Manual

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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: Q18QY

Calculation Name: 5RUL-B-Xray89

Preferred Name:

Target Type:

Ligand Name: 4,6-dimethylpyrimidin-2-amine

ligand 3-letter code: 5ZE

PDB ID: 5RUL

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 206
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1785621.78422
FMO2-HF: Nuclear repulsion 1719239.550564
FMO2-HF: Total energy -66382.233656
FMO2-MP2: Total energy -66575.823801


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.
-1.880.762-0.003-1.198-1.4410.006
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 : 0.005 / q_NPA : 0.005
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 00.0380.0123.587-0.8031.839-0.003-1.198-1.4410.006
4B4ASN 0-0.003-0.0095.931-0.599-0.5990.0000.0000.0000.000
5B5SER 00.0220.0208.179-0.248-0.2480.0000.0000.0000.000
6B6PHE 0-0.017-0.01510.1290.1210.1210.0000.0000.0000.000
7B7SER 00.016-0.00113.878-0.049-0.0490.0000.0000.0000.000
8B8GLY 00.0210.00815.8300.0490.0490.0000.0000.0000.000
9B9TYR 0-0.079-0.06016.5690.0300.0300.0000.0000.0000.000
10B10LEU 00.0200.02320.937-0.022-0.0220.0000.0000.0000.000
11B11LYS 10.8500.92022.9560.1890.1890.0000.0000.0000.000
12B12LEU 0-0.040-0.00824.9360.0060.0060.0000.0000.0000.000
13B13THR 00.036-0.00526.5130.0010.0010.0000.0000.0000.000
14B14ASP -1-0.870-0.94425.398-0.157-0.1570.0000.0000.0000.000
15B15ASN 0-0.048-0.02322.433-0.021-0.0210.0000.0000.0000.000
16B16VAL 00.0210.02322.2620.0100.0100.0000.0000.0000.000
17B17TYR 00.0000.00320.621-0.022-0.0220.0000.0000.0000.000
18B18ILE 00.0110.00922.6690.0210.0210.0000.0000.0000.000
19B19LYS 10.8400.90217.8450.0820.0820.0000.0000.0000.000
20B20ASN 0-0.042-0.01122.7790.0120.0120.0000.0000.0000.000
21B21ALA 00.007-0.01219.897-0.008-0.0080.0000.0000.0000.000
22B22ASP -1-0.815-0.89220.9570.0970.0970.0000.0000.0000.000
23B23ILE 00.0370.00518.6550.0030.0030.0000.0000.0000.000
24B24VAL 00.0200.01817.3830.0270.0270.0000.0000.0000.000
25B25GLU -1-0.815-0.89716.0980.1880.1880.0000.0000.0000.000
26B26GLU -1-0.776-0.85615.071-0.066-0.0660.0000.0000.0000.000
27B27ALA 00.0020.00113.318-0.008-0.0080.0000.0000.0000.000
28B28LYS 10.8420.90911.371-0.140-0.1400.0000.0000.0000.000
29B29LYS 10.7720.88110.3460.1300.1300.0000.0000.0000.000
30B30VAL 0-0.070-0.0309.533-0.067-0.0670.0000.0000.0000.000
31B31LYS 10.9560.9975.111-0.454-0.4540.0000.0000.0000.000
32B32PRO 00.0200.0287.9100.1570.1570.0000.0000.0000.000
33B33THR 00.0120.00210.1860.2410.2410.0000.0000.0000.000
34B34VAL 0-0.013-0.01210.9030.0270.0270.0000.0000.0000.000
35B35VAL 0-0.0070.00614.603-0.049-0.0490.0000.0000.0000.000
36B36VAL 0-0.016-0.00816.5770.0110.0110.0000.0000.0000.000
37B37ASN 00.009-0.02520.360-0.014-0.0140.0000.0000.0000.000
38B38ALA 0-0.0120.01922.778-0.009-0.0090.0000.0000.0000.000
39B39ALA 00.0280.02926.0510.0000.0000.0000.0000.0000.000
40B40ASN 00.0240.00127.807-0.009-0.0090.0000.0000.0000.000
41B41VAL 00.0260.00730.5020.0080.0080.0000.0000.0000.000
42B42TYR 00.0340.01432.4420.0030.0030.0000.0000.0000.000
43B43LEU 0-0.035-0.00626.4210.0060.0060.0000.0000.0000.000
44B44LYS 10.8620.94028.937-0.103-0.1030.0000.0000.0000.000
45B45HIS 00.000-0.00125.610-0.019-0.0190.0000.0000.0000.000
46B46GLY 00.0340.02528.3630.0030.0030.0000.0000.0000.000
47B47GLY 00.0210.00130.3150.0010.0010.0000.0000.0000.000
48B48GLY 00.0070.00028.9430.0050.0050.0000.0000.0000.000
49B49VAL 00.0640.02622.9910.0070.0070.0000.0000.0000.000
50B50ALA 00.0150.02024.1160.0150.0150.0000.0000.0000.000
51B51GLY 0-0.0110.00824.9390.0140.0140.0000.0000.0000.000
52B52ALA 0-0.040-0.03123.4640.0100.0100.0000.0000.0000.000
53B53LEU 00.0160.00118.7250.0160.0160.0000.0000.0000.000
54B54ASN 00.0620.01820.7120.0370.0370.0000.0000.0000.000
55B55LYS 10.9310.97122.733-0.109-0.1090.0000.0000.0000.000
56B56ALA 00.0130.02218.4290.0070.0070.0000.0000.0000.000
57B57THR 0-0.039-0.01117.8200.0250.0250.0000.0000.0000.000
58B58ASN 0-0.022-0.01619.645-0.008-0.0080.0000.0000.0000.000
59B59ASN 0-0.019-0.01022.733-0.012-0.0120.0000.0000.0000.000
60B60ALA 00.0520.04020.383-0.009-0.0090.0000.0000.0000.000
61B61MET 00.0360.03719.664-0.012-0.0120.0000.0000.0000.000
62B62GLN 0-0.042-0.03322.355-0.015-0.0150.0000.0000.0000.000
63B63VAL 0-0.0030.00525.325-0.010-0.0100.0000.0000.0000.000
64B64GLU -1-0.728-0.84520.5060.2860.2860.0000.0000.0000.000
65B65SER 0-0.023-0.02024.700-0.010-0.0100.0000.0000.0000.000
66B66ASP -1-0.817-0.89126.5140.1120.1120.0000.0000.0000.000
67B67ASP -1-0.913-0.94327.3340.1510.1510.0000.0000.0000.000
68B68TYR 00.0440.00626.056-0.007-0.0070.0000.0000.0000.000
69B69ILE 0-0.034-0.01728.328-0.011-0.0110.0000.0000.0000.000
70B70ALA 0-0.0270.00231.656-0.009-0.0090.0000.0000.0000.000
71B71THR 0-0.037-0.00930.154-0.008-0.0080.0000.0000.0000.000
72B72ASN 0-0.089-0.05528.651-0.009-0.0090.0000.0000.0000.000
73B73GLY 0-0.0200.00432.405-0.008-0.0080.0000.0000.0000.000
74B74PRO 0-0.057-0.03332.6220.0060.0060.0000.0000.0000.000
75B75LEU 0-0.027-0.01327.672-0.003-0.0030.0000.0000.0000.000
76B76LYS 10.9990.99232.202-0.054-0.0540.0000.0000.0000.000
77B77VAL 00.0240.00032.6380.0040.0040.0000.0000.0000.000
78B78GLY 00.0010.00932.055-0.005-0.0050.0000.0000.0000.000
79B79GLY 00.0060.02229.995-0.003-0.0030.0000.0000.0000.000
80B80SER 0-0.050-0.05324.7810.0060.0060.0000.0000.0000.000
81B81CYS 0-0.0110.02524.709-0.004-0.0040.0000.0000.0000.000
82B82VAL 00.0130.01418.2280.0040.0040.0000.0000.0000.000
83B83LEU 0-0.0030.00920.014-0.005-0.0050.0000.0000.0000.000
84B84SER 00.0340.01316.3520.0580.0580.0000.0000.0000.000
85B85GLY 00.0200.02214.457-0.054-0.0540.0000.0000.0000.000
86B86HIS 0-0.037-0.03014.7490.0170.0170.0000.0000.0000.000
87B87ASN 0-0.042-0.03212.5360.0950.0950.0000.0000.0000.000
88B88LEU 0-0.026-0.00512.610-0.012-0.0120.0000.0000.0000.000
89B89ALA 00.0360.02010.895-0.024-0.0240.0000.0000.0000.000
90B90LYS 10.9160.9889.536-0.760-0.7600.0000.0000.0000.000
91B91HIS 00.016-0.00311.404-0.031-0.0310.0000.0000.0000.000
92B92CYS 0-0.031-0.01515.045-0.018-0.0180.0000.0000.0000.000
93B93LEU 0-0.0300.00318.017-0.011-0.0110.0000.0000.0000.000
94B94HIS 00.0500.00720.586-0.036-0.0360.0000.0000.0000.000
95B95VAL 00.005-0.00223.742-0.007-0.0070.0000.0000.0000.000
96B96VAL 0-0.0240.01526.323-0.001-0.0010.0000.0000.0000.000
97B97GLY 00.0310.01730.002-0.007-0.0070.0000.0000.0000.000
98B98PRO 00.0010.01431.6730.0050.0050.0000.0000.0000.000
99B99ASN 00.0050.00634.624-0.004-0.0040.0000.0000.0000.000
100B100VAL 00.0880.04336.460-0.001-0.0010.0000.0000.0000.000
101B101ASN 0-0.046-0.02037.386-0.005-0.0050.0000.0000.0000.000
102B102LYS 10.7630.87936.289-0.052-0.0520.0000.0000.0000.000
103B103GLY 00.0030.01041.0570.0000.0000.0000.0000.0000.000
104B104GLU -1-0.819-0.86336.8380.0470.0470.0000.0000.0000.000
105B105ASP -1-0.819-0.91540.5370.0140.0140.0000.0000.0000.000
106B106ILE 00.0310.00136.4770.0020.0020.0000.0000.0000.000
107B107GLN 0-0.032-0.01837.3790.0010.0010.0000.0000.0000.000
108B108LEU 00.0220.00535.722-0.001-0.0010.0000.0000.0000.000
109B109LEU 0-0.035-0.01831.3830.0040.0040.0000.0000.0000.000
110B110LYS 10.8780.93231.8310.0120.0120.0000.0000.0000.000
111B111SER 00.0220.01131.397-0.001-0.0010.0000.0000.0000.000
112B112ALA 00.0280.01029.7350.0040.0040.0000.0000.0000.000
113B113TYR 00.024-0.01426.2910.0080.0080.0000.0000.0000.000
114B114GLU -1-0.872-0.91626.5750.0070.0070.0000.0000.0000.000
115B115ASN 0-0.024-0.00624.9420.0060.0060.0000.0000.0000.000
116B116PHE 00.027-0.00922.2350.0130.0130.0000.0000.0000.000
117B117ASN 0-0.038-0.01621.624-0.013-0.0130.0000.0000.0000.000
118B118GLN 0-0.0380.00522.116-0.009-0.0090.0000.0000.0000.000
119B119HIS 00.0050.00317.2050.0320.0320.0000.0000.0000.000
120B120GLU -1-0.835-0.89915.555-0.098-0.0980.0000.0000.0000.000
121B121VAL 0-0.017-0.01312.747-0.042-0.0420.0000.0000.0000.000
122B122LEU 0-0.0110.02515.1720.0720.0720.0000.0000.0000.000
123B123LEU 0-0.0070.01314.716-0.044-0.0440.0000.0000.0000.000
124B124ALA 00.006-0.00817.0930.0340.0340.0000.0000.0000.000
125B125PRO 00.0010.01520.696-0.018-0.0180.0000.0000.0000.000
126B126LEU 00.0070.00223.839-0.002-0.0020.0000.0000.0000.000
127B127LEU 00.0200.02125.8470.0070.0070.0000.0000.0000.000
128B128SER 00.014-0.02428.739-0.008-0.0080.0000.0000.0000.000
129B129ALA 00.0140.02429.930-0.004-0.0040.0000.0000.0000.000
130B130GLY 00.0380.01831.6980.0070.0070.0000.0000.0000.000
131B131ILE 0-0.002-0.00631.341-0.003-0.0030.0000.0000.0000.000
132B132PHE 0-0.069-0.02330.6780.0000.0000.0000.0000.0000.000
133B133GLY 00.0280.01134.515-0.002-0.0020.0000.0000.0000.000
134B134ALA 0-0.019-0.00134.748-0.004-0.0040.0000.0000.0000.000
135B135ASP -1-0.817-0.91335.821-0.002-0.0020.0000.0000.0000.000
136B136PRO 0-0.032-0.02332.247-0.001-0.0010.0000.0000.0000.000
137B137ILE 00.014-0.00132.659-0.003-0.0030.0000.0000.0000.000
138B138HIS 00.0590.03434.580-0.006-0.0060.0000.0000.0000.000
139B139SER 0-0.028-0.03230.657-0.003-0.0030.0000.0000.0000.000
140B140LEU 0-0.020-0.01028.3100.0000.0000.0000.0000.0000.000
141B141ARG 10.8210.87830.8160.0310.0310.0000.0000.0000.000
142B142VAL 00.0200.01531.841-0.003-0.0030.0000.0000.0000.000
143B143CYS 0-0.0110.00826.4550.0000.0000.0000.0000.0000.000
144B144VAL 0-0.0060.00528.383-0.004-0.0040.0000.0000.0000.000
145B145ASP -1-0.765-0.83329.592-0.040-0.0400.0000.0000.0000.000
146B146THR 0-0.113-0.06329.1670.0020.0020.0000.0000.0000.000
147B147VAL 0-0.058-0.01823.4070.0030.0030.0000.0000.0000.000
148B148ARG 10.9190.96825.4040.0240.0240.0000.0000.0000.000
149B149THR 0-0.0150.02019.863-0.020-0.0200.0000.0000.0000.000
150B150ASN 0-0.034-0.01017.566-0.009-0.0090.0000.0000.0000.000
151B151VAL 00.0390.01518.3760.0240.0240.0000.0000.0000.000
152B152TYR 0-0.018-0.00816.550-0.028-0.0280.0000.0000.0000.000
153B153LEU 00.021-0.00219.4330.0320.0320.0000.0000.0000.000
154B154ALA 0-0.003-0.00319.883-0.016-0.0160.0000.0000.0000.000
155B155VAL 0-0.017-0.01221.9720.0130.0130.0000.0000.0000.000
156B156PHE 00.0170.00824.573-0.010-0.0100.0000.0000.0000.000
157B157ASP -1-0.792-0.89226.103-0.001-0.0010.0000.0000.0000.000
158B158LYS 10.8710.91729.0230.0380.0380.0000.0000.0000.000
159B159ASN 0-0.012-0.02730.052-0.009-0.0090.0000.0000.0000.000
160B160LEU 0-0.0070.00430.522-0.003-0.0030.0000.0000.0000.000
161B161TYR 0-0.015-0.01525.469-0.003-0.0030.0000.0000.0000.000
162B162ASP -1-0.763-0.85829.852-0.045-0.0450.0000.0000.0000.000
163B163LYS 10.9431.00832.6810.0080.0080.0000.0000.0000.000
164B164LEU 0-0.0350.00529.441-0.001-0.0010.0000.0000.0000.000
165B165VAL 00.0350.00528.887-0.003-0.0030.0000.0000.0000.000
166B166SER 0-0.069-0.04031.777-0.002-0.0020.0000.0000.0000.000
167B167SER 0-0.016-0.02635.352-0.001-0.0010.0000.0000.0000.000
168B168PHE 0-0.0090.00531.2580.0020.0020.0000.0000.0000.000
169B169LEU -1-0.913-0.93234.166-0.053-0.0530.0000.0000.0000.000
170B204HOH 0-0.066-0.04611.8430.0400.0400.0000.0000.0000.000
171B218HOH 0-0.006-0.01233.6970.0010.0010.0000.0000.0000.000
172B226HOH 0-0.039-0.03138.7890.0010.0010.0000.0000.0000.000
173B235HOH 0-0.034-0.02911.414-0.025-0.0250.0000.0000.0000.000
174B242HOH 0-0.043-0.03327.6510.0000.0000.0000.0000.0000.000
175B248HOH 0-0.050-0.05033.9230.0020.0020.0000.0000.0000.000
176B250HOH 0-0.041-0.03034.8570.0010.0010.0000.0000.0000.000
177B251HOH 0-0.024-0.03413.6970.0020.0020.0000.0000.0000.000
178B252HOH 0-0.011-0.01328.454-0.004-0.0040.0000.0000.0000.000
179B254HOH 0-0.035-0.02931.1190.0020.0020.0000.0000.0000.000
180B256HOH 00.0160.00424.0630.0060.0060.0000.0000.0000.000
181B261HOH 0-0.011-0.03519.449-0.014-0.0140.0000.0000.0000.000
182B263HOH 0-0.021-0.02222.8280.0040.0040.0000.0000.0000.000
183B273HOH 0-0.022-0.00827.479-0.002-0.0020.0000.0000.0000.000
184B274HOH 00.0230.00029.531-0.002-0.0020.0000.0000.0000.000
185B277HOH 0-0.030-0.02923.0380.0060.0060.0000.0000.0000.000
186B280HOH 0-0.023-0.02328.3950.0010.0010.0000.0000.0000.000
187B281HOH 0-0.033-0.03022.9020.0010.0010.0000.0000.0000.000
188B282HOH 0-0.069-0.05229.042-0.003-0.0030.0000.0000.0000.000
189B285HOH 00.000-0.00322.1710.0040.0040.0000.0000.0000.000
190B290HOH 0-0.019-0.03012.4940.0320.0320.0000.0000.0000.000
191B292HOH 00.0220.01428.041-0.002-0.0020.0000.0000.0000.000
192B296HOH 0-0.017-0.01115.3560.0150.0150.0000.0000.0000.000
193B297HOH 0-0.084-0.06237.085-0.001-0.0010.0000.0000.0000.000
194B302HOH 00.008-0.01427.959-0.003-0.0030.0000.0000.0000.000
195B308HOH 0-0.041-0.03234.008-0.002-0.0020.0000.0000.0000.000
196B312HOH 00.0350.02433.7210.0020.0020.0000.0000.0000.000
197B316HOH 0-0.020-0.00229.5010.0030.0030.0000.0000.0000.000
198B319HOH 00.0020.00331.6590.0030.0030.0000.0000.0000.000
199B326HOH 0-0.001-0.02015.8460.0190.0190.0000.0000.0000.000
200B330HOH 00.003-0.01334.7110.0020.0020.0000.0000.0000.000
201B332HOH 00.0180.00830.0770.0020.0020.0000.0000.0000.000
202B335HOH 00.0280.01831.7600.0010.0010.0000.0000.0000.000
203B341HOH 00.0160.00628.396-0.003-0.0030.0000.0000.0000.000
204B350HOH 00.006-0.00430.620-0.002-0.0020.0000.0000.0000.000
205B354HOH 0-0.015-0.02728.634-0.001-0.0010.0000.0000.0000.000
206B363HOH 0-0.029-0.02028.9030.0000.0000.0000.0000.0000.000