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: LJ3L9

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 OptHSide
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 -2817878.655116
FMO2-HF: Nuclear repulsion 2726212.758302
FMO2-HF: Total energy -91665.896814
FMO2-MP2: Total energy -91930.985995


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.
-69.068-73.24833.063-16.97-11.9130.118
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 : -0.753 / q_NPA : -0.852
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].
3A70LYS10.8490.9143.045-75.348-71.0230.013-2.202-2.1360.010
4A71LYS10.8810.9553.498-34.354-33.9870.001-0.074-0.2940.000
5A72PRO00.0130.0215.1401.6151.713-0.001-0.001-0.0960.000
6A73PHE0-0.0290.0005.8140.2450.2450.0000.0000.0000.000
7A74SER00.039-0.0188.284-1.029-1.0290.0000.0000.0000.000
8A75VAL0-0.018-0.01210.9130.9280.9280.0000.0000.0000.000
9A76LEU00.0150.01513.046-0.773-0.7730.0000.0000.0000.000
10A77LEU0-0.0060.00515.7560.0940.0940.0000.0000.0000.000
11A78MET0-0.030-0.01718.711-0.906-0.9060.0000.0000.0000.000
12A79GLY00.0330.02422.0480.2380.2380.0000.0000.0000.000
13A80SER0-0.063-0.06725.088-0.556-0.5560.0000.0000.0000.000
14A89GLY00.0500.02731.422-0.049-0.0490.0000.0000.0000.000
15A90ARG10.8590.91729.533-8.869-8.8690.0000.0000.0000.000
16A91ALA00.0170.03625.5010.1320.1320.0000.0000.0000.000
17A92ASP-1-0.822-0.90327.5449.1469.1460.0000.0000.0000.000
18A93THR0-0.098-0.05524.547-0.188-0.1880.0000.0000.0000.000
19A94ILE00.0510.02622.4130.3970.3970.0000.0000.0000.000
20A95ILE00.0410.03019.151-0.229-0.2290.0000.0000.0000.000
21A96LEU0-0.0060.01515.8090.6500.6500.0000.0000.0000.000
22A97ALA00.009-0.00814.948-0.333-0.3330.0000.0000.0000.000
23A98THR00.0050.00311.9860.7280.7280.0000.0000.0000.000
24A99ALA0-0.0100.0179.049-0.676-0.6760.0000.0000.0000.000
25A100ASN00.025-0.0069.0612.2362.2360.0000.0000.0000.000
26A101LYS10.9250.9487.726-27.268-27.2680.0000.0000.0000.000
27A102GLN0-0.044-0.0287.964-1.667-1.6670.0000.0000.0000.000
28A103GLN0-0.029-0.01911.857-0.794-0.7940.0000.0000.0000.000
29A104ASN0-0.032-0.00412.6220.8010.8010.0000.0000.0000.000
30A105ALA00.0360.00713.227-1.087-1.0870.0000.0000.0000.000
31A106VAL0-0.063-0.04012.8781.2991.2990.0000.0000.0000.000
32A107GLU-1-0.883-0.93814.97113.13813.1380.0000.0000.0000.000
33A108MET0-0.019-0.02416.5730.6650.6650.0000.0000.0000.000
34A109VAL0-0.0060.01318.768-0.633-0.6330.0000.0000.0000.000
35A110SER0-0.041-0.03821.5900.4000.4000.0000.0000.0000.000
36A111ILE00.021-0.00223.173-0.377-0.3770.0000.0000.0000.000
37A112PRO00.0500.03926.033-0.045-0.0450.0000.0000.0000.000
38A113ARG10.8950.96129.162-9.090-9.0900.0000.0000.0000.000
39A114ASP-1-0.837-0.93030.1478.5648.5640.0000.0000.0000.000
40A115THR0-0.032-0.02728.768-0.218-0.2180.0000.0000.0000.000
41A116LYS10.8210.90931.341-7.736-7.7360.0000.0000.0000.000
42A117VAL0-0.019-0.01727.7120.1750.1750.0000.0000.0000.000
43A118ASP-1-0.953-0.96930.8538.4758.4750.0000.0000.0000.000
44A119TYR0-0.013-0.01728.5950.4120.4120.0000.0000.0000.000
45A120GLY00.1080.06531.777-0.094-0.0940.0000.0000.0000.000
46A121ASN0-0.076-0.03534.4050.0680.0680.0000.0000.0000.000
47A122GLY00.018-0.00937.375-0.233-0.2330.0000.0000.0000.000
48A123ASP-1-0.966-0.96834.2728.3178.3170.0000.0000.0000.000
49A124ILE00.004-0.00535.1120.1480.1480.0000.0000.0000.000
50A125GLY00.0290.00434.327-0.142-0.1420.0000.0000.0000.000
51A126LYS10.8230.90832.779-8.254-8.2540.0000.0000.0000.000
52A127ILE00.003-0.01025.9860.0830.0830.0000.0000.0000.000
53A128ASN0-0.001-0.00328.4450.0160.0160.0000.0000.0000.000
54A129ALA0-0.027-0.02429.7940.0930.0930.0000.0000.0000.000
55A130SER00.0420.03131.8340.0610.0610.0000.0000.0000.000
56A131TYR00.0240.02827.4230.1450.1450.0000.0000.0000.000
57A132SER0-0.004-0.00326.0170.1020.1020.0000.0000.0000.000
58A133ASN0-0.114-0.06226.986-0.095-0.0950.0000.0000.0000.000
59A134GLY00.0370.01128.095-0.267-0.2670.0000.0000.0000.000
60A135GLY0-0.0010.01124.6190.2070.2070.0000.0000.0000.000
61A136PRO00.0560.02220.916-0.056-0.0560.0000.0000.0000.000
62A137SER00.0260.01119.9860.1150.1150.0000.0000.0000.000
63A138GLY00.0140.01021.0080.0080.0080.0000.0000.0000.000
64A139THR00.031-0.01322.323-0.306-0.3060.0000.0000.0000.000
65A140VAL0-0.0220.00417.300-0.025-0.0250.0000.0000.0000.000
66A141SER00.0680.04420.368-0.103-0.1030.0000.0000.0000.000
67A142ALA0-0.018-0.01022.695-0.224-0.2240.0000.0000.0000.000
68A143VAL0-0.034-0.03519.999-0.257-0.2570.0000.0000.0000.000
69A144GLU-1-0.894-0.95018.40514.10914.1090.0000.0000.0000.000
70A145LYS10.7960.90221.661-10.373-10.3730.0000.0000.0000.000
71A146LEU0-0.043-0.01924.958-0.288-0.2880.0000.0000.0000.000
72A147MET0-0.045-0.03721.623-0.041-0.0410.0000.0000.0000.000
73A148PRO00.0010.00421.4270.4820.4820.0000.0000.0000.000
74A149GLY0-0.046-0.01520.6450.3120.3120.0000.0000.0000.000
75A150VAL0-0.001-0.00516.2610.5660.5660.0000.0000.0000.000
76A151PRO00.0380.05013.264-0.432-0.4320.0000.0000.0000.000
77A152VAL00.0250.01213.9740.8020.8020.0000.0000.0000.000
78A153ASP-1-0.862-0.9278.65024.40424.4040.0000.0000.0000.000
79A154TYR0-0.049-0.0346.1900.9010.9010.0000.0000.0000.000
80A155PHE00.0430.00312.076-1.053-1.0530.0000.0000.0000.000
81A156ILE0-0.0220.00313.9400.3570.3570.0000.0000.0000.000
82A157SER0-0.012-0.00217.314-0.489-0.4890.0000.0000.0000.000
83A158ILE00.0060.01620.870-0.004-0.0040.0000.0000.0000.000
84A159ASN00.0470.02123.480-0.061-0.0610.0000.0000.0000.000
85A160MET0-0.012-0.02927.0250.2560.2560.0000.0000.0000.000
86A161GLU-1-0.816-0.88729.2219.4039.4030.0000.0000.0000.000
87A162GLY00.040-0.00725.7930.1180.1180.0000.0000.0000.000
88A163PHE0-0.069-0.02424.3380.4370.4370.0000.0000.0000.000
89A164LYS10.8590.91925.692-9.312-9.3120.0000.0000.0000.000
90A165ASP-1-0.838-0.91826.62111.01011.0100.0000.0000.0000.000
91A166LEU0-0.071-0.04119.7560.4170.4170.0000.0000.0000.000
92A167VAL0-0.026-0.01122.9080.4960.4960.0000.0000.0000.000
93A168ASP-1-0.812-0.90425.33310.59310.5930.0000.0000.0000.000
94A169ALA0-0.0440.00123.4810.0430.0430.0000.0000.0000.000
95A170VAL0-0.043-0.00519.4950.3570.3570.0000.0000.0000.000
96A171GLY0-0.009-0.01422.2330.2130.2130.0000.0000.0000.000
97A172GLY0-0.014-0.01525.355-0.080-0.0800.0000.0000.0000.000
98A173ILE0-0.0440.00922.9660.6860.6860.0000.0000.0000.000
99A174THR0-0.022-0.00824.210-0.553-0.5530.0000.0000.0000.000
100A175VAL00.0490.01825.4730.5000.5000.0000.0000.0000.000
101A176TYR0-0.017-0.00627.610-0.503-0.5030.0000.0000.0000.000
102A177ASN00.0170.00929.5740.1310.1310.0000.0000.0000.000
103A178ASP-1-0.892-0.94731.9079.2059.2050.0000.0000.0000.000
104A179ILE0-0.027-0.00633.679-0.341-0.3410.0000.0000.0000.000
105A180ASP-1-0.926-0.99236.2537.7227.7220.0000.0000.0000.000
106A181LEU0-0.057-0.01235.077-0.161-0.1610.0000.0000.0000.000
107A182THR00.0680.02139.0620.0610.0610.0000.0000.0000.000
108A183GLU-1-0.901-0.94741.4727.2517.2510.0000.0000.0000.000
109A184VAL0-0.107-0.04442.362-0.121-0.1210.0000.0000.0000.000
110A185ASN0-0.061-0.05839.0220.0110.0110.0000.0000.0000.000
111A186SER00.0300.01338.321-0.043-0.0430.0000.0000.0000.000
112A187LYS10.8810.96336.864-8.558-8.5580.0000.0000.0000.000
113A188PHE0-0.054-0.04935.1860.2150.2150.0000.0000.0000.000
114A189VAL00.0300.01837.472-0.034-0.0340.0000.0000.0000.000
115A190LYS10.9680.99336.524-7.782-7.7820.0000.0000.0000.000
116A191GLY0-0.021-0.01233.922-0.058-0.0580.0000.0000.0000.000
117A192ASN0-0.008-0.02429.0940.3890.3890.0000.0000.0000.000
118A193ILE0-0.0360.00431.604-0.216-0.2160.0000.0000.0000.000
119A194THR0-0.034-0.03428.1280.2300.2300.0000.0000.0000.000
120A195LEU0-0.0360.01129.178-0.374-0.3740.0000.0000.0000.000
121A196ASN00.0570.00829.1440.3700.3700.0000.0000.0000.000
122A197GLY00.0600.02528.8730.0880.0880.0000.0000.0000.000
123A198THR0-0.005-0.02229.815-0.020-0.0200.0000.0000.0000.000
124A199GLU-1-0.870-0.93432.7569.1029.1020.0000.0000.0000.000
125A200ALA00.0450.02928.067-0.105-0.1050.0000.0000.0000.000
126A201LEU0-0.036-0.01429.938-0.041-0.0410.0000.0000.0000.000
127A202GLN0-0.036-0.02931.055-0.047-0.0470.0000.0000.0000.000
128A203TYR0-0.022-0.01528.899-0.316-0.3160.0000.0000.0000.000
129A204VAL00.0280.01327.392-0.154-0.1540.0000.0000.0000.000
130A205ARG10.8780.93430.523-9.111-9.1110.0000.0000.0000.000
131A206ILE0-0.0250.02333.353-0.250-0.2500.0000.0000.0000.000
132A207ARG10.9150.93235.044-8.097-8.0970.0000.0000.0000.000
133A208HIS00.0090.00537.5780.1460.1460.0000.0000.0000.000
134A209GLU-1-0.813-0.90339.5387.8087.8080.0000.0000.0000.000
135A210ASP-1-0.707-0.82934.6448.7918.7910.0000.0000.0000.000
136A211PRO00.0230.01738.2830.0070.0070.0000.0000.0000.000
137A212ARG10.7720.87931.905-9.383-9.3830.0000.0000.0000.000
138A213GLY0-0.024-0.01936.2320.1060.1060.0000.0000.0000.000
139A214ASP-1-0.846-0.91733.6828.7488.7480.0000.0000.0000.000
140A215PHE00.0220.01729.7500.2640.2640.0000.0000.0000.000
141A216GLY00.0390.02230.9150.3130.3130.0000.0000.0000.000
142A217ARG10.8190.88730.779-8.950-8.9500.0000.0000.0000.000
143A218GLN0-0.032-0.01525.2230.7130.7130.0000.0000.0000.000
144A219ASP-1-0.871-0.91726.36911.01211.0120.0000.0000.0000.000
145A220ARG10.8470.91026.676-8.856-8.8560.0000.0000.0000.000
146A221GLN0-0.012-0.01524.1850.4060.4060.0000.0000.0000.000
147A222ARG10.8940.95221.643-11.619-11.6190.0000.0000.0000.000
148A223ASP-1-0.837-0.90722.46911.83411.8340.0000.0000.0000.000
149A224VAL00.005-0.01623.6080.4270.4270.0000.0000.0000.000
150A225ILE0-0.0300.00118.1590.4850.4850.0000.0000.0000.000
151A226ILE0-0.014-0.01617.8140.9100.9100.0000.0000.0000.000
152A227GLY00.0230.00519.8260.4730.4730.0000.0000.0000.000
153A228ILE00.003-0.01018.7780.1340.1340.0000.0000.0000.000
154A229ALA00.0160.00015.3220.6890.6890.0000.0000.0000.000
155A230ASN0-0.057-0.02715.8381.8981.8980.0000.0000.0000.000
156A231LYS10.7750.89217.652-13.973-13.9730.0000.0000.0000.000
157A232VAL0-0.063-0.00912.3580.4550.4550.0000.0000.0000.000
158A243SER00.0230.01413.7790.2250.2250.0000.0000.0000.000
159A244ILE0-0.029-0.02712.642-1.028-1.0280.0000.0000.0000.000
160A245MET00.0330.02215.877-0.276-0.2760.0000.0000.0000.000
161A246LYS10.8480.92016.361-17.145-17.1450.0000.0000.0000.000
162A247ALA00.0280.03521.415-0.246-0.2460.0000.0000.0000.000
163A248VAL00.0150.01922.910-0.383-0.3830.0000.0000.0000.000
164A249GLY00.060-0.00523.9040.2450.2450.0000.0000.0000.000
165A250ASP-1-0.881-0.92923.73311.39511.3950.0000.0000.0000.000
166A251ASN0-0.083-0.02425.874-0.304-0.3040.0000.0000.0000.000
167A252PHE00.025-0.00716.7710.4010.4010.0000.0000.0000.000
168A253GLN00.0210.02719.536-0.504-0.5040.0000.0000.0000.000
169A254THR0-0.019-0.03014.4340.6490.6490.0000.0000.0000.000
170A255ASN00.0260.01812.001-0.475-0.4750.0000.0000.0000.000
171A256MET0-0.033-0.0049.9370.6030.6030.0000.0000.0000.000
172A257THR0-0.004-0.0148.792-2.219-2.2190.0000.0000.0000.000
173A258LEU00.0610.0209.6632.0072.0070.0000.0000.0000.000
174A259THR0-0.034-0.0278.373-0.132-0.1320.0000.0000.0000.000
175A260ASP-1-0.866-0.9235.39434.21934.2190.0000.0000.0000.000
176A261ILE00.0460.0196.3673.1293.1290.0000.0000.0000.000
177A262THR0-0.010-0.0247.056-0.156-0.1560.0000.0000.0000.000
178A263SER0-0.064-0.0431.550-18.689-31.95228.575-10.658-4.6540.059
179A264MET0-0.019-0.0153.8871.0901.294-0.001-0.003-0.2000.001
180A265ALA00.0030.0146.336-4.094-4.0940.0000.0000.0000.000
181A266ALA0-0.020-0.0054.628-2.380-2.326-0.001-0.004-0.0480.000
182A267ASN0-0.045-0.0162.268-34.294-31.2714.409-3.597-3.8360.051
183A268TYR0-0.058-0.0442.917-5.348-4.3360.068-0.431-0.649-0.003
184A269SER00.0890.0428.264-0.354-0.3540.0000.0000.0000.000
185A270SER0-0.033-0.02111.511-1.104-1.1040.0000.0000.0000.000
186A271VAL0-0.040-0.00113.267-1.134-1.1340.0000.0000.0000.000
187A272LEU00.0080.01215.225-1.095-1.0950.0000.0000.0000.000
188A273LYS10.8500.92217.698-14.244-14.2440.0000.0000.0000.000
189A274ASN0-0.020-0.03517.330-0.405-0.4050.0000.0000.0000.000
190A275VAL00.0270.03916.9400.3960.3960.0000.0000.0000.000
191A276ASP-1-0.842-0.91519.01712.48312.4830.0000.0000.0000.000
192A277SER00.0020.00120.8070.1740.1740.0000.0000.0000.000
193A278GLN0-0.019-0.01722.398-0.322-0.3220.0000.0000.0000.000
194A279GLU-1-0.848-0.90024.54110.54310.5430.0000.0000.0000.000
195A280LEU0-0.076-0.01726.059-0.224-0.2240.0000.0000.0000.000
196A281LYS10.9070.93627.679-9.566-9.5660.0000.0000.0000.000
197A282GLY00.005-0.02131.2540.1580.1580.0000.0000.0000.000
198A283GLU-1-0.972-0.97534.0197.2067.2060.0000.0000.0000.000
199A284GLY0-0.0070.00137.2650.0920.0920.0000.0000.0000.000
200A285GLU-1-0.815-0.90338.6757.4067.4060.0000.0000.0000.000
201A286MET0-0.028-0.02140.7060.1630.1630.0000.0000.0000.000
202A287ILE0-0.024-0.01739.332-0.067-0.0670.0000.0000.0000.000
203A288TYR00.0030.00343.4440.0790.0790.0000.0000.0000.000
204A289SER0-0.013-0.01743.0280.1770.1770.0000.0000.0000.000
205A290GLU-1-0.841-0.91244.9786.0556.0550.0000.0000.0000.000
206A291SER0-0.070-0.02143.798-0.034-0.0340.0000.0000.0000.000
207A292TYR0-0.043-0.02540.654-0.051-0.0510.0000.0000.0000.000
208A293GLY00.0340.03446.778-0.118-0.1180.0000.0000.0000.000
209A294PHE0-0.062-0.04145.591-0.112-0.1120.0000.0000.0000.000
210A295ASP-1-0.884-0.95045.4806.4896.4890.0000.0000.0000.000
211A296LEU0-0.069-0.03140.0830.0400.0400.0000.0000.0000.000
212A297TYR0-0.011-0.01436.526-0.046-0.0460.0000.0000.0000.000
213A298TYR00.002-0.00135.7070.2880.2880.0000.0000.0000.000
214A299PHE0-0.0120.01431.451-0.168-0.1680.0000.0000.0000.000
215A300ALA00.0550.02133.5300.2900.2900.0000.0000.0000.000
216A301PRO0-0.0010.00230.067-0.016-0.0160.0000.0000.0000.000
217A302ASP-1-0.840-0.91232.0948.4088.4080.0000.0000.0000.000
218A303LYS10.9670.97731.394-8.494-8.4940.0000.0000.0000.000
219A304THR00.0480.03130.5660.2330.2330.0000.0000.0000.000
220A305ASP-1-0.854-0.92029.14910.15710.1570.0000.0000.0000.000
221A306LEU00.019-0.00825.9410.3710.3710.0000.0000.0000.000
222A307GLU-1-0.890-0.94325.85110.96410.9640.0000.0000.0000.000
223A308ARG10.9270.98123.620-11.036-11.0360.0000.0000.0000.000
224A309ILE0-0.001-0.00622.0120.5040.5040.0000.0000.0000.000
225A310ILE00.0130.01721.5830.7080.7080.0000.0000.0000.000
226A311THR0-0.079-0.05521.1100.5950.5950.0000.0000.0000.000
227A312MET0-0.085-0.03119.4990.6500.6500.0000.0000.0000.000
228A313PHE00.050-0.00516.8180.5290.5290.0000.0000.0000.000
229A314LYS10.9350.98616.000-11.890-11.8900.0000.0000.0000.000
230A315LYS10.8940.94316.411-12.557-12.5570.0000.0000.0000.000
231A316SER00.0210.02414.1520.5210.5210.0000.0000.0000.000
232A317LEU0-0.0330.00010.7651.4881.4880.0000.0000.0000.000
233A318ASP-1-0.877-0.96312.26919.56219.5620.0000.0000.0000.000
234A319ILE0-0.059-0.01314.520-0.492-0.4920.0000.0000.0000.000
235A320THR0-0.047-0.00615.831-1.035-1.0350.0000.0000.0000.000