FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: RY6G8

Calculation Name: 2NO2-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

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 OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
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 -483183.868395
FMO2-HF: Nuclear repulsion 442676.836841
FMO2-HF: Total energy -40507.031554
FMO2-MP2: Total energy -40625.62075


3D Structure
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.
-0.8842.2950.59-1.663-2.109-0.007
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 : 0.059 / q_NPA : 0.018
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].
3A481SER00.0250.0954.3630.5740.786-0.001-0.082-0.1290.000
4A482HIS00.102-0.0503.854-0.6430.317-0.003-0.454-0.5030.001
5A482HIS0-0.0420.0945.313-0.012-0.0120.0000.0000.0000.000
6A483ALA00.130-0.1023.4360.4400.6330.0090.030-0.2320.000
7A483ALA0-0.0690.1192.519-0.2070.1010.241-0.263-0.2880.000
8A484ASP00.038-0.1244.1230.8751.179-0.001-0.130-0.1730.000
9A484ASP-1-0.917-0.8022.962-7.126-5.9240.345-0.764-0.784-0.008
10A485LEU00.034-0.1135.5240.6050.6050.0000.0000.0000.000
11A485LEU0-0.0790.1067.7340.0370.0370.0000.0000.0000.000
12A486LEU00.098-0.0997.8210.2130.2130.0000.0000.0000.000
13A486LEU0-0.0770.1037.4050.0270.0270.0000.0000.0000.000
14A487ARG00.111-0.0797.9950.2790.2790.0000.0000.0000.000
15A487ARG10.7551.0014.9232.4832.4830.0000.0000.0000.000
16A488LYS00.120-0.0729.5280.1810.1810.0000.0000.0000.000
17A488LYS10.8341.0559.2001.0651.0650.0000.0000.0000.000
18A489ASN00.144-0.06311.3770.1000.1000.0000.0000.0000.000
19A489ASN0-0.1060.06912.7810.0260.0260.0000.0000.0000.000
20A490ALA00.105-0.09312.7970.1000.1000.0000.0000.0000.000
21A490ALA0-0.0950.10513.031-0.003-0.0030.0000.0000.0000.000
22A491GLU00.079-0.09913.9250.0840.0840.0000.0000.0000.000
23A491GLU-1-0.946-0.81114.216-0.419-0.4190.0000.0000.0000.000
24A492VAL00.070-0.10315.5250.0530.0530.0000.0000.0000.000
25A492VAL0-0.0730.10215.5480.0000.0000.0000.0000.0000.000
26A493THR00.044-0.08617.2950.0430.0430.0000.0000.0000.000
27A493THR0-0.0760.04217.1930.0160.0160.0000.0000.0000.000
28A494LYS00.011-0.12118.5100.0440.0440.0000.0000.0000.000
29A494LYS10.8911.08518.3770.2460.2460.0000.0000.0000.000
30A495GLN00.134-0.08119.8000.0350.0350.0000.0000.0000.000
31A495GLN0-0.1330.06517.9360.0100.0100.0000.0000.0000.000
32A496VAL00.107-0.08021.5450.0210.0210.0000.0000.0000.000
33A496VAL0-0.0950.09021.6950.0020.0020.0000.0000.0000.000
34A497SER00.041-0.08323.2320.0200.0200.0000.0000.0000.000
35A497SER0-0.0400.07123.9020.0040.0040.0000.0000.0000.000
36A498MET00.048-0.10224.3810.0200.0200.0000.0000.0000.000
37A498MET0-0.1050.08123.143-0.009-0.0090.0000.0000.0000.000
38A499ALA00.126-0.07525.6560.0130.0130.0000.0000.0000.000
39A499ALA0-0.0780.10426.074-0.001-0.0010.0000.0000.0000.000
40A500ARG00.134-0.05427.5100.0110.0110.0000.0000.0000.000
41A500ARG10.7951.02625.3410.1430.1430.0000.0000.0000.000
42A501GLN00.091-0.10628.9960.0110.0110.0000.0000.0000.000
43A501GLN0-0.1490.06229.562-0.002-0.0020.0000.0000.0000.000
44A502ALA00.122-0.08030.0890.0100.0100.0000.0000.0000.000
45A502ALA0-0.0910.08930.151-0.002-0.0020.0000.0000.0000.000
46A503GLN00.096-0.07331.6990.0060.0060.0000.0000.0000.000
47A503GLN0-0.1830.03132.120-0.008-0.0080.0000.0000.0000.000
48A504VAL00.108-0.08733.6720.0060.0060.0000.0000.0000.000
49A504VAL0-0.1090.08834.1210.0000.0000.0000.0000.0000.000
50A505ASP00.067-0.09034.8600.0080.0080.0000.0000.0000.000
51A505ASP-1-0.899-0.79734.542-0.099-0.0990.0000.0000.0000.000
52A506LEU00.120-0.09235.8060.0060.0060.0000.0000.0000.000
53A506LEU0-0.0840.09934.274-0.001-0.0010.0000.0000.0000.000
54A507GLU00.116-0.10037.5150.0040.0040.0000.0000.0000.000
55A507GLU-1-0.970-0.82037.454-0.085-0.0850.0000.0000.0000.000
56A508ARG00.051-0.10039.5010.0050.0050.0000.0000.0000.000
57A508ARG10.7180.99038.2140.0800.0800.0000.0000.0000.000
58A509GLU00.118-0.11640.2640.0050.0050.0000.0000.0000.000
59A509GLU-1-1.029-0.85638.979-0.087-0.0870.0000.0000.0000.000
60A510LYS00.102-0.09941.4280.0040.0040.0000.0000.0000.000
61A510LYS10.7390.99441.6960.0630.0630.0000.0000.0000.000
62A511LYS00.108-0.08343.3110.0030.0030.0000.0000.0000.000
63A511LYS10.6810.96844.4470.0510.0510.0000.0000.0000.000
64A512GLU00.065-0.11845.2660.0040.0040.0000.0000.0000.000
65A512GLU-1-0.999-0.84543.820-0.065-0.0650.0000.0000.0000.000
66A513LEU00.050-0.10545.9060.0040.0040.0000.0000.0000.000
67A513LEU0-0.0640.10643.5620.0000.0000.0000.0000.0000.000
68A514GLU00.099-0.09147.3350.0020.0020.0000.0000.0000.000
69A514GLU-1-0.909-0.80046.895-0.059-0.0590.0000.0000.0000.000
70A515ASP00.121-0.10349.2230.0020.0020.0000.0000.0000.000
71A515ASP-1-0.892-0.80350.496-0.050-0.0500.0000.0000.0000.000
72A516SER00.005-0.09250.6480.0030.0030.0000.0000.0000.000
73A516SER0-0.0710.04949.9590.0000.0000.0000.0000.0000.000
74A517LEU00.042-0.11451.4340.0020.0020.0000.0000.0000.000
75A517LEU0-0.0980.10649.7290.0000.0000.0000.0000.0000.000
76A518GLU00.162-0.10452.9760.0020.0020.0000.0000.0000.000
77A518GLU-1-1.041-0.84854.321-0.041-0.0410.0000.0000.0000.000
78A519ARG00.053-0.10955.2760.0020.0020.0000.0000.0000.000
79A519ARG10.8191.05651.4880.0460.0460.0000.0000.0000.000
80A520ILE00.053-0.08155.9690.0020.0020.0000.0000.0000.000
81A520ILE0-0.0690.09954.7310.0000.0000.0000.0000.0000.000
82A521SER00.071-0.08257.1430.0010.0010.0000.0000.0000.000
83A521SER0-0.0120.08557.0750.0000.0000.0000.0000.0000.000
84A522ASP00.020-0.11458.8130.0010.0010.0000.0000.0000.000
85A522ASP-1-0.901-0.79160.606-0.033-0.0330.0000.0000.0000.000
86A523GLN00.049-0.12860.7810.0020.0020.0000.0000.0000.000
87A523GLN0-0.1090.09660.4960.0000.0000.0000.0000.0000.000
88A524GLY00.020-0.09161.4330.0010.0010.0000.0000.0000.000
89A525GLN00.1320.03962.9360.0010.0010.0000.0000.0000.000
90A525GLN0-0.0910.09063.3380.0000.0000.0000.0000.0000.000
91A526ARG00.067-0.10264.8250.0010.0010.0000.0000.0000.000
92A526ARG10.7431.00462.8040.0320.0320.0000.0000.0000.000
93A527LYS00.138-0.07066.1860.0010.0010.0000.0000.0000.000
94A527LYS10.8401.04665.0540.0310.0310.0000.0000.0000.000
95A528THR00.037-0.07967.1980.0010.0010.0000.0000.0000.000
96A528THR0-0.0820.04366.2420.0000.0000.0000.0000.0000.000
97A529GLN00.000-0.11468.7980.0010.0010.0000.0000.0000.000
98A529GLN0-0.0670.10169.7850.0010.0010.0000.0000.0000.000
99A530GLU00.147-0.07070.9030.0010.0010.0000.0000.0000.000
100A530GLU-1-0.976-0.86968.720-0.029-0.0290.0000.0000.0000.000
101A531GLN00.098-0.08071.5800.0010.0010.0000.0000.0000.000
102A531GLN0-0.1300.07271.375-0.001-0.0010.0000.0000.0000.000
103A532LEU00.040-0.10373.1810.0010.0010.0000.0000.0000.000
104A532LEU0-0.0710.09372.3660.0000.0000.0000.0000.0000.000
105A533GLU00.080-0.12775.1780.0010.0010.0000.0000.0000.000
106A533GLU-1-1.008-0.84174.375-0.024-0.0240.0000.0000.0000.000
107A534VAL00.106-0.09076.3320.0010.0010.0000.0000.0000.000
108A534VAL0-0.1150.09575.8080.0000.0000.0000.0000.0000.000
109A535LEU00.118-0.06877.2720.0010.0010.0000.0000.0000.000
110A535LEU0-0.1230.06976.6680.0000.0000.0000.0000.0000.000
111A536GLU00.051-0.13178.9070.0010.0010.0000.0000.0000.000
112A536GLU-1-0.879-0.78079.939-0.020-0.0200.0000.0000.0000.000
113A537SER00.034-0.10080.8890.0010.0010.0000.0000.0000.000
114A537SER0-0.0680.05281.4080.0000.0000.0000.0000.0000.000
115A538LEU00.151-0.07581.8740.0010.0010.0000.0000.0000.000
116A538LEU0-0.1020.10581.0510.0000.0000.0000.0000.0000.000
117A539LYS00.019-0.13383.5110.0000.0000.0000.0000.0000.000
118A539LYS10.7820.99581.3800.0200.0200.0000.0000.0000.000
119A540GLN00.067-0.08485.4580.0010.0010.0000.0000.0000.000
120A540GLN0-0.1620.07184.7000.0000.0000.0000.0000.0000.000
121A541GLU00.089-0.11086.5700.0010.0010.0000.0000.0000.000
122A541GLU-1-0.939-0.78383.983-0.020-0.0200.0000.0000.0000.000
123A542LEU00.138-0.07887.5590.0010.0010.0000.0000.0000.000
124A542LEU0-0.0920.10787.5070.0000.0000.0000.0000.0000.000
125A543ALA00.094-0.11289.3500.0000.0000.0000.0000.0000.000
126A543ALA0-0.0790.10090.0750.0000.0000.0000.0000.0000.000
127A544THR0-0.082-0.14491.1650.0000.0000.0000.0000.0000.000
128A544THR0-0.0760.06891.0120.0000.0000.0000.0000.0000.000
129A545SER00.144-0.02692.0820.0000.0000.0000.0000.0000.000
130A545SER0-0.0270.08391.8770.0000.0000.0000.0000.0000.000
131A546GLN00.057-0.11593.4790.0000.0000.0000.0000.0000.000
132A546GLN0-0.1010.07792.8920.0000.0000.0000.0000.0000.000
133A547ARG00.092-0.07295.3860.0000.0000.0000.0000.0000.000
134A547ARG10.8101.03292.8940.0150.0150.0000.0000.0000.000
135A548GLU00.072-0.11696.8040.0000.0000.0000.0000.0000.000
136A548GLU-1-0.975-0.84394.586-0.015-0.0150.0000.0000.0000.000
137A549LEU00.066-0.10497.6560.0000.0000.0000.0000.0000.000
138A549LEU0-0.0720.10795.5280.0000.0000.0000.0000.0000.000
139A550GLN00.183-0.05799.3300.0000.0000.0000.0000.0000.000
140A550GLN0-0.1400.077100.1510.0000.0000.0000.0000.0000.000
141A551VAL00.036-0.129101.4200.0000.0000.0000.0000.0000.000
142A551VAL0-0.0940.108101.8870.0000.0000.0000.0000.0000.000
143A552LEU00.091-0.091102.2690.0000.0000.0000.0000.0000.000
144A552LEU0-0.0770.112100.1250.0000.0000.0000.0000.0000.000
145A553GLN00.064-0.100103.4890.0000.0000.0000.0000.0000.000
146A553GLN0-0.0950.081102.1230.0000.0000.0000.0000.0000.000
147A554GLY00.034-0.084105.2850.0000.0000.0000.0000.0000.000
148A555SER00.0520.021106.9340.0000.0000.0000.0000.0000.000
149A555SER0-0.0780.046106.3660.0000.0000.0000.0000.0000.000
150A556LEU00.106-0.070107.6860.0000.0000.0000.0000.0000.000
151A556LEU0-0.1250.089107.1720.0000.0000.0000.0000.0000.000
152A557GLU00.135-0.100109.2040.0000.0000.0000.0000.0000.000
153A557GLU-1-1.049-0.872109.992-0.011-0.0110.0000.0000.0000.000
154A558THR0-0.015-0.110111.4140.0000.0000.0000.0000.0000.000
155A558THR0-0.0870.046111.4270.0000.0000.0000.0000.0000.000
156A559SER00.043-0.079112.2500.0000.0000.0000.0000.0000.000
157A559SER0-0.0840.043111.9890.0000.0000.0000.0000.0000.000
158A560ALA00.129-0.073113.2970.0000.0000.0000.0000.0000.000
159A560ALA0-0.0820.109113.2620.0000.0000.0000.0000.0000.000
160A561GLN00.086-0.111115.0320.0000.0000.0000.0000.0000.000
161A561GLN0-0.1250.087116.8290.0000.0000.0000.0000.0000.000
162A562SER00.023-0.102116.9530.0000.0000.0000.0000.0000.000
163A562SER0-0.0250.077117.1690.0000.0000.0000.0000.0000.000
164A563GLU00.009-0.116117.6160.0000.0000.0000.0000.0000.000
165A563GLU-1-0.950-0.811114.541-0.011-0.0110.0000.0000.0000.000
166A564ALA00.110-0.096119.0250.0000.0000.0000.0000.0000.000
167A564ALA0-0.0940.100119.7740.0000.0000.0000.0000.0000.000
168A565ASN00.047-0.093121.1160.0000.0000.0000.0000.0000.000
169A565ASN0-0.1010.065121.8730.0000.0000.0000.0000.0000.000
170A566TRP00.091-0.083122.1210.0000.0000.0000.0000.0000.000
171A566TRP0-0.0960.082119.8240.0000.0000.0000.0000.0000.000
172A567ALA00.167-0.068123.1580.0000.0000.0000.0000.0000.000
173A567ALA0-0.0980.096123.1280.0000.0000.0000.0000.0000.000
174A568ALA00.072-0.100124.8730.0000.0000.0000.0000.0000.000
175A568ALA0-0.1000.091126.3590.0000.0000.0000.0000.0000.000
176A569GLU00.032-0.130126.8980.0000.0000.0000.0000.0000.000
177A569GLU-1-1.037-0.877126.589-0.008-0.0080.0000.0000.0000.000
178A570PHE00.133-0.072127.5290.0000.0000.0000.0000.0000.000
179A570PHE0-0.1350.075127.1240.0000.0000.0000.0000.0000.000
180A571ALA00.109-0.091129.0310.0000.0000.0000.0000.0000.000
181A571ALA0-0.0980.095129.3440.0000.0000.0000.0000.0000.000
182A572GLU00.057-0.125130.8670.0000.0000.0000.0000.0000.000
183A572GLU-1-0.878-0.763132.544-0.008-0.0080.0000.0000.0000.000
184A573LEU00.149-0.076132.4600.0000.0000.0000.0000.0000.000
185A573LEU0-0.1210.099132.1720.0000.0000.0000.0000.0000.000
186A574GLU00.108-0.097132.8610.0000.0000.0000.0000.0000.000
187A574GLU-1-0.954-0.818131.312-0.008-0.0080.0000.0000.0000.000
188A575LYS00.129-0.084134.1510.0000.0000.0000.0000.0000.000
189A575LYS10.6660.971135.8890.0080.0080.0000.0000.0000.000
190A576GLU00.059-0.136136.8620.0000.0000.0000.0000.0000.000
191A576GLU-1-1.004-0.849137.024-0.007-0.0070.0000.0000.0000.000
192A577ARG00.114-0.080136.9960.0000.0000.0000.0000.0000.000
193A577ARG10.6090.911133.7400.0080.0080.0000.0000.0000.000
194A578ASP00.070-0.130138.2460.0000.0000.0000.0000.0000.000
195A578ASP-1-0.926-0.790137.143-0.008-0.0080.0000.0000.0000.000
196A579SER00.001-0.106139.9640.0000.0000.0000.0000.0000.000
197A579SER0-0.0950.044140.8220.0000.0000.0000.0000.0000.000
198A580LEU0-0.040-0.114142.0210.0000.0000.0000.0000.0000.000
199A580LEU0-0.1070.094141.9240.0000.0000.0000.0000.0000.000
200A581VAL0-0.123-0.165142.3620.0000.0000.0000.0000.0000.000
201A581VAL00.0530.038140.8130.0000.0000.0000.0000.0000.000