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: 531NZ

Calculation Name: 3Q5W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q5W

Chain ID: A

ChEMBL ID:

UniProt ID: P38937

Base Structure: X-ray

Registration Date: 2023-06-20

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2022071.440021
FMO2-HF: Nuclear repulsion 1941240.687373
FMO2-HF: Total energy -80830.752647
FMO2-MP2: Total energy -81065.907556


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:19:ASP)


Summations of interaction energy for fragment #1(A:19: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.
-120.848-135.10933.844-10.76-8.8220.041
Interaction energy analysis for fragmet #1(A:19:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.913 / q_NPA : -0.936
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].
3A21SER00.0240.0283.498-11.216-8.665-0.006-1.185-1.359-0.002
4A22LYS10.9430.9654.683-18.138-18.098-0.001-0.017-0.0220.000
5A23ARG10.9180.9251.801-99.381-116.23333.851-9.558-7.4410.043
6A24ALA00.0260.0187.5010.2870.2870.0000.0000.0000.000
7A25ARG10.9600.98910.713-15.748-15.7480.0000.0000.0000.000
8A26GLN00.0210.00512.515-0.446-0.4460.0000.0000.0000.000
9A27LEU0-0.010-0.01813.920-0.919-0.9190.0000.0000.0000.000
10A28PRO0-0.045-0.01417.5040.3890.3890.0000.0000.0000.000
11A29VAL00.0550.02117.763-0.227-0.2270.0000.0000.0000.000
12A30GLY0-0.027-0.00620.729-0.205-0.2050.0000.0000.0000.000
13A31GLU-1-0.928-0.96722.71613.89913.8990.0000.0000.0000.000
14A32GLN0-0.024-0.00725.734-0.286-0.2860.0000.0000.0000.000
15A33LEU0-0.013-0.00828.1690.2620.2620.0000.0000.0000.000
16A34PRO00.0590.02126.968-0.197-0.1970.0000.0000.0000.000
17A35LEU00.0950.02928.915-0.339-0.3390.0000.0000.0000.000
18A36SER00.0030.00030.549-0.188-0.1880.0000.0000.0000.000
19A37ARG10.8850.96231.235-10.037-10.0370.0000.0000.0000.000
20A38LEU00.0470.01433.175-0.291-0.2910.0000.0000.0000.000
21A39LEU00.0240.00735.399-0.263-0.2630.0000.0000.0000.000
22A40GLN0-0.049-0.01535.579-0.065-0.0650.0000.0000.0000.000
23A41TYR0-0.079-0.03636.227-0.067-0.0670.0000.0000.0000.000
24A42SER00.0160.00040.602-0.078-0.0780.0000.0000.0000.000
25A43ASP-1-0.845-0.91342.6386.9496.9490.0000.0000.0000.000
26A44LYS11.0030.96945.128-6.633-6.6330.0000.0000.0000.000
27A45GLN0-0.0210.01746.4420.1200.1200.0000.0000.0000.000
28A46GLN00.0940.03144.5840.0900.0900.0000.0000.0000.000
29A47LEU0-0.0020.01240.6350.0520.0520.0000.0000.0000.000
30A48PHE00.0150.00443.5590.0610.0610.0000.0000.0000.000
31A49THR00.012-0.00546.509-0.049-0.0490.0000.0000.0000.000
32A50ILE0-0.031-0.00940.2480.0170.0170.0000.0000.0000.000
33A51LEU00.0010.00241.7620.1010.1010.0000.0000.0000.000
34A52LEU00.011-0.01143.1330.0370.0370.0000.0000.0000.000
35A53GLN00.0060.01244.3680.1030.1030.0000.0000.0000.000
36A54CYS0-0.095-0.04240.4060.1360.1360.0000.0000.0000.000
37A55VAL0-0.015-0.00742.3000.0750.0750.0000.0000.0000.000
38A56GLU-1-0.946-0.96844.3736.5626.5620.0000.0000.0000.000
39A57LYS10.8880.96138.695-8.221-8.2210.0000.0000.0000.000
40A58HIS0-0.042-0.02538.5760.1750.1750.0000.0000.0000.000
41A59PRO00.1180.05841.9830.0870.0870.0000.0000.0000.000
42A60ASP-1-1.000-0.99939.2038.0608.0600.0000.0000.0000.000
43A61LEU00.0590.01237.6950.0680.0680.0000.0000.0000.000
44A62ALA0-0.014-0.00841.3930.0020.0020.0000.0000.0000.000
45A63ARG10.8660.94340.942-7.851-7.8510.0000.0000.0000.000
46A64ASP-1-0.880-0.95338.9838.2398.2390.0000.0000.0000.000
47A65ILE0-0.013-0.01441.1930.0020.0020.0000.0000.0000.000
48A66ARG10.9720.98542.859-6.645-6.6450.0000.0000.0000.000
49A67GLY0-0.021-0.00645.165-0.057-0.0570.0000.0000.0000.000
50A68ILE0-0.0160.00640.0130.0370.0370.0000.0000.0000.000
51A69LEU0-0.057-0.02143.4520.0480.0480.0000.0000.0000.000
52A70PRO0-0.065-0.01945.916-0.102-0.1020.0000.0000.0000.000
53A71ALA00.0250.00648.694-0.058-0.0580.0000.0000.0000.000
54A72PRO0-0.024-0.00452.076-0.019-0.0190.0000.0000.0000.000
55A73SER00.0540.02254.970-0.057-0.0570.0000.0000.0000.000
56A74MET00.0580.02357.834-0.020-0.0200.0000.0000.0000.000
57A75ASP-1-0.885-0.94461.2935.1765.1760.0000.0000.0000.000
58A76THR00.0020.01356.1140.0090.0090.0000.0000.0000.000
59A77CYS0-0.0250.00058.6190.0080.0080.0000.0000.0000.000
60A78VAL00.0360.01460.460-0.046-0.0460.0000.0000.0000.000
61A79GLU-1-0.883-0.97061.3025.1665.1660.0000.0000.0000.000
62A80THR0-0.117-0.07758.7050.0200.0200.0000.0000.0000.000
63A81LEU00.0150.01161.256-0.024-0.0240.0000.0000.0000.000
64A82ARG10.9370.99064.483-4.860-4.8600.0000.0000.0000.000
65A83LYS10.9860.98659.861-5.465-5.4650.0000.0000.0000.000
66A84LEU00.0060.01060.895-0.017-0.0170.0000.0000.0000.000
67A85LEU00.0400.00864.235-0.026-0.0260.0000.0000.0000.000
68A86ILE0-0.045-0.01666.862-0.065-0.0650.0000.0000.0000.000
69A87ASN0-0.069-0.01462.8200.0000.0000.0000.0000.0000.000
70A88LEU0-0.025-0.00765.950-0.020-0.0200.0000.0000.0000.000
71A89ASN0-0.009-0.01368.059-0.075-0.0750.0000.0000.0000.000
72A90ASP-1-0.896-0.93568.0504.6984.6980.0000.0000.0000.000
73A91SER0-0.128-0.07767.0440.0320.0320.0000.0000.0000.000
74A92PHE0-0.016-0.01368.964-0.028-0.0280.0000.0000.0000.000
75A93PRO0-0.092-0.04472.6550.0060.0060.0000.0000.0000.000
76A94TYR00.016-0.01073.794-0.049-0.0490.0000.0000.0000.000
77A95GLY00.0530.04575.6860.0030.0030.0000.0000.0000.000
78A96GLY0-0.044-0.01178.294-0.058-0.0580.0000.0000.0000.000
79A97ASP-1-0.813-0.91479.9783.9483.9480.0000.0000.0000.000
80A98LYS10.9560.97377.614-4.104-4.1040.0000.0000.0000.000
81A99ARG10.9210.96778.208-3.953-3.9530.0000.0000.0000.000
82A100GLY00.0480.03379.952-0.028-0.0280.0000.0000.0000.000
83A101ASP-1-0.831-0.94377.5494.1774.1770.0000.0000.0000.000
84A102TYR0-0.022-0.01573.7140.0790.0790.0000.0000.0000.000
85A103ALA00.0220.00073.9730.0690.0690.0000.0000.0000.000
86A104PHE00.0310.02271.9810.0690.0690.0000.0000.0000.000
87A105ASN00.0220.00870.6410.0370.0370.0000.0000.0000.000
88A106ARG10.8930.95768.957-4.596-4.5960.0000.0000.0000.000
89A107ILE00.005-0.00268.4850.0570.0570.0000.0000.0000.000
90A108ARG10.9721.01967.182-4.746-4.7460.0000.0000.0000.000
91A109GLU-1-0.895-0.95763.1734.9784.9780.0000.0000.0000.000
92A110LYS10.9630.98262.938-5.089-5.0890.0000.0000.0000.000
93A111TYR00.0380.01465.339-0.001-0.0010.0000.0000.0000.000
94A112MET0-0.047-0.05064.6710.0150.0150.0000.0000.0000.000
95A113ALA0-0.0180.00461.8380.0440.0440.0000.0000.0000.000
96A114VAL00.0200.00763.0680.0480.0480.0000.0000.0000.000
97A115LEU00.0170.00865.3830.0050.0050.0000.0000.0000.000
98A116HIS00.0080.01360.7520.0090.0090.0000.0000.0000.000
99A117ALA00.0510.03560.8120.0480.0480.0000.0000.0000.000
100A118LEU0-0.031-0.02261.8650.0180.0180.0000.0000.0000.000
101A119ASN00.003-0.01362.865-0.030-0.0300.0000.0000.0000.000
102A120ASP-1-0.970-0.96858.3635.6565.6560.0000.0000.0000.000
103A121MET0-0.053-0.04358.575-0.003-0.0030.0000.0000.0000.000
104A122VAL00.0220.00361.212-0.012-0.0120.0000.0000.0000.000
105A123PRO00.0210.02061.156-0.034-0.0340.0000.0000.0000.000
106A124CYS0-0.093-0.04658.5190.0530.0530.0000.0000.0000.000
107A125TYR0-0.101-0.05060.7920.0410.0410.0000.0000.0000.000
108A126LEU00.0490.02863.971-0.105-0.1050.0000.0000.0000.000
109A127PRO00.0800.02364.4210.0750.0750.0000.0000.0000.000
110A128PRO0-0.097-0.02162.4510.0790.0790.0000.0000.0000.000
111A129TYR0-0.037-0.00255.5650.0570.0570.0000.0000.0000.000
112A130SER00.011-0.00861.0770.0710.0710.0000.0000.0000.000
113A131THR00.0110.00763.195-0.083-0.0830.0000.0000.0000.000
114A132CYS0-0.059-0.02564.771-0.081-0.0810.0000.0000.0000.000
115A133PHE00.1230.06066.4510.0130.0130.0000.0000.0000.000
116A134GLU-1-0.884-0.96268.5594.7244.7240.0000.0000.0000.000
117A135LYS10.8720.94064.416-4.867-4.8670.0000.0000.0000.000
118A136ASN00.0630.02065.6880.0670.0670.0000.0000.0000.000
119A137ILE00.0270.03167.823-0.005-0.0050.0000.0000.0000.000
120A138THR0-0.007-0.00768.036-0.035-0.0350.0000.0000.0000.000
121A139PHE0-0.0110.00463.5120.0040.0040.0000.0000.0000.000
122A140LEU00.014-0.00467.734-0.003-0.0030.0000.0000.0000.000
123A141ASP-1-0.865-0.91170.2584.3974.3970.0000.0000.0000.000
124A142ALA00.018-0.00468.441-0.025-0.0250.0000.0000.0000.000
125A143ALA0-0.022-0.01868.0810.0140.0140.0000.0000.0000.000
126A144THR00.012-0.02169.685-0.021-0.0210.0000.0000.0000.000
127A145ASN00.0400.01272.683-0.078-0.0780.0000.0000.0000.000
128A146VAL0-0.082-0.02868.169-0.012-0.0120.0000.0000.0000.000
129A147VAL00.005-0.01871.157-0.010-0.0100.0000.0000.0000.000
130A148HIS00.0270.09573.117-0.048-0.0480.0000.0000.0000.000
131A149GLU-1-0.952-0.96873.1504.3414.3410.0000.0000.0000.000
132A150LEU0-0.058-0.00271.0850.0160.0160.0000.0000.0000.000
133A151PRO0-0.0100.01273.099-0.079-0.0790.0000.0000.0000.000
134A152GLU-1-0.893-0.94076.0774.0214.0210.0000.0000.0000.000
135A153PHE0-0.046-0.05874.9270.0180.0180.0000.0000.0000.000
136A154HIS0-0.032-0.01480.042-0.027-0.0270.0000.0000.0000.000
137A155ASN0-0.0190.00179.609-0.037-0.0370.0000.0000.0000.000
138A156PRO00.0730.02080.8630.0380.0380.0000.0000.0000.000
139A157ASN00.0500.00977.6260.0380.0380.0000.0000.0000.000
140A158HIS10.7480.88775.639-4.223-4.2230.0000.0000.0000.000
141A159ASN00.0610.04576.1130.0640.0640.0000.0000.0000.000
142A160VAL00.0300.02574.7820.0020.0020.0000.0000.0000.000
143A161TYR0-0.0020.00971.5740.0210.0210.0000.0000.0000.000
144A162LYS10.8890.94173.406-4.225-4.2250.0000.0000.0000.000
145A163SER0-0.075-0.03275.218-0.024-0.0240.0000.0000.0000.000
146A164GLN0-0.001-0.02271.3300.0310.0310.0000.0000.0000.000
147A165ALA0-0.0080.00872.1330.0200.0200.0000.0000.0000.000
148A166TYR0-0.018-0.11473.085-0.002-0.0020.0000.0000.0000.000
149A167TYR0-0.0200.02974.633-0.005-0.0050.0000.0000.0000.000
150A168GLU-1-0.851-0.94070.2714.5934.5930.0000.0000.0000.000
151A169LEU00.0070.00169.8770.0230.0230.0000.0000.0000.000
152A170THR0-0.021-0.01072.642-0.029-0.0290.0000.0000.0000.000
153A171GLY00.0500.02173.581-0.015-0.0150.0000.0000.0000.000
154A172ALA0-0.041-0.03169.6290.0240.0240.0000.0000.0000.000
155A173TRP00.045-0.00571.2460.0380.0380.0000.0000.0000.000
156A174LEU00.0300.02673.694-0.008-0.0080.0000.0000.0000.000
157A175VAL0-0.056-0.02069.526-0.007-0.0070.0000.0000.0000.000
158A176VAL00.002-0.00369.2520.0190.0190.0000.0000.0000.000
159A177LEU0-0.023-0.02271.4840.0020.0020.0000.0000.0000.000
160A178ARG11.0051.01470.612-4.563-4.5630.0000.0000.0000.000
161A179GLN0-0.095-0.03868.0500.0060.0060.0000.0000.0000.000
162A180LEU0-0.099-0.05772.0830.0440.0440.0000.0000.0000.000
163A181GLU-1-0.873-0.94074.6914.1624.1620.0000.0000.0000.000
164A182ASP-1-0.993-0.99274.4894.3064.3060.0000.0000.0000.000
165A183ARG10.9260.99170.457-4.513-4.5130.0000.0000.0000.000
166A184PRO00.004-0.01373.752-0.044-0.0440.0000.0000.0000.000
167A185VAL0-0.057-0.02776.1180.0300.0300.0000.0000.0000.000
168A186VAL00.0850.03777.9580.0310.0310.0000.0000.0000.000
169A187PRO0-0.054-0.02674.617-0.029-0.0290.0000.0000.0000.000
170A188LEU00.0260.01277.603-0.042-0.0420.0000.0000.0000.000
171A189LEU00.0030.00477.1960.0400.0400.0000.0000.0000.000
172A190PRO00.0550.04675.974-0.053-0.0530.0000.0000.0000.000
173A191LEU0-0.055-0.04979.147-0.002-0.0020.0000.0000.0000.000
174A192GLU-1-0.957-0.99382.5313.8873.8870.0000.0000.0000.000
175A193GLU-1-0.883-0.92977.5274.2584.2580.0000.0000.0000.000
176A194LEU0-0.012-0.03277.387-0.006-0.0060.0000.0000.0000.000
177A195GLU-1-0.848-0.91980.3913.8083.8080.0000.0000.0000.000
178A196GLU-1-0.892-0.96082.1133.9233.9230.0000.0000.0000.000
179A197HIS00.0090.04375.869-0.017-0.0170.0000.0000.0000.000
180A198ASN00.018-0.00280.5050.0210.0210.0000.0000.0000.000
181A199LYS10.8860.98282.663-3.932-3.9320.0000.0000.0000.000
182A200THR0-0.068-0.06980.809-0.041-0.0410.0000.0000.0000.000
183A201SER0-0.0240.00279.872-0.018-0.0180.0000.0000.0000.000
184A202GLN0-0.073-0.06381.641-0.014-0.0140.0000.0000.0000.000
185A203ASN00.0400.00884.536-0.021-0.0210.0000.0000.0000.000
186A204ARG10.8700.95480.142-4.019-4.0190.0000.0000.0000.000
187A205MET00.0130.00275.7960.0460.0460.0000.0000.0000.000
188A206GLU-1-0.889-0.91580.6663.7973.7970.0000.0000.0000.000
189A207GLU-1-0.943-0.95880.5664.0774.0770.0000.0000.0000.000
190A208ALA00.001-0.01277.8270.0030.0030.0000.0000.0000.000
191A209LEU00.004-0.00379.6370.0120.0120.0000.0000.0000.000
192A210ASN0-0.076-0.06582.285-0.038-0.0380.0000.0000.0000.000
193A211TYR0-0.047-0.03478.053-0.031-0.0310.0000.0000.0000.000
194A212LEU0-0.0110.02779.2130.0070.0070.0000.0000.0000.000
195A213LYS10.9310.94981.911-3.760-3.7600.0000.0000.0000.000
196A214GLN0-0.101-0.02683.859-0.055-0.0550.0000.0000.0000.000
197A215LEU0-0.016-0.00877.991-0.015-0.0150.0000.0000.0000.000
198A216GLN0-0.058-0.00982.600-0.044-0.0440.0000.0000.0000.000