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

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FMODB ID: 52QMZ

Calculation Name: 5I66-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5I66

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 211
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2213202.953546
FMO2-HF: Nuclear repulsion 2129747.866743
FMO2-HF: Total energy -83455.086803
FMO2-MP2: Total energy -83697.357398


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:21:ASP)


Summations of interaction energy for fragment #1(B:21:ASP)
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.
-68.948-62.5072.668-3.578-5.530.034
Interaction energy analysis for fragmet #1(B:21:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.900 / q_NPA : -0.962
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].
3B23VAL00.0320.0313.860-0.5161.183-0.009-0.724-0.9660.005
4B24MET0-0.0200.0055.285-4.197-4.127-0.001-0.004-0.0650.000
5B25THR0-0.007-0.0138.351-0.292-0.2920.0000.0000.0000.000
6B26GLN00.036-0.01410.934-0.035-0.0350.0000.0000.0000.000
7B27SER00.0080.00014.0190.1260.1260.0000.0000.0000.000
8B28HIS00.0350.02416.053-0.438-0.4380.0000.0000.0000.000
9B29LYS10.8410.91414.485-18.553-18.5530.0000.0000.0000.000
10B30PHE00.0200.01218.8700.1010.1010.0000.0000.0000.000
11B31MET0-0.024-0.00520.8950.0600.0600.0000.0000.0000.000
12B32SER0-0.0070.00924.498-0.077-0.0770.0000.0000.0000.000
13B33THR0-0.0060.00528.2840.0130.0130.0000.0000.0000.000
14B34SER00.028-0.00230.383-0.127-0.1270.0000.0000.0000.000
15B35VAL0-0.054-0.03133.3420.1410.1410.0000.0000.0000.000
16B36GLY00.0170.01734.622-0.280-0.2800.0000.0000.0000.000
17B37ASP-1-0.848-0.88732.4248.9628.9620.0000.0000.0000.000
18B38ARG10.9010.95926.932-10.536-10.5360.0000.0000.0000.000
19B39VAL0-0.0080.00125.0920.0380.0380.0000.0000.0000.000
20B40SER0-0.012-0.02024.267-0.148-0.1480.0000.0000.0000.000
21B41ILE00.0220.01618.4020.0570.0570.0000.0000.0000.000
22B42THR00.0000.01018.1550.1580.1580.0000.0000.0000.000
23B43CYS0-0.080-0.02712.6200.6430.6430.0000.0000.0000.000
24B44LYS10.8230.90212.817-18.000-18.0000.0000.0000.0000.000
25B45ALA00.0470.0259.2811.4771.4770.0000.0000.0000.000
26B46SER0-0.026-0.0146.435-0.608-0.6080.0000.0000.0000.000
27B47GLN0-0.041-0.0246.6232.2662.2660.0000.0000.0000.000
28B48ASP-1-0.819-0.9009.83719.31519.3150.0000.0000.0000.000
29B49VAL00.003-0.0078.7592.3872.3870.0000.0000.0000.000
30B50SER00.0230.01311.450-0.959-0.9590.0000.0000.0000.000
31B51THR00.0620.03015.275-0.243-0.2430.0000.0000.0000.000
32B52ALA0-0.0130.01712.383-0.538-0.5380.0000.0000.0000.000
33B53VAL0-0.019-0.01711.9391.9961.9960.0000.0000.0000.000
34B54ALA0-0.028-0.00913.764-1.523-1.5230.0000.0000.0000.000
35B55TRP00.006-0.01015.0461.0871.0870.0000.0000.0000.000
36B56TYR0-0.010-0.01814.638-1.224-1.2240.0000.0000.0000.000
37B57GLN0-0.008-0.02218.839-0.077-0.0770.0000.0000.0000.000
38B58GLN0-0.0120.00218.5420.5350.5350.0000.0000.0000.000
39B59LYS10.8990.95621.559-11.189-11.1890.0000.0000.0000.000
40B60PRO00.019-0.00324.3680.3490.3490.0000.0000.0000.000
41B61GLY0-0.0010.00624.854-0.370-0.3700.0000.0000.0000.000
42B62GLN0-0.0180.00624.466-0.072-0.0720.0000.0000.0000.000
43B63SER00.0420.01120.9680.5850.5850.0000.0000.0000.000
44B64PRO0-0.014-0.01516.781-0.546-0.5460.0000.0000.0000.000
45B65LYS10.9170.97819.781-11.585-11.5850.0000.0000.0000.000
46B66LEU00.0010.00318.0060.2550.2550.0000.0000.0000.000
47B67LEU0-0.058-0.03020.665-0.816-0.8160.0000.0000.0000.000
48B68ILE0-0.0010.00219.901-0.605-0.6050.0000.0000.0000.000
49B69TYR00.0100.00118.0011.0241.0240.0000.0000.0000.000
50B70SER00.0430.01217.710-0.394-0.3940.0000.0000.0000.000
51B71ALA00.0200.00417.282-0.744-0.7440.0000.0000.0000.000
52B72SER0-0.086-0.04118.421-0.441-0.4410.0000.0000.0000.000
53B73TYR0-0.0150.01421.845-0.738-0.7380.0000.0000.0000.000
54B74ARG10.8290.89822.734-9.839-9.8390.0000.0000.0000.000
55B75TYR00.0140.00722.718-0.166-0.1660.0000.0000.0000.000
56B76THR00.0330.00124.713-0.402-0.4020.0000.0000.0000.000
57B77GLY00.0180.01727.7150.1550.1550.0000.0000.0000.000
58B78VAL0-0.067-0.02125.1550.1020.1020.0000.0000.0000.000
59B79PRO00.011-0.00128.485-0.134-0.1340.0000.0000.0000.000
60B80ASP-1-0.786-0.89529.8579.8569.8560.0000.0000.0000.000
61B81ARG10.7010.83429.946-9.926-9.9260.0000.0000.0000.000
62B82PHE0-0.0090.01125.6890.2210.2210.0000.0000.0000.000
63B83THR0-0.011-0.00825.610-0.185-0.1850.0000.0000.0000.000
64B84GLY00.0220.01021.5250.4360.4360.0000.0000.0000.000
65B85SER0-0.028-0.01321.045-0.619-0.6190.0000.0000.0000.000
66B86GLY00.0500.01819.3370.5810.5810.0000.0000.0000.000
67B87SER0-0.030-0.04317.348-0.198-0.1980.0000.0000.0000.000
68B88GLY00.0240.03115.485-0.279-0.2790.0000.0000.0000.000
69B89THR00.009-0.02312.4851.2191.2190.0000.0000.0000.000
70B90ASP-1-0.826-0.85913.93017.63217.6320.0000.0000.0000.000
71B91PHE00.0250.01213.449-0.660-0.6600.0000.0000.0000.000
72B92THR0-0.038-0.03717.630-0.180-0.1800.0000.0000.0000.000
73B93PHE00.0160.03420.009-0.379-0.3790.0000.0000.0000.000
74B94THR0-0.027-0.04721.413-0.165-0.1650.0000.0000.0000.000
75B95ILE00.0040.02725.097-0.023-0.0230.0000.0000.0000.000
76B96SER0-0.020-0.03227.815-0.132-0.1320.0000.0000.0000.000
77B97SER0-0.016-0.02230.953-0.303-0.3030.0000.0000.0000.000
78B98VAL0-0.016-0.00128.9490.0900.0900.0000.0000.0000.000
79B99GLN00.0430.00931.555-0.366-0.3660.0000.0000.0000.000
80B100ALA00.0490.01831.7120.2990.2990.0000.0000.0000.000
81B101GLU-1-0.821-0.88531.0259.7819.7810.0000.0000.0000.000
82B102ASP-1-0.772-0.86327.68711.04111.0410.0000.0000.0000.000
83B103LEU0-0.0100.02126.5550.5140.5140.0000.0000.0000.000
84B104ALA0-0.001-0.01022.8440.0080.0080.0000.0000.0000.000
85B105VAL00.0000.01717.630-0.099-0.0990.0000.0000.0000.000
86B106TYR0-0.008-0.01719.0290.0260.0260.0000.0000.0000.000
87B107TYR0-0.021-0.01713.7120.5430.5430.0000.0000.0000.000
88B109GLN0-0.003-0.00910.132-0.450-0.4500.0000.0000.0000.000
89B110GLN00.0580.0274.971-6.560-6.5600.0000.0000.0000.000
90B111HIS00.0290.0018.9093.3933.3930.0000.0000.0000.000
91B112TYR0-0.038-0.0198.630-1.643-1.6430.0000.0000.0000.000
92B113SER0-0.004-0.0014.581-1.404-1.359-0.001-0.003-0.0410.000
93B114ILE0-0.0200.0136.357-1.744-1.7440.0000.0000.0000.000
94B115PRO00.0830.0392.630-9.233-5.5262.616-2.564-3.7590.028
95B116ARG10.8270.9084.491-30.315-30.244-0.001-0.011-0.0590.000
96B117THR0-0.019-0.0173.111-0.1240.7250.064-0.272-0.6400.001
97B118PHE00.028-0.0036.523-4.483-4.4830.0000.0000.0000.000
98B119GLY00.0520.0148.1682.3142.3140.0000.0000.0000.000
99B120GLY0-0.028-0.01910.499-0.487-0.4870.0000.0000.0000.000
100B121GLY00.0110.02111.795-1.231-1.2310.0000.0000.0000.000
101B122THR0-0.051-0.03415.2220.2190.2190.0000.0000.0000.000
102B123LYS10.7940.88418.557-12.003-12.0030.0000.0000.0000.000
103B124LEU0-0.014-0.00321.703-0.228-0.2280.0000.0000.0000.000
104B125GLU-1-0.802-0.87324.86610.91810.9180.0000.0000.0000.000
105B126ILE0-0.010-0.01427.964-0.082-0.0820.0000.0000.0000.000
106B127LYS10.8770.95031.227-8.479-8.4790.0000.0000.0000.000
107B128ARG10.8820.93934.137-8.023-8.0230.0000.0000.0000.000
108B129ALA00.0250.00537.573-0.006-0.0060.0000.0000.0000.000
109B130ASP-1-0.816-0.91040.2437.8287.8280.0000.0000.0000.000
110B131ALA0-0.029-0.01341.379-0.144-0.1440.0000.0000.0000.000
111B132ALA00.0380.02442.5060.1310.1310.0000.0000.0000.000
112B133PRO0-0.025-0.00142.8420.0170.0170.0000.0000.0000.000
113B134THR00.0390.01344.364-0.236-0.2360.0000.0000.0000.000
114B135VAL0-0.053-0.02945.6830.1130.1130.0000.0000.0000.000
115B136SER0-0.037-0.01746.729-0.204-0.2040.0000.0000.0000.000
116B137ILE0-0.023-0.01647.1810.1520.1520.0000.0000.0000.000
117B138PHE0-0.005-0.00746.251-0.107-0.1070.0000.0000.0000.000
118B139PRO00.0220.01949.4260.0840.0840.0000.0000.0000.000
119B140PRO00.0040.00549.0450.0880.0880.0000.0000.0000.000
120B141SER0-0.023-0.02849.383-0.115-0.1150.0000.0000.0000.000
121B142SER00.049-0.00451.130-0.033-0.0330.0000.0000.0000.000
122B143GLU-1-0.798-0.85149.5866.2776.2770.0000.0000.0000.000
123B144GLN00.0320.02645.311-0.044-0.0440.0000.0000.0000.000
124B145LEU00.0420.01649.499-0.015-0.0150.0000.0000.0000.000
125B146THR0-0.073-0.04652.893-0.146-0.1460.0000.0000.0000.000
126B147SER0-0.069-0.04148.720-0.014-0.0140.0000.0000.0000.000
127B148GLY0-0.0010.01249.9630.0770.0770.0000.0000.0000.000
128B149GLY0-0.022-0.01048.0150.0230.0230.0000.0000.0000.000
129B150ALA0-0.013-0.02348.296-0.092-0.0920.0000.0000.0000.000
130B151SER0-0.033-0.02243.8650.0360.0360.0000.0000.0000.000
131B152VAL0-0.0040.01846.223-0.052-0.0520.0000.0000.0000.000
132B153VAL0-0.002-0.00242.8250.1620.1620.0000.0000.0000.000
133B154CYS0-0.034-0.00244.241-0.103-0.1030.0000.0000.0000.000
134B155PHE0-0.028-0.00641.4190.2380.2380.0000.0000.0000.000
135B156LEU00.0250.00041.366-0.212-0.2120.0000.0000.0000.000
136B157ASN00.021-0.00640.7780.3400.3400.0000.0000.0000.000
137B158ASN0-0.026-0.03539.010-0.306-0.3060.0000.0000.0000.000
138B159PHE00.0170.02737.673-0.156-0.1560.0000.0000.0000.000
139B160TYR00.0310.00532.7920.1980.1980.0000.0000.0000.000
140B161PRO00.0250.01235.792-0.238-0.2380.0000.0000.0000.000
141B162LYS10.9130.95529.808-10.406-10.4060.0000.0000.0000.000
142B163ASP-1-0.903-0.94635.1738.8498.8490.0000.0000.0000.000
143B164ILE0-0.035-0.01637.131-0.252-0.2520.0000.0000.0000.000
144B165ASN0-0.043-0.02239.448-0.004-0.0040.0000.0000.0000.000
145B166VAL00.0340.01041.331-0.145-0.1450.0000.0000.0000.000
146B167LYS10.8250.91743.878-6.588-6.5880.0000.0000.0000.000
147B168TRP00.0450.00144.107-0.190-0.1900.0000.0000.0000.000
148B169LYS10.7920.86748.257-6.044-6.0440.0000.0000.0000.000
149B170ILE00.0140.00350.7610.0350.0350.0000.0000.0000.000
150B171ASP-1-0.783-0.88854.1575.4885.4880.0000.0000.0000.000
151B172GLY00.0050.00956.562-0.081-0.0810.0000.0000.0000.000
152B173SER0-0.0130.00053.6900.0240.0240.0000.0000.0000.000
153B174GLU-1-0.804-0.88247.6356.7056.7050.0000.0000.0000.000
154B175ARG10.7960.87547.901-6.528-6.5280.0000.0000.0000.000
155B176GLN00.016-0.00243.5000.2430.2430.0000.0000.0000.000
156B177ASN0-0.009-0.01643.9160.1300.1300.0000.0000.0000.000
157B178GLY00.0860.04243.079-0.162-0.1620.0000.0000.0000.000
158B179VAL0-0.0380.00341.1920.0410.0410.0000.0000.0000.000
159B180LEU0-0.0060.00736.7050.2030.2030.0000.0000.0000.000
160B181ASN00.0170.01937.188-0.239-0.2390.0000.0000.0000.000
161B182SER0-0.001-0.00133.6420.3560.3560.0000.0000.0000.000
162B183TRP00.018-0.00332.696-0.171-0.1710.0000.0000.0000.000
163B184THR00.002-0.01432.1720.1670.1670.0000.0000.0000.000
164B185ASP-1-0.783-0.89426.56011.67211.6720.0000.0000.0000.000
165B186GLN0-0.048-0.03129.776-0.109-0.1090.0000.0000.0000.000
166B187ASP-1-0.783-0.87231.5058.8318.8310.0000.0000.0000.000
167B188SER00.013-0.00631.391-0.005-0.0050.0000.0000.0000.000
168B189LYS10.7850.88133.092-8.273-8.2730.0000.0000.0000.000
169B190ASP-1-0.789-0.88336.6408.1168.1160.0000.0000.0000.000
170B191SER00.0150.00833.260-0.157-0.1570.0000.0000.0000.000
171B192THR0-0.093-0.03934.8700.0450.0450.0000.0000.0000.000
172B193TYR0-0.058-0.05529.7760.3650.3650.0000.0000.0000.000
173B194SER00.0490.03335.723-0.394-0.3940.0000.0000.0000.000
174B195MET0-0.069-0.01436.1000.2800.2800.0000.0000.0000.000
175B196SER0-0.0070.00937.248-0.241-0.2410.0000.0000.0000.000
176B197SER00.019-0.00738.7950.1110.1110.0000.0000.0000.000
177B198THR00.0270.00140.143-0.226-0.2260.0000.0000.0000.000
178B199LEU00.0010.02542.3010.1160.1160.0000.0000.0000.000
179B200THR0-0.020-0.01142.770-0.125-0.1250.0000.0000.0000.000
180B201LEU0-0.057-0.01945.114-0.013-0.0130.0000.0000.0000.000
181B202THR00.0440.00748.2450.0860.0860.0000.0000.0000.000
182B203LYS10.8690.93950.380-5.751-5.7510.0000.0000.0000.000
183B204ASP-1-0.781-0.87953.2075.9145.9140.0000.0000.0000.000
184B205GLU-1-0.805-0.90351.2945.9685.9680.0000.0000.0000.000
185B206TYR00.014-0.00252.194-0.066-0.0660.0000.0000.0000.000
186B207GLU-1-0.873-0.95854.0585.5425.5420.0000.0000.0000.000
187B208ARG10.8020.91054.115-5.920-5.9200.0000.0000.0000.000
188B209HIS10.7910.91154.977-5.770-5.7700.0000.0000.0000.000
189B210ASN0-0.017-0.02158.3770.0180.0180.0000.0000.0000.000
190B211SER00.0230.03057.1480.0150.0150.0000.0000.0000.000
191B212TYR0-0.030-0.02651.9030.1150.1150.0000.0000.0000.000
192B213THR00.013-0.01552.174-0.042-0.0420.0000.0000.0000.000
193B215GLU-1-0.797-0.89548.2786.0456.0450.0000.0000.0000.000
194B216ALA00.0210.01444.9750.1350.1350.0000.0000.0000.000
195B217THR0-0.0110.00145.144-0.169-0.1690.0000.0000.0000.000
196B218HIS00.0610.02239.705-0.016-0.0160.0000.0000.0000.000
197B219LYS10.8710.92940.404-7.544-7.5440.0000.0000.0000.000
198B220THR0-0.033-0.03443.612-0.075-0.0750.0000.0000.0000.000
199B221SER0-0.033-0.02546.047-0.184-0.1840.0000.0000.0000.000
200B222THR00.0010.00248.6040.0820.0820.0000.0000.0000.000
201B223SER0-0.0120.00850.861-0.091-0.0910.0000.0000.0000.000
202B224PRO00.0140.00749.0910.0560.0560.0000.0000.0000.000
203B225ILE00.0140.01047.581-0.150-0.1500.0000.0000.0000.000
204B226VAL00.0160.01149.3870.1210.1210.0000.0000.0000.000
205B227LYS10.8470.93050.198-6.272-6.2720.0000.0000.0000.000
206B228SER00.0490.01952.0560.0800.0800.0000.0000.0000.000
207B229PHE0-0.0250.00251.625-0.040-0.0400.0000.0000.0000.000
208B230ASN00.010-0.00456.4190.0700.0700.0000.0000.0000.000
209B231ARG10.8500.92756.668-5.478-5.4780.0000.0000.0000.000
210B232ASN0-0.0040.01158.7310.0560.0560.0000.0000.0000.000
211B233GLU-1-0.943-0.96061.3614.8444.8440.0000.0000.0000.000