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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: M3MGZ

Calculation Name: 5RTY-B-Xray89

Preferred Name:

Target Type:

Ligand Name: 4-hydroxybenzamide

ligand 3-letter code: HBD

PDB ID: 5RTY

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-09-27

Reference: T. Ohyama, K. Kamisaka, C. Watanabe, T. Honma et. al., FMO-based interaction energy analysis of SARS-Cov-2 related protein and ligand complexes, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHLSideSolv
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water Waters within average of the temperature factors of receptor.
Procedure Auto-FMO protocol ver. 1.20200406
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 210
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1798413.607158
FMO2-HF: Nuclear repulsion 1731727.255349
FMO2-HF: Total energy -66686.351809
FMO2-MP2: Total energy -66880.710505


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:1:SER )


Summations of interaction energy for fragment #1(B:1:SER )
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.
-1.7770.841-0.001-1.205-1.4120.006
Interaction energy analysis for fragmet #1(B:1:SER )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / 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].
3B3VAL 00.0370.0133.593-0.8051.813-0.001-1.205-1.4120.006
4B4ASN 0-0.005-0.0105.898-0.568-0.5680.0000.0000.0000.000
5B5SER 00.0150.0178.223-0.236-0.2360.0000.0000.0000.000
6B6PHE 0-0.009-0.01010.1700.1120.1120.0000.0000.0000.000
7B7SER 00.016-0.00213.911-0.045-0.0450.0000.0000.0000.000
8B8GLY 00.0180.00615.9050.0480.0480.0000.0000.0000.000
9B9TYR 0-0.078-0.06016.5870.0310.0310.0000.0000.0000.000
10B10LEU 00.0140.01921.013-0.022-0.0220.0000.0000.0000.000
11B11LYS 10.8540.92223.0060.1900.1900.0000.0000.0000.000
12B12LEU 0-0.043-0.00924.9940.0060.0060.0000.0000.0000.000
13B13THR 00.035-0.00626.5370.0010.0010.0000.0000.0000.000
14B14ASP -1-0.868-0.94025.415-0.157-0.1570.0000.0000.0000.000
15B15ASN 0-0.047-0.02322.444-0.021-0.0210.0000.0000.0000.000
16B16VAL 00.0220.02322.2720.0100.0100.0000.0000.0000.000
17B17TYR 0-0.0050.00120.607-0.023-0.0230.0000.0000.0000.000
18B18ILE 00.0140.01122.6660.0200.0200.0000.0000.0000.000
19B19LYS 10.8460.90617.9130.0990.0990.0000.0000.0000.000
20B20ASN 0-0.048-0.01522.7850.0120.0120.0000.0000.0000.000
21B21ALA 00.006-0.01319.923-0.009-0.0090.0000.0000.0000.000
22B22ASP -1-0.808-0.88520.9610.0860.0860.0000.0000.0000.000
23B23ILE 00.0310.00318.6090.0010.0010.0000.0000.0000.000
24B24VAL 00.0090.01317.3820.0250.0250.0000.0000.0000.000
25B25GLU -1-0.809-0.89216.0930.1650.1650.0000.0000.0000.000
26B26GLU -1-0.775-0.85815.085-0.090-0.0900.0000.0000.0000.000
27B27ALA 00.0030.00413.301-0.013-0.0130.0000.0000.0000.000
28B28LYS 10.8380.90511.364-0.127-0.1270.0000.0000.0000.000
29B29LYS 10.7750.88510.3660.1480.1480.0000.0000.0000.000
30B30VAL 0-0.065-0.0309.599-0.078-0.0780.0000.0000.0000.000
31B31LYS 10.9500.9935.167-0.349-0.3490.0000.0000.0000.000
32B32PRO 00.0210.0297.8760.1520.1520.0000.0000.0000.000
33B33THR 00.0170.00310.1570.2440.2440.0000.0000.0000.000
34B34VAL 0-0.009-0.00910.8780.0290.0290.0000.0000.0000.000
35B35VAL 0-0.0120.00214.585-0.051-0.0510.0000.0000.0000.000
36B36VAL 0-0.015-0.00516.5350.0110.0110.0000.0000.0000.000
37B37ASN 00.002-0.03220.309-0.015-0.0150.0000.0000.0000.000
38B38ALA 0-0.0050.02022.734-0.008-0.0080.0000.0000.0000.000
39B39ALA 00.0320.03526.0020.0000.0000.0000.0000.0000.000
40B40ASN 00.022-0.00327.757-0.009-0.0090.0000.0000.0000.000
41B41VAL 00.0320.01130.4570.0080.0080.0000.0000.0000.000
42B42TYR 00.0390.01532.3780.0030.0030.0000.0000.0000.000
43B43LEU 0-0.033-0.00526.3360.0060.0060.0000.0000.0000.000
44B44LYS 10.8580.93728.871-0.101-0.1010.0000.0000.0000.000
45B45HIS 00.0050.00225.546-0.019-0.0190.0000.0000.0000.000
46B46GLY 00.0250.02228.3210.0030.0030.0000.0000.0000.000
47B47GLY 00.0290.00230.3580.0000.0000.0000.0000.0000.000
48B48GLY 00.0060.00128.8990.0040.0040.0000.0000.0000.000
49B49VAL 00.0620.02722.9300.0070.0070.0000.0000.0000.000
50B50ALA 00.0160.02224.0870.0140.0140.0000.0000.0000.000
51B51GLY 0-0.0060.01224.8990.0140.0140.0000.0000.0000.000
52B52ALA 0-0.028-0.02123.4300.0100.0100.0000.0000.0000.000
53B53LEU 00.0340.01318.6850.0150.0150.0000.0000.0000.000
54B54ASN 00.0650.02020.6870.0360.0360.0000.0000.0000.000
55B55LYS 10.9250.97122.712-0.101-0.1010.0000.0000.0000.000
56B56ALA 00.0220.02518.4230.0060.0060.0000.0000.0000.000
57B57THR 0-0.041-0.01317.7820.0250.0250.0000.0000.0000.000
58B58ASN 0-0.025-0.01919.612-0.007-0.0070.0000.0000.0000.000
59B59ASN 0-0.016-0.00822.726-0.010-0.0100.0000.0000.0000.000
60B60ALA 00.0520.03920.334-0.009-0.0090.0000.0000.0000.000
61B61MET 00.0380.03619.625-0.011-0.0110.0000.0000.0000.000
62B62GLN 0-0.037-0.03022.312-0.014-0.0140.0000.0000.0000.000
63B63VAL 00.0110.01825.259-0.009-0.0090.0000.0000.0000.000
64B64GLU -1-0.697-0.82220.4030.2820.2820.0000.0000.0000.000
65B65SER 0-0.001-0.00524.624-0.010-0.0100.0000.0000.0000.000
66B66ASP -1-0.808-0.88426.4330.1100.1100.0000.0000.0000.000
67B67ASP -1-0.880-0.91527.2590.1580.1580.0000.0000.0000.000
68B68TYR 00.0570.01826.001-0.008-0.0080.0000.0000.0000.000
69B69ILE 0-0.048-0.02428.267-0.011-0.0110.0000.0000.0000.000
70B70ALA 0-0.033-0.00131.578-0.008-0.0080.0000.0000.0000.000
71B71THR 0-0.034-0.00630.080-0.007-0.0070.0000.0000.0000.000
72B72ASN 0-0.087-0.05628.588-0.009-0.0090.0000.0000.0000.000
73B73GLY 0-0.0180.00732.370-0.008-0.0080.0000.0000.0000.000
74B74PRO 0-0.057-0.03332.5770.0060.0060.0000.0000.0000.000
75B75LEU 0-0.023-0.01227.632-0.003-0.0030.0000.0000.0000.000
76B76LYS 10.9980.99332.164-0.055-0.0550.0000.0000.0000.000
77B77VAL 00.0280.00332.6050.0040.0040.0000.0000.0000.000
78B78GLY 00.0030.01032.010-0.005-0.0050.0000.0000.0000.000
79B79GLY 0-0.0060.01329.943-0.003-0.0030.0000.0000.0000.000
80B80SER 0-0.045-0.05024.7550.0060.0060.0000.0000.0000.000
81B81CYS 0-0.0150.02224.670-0.004-0.0040.0000.0000.0000.000
82B82VAL 00.0160.01518.1880.0030.0030.0000.0000.0000.000
83B83LEU 0-0.0010.01019.963-0.005-0.0050.0000.0000.0000.000
84B84SER 00.0420.02016.2670.0580.0580.0000.0000.0000.000
85B85GLY 00.0140.02014.402-0.055-0.0550.0000.0000.0000.000
86B86HIS 0-0.038-0.03314.7320.0120.0120.0000.0000.0000.000
87B87ASN 0-0.038-0.03012.5090.0930.0930.0000.0000.0000.000
88B88LEU 0-0.028-0.00612.616-0.018-0.0180.0000.0000.0000.000
89B89ALA 00.0330.01810.857-0.027-0.0270.0000.0000.0000.000
90B90LYS 10.9160.9889.521-0.763-0.7630.0000.0000.0000.000
91B91HIS 00.019-0.00311.393-0.028-0.0280.0000.0000.0000.000
92B92CYS 0-0.037-0.01715.017-0.020-0.0200.0000.0000.0000.000
93B93LEU 0-0.0270.00717.970-0.009-0.0090.0000.0000.0000.000
94B94HIS 00.0520.00420.557-0.037-0.0370.0000.0000.0000.000
95B95VAL 00.003-0.00323.715-0.006-0.0060.0000.0000.0000.000
96B96VAL 0-0.0320.00926.301-0.001-0.0010.0000.0000.0000.000
97B97GLY 00.0250.01129.950-0.006-0.0060.0000.0000.0000.000
98B98PRO 0-0.0190.00231.6260.0040.0040.0000.0000.0000.000
99B99ASN 00.0010.00334.507-0.004-0.0040.0000.0000.0000.000
100B100VAL 00.0820.04136.3880.0000.0000.0000.0000.0000.000
101B101ASN 0-0.040-0.01737.336-0.004-0.0040.0000.0000.0000.000
102B102LYS 10.7630.87536.360-0.050-0.0500.0000.0000.0000.000
103B103GLY 00.0040.00941.0020.0000.0000.0000.0000.0000.000
104B104GLU -1-0.830-0.87736.8000.0460.0460.0000.0000.0000.000
105B105ASP -1-0.816-0.91240.4990.0130.0130.0000.0000.0000.000
106B106ILE 00.0380.00236.3890.0020.0020.0000.0000.0000.000
107B107GLN 0-0.032-0.01737.3570.0010.0010.0000.0000.0000.000
108B108LEU 00.0200.00335.688-0.001-0.0010.0000.0000.0000.000
109B109LEU 0-0.033-0.01831.3360.0040.0040.0000.0000.0000.000
110B110LYS 10.8910.93431.8130.0130.0130.0000.0000.0000.000
111B111SER 00.0260.01431.374-0.001-0.0010.0000.0000.0000.000
112B112ALA 00.0290.00929.7040.0040.0040.0000.0000.0000.000
113B113TYR 00.029-0.01026.2780.0080.0080.0000.0000.0000.000
114B114GLU -1-0.836-0.87126.5640.0050.0050.0000.0000.0000.000
115B115ASN 0-0.035-0.01124.9060.0060.0060.0000.0000.0000.000
116B116PHE 00.035-0.00522.2270.0130.0130.0000.0000.0000.000
117B117ASN 0-0.034-0.01421.612-0.012-0.0120.0000.0000.0000.000
118B118GLN 0-0.0470.00122.086-0.008-0.0080.0000.0000.0000.000
119B119HIS 00.0090.00617.2000.0330.0330.0000.0000.0000.000
120B120GLU -1-0.839-0.90215.501-0.087-0.0870.0000.0000.0000.000
121B121VAL 0-0.016-0.01312.717-0.042-0.0420.0000.0000.0000.000
122B122LEU 0-0.0050.02815.1580.0720.0720.0000.0000.0000.000
123B123LEU 0-0.0100.01014.694-0.045-0.0450.0000.0000.0000.000
124B124ALA 00.005-0.00917.0540.0340.0340.0000.0000.0000.000
125B125PRO 0-0.0260.00120.662-0.018-0.0180.0000.0000.0000.000
126B126LEU 00.0180.00523.818-0.001-0.0010.0000.0000.0000.000
127B127LEU 00.0150.01625.7800.0070.0070.0000.0000.0000.000
128B128SER 00.003-0.02828.709-0.008-0.0080.0000.0000.0000.000
129B129ALA 00.0220.02929.935-0.004-0.0040.0000.0000.0000.000
130B130GLY 00.0360.01631.6850.0070.0070.0000.0000.0000.000
131B131ILE 0-0.003-0.00631.308-0.003-0.0030.0000.0000.0000.000
132B132PHE 0-0.067-0.02330.7360.0010.0010.0000.0000.0000.000
133B133GLY 00.0270.01334.496-0.002-0.0020.0000.0000.0000.000
134B134ALA 0-0.021-0.00234.703-0.003-0.0030.0000.0000.0000.000
135B135ASP -1-0.813-0.91235.785-0.005-0.0050.0000.0000.0000.000
136B136PRO 0-0.028-0.02232.271-0.001-0.0010.0000.0000.0000.000
137B137ILE 00.012-0.00232.649-0.003-0.0030.0000.0000.0000.000
138B138HIS 00.0590.03334.560-0.006-0.0060.0000.0000.0000.000
139B139SER 0-0.030-0.03230.633-0.003-0.0030.0000.0000.0000.000
140B140LEU 0-0.019-0.00928.2890.0000.0000.0000.0000.0000.000
141B141ARG 10.8250.88130.8150.0330.0330.0000.0000.0000.000
142B142VAL 00.0210.01431.830-0.003-0.0030.0000.0000.0000.000
143B143CYS 0-0.0150.00826.4700.0000.0000.0000.0000.0000.000
144B144VAL 0-0.0050.00628.392-0.004-0.0040.0000.0000.0000.000
145B145ASP -1-0.761-0.83329.598-0.041-0.0410.0000.0000.0000.000
146B146THR 0-0.112-0.05929.2150.0030.0030.0000.0000.0000.000
147B147VAL 0-0.049-0.01323.4060.0030.0030.0000.0000.0000.000
148B148ARG 10.9080.96325.4210.0210.0210.0000.0000.0000.000
149B149THR 0-0.0200.01919.859-0.020-0.0200.0000.0000.0000.000
150B150ASN 0-0.031-0.01017.573-0.011-0.0110.0000.0000.0000.000
151B151VAL 00.0400.01818.3820.0230.0230.0000.0000.0000.000
152B152TYR 0-0.021-0.01016.539-0.028-0.0280.0000.0000.0000.000
153B153LEU 00.0260.00119.4150.0300.0300.0000.0000.0000.000
154B154ALA 00.0140.00819.867-0.016-0.0160.0000.0000.0000.000
155B155VAL 0-0.016-0.00521.9550.0140.0140.0000.0000.0000.000
156B156PHE 00.0300.01724.583-0.010-0.0100.0000.0000.0000.000
157B157ASP -1-0.794-0.89226.108-0.007-0.0070.0000.0000.0000.000
158B158LYS 10.8700.91629.0260.0450.0450.0000.0000.0000.000
159B159ASN 0-0.012-0.02530.059-0.008-0.0080.0000.0000.0000.000
160B160LEU 0-0.0020.00530.481-0.002-0.0020.0000.0000.0000.000
161B161TYR 0-0.018-0.01925.483-0.003-0.0030.0000.0000.0000.000
162B162ASP -1-0.766-0.85729.863-0.050-0.0500.0000.0000.0000.000
163B163LYS 10.9511.01532.7090.0120.0120.0000.0000.0000.000
164B164LEU 0-0.0390.00029.441-0.001-0.0010.0000.0000.0000.000
165B165VAL 00.0390.00828.916-0.003-0.0030.0000.0000.0000.000
166B166SER 0-0.074-0.04631.784-0.002-0.0020.0000.0000.0000.000
167B167SER 0-0.017-0.02435.3700.0000.0000.0000.0000.0000.000
168B168PHE 0-0.0080.00831.2830.0020.0020.0000.0000.0000.000
169B169LEU -1-0.911-0.93234.251-0.055-0.0550.0000.0000.0000.000
170B214HOH 0-0.006-0.01233.6900.0010.0010.0000.0000.0000.000
171B218HOH 0-0.037-0.03138.7840.0010.0010.0000.0000.0000.000
172B219HOH 0-0.012-0.02331.783-0.003-0.0030.0000.0000.0000.000
173B222HOH 0-0.064-0.04211.8250.0410.0410.0000.0000.0000.000
174B224HOH 0-0.042-0.03327.5890.0010.0010.0000.0000.0000.000
175B225HOH 0-0.036-0.03011.286-0.022-0.0220.0000.0000.0000.000
176B240HOH 0-0.026-0.03513.6970.0030.0030.0000.0000.0000.000
177B244HOH 0-0.011-0.03519.402-0.014-0.0140.0000.0000.0000.000
178B249HOH 0-0.032-0.02531.1410.0020.0020.0000.0000.0000.000
179B250HOH 0-0.032-0.02822.586-0.003-0.0030.0000.0000.0000.000
180B251HOH 0-0.019-0.02122.6640.0040.0040.0000.0000.0000.000
181B253HOH 0-0.041-0.03034.7820.0010.0010.0000.0000.0000.000
182B254HOH 0-0.010-0.01328.411-0.004-0.0040.0000.0000.0000.000
183B257HOH 0-0.068-0.05129.039-0.003-0.0030.0000.0000.0000.000
184B259HOH 0-0.080-0.06425.3210.0050.0050.0000.0000.0000.000
185B261HOH 00.0240.00029.517-0.002-0.0020.0000.0000.0000.000
186B264HOH 00.0160.00424.0230.0060.0060.0000.0000.0000.000
187B271HOH 00.001-0.00322.1410.0030.0030.0000.0000.0000.000
188B273HOH 0-0.021-0.00827.481-0.002-0.0020.0000.0000.0000.000
189B274HOH 0-0.032-0.02922.8060.0000.0000.0000.0000.0000.000
190B275HOH 0-0.030-0.03123.0460.0060.0060.0000.0000.0000.000
191B279HOH 0-0.025-0.02328.3890.0010.0010.0000.0000.0000.000
192B284HOH 0-0.017-0.02912.4840.0310.0310.0000.0000.0000.000
193B289HOH 0-0.085-0.06337.095-0.001-0.0010.0000.0000.0000.000
194B291HOH 00.0210.01427.984-0.002-0.0020.0000.0000.0000.000
195B298HOH 0-0.017-0.01115.3290.0150.0150.0000.0000.0000.000
196B299HOH 00.006-0.01627.908-0.003-0.0030.0000.0000.0000.000
197B300HOH 0-0.036-0.03128.647-0.002-0.0020.0000.0000.0000.000
198B306HOH 0-0.041-0.03233.992-0.002-0.0020.0000.0000.0000.000
199B313HOH 0-0.019-0.00229.5240.0030.0030.0000.0000.0000.000
200B315HOH 0-0.006-0.01225.158-0.001-0.0010.0000.0000.0000.000
201B319HOH 00.0350.02433.7570.0020.0020.0000.0000.0000.000
202B323HOH 0-0.030-0.03134.7440.0020.0020.0000.0000.0000.000
203B324HOH 0-0.009-0.00932.0220.0010.0010.0000.0000.0000.000
204B328HOH 0-0.024-0.02030.1380.0010.0010.0000.0000.0000.000
205B330HOH 0-0.001-0.01815.7540.0180.0180.0000.0000.0000.000
206B338HOH 00.0280.01831.8920.0010.0010.0000.0000.0000.000
207B339HOH 00.0160.00628.341-0.003-0.0030.0000.0000.0000.000
208B343HOH 00.006-0.00530.562-0.002-0.0020.0000.0000.0000.000
209B347HOH 0-0.017-0.02828.572-0.001-0.0010.0000.0000.0000.000
210B358HOH 0-0.027-0.01828.9950.0000.0000.0000.0000.0000.000