Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 3QVNL

Calculation Name: 3NRO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NRO

Chain ID: A

ChEMBL ID:

UniProt ID: Q8Y889

Base Structure: X-ray

Registration Date: 2023-06-19

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

DOI:


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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2816368.577786
FMO2-HF: Nuclear repulsion 2724705.216481
FMO2-HF: Total energy -91663.361305
FMO2-MP2: Total energy -91928.722093


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:68:GLU)


Summations of interaction energy for fragment #1(A:68:GLU)
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.
-20.214-16.85914.951-9.577-8.730.061
Interaction energy analysis for fragmet #1(A:68:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.814 / q_NPA : -0.898
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].
3A70LYS10.8970.9443.153-51.023-47.0490.011-2.146-1.8400.011
4A71LYS10.9370.9883.573-34.303-33.9540.001-0.070-0.2790.000
5A72PRO0-0.0120.0165.1931.5741.664-0.001-0.001-0.0880.000
6A73PHE0-0.0180.0026.3820.4290.4290.0000.0000.0000.000
7A74SER00.020-0.0248.306-1.250-1.2500.0000.0000.0000.000
8A75VAL00.006-0.00110.9000.9450.9450.0000.0000.0000.000
9A76LEU00.0180.01913.024-0.775-0.7750.0000.0000.0000.000
10A77LEU0-0.011-0.00115.9430.1090.1090.0000.0000.0000.000
11A78MET0-0.037-0.02618.675-0.848-0.8480.0000.0000.0000.000
12A79GLY00.0230.01922.0440.2440.2440.0000.0000.0000.000
13A80SER0-0.035-0.03825.085-0.331-0.3310.0000.0000.0000.000
14A89GLY0-0.004-0.01931.451-0.093-0.0930.0000.0000.0000.000
15A90ARG10.8810.94429.541-8.807-8.8070.0000.0000.0000.000
16A91ALA00.0040.01325.6010.1310.1310.0000.0000.0000.000
17A92ASP-1-0.879-0.93127.5899.0909.0900.0000.0000.0000.000
18A93THR0-0.074-0.04424.656-0.232-0.2320.0000.0000.0000.000
19A94ILE00.0420.02222.1620.4010.4010.0000.0000.0000.000
20A95ILE00.0310.02418.974-0.265-0.2650.0000.0000.0000.000
21A96LEU0-0.0040.01215.9350.6130.6130.0000.0000.0000.000
22A97ALA00.016-0.00514.760-0.358-0.3580.0000.0000.0000.000
23A98THR00.0100.00211.9890.8400.8400.0000.0000.0000.000
24A99ALA0-0.0120.0209.111-0.583-0.5830.0000.0000.0000.000
25A100ASN00.1120.0499.0633.0883.0880.0000.0000.0000.000
26A101LYS10.9300.9747.714-26.280-26.2800.0000.0000.0000.000
27A102GLN0-0.073-0.0418.048-1.460-1.4600.0000.0000.0000.000
28A103GLN0-0.025-0.03411.911-0.427-0.4270.0000.0000.0000.000
29A104ASN0-0.055-0.02312.6520.5360.5360.0000.0000.0000.000
30A105ALA00.021-0.00713.283-0.902-0.9020.0000.0000.0000.000
31A106VAL0-0.069-0.04013.0471.2881.2880.0000.0000.0000.000
32A107GLU-1-0.839-0.91514.97713.05313.0530.0000.0000.0000.000
33A108MET0-0.032-0.03516.5800.6180.6180.0000.0000.0000.000
34A109VAL0-0.0060.00518.787-0.595-0.5950.0000.0000.0000.000
35A110SER0-0.007-0.00921.5850.3380.3380.0000.0000.0000.000
36A111ILE00.020-0.00423.204-0.339-0.3390.0000.0000.0000.000
37A112PRO00.0280.03526.026-0.014-0.0140.0000.0000.0000.000
38A113ARG10.9530.97829.146-8.938-8.9380.0000.0000.0000.000
39A114ASP-1-0.887-0.97130.1288.4118.4110.0000.0000.0000.000
40A115THR0-0.025-0.02028.766-0.208-0.2080.0000.0000.0000.000
41A116LYS10.9210.96631.337-7.778-7.7780.0000.0000.0000.000
42A117VAL0-0.036-0.02127.9070.1610.1610.0000.0000.0000.000
43A118ASP-1-0.962-0.97930.8588.3568.3560.0000.0000.0000.000
44A119TYR0-0.041-0.03228.8930.4120.4120.0000.0000.0000.000
45A120GLY00.1160.06231.780-0.088-0.0880.0000.0000.0000.000
46A121ASN0-0.063-0.02934.4020.0880.0880.0000.0000.0000.000
47A122GLY00.012-0.01037.378-0.232-0.2320.0000.0000.0000.000
48A123ASP-1-1.002-0.97334.5858.1908.1900.0000.0000.0000.000
49A124ILE00.004-0.00835.1230.1550.1550.0000.0000.0000.000
50A125GLY00.012-0.00934.332-0.133-0.1330.0000.0000.0000.000
51A126LYS10.8860.95332.802-8.003-8.0030.0000.0000.0000.000
52A127ILE00.008-0.01026.1010.0870.0870.0000.0000.0000.000
53A128ASN00.0220.00728.4770.0830.0830.0000.0000.0000.000
54A129ALA0-0.028-0.02929.8220.0790.0790.0000.0000.0000.000
55A130SER0-0.0070.01731.8610.0200.0200.0000.0000.0000.000
56A131TYR00.0340.02927.3450.1330.1330.0000.0000.0000.000
57A132SER0-0.009-0.00926.0360.1150.1150.0000.0000.0000.000
58A133ASN0-0.0270.00627.0110.2100.2100.0000.0000.0000.000
59A134GLY00.018-0.00528.098-0.265-0.2650.0000.0000.0000.000
60A135GLY0-0.0030.01024.6340.2200.2200.0000.0000.0000.000
61A136PRO00.0610.02121.004-0.052-0.0520.0000.0000.0000.000
62A137SER00.003-0.00620.071-0.006-0.0060.0000.0000.0000.000
63A138GLY00.0640.03521.0220.0240.0240.0000.0000.0000.000
64A139THR00.018-0.00922.517-0.343-0.3430.0000.0000.0000.000
65A140VAL00.0030.01217.241-0.038-0.0380.0000.0000.0000.000
66A141SER00.0720.04420.387-0.101-0.1010.0000.0000.0000.000
67A142ALA0-0.009-0.00822.702-0.232-0.2320.0000.0000.0000.000
68A143VAL0-0.043-0.03320.026-0.268-0.2680.0000.0000.0000.000
69A144GLU-1-0.904-0.95618.25514.08014.0800.0000.0000.0000.000
70A145LYS10.7930.91121.671-10.492-10.4920.0000.0000.0000.000
71A146LEU0-0.038-0.01424.941-0.282-0.2820.0000.0000.0000.000
72A147MET0-0.045-0.03421.581-0.044-0.0440.0000.0000.0000.000
73A148PRO00.0050.02121.4710.4640.4640.0000.0000.0000.000
74A149GLY0-0.046-0.03220.6840.3300.3300.0000.0000.0000.000
75A150VAL0-0.006-0.01016.2250.5280.5280.0000.0000.0000.000
76A151PRO00.0330.05113.330-0.427-0.4270.0000.0000.0000.000
77A152VAL00.0380.01913.9910.7010.7010.0000.0000.0000.000
78A153ASP-1-0.895-0.9518.77823.80023.8000.0000.0000.0000.000
79A154TYR0-0.034-0.0266.1021.0791.0790.0000.0000.0000.000
80A155PHE00.033-0.00412.107-1.049-1.0490.0000.0000.0000.000
81A156ILE0-0.028-0.00813.9980.3780.3780.0000.0000.0000.000
82A157SER0-0.016-0.00817.364-0.467-0.4670.0000.0000.0000.000
83A158ILE00.0070.01621.0400.0490.0490.0000.0000.0000.000
84A159ASN00.1190.08423.5360.0780.0780.0000.0000.0000.000
85A160MET0-0.039-0.03727.0870.2150.2150.0000.0000.0000.000
86A161GLU-1-0.969-1.00228.7849.4709.4700.0000.0000.0000.000
87A162GLY00.0660.01225.8390.1000.1000.0000.0000.0000.000
88A163PHE0-0.066-0.02723.9440.3420.3420.0000.0000.0000.000
89A164LYS10.9130.95825.716-9.203-9.2030.0000.0000.0000.000
90A165ASP-1-0.792-0.89026.79110.89410.8940.0000.0000.0000.000
91A166LEU0-0.081-0.04120.1500.4180.4180.0000.0000.0000.000
92A167VAL0-0.024-0.00623.3500.4540.4540.0000.0000.0000.000
93A168ASP-1-0.822-0.92825.68310.52610.5260.0000.0000.0000.000
94A169ALA0-0.0350.00223.6090.0460.0460.0000.0000.0000.000
95A170VAL0-0.055-0.00420.2560.3770.3770.0000.0000.0000.000
96A171GLY0-0.038-0.03122.6080.2020.2020.0000.0000.0000.000
97A172GLY0-0.037-0.02325.752-0.123-0.1230.0000.0000.0000.000
98A173ILE0-0.0570.00222.9390.6360.6360.0000.0000.0000.000
99A174THR0-0.036-0.00124.681-0.673-0.6730.0000.0000.0000.000
100A175VAL00.0550.01525.5030.4620.4620.0000.0000.0000.000
101A176TYR0-0.025-0.01227.588-0.508-0.5080.0000.0000.0000.000
102A177ASN00.0280.01529.5410.1140.1140.0000.0000.0000.000
103A178ASP-1-0.907-0.94331.9179.1939.1930.0000.0000.0000.000
104A179ILE0-0.045-0.01733.655-0.323-0.3230.0000.0000.0000.000
105A180ASP-1-0.902-0.97836.2277.5307.5300.0000.0000.0000.000
106A181LEU0-0.052-0.01635.176-0.132-0.1320.0000.0000.0000.000
107A182THR00.0910.02239.0260.0650.0650.0000.0000.0000.000
108A183GLU-1-0.956-0.96241.4307.0157.0150.0000.0000.0000.000
109A184VAL0-0.101-0.03942.363-0.113-0.1130.0000.0000.0000.000
110A185ASN00.005-0.00438.872-0.078-0.0780.0000.0000.0000.000
111A186SER00.007-0.01338.311-0.025-0.0250.0000.0000.0000.000
112A187LYS10.9411.00736.872-8.420-8.4200.0000.0000.0000.000
113A188PHE0-0.066-0.07634.4490.2160.2160.0000.0000.0000.000
114A189VAL00.0280.02137.090-0.049-0.0490.0000.0000.0000.000
115A190LYS10.9760.99036.301-7.746-7.7460.0000.0000.0000.000
116A191GLY0-0.029-0.02333.896-0.060-0.0600.0000.0000.0000.000
117A192ASN0-0.021-0.02628.9220.4630.4630.0000.0000.0000.000
118A193ILE0-0.0380.03131.550-0.221-0.2210.0000.0000.0000.000
119A194THR0-0.017-0.03428.8950.1990.1990.0000.0000.0000.000
120A195LEU0-0.072-0.00629.529-0.372-0.3720.0000.0000.0000.000
121A196ASN00.0920.03829.6850.3800.3800.0000.0000.0000.000
122A197GLY00.0650.03629.0050.0740.0740.0000.0000.0000.000
123A198THR0-0.021-0.03329.963-0.037-0.0370.0000.0000.0000.000
124A199GLU-1-0.928-0.97532.6169.0919.0910.0000.0000.0000.000
125A200ALA00.0540.03028.013-0.122-0.1220.0000.0000.0000.000
126A201LEU0-0.039-0.01629.538-0.053-0.0530.0000.0000.0000.000
127A202GLN0-0.028-0.02731.001-0.061-0.0610.0000.0000.0000.000
128A203TYR00.0000.01329.028-0.305-0.3050.0000.0000.0000.000
129A204VAL00.0240.00927.412-0.159-0.1590.0000.0000.0000.000
130A205ARG10.8690.93230.482-9.018-9.0180.0000.0000.0000.000
131A206ILE0-0.0070.02933.311-0.293-0.2930.0000.0000.0000.000
132A207ARG10.9100.92434.924-8.032-8.0320.0000.0000.0000.000
133A208HIS00.0210.01037.5470.1430.1430.0000.0000.0000.000
134A209GLU-1-0.890-0.94139.4057.4657.4650.0000.0000.0000.000
135A210ASP-1-0.742-0.84535.0608.5408.5400.0000.0000.0000.000
136A211PRO00.0520.02638.2570.0070.0070.0000.0000.0000.000
137A212ARG10.7810.88431.763-9.122-9.1220.0000.0000.0000.000
138A213GLY0-0.031-0.02436.2190.1010.1010.0000.0000.0000.000
139A214ASP-1-0.850-0.93133.7468.6648.6640.0000.0000.0000.000
140A215PHE0-0.0020.00329.6050.2490.2490.0000.0000.0000.000
141A216GLY00.0510.02930.9000.3030.3030.0000.0000.0000.000
142A217ARG10.8640.91830.810-8.785-8.7850.0000.0000.0000.000
143A218GLN0-0.003-0.00325.2940.6550.6550.0000.0000.0000.000
144A219ASP-1-0.916-0.94526.34910.60910.6090.0000.0000.0000.000
145A220ARG10.8940.94126.651-8.656-8.6560.0000.0000.0000.000
146A221GLN0-0.021-0.01924.1700.4460.4460.0000.0000.0000.000
147A222ARG10.9430.98021.878-11.737-11.7370.0000.0000.0000.000
148A223ASP-1-0.876-0.94522.43611.66911.6690.0000.0000.0000.000
149A224VAL0-0.004-0.01523.5680.3930.3930.0000.0000.0000.000
150A225ILE0-0.0190.00718.1980.4620.4620.0000.0000.0000.000
151A226ILE0-0.026-0.01918.0880.8180.8180.0000.0000.0000.000
152A227GLY00.019-0.01619.7870.4390.4390.0000.0000.0000.000
153A228ILE00.013-0.00318.6360.1500.1500.0000.0000.0000.000
154A229ALA00.0280.00215.2590.6520.6520.0000.0000.0000.000
155A230ASN0-0.051-0.02816.2711.7021.7020.0000.0000.0000.000
156A231LYS10.8670.94618.200-13.856-13.8560.0000.0000.0000.000
157A232VAL0-0.062-0.00912.9050.5860.5860.0000.0000.0000.000
158A243SER00.014-0.01113.7160.2650.2650.0000.0000.0000.000
159A244ILE0-0.021-0.00112.836-1.039-1.0390.0000.0000.0000.000
160A245MET00.0340.01315.857-0.152-0.1520.0000.0000.0000.000
161A246LYS10.8430.92916.130-17.422-17.4220.0000.0000.0000.000
162A247ALA00.0370.03521.310-0.221-0.2210.0000.0000.0000.000
163A248VAL00.0280.02222.783-0.389-0.3890.0000.0000.0000.000
164A249GLY00.049-0.01223.6950.2680.2680.0000.0000.0000.000
165A250ASP-1-0.868-0.92423.76811.46611.4660.0000.0000.0000.000
166A251ASN0-0.109-0.04225.915-0.323-0.3230.0000.0000.0000.000
167A252PHE00.0370.00116.8710.3780.3780.0000.0000.0000.000
168A253GLN00.0380.03319.792-0.341-0.3410.0000.0000.0000.000
169A254THR0-0.014-0.01814.3830.6280.6280.0000.0000.0000.000
170A255ASN00.0200.01511.991-0.341-0.3410.0000.0000.0000.000
171A256MET0-0.054-0.0069.9660.6890.6890.0000.0000.0000.000
172A257THR0-0.025-0.0448.457-2.037-2.0370.0000.0000.0000.000
173A258LEU00.0740.0199.4451.8601.8600.0000.0000.0000.000
174A259THR0-0.051-0.0337.802-0.464-0.4640.0000.0000.0000.000
175A260ASP-1-0.830-0.8805.20734.94934.9490.0000.0000.0000.000
176A261ILE00.0250.0116.1532.2492.2490.0000.0000.0000.000
177A262THR0-0.014-0.0276.632-0.739-0.7390.0000.0000.0000.000
178A263SER0-0.031-0.0161.759-16.336-19.16014.876-6.612-5.4400.048
179A264MET0-0.008-0.0034.306-1.983-1.8440.000-0.069-0.0700.000
180A265ALA0-0.025-0.0056.286-1.616-1.6160.0000.0000.0000.000
181A266ALA0-0.0050.0055.157-1.971-1.910-0.001-0.001-0.0590.000
182A267ASN0-0.028-0.0293.252-15.314-14.4020.022-0.420-0.5140.003
183A268TYR0-0.076-0.0382.926-3.640-2.9860.043-0.258-0.440-0.001
184A269SER00.0770.0368.244-0.282-0.2820.0000.0000.0000.000
185A270SER0-0.014-0.01511.161-0.990-0.9900.0000.0000.0000.000
186A271VAL0-0.0410.00313.261-1.020-1.0200.0000.0000.0000.000
187A272LEU00.0030.01015.202-1.023-1.0230.0000.0000.0000.000
188A273LYS10.9230.94117.681-13.690-13.6900.0000.0000.0000.000
189A274ASN00.001-0.00117.122-0.452-0.4520.0000.0000.0000.000
190A275VAL00.0170.03416.9950.4000.4000.0000.0000.0000.000
191A276ASP-1-0.912-0.94619.01412.26112.2610.0000.0000.0000.000
192A277SER0-0.027-0.00720.8140.0980.0980.0000.0000.0000.000
193A278GLN0-0.023-0.01922.397-0.190-0.1900.0000.0000.0000.000
194A279GLU-1-0.941-0.96124.5419.9729.9720.0000.0000.0000.000
195A280LEU0-0.070-0.01126.143-0.194-0.1940.0000.0000.0000.000
196A281LYS10.9840.99027.686-8.937-8.9370.0000.0000.0000.000
197A282GLY00.017-0.01531.2660.1530.1530.0000.0000.0000.000
198A283GLU-1-0.979-0.98134.0307.1027.1020.0000.0000.0000.000
199A284GLY0-0.0120.00037.2700.0990.0990.0000.0000.0000.000
200A285GLU-1-0.898-0.95938.6757.2487.2480.0000.0000.0000.000
201A286MET0-0.037-0.02340.7020.1600.1600.0000.0000.0000.000
202A287ILE0-0.011-0.00339.604-0.074-0.0740.0000.0000.0000.000
203A288TYR00.0200.03243.4400.0760.0760.0000.0000.0000.000
204A289SER0-0.021-0.02343.0600.1780.1780.0000.0000.0000.000
205A290GLU-1-0.893-0.96045.0006.0146.0140.0000.0000.0000.000
206A291SER0-0.088-0.02343.252-0.095-0.0950.0000.0000.0000.000
207A292TYR0-0.001-0.01140.694-0.040-0.0400.0000.0000.0000.000
208A293GLY00.0320.03546.805-0.115-0.1150.0000.0000.0000.000
209A294PHE0-0.058-0.03845.237-0.119-0.1190.0000.0000.0000.000
210A295ASP-1-0.877-0.94745.4556.4676.4670.0000.0000.0000.000
211A296LEU0-0.080-0.04140.5580.0410.0410.0000.0000.0000.000
212A297TYR0-0.006-0.00936.410-0.069-0.0690.0000.0000.0000.000
213A298TYR00.0150.00135.6400.2960.2960.0000.0000.0000.000
214A299PHE0-0.0110.02331.431-0.170-0.1700.0000.0000.0000.000
215A300ALA00.0340.00933.5320.2800.2800.0000.0000.0000.000
216A301PRO00.0010.00130.087-0.030-0.0300.0000.0000.0000.000
217A302ASP-1-0.805-0.89532.0988.3318.3310.0000.0000.0000.000
218A303LYS10.9680.98131.417-8.281-8.2810.0000.0000.0000.000
219A304THR00.0300.02030.5970.2460.2460.0000.0000.0000.000
220A305ASP-1-0.882-0.95229.32010.00010.0000.0000.0000.0000.000
221A306LEU0-0.016-0.01825.7460.3710.3710.0000.0000.0000.000
222A307GLU-1-0.902-0.94925.88010.68510.6850.0000.0000.0000.000
223A308ARG10.9280.97923.987-10.620-10.6200.0000.0000.0000.000
224A309ILE00.0260.00222.0630.4940.4940.0000.0000.0000.000
225A310ILE00.0140.01221.6160.6930.6930.0000.0000.0000.000
226A311THR0-0.088-0.04921.1500.5210.5210.0000.0000.0000.000
227A312MET0-0.101-0.04719.7760.6500.6500.0000.0000.0000.000
228A313PHE00.0940.02317.3010.5850.5850.0000.0000.0000.000
229A314LYS10.9330.99916.042-11.963-11.9630.0000.0000.0000.000
230A315LYS10.8800.93716.468-12.057-12.0570.0000.0000.0000.000
231A316SER0-0.059-0.02914.2090.5110.5110.0000.0000.0000.000
232A317LEU0-0.040-0.02110.8121.2161.2160.0000.0000.0000.000
233A318ASP-1-0.837-0.93712.33620.16520.1650.0000.0000.0000.000
234A319ILE0-0.094-0.02814.588-0.515-0.5150.0000.0000.0000.000
235A320THR0-0.047-0.01216.114-0.475-0.4750.0000.0000.0000.000