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: ZVVZN

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 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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1586711.056502
FMO2-HF: Nuclear repulsion 1516032.574291
FMO2-HF: Total energy -70678.482211
FMO2-MP2: Total energy -70881.255949


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.
-3.498-1.445-0.011-1.048-0.9920.002
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 : 0.000 / q_NPA : -0.019
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].
3B25THR0-0.037-0.0273.831-0.9310.617-0.016-0.924-0.6080.002
4B26VAL0-0.010-0.0026.5230.3900.3900.0000.0000.0000.000
5B27PHE0-0.025-0.0148.7770.0270.0270.0000.0000.0000.000
6B28THR00.0400.00712.3770.1040.1040.0000.0000.0000.000
7B29THR0-0.057-0.03014.897-0.010-0.0100.0000.0000.0000.000
8B30VAL00.0080.01518.6690.0190.0190.0000.0000.0000.000
9B31GLU-1-0.912-0.95621.977-0.144-0.1440.0000.0000.0000.000
10B32ASP-1-0.858-0.94024.956-0.081-0.0810.0000.0000.0000.000
11B33LEU0-0.078-0.04626.8910.0040.0040.0000.0000.0000.000
12B34GLY0-0.048-0.00930.5240.0090.0090.0000.0000.0000.000
13B35SER0-0.026-0.00233.558-0.002-0.0020.0000.0000.0000.000
14B36LYS10.9240.95529.3600.0250.0250.0000.0000.0000.000
15B37ILE00.0490.03424.695-0.005-0.0050.0000.0000.0000.000
16B38LEU0-0.040-0.01222.4370.0140.0140.0000.0000.0000.000
17B39LEU0-0.0130.00919.288-0.021-0.0210.0000.0000.0000.000
18B40THR0-0.009-0.03017.7350.0230.0230.0000.0000.0000.000
19B41CYS0-0.088-0.01712.553-0.032-0.0320.0000.0000.0000.000
20B42SER00.0160.00312.7500.1070.1070.0000.0000.0000.000
21B43LEU0-0.055-0.0125.181-0.164-0.1640.0000.0000.0000.000
22B44ASN0-0.023-0.0128.2830.3200.3200.0000.0000.0000.000
23B45ASP-1-0.869-0.9516.397-1.959-1.9590.0000.0000.0000.000
24B46SER0-0.018-0.0063.606-0.222-0.0450.007-0.081-0.1030.000
25B47ALA00.001-0.0013.844-0.295-0.1360.000-0.021-0.1370.000
26B48THR0-0.075-0.0334.779-0.698-0.644-0.001-0.003-0.0490.000
27B49GLU-1-0.822-0.9237.1490.1840.1840.0000.0000.0000.000
28B50VAL0-0.080-0.0319.3530.0490.0490.0000.0000.0000.000
29B51THR0-0.068-0.03711.359-0.055-0.0550.0000.0000.0000.000
30B52GLY00.0660.03113.935-0.054-0.0540.0000.0000.0000.000
31B53HIS10.7270.86813.326-0.118-0.1180.0000.0000.0000.000
32B54ARG10.8530.91614.907-0.231-0.2310.0000.0000.0000.000
33B55TRP00.0600.03115.659-0.031-0.0310.0000.0000.0000.000
34B56LEU0-0.053-0.04116.0810.0250.0250.0000.0000.0000.000
35B57LYS10.9770.99919.3690.0310.0310.0000.0000.0000.000
36B58GLY00.0080.00921.634-0.007-0.0070.0000.0000.0000.000
37B59GLY0-0.0150.01222.1530.0130.0130.0000.0000.0000.000
38B60VAL0-0.045-0.04219.669-0.003-0.0030.0000.0000.0000.000
39B61VAL00.0040.01021.6540.0030.0030.0000.0000.0000.000
40B62LEU00.0250.01720.5740.0000.0000.0000.0000.0000.000
41B63LYS10.9040.94118.709-0.157-0.1570.0000.0000.0000.000
42B64GLU-1-0.826-0.89518.2680.1140.1140.0000.0000.0000.000
43B65ASP-1-0.868-0.94917.8520.2470.2470.0000.0000.0000.000
44B66ALA0-0.019-0.00518.3280.0300.0300.0000.0000.0000.000
45B67LEU0-0.030-0.01119.006-0.006-0.0060.0000.0000.0000.000
46B68PRO00.0660.04815.3710.0130.0130.0000.0000.0000.000
47B69GLY00.0250.01014.699-0.051-0.0510.0000.0000.0000.000
48B70GLN00.026-0.00310.274-0.028-0.0280.0000.0000.0000.000
49B71LYS10.9340.97612.3550.0660.0660.0000.0000.0000.000
50B72THR0-0.0170.00714.1320.0410.0410.0000.0000.0000.000
51B73GLU-1-0.882-0.95216.769-0.106-0.1060.0000.0000.0000.000
52B74PHE00.007-0.00319.9170.0260.0260.0000.0000.0000.000
53B75LYS10.9500.97921.8850.0140.0140.0000.0000.0000.000
54B76VAL0-0.0050.00523.8390.0080.0080.0000.0000.0000.000
55B77ASP-1-0.831-0.92326.686-0.032-0.0320.0000.0000.0000.000
56B78SER00.008-0.01629.916-0.003-0.0030.0000.0000.0000.000
57B79ASP-1-0.923-0.95131.810-0.040-0.0400.0000.0000.0000.000
58B80ASP-1-0.901-0.95127.866-0.031-0.0310.0000.0000.0000.000
59B81GLN0-0.098-0.03026.982-0.012-0.0120.0000.0000.0000.000
60B82TRP0-0.089-0.06126.686-0.009-0.0090.0000.0000.0000.000
61B83GLY0-0.008-0.00124.5230.0100.0100.0000.0000.0000.000
62B84GLU-1-0.935-0.97618.042-0.192-0.1920.0000.0000.0000.000
63B85TYR0-0.040-0.03519.1240.0260.0260.0000.0000.0000.000
64B86SER0-0.007-0.00814.633-0.026-0.0260.0000.0000.0000.000
65B88VAL0-0.007-0.02711.186-0.040-0.0400.0000.0000.0000.000
66B89PHE0-0.003-0.0128.667-0.005-0.0050.0000.0000.0000.000
67B90LEU0-0.052-0.0129.9070.1110.1110.0000.0000.0000.000
68B91PRO00.0400.0209.779-0.047-0.0470.0000.0000.0000.000
69B92GLU-1-0.846-0.9239.1380.5260.5260.0000.0000.0000.000
70B93PRO0-0.048-0.0266.2490.0550.0550.0000.0000.0000.000
71B94MET0-0.011-0.0084.8170.0190.0190.0000.0000.0000.000
72B95GLY00.0530.0254.486-0.407-0.292-0.001-0.019-0.0950.000
73B96THR0-0.059-0.0296.1550.1670.1670.0000.0000.0000.000
74B97ALA00.0050.0128.372-0.182-0.1820.0000.0000.0000.000
75B98ASN00.0420.01811.1540.0870.0870.0000.0000.0000.000
76B99ILE00.0020.00114.700-0.039-0.0390.0000.0000.0000.000
77B100GLN0-0.010-0.00317.6600.0450.0450.0000.0000.0000.000
78B101LEU0-0.0060.01220.444-0.009-0.0090.0000.0000.0000.000
79B102HIS00.029-0.00623.3470.0200.0200.0000.0000.0000.000
80B103GLY00.0380.01125.9890.0070.0070.0000.0000.0000.000
81B104PRO00.0150.02028.607-0.004-0.0040.0000.0000.0000.000
82B105PRO0-0.059-0.02031.673-0.002-0.0020.0000.0000.0000.000
83B106ARG10.9460.97132.6750.0630.0630.0000.0000.0000.000
84B107VAL0-0.088-0.03835.056-0.004-0.0040.0000.0000.0000.000
85B108LYS10.9630.98036.9020.0430.0430.0000.0000.0000.000
86B109ALA00.0580.03040.326-0.002-0.0020.0000.0000.0000.000
87B110VAL0-0.105-0.04441.9690.0000.0000.0000.0000.0000.000
88B111LYS10.9600.97043.5210.0260.0260.0000.0000.0000.000
89B112SER00.0550.02845.2870.0000.0000.0000.0000.0000.000
90B113SER0-0.0280.00947.7430.0010.0010.0000.0000.0000.000
91B114GLU-1-0.894-0.96150.173-0.030-0.0300.0000.0000.0000.000
92B115HIS0-0.033-0.01953.5550.0000.0000.0000.0000.0000.000
93B116ILE0-0.0040.01254.4600.0000.0000.0000.0000.0000.000
94B117ASN00.016-0.01958.6540.0020.0020.0000.0000.0000.000
95B118GLU-1-0.909-0.95362.091-0.018-0.0180.0000.0000.0000.000
96B119GLY0-0.038-0.01664.5610.0000.0000.0000.0000.0000.000
97B120GLU-1-0.943-0.97460.098-0.025-0.0250.0000.0000.0000.000
98B121THR0-0.002-0.00756.2870.0000.0000.0000.0000.0000.000
99B122ALA0-0.039-0.00955.3800.0000.0000.0000.0000.0000.000
100B123MET0-0.010-0.00948.474-0.002-0.0020.0000.0000.0000.000
101B124LEU00.0110.02649.7920.0000.0000.0000.0000.0000.000
102B125VAL00.000-0.00543.746-0.002-0.0020.0000.0000.0000.000
103B126CYS0-0.081-0.01142.7120.0010.0010.0000.0000.0000.000
104B127LYS10.9590.97937.7500.0500.0500.0000.0000.0000.000
105B128SER0-0.057-0.06035.4910.0010.0010.0000.0000.0000.000
106B129GLU-1-0.952-0.98031.204-0.075-0.0750.0000.0000.0000.000
107B130SER0-0.0130.01430.485-0.004-0.0040.0000.0000.0000.000
108B131VAL00.0350.02526.451-0.002-0.0020.0000.0000.0000.000
109B132PRO0-0.001-0.01128.162-0.003-0.0030.0000.0000.0000.000
110B133PRO00.0150.02030.3800.0070.0070.0000.0000.0000.000
111B134VAL0-0.028-0.01933.3320.0010.0010.0000.0000.0000.000
112B135THR0-0.078-0.03236.654-0.002-0.0020.0000.0000.0000.000
113B136ASP-1-0.866-0.92838.735-0.066-0.0660.0000.0000.0000.000
114B137TRP0-0.036-0.02839.1010.0020.0020.0000.0000.0000.000
115B138ALA0-0.0090.00444.1350.0010.0010.0000.0000.0000.000
116B139TRP00.019-0.01346.6010.0020.0020.0000.0000.0000.000
117B140TYR00.0260.01648.0920.0000.0000.0000.0000.0000.000
118B141LYS10.8890.96352.3800.0230.0230.0000.0000.0000.000
119B142ILE0-0.055-0.03650.4590.0000.0000.0000.0000.0000.000
120B143THR0-0.036-0.02654.9370.0010.0010.0000.0000.0000.000
121B144ASP-1-0.936-0.96757.055-0.017-0.0170.0000.0000.0000.000
122B145SER0-0.065-0.01757.8870.0000.0000.0000.0000.0000.000
123B146GLU-1-0.912-0.97055.850-0.026-0.0260.0000.0000.0000.000
124B147ASP-1-0.860-0.91651.790-0.027-0.0270.0000.0000.0000.000
125B148LYS10.9640.98855.0820.0250.0250.0000.0000.0000.000
126B149ALA00.017-0.01253.628-0.001-0.0010.0000.0000.0000.000
127B150LEU0-0.059-0.01253.7330.0010.0010.0000.0000.0000.000
128B151MET00.0040.00051.664-0.002-0.0020.0000.0000.0000.000
129B152ASN00.0460.01052.7070.0010.0010.0000.0000.0000.000
130B153GLY00.0200.00654.7260.0000.0000.0000.0000.0000.000
131B154SER0-0.031-0.00857.8470.0010.0010.0000.0000.0000.000
132B155GLU-1-0.955-1.00859.657-0.025-0.0250.0000.0000.0000.000
133B156SER0-0.029-0.01961.9500.0010.0010.0000.0000.0000.000
134B157ARG10.8650.92460.7060.0250.0250.0000.0000.0000.000
135B158PHE00.0140.03256.4730.0000.0000.0000.0000.0000.000
136B159PHE00.0120.01654.575-0.001-0.0010.0000.0000.0000.000
137B160VAL00.006-0.00748.6460.0000.0000.0000.0000.0000.000
138B161SER0-0.0150.01547.773-0.002-0.0020.0000.0000.0000.000
139B162SER00.013-0.01043.9840.0010.0010.0000.0000.0000.000
140B163SER0-0.0110.00741.039-0.002-0.0020.0000.0000.0000.000
141B164GLN00.0450.00434.958-0.002-0.0020.0000.0000.0000.000
142B165GLY00.0360.02736.510-0.001-0.0010.0000.0000.0000.000
143B166ARG10.8580.92537.4170.0570.0570.0000.0000.0000.000
144B167SER00.0390.03440.9060.0000.0000.0000.0000.0000.000
145B168GLU-1-0.886-0.95444.485-0.046-0.0460.0000.0000.0000.000
146B169LEU00.002-0.00147.8380.0000.0000.0000.0000.0000.000
147B170HIS0-0.010-0.00850.5210.0020.0020.0000.0000.0000.000
148B171ILE0-0.0260.00354.2550.0000.0000.0000.0000.0000.000
149B172GLU-1-0.922-0.96957.580-0.031-0.0310.0000.0000.0000.000
150B173ASN00.0090.00460.2920.0000.0000.0000.0000.0000.000
151B174LEU0-0.054-0.01758.7190.0010.0010.0000.0000.0000.000
152B175ASN00.0710.03762.7410.0000.0000.0000.0000.0000.000
153B176MET0-0.015-0.02463.9390.0000.0000.0000.0000.0000.000
154B177GLU-1-0.967-0.97565.863-0.016-0.0160.0000.0000.0000.000
155B178ALA0-0.013-0.01063.4340.0000.0000.0000.0000.0000.000
156B179ASP-1-0.781-0.88260.001-0.024-0.0240.0000.0000.0000.000
157B180PRO0-0.0330.00059.080-0.001-0.0010.0000.0000.0000.000
158B181GLY00.0270.00457.9000.0010.0010.0000.0000.0000.000
159B182GLN0-0.028-0.01652.710-0.001-0.0010.0000.0000.0000.000
160B183TYR00.0080.00451.790-0.001-0.0010.0000.0000.0000.000
161B184ARG10.9110.95247.1200.0280.0280.0000.0000.0000.000
162B186ASN00.023-0.00743.3510.0020.0020.0000.0000.0000.000
163B187GLY00.0030.00940.331-0.001-0.0010.0000.0000.0000.000
164B188THR00.002-0.02039.1150.0020.0020.0000.0000.0000.000
165B189SER0-0.011-0.00634.221-0.004-0.0040.0000.0000.0000.000
166B190SER00.0320.00832.0860.0030.0030.0000.0000.0000.000
167B191LYS10.9250.97127.9680.1070.1070.0000.0000.0000.000
168B192GLY00.0580.03433.0430.0040.0040.0000.0000.0000.000
169B193SER0-0.003-0.02236.278-0.003-0.0030.0000.0000.0000.000
170B194ASP-1-0.794-0.86237.565-0.041-0.0410.0000.0000.0000.000
171B195GLN0-0.039-0.03239.6140.0010.0010.0000.0000.0000.000
172B196ALA0-0.001-0.00541.9960.0010.0010.0000.0000.0000.000
173B197ILE0-0.025-0.01944.1040.0000.0000.0000.0000.0000.000
174B198ILE0-0.036-0.01346.5710.0010.0010.0000.0000.0000.000
175B199THR0-0.038-0.02949.6190.0010.0010.0000.0000.0000.000
176B200LEU00.0070.00253.0110.0000.0000.0000.0000.0000.000
177B201ARG10.9110.94855.7920.0160.0160.0000.0000.0000.000
178B202VAL00.0470.02658.736-0.001-0.0010.0000.0000.0000.000
179B203ARG10.9260.97959.5370.0190.0190.0000.0000.0000.000