Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: R51R8

Calculation Name: 5RTZ-B-Xray89

Preferred Name:

Target Type:

Ligand Name: 3-fluoro-4-hydroxybenzoic acid

ligand 3-letter code: FHB

PDB ID: 5RTZ

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 205
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1780742.265875
FMO2-HF: Nuclear repulsion 1714436.057019
FMO2-HF: Total energy -66306.208856
FMO2-MP2: Total energy -66499.589819


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.
-1.6960.866-0.008-1.165-1.3890.005
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 : 0.004 / q_NPA : 0.004
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 00.0400.0153.683-0.7521.810-0.008-1.165-1.3890.005
4B4ASN 00.000-0.0075.959-0.565-0.5650.0000.0000.0000.000
5B5SER 00.0130.0118.096-0.156-0.1560.0000.0000.0000.000
6B6PHE 0-0.022-0.01010.0950.0820.0820.0000.0000.0000.000
7B7SER 00.0310.00613.891-0.047-0.0470.0000.0000.0000.000
8B8GLY 00.0160.00415.8360.0490.0490.0000.0000.0000.000
9B9TYR 0-0.078-0.05716.5790.0300.0300.0000.0000.0000.000
10B10LEU 00.0160.02020.940-0.022-0.0220.0000.0000.0000.000
11B11LYS 10.8570.92322.9670.1900.1900.0000.0000.0000.000
12B12LEU 0-0.044-0.00824.9710.0060.0060.0000.0000.0000.000
13B13THR 00.037-0.00526.5910.0010.0010.0000.0000.0000.000
14B14ASP -1-0.871-0.94625.471-0.158-0.1580.0000.0000.0000.000
15B15ASN 0-0.045-0.01922.497-0.021-0.0210.0000.0000.0000.000
16B16VAL 00.0180.02022.3370.0100.0100.0000.0000.0000.000
17B17TYR 0-0.0020.00320.645-0.022-0.0220.0000.0000.0000.000
18B18ILE 00.0140.01022.7150.0200.0200.0000.0000.0000.000
19B19LYS 10.8410.90217.8540.0910.0910.0000.0000.0000.000
20B20ASN 0-0.043-0.01222.8070.0120.0120.0000.0000.0000.000
21B21ALA 00.003-0.01519.940-0.008-0.0080.0000.0000.0000.000
22B22ASP -1-0.813-0.89020.9690.0900.0900.0000.0000.0000.000
23B23ILE 00.0370.00618.6750.0020.0020.0000.0000.0000.000
24B24VAL 00.0170.01617.4100.0260.0260.0000.0000.0000.000
25B25GLU -1-0.811-0.89416.1280.1750.1750.0000.0000.0000.000
26B26GLU -1-0.780-0.85915.087-0.080-0.0800.0000.0000.0000.000
27B27ALA 00.0030.00413.346-0.011-0.0110.0000.0000.0000.000
28B28LYS 10.8380.90411.385-0.133-0.1330.0000.0000.0000.000
29B29LYS 10.7810.88710.3750.1400.1400.0000.0000.0000.000
30B30VAL 0-0.076-0.0369.533-0.077-0.0770.0000.0000.0000.000
31B31LYS 10.9661.0035.086-0.349-0.3490.0000.0000.0000.000
32B32PRO 00.0180.0247.9480.1510.1510.0000.0000.0000.000
33B33THR 00.0190.00510.2470.2370.2370.0000.0000.0000.000
34B34VAL 0-0.017-0.01310.9650.0280.0280.0000.0000.0000.000
35B35VAL 0-0.0050.00514.674-0.050-0.0500.0000.0000.0000.000
36B36VAL 0-0.013-0.00616.6010.0100.0100.0000.0000.0000.000
37B37ASN 00.002-0.02920.385-0.014-0.0140.0000.0000.0000.000
38B38ALA 0-0.0080.02122.805-0.009-0.0090.0000.0000.0000.000
39B39ALA 00.0270.02926.0870.0000.0000.0000.0000.0000.000
40B40ASN 00.021-0.00327.842-0.009-0.0090.0000.0000.0000.000
41B41VAL 00.0350.01030.5300.0080.0080.0000.0000.0000.000
42B42TYR 00.0400.01732.4980.0030.0030.0000.0000.0000.000
43B43LEU 0-0.037-0.00826.4470.0060.0060.0000.0000.0000.000
44B44LYS 10.8620.93928.973-0.101-0.1010.0000.0000.0000.000
45B45HIS 00.003-0.00125.639-0.019-0.0190.0000.0000.0000.000
46B46GLY 00.0300.02428.3880.0030.0030.0000.0000.0000.000
47B47GLY 00.0210.00130.3630.0010.0010.0000.0000.0000.000
48B48GLY 00.0120.00328.9820.0040.0040.0000.0000.0000.000
49B49VAL 00.0580.02423.0160.0070.0070.0000.0000.0000.000
50B50ALA 00.0170.02224.1490.0140.0140.0000.0000.0000.000
51B51GLY 0-0.0090.00924.9760.0140.0140.0000.0000.0000.000
52B52ALA 0-0.038-0.03023.4840.0100.0100.0000.0000.0000.000
53B53LEU 00.0140.00018.7590.0150.0150.0000.0000.0000.000
54B54ASN 00.0630.01920.7410.0360.0360.0000.0000.0000.000
55B55LYS 10.9300.97222.748-0.105-0.1050.0000.0000.0000.000
56B56ALA 00.0170.02418.4510.0070.0070.0000.0000.0000.000
57B57THR 0-0.042-0.01517.8440.0250.0250.0000.0000.0000.000
58B58ASN 0-0.022-0.01519.661-0.008-0.0080.0000.0000.0000.000
59B59ASN 0-0.020-0.01222.747-0.011-0.0110.0000.0000.0000.000
60B60ALA 00.0560.04320.396-0.009-0.0090.0000.0000.0000.000
61B61MET 00.0390.04019.684-0.012-0.0120.0000.0000.0000.000
62B62GLN 0-0.043-0.03822.375-0.015-0.0150.0000.0000.0000.000
63B63VAL 0-0.0080.00425.340-0.010-0.0100.0000.0000.0000.000
64B64GLU -1-0.727-0.84420.5260.2810.2810.0000.0000.0000.000
65B65SER 0-0.023-0.01924.723-0.010-0.0100.0000.0000.0000.000
66B66ASP -1-0.822-0.89426.5470.1100.1100.0000.0000.0000.000
67B67ASP -1-0.908-0.94127.3800.1490.1490.0000.0000.0000.000
68B68TYR 00.0430.00626.129-0.007-0.0070.0000.0000.0000.000
69B69ILE 0-0.032-0.01628.396-0.011-0.0110.0000.0000.0000.000
70B70ALA 0-0.029-0.00231.696-0.009-0.0090.0000.0000.0000.000
71B71THR 0-0.037-0.00730.202-0.007-0.0070.0000.0000.0000.000
72B72ASN 0-0.089-0.05528.716-0.009-0.0090.0000.0000.0000.000
73B73GLY 0-0.0200.00332.470-0.008-0.0080.0000.0000.0000.000
74B74PRO 0-0.056-0.03232.6710.0060.0060.0000.0000.0000.000
75B75LEU 0-0.028-0.01327.752-0.003-0.0030.0000.0000.0000.000
76B76LYS 10.9980.99232.282-0.053-0.0530.0000.0000.0000.000
77B77VAL 00.0290.00432.7090.0040.0040.0000.0000.0000.000
78B78GLY 00.0010.00932.122-0.005-0.0050.0000.0000.0000.000
79B79GLY 00.0050.02030.052-0.003-0.0030.0000.0000.0000.000
80B80SER 0-0.048-0.05324.8490.0060.0060.0000.0000.0000.000
81B81CYS 0-0.0120.02524.773-0.004-0.0040.0000.0000.0000.000
82B82VAL 00.0170.01618.3020.0030.0030.0000.0000.0000.000
83B83LEU 0-0.0070.00720.081-0.005-0.0050.0000.0000.0000.000
84B84SER 00.0390.01716.3500.0560.0560.0000.0000.0000.000
85B85GLY 00.0210.02314.443-0.053-0.0530.0000.0000.0000.000
86B86HIS 0-0.044-0.03414.7640.0140.0140.0000.0000.0000.000
87B87ASN 0-0.039-0.03212.5230.0930.0930.0000.0000.0000.000
88B88LEU 0-0.028-0.00812.608-0.015-0.0150.0000.0000.0000.000
89B89ALA 00.0330.02010.900-0.027-0.0270.0000.0000.0000.000
90B90LYS 10.9190.9879.590-0.760-0.7600.0000.0000.0000.000
91B91HIS 00.014-0.00511.454-0.030-0.0300.0000.0000.0000.000
92B92CYS 0-0.029-0.01415.095-0.019-0.0190.0000.0000.0000.000
93B93LEU 0-0.0220.00818.045-0.010-0.0100.0000.0000.0000.000
94B94HIS 00.0480.00420.643-0.036-0.0360.0000.0000.0000.000
95B95VAL 00.005-0.00123.801-0.007-0.0070.0000.0000.0000.000
96B96VAL 0-0.0300.01026.387-0.001-0.0010.0000.0000.0000.000
97B97GLY 00.0190.00730.033-0.006-0.0060.0000.0000.0000.000
98B98PRO 0-0.0160.00231.7130.0040.0040.0000.0000.0000.000
99B99ASN 00.0050.00534.641-0.004-0.0040.0000.0000.0000.000
100B100VAL 00.0850.04136.5090.0000.0000.0000.0000.0000.000
101B101ASN 0-0.042-0.01837.417-0.004-0.0040.0000.0000.0000.000
102B102LYS 10.7640.87836.532-0.050-0.0500.0000.0000.0000.000
103B103GLY 00.0030.01041.1270.0000.0000.0000.0000.0000.000
104B104GLU -1-0.832-0.88036.9010.0460.0460.0000.0000.0000.000
105B105ASP -1-0.819-0.91440.5870.0130.0130.0000.0000.0000.000
106B106ILE 00.0330.00136.5260.0020.0020.0000.0000.0000.000
107B107GLN 0-0.031-0.01837.4650.0010.0010.0000.0000.0000.000
108B108LEU 00.0240.00635.800-0.001-0.0010.0000.0000.0000.000
109B109LEU 0-0.032-0.01731.4420.0040.0040.0000.0000.0000.000
110B110LYS 10.8900.93231.9080.0140.0140.0000.0000.0000.000
111B111SER 00.0240.01231.487-0.001-0.0010.0000.0000.0000.000
112B112ALA 00.0300.01129.8000.0040.0040.0000.0000.0000.000
113B113TYR 00.024-0.01426.3570.0080.0080.0000.0000.0000.000
114B114GLU -1-0.835-0.86926.6530.0040.0040.0000.0000.0000.000
115B115ASN 0-0.027-0.00525.0040.0060.0060.0000.0000.0000.000
116B116PHE 00.032-0.00822.3240.0130.0130.0000.0000.0000.000
117B117ASN 0-0.036-0.01421.691-0.012-0.0120.0000.0000.0000.000
118B118GLN 0-0.0370.00722.187-0.009-0.0090.0000.0000.0000.000
119B119HIS 00.0000.00017.2690.0320.0320.0000.0000.0000.000
120B120GLU -1-0.838-0.90315.650-0.096-0.0960.0000.0000.0000.000
121B121VAL 0-0.016-0.01112.825-0.041-0.0410.0000.0000.0000.000
122B122LEU 0-0.0090.02615.2480.0710.0710.0000.0000.0000.000
123B123LEU 0-0.0080.01314.764-0.044-0.0440.0000.0000.0000.000
124B124ALA 00.004-0.01017.1180.0340.0340.0000.0000.0000.000
125B125PRO 0-0.0010.01620.729-0.018-0.0180.0000.0000.0000.000
126B126LEU 00.0120.00623.877-0.002-0.0020.0000.0000.0000.000
127B127LEU 00.0210.01925.8570.0070.0070.0000.0000.0000.000
128B128SER 00.007-0.02828.777-0.008-0.0080.0000.0000.0000.000
129B129ALA 00.0200.02929.993-0.004-0.0040.0000.0000.0000.000
130B130GLY 00.0340.01331.7450.0070.0070.0000.0000.0000.000
131B131ILE 0-0.002-0.00631.366-0.003-0.0030.0000.0000.0000.000
132B132PHE 0-0.065-0.02130.8090.0010.0010.0000.0000.0000.000
133B133GLY 00.0290.01234.557-0.002-0.0020.0000.0000.0000.000
134B134ALA 0-0.025-0.00334.775-0.003-0.0030.0000.0000.0000.000
135B135ASP -1-0.807-0.90935.877-0.004-0.0040.0000.0000.0000.000
136B136PRO 0-0.032-0.02332.313-0.001-0.0010.0000.0000.0000.000
137B137ILE 00.012-0.00232.700-0.003-0.0030.0000.0000.0000.000
138B138HIS 00.0570.03334.623-0.006-0.0060.0000.0000.0000.000
139B139SER 0-0.027-0.03230.707-0.003-0.0030.0000.0000.0000.000
140B140LEU 0-0.019-0.00928.3630.0000.0000.0000.0000.0000.000
141B141ARG 10.8590.90430.8770.0320.0320.0000.0000.0000.000
142B142VAL 00.0170.01231.901-0.003-0.0030.0000.0000.0000.000
143B143CYS 0-0.0110.01126.5270.0000.0000.0000.0000.0000.000
144B144VAL 0-0.0100.00328.457-0.004-0.0040.0000.0000.0000.000
145B145ASP -1-0.753-0.82729.662-0.041-0.0410.0000.0000.0000.000
146B146THR 0-0.115-0.06029.3110.0020.0020.0000.0000.0000.000
147B147VAL 0-0.048-0.01223.4970.0030.0030.0000.0000.0000.000
148B148ARG 10.9090.96325.4920.0230.0230.0000.0000.0000.000
149B149THR 0-0.0160.02119.941-0.020-0.0200.0000.0000.0000.000
150B150ASN 0-0.035-0.01017.647-0.009-0.0090.0000.0000.0000.000
151B151VAL 00.0450.01718.4550.0230.0230.0000.0000.0000.000
152B152TYR 0-0.022-0.00916.608-0.028-0.0280.0000.0000.0000.000
153B153LEU 00.018-0.00219.4570.0310.0310.0000.0000.0000.000
154B154ALA 00.0040.00119.914-0.016-0.0160.0000.0000.0000.000
155B155VAL 0-0.025-0.01721.9990.0130.0130.0000.0000.0000.000
156B156PHE 00.0170.00924.603-0.009-0.0090.0000.0000.0000.000
157B157ASP -1-0.786-0.88726.149-0.004-0.0040.0000.0000.0000.000
158B158LYS 10.8660.91429.0580.0420.0420.0000.0000.0000.000
159B159ASN 0-0.013-0.02730.100-0.009-0.0090.0000.0000.0000.000
160B160LEU 0-0.0050.00530.557-0.002-0.0020.0000.0000.0000.000
161B161TYR 0-0.022-0.02025.498-0.003-0.0030.0000.0000.0000.000
162B162ASP -1-0.756-0.85529.903-0.048-0.0480.0000.0000.0000.000
163B163LYS 10.9471.01232.7250.0110.0110.0000.0000.0000.000
164B164LEU 0-0.0340.00529.479-0.001-0.0010.0000.0000.0000.000
165B165VAL 00.0310.00228.941-0.003-0.0030.0000.0000.0000.000
166B166SER 0-0.068-0.03931.824-0.002-0.0020.0000.0000.0000.000
167B167SER 0-0.019-0.02735.3950.0000.0000.0000.0000.0000.000
168B168PHE 0-0.020-0.00231.3900.0020.0020.0000.0000.0000.000
169B169LEU -1-0.907-0.92934.191-0.054-0.0540.0000.0000.0000.000
170B209HOH 0-0.061-0.03711.8900.0390.0390.0000.0000.0000.000
171B215HOH 0-0.016-0.02632.028-0.003-0.0030.0000.0000.0000.000
172B217HOH 0-0.006-0.01133.7460.0010.0010.0000.0000.0000.000
173B226HOH 0-0.039-0.03138.8380.0010.0010.0000.0000.0000.000
174B234HOH 0-0.043-0.03427.6590.0000.0000.0000.0000.0000.000
175B241HOH 0-0.034-0.02911.380-0.025-0.0250.0000.0000.0000.000
176B243HOH 0-0.019-0.02122.8360.0040.0040.0000.0000.0000.000
177B246HOH 0-0.010-0.01328.491-0.004-0.0040.0000.0000.0000.000
178B247HOH 0-0.031-0.02531.2430.0020.0020.0000.0000.0000.000
179B249HOH 0-0.026-0.03513.7910.0020.0020.0000.0000.0000.000
180B252HOH 0-0.042-0.03034.9270.0010.0010.0000.0000.0000.000
181B255HOH 0-0.011-0.03419.465-0.014-0.0140.0000.0000.0000.000
182B257HOH 00.0160.00424.1260.0060.0060.0000.0000.0000.000
183B262HOH 0-0.030-0.02923.0750.0060.0060.0000.0000.0000.000
184B263HOH 0-0.066-0.05029.134-0.003-0.0030.0000.0000.0000.000
185B268HOH 00.0240.00129.567-0.002-0.0020.0000.0000.0000.000
186B269HOH 0-0.022-0.00827.528-0.002-0.0020.0000.0000.0000.000
187B270HOH 0-0.033-0.03022.9190.0020.0020.0000.0000.0000.000
188B280HOH 00.000-0.00322.2370.0030.0030.0000.0000.0000.000
189B284HOH 00.0190.01328.069-0.002-0.0020.0000.0000.0000.000
190B285HOH 0-0.024-0.02428.4720.0010.0010.0000.0000.0000.000
191B292HOH 0-0.085-0.06237.129-0.001-0.0010.0000.0000.0000.000
192B293HOH 0-0.019-0.03012.5690.0310.0310.0000.0000.0000.000
193B294HOH 0-0.015-0.00915.4280.0140.0140.0000.0000.0000.000
194B304HOH 0-0.041-0.03134.101-0.002-0.0020.0000.0000.0000.000
195B305HOH 00.005-0.01527.976-0.003-0.0030.0000.0000.0000.000
196B315HOH 0-0.021-0.00329.5760.0030.0030.0000.0000.0000.000
197B320HOH 0-0.006-0.00832.2090.0010.0010.0000.0000.0000.000
198B324HOH 00.001-0.01815.9620.0180.0180.0000.0000.0000.000
199B329HOH 0-0.029-0.03134.9110.0020.0020.0000.0000.0000.000
200B335HOH 0-0.026-0.01930.2090.0010.0010.0000.0000.0000.000
201B338HOH 00.0280.01831.8350.0010.0010.0000.0000.0000.000
202B340HOH 00.0150.00428.461-0.003-0.0030.0000.0000.0000.000
203B344HOH 00.005-0.00530.691-0.002-0.0020.0000.0000.0000.000
204B349HOH 0-0.016-0.02828.661-0.001-0.0010.0000.0000.0000.000
205B360HOH 0-0.027-0.01829.0850.0000.0000.0000.0000.0000.000