FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

tag_button

FMODB ID: 3QQQL

Calculation Name: 5RU6-B-Xray89

Preferred Name:

Target Type:

Ligand Name: naphthalene-2-carboximidamide

ligand 3-letter code: 2UP

PDB ID: 5RU6

Chain ID: B

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 205
LigandCharge 2UP=1
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1809001.514982
FMO2-HF: Nuclear repulsion 1742239.586473
FMO2-HF: Total energy -66761.928509
FMO2-MP2: Total energy -66956.847854


3D Structure
Snapshot
 
Ligand structure

2UP

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.
-93.925-98.42241.598-16.729-20.3720.133


Interactive mode: IFIE and PIEDA for fragment #205(B:201:2UP )


Summations of interaction energy for fragment #205(B:201:2UP )
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.
-93.925-98.42241.598-16.729-20.372-0.133
Interaction energy analysis for fragmet #205(B:201:2UP )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.868 / q_NPA : 0.895
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].
1B1SER 00.0060.00522.247-0.100-0.1000.0000.0000.0000.000
2B2MET 0-0.044-0.03219.7460.3170.3170.0000.0000.0000.000
3B3VAL 00.0360.01118.377-0.762-0.7620.0000.0000.0000.000
4B4ASN 00.001-0.00717.214-0.073-0.0730.0000.0000.0000.000
5B5SER 00.0150.01717.1791.0371.0370.0000.0000.0000.000
6B6PHE 0-0.012-0.01413.918-1.393-1.3930.0000.0000.0000.000
7B7SER 00.015-0.00315.4641.0591.0590.0000.0000.0000.000
8B8GLY 00.0260.01215.284-1.404-1.4040.0000.0000.0000.000
9B9TYR 0-0.083-0.06111.847-0.823-0.8230.0000.0000.0000.000
10B10LEU 00.0190.02117.3700.8510.8510.0000.0000.0000.000
11B11LYS 10.8520.92019.82211.17011.1700.0000.0000.0000.000
12B12LEU 0-0.047-0.01019.6030.2170.2170.0000.0000.0000.000
13B13THR 00.042-0.00423.3180.4410.4410.0000.0000.0000.000
14B14ASP -1-0.870-0.94324.866-10.971-10.9710.0000.0000.0000.000
15B15ASN 0-0.045-0.02223.5610.3030.3030.0000.0000.0000.000
16B16VAL 00.0190.02119.551-0.692-0.6920.0000.0000.0000.000
17B17TYR 00.0040.00718.1820.4780.4780.0000.0000.0000.000
18B18ILE 00.0070.00815.055-1.100-1.1000.0000.0000.0000.000
19B19LYS 10.8540.91011.99224.21424.2140.0000.0000.0000.000
20B20ASN 0-0.040-0.01110.516-0.279-0.2790.0000.0000.0000.000
21B21ALA 00.018-0.0068.3760.2710.2710.0000.0000.0000.000
22B22ASP -1-0.759-0.8281.677-138.046-150.08931.972-12.243-7.686-0.135
23B23ILE 00.0540.0124.6120.9421.043-0.001-0.006-0.0940.000
24B24VAL 00.0200.0192.2894.5425.6911.345-0.631-1.863-0.005
25B25GLU -1-0.819-0.9013.481-48.899-48.2250.008-0.118-0.564-0.001
26B26GLU -1-0.764-0.8505.742-19.100-19.1000.0000.0000.0000.000
27B27ALA 00.0030.0007.6243.7503.7500.0000.0000.0000.000
28B28LYS 10.8420.9125.42948.88248.8820.0000.0000.0000.000
29B29LYS 10.7780.8859.96727.27927.2790.0000.0000.0000.000
30B30VAL 0-0.063-0.02711.7661.8031.8030.0000.0000.0000.000
31B31LYS 10.9530.99513.03920.60720.6070.0000.0000.0000.000
32B32PRO 00.0190.02912.4121.4631.4630.0000.0000.0000.000
33B33THR 00.0140.00215.524-0.283-0.2830.0000.0000.0000.000
34B34VAL 0-0.005-0.00616.0880.0710.0710.0000.0000.0000.000
35B35VAL 0-0.018-0.0019.335-0.596-0.5960.0000.0000.0000.000
36B36VAL 0-0.007-0.00212.6070.7280.7280.0000.0000.0000.000
37B37ASN 0-0.002-0.03210.559-3.905-3.9050.0000.0000.0000.000
38B38ALA 0-0.0110.01910.8781.8231.8230.0000.0000.0000.000
39B39ALA 00.0270.02911.723-0.952-0.9520.0000.0000.0000.000
40B40ASN 00.023-0.00113.1031.3571.3570.0000.0000.0000.000
41B41VAL 00.0280.01116.002-0.160-0.1600.0000.0000.0000.000
42B42TYR 00.0380.01517.9510.4670.4670.0000.0000.0000.000
43B43LEU 0-0.040-0.00915.035-0.185-0.1850.0000.0000.0000.000
44B44LYS 10.8640.94213.10915.14615.1460.0000.0000.0000.000
45B45HIS 00.001-0.0018.981-1.376-1.3760.0000.0000.0000.000
46B46GLY 00.0310.0227.685-1.336-1.3360.0000.0000.0000.000
47B47GLY 00.0220.0015.536-2.397-2.3970.0000.0000.0000.000
48B48GLY 00.0030.0006.1100.2970.2970.0000.0000.0000.000
49B49VAL 00.0580.0244.720-5.855-5.708-0.001-0.010-0.1370.000
50B50ALA 00.0210.0246.332-3.005-3.0050.0000.0000.0000.000
51B51GLY 0-0.0080.0114.7440.2220.315-0.001-0.012-0.0800.000
52B52ALA 0-0.050-0.0402.325-4.182-2.2571.859-1.261-2.5220.001
53B53LEU 00.003-0.0013.391-0.470-0.4720.0340.401-0.4330.000
54B54ASN 00.0700.0206.2132.8102.8100.0000.0000.0000.000
55B55LYS 10.8970.9652.39031.37733.0915.585-1.805-5.4940.024
56B56ALA 00.0200.0204.9601.6771.6770.0000.0000.0000.000
57B57THR 0-0.040-0.0106.8553.2853.2850.0000.0000.0000.000
58B58ASN 0-0.029-0.0198.8750.9580.9580.0000.0000.0000.000
59B59ASN 0-0.017-0.00910.0460.9790.9790.0000.0000.0000.000
60B60ALA 00.0440.03111.3411.2591.2590.0000.0000.0000.000
61B61MET 00.0140.02110.4470.5170.5170.0000.0000.0000.000
62B62GLN 0-0.044-0.03711.389-0.085-0.0850.0000.0000.0000.000
63B63VAL 0-0.0050.00313.4040.9610.9610.0000.0000.0000.000
64B64GLU -1-0.718-0.83816.609-16.468-16.4680.0000.0000.0000.000
65B65SER 0-0.019-0.01915.1590.4860.4860.0000.0000.0000.000
66B66ASP -1-0.818-0.89116.394-14.977-14.9770.0000.0000.0000.000
67B67ASP -1-0.906-0.93918.804-11.632-11.6320.0000.0000.0000.000
68B68TYR 00.0440.00620.3010.5410.5410.0000.0000.0000.000
69B69ILE 0-0.036-0.01919.2590.5280.5280.0000.0000.0000.000
70B70ALA 0-0.0270.00022.3210.4850.4850.0000.0000.0000.000
71B71THR 0-0.037-0.00824.7740.5870.5870.0000.0000.0000.000
72B72ASN 0-0.093-0.05824.7370.6620.6620.0000.0000.0000.000
73B73GLY 0-0.0170.00725.2300.2560.2560.0000.0000.0000.000
74B74PRO 0-0.057-0.03322.235-0.420-0.4200.0000.0000.0000.000
75B75LEU 0-0.028-0.01419.0640.3600.3600.0000.0000.0000.000
76B76LYS 10.9990.99322.84210.44810.4480.0000.0000.0000.000
77B77VAL 00.0230.00121.341-0.503-0.5030.0000.0000.0000.000
78B78GLY 00.0040.01121.8190.6350.6350.0000.0000.0000.000
79B79GLY 00.0050.02022.9250.2070.2070.0000.0000.0000.000
80B80SER 0-0.051-0.05419.953-0.737-0.7370.0000.0000.0000.000
81B81CYS 0-0.0090.02619.7320.5320.5320.0000.0000.0000.000
82B82VAL 00.0130.01318.983-0.962-0.9620.0000.0000.0000.000
83B83LEU 0-0.0050.00817.0910.6530.6530.0000.0000.0000.000
84B84SER 00.0420.01917.070-0.420-0.4200.0000.0000.0000.000
85B85GLY 00.0160.02113.627-0.904-0.9040.0000.0000.0000.000
86B86HIS 0-0.038-0.03312.407-2.060-2.0600.0000.0000.0000.000
87B87ASN 0-0.040-0.0309.7170.9020.9020.0000.0000.0000.000
88B88LEU 0-0.032-0.0107.238-2.029-2.0290.0000.0000.0000.000
89B89ALA 00.0320.02010.772-0.258-0.2580.0000.0000.0000.000
90B90LYS 10.9250.99113.99014.59914.5990.0000.0000.0000.000
91B91HIS 00.018-0.00116.8830.1700.1700.0000.0000.0000.000
92B92CYS 0-0.038-0.01912.842-1.789-1.7890.0000.0000.0000.000
93B93LEU 0-0.0260.00614.7401.0761.0760.0000.0000.0000.000
94B94HIS 00.0550.00913.356-1.616-1.6160.0000.0000.0000.000
95B95VAL 00.005-0.00215.6931.2871.2870.0000.0000.0000.000
96B96VAL 0-0.0230.01616.395-1.134-1.1340.0000.0000.0000.000
97B97GLY 00.0300.01617.3230.8890.8890.0000.0000.0000.000
98B98PRO 00.0050.01818.578-0.341-0.3410.0000.0000.0000.000
99B99ASN 00.0010.00215.194-0.262-0.2620.0000.0000.0000.000
100B100VAL 00.0880.04418.6840.6090.6090.0000.0000.0000.000
101B101ASN 0-0.050-0.02315.7021.1461.1460.0000.0000.0000.000
102B102LYS 10.7660.87916.91714.75414.7540.0000.0000.0000.000
103B103GLY 00.0070.01220.8660.4280.4280.0000.0000.0000.000
104B104GLU -1-0.816-0.86020.687-13.538-13.5380.0000.0000.0000.000
105B105ASP -1-0.817-0.91323.932-10.771-10.7710.0000.0000.0000.000
106B106ILE 00.0310.00022.246-0.358-0.3580.0000.0000.0000.000
107B107GLN 0-0.035-0.02024.792-0.437-0.4370.0000.0000.0000.000
108B108LEU 00.0280.00724.4360.0000.0000.0000.0000.0000.000
109B109LEU 0-0.038-0.01919.882-0.351-0.3510.0000.0000.0000.000
110B110LYS 10.8760.92923.13110.56510.5650.0000.0000.0000.000
111B111SER 00.0250.01525.263-0.053-0.0530.0000.0000.0000.000
112B112ALA 00.0300.01120.463-0.115-0.1150.0000.0000.0000.000
113B113TYR 00.020-0.01618.192-0.737-0.7370.0000.0000.0000.000
114B114GLU -1-0.871-0.91721.978-10.978-10.9780.0000.0000.0000.000
115B115ASN 0-0.024-0.00521.1730.3930.3930.0000.0000.0000.000
116B116PHE 00.027-0.01016.272-0.239-0.2390.0000.0000.0000.000
117B117ASN 0-0.041-0.01721.3450.0500.0500.0000.0000.0000.000
118B118GLN 0-0.0330.00723.9290.6250.6250.0000.0000.0000.000
119B119HIS 0-0.0010.00020.909-0.124-0.1240.0000.0000.0000.000
120B120GLU -1-0.834-0.90022.893-11.687-11.6870.0000.0000.0000.000
121B121VAL 0-0.013-0.01018.5780.0140.0140.0000.0000.0000.000
122B122LEU 0-0.0080.02816.430-0.315-0.3150.0000.0000.0000.000
123B123LEU 0-0.0130.0119.3490.0820.0820.0000.0000.0000.000
124B124ALA 00.007-0.00812.398-0.394-0.3940.0000.0000.0000.000
125B125PRO 0-0.0060.0129.803-0.659-0.6590.0000.0000.0000.000
126B126LEU 00.0140.00711.7791.3971.3970.0000.0000.0000.000
127B127LEU 00.0170.01914.383-0.881-0.8810.0000.0000.0000.000
128B128SER 00.010-0.02615.9850.7630.7630.0000.0000.0000.000
129B129ALA 00.0190.02914.2210.5400.5400.0000.0000.0000.000
130B130GLY 00.0310.01211.988-0.904-0.9040.0000.0000.0000.000
131B131ILE 0-0.003-0.0058.8541.1921.1920.0000.0000.0000.000
132B132PHE 0-0.069-0.02311.8961.0261.0260.0000.0000.0000.000
133B133GLY 00.0330.01615.2161.0561.0560.0000.0000.0000.000
134B134ALA 0-0.022-0.00417.5980.9000.9000.0000.0000.0000.000
135B135ASP -1-0.813-0.91018.670-14.866-14.8660.0000.0000.0000.000
136B136PRO 0-0.030-0.02316.6080.0400.0400.0000.0000.0000.000
137B137ILE 00.014-0.00218.642-0.146-0.1460.0000.0000.0000.000
138B138HIS 00.0610.03521.5890.3430.3430.0000.0000.0000.000
139B139SER 0-0.027-0.03118.1930.2640.2640.0000.0000.0000.000
140B140LEU 0-0.027-0.01418.654-0.042-0.0420.0000.0000.0000.000
141B141ARG 10.8590.90420.47811.92911.9290.0000.0000.0000.000
142B142VAL 00.0230.01723.0650.3800.3800.0000.0000.0000.000
143B143CYS 0-0.0120.00719.9520.0920.0920.0000.0000.0000.000
144B144VAL 0-0.0100.00322.0190.2890.2890.0000.0000.0000.000
145B145ASP -1-0.764-0.83424.263-10.782-10.7820.0000.0000.0000.000
146B146THR 0-0.109-0.06024.5830.6670.6670.0000.0000.0000.000
147B147VAL 0-0.059-0.02021.0110.2650.2650.0000.0000.0000.000
148B148ARG 10.9200.96924.35410.88310.8830.0000.0000.0000.000
149B149THR 0-0.0140.02222.9670.2080.2080.0000.0000.0000.000
150B150ASN 0-0.033-0.00921.575-0.105-0.1050.0000.0000.0000.000
151B151VAL 00.0320.01116.898-0.609-0.6090.0000.0000.0000.000
152B152TYR 0-0.011-0.00414.8620.4250.4250.0000.0000.0000.000
153B153LEU 00.023-0.00213.537-1.505-1.5050.0000.0000.0000.000
154B154ALA 0-0.002-0.0028.4170.0800.0800.0000.0000.0000.000
155B155VAL 0-0.021-0.01310.133-0.873-0.8730.0000.0000.0000.000
156B156PHE 00.0100.0023.6670.9811.2760.001-0.032-0.2640.000
157B157ASP -1-0.792-0.8928.100-22.812-22.8120.0000.0000.0000.000
158B158LYS 10.8700.91611.02419.30319.3030.0000.0000.0000.000
159B159ASN 0-0.006-0.02313.4402.3932.3930.0000.0000.0000.000
160B160LEU 0-0.0080.00413.2091.1551.1550.0000.0000.0000.000
161B161TYR 0-0.016-0.01513.6261.0491.0490.0000.0000.0000.000
162B162ASP -1-0.757-0.85715.524-16.061-16.0610.0000.0000.0000.000
163B163LYS 10.9471.01218.66315.06015.0600.0000.0000.0000.000
164B164LEU 0-0.0360.00215.7200.7300.7300.0000.0000.0000.000
165B165VAL 00.0330.00418.3730.6980.6980.0000.0000.0000.000
166B166SER 0-0.068-0.04020.9800.7870.7870.0000.0000.0000.000
167B167SER 0-0.018-0.02722.7810.5880.5880.0000.0000.0000.000
168B168PHE 0-0.018-0.00222.8170.3010.3010.0000.0000.0000.000
169B169LEU -1-0.905-0.92624.831-10.578-10.5780.0000.0000.0000.000
170B313HOH 0-0.005-0.01122.239-0.029-0.0290.0000.0000.0000.000
171B318HOH 0-0.037-0.03127.7700.0740.0740.0000.0000.0000.000
172B326HOH 0-0.065-0.04416.1970.5320.5320.0000.0000.0000.000
173B331HOH 0-0.035-0.03011.585-0.337-0.3370.0000.0000.0000.000
174B332HOH 0-0.028-0.0312.568-4.965-3.5150.797-1.012-1.235-0.017
175B341HOH 0-0.019-0.02126.836-0.039-0.0390.0000.0000.0000.000
176B345HOH 0-0.050-0.05118.464-0.179-0.1790.0000.0000.0000.000
177B347HOH 0-0.035-0.02826.6250.0620.0620.0000.0000.0000.000
178B351HOH 00.0160.00422.311-0.050-0.0500.0000.0000.0000.000
179B354HOH 0-0.024-0.03520.3550.0830.0830.0000.0000.0000.000
180B356HOH 0-0.010-0.01215.203-0.091-0.0910.0000.0000.0000.000
181B361HOH 0-0.040-0.02926.2240.0820.0820.0000.0000.0000.000
182B363HOH 00.0240.00114.518-0.242-0.2420.0000.0000.0000.000
183B365HOH 0-0.011-0.03514.895-0.329-0.3290.0000.0000.0000.000
184B370HOH 0-0.025-0.0266.583-2.376-2.3760.0000.0000.0000.000
185B375HOH 0-0.020-0.00625.734-0.096-0.0960.0000.0000.0000.000
186B378HOH 00.000-0.00322.851-0.166-0.1660.0000.0000.0000.000
187B380HOH 0-0.069-0.05211.7760.1450.1450.0000.0000.0000.000
188B386HOH 0-0.022-0.02126.6780.1890.1890.0000.0000.0000.000
189B387HOH 0-0.085-0.06326.8490.0050.0050.0000.0000.0000.000
190B390HOH 00.0220.0149.237-0.732-0.7320.0000.0000.0000.000
191B391HOH 0-0.018-0.03017.494-0.422-0.4220.0000.0000.0000.000
192B402HOH 0-0.016-0.01022.092-0.236-0.2360.0000.0000.0000.000
193B405HOH 00.009-0.01312.2550.1630.1630.0000.0000.0000.000
194B411HOH 0-0.020-0.00312.252-0.866-0.8660.0000.0000.0000.000
195B413HOH 0-0.041-0.03223.0890.1270.1270.0000.0000.0000.000
196B424HOH 00.001-0.01724.825-0.271-0.2710.0000.0000.0000.000
197B427HOH 00.0030.00329.575-0.078-0.0780.0000.0000.0000.000
198B431HOH 00.004-0.01418.558-0.144-0.1440.0000.0000.0000.000
199B433HOH 00.0190.00928.5840.0540.0540.0000.0000.0000.000
200B439HOH 00.0290.0185.412-0.193-0.1930.0000.0000.0000.000
201B443HOH 00.0160.00524.3580.0330.0330.0000.0000.0000.000
202B447HOH 00.006-0.00524.701-0.009-0.0090.0000.0000.0000.000
203B455HOH 0-0.015-0.0279.506-1.060-1.0600.0000.0000.0000.000
204B463HOH 0-0.029-0.02025.610-0.016-0.0160.0000.0000.0000.000