000.0000.000
176A569GLU00.032-0.131126.7160.0000.0000.0000.0000.0000.000
177A569GLU-1-1.042-0.869126.247-0.007-0.0070.0000.0000.0000.000
178A570PHE00.112-0.100127.3900.0000.0000.0000.0000.0000.000
179A570PHE0-0.1560.062126.9390.0000.0000.0000.0000.0000.000
180A571ALA00.100-0.100128.8750.0000.0000.0000.0000.0000.000
181A571ALA0-0.1300.093129.3950.0000.0000.0000.0000.0000.000
182A572GLU00.055-0.129130.8390.0000.0000.0000.0000.0000.000
183A572GLU-1-1.018-0.842132.247-0.006-0.0060.0000.0000.0000.000
184A573LEU00.137-0.094132.4030.0000.0000.0000.0000.0000.000
185A573LEU0-0.1180.103131.9770.0000.0000.0000.0000.0000.000
186A574GLU00.097-0.127132.9110.0000.0000.0000.0000.0000.000
187A574GLU-1-1.036-0.845131.734-0.006-0.0060.0000.0000.0000.000
188A575LYS00.173-0.086134.2940.0000.0000.0000.0000.0000.000
189A575LYS10.8261.071135.9350.0060.0060.0000.0000.0000.000
190A576GLU00.023-0.149136.9380.0000.0000.0000.0000.0000.000
191A576GLU-1-1.007-0.840137.086-0.006-0.0060.0000.0000.0000.000
192A577ARG00.144-0.087137.1540.0000.0000.0000.0000.0000.000
193A577ARG10.7491.027134.0370.0060.0060.0000.0000.0000.000
194A578ASP00.029-0.169138.2010.0000.0000.0000.0000.0000.000
195A578ASP-1-0.934-0.807136.964-0.006-0.0060.0000.0000.0000.000
196A579SER0-0.004-0.107139.7760.0000.0000.0000.0000.0000.000
197A579SER0-0.1090.049141.1280.0000.0000.0000.0000.0000.000
198A580LEU0-0.021-0.130142.0220.0000.0000.0000.0000.0000.000
199A580LEU0-0.1370.100141.1340.0000.0000.0000.0000.0000.000
200A581VAL0-0.078-0.119142.1570.0000.0000.0000.0000.0000.000
201A581VAL00.0050.013140.5340.0000.0000.0000.0000.0000.000