FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: YY5V2

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2020706.099307
FMO2-HF: Nuclear repulsion 1939873.225159
FMO2-HF: Total energy -80832.874148
FMO2-MP2: Total energy -81067.75212


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.
-150.246-161.29136.694-14.793-10.8560.128
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 : -0.848 / q_NPA : -0.884
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].
3A21SER00.0120.0243.409-10.824-8.262-0.009-1.255-1.298-0.001
4A22LYS10.9510.9634.517-18.526-18.449-0.001-0.019-0.0570.000
5A23ARG10.8430.8781.712-127.399-141.08336.704-13.519-9.5010.129
6A24ALA00.0270.0167.4020.5430.5430.0000.0000.0000.000
7A25ARG10.9240.97310.679-16.905-16.9050.0000.0000.0000.000
8A26GLN00.0450.01012.486-0.687-0.6870.0000.0000.0000.000
9A27LEU0-0.006-0.00913.868-0.946-0.9460.0000.0000.0000.000
10A28PRO0-0.019-0.00917.4340.3560.3560.0000.0000.0000.000
11A29VAL00.0310.01617.708-0.237-0.2370.0000.0000.0000.000
12A30GLY0-0.021-0.00120.628-0.212-0.2120.0000.0000.0000.000
13A31GLU-1-0.931-0.96922.29514.01014.0100.0000.0000.0000.000
14A32GLN0-0.034-0.00725.632-0.441-0.4410.0000.0000.0000.000
15A33LEU0-0.004-0.00928.0870.2670.2670.0000.0000.0000.000
16A34PRO00.0610.01826.928-0.210-0.2100.0000.0000.0000.000
17A35LEU00.0840.03228.857-0.333-0.3330.0000.0000.0000.000
18A36SER00.0160.00030.531-0.186-0.1860.0000.0000.0000.000
19A37ARG10.8560.93831.353-9.976-9.9760.0000.0000.0000.000
20A38LEU00.0390.01533.139-0.294-0.2940.0000.0000.0000.000
21A39LEU00.0240.00835.344-0.263-0.2630.0000.0000.0000.000
22A40GLN0-0.0240.00235.389-0.092-0.0920.0000.0000.0000.000
23A41TYR0-0.069-0.03435.859-0.052-0.0520.0000.0000.0000.000
24A42SER00.0300.01340.563-0.073-0.0730.0000.0000.0000.000
25A43ASP-1-0.840-0.90242.6086.9686.9680.0000.0000.0000.000
26A44LYS10.9950.96545.094-6.615-6.6150.0000.0000.0000.000
27A45GLN0-0.0100.01946.4190.0690.0690.0000.0000.0000.000
28A46GLN00.0580.00944.5790.0910.0910.0000.0000.0000.000
29A47LEU00.0010.01340.2550.0490.0490.0000.0000.0000.000
30A48PHE0-0.001-0.00143.5170.0550.0550.0000.0000.0000.000
31A49THR00.009-0.01246.469-0.047-0.0470.0000.0000.0000.000
32A50ILE0-0.0060.00440.1490.0210.0210.0000.0000.0000.000
33A51LEU00.0050.00841.3190.1030.1030.0000.0000.0000.000
34A52LEU00.008-0.01243.0790.0330.0330.0000.0000.0000.000
35A53GLN00.0070.01344.4550.0920.0920.0000.0000.0000.000
36A54CYS0-0.101-0.05040.4380.1320.1320.0000.0000.0000.000
37A55VAL0-0.014-0.01042.3010.0690.0690.0000.0000.0000.000
38A56GLU-1-0.922-0.95844.4876.5396.5390.0000.0000.0000.000
39A57LYS10.8320.92138.849-8.169-8.1690.0000.0000.0000.000
40A58HIS00.0070.01138.4010.1450.1450.0000.0000.0000.000
41A59PRO00.1260.06342.1220.0910.0910.0000.0000.0000.000
42A60ASP-1-0.949-0.97839.6007.9417.9410.0000.0000.0000.000
43A61LEU00.033-0.00237.8710.0840.0840.0000.0000.0000.000
44A62ALA0-0.014-0.00141.7400.0050.0050.0000.0000.0000.000
45A63ARG10.8460.92441.781-7.807-7.8070.0000.0000.0000.000
46A64ASP-1-0.905-0.95439.2258.1818.1810.0000.0000.0000.000
47A65ILE0-0.007-0.01541.3390.0060.0060.0000.0000.0000.000
48A66ARG10.9590.98243.294-6.587-6.5870.0000.0000.0000.000
49A67GLY0-0.0100.00145.592-0.052-0.0520.0000.0000.0000.000
50A68ILE0-0.0210.00440.1650.0390.0390.0000.0000.0000.000
51A69LEU0-0.050-0.02043.8260.0540.0540.0000.0000.0000.000
52A70PRO0-0.051-0.01646.188-0.105-0.1050.0000.0000.0000.000
53A71ALA00.0160.00649.008-0.058-0.0580.0000.0000.0000.000
54A72PRO0-0.021-0.00452.415-0.018-0.0180.0000.0000.0000.000
55A73SER00.017-0.00355.285-0.040-0.0400.0000.0000.0000.000
56A74MET00.0670.02558.135-0.023-0.0230.0000.0000.0000.000
57A75ASP-1-0.811-0.90361.5585.2665.2660.0000.0000.0000.000
58A76THR0-0.021-0.00156.3540.0040.0040.0000.0000.0000.000
59A77CYS0-0.050-0.01859.1900.0150.0150.0000.0000.0000.000
60A78VAL00.0490.01460.778-0.044-0.0440.0000.0000.0000.000
61A79GLU-1-0.913-0.97761.3515.1155.1150.0000.0000.0000.000
62A80THR0-0.133-0.07158.7900.0210.0210.0000.0000.0000.000
63A81LEU00.0230.01361.358-0.022-0.0220.0000.0000.0000.000
64A82ARG10.9500.99664.570-4.834-4.8340.0000.0000.0000.000
65A83LYS10.9780.98760.037-5.462-5.4620.0000.0000.0000.000
66A84LEU00.0040.01360.597-0.017-0.0170.0000.0000.0000.000
67A85LEU00.0460.01564.217-0.025-0.0250.0000.0000.0000.000
68A86ILE0-0.025-0.01666.973-0.065-0.0650.0000.0000.0000.000
69A87ASN0-0.031-0.00363.1830.0010.0010.0000.0000.0000.000
70A88LEU0-0.028-0.02465.932-0.016-0.0160.0000.0000.0000.000
71A89ASN0-0.001-0.01668.030-0.095-0.0950.0000.0000.0000.000
72A90ASP-1-0.882-0.92368.0364.7014.7010.0000.0000.0000.000
73A91SER0-0.119-0.06166.8190.0380.0380.0000.0000.0000.000
74A92PHE0-0.012-0.00668.930-0.026-0.0260.0000.0000.0000.000
75A93PRO0-0.084-0.04372.6180.0070.0070.0000.0000.0000.000
76A94TYR00.021-0.00973.752-0.050-0.0500.0000.0000.0000.000
77A95GLY00.0520.04675.6500.0040.0040.0000.0000.0000.000
78A96GLY0-0.048-0.01278.254-0.058-0.0580.0000.0000.0000.000
79A97ASP-1-0.755-0.86879.9353.9543.9540.0000.0000.0000.000
80A98LYS10.9500.97077.501-4.162-4.1620.0000.0000.0000.000
81A99ARG10.8520.91578.165-3.938-3.9380.0000.0000.0000.000
82A100GLY00.0330.02379.936-0.028-0.0280.0000.0000.0000.000
83A101ASP-1-0.803-0.89877.4934.1834.1830.0000.0000.0000.000
84A102TYR0-0.014-0.01273.3560.0750.0750.0000.0000.0000.000
85A103ALA00.0270.00273.9120.0690.0690.0000.0000.0000.000
86A104PHE00.0310.02571.7460.0710.0710.0000.0000.0000.000
87A105ASN00.0310.01270.6290.0450.0450.0000.0000.0000.000
88A106ARG10.8820.95568.921-4.606-4.6060.0000.0000.0000.000
89A107ILE0-0.025-0.01968.4340.0600.0600.0000.0000.0000.000
90A108ARG10.9721.01867.561-4.731-4.7310.0000.0000.0000.000
91A109GLU-1-0.894-0.95063.0844.9914.9910.0000.0000.0000.000
92A110LYS10.9010.94362.893-5.073-5.0730.0000.0000.0000.000
93A111TYR00.0250.01665.2970.0030.0030.0000.0000.0000.000
94A112MET0-0.036-0.04264.7750.0050.0050.0000.0000.0000.000
95A113ALA0-0.0150.00561.7860.0500.0500.0000.0000.0000.000
96A114VAL00.0200.01063.0320.0470.0470.0000.0000.0000.000
97A115LEU00.0150.00665.4000.0020.0020.0000.0000.0000.000
98A116HIS0-0.0010.00760.724-0.009-0.0090.0000.0000.0000.000
99A117ALA00.0570.03660.9170.0470.0470.0000.0000.0000.000
100A118LEU0-0.028-0.01961.9520.0210.0210.0000.0000.0000.000
101A119ASN0-0.017-0.02363.318-0.042-0.0420.0000.0000.0000.000
102A120ASP-1-0.961-0.96558.5275.6485.6480.0000.0000.0000.000
103A121MET0-0.053-0.03758.875-0.004-0.0040.0000.0000.0000.000
104A122VAL00.010-0.00261.588-0.013-0.0130.0000.0000.0000.000
105A123PRO00.0490.02461.839-0.031-0.0310.0000.0000.0000.000
106A124CYS0-0.101-0.03959.0610.0520.0520.0000.0000.0000.000
107A125TYR0-0.062-0.03860.9890.0410.0410.0000.0000.0000.000
108A126LEU00.0120.01764.420-0.104-0.1040.0000.0000.0000.000
109A127PRO00.1010.02464.8760.0760.0760.0000.0000.0000.000
110A128PRO0-0.126-0.04563.1300.0460.0460.0000.0000.0000.000
111A129TYR0-0.0270.00556.3040.0770.0770.0000.0000.0000.000
112A130SER00.0050.00261.5420.0660.0660.0000.0000.0000.000
113A131THR00.0300.02063.626-0.089-0.0890.0000.0000.0000.000
114A132CYS0-0.066-0.03165.094-0.079-0.0790.0000.0000.0000.000
115A133PHE00.1290.06866.8440.0130.0130.0000.0000.0000.000
116A134GLU-1-0.843-0.93369.0904.7064.7060.0000.0000.0000.000
117A135LYS10.8420.92064.911-4.815-4.8150.0000.0000.0000.000
118A136ASN00.0510.01566.1570.0630.0630.0000.0000.0000.000
119A137ILE00.0110.02668.208-0.005-0.0050.0000.0000.0000.000
120A138THR0-0.003-0.00568.449-0.026-0.0260.0000.0000.0000.000
121A139PHE00.0000.00663.8610.0050.0050.0000.0000.0000.000
122A140LEU00.0220.00668.089-0.004-0.0040.0000.0000.0000.000
123A141ASP-1-0.804-0.87670.6384.3934.3930.0000.0000.0000.000
124A142ALA0-0.019-0.01468.794-0.028-0.0280.0000.0000.0000.000
125A143ALA0-0.020-0.01768.4570.0140.0140.0000.0000.0000.000
126A144THR00.010-0.01970.023-0.021-0.0210.0000.0000.0000.000
127A145ASN0-0.002-0.00573.120-0.083-0.0830.0000.0000.0000.000
128A146VAL0-0.067-0.02068.194-0.011-0.0110.0000.0000.0000.000
129A147VAL00.000-0.01371.231-0.009-0.0090.0000.0000.0000.000
130A148HIS0-0.0010.00573.230-0.048-0.0480.0000.0000.0000.000
131A149GLU-1-0.931-0.96373.1224.3224.3220.0000.0000.0000.000
132A150LEU0-0.059-0.01070.5800.0180.0180.0000.0000.0000.000
133A151PRO0-0.0170.00573.078-0.075-0.0750.0000.0000.0000.000
134A152GLU-1-0.841-0.90476.0414.0034.0030.0000.0000.0000.000
135A153PHE0-0.046-0.05274.6220.0150.0150.0000.0000.0000.000
136A154HIS0-0.045-0.03079.992-0.034-0.0340.0000.0000.0000.000
137A155ASN0-0.020-0.01579.575-0.043-0.0430.0000.0000.0000.000
138A156PRO00.0790.03580.8020.0350.0350.0000.0000.0000.000
139A157ASN0-0.003-0.01777.6800.0460.0460.0000.0000.0000.000
140A158HIS10.7620.87775.583-4.231-4.2310.0000.0000.0000.000
141A159ASN00.0590.02376.0570.0730.0730.0000.0000.0000.000
142A160VAL00.0290.02274.7960.0010.0010.0000.0000.0000.000
143A161TYR00.0070.01971.1800.0230.0230.0000.0000.0000.000
144A162LYS10.8920.95173.376-4.210-4.2100.0000.0000.0000.000
145A163SER0-0.027-0.01175.173-0.040-0.0400.0000.0000.0000.000
146A164GLN0-0.078-0.05571.456-0.018-0.0180.0000.0000.0000.000
147A165ALA0-0.016-0.00172.2300.0200.0200.0000.0000.0000.000
148A166TYR00.002-0.03273.2090.0020.0020.0000.0000.0000.000
149A167TYR00.0010.03674.961-0.001-0.0010.0000.0000.0000.000
150A168GLU-1-0.806-0.91070.4924.5644.5640.0000.0000.0000.000
151A169LEU00.000-0.00469.9880.0240.0240.0000.0000.0000.000
152A170THR0-0.021-0.01073.034-0.027-0.0270.0000.0000.0000.000
153A171GLY00.0500.02174.043-0.015-0.0150.0000.0000.0000.000
154A172ALA0-0.053-0.03670.0100.0230.0230.0000.0000.0000.000
155A173TRP00.049-0.00971.7010.0350.0350.0000.0000.0000.000
156A174LEU00.0090.02674.130-0.008-0.0080.0000.0000.0000.000
157A175VAL0-0.047-0.01969.601-0.005-0.0050.0000.0000.0000.000
158A176VAL0-0.007-0.00669.5190.0170.0170.0000.0000.0000.000
159A177LEU0-0.015-0.01771.9280.0020.0020.0000.0000.0000.000
160A178ARG11.0181.01671.375-4.518-4.5180.0000.0000.0000.000
161A179GLN0-0.118-0.06469.1400.0220.0220.0000.0000.0000.000
162A180LEU0-0.097-0.05572.5490.0450.0450.0000.0000.0000.000
163A181GLU-1-0.879-0.92975.1344.1184.1180.0000.0000.0000.000
164A182ASP-1-0.978-0.97774.9964.3034.3030.0000.0000.0000.000
165A183ARG10.9120.97871.597-4.474-4.4740.0000.0000.0000.000
166A184PRO00.017-0.00874.200-0.044-0.0440.0000.0000.0000.000
167A185VAL0-0.074-0.04176.5330.0340.0340.0000.0000.0000.000
168A186VAL00.1010.04978.3750.0300.0300.0000.0000.0000.000
169A187PRO0-0.057-0.02974.998-0.030-0.0300.0000.0000.0000.000
170A188LEU00.0290.01677.977-0.042-0.0420.0000.0000.0000.000
171A189LEU00.0080.01077.7250.0400.0400.0000.0000.0000.000
172A190PRO00.0500.04676.398-0.052-0.0520.0000.0000.0000.000
173A191LEU0-0.053-0.04479.508-0.003-0.0030.0000.0000.0000.000
174A192GLU-1-0.952-0.98682.8993.8493.8490.0000.0000.0000.000
175A193GLU-1-0.910-0.95377.3554.2724.2720.0000.0000.0000.000
176A194LEU00.011-0.02077.669-0.007-0.0070.0000.0000.0000.000
177A195GLU-1-0.812-0.86880.7703.7713.7710.0000.0000.0000.000
178A196GLU-1-0.821-0.92582.5883.9123.9120.0000.0000.0000.000
179A197HIS00.0150.02476.617-0.013-0.0130.0000.0000.0000.000
180A198ASN00.020-0.01680.8730.0360.0360.0000.0000.0000.000
181A199LYS10.8060.92483.048-3.940-3.9400.0000.0000.0000.000
182A200THR0-0.021-0.02180.919-0.038-0.0380.0000.0000.0000.000
183A201SER0-0.059-0.01979.929-0.005-0.0050.0000.0000.0000.000
184A202GLN0-0.078-0.07381.844-0.014-0.0140.0000.0000.0000.000
185A203ASN0-0.018-0.00584.792-0.023-0.0230.0000.0000.0000.000
186A204ARG10.8790.95780.266-4.030-4.0300.0000.0000.0000.000
187A205MET00.0220.00476.1730.0490.0490.0000.0000.0000.000
188A206GLU-1-0.845-0.89381.0473.7633.7630.0000.0000.0000.000
189A207GLU-1-0.959-0.97080.7394.0774.0770.0000.0000.0000.000
190A208ALA00.015-0.00678.2750.0030.0030.0000.0000.0000.000
191A209LEU0-0.011-0.00980.0850.0080.0080.0000.0000.0000.000
192A210ASN0-0.063-0.06182.711-0.036-0.0360.0000.0000.0000.000
193A211TYR0-0.038-0.04377.986-0.017-0.0170.0000.0000.0000.000
194A212LEU0-0.0170.02079.4120.0060.0060.0000.0000.0000.000
195A213LYS10.8640.90482.336-3.772-3.7720.0000.0000.0000.000
196A214GLN0-0.080-0.00984.461-0.053-0.0530.0000.0000.0000.000
197A215LEU0-0.029-0.00878.474-0.017-0.0170.0000.0000.0000.000
198A216GLN0-0.075-0.04483.032-0.060-0.0600.0000.0000.0000.000