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: 9GVY2

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 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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2816640.949212
FMO2-HF: Nuclear repulsion 2724973.318832
FMO2-HF: Total energy -91667.63038
FMO2-MP2: Total energy -91932.558137


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.
-107.114-119.85748.758-20.925-15.090.146
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 : -0.727 / q_NPA : -0.838
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].
3A70LYS10.8340.9042.009-120.031-115.6566.346-5.563-5.1580.051
4A71LYS10.8220.9164.404-32.870-32.660-0.001-0.019-0.1890.000
5A72PRO00.0220.0355.8241.6461.6460.0000.0000.0000.000
6A73PHE0-0.0360.0016.3000.2120.2120.0000.0000.0000.000
7A74SER00.031-0.0098.449-0.855-0.8550.0000.0000.0000.000
8A75VAL0-0.014-0.01110.9280.7750.7750.0000.0000.0000.000
9A76LEU00.0130.01913.361-0.723-0.7230.0000.0000.0000.000
10A77LEU00.0030.00215.9040.1530.1530.0000.0000.0000.000
11A78MET0-0.029-0.00718.978-0.882-0.8820.0000.0000.0000.000
12A79GLY00.0330.01522.3890.2190.2190.0000.0000.0000.000
13A80SER0-0.073-0.06125.633-0.516-0.5160.0000.0000.0000.000
14A89GLY00.0450.02931.170-0.014-0.0140.0000.0000.0000.000
15A90ARG10.8540.89529.876-8.811-8.8110.0000.0000.0000.000
16A91ALA00.0040.03125.5740.1930.1930.0000.0000.0000.000
17A92ASP-1-0.794-0.88527.6359.0949.0940.0000.0000.0000.000
18A93THR0-0.042-0.03525.128-0.236-0.2360.0000.0000.0000.000
19A94ILE00.0230.01822.6450.2910.2910.0000.0000.0000.000
20A95ILE00.0230.02120.025-0.263-0.2630.0000.0000.0000.000
21A96LEU00.0140.02816.2190.6340.6340.0000.0000.0000.000
22A97ALA00.004-0.00315.585-0.375-0.3750.0000.0000.0000.000
23A98THR0-0.010-0.01012.8030.6020.6020.0000.0000.0000.000
24A99ALA00.0110.01010.082-0.580-0.5800.0000.0000.0000.000
25A100ASN00.000-0.0119.8562.5372.5370.0000.0000.0000.000
26A101LYS10.9100.9468.712-29.242-29.2420.0000.0000.0000.000
27A102GLN0-0.057-0.0428.785-1.549-1.5490.0000.0000.0000.000
28A103GLN0-0.014-0.02113.268-0.992-0.9920.0000.0000.0000.000
29A104ASN0-0.0050.02213.6480.9430.9430.0000.0000.0000.000
30A105ALA00.0110.00414.474-0.862-0.8620.0000.0000.0000.000
31A106VAL0-0.005-0.01113.7561.4141.4140.0000.0000.0000.000
32A107GLU-1-0.746-0.84816.02212.45512.4550.0000.0000.0000.000
33A108MET0-0.027-0.02417.4100.7660.7660.0000.0000.0000.000
34A109VAL00.0010.00319.535-0.622-0.6220.0000.0000.0000.000
35A110SER0-0.020-0.02622.1830.3160.3160.0000.0000.0000.000
36A111ILE00.021-0.00423.189-0.284-0.2840.0000.0000.0000.000
37A112PRO00.0400.03026.156-0.052-0.0520.0000.0000.0000.000
38A113ARG10.8470.93929.181-9.198-9.1980.0000.0000.0000.000
39A114ASP-1-0.822-0.90730.1798.5358.5350.0000.0000.0000.000
40A115THR0-0.046-0.04128.989-0.237-0.2370.0000.0000.0000.000
41A116LYS10.8070.88931.214-7.591-7.5910.0000.0000.0000.000
42A117VAL0-0.049-0.02127.7360.1510.1510.0000.0000.0000.000
43A118ASP-1-0.853-0.92031.0618.7688.7680.0000.0000.0000.000
44A119TYR0-0.032-0.01728.3570.4980.4980.0000.0000.0000.000
45A120GLY00.0870.05531.594-0.058-0.0580.0000.0000.0000.000
46A121ASN0-0.066-0.04334.0660.0340.0340.0000.0000.0000.000
47A122GLY00.001-0.01037.291-0.228-0.2280.0000.0000.0000.000
48A123ASP-1-0.881-0.91133.5968.3678.3670.0000.0000.0000.000
49A124ILE0-0.015-0.01434.8930.1530.1530.0000.0000.0000.000
50A125GLY00.0470.02533.468-0.158-0.1580.0000.0000.0000.000
51A126LYS10.8170.89332.266-8.339-8.3390.0000.0000.0000.000
52A127ILE00.012-0.00925.6860.0450.0450.0000.0000.0000.000
53A128ASN0-0.043-0.02328.2540.0510.0510.0000.0000.0000.000
54A129ALA00.010-0.00129.7570.0970.0970.0000.0000.0000.000
55A130SER00.0220.03732.244-0.103-0.1030.0000.0000.0000.000
56A131TYR0-0.004-0.00327.4120.1030.1030.0000.0000.0000.000
57A132SER0-0.008-0.00125.406-0.121-0.1210.0000.0000.0000.000
58A133ASN0-0.075-0.06127.1270.1100.1100.0000.0000.0000.000
59A134GLY0-0.007-0.01027.948-0.294-0.2940.0000.0000.0000.000
60A135GLY0-0.0100.01824.5620.2300.2300.0000.0000.0000.000
61A136PRO00.035-0.00320.742-0.110-0.1100.0000.0000.0000.000
62A137SER00.0250.01420.1750.1390.1390.0000.0000.0000.000
63A138GLY00.0470.03221.203-0.024-0.0240.0000.0000.0000.000
64A139THR00.015-0.01422.444-0.368-0.3680.0000.0000.0000.000
65A140VAL0-0.022-0.00417.431-0.010-0.0100.0000.0000.0000.000
66A141SER00.0340.00220.455-0.065-0.0650.0000.0000.0000.000
67A142ALA0-0.027-0.00122.553-0.308-0.3080.0000.0000.0000.000
68A143VAL0-0.016-0.01920.323-0.232-0.2320.0000.0000.0000.000
69A144GLU-1-0.869-0.92718.53213.51613.5160.0000.0000.0000.000
70A145LYS10.7820.87121.649-10.060-10.0600.0000.0000.0000.000
71A146LEU0-0.044-0.01024.809-0.373-0.3730.0000.0000.0000.000
72A147MET0-0.035-0.02821.5730.0000.0000.0000.0000.0000.000
73A148PRO00.0360.02021.2470.5440.5440.0000.0000.0000.000
74A149GLY0-0.034-0.01020.5420.1070.1070.0000.0000.0000.000
75A150VAL0-0.042-0.02316.7060.5600.5600.0000.0000.0000.000
76A151PRO00.0290.03313.206-0.303-0.3030.0000.0000.0000.000
77A152VAL00.0110.01313.9260.4800.4800.0000.0000.0000.000
78A153ASP-1-0.820-0.8948.51123.68123.6810.0000.0000.0000.000
79A154TYR0-0.059-0.0436.3721.0801.0800.0000.0000.0000.000
80A155PHE00.0460.01211.950-0.941-0.9410.0000.0000.0000.000
81A156ILE0-0.0110.00414.2850.5170.5170.0000.0000.0000.000
82A157SER0-0.016-0.00317.523-0.434-0.4340.0000.0000.0000.000
83A158ILE00.0180.02221.3430.0720.0720.0000.0000.0000.000
84A159ASN00.0240.01123.956-0.152-0.1520.0000.0000.0000.000
85A160MET00.014-0.01627.4380.2930.2930.0000.0000.0000.000
86A161GLU-1-0.816-0.87329.9149.3059.3050.0000.0000.0000.000
87A162GLY00.0550.00826.1000.1440.1440.0000.0000.0000.000
88A163PHE0-0.055-0.02125.1620.4940.4940.0000.0000.0000.000
89A164LYS10.8370.90426.172-9.175-9.1750.0000.0000.0000.000
90A165ASP-1-0.826-0.92626.60110.95110.9510.0000.0000.0000.000
91A166LEU0-0.055-0.02419.6870.3210.3210.0000.0000.0000.000
92A167VAL0-0.0120.00223.1990.4040.4040.0000.0000.0000.000
93A168ASP-1-0.803-0.90825.25810.53310.5330.0000.0000.0000.000
94A169ALA0-0.052-0.01823.784-0.001-0.0010.0000.0000.0000.000
95A170VAL0-0.044-0.00419.6280.3170.3170.0000.0000.0000.000
96A171GLY0-0.004-0.00722.4030.1830.1830.0000.0000.0000.000
97A172GLY00.0020.00625.602-0.136-0.1360.0000.0000.0000.000
98A173ILE0-0.0320.00022.4530.6760.6760.0000.0000.0000.000
99A174THR0-0.018-0.00724.522-0.712-0.7120.0000.0000.0000.000
100A175VAL00.0260.02025.4180.5530.5530.0000.0000.0000.000
101A176TYR0-0.021-0.01127.767-0.448-0.4480.0000.0000.0000.000
102A177ASN00.0390.02829.7120.0680.0680.0000.0000.0000.000
103A178ASP-1-0.818-0.91432.7359.1539.1530.0000.0000.0000.000
104A179ILE0-0.029-0.00234.554-0.371-0.3710.0000.0000.0000.000
105A180ASP-1-0.866-0.93837.4767.7737.7730.0000.0000.0000.000
106A181LEU0-0.055-0.01135.829-0.217-0.2170.0000.0000.0000.000
107A182THR00.0380.01139.7850.0290.0290.0000.0000.0000.000
108A183GLU-1-0.915-0.97142.4707.3157.3150.0000.0000.0000.000
109A184VAL0-0.089-0.03243.399-0.131-0.1310.0000.0000.0000.000
110A185ASN0-0.057-0.05239.7260.0310.0310.0000.0000.0000.000
111A186SER00.0220.01138.531-0.028-0.0280.0000.0000.0000.000
112A187LYS10.8690.93736.905-8.492-8.4920.0000.0000.0000.000
113A188PHE0-0.050-0.02535.3490.2530.2530.0000.0000.0000.000
114A189VAL00.0430.02037.559-0.020-0.0200.0000.0000.0000.000
115A190LYS10.8520.92936.566-7.808-7.8080.0000.0000.0000.000
116A191GLY00.000-0.00234.247-0.139-0.1390.0000.0000.0000.000
117A192ASN0-0.040-0.03328.8820.4060.4060.0000.0000.0000.000
118A193ILE00.0150.02031.171-0.262-0.2620.0000.0000.0000.000
119A194THR0-0.057-0.04328.1260.2990.2990.0000.0000.0000.000
120A195LEU0-0.0260.00429.390-0.395-0.3950.0000.0000.0000.000
121A196ASN00.0290.00229.1700.4130.4130.0000.0000.0000.000
122A197GLY00.0440.00529.0870.0530.0530.0000.0000.0000.000
123A198THR0-0.014-0.02530.009-0.048-0.0480.0000.0000.0000.000
124A199GLU-1-0.822-0.90532.9169.0099.0090.0000.0000.0000.000
125A200ALA00.0240.01728.375-0.077-0.0770.0000.0000.0000.000
126A201LEU0-0.018-0.00530.4960.0060.0060.0000.0000.0000.000
127A202GLN0-0.030-0.02631.657-0.055-0.0550.0000.0000.0000.000
128A203TYR0-0.029-0.03829.682-0.266-0.2660.0000.0000.0000.000
129A204VAL00.0090.00627.790-0.083-0.0830.0000.0000.0000.000
130A205ARG10.8760.93131.020-9.001-9.0010.0000.0000.0000.000
131A206ILE0-0.0220.02234.036-0.231-0.2310.0000.0000.0000.000
132A207ARG10.8220.88835.626-8.005-8.0050.0000.0000.0000.000
133A208HIS00.0130.00138.0150.1250.1250.0000.0000.0000.000
134A209GLU-1-0.779-0.88640.3437.8017.8010.0000.0000.0000.000
135A210ASP-1-0.695-0.81935.4258.8438.8430.0000.0000.0000.000
136A211PRO0-0.0060.00139.0570.0050.0050.0000.0000.0000.000
137A212ARG10.7640.85532.373-9.450-9.4500.0000.0000.0000.000
138A213GLY00.0010.00336.5410.1340.1340.0000.0000.0000.000
139A214ASP-1-0.782-0.87834.2608.7548.7540.0000.0000.0000.000
140A215PHE00.0220.01630.2920.2800.2800.0000.0000.0000.000
141A216GLY00.0420.01731.6250.3110.3110.0000.0000.0000.000
142A217ARG10.7870.87231.478-8.930-8.9300.0000.0000.0000.000
143A218GLN0-0.040-0.02525.6720.6910.6910.0000.0000.0000.000
144A219ASP-1-0.836-0.89227.02511.23311.2330.0000.0000.0000.000
145A220ARG10.8230.89127.407-8.907-8.9070.0000.0000.0000.000
146A221GLN0-0.014-0.00824.6310.3140.3140.0000.0000.0000.000
147A222ARG10.8390.90822.279-11.722-11.7220.0000.0000.0000.000
148A223ASP-1-0.816-0.88523.09411.83611.8360.0000.0000.0000.000
149A224VAL00.001-0.00424.2120.4430.4430.0000.0000.0000.000
150A225ILE0-0.019-0.00218.8850.5120.5120.0000.0000.0000.000
151A226ILE0-0.001-0.00918.3300.9890.9890.0000.0000.0000.000
152A227GLY00.0410.01619.8290.5430.5430.0000.0000.0000.000
153A228ILE0-0.033-0.02518.7430.2120.2120.0000.0000.0000.000
154A229ALA0-0.009-0.00315.6130.6970.6970.0000.0000.0000.000
155A230ASN0-0.077-0.04315.4571.9511.9510.0000.0000.0000.000
156A231LYS10.7840.89817.368-13.922-13.9220.0000.0000.0000.000
157A232VAL0-0.036-0.00312.1050.2640.2640.0000.0000.0000.000
158A243SER00.0310.01714.2380.3490.3490.0000.0000.0000.000
159A244ILE0-0.020-0.01612.686-0.989-0.9890.0000.0000.0000.000
160A245MET00.0260.01715.996-0.436-0.4360.0000.0000.0000.000
161A246LYS10.8520.91616.717-16.324-16.3240.0000.0000.0000.000
162A247ALA00.0350.03221.507-0.304-0.3040.0000.0000.0000.000
163A248VAL0-0.0210.00822.903-0.418-0.4180.0000.0000.0000.000
164A249GLY00.0390.00524.0210.3930.3930.0000.0000.0000.000
165A250ASP-1-0.876-0.94524.39711.15311.1530.0000.0000.0000.000
166A251ASN0-0.0590.00026.064-0.186-0.1860.0000.0000.0000.000
167A252PHE0-0.013-0.02717.3670.3440.3440.0000.0000.0000.000
168A253GLN0-0.0080.01018.930-0.376-0.3760.0000.0000.0000.000
169A254THR0-0.034-0.04114.7460.6110.6110.0000.0000.0000.000
170A255ASN00.0330.01311.871-0.809-0.8090.0000.0000.0000.000
171A256MET0-0.0190.00110.4200.6880.6880.0000.0000.0000.000
172A257THR0-0.006-0.0078.824-1.967-1.9670.0000.0000.0000.000
173A258LEU00.002-0.00810.3531.7431.7430.0000.0000.0000.000
174A259THR0-0.019-0.0148.193-0.434-0.4340.0000.0000.0000.000
175A260ASP-1-0.835-0.9005.48831.70431.7040.0000.0000.0000.000
176A261ILE00.0650.0176.4674.4694.4690.0000.0000.0000.000
177A262THR00.002-0.0117.0070.1320.1320.0000.0000.0000.000
178A263SER0-0.043-0.0341.578-16.854-28.42226.376-9.808-5.0000.036
179A264MET0-0.024-0.0183.9511.1251.2840.000-0.012-0.1470.001
180A265ALA00.0270.0236.548-3.974-3.9740.0000.0000.0000.000
181A266ALA0-0.028-0.0045.174-2.711-2.717-0.001-0.0010.0070.000
182A267ASN0-0.060-0.0501.776-26.872-33.08416.036-5.462-4.3620.058
183A268TYR0-0.067-0.0463.634-3.389-3.0900.002-0.060-0.2410.000
184A269SER00.0540.0238.288-1.419-1.4190.0000.0000.0000.000
185A270SER0-0.028-0.03211.761-1.283-1.2830.0000.0000.0000.000
186A271VAL0-0.0070.00513.766-1.250-1.2500.0000.0000.0000.000
187A272LEU0-0.0180.01315.689-1.213-1.2130.0000.0000.0000.000
188A273LYS10.8460.89217.881-14.508-14.5080.0000.0000.0000.000
189A274ASN0-0.044-0.03318.447-0.541-0.5410.0000.0000.0000.000
190A275VAL00.0480.05317.4740.3950.3950.0000.0000.0000.000
191A276ASP-1-0.850-0.91719.72112.35012.3500.0000.0000.0000.000
192A277SER00.007-0.00521.3060.3390.3390.0000.0000.0000.000
193A278GLN0-0.0130.00323.674-0.269-0.2690.0000.0000.0000.000
194A279GLU-1-0.840-0.89325.35510.60410.6040.0000.0000.0000.000
195A280LEU0-0.045-0.01226.729-0.182-0.1820.0000.0000.0000.000
196A281LYS10.8890.91928.368-9.794-9.7940.0000.0000.0000.000
197A282GLY00.027-0.00431.8980.1450.1450.0000.0000.0000.000
198A283GLU-1-0.972-0.96834.5707.1787.1780.0000.0000.0000.000
199A284GLY0-0.016-0.00637.5080.1200.1200.0000.0000.0000.000
200A285GLU-1-0.792-0.89538.7617.3807.3800.0000.0000.0000.000
201A286MET0-0.034-0.01640.9040.1380.1380.0000.0000.0000.000
202A287ILE0-0.005-0.00139.152-0.060-0.0600.0000.0000.0000.000
203A288TYR0-0.022-0.01543.3840.0550.0550.0000.0000.0000.000
204A289SER0-0.025-0.01843.2250.1560.1560.0000.0000.0000.000
205A290GLU-1-0.787-0.89045.1585.9915.9910.0000.0000.0000.000
206A291SER0-0.101-0.04843.548-0.025-0.0250.0000.0000.0000.000
207A292TYR0-0.047-0.02740.9240.0380.0380.0000.0000.0000.000
208A293GLY00.0040.02147.128-0.111-0.1110.0000.0000.0000.000
209A294PHE0-0.053-0.03545.678-0.105-0.1050.0000.0000.0000.000
210A295ASP-1-0.867-0.93745.5036.4736.4730.0000.0000.0000.000
211A296LEU0-0.049-0.01739.9360.0350.0350.0000.0000.0000.000
212A297TYR00.006-0.00636.885-0.024-0.0240.0000.0000.0000.000
213A298TYR0-0.012-0.01535.5000.2740.2740.0000.0000.0000.000
214A299PHE0-0.0230.00131.637-0.163-0.1630.0000.0000.0000.000
215A300ALA00.0560.03733.7210.2780.2780.0000.0000.0000.000
216A301PRO0-0.014-0.00630.289-0.021-0.0210.0000.0000.0000.000
217A302ASP-1-0.791-0.88632.4118.5198.5190.0000.0000.0000.000
218A303LYS10.9510.96031.535-8.587-8.5870.0000.0000.0000.000
219A304THR0-0.023-0.02030.8420.2140.2140.0000.0000.0000.000
220A305ASP-1-0.819-0.90529.29910.34810.3480.0000.0000.0000.000
221A306LEU00.0160.01226.0970.3780.3780.0000.0000.0000.000
222A307GLU-1-0.880-0.94625.98111.17111.1710.0000.0000.0000.000
223A308ARG10.7270.86123.137-11.717-11.7170.0000.0000.0000.000
224A309ILE0-0.007-0.00822.4030.5270.5270.0000.0000.0000.000
225A310ILE00.0330.02621.6900.7380.7380.0000.0000.0000.000
226A311THR0-0.014-0.02020.8980.7170.7170.0000.0000.0000.000
227A312MET0-0.110-0.01219.6550.7190.7190.0000.0000.0000.000
228A313PHE00.037-0.01117.1520.6400.6400.0000.0000.0000.000
229A314LYS10.9220.96416.268-11.817-11.8170.0000.0000.0000.000
230A315LYS10.9240.95716.746-12.734-12.7340.0000.0000.0000.000
231A316SER0-0.0090.00815.2500.7250.7250.0000.0000.0000.000
232A317LEU0-0.0170.00311.0721.5871.5870.0000.0000.0000.000
233A318ASP-1-0.821-0.92012.21119.22719.2270.0000.0000.0000.000
234A319ILE0-0.085-0.01114.807-0.585-0.5850.0000.0000.0000.000
235A320THR0-0.094-0.05915.397-1.343-1.3430.0000.0000.0000.000