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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: 2KY7R

Calculation Name: 7CZ4-B-Xray89

Preferred Name:

Target Type:

Ligand Name: adenosine-5-diphosphoribose

ligand 3-letter code: APR

PDB ID: 7CZ4

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-03-24

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 191
LigandCharge APR=-2
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1806203.104342
FMO2-HF: Nuclear repulsion 1739593.026026
FMO2-HF: Total energy -66610.078316
FMO2-MP2: Total energy -66803.566027


3D Structure
Snapshot
 
Ligand structure

APR

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.
-497.225-519.259236.851-92.039-122.779-0.310


Interactive mode: IFIE and PIEDA for fragment #191(B:201:APR )


Summations of interaction energy for fragment #191(B:201:APR )
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.
-497.225-519.259236.851-92.039-122.7790.31
Interaction energy analysis for fragmet #191(B:201:APR )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -2 / q_Mulliken : -1.688 / q_NPA : -1.820
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].
1B4ASN 00.0380.00015.7021.3971.3970.0000.0000.0000.000
2B5SER 0-0.025-0.00816.325-0.352-0.3520.0000.0000.0000.000
3B6PHE 00.0430.02910.2110.3530.3530.0000.0000.0000.000
4B7SER 00.007-0.00712.853-1.971-1.9710.0000.0000.0000.000
5B8GLY 0-0.004-0.00212.2701.4931.4930.0000.0000.0000.000
6B9TYR 0-0.044-0.0187.3850.2360.2360.0000.0000.0000.000
7B10LEU 00.0270.03112.371-1.815-1.8150.0000.0000.0000.000
8B11LYS 10.8200.90113.633-24.928-24.9280.0000.0000.0000.000
9B12LEU 0-0.0140.00611.863-0.467-0.4670.0000.0000.0000.000
10B13THR 00.0330.01116.347-0.686-0.6860.0000.0000.0000.000
11B14ASP -1-0.913-0.95718.54824.74824.7480.0000.0000.0000.000
12B15ASN 0-0.033-0.02616.491-1.085-1.0850.0000.0000.0000.000
13B16VAL 00.0290.02811.9621.6521.6520.0000.0000.0000.000
14B17TYR 0-0.002-0.00312.225-2.244-2.2440.0000.0000.0000.000
15B18ILE 00.0120.0248.0923.2023.2020.0000.0000.0000.000
16B19LYS 10.8260.8807.613-38.633-38.6330.0000.0000.0000.000
17B20ASN 0-0.063-0.0266.1760.7200.7200.0000.0000.0000.000
18B21ALA 00.013-0.0074.676-4.099-3.925-0.001-0.020-0.1530.000
19B22ASP -1-0.776-0.8771.75544.07642.15513.374-5.796-5.656-0.048
20B23ILE 00.032-0.0021.958-16.474-19.45913.261-3.978-6.2980.024
21B24VAL 0-0.002-0.0032.963-7.099-5.9720.035-0.377-0.7850.003
22B25GLU -1-0.840-0.9114.80931.42831.4280.0000.0000.0000.000
23B26GLU -1-0.837-0.9076.59333.24833.2480.0000.0000.0000.000
24B27ALA 00.0150.0047.502-2.760-2.7600.0000.0000.0000.000
25B28LYS 10.8180.9098.234-39.637-39.6370.0000.0000.0000.000
26B29LYS 10.8340.9089.806-35.925-35.9250.0000.0000.0000.000
27B30VAL 0-0.039-0.02111.460-1.512-1.5120.0000.0000.0000.000
28B31LYS 10.8570.94013.089-31.000-31.0000.0000.0000.0000.000
29B32PRO 0-0.0100.01311.226-1.517-1.5170.0000.0000.0000.000
30B33THR 00.0340.00514.533-0.204-0.2040.0000.0000.0000.000
31B34VAL 00.0090.01213.835-0.200-0.2000.0000.0000.0000.000
32B35VAL 0-0.0020.0118.5500.3300.3300.0000.0000.0000.000
33B36VAL 0-0.023-0.0147.817-0.805-0.8050.0000.0000.0000.000
34B37ASN 0-0.023-0.0375.16712.61612.6160.0000.0000.0000.000
35B38ALA 00.0060.0172.506-9.169-7.1992.355-1.800-2.5240.022
36B39ALA 0-0.0030.0022.426-2.3791.6471.613-2.134-3.505-0.027
37B40ASN 00.0200.0311.649-15.494-25.30027.842-10.796-7.240-0.058
38B41VAL 00.0250.0023.549-1.802-1.6010.025-0.019-0.2080.000
39B42TYR 0-0.009-0.0055.995-3.253-3.2530.0000.0000.0000.000
40B43LEU 0-0.017-0.0015.523-1.211-1.2110.0000.0000.0000.000
41B44LYS 10.8280.9114.818-39.874-39.8740.0000.0000.0000.000
42B45HIS 00.0240.0112.9068.48510.7240.448-1.096-1.5920.002
43B46GLY 00.0110.0122.931-7.617-5.9350.118-0.701-1.0990.007
44B47GLY 0-0.015-0.0212.819-3.287-1.4790.241-0.748-1.301-0.003
45B48GLY 00.0800.0631.601-15.546-24.17625.304-10.604-6.070-0.032
46B49VAL 00.005-0.0031.780-41.818-44.01216.536-4.025-10.3170.067
47B50ALA 00.0260.0332.423-27.338-24.0711.449-1.952-2.7630.013
48B51GLY 00.0280.0083.022-12.349-11.9100.008-0.183-0.2640.000
49B52ALA 0-0.076-0.0343.170-9.893-9.2600.065-0.151-0.5470.000
50B53LEU 00.025-0.0054.962-8.127-7.955-0.001-0.005-0.1660.000
51B54ASN 00.0270.0047.160-7.360-7.3600.0000.0000.0000.000
52B55LYS 10.9240.9637.062-57.445-57.4450.0000.0000.0000.000
53B56ALA 0-0.0090.0167.664-3.496-3.4960.0000.0000.0000.000
54B57THR 0-0.029-0.0059.724-2.337-2.3370.0000.0000.0000.000
55B58ASN 0-0.056-0.04312.742-1.734-1.7340.0000.0000.0000.000
56B59ASN 0-0.0070.00311.7740.4170.4170.0000.0000.0000.000
57B60ALA 00.0480.03313.344-0.526-0.5260.0000.0000.0000.000
58B61MET 00.0270.0259.4041.2471.2470.0000.0000.0000.000
59B62GLN 0-0.0110.0017.3653.3293.3290.0000.0000.0000.000
60B63VAL 00.0060.00910.350-0.837-0.8370.0000.0000.0000.000
61B64GLU -1-0.737-0.85713.50132.86632.8660.0000.0000.0000.000
62B65SER 0-0.031-0.0339.2050.9010.9010.0000.0000.0000.000
63B66ASP -1-0.784-0.86710.97334.82034.8200.0000.0000.0000.000
64B67ASP -1-0.876-0.91912.66025.88425.8840.0000.0000.0000.000
65B68TYR 0-0.0050.00012.482-0.935-0.9350.0000.0000.0000.000
66B69ILE 00.002-0.0059.940-0.750-0.7500.0000.0000.0000.000
67B70ALA 0-0.0030.01713.424-0.991-0.9910.0000.0000.0000.000
68B71THR 0-0.050-0.02016.292-1.635-1.6350.0000.0000.0000.000
69B72ASN 0-0.093-0.05315.995-1.647-1.6470.0000.0000.0000.000
70B73GLY 00.0140.02015.104-0.227-0.2270.0000.0000.0000.000
71B74PRO 0-0.059-0.04210.5991.1811.1810.0000.0000.0000.000
72B75LEU 00.0160.0158.797-1.490-1.4900.0000.0000.0000.000
73B76LYS 10.9200.94411.060-30.193-30.1930.0000.0000.0000.000
74B77VAL 00.0400.0208.3041.8821.8820.0000.0000.0000.000
75B78GLY 0-0.0110.0019.270-3.292-3.2920.0000.0000.0000.000
76B79GLY 0-0.050-0.01710.864-2.006-2.0060.0000.0000.0000.000
77B80SER 0-0.030-0.04010.2543.3193.3190.0000.0000.0000.000
78B81CYS 0-0.0520.00411.823-2.190-2.1900.0000.0000.0000.000
79B82VAL 00.0100.00412.6012.7352.7350.0000.0000.0000.000
80B83LEU 0-0.012-0.00411.239-1.660-1.6600.0000.0000.0000.000
81B84SER 00.0270.01914.9080.1890.1890.0000.0000.0000.000
82B85GLY 00.0050.00614.3542.3462.3460.0000.0000.0000.000
83B86HIS 0-0.023-0.02313.923-0.336-0.3360.0000.0000.0000.000
84B87ASN 0-0.049-0.04012.259-0.880-0.8800.0000.0000.0000.000
85B88LEU 0-0.020-0.0148.425-0.585-0.5850.0000.0000.0000.000
86B89ALA 00.0470.02912.0880.4670.4670.0000.0000.0000.000
87B90LYS 10.8730.96714.393-26.818-26.8180.0000.0000.0000.000
88B91HIS 0-0.005-0.01316.734-2.001-2.0010.0000.0000.0000.000
89B92CYS 00.010-0.00410.2492.7202.7200.0000.0000.0000.000
90B93LEU 0-0.0420.00812.109-1.990-1.9900.0000.0000.0000.000
91B94HIS 00.0620.0188.0298.8348.8340.0000.0000.0000.000
92B95VAL 00.010-0.0077.756-5.181-5.1810.0000.0000.0000.000
93B96VAL 0-0.0330.0075.1478.9758.9750.0000.0000.0000.000
94B97GLY 00.0560.0284.783-8.250-8.172-0.001-0.015-0.0620.000
95B98PRO 0-0.021-0.0045.6480.5730.665-0.001-0.011-0.0800.000
96B99ASN 00.0240.0104.51310.69310.953-0.001-0.020-0.2400.000
97B100VAL 00.0400.0196.671-8.209-8.2090.0000.0000.0000.000
98B101ASN 0-0.047-0.0156.457-12.194-12.1940.0000.0000.0000.000
99B102LYS 10.8650.9286.982-57.491-57.4910.0000.0000.0000.000
100B103GLY 0-0.0080.0029.883-3.231-3.2310.0000.0000.0000.000
101B104GLU -1-0.841-0.8908.26452.34752.3470.0000.0000.0000.000
102B105ASP -1-0.773-0.87611.70037.96837.9680.0000.0000.0000.000
103B106ILE 00.0570.0189.2472.3342.3340.0000.0000.0000.000
104B107GLN 0-0.039-0.03011.5731.3071.3070.0000.0000.0000.000
105B108LEU 0-0.022-0.00910.922-0.824-0.8240.0000.0000.0000.000
106B109LEU 0-0.019-0.0146.7391.8521.8520.0000.0000.0000.000
107B110LYS 10.9140.9559.753-32.471-32.4710.0000.0000.0000.000
108B111SER 00.0240.00912.753-0.890-0.8900.0000.0000.0000.000
109B112ALA 0-0.0050.0018.072-0.536-0.5360.0000.0000.0000.000
110B113TYR 00.045-0.0026.612-0.158-0.1580.0000.0000.0000.000
111B114GLU -1-0.890-0.94811.56031.07131.0710.0000.0000.0000.000
112B115ASN 0-0.0100.00811.743-4.780-4.7800.0000.0000.0000.000
113B116PHE 00.0440.0018.288-0.864-0.8640.0000.0000.0000.000
114B117ASN 0-0.040-0.01014.571-2.077-2.0770.0000.0000.0000.000
115B118GLN 0-0.0140.02517.510-2.792-2.7920.0000.0000.0000.000
116B119HIS 00.005-0.00716.496-1.204-1.2040.0000.0000.0000.000
117B120GLU -1-0.875-0.93218.26526.56526.5650.0000.0000.0000.000
118B121VAL 0-0.021-0.02714.717-0.035-0.0350.0000.0000.0000.000
119B122LEU 0-0.068-0.01912.4640.7520.7520.0000.0000.0000.000
120B123LEU 0-0.0250.0106.448-0.383-0.3830.0000.0000.0000.000
121B124ALA 00.0370.0147.7181.6101.6100.0000.0000.0000.000
122B125PRO 00.0180.0232.836-4.529-2.4630.391-0.628-1.8290.005
123B126LEU 0-0.008-0.0032.472-8.386-5.9540.620-0.780-2.2710.003
124B127LEU 00.0200.0062.5236.6899.7271.600-1.717-2.921-0.024
125B128SER 00.0510.0032.548-19.802-16.7492.284-2.442-2.8950.027
126B129ALA 0-0.0360.0032.183-4.998-4.2854.558-0.584-4.687-0.003
127B130GLY 00.0140.0001.847-26.699-31.41318.374-6.692-6.9690.039
128B131ILE 0-0.052-0.0341.786-43.623-46.97315.717-2.181-10.1870.065
129B132PHE 0-0.069-0.0341.985-51.815-47.20616.060-6.664-14.0050.043
130B133GLY 00.0370.0213.757-19.487-19.0560.020-0.012-0.4390.002
131B134ALA 0-0.017-0.0044.964-12.041-11.975-0.001-0.006-0.0590.000
132B135ASP -1-0.832-0.9326.14651.85951.8590.0000.0000.0000.000
133B136PRO 0-0.010-0.0173.935-0.887-0.4980.002-0.081-0.3090.000
134B137ILE 00.0190.0075.793-1.083-1.040-0.0010.000-0.0430.000
135B138HIS 00.0030.0009.145-3.067-3.0670.0000.0000.0000.000
136B139SER 0-0.019-0.0315.743-3.832-3.8320.0000.0000.0000.000
137B140LEU 00.007-0.0017.917-1.499-1.4990.0000.0000.0000.000
138B141ARG 10.8430.9029.002-34.732-34.7320.0000.0000.0000.000
139B142VAL 00.0370.02711.077-2.082-2.0820.0000.0000.0000.000
140B143CYS 0-0.067-0.0039.200-2.232-2.2320.0000.0000.0000.000
141B144VAL 00.0270.00511.347-2.217-2.2170.0000.0000.0000.000
142B145ASP -1-0.788-0.83914.25830.30830.3080.0000.0000.0000.000
143B146THR 0-0.104-0.04914.230-2.304-2.3040.0000.0000.0000.000
144B147VAL 0-0.083-0.03512.400-1.222-1.2220.0000.0000.0000.000
145B148ARG 10.9510.98015.677-29.543-29.5430.0000.0000.0000.000
146B149THR 0-0.0070.01617.218-1.002-1.0020.0000.0000.0000.000
147B150ASN 0-0.030-0.01216.2830.6990.6990.0000.0000.0000.000
148B151VAL 00.0410.02910.4481.0641.0640.0000.0000.0000.000
149B152TYR 0-0.012-0.0119.866-1.266-1.2660.0000.0000.0000.000
150B153LEU 00.019-0.0186.7432.8642.8640.0000.0000.0000.000
151B154ALA 0-0.010-0.0113.140-4.734-4.2070.034-0.128-0.4330.000
152B155VAL 00.0030.0062.5606.7539.6911.478-1.640-2.776-0.015
153B156PHE 00.0190.0042.416-15.479-11.8576.088-2.737-6.9730.023
154B157ASP -1-0.811-0.9023.78340.00640.5420.1010.042-0.6780.002
155B158LYS 10.8690.9226.295-34.079-34.0790.0000.0000.0000.000
156B159ASN 00.0100.0029.187-2.950-2.9500.0000.0000.0000.000
157B160LEU 0-0.031-0.0212.753-2.407-1.4680.174-0.298-0.8160.000
158B161TYR 0-0.035-0.0196.903-1.351-1.3510.0000.0000.0000.000
159B162ASP -1-0.779-0.8967.93632.38132.3810.0000.0000.0000.000
160B163LYS 10.9460.9998.885-44.074-44.0740.0000.0000.0000.000
161B164LEU 0-0.034-0.0035.245-1.040-1.0400.0000.0000.0000.000
162B165VAL 00.0130.0019.818-1.542-1.5420.0000.0000.0000.000
163B166SER 00.003-0.00812.790-1.099-1.0990.0000.0000.0000.000
164B167SER 0-0.091-0.05912.384-1.138-1.1380.0000.0000.0000.000
165B168PHE 0-0.091-0.04413.261-0.440-0.4400.0000.0000.0000.000
166B169LEU -1-0.960-0.95915.18425.04225.0420.0000.0000.0000.000
167B301HOH 0-0.064-0.04515.240-0.423-0.4230.0000.0000.0000.000
168B304HOH 0-0.051-0.03618.1040.0570.0570.0000.0000.0000.000
169B305HOH 0-0.034-0.0287.3760.8040.8040.0000.0000.0000.000
170B306HOH 0-0.053-0.05115.8450.7480.7480.0000.0000.0000.000
171B307HOH 0-0.065-0.04917.456-0.626-0.6260.0000.0000.0000.000
172B308HOH 0-0.026-0.02722.721-0.322-0.3220.0000.0000.0000.000
173B309HOH 0-0.065-0.05611.3110.8150.8150.0000.0000.0000.000
174B310HOH 0-0.034-0.0221.739-19.060-24.17012.101-4.547-2.4430.051
175B311HOH 00.0290.01610.4852.0562.0560.0000.0000.0000.000
176B312HOH 00.005-0.0351.695-24.423-43.60935.925-10.494-6.2450.058
177B313HOH 0-0.008-0.00617.699-0.690-0.6900.0000.0000.0000.000
178B314HOH 0-0.011-0.0271.895-11.208-13.1186.615-2.524-2.1820.032
179B315HOH 0-0.044-0.03417.547-0.349-0.3490.0000.0000.0000.000
180B316HOH 0-0.041-0.03715.236-0.850-0.8500.0000.0000.0000.000
181B317HOH 00.0100.01022.524-0.337-0.3370.0000.0000.0000.000
182B318HOH 00.014-0.0065.360-0.040-0.0400.0000.0000.0000.000
183B319HOH 00.0380.02720.1020.5430.5430.0000.0000.0000.000
184B320HOH 0-0.025-0.02221.669-0.098-0.0980.0000.0000.0000.000
185B322HOH 00.000-0.01319.441-0.150-0.1500.0000.0000.0000.000
186B324HOH 0-0.027-0.0241.881-8.528-14.32612.042-3.495-2.7490.032
187B329HOH 00.0270.01513.3500.3170.3170.0000.0000.0000.000
188B330HOH 0-0.025-0.01815.850-0.438-0.4380.0000.0000.0000.000
189B331HOH 00.0040.00015.0540.2440.2440.0000.0000.0000.000
190B332HOH 00.0130.00317.5890.0820.0820.0000.0000.0000.000