FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: VQJL1

Calculation Name: 3RD3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RD3

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I1S1

Base Structure: X-ray

Registration Date: 2023-09-23

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1957892.198777
FMO2-HF: Nuclear repulsion 1883055.318923
FMO2-HF: Total energy -74836.879854
FMO2-MP2: Total energy -75050.041744


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:7:ASP)


Summations of interaction energy for fragment #1(A:7:ASP)
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.
-65.053-60.6120.04-2.215-2.2650.011
Interaction energy analysis for fragmet #1(A:7:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.849 / q_NPA : -0.912
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].
3A9ARG10.9630.9933.645-47.960-44.5850.018-1.855-1.5370.010
4A10GLN0-0.001-0.0203.343-6.406-5.8470.024-0.158-0.4250.000
5A11HIS00.0130.0144.225-5.209-4.796-0.001-0.198-0.2140.001
6A12LEU0-0.003-0.0156.012-5.728-5.7280.0000.0000.0000.000
7A13LEU0-0.0220.0047.917-3.461-3.4610.0000.0000.0000.000
8A14ASP-1-0.818-0.9067.78126.01526.0150.0000.0000.0000.000
9A15THR0-0.074-0.0539.843-2.749-2.7490.0000.0000.0000.000
10A16GLY00.003-0.00411.733-1.688-1.6880.0000.0000.0000.000
11A17TYR0-0.034-0.01413.038-1.699-1.6990.0000.0000.0000.000
12A18ARG10.9630.98210.807-23.120-23.1200.0000.0000.0000.000
13A19ILE0-0.0030.00315.717-0.983-0.9830.0000.0000.0000.000
14A20MET00.0070.02117.383-1.027-1.0270.0000.0000.0000.000
15A21ALA00.0260.00718.715-0.884-0.8840.0000.0000.0000.000
16A22VAL00.0090.00720.607-0.796-0.7960.0000.0000.0000.000
17A23LYS10.8490.91721.967-14.180-14.1800.0000.0000.0000.000
18A24GLY00.0360.05022.531-0.395-0.3950.0000.0000.0000.000
19A25PHE0-0.047-0.04818.6220.8480.8480.0000.0000.0000.000
20A26SER0-0.006-0.00922.1060.4990.4990.0000.0000.0000.000
21A27GLY00.0410.03525.178-0.217-0.2170.0000.0000.0000.000
22A28VAL0-0.0210.00519.6630.0530.0530.0000.0000.0000.000
23A29GLY00.0200.01621.8580.2730.2730.0000.0000.0000.000
24A30LEU00.004-0.01615.8420.4600.4600.0000.0000.0000.000
25A31ASN00.009-0.00717.7611.0941.0940.0000.0000.0000.000
26A32GLU-1-0.772-0.87318.85914.36014.3600.0000.0000.0000.000
27A33ILE00.0160.01513.8700.7210.7210.0000.0000.0000.000
28A34LEU0-0.032-0.01713.8781.1511.1510.0000.0000.0000.000
29A35GLN0-0.013-0.01814.2470.9060.9060.0000.0000.0000.000
30A36SER0-0.033-0.00915.445-0.449-0.4490.0000.0000.0000.000
31A37ALA0-0.041-0.01510.2340.5560.5560.0000.0000.0000.000
32A38GLY00.0220.02410.4451.9901.9900.0000.0000.0000.000
33A39VAL0-0.040-0.0108.1961.7781.7780.0000.0000.0000.000
34A40PRO00.0390.01110.102-2.688-2.6880.0000.0000.0000.000
35A41LYS10.9860.98412.021-15.899-15.8990.0000.0000.0000.000
36A42GLY0-0.015-0.01213.8910.1950.1950.0000.0000.0000.000
37A43SER00.0340.0088.237-0.544-0.5440.0000.0000.0000.000
38A44PHE00.0460.0269.1982.7842.7840.0000.0000.0000.000
39A45TYR0-0.024-0.02811.4530.1850.1850.0000.0000.0000.000
40A46HIS0-0.0170.0158.297-2.504-2.5040.0000.0000.0000.000
41A47TYR0-0.031-0.0214.6441.0231.117-0.001-0.004-0.0890.000
42A48PHE0-0.027-0.0079.374-1.455-1.4550.0000.0000.0000.000
43A49LYS10.9400.96813.243-19.125-19.1250.0000.0000.0000.000
44A50SER0-0.014-0.01616.468-0.917-0.9170.0000.0000.0000.000
45A51LYS10.9030.95016.742-13.356-13.3560.0000.0000.0000.000
46A52GLU-1-0.781-0.87318.52513.74613.7460.0000.0000.0000.000
47A53GLN00.010-0.01114.183-0.093-0.0930.0000.0000.0000.000
48A54PHE0-0.007-0.00111.2380.1860.1860.0000.0000.0000.000
49A55GLY00.0690.03515.1450.5980.5980.0000.0000.0000.000
50A56GLN0-0.003-0.02117.893-0.495-0.4950.0000.0000.0000.000
51A57ALA0-0.0200.00012.897-0.034-0.0340.0000.0000.0000.000
52A58LEU00.0060.00912.7850.1680.1680.0000.0000.0000.000
53A59LEU00.0230.01614.812-0.294-0.2940.0000.0000.0000.000
54A60GLU-1-0.928-0.94415.69817.88917.8890.0000.0000.0000.000
55A61ASP-1-0.822-0.92111.88922.77222.7720.0000.0000.0000.000
56A62TYR0-0.027-0.00214.780-0.324-0.3240.0000.0000.0000.000
57A63PHE00.0210.00116.929-0.577-0.5770.0000.0000.0000.000
58A64ARG10.7660.87912.740-20.185-20.1850.0000.0000.0000.000
59A65VAL00.0180.00614.088-0.434-0.4340.0000.0000.0000.000
60A66TYR00.0060.01117.356-0.717-0.7170.0000.0000.0000.000
61A67LEU0-0.019-0.02220.628-0.545-0.5450.0000.0000.0000.000
62A68ALA00.0330.02619.571-0.442-0.4420.0000.0000.0000.000
63A69ASP-1-0.867-0.92320.86311.79511.7950.0000.0000.0000.000
64A70MET0-0.018-0.01122.372-0.629-0.6290.0000.0000.0000.000
65A71ASP-1-0.779-0.85424.77310.86710.8670.0000.0000.0000.000
66A72GLN0-0.067-0.00622.647-0.362-0.3620.0000.0000.0000.000
67A73ARG10.8340.91324.873-11.341-11.3410.0000.0000.0000.000
68A74PHE0-0.043-0.02828.152-0.360-0.3600.0000.0000.0000.000
69A75SER0-0.059-0.04628.381-0.292-0.2920.0000.0000.0000.000
70A76ALA00.0240.02429.863-0.084-0.0840.0000.0000.0000.000
71A77PRO00.0170.01031.090-0.327-0.3270.0000.0000.0000.000
72A78GLY0-0.022-0.01934.0990.0760.0760.0000.0000.0000.000
73A79LEU0-0.0370.00332.485-0.056-0.0560.0000.0000.0000.000
74A80ASN0-0.016-0.00636.4480.1110.1110.0000.0000.0000.000
75A81ALA00.0500.02636.9890.2020.2020.0000.0000.0000.000
76A82ARG10.8330.87537.000-6.912-6.9120.0000.0000.0000.000
77A83GLU-1-0.831-0.91436.0547.8427.8420.0000.0000.0000.000
78A84ARG10.8080.89732.908-8.307-8.3070.0000.0000.0000.000
79A85LEU00.0160.00532.1960.3250.3250.0000.0000.0000.000
80A86MET0-0.004-0.00733.3830.1890.1890.0000.0000.0000.000
81A87SER0-0.027-0.00530.8660.2600.2600.0000.0000.0000.000
82A88TYR0-0.017-0.02226.6510.2470.2470.0000.0000.0000.000
83A89TRP00.0450.01029.3650.2860.2860.0000.0000.0000.000
84A90GLN0-0.063-0.03431.110-0.146-0.1460.0000.0000.0000.000
85A91LYS10.9350.95722.057-12.119-12.1190.0000.0000.0000.000
86A92TRP0-0.058-0.03426.4780.4130.4130.0000.0000.0000.000
87A93LEU0-0.044-0.02728.0570.1390.1390.0000.0000.0000.000
88A94ASP-1-0.845-0.90927.8499.7029.7020.0000.0000.0000.000
89A95ASN0-0.055-0.01522.3640.6030.6030.0000.0000.0000.000
90A96ALA0-0.0420.00023.8980.4660.4660.0000.0000.0000.000
91A97CYS00.0040.01023.8180.0630.0630.0000.0000.0000.000
92A98PRO00.0050.00326.9990.2420.2420.0000.0000.0000.000
93A99PRO00.007-0.00328.6810.0420.0420.0000.0000.0000.000
94A101ASP-1-0.804-0.89524.49911.04811.0480.0000.0000.0000.000
95A102GLU-1-0.949-0.97518.39315.62415.6240.0000.0000.0000.000
96A103GLN0-0.024-0.00822.564-0.057-0.0570.0000.0000.0000.000
97A104ARG10.9760.97517.876-14.525-14.5250.0000.0000.0000.000
98A105CYS00.0070.02121.1810.3680.3680.0000.0000.0000.000
99A106LEU00.0720.01818.486-0.307-0.3070.0000.0000.0000.000
100A107VAL00.0740.05723.115-0.149-0.1490.0000.0000.0000.000
101A108VAL0-0.012-0.00126.335-0.289-0.2890.0000.0000.0000.000
102A109LYS10.7740.88723.110-12.477-12.4770.0000.0000.0000.000
103A110LEU0-0.010-0.01321.364-0.035-0.0350.0000.0000.0000.000
104A111SER0-0.012-0.02825.921-0.198-0.1980.0000.0000.0000.000
105A112ALA0-0.055-0.01629.241-0.356-0.3560.0000.0000.0000.000
106A113GLU-1-0.804-0.90225.44311.90211.9020.0000.0000.0000.000
107A114VAL00.024-0.00528.7360.0900.0900.0000.0000.0000.000
108A115ALA0-0.060-0.01530.0080.0410.0410.0000.0000.0000.000
109A116ASP-1-0.880-0.93729.45810.00510.0050.0000.0000.0000.000
110A117LEU0-0.092-0.02624.6320.5120.5120.0000.0000.0000.000
111A118SER0-0.013-0.03524.801-0.351-0.3510.0000.0000.0000.000
112A119GLU-1-0.808-0.90327.7119.7609.7600.0000.0000.0000.000
113A120SER0-0.026-0.01824.481-0.200-0.2000.0000.0000.0000.000
114A121MET00.0220.03320.8410.2730.2730.0000.0000.0000.000
115A122ARG10.8450.90824.672-9.891-9.8910.0000.0000.0000.000
116A123ILE0-0.042-0.03827.516-0.166-0.1660.0000.0000.0000.000
117A124THR00.0230.01321.4500.0800.0800.0000.0000.0000.000
118A125LEU0-0.027-0.00624.1210.1340.1340.0000.0000.0000.000
119A126ARG10.8400.92225.784-9.838-9.8380.0000.0000.0000.000
120A127ASP-1-0.822-0.89726.61910.36710.3670.0000.0000.0000.000
121A128GLY0-0.003-0.01624.613-0.088-0.0880.0000.0000.0000.000
122A129SER0-0.012-0.00725.413-0.088-0.0880.0000.0000.0000.000
123A130ASP-1-0.890-0.96228.2809.1429.1420.0000.0000.0000.000
124A131GLY0-0.0150.00127.662-0.222-0.2220.0000.0000.0000.000
125A132ILE0-0.023-0.02225.515-0.017-0.0170.0000.0000.0000.000
126A133ILE00.0100.00728.899-0.239-0.2390.0000.0000.0000.000
127A134GLU-1-0.903-0.95031.6318.3978.3970.0000.0000.0000.000
128A135ARG10.7950.86825.917-11.175-11.1750.0000.0000.0000.000
129A136LEU0-0.011-0.00431.730-0.207-0.2070.0000.0000.0000.000
130A137VAL0-0.0050.00333.929-0.295-0.2950.0000.0000.0000.000
131A138GLY0-0.0180.00035.224-0.222-0.2220.0000.0000.0000.000
132A139CYS0-0.032-0.02033.942-0.152-0.1520.0000.0000.0000.000
133A140LEU00.002-0.00136.033-0.191-0.1910.0000.0000.0000.000
134A141GLY0-0.063-0.04039.219-0.224-0.2240.0000.0000.0000.000
135A142GLN00.0420.02434.969-0.130-0.1300.0000.0000.0000.000
136A143GLY00.0510.00840.051-0.063-0.0630.0000.0000.0000.000
137A144ARG10.8120.91341.635-7.086-7.0860.0000.0000.0000.000
138A145ASP-1-0.924-0.95142.9496.8616.8610.0000.0000.0000.000
139A146ASP-1-0.833-0.89741.0497.2397.2390.0000.0000.0000.000
140A147GLY0-0.032-0.01344.483-0.057-0.0570.0000.0000.0000.000
141A148SER0-0.048-0.03941.743-0.040-0.0400.0000.0000.0000.000
142A149LEU0-0.081-0.05439.4290.0610.0610.0000.0000.0000.000
143A150ALA00.0240.02044.115-0.099-0.0990.0000.0000.0000.000
144A151PRO00.001-0.01045.9430.1260.1260.0000.0000.0000.000
145A152CYS0-0.0020.00444.1050.0300.0300.0000.0000.0000.000
146A153ASP-1-0.850-0.91944.4326.9076.9070.0000.0000.0000.000
147A154ALA00.033-0.00540.5900.0790.0790.0000.0000.0000.000
148A155ARG10.9971.00839.674-7.147-7.1470.0000.0000.0000.000
149A156HIS00.0080.00739.8520.2460.2460.0000.0000.0000.000
150A157MET00.0300.01540.2430.1260.1260.0000.0000.0000.000
151A158ALA00.0090.01636.0390.1270.1270.0000.0000.0000.000
152A159SER0-0.004-0.01136.3980.2670.2670.0000.0000.0000.000
153A160ALA0-0.038-0.00837.4490.1040.1040.0000.0000.0000.000
154A161LEU00.019-0.00336.5300.0550.0550.0000.0000.0000.000
155A162TYR00.041-0.00429.0720.2380.2380.0000.0000.0000.000
156A163GLN0-0.044-0.02733.6100.2230.2230.0000.0000.0000.000
157A164LEU0-0.0150.00835.8000.0800.0800.0000.0000.0000.000
158A165TRP00.0470.01831.7660.1130.1130.0000.0000.0000.000
159A166LEU0-0.0060.00029.6440.2350.2350.0000.0000.0000.000
160A167GLY0-0.0060.00132.1480.1320.1320.0000.0000.0000.000
161A168ALA00.0240.01634.167-0.039-0.0390.0000.0000.0000.000
162A169SER0-0.023-0.02128.9280.2270.2270.0000.0000.0000.000
163A170LEU0-0.023-0.01330.9450.1590.1590.0000.0000.0000.000
164A171LEU00.015-0.00232.1890.0170.0170.0000.0000.0000.000
165A172SER0-0.015-0.03231.587-0.138-0.1380.0000.0000.0000.000
166A173LYS10.7510.86825.454-11.209-11.2090.0000.0000.0000.000
167A174LEU0-0.070-0.01430.8660.0160.0160.0000.0000.0000.000
168A175HIS00.016-0.01033.974-0.031-0.0310.0000.0000.0000.000
169A176ARG10.8640.94429.522-10.014-10.0140.0000.0000.0000.000
170A177SER00.0170.01332.916-0.052-0.0520.0000.0000.0000.000
171A178PRO00.0410.01133.5250.1890.1890.0000.0000.0000.000
172A179GLY00.0740.04534.526-0.024-0.0240.0000.0000.0000.000
173A180PRO0-0.025-0.02635.564-0.119-0.1190.0000.0000.0000.000
174A181LEU00.0160.01530.631-0.011-0.0110.0000.0000.0000.000
175A182GLU-1-0.897-0.95034.8337.9447.9440.0000.0000.0000.000
176A183THR0-0.0110.00037.571-0.215-0.2150.0000.0000.0000.000
177A184ALA00.0260.02935.678-0.153-0.1530.0000.0000.0000.000
178A185MET0-0.0120.00935.845-0.048-0.0480.0000.0000.0000.000
179A186GLN0-0.006-0.00637.673-0.046-0.0460.0000.0000.0000.000
180A187THR0-0.013-0.01740.763-0.225-0.2250.0000.0000.0000.000
181A188THR0-0.005-0.02736.908-0.065-0.0650.0000.0000.0000.000
182A189ARG10.9130.94736.710-7.896-7.8960.0000.0000.0000.000
183A190SER0-0.047-0.01041.993-0.151-0.1510.0000.0000.0000.000
184A191LEU0-0.039-0.01642.222-0.118-0.1180.0000.0000.0000.000
185A192LEU0-0.0260.00638.793-0.027-0.0270.0000.0000.0000.000
186A193GLU-1-0.827-0.87442.5156.9596.9590.0000.0000.0000.000