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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: YYYQ2

Calculation Name: 5RSG-A-Xray89

Preferred Name:

Target Type:

Ligand Name: n-methyl-n-7h-pyrrolo[2,3-d]pyrimidin-4-yl-beta-alanine

ligand 3-letter code: W5J

PDB ID: 5RSG

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-10-07

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 W5J=-1
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1817933.274741
FMO2-HF: Nuclear repulsion 1751460.39218
FMO2-HF: Total energy -66472.882561
FMO2-MP2: Total energy -66667.729445


3D Structure
Snapshot
 
Ligand structure

W5J

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.
-190.494-187.86693.133-39.543-56.218-0.195


Interactive mode: IFIE and PIEDA for fragment #210(A:201:W5J )


Summations of interaction energy for fragment #210(A:201:W5J )
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.
-190.494-187.86693.133-39.543-56.2180.195
Interaction energy analysis for fragmet #210(A:201:W5J )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.804 / q_NPA : -0.879
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].
1A3VAL 00.005-0.01021.6740.0620.0620.0000.0000.0000.000
2A4ASN 0-0.014-0.01416.4670.2450.2450.0000.0000.0000.000
3A5SER 00.0250.00016.466-0.334-0.3340.0000.0000.0000.000
4A6PHE 0-0.0410.00710.2000.5060.5060.0000.0000.0000.000
5A7SER 00.0280.01113.271-0.631-0.6310.0000.0000.0000.000
6A8GLY 00.0210.00312.8961.5281.5280.0000.0000.0000.000
7A9TYR 0-0.045-0.0178.2191.7941.7940.0000.0000.0000.000
8A10LEU 0-0.0140.00912.666-2.002-2.0020.0000.0000.0000.000
9A11LYS 10.8440.92013.781-15.015-15.0150.0000.0000.0000.000
10A12LEU 0-0.030-0.00911.238-0.248-0.2480.0000.0000.0000.000
11A13THR 00.026-0.00415.772-0.887-0.8870.0000.0000.0000.000
12A14ASP -1-0.911-0.95718.43514.15014.1500.0000.0000.0000.000
13A15ASN 0-0.016-0.01116.860-0.365-0.3650.0000.0000.0000.000
14A16VAL 00.0180.02512.2480.9430.9430.0000.0000.0000.000
15A17TYR 00.0240.01512.264-1.214-1.2140.0000.0000.0000.000
16A18ILE 00.0180.0107.2082.4742.4740.0000.0000.0000.000
17A19LYS 10.8440.9107.799-29.950-29.9500.0000.0000.0000.000
18A20ASN 0-0.057-0.0276.0560.4830.4830.0000.0000.0000.000
19A21ALA 0-0.027-0.0295.429-7.079-7.0790.0000.0000.0000.000
20A22ASP -1-0.773-0.8721.77822.30221.98411.690-5.581-5.791-0.058
21A23ILE 00.0360.0032.021-17.371-18.70912.947-4.381-7.2280.038
22A24VAL 00.0000.0022.855-6.629-5.3410.106-0.205-1.1900.004
23A25GLU -1-0.821-0.8954.78018.73718.873-0.001-0.006-0.1290.000
24A26GLU -1-0.782-0.8606.36823.18323.1830.0000.0000.0000.000
25A27ALA 0-0.010-0.0117.426-2.237-2.2370.0000.0000.0000.000
26A28LYS 10.8150.8948.000-21.553-21.5530.0000.0000.0000.000
27A29LYS 10.8210.91210.641-23.228-23.2280.0000.0000.0000.000
28A30VAL 0-0.048-0.03111.886-1.030-1.0300.0000.0000.0000.000
29A31LYS 10.8760.96412.895-16.968-16.9680.0000.0000.0000.000
30A32PRO 0-0.0070.01110.743-0.846-0.8460.0000.0000.0000.000
31A33THR 00.034-0.00214.081-0.325-0.3250.0000.0000.0000.000
32A34VAL 0-0.021-0.01512.778-0.484-0.4840.0000.0000.0000.000
33A35VAL 00.0210.0177.9031.0181.0180.0000.0000.0000.000
34A36VAL 00.005-0.0028.455-1.460-1.4600.0000.0000.0000.000
35A37ASN 0-0.003-0.0237.5865.5335.5330.0000.0000.0000.000
36A38ALA 0-0.0010.0205.605-1.434-1.4340.0000.0000.0000.000
37A39ALA 00.0340.0447.497-0.189-0.1890.0000.0000.0000.000
38A40ASN 0-0.011-0.02210.730-0.775-0.7750.0000.0000.0000.000
39A41VAL 00.0450.01712.914-0.189-0.1890.0000.0000.0000.000
40A42TYR 0-0.004-0.00116.318-0.559-0.5590.0000.0000.0000.000
41A43LEU 0-0.0010.00814.526-0.278-0.2780.0000.0000.0000.000
42A44LYS 10.9971.01914.582-14.759-14.7590.0000.0000.0000.000
43A45HIS 00.0150.01110.2402.6692.6690.0000.0000.0000.000
44A46GLY 00.0220.02710.396-0.538-0.5380.0000.0000.0000.000
45A47GLY 00.0640.0186.814-0.535-0.5350.0000.0000.0000.000
46A48GLY 0-0.009-0.0012.757-0.2710.2650.422-0.379-0.5790.001
47A49VAL 00.0760.0422.831-6.587-2.6673.282-1.420-5.7810.012
48A50ALA 00.0170.0284.145-4.779-4.4700.0210.027-0.3570.001
49A51GLY 0-0.0270.0006.594-2.392-2.3920.0000.0000.0000.000
50A52ALA 00.0300.0182.679-3.325-2.6290.623-0.445-0.8730.002
51A53LEU 00.0340.0064.592-2.471-2.301-0.001-0.017-0.1530.000
52A54ASN 00.0530.0047.137-2.291-2.2910.0000.0000.0000.000
53A55LYS 10.9510.9877.387-19.852-19.8520.0000.0000.0000.000
54A56ALA 0-0.027-0.0057.619-1.168-1.1680.0000.0000.0000.000
55A57THR 0-0.051-0.0159.678-0.950-0.9500.0000.0000.0000.000
56A58ASN 0-0.038-0.02312.378-0.774-0.7740.0000.0000.0000.000
57A59ASN 0-0.0020.00213.055-0.127-0.1270.0000.0000.0000.000
58A60ALA 00.0290.02114.592-0.354-0.3540.0000.0000.0000.000
59A61MET 00.0050.01210.7250.2180.2180.0000.0000.0000.000
60A62GLN 0-0.048-0.02514.2190.8850.8850.0000.0000.0000.000
61A63VAL 00.0230.02415.730-0.396-0.3960.0000.0000.0000.000
62A64GLU -1-0.728-0.84217.62914.26914.2690.0000.0000.0000.000
63A65SER 00.006-0.00816.2540.1000.1000.0000.0000.0000.000
64A66ASP -1-0.809-0.89218.62413.25613.2560.0000.0000.0000.000
65A67ASP -1-0.849-0.88120.96510.59110.5910.0000.0000.0000.000
66A68TYR 00.009-0.01420.916-0.239-0.2390.0000.0000.0000.000
67A69ILE 0-0.039-0.02419.259-0.292-0.2920.0000.0000.0000.000
68A70ALA 0-0.029-0.00222.907-0.326-0.3260.0000.0000.0000.000
69A71THR 0-0.045-0.00926.155-0.524-0.5240.0000.0000.0000.000
70A72ASN 0-0.076-0.04424.230-0.531-0.5310.0000.0000.0000.000
71A73GLY 00.0230.02524.793-0.068-0.0680.0000.0000.0000.000
72A74PRO 0-0.042-0.02420.5880.4300.4300.0000.0000.0000.000
73A75LEU 0-0.014-0.00115.945-0.307-0.3070.0000.0000.0000.000
74A76LYS 10.9700.97819.498-12.230-12.2300.0000.0000.0000.000
75A77VAL 00.0320.00914.6950.6530.6530.0000.0000.0000.000
76A78GLY 00.0210.02115.122-0.676-0.6760.0000.0000.0000.000
77A79GLY 0-0.034-0.01116.324-0.203-0.2030.0000.0000.0000.000
78A80SER 0-0.011-0.03815.5251.0001.0000.0000.0000.0000.000
79A81CYS 0-0.0290.01116.785-0.743-0.7430.0000.0000.0000.000
80A82VAL 00.0090.00817.0731.1011.1010.0000.0000.0000.000
81A83LEU 00.0050.01017.112-0.804-0.8040.0000.0000.0000.000
82A84SER 00.0300.01117.6230.5540.5540.0000.0000.0000.000
83A85GLY 0-0.0170.00314.0840.8770.8770.0000.0000.0000.000
84A86HIS 0-0.032-0.03513.6630.3500.3500.0000.0000.0000.000
85A87ASN 0-0.020-0.02212.538-0.008-0.0080.0000.0000.0000.000
86A88LEU 0-0.015-0.0198.3210.1800.1800.0000.0000.0000.000
87A89ALA 0-0.010-0.00411.9410.8200.8200.0000.0000.0000.000
88A90LYS 10.8490.94414.154-13.513-13.5130.0000.0000.0000.000
89A91HIS 00.0300.01516.196-1.119-1.1190.0000.0000.0000.000
90A92CYS 0-0.018-0.00712.2121.7561.7560.0000.0000.0000.000
91A93LEU 0-0.0240.01012.861-1.131-1.1310.0000.0000.0000.000
92A94HIS 00.040-0.00112.2683.1583.1580.0000.0000.0000.000
93A95VAL 00.0210.00411.183-1.628-1.6280.0000.0000.0000.000
94A96VAL 0-0.0400.00410.7711.8511.8510.0000.0000.0000.000
95A97GLY 00.0520.03010.259-0.990-0.9900.0000.0000.0000.000
96A98PRO 0-0.0160.00411.187-0.160-0.1600.0000.0000.0000.000
97A99ASN 0-0.039-0.02010.7891.8901.8900.0000.0000.0000.000
98A100VAL 00.0760.03311.436-1.541-1.5410.0000.0000.0000.000
99A101ASN 0-0.059-0.03210.265-2.048-2.0480.0000.0000.0000.000
100A102LYS 10.8120.90713.420-18.832-18.8320.0000.0000.0000.000
101A103GLY 0-0.0010.00816.060-0.810-0.8100.0000.0000.0000.000
102A104GLU -1-0.795-0.84914.48317.25917.2590.0000.0000.0000.000
103A105ASP -1-0.815-0.91116.46315.08015.0800.0000.0000.0000.000
104A106ILE 00.0480.01212.1100.6540.6540.0000.0000.0000.000
105A107GLN 00.0090.00715.4671.0051.0050.0000.0000.0000.000
106A108LEU 0-0.047-0.02816.2110.0510.0510.0000.0000.0000.000
107A109LEU 0-0.031-0.02210.2120.4990.4990.0000.0000.0000.000
108A110LYS 10.8940.93914.015-15.049-15.0490.0000.0000.0000.000
109A111SER 00.0210.00316.644-0.049-0.0490.0000.0000.0000.000
110A112ALA 00.0040.00312.630-0.067-0.0670.0000.0000.0000.000
111A113TYR 00.020-0.0048.7091.0101.0100.0000.0000.0000.000
112A114GLU -1-0.802-0.85714.10514.14914.1490.0000.0000.0000.000
113A115ASN 0-0.067-0.02415.407-1.360-1.3600.0000.0000.0000.000
114A116PHE 00.0450.0029.462-0.161-0.1610.0000.0000.0000.000
115A117ASN 0-0.021-0.00615.601-0.293-0.2930.0000.0000.0000.000
116A118GLN 0-0.0440.00418.805-1.118-1.1180.0000.0000.0000.000
117A119HIS 0-0.038-0.02416.317-0.323-0.3230.0000.0000.0000.000
118A120GLU -1-0.817-0.89117.67913.47713.4770.0000.0000.0000.000
119A121VAL 0-0.012-0.01314.2690.3150.3150.0000.0000.0000.000
120A122LEU 0-0.0410.02111.524-0.284-0.2840.0000.0000.0000.000
121A123LEU 0-0.0170.0126.3140.3190.3190.0000.0000.0000.000
122A124ALA 00.013-0.0126.785-1.230-1.2300.0000.0000.0000.000
123A125PRO 0-0.0250.0043.0671.2642.5030.141-0.375-1.0060.002
124A126LEU 00.0550.0283.632-9.526-8.6420.005-0.234-0.6550.001
125A127LEU 0-0.046-0.0204.2211.9122.1810.000-0.032-0.2370.000
126A128SER 00.013-0.0296.8260.1230.1230.0000.0000.0000.000
127A129ALA 00.0140.0443.721-2.291-2.0440.002-0.032-0.2170.000
128A130GLY 00.0560.0303.358-0.0120.4640.043-0.179-0.3400.000
129A131ILE 00.008-0.0214.052-5.290-4.9410.005-0.028-0.3260.000
130A132PHE 0-0.101-0.0326.027-3.206-3.2060.0000.0000.0000.000
131A133GLY 00.0360.0147.623-2.449-2.4490.0000.0000.0000.000
132A134ALA 0-0.009-0.0058.370-1.738-1.7380.0000.0000.0000.000
133A135ASP -1-0.800-0.9027.79729.19029.1900.0000.0000.0000.000
134A136PRO 00.007-0.0134.844-0.441-0.4410.0000.0000.0000.000
135A137ILE 00.003-0.0016.8820.6060.6060.0000.0000.0000.000
136A138HIS 00.0480.02710.274-1.072-1.0720.0000.0000.0000.000
137A139SER 0-0.012-0.0217.424-1.256-1.2560.0000.0000.0000.000
138A140LEU 0-0.0040.0028.847-0.511-0.5110.0000.0000.0000.000
139A141ARG 10.8390.91510.323-20.005-20.0050.0000.0000.0000.000
140A142VAL 00.0020.00812.809-1.292-1.2920.0000.0000.0000.000
141A143CYS 0-0.0160.00710.489-1.821-1.8210.0000.0000.0000.000
142A144VAL 00.0130.01613.129-1.266-1.2660.0000.0000.0000.000
143A145ASP -1-0.810-0.90315.42615.96915.9690.0000.0000.0000.000
144A146THR 0-0.117-0.06115.991-1.569-1.5690.0000.0000.0000.000
145A147VAL 0-0.048-0.01113.564-0.868-0.8680.0000.0000.0000.000
146A148ARG 10.9100.95916.954-14.273-14.2730.0000.0000.0000.000
147A149THR 0-0.0390.00217.105-0.304-0.3040.0000.0000.0000.000
148A150ASN 0-0.022-0.00216.0950.8710.8710.0000.0000.0000.000
149A151VAL 00.0200.00610.0610.2330.2330.0000.0000.0000.000
150A152TYR 00.0170.0209.820-0.552-0.5520.0000.0000.0000.000
151A153LEU 00.026-0.0026.5931.1861.1860.0000.0000.0000.000
152A154ALA 0-0.019-0.0113.078-2.567-2.0020.039-0.137-0.4660.000
153A155VAL 00.0040.0122.3461.5306.3244.383-3.910-5.2670.010
154A156PHE 0-0.0110.0001.941-41.893-38.26717.296-6.224-14.6980.071
155A157ASP -1-0.877-0.9481.80215.83213.74711.246-4.433-4.7280.055
156A158LYS 10.8460.9223.697-36.279-35.9930.021-0.049-0.2580.002
157A159ASN 00.0130.0017.220-2.237-2.2370.0000.0000.0000.000
158A160LEU 0-0.002-0.0083.275-6.212-5.1840.073-0.466-0.6350.004
159A161TYR 00.0070.0056.011-4.199-4.1990.0000.0000.0000.000
160A162ASP -1-0.804-0.8987.41624.72024.7200.0000.0000.0000.000
161A163LYS 10.9440.9899.436-29.522-29.5220.0000.0000.0000.000
162A164LEU 0-0.041-0.0165.739-2.039-2.0390.0000.0000.0000.000
163A165VAL 00.0040.00710.069-2.246-2.2460.0000.0000.0000.000
164A166SER 0-0.051-0.03412.470-2.309-2.3090.0000.0000.0000.000
165A167SER 0-0.107-0.07212.836-1.332-1.3320.0000.0000.0000.000
166A168PHE 0-0.0020.00313.198-0.291-0.2910.0000.0000.0000.000
167A169LEU -1-0.890-0.93115.11016.05016.0500.0000.0000.0000.000
168A304HOH 0-0.051-0.04026.085-0.144-0.1440.0000.0000.0000.000
169A305HOH 0-0.035-0.0256.5251.5881.5880.0000.0000.0000.000
170A308HOH 0-0.059-0.04512.592-0.302-0.3020.0000.0000.0000.000
171A321HOH 0-0.008-0.02121.6460.1360.1360.0000.0000.0000.000
172A324HOH 0-0.0060.00710.917-0.460-0.4600.0000.0000.0000.000
173A335HOH 0-0.074-0.06122.1740.0920.0920.0000.0000.0000.000
174A339HOH 0-0.021-0.02423.0260.0170.0170.0000.0000.0000.000
175A343HOH 0-0.023-0.02720.133-0.154-0.1540.0000.0000.0000.000
176A345HOH 00.011-0.00512.6601.0391.0390.0000.0000.0000.000
177A346HOH 0-0.031-0.0275.560-0.377-0.3770.0000.0000.0000.000
178A351HOH 0-0.043-0.0651.538-22.963-38.14228.186-9.755-3.2520.054
179A356HOH 0-0.009-0.0138.9840.8600.8600.0000.0000.0000.000
180A359HOH 0-0.028-0.01617.8630.2110.2110.0000.0000.0000.000
181A362HOH 0-0.031-0.03912.1910.0190.0190.0000.0000.0000.000
182A366HOH 0-0.013-0.03415.3850.4070.4070.0000.0000.0000.000
183A367HOH 0-0.060-0.03823.858-0.147-0.1470.0000.0000.0000.000
184A374HOH 0-0.004-0.00522.4880.1920.1920.0000.0000.0000.000
185A376HOH 0-0.051-0.0398.909-0.060-0.0600.0000.0000.0000.000
186A377HOH 00.0140.00218.847-0.063-0.0630.0000.0000.0000.000
187A380HOH 00.000-0.00319.5330.2330.2330.0000.0000.0000.000
188A385HOH 00.010-0.01511.5030.4660.4660.0000.0000.0000.000
189A386HOH 0-0.001-0.01116.495-0.294-0.2940.0000.0000.0000.000
190A390HOH 0-0.020-0.02713.020-0.300-0.3000.0000.0000.0000.000
191A394HOH 00.0280.0145.8522.0272.0270.0000.0000.0000.000
192A397HOH 00.0410.0136.8081.4341.4340.0000.0000.0000.000
193A399HOH 0-0.007-0.00911.2481.1951.1950.0000.0000.0000.000
194A400HOH 0-0.020-0.02019.080-0.393-0.3930.0000.0000.0000.000
195A404HOH 0-0.032-0.02121.3050.1040.1040.0000.0000.0000.000
196A408HOH 0-0.046-0.0348.847-0.191-0.1910.0000.0000.0000.000
197A410HOH 0-0.020-0.01617.8140.0390.0390.0000.0000.0000.000
198A418HOH 0-0.063-0.05914.120-0.123-0.1230.0000.0000.0000.000
199A419HOH 00.0250.01219.8910.0540.0540.0000.0000.0000.000
200A421HOH 0-0.020-0.01912.481-0.271-0.2710.0000.0000.0000.000
201A422HOH 0-0.036-0.04021.1960.3190.3190.0000.0000.0000.000
202A426HOH 0-0.009-0.0169.402-0.895-0.8950.0000.0000.0000.000
203A431HOH 0-0.021-0.0079.670-0.357-0.3570.0000.0000.0000.000
204A433HOH 00.0060.00220.632-0.241-0.2410.0000.0000.0000.000
205A451HOH 0-0.029-0.02418.5890.0690.0690.0000.0000.0000.000
206A454HOH 0-0.011-0.0173.6061.1051.4480.011-0.139-0.215-0.001
207A455HOH 00.003-0.0102.038-3.003-2.7812.588-1.094-1.716-0.003
208A459HOH 0-0.0060.0063.5240.0200.1850.005-0.049-0.1210.000
209A469HOH 00.0090.00610.3190.1220.1220.0000.0000.0000.000