Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: QVVLY

Calculation Name: 4U0Q-B-Xray372

Preferred Name: Basigin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4U0Q

Chain ID: B

ChEMBL ID: CHEMBL3580492

UniProt ID: P35613

Base Structure: X-ray

Registration Date: 2023-09-21

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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1593207.10528
FMO2-HF: Nuclear repulsion 1522526.619889
FMO2-HF: Total energy -70680.485391
FMO2-MP2: Total energy -70883.309078


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(B:23:ALA)


Summations of interaction energy for fragment #1(B:23:ALA)
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.
-3.694-1.189-0.003-1.282-1.220.004
Interaction energy analysis for fragmet #1(B:23:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.006
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].
3B25THR0-0.065-0.0433.875-0.8741.015-0.008-1.144-0.7370.004
4B26VAL0-0.016-0.0046.3780.2580.2580.0000.0000.0000.000
5B27PHE00.0090.0098.7330.1480.1480.0000.0000.0000.000
6B28THR00.0210.00812.0570.0930.0930.0000.0000.0000.000
7B29THR0-0.078-0.04914.699-0.007-0.0070.0000.0000.0000.000
8B30VAL00.0100.00818.4850.0190.0190.0000.0000.0000.000
9B31GLU-1-0.850-0.90221.675-0.213-0.2130.0000.0000.0000.000
10B32ASP-1-0.851-0.92324.852-0.088-0.0880.0000.0000.0000.000
11B33LEU0-0.059-0.03927.119-0.002-0.0020.0000.0000.0000.000
12B34GLY0-0.028-0.00630.7190.0070.0070.0000.0000.0000.000
13B35SER0-0.041-0.02832.6670.0050.0050.0000.0000.0000.000
14B36LYS10.8170.90929.6880.0440.0440.0000.0000.0000.000
15B37ILE00.0360.02324.721-0.006-0.0060.0000.0000.0000.000
16B38LEU0-0.065-0.02822.6540.0160.0160.0000.0000.0000.000
17B39LEU0-0.0160.00519.385-0.014-0.0140.0000.0000.0000.000
18B40THR0-0.006-0.04616.9380.0150.0150.0000.0000.0000.000
19B41CYS0-0.107-0.04112.533-0.017-0.0170.0000.0000.0000.000
20B42SER00.009-0.01212.6730.0980.0980.0000.0000.0000.000
21B43LEU0-0.0390.0005.249-0.141-0.1410.0000.0000.0000.000
22B44ASN00.0240.0208.7920.1790.1790.0000.0000.0000.000
23B45ASP-1-0.891-0.9666.746-2.339-2.3390.0000.0000.0000.000
24B46SER0-0.013-0.0133.741-1.233-1.1500.003-0.050-0.0360.000
25B47ALA0-0.019-0.0083.5970.3030.5990.004-0.059-0.2410.000
26B48THR0-0.046-0.0224.9180.4940.4940.0000.0000.0000.000
27B49GLU-1-0.792-0.8837.192-0.364-0.3640.0000.0000.0000.000
28B50VAL0-0.056-0.0259.9700.1690.1690.0000.0000.0000.000
29B51THR0-0.062-0.04411.139-0.019-0.0190.0000.0000.0000.000
30B52GLY00.0200.01213.705-0.028-0.0280.0000.0000.0000.000
31B53HIS10.7840.86913.1880.0750.0750.0000.0000.0000.000
32B54ARG10.7730.84214.562-0.226-0.2260.0000.0000.0000.000
33B55TRP00.0520.02915.532-0.019-0.0190.0000.0000.0000.000
34B56LEU0-0.053-0.03716.0680.0270.0270.0000.0000.0000.000
35B57LYS10.8580.95519.4880.0060.0060.0000.0000.0000.000
36B58GLY00.0100.01721.067-0.003-0.0030.0000.0000.0000.000
37B59GLY0-0.0010.00622.3870.0170.0170.0000.0000.0000.000
38B60VAL0-0.034-0.03319.992-0.006-0.0060.0000.0000.0000.000
39B61VAL0-0.009-0.00321.367-0.002-0.0020.0000.0000.0000.000
40B62LEU00.0140.01020.847-0.008-0.0080.0000.0000.0000.000
41B63LYS10.8230.87818.706-0.121-0.1210.0000.0000.0000.000
42B64GLU-1-0.812-0.87718.1940.0030.0030.0000.0000.0000.000
43B65ASP-1-0.812-0.89917.7220.1480.1480.0000.0000.0000.000
44B66ALA0-0.008-0.00318.5610.0230.0230.0000.0000.0000.000
45B67LEU0-0.033-0.00818.750-0.015-0.0150.0000.0000.0000.000
46B68PRO00.0320.02615.223-0.003-0.0030.0000.0000.0000.000
47B69GLY00.0160.01214.239-0.022-0.0220.0000.0000.0000.000
48B70GLN0-0.002-0.01610.6900.0300.0300.0000.0000.0000.000
49B71LYS10.8250.91412.4200.1610.1610.0000.0000.0000.000
50B72THR0-0.011-0.00114.1770.0570.0570.0000.0000.0000.000
51B73GLU-1-0.834-0.91516.644-0.189-0.1890.0000.0000.0000.000
52B74PHE00.0040.00519.6380.0270.0270.0000.0000.0000.000
53B75LYS10.9490.97421.8220.0660.0660.0000.0000.0000.000
54B76VAL00.0040.01124.0120.0110.0110.0000.0000.0000.000
55B77ASP-1-0.756-0.86926.942-0.045-0.0450.0000.0000.0000.000
56B78SER00.0600.00230.158-0.002-0.0020.0000.0000.0000.000
57B79ASP-1-0.919-0.93831.919-0.033-0.0330.0000.0000.0000.000
58B80ASP-1-0.847-0.92728.214-0.015-0.0150.0000.0000.0000.000
59B81GLN0-0.092-0.03326.989-0.004-0.0040.0000.0000.0000.000
60B82TRP0-0.079-0.06026.995-0.004-0.0040.0000.0000.0000.000
61B83GLY00.0070.00424.8850.0070.0070.0000.0000.0000.000
62B84GLU-1-0.862-0.92017.802-0.078-0.0780.0000.0000.0000.000
63B85TYR00.000-0.00719.2730.0230.0230.0000.0000.0000.000
64B86SER0-0.026-0.03014.579-0.018-0.0180.0000.0000.0000.000
65B88VAL0-0.002-0.01111.052-0.026-0.0260.0000.0000.0000.000
66B89PHE00.009-0.0048.897-0.060-0.0600.0000.0000.0000.000
67B90LEU0-0.0350.00510.1270.1520.1520.0000.0000.0000.000
68B91PRO00.0380.0199.633-0.097-0.0970.0000.0000.0000.000
69B92GLU-1-0.753-0.8459.0060.5570.5570.0000.0000.0000.000
70B93PRO0-0.048-0.0305.7640.0180.0180.0000.0000.0000.000
71B94MET0-0.044-0.0134.659-0.0580.073-0.001-0.005-0.1250.000
72B95GLY00.0790.0354.414-0.638-0.532-0.001-0.024-0.0810.000
73B96THR0-0.073-0.0516.1090.1710.1710.0000.0000.0000.000
74B97ALA00.0010.0168.164-0.136-0.1360.0000.0000.0000.000
75B98ASN00.0100.00210.9760.0750.0750.0000.0000.0000.000
76B99ILE00.0090.00614.607-0.042-0.0420.0000.0000.0000.000
77B100GLN0-0.028-0.01817.6670.0330.0330.0000.0000.0000.000
78B101LEU00.0100.00520.436-0.015-0.0150.0000.0000.0000.000
79B102HIS00.0430.00823.8060.0040.0040.0000.0000.0000.000
80B103GLY00.0130.01126.0640.0030.0030.0000.0000.0000.000
81B104PRO00.0270.01828.807-0.005-0.0050.0000.0000.0000.000
82B105PRO0-0.047-0.01731.8850.0020.0020.0000.0000.0000.000
83B106ARG10.8690.93933.0240.0070.0070.0000.0000.0000.000
84B107VAL0-0.051-0.01235.0760.0000.0000.0000.0000.0000.000
85B108LYS10.9190.95437.661-0.007-0.0070.0000.0000.0000.000
86B109ALA00.0750.03640.396-0.002-0.0020.0000.0000.0000.000
87B110VAL0-0.087-0.04341.8980.0020.0020.0000.0000.0000.000
88B111LYS10.8110.88643.382-0.003-0.0030.0000.0000.0000.000
89B112SER00.0430.02145.630-0.001-0.0010.0000.0000.0000.000
90B113SER0-0.053-0.02947.7990.0000.0000.0000.0000.0000.000
91B114GLU-1-0.747-0.86651.4080.0050.0050.0000.0000.0000.000
92B115HIS0-0.050-0.02753.7370.0000.0000.0000.0000.0000.000
93B116ILE00.0180.03854.6550.0010.0010.0000.0000.0000.000
94B117ASN0-0.009-0.02658.9980.0010.0010.0000.0000.0000.000
95B118GLU-1-0.837-0.88062.4250.0000.0000.0000.0000.0000.000
96B119GLY0-0.039-0.02164.9610.0000.0000.0000.0000.0000.000
97B120GLU-1-0.872-0.92560.3120.0000.0000.0000.0000.0000.000
98B121THR0-0.017-0.01756.402-0.001-0.0010.0000.0000.0000.000
99B122ALA0-0.034-0.00355.7290.0010.0010.0000.0000.0000.000
100B123MET00.001-0.00249.184-0.002-0.0020.0000.0000.0000.000
101B124LEU0-0.0330.00249.9850.0020.0020.0000.0000.0000.000
102B125VAL00.016-0.00443.903-0.002-0.0020.0000.0000.0000.000
103B126CYS0-0.079-0.01142.5110.0020.0020.0000.0000.0000.000
104B127LYS10.8800.92636.2870.0010.0010.0000.0000.0000.000
105B128SER0-0.028-0.05735.1420.0010.0010.0000.0000.0000.000
106B129GLU-1-0.779-0.86730.987-0.007-0.0070.0000.0000.0000.000
107B130SER00.0030.01830.2760.0000.0000.0000.0000.0000.000
108B131VAL0-0.0050.01026.340-0.004-0.0040.0000.0000.0000.000
109B132PRO00.0200.00628.036-0.001-0.0010.0000.0000.0000.000
110B133PRO00.0080.00630.3670.0060.0060.0000.0000.0000.000
111B134VAL0-0.038-0.02733.238-0.002-0.0020.0000.0000.0000.000
112B135THR0-0.069-0.02836.372-0.001-0.0010.0000.0000.0000.000
113B136ASP-1-0.887-0.93838.592-0.040-0.0400.0000.0000.0000.000
114B137TRP0-0.040-0.05239.5520.0030.0030.0000.0000.0000.000
115B138ALA0-0.0100.00844.154-0.001-0.0010.0000.0000.0000.000
116B139TRP00.001-0.01946.4270.0020.0020.0000.0000.0000.000
117B140TYR0-0.0030.00648.273-0.001-0.0010.0000.0000.0000.000
118B141LYS10.7940.90352.5790.0050.0050.0000.0000.0000.000
119B142ILE0-0.050-0.01950.5940.0000.0000.0000.0000.0000.000
120B143THR0-0.034-0.04954.9950.0010.0010.0000.0000.0000.000
121B144ASP-1-0.956-0.97357.314-0.004-0.0040.0000.0000.0000.000
122B145SER0-0.014-0.00158.1120.0000.0000.0000.0000.0000.000
123B146GLU-1-0.942-0.97555.789-0.014-0.0140.0000.0000.0000.000
124B147ASP-1-0.772-0.84452.258-0.007-0.0070.0000.0000.0000.000
125B148LYS10.9320.97055.0700.0080.0080.0000.0000.0000.000
126B149ALA00.015-0.00153.7380.0000.0000.0000.0000.0000.000
127B150LEU0-0.054-0.02453.5590.0000.0000.0000.0000.0000.000
128B151MET00.0040.00251.459-0.001-0.0010.0000.0000.0000.000
129B152ASN00.0370.01352.9520.0020.0020.0000.0000.0000.000
130B153GLY00.0470.02254.921-0.001-0.0010.0000.0000.0000.000
131B154SER0-0.016-0.00157.8660.0000.0000.0000.0000.0000.000
132B155GLU-1-0.837-0.93459.612-0.008-0.0080.0000.0000.0000.000
133B156SER0-0.047-0.02362.2620.0000.0000.0000.0000.0000.000
134B157ARG10.7580.85961.2320.0070.0070.0000.0000.0000.000
135B158PHE0-0.0410.00156.2310.0010.0010.0000.0000.0000.000
136B159PHE00.0050.00554.790-0.002-0.0020.0000.0000.0000.000
137B160VAL0-0.001-0.00948.8950.0010.0010.0000.0000.0000.000
138B161SER00.0040.02647.629-0.002-0.0020.0000.0000.0000.000
139B162SER00.0050.00044.4150.0020.0020.0000.0000.0000.000
140B163SER0-0.028-0.01040.995-0.002-0.0020.0000.0000.0000.000
141B164GLN00.0540.01335.2810.0010.0010.0000.0000.0000.000
142B165GLY00.0290.03736.3090.0010.0010.0000.0000.0000.000
143B166ARG10.7880.87137.1100.0160.0160.0000.0000.0000.000
144B167SER00.001-0.00440.730-0.003-0.0030.0000.0000.0000.000
145B168GLU-1-0.811-0.89044.291-0.010-0.0100.0000.0000.0000.000
146B169LEU00.0130.01147.703-0.002-0.0020.0000.0000.0000.000
147B170HIS0-0.022-0.02750.0810.0020.0020.0000.0000.0000.000
148B171ILE0-0.005-0.00954.156-0.001-0.0010.0000.0000.0000.000
149B172GLU-1-0.874-0.95457.628-0.010-0.0100.0000.0000.0000.000
150B173ASN0-0.0090.00360.0880.0010.0010.0000.0000.0000.000
151B174LEU0-0.0110.00658.7930.0000.0000.0000.0000.0000.000
152B175ASN00.0350.01562.7760.0000.0000.0000.0000.0000.000
153B176MET00.004-0.01764.0100.0010.0010.0000.0000.0000.000
154B177GLU-1-0.894-0.94865.638-0.002-0.0020.0000.0000.0000.000
155B178ALA0-0.023-0.00963.8290.0000.0000.0000.0000.0000.000
156B179ASP-1-0.732-0.81760.195-0.005-0.0050.0000.0000.0000.000
157B180PRO00.0120.02059.1140.0000.0000.0000.0000.0000.000
158B181GLY00.0130.01657.9750.0000.0000.0000.0000.0000.000
159B182GLN0-0.027-0.02552.5980.0000.0000.0000.0000.0000.000
160B183TYR00.002-0.01051.876-0.001-0.0010.0000.0000.0000.000
161B184ARG10.8120.86947.4950.0090.0090.0000.0000.0000.000
162B186ASN00.0570.01743.6630.0020.0020.0000.0000.0000.000
163B187GLY00.0050.00840.464-0.001-0.0010.0000.0000.0000.000
164B188THR00.012-0.01038.9510.0010.0010.0000.0000.0000.000
165B189SER00.0360.01433.446-0.001-0.0010.0000.0000.0000.000
166B190SER00.0200.00132.2870.0030.0030.0000.0000.0000.000
167B191LYS10.8590.94227.8840.0650.0650.0000.0000.0000.000
168B192GLY00.0130.01533.2080.0030.0030.0000.0000.0000.000
169B193SER0-0.002-0.01136.424-0.002-0.0020.0000.0000.0000.000
170B194ASP-1-0.809-0.88537.612-0.008-0.0080.0000.0000.0000.000
171B195GLN0-0.027-0.02839.7270.0010.0010.0000.0000.0000.000
172B196ALA0-0.020-0.00842.2150.0020.0020.0000.0000.0000.000
173B197ILE00.0060.00744.098-0.001-0.0010.0000.0000.0000.000
174B198ILE0-0.054-0.02446.5790.0020.0020.0000.0000.0000.000
175B199THR0-0.029-0.00949.6500.0000.0000.0000.0000.0000.000
176B200LEU00.0070.00653.1270.0000.0000.0000.0000.0000.000
177B201ARG10.9120.95455.809-0.007-0.0070.0000.0000.0000.000
178B202VAL00.0560.02658.8810.0000.0000.0000.0000.0000.000
179B203ARG10.7840.85158.801-0.004-0.0040.0000.0000.0000.000