Manual

About

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: 49K7N

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 OptHSide
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
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2224355.171345
FMO2-HF: Nuclear repulsion 2140900.741369
FMO2-HF: Total energy -83454.429977
FMO2-MP2: Total energy -83696.892332


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.
-67.647-60.4113.461-4.086-6.6090.036
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 : -0.908 / q_NPA : -0.961
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].
3B23VAL00.0210.0273.4620.2772.8430.024-1.154-1.4360.006
4B24MET00.0050.0105.375-3.868-3.803-0.001-0.004-0.0590.000
5B25THR00.003-0.0098.3120.0410.0410.0000.0000.0000.000
6B26GLN00.021-0.01211.1410.1060.1060.0000.0000.0000.000
7B27SER00.010-0.00214.3200.2240.2240.0000.0000.0000.000
8B28HIS0-0.0040.01816.378-0.530-0.5300.0000.0000.0000.000
9B29LYS10.8900.94814.668-18.269-18.2690.0000.0000.0000.000
10B30PHE00.0120.01119.1160.0060.0060.0000.0000.0000.000
11B31MET0-0.0190.00420.6820.0560.0560.0000.0000.0000.000
12B32SER0-0.0040.01024.626-0.043-0.0430.0000.0000.0000.000
13B33THR00.0060.00728.341-0.024-0.0240.0000.0000.0000.000
14B34SER00.0300.01030.300-0.108-0.1080.0000.0000.0000.000
15B35VAL0-0.031-0.02533.1250.1360.1360.0000.0000.0000.000
16B36GLY0-0.011-0.00334.185-0.243-0.2430.0000.0000.0000.000
17B37ASP-1-0.868-0.90832.3018.8328.8320.0000.0000.0000.000
18B38ARG10.9260.97726.764-10.418-10.4180.0000.0000.0000.000
19B39VAL0-0.042-0.02025.1350.0140.0140.0000.0000.0000.000
20B40SER0-0.025-0.04423.674-0.037-0.0370.0000.0000.0000.000
21B41ILE00.018-0.00118.1220.0310.0310.0000.0000.0000.000
22B42THR00.0130.01717.916-0.073-0.0730.0000.0000.0000.000
23B43CYS0-0.072-0.02212.1760.5980.5980.0000.0000.0000.000
24B44LYS10.8410.92612.690-17.743-17.7430.0000.0000.0000.000
25B45ALA00.0280.0019.3761.4821.4820.0000.0000.0000.000
26B46SER0-0.030-0.0096.245-0.556-0.5560.0000.0000.0000.000
27B47GLN0-0.010-0.0116.3261.9761.9760.0000.0000.0000.000
28B48ASP-1-0.868-0.9339.52118.97318.9730.0000.0000.0000.000
29B49VAL0-0.003-0.0208.6461.7171.7170.0000.0000.0000.000
30B50SER00.0120.01511.312-0.897-0.8970.0000.0000.0000.000
31B51THR00.0500.01115.020-0.003-0.0030.0000.0000.0000.000
32B52ALA0-0.0170.01512.158-0.587-0.5870.0000.0000.0000.000
33B53VAL0-0.008-0.01011.9921.9711.9710.0000.0000.0000.000
34B54ALA0-0.032-0.01213.471-1.572-1.5720.0000.0000.0000.000
35B55TRP0-0.009-0.01814.4551.1891.1890.0000.0000.0000.000
36B56TYR0-0.009-0.02314.045-1.299-1.2990.0000.0000.0000.000
37B57GLN0-0.002-0.01017.9520.0190.0190.0000.0000.0000.000
38B58GLN00.001-0.01018.4950.6100.6100.0000.0000.0000.000
39B59LYS10.9020.95521.066-11.185-11.1850.0000.0000.0000.000
40B60PRO00.0530.01524.0880.3700.3700.0000.0000.0000.000
41B61GLY00.0020.00624.577-0.385-0.3850.0000.0000.0000.000
42B62GLN0-0.037-0.00624.362-0.007-0.0070.0000.0000.0000.000
43B63SER00.0290.00821.0350.6250.6250.0000.0000.0000.000
44B64PRO0-0.020-0.01616.852-0.495-0.4950.0000.0000.0000.000
45B65LYS10.9650.99819.653-11.931-11.9310.0000.0000.0000.000
46B66LEU0-0.0140.00517.6300.2310.2310.0000.0000.0000.000
47B67LEU0-0.053-0.02920.001-0.787-0.7870.0000.0000.0000.000
48B68ILE00.0090.00619.535-0.545-0.5450.0000.0000.0000.000
49B69TYR00.0100.00417.8220.9950.9950.0000.0000.0000.000
50B70SER00.0370.00817.437-0.422-0.4220.0000.0000.0000.000
51B71ALA00.0080.00817.330-0.731-0.7310.0000.0000.0000.000
52B72SER0-0.057-0.04218.466-0.473-0.4730.0000.0000.0000.000
53B73TYR0-0.0270.01121.682-0.796-0.7960.0000.0000.0000.000
54B74ARG10.8390.92322.499-9.849-9.8490.0000.0000.0000.000
55B75TYR00.0120.00122.480-0.220-0.2200.0000.0000.0000.000
56B76THR00.0520.00724.507-0.378-0.3780.0000.0000.0000.000
57B77GLY0-0.0070.00227.5360.1690.1690.0000.0000.0000.000
58B78VAL0-0.099-0.02624.551-0.131-0.1310.0000.0000.0000.000
59B79PRO0-0.006-0.00627.852-0.159-0.1590.0000.0000.0000.000
60B80ASP-1-0.765-0.90128.8209.9179.9170.0000.0000.0000.000
61B81ARG10.7200.84529.174-9.877-9.8770.0000.0000.0000.000
62B82PHE0-0.0030.01424.7450.2080.2080.0000.0000.0000.000
63B83THR0-0.007-0.01425.071-0.107-0.1070.0000.0000.0000.000
64B84GLY00.0280.01321.0910.3720.3720.0000.0000.0000.000
65B85SER0-0.032-0.01320.788-0.576-0.5760.0000.0000.0000.000
66B86GLY00.0570.02019.0810.5410.5410.0000.0000.0000.000
67B87SER0-0.015-0.02717.5150.0730.0730.0000.0000.0000.000
68B88GLY00.0350.03815.186-0.466-0.4660.0000.0000.0000.000
69B89THR00.009-0.01512.1371.2621.2620.0000.0000.0000.000
70B90ASP-1-0.827-0.86913.87417.40517.4050.0000.0000.0000.000
71B91PHE0-0.0140.00013.103-0.677-0.6770.0000.0000.0000.000
72B92THR0-0.029-0.02817.102-0.098-0.0980.0000.0000.0000.000
73B93PHE00.0110.01719.326-0.218-0.2180.0000.0000.0000.000
74B94THR00.000-0.00420.899-0.280-0.2800.0000.0000.0000.000
75B95ILE00.0020.02224.588-0.021-0.0210.0000.0000.0000.000
76B96SER0-0.035-0.03227.135-0.157-0.1570.0000.0000.0000.000
77B97SER00.020-0.00230.354-0.306-0.3060.0000.0000.0000.000
78B98VAL0-0.024-0.00228.5430.0550.0550.0000.0000.0000.000
79B99GLN00.0300.00630.895-0.411-0.4110.0000.0000.0000.000
80B100ALA00.0710.03531.0210.3200.3200.0000.0000.0000.000
81B101GLU-1-0.850-0.90630.3549.8349.8340.0000.0000.0000.000
82B102ASP-1-0.796-0.86927.11910.93110.9310.0000.0000.0000.000
83B103LEU0-0.0080.02226.1430.5370.5370.0000.0000.0000.000
84B104ALA0-0.018-0.01422.9220.0250.0250.0000.0000.0000.000
85B105VAL0-0.0140.00617.620-0.091-0.0910.0000.0000.0000.000
86B106TYR0-0.008-0.01918.6780.0590.0590.0000.0000.0000.000
87B107TYR0-0.0060.00213.3550.4580.4580.0000.0000.0000.000
88B109GLN00.027-0.0019.682-0.360-0.3600.0000.0000.0000.000
89B110GLN00.0790.0384.992-6.488-6.4880.0000.0000.0000.000
90B111HIS00.002-0.0138.7803.5373.5370.0000.0000.0000.000
91B112TYR0-0.0010.0028.285-1.881-1.8810.0000.0000.0000.000
92B113SER0-0.021-0.0084.331-1.426-1.350-0.001-0.004-0.0710.000
93B114ILE0-0.0360.0166.284-0.777-0.7770.0000.0000.0000.000
94B115PRO00.0750.0342.619-9.899-6.1852.996-2.621-4.0890.030
95B116ARG10.8560.9224.848-29.908-29.816-0.001-0.004-0.0860.000
96B117THR0-0.018-0.0192.4750.1640.8870.444-0.299-0.8680.000
97B118PHE00.016-0.0055.851-4.459-4.4590.0000.0000.0000.000
98B119GLY00.0420.0128.1541.6741.6740.0000.0000.0000.000
99B120GLY0-0.033-0.02410.479-0.144-0.1440.0000.0000.0000.000
100B121GLY00.0050.00212.344-0.976-0.9760.0000.0000.0000.000
101B122THR0-0.046-0.04015.4120.1010.1010.0000.0000.0000.000
102B123LYS10.8040.89118.670-11.990-11.9900.0000.0000.0000.000
103B124LEU0-0.018-0.00221.833-0.222-0.2220.0000.0000.0000.000
104B125GLU-1-0.819-0.90924.84710.86010.8600.0000.0000.0000.000
105B126ILE0-0.006-0.00627.930-0.102-0.1020.0000.0000.0000.000
106B127LYS10.9400.97531.216-8.464-8.4640.0000.0000.0000.000
107B128ARG10.8540.92434.030-8.062-8.0620.0000.0000.0000.000
108B129ALA00.004-0.00837.3190.0010.0010.0000.0000.0000.000
109B130ASP-1-0.838-0.92440.4207.7197.7190.0000.0000.0000.000
110B131ALA0-0.036-0.01841.402-0.138-0.1380.0000.0000.0000.000
111B132ALA00.0460.02442.6080.1340.1340.0000.0000.0000.000
112B133PRO0-0.0260.00342.8810.0300.0300.0000.0000.0000.000
113B134THR00.0130.00344.370-0.239-0.2390.0000.0000.0000.000
114B135VAL0-0.029-0.02345.4390.1370.1370.0000.0000.0000.000
115B136SER0-0.030-0.01246.776-0.198-0.1980.0000.0000.0000.000
116B137ILE0-0.0140.00147.1470.1590.1590.0000.0000.0000.000
117B138PHE0-0.016-0.01146.158-0.102-0.1020.0000.0000.0000.000
118B139PRO00.0250.01349.3580.0950.0950.0000.0000.0000.000
119B140PRO00.002-0.00249.5220.0820.0820.0000.0000.0000.000
120B141SER0-0.014-0.01749.597-0.113-0.1130.0000.0000.0000.000
121B142SER00.0500.00751.326-0.035-0.0350.0000.0000.0000.000
122B143GLU-1-0.827-0.88749.7776.2496.2490.0000.0000.0000.000
123B144GLN00.0410.00845.586-0.045-0.0450.0000.0000.0000.000
124B145LEU00.0310.01649.622-0.008-0.0080.0000.0000.0000.000
125B146THR0-0.079-0.04152.820-0.113-0.1130.0000.0000.0000.000
126B147SER0-0.070-0.02748.8310.0000.0000.0000.0000.0000.000
127B148GLY0-0.006-0.00650.3040.0580.0580.0000.0000.0000.000
128B149GLY0-0.023-0.00648.1600.0590.0590.0000.0000.0000.000
129B150ALA00.004-0.01348.536-0.118-0.1180.0000.0000.0000.000
130B151SER0-0.0250.00044.2130.0660.0660.0000.0000.0000.000
131B152VAL0-0.0260.00546.661-0.094-0.0940.0000.0000.0000.000
132B153VAL00.0080.01042.6410.1600.1600.0000.0000.0000.000
133B154CYS0-0.042-0.00244.245-0.122-0.1220.0000.0000.0000.000
134B155PHE0-0.032-0.01241.3650.2310.2310.0000.0000.0000.000
135B156LEU00.0130.00041.491-0.220-0.2200.0000.0000.0000.000
136B157ASN00.039-0.00540.7190.3800.3800.0000.0000.0000.000
137B158ASN0-0.009-0.02239.300-0.314-0.3140.0000.0000.0000.000
138B159PHE00.0080.00637.782-0.162-0.1620.0000.0000.0000.000
139B160TYR00.0420.02733.1700.2350.2350.0000.0000.0000.000
140B161PRO00.0060.00236.197-0.241-0.2410.0000.0000.0000.000
141B162LYS10.9991.00129.822-10.428-10.4280.0000.0000.0000.000
142B163ASP-1-0.931-0.95335.4958.8088.8080.0000.0000.0000.000
143B164ILE0-0.041-0.02037.304-0.235-0.2350.0000.0000.0000.000
144B165ASN0-0.036-0.01739.789-0.007-0.0070.0000.0000.0000.000
145B166VAL00.0360.01241.437-0.138-0.1380.0000.0000.0000.000
146B167LYS10.7890.89944.063-6.548-6.5480.0000.0000.0000.000
147B168TRP00.0520.01344.186-0.175-0.1750.0000.0000.0000.000
148B169LYS10.7960.88248.535-6.024-6.0240.0000.0000.0000.000
149B170ILE00.007-0.00350.8180.0180.0180.0000.0000.0000.000
150B171ASP-1-0.765-0.87954.2295.4535.4530.0000.0000.0000.000
151B172GLY0-0.012-0.00356.785-0.057-0.0570.0000.0000.0000.000
152B173SER0-0.007-0.00154.044-0.002-0.0020.0000.0000.0000.000
153B174GLU-1-0.820-0.88647.9276.6826.6820.0000.0000.0000.000
154B175ARG10.8040.88647.671-6.547-6.5470.0000.0000.0000.000
155B176GLN0-0.001-0.02243.9960.2310.2310.0000.0000.0000.000
156B177ASN00.004-0.00343.8580.1930.1930.0000.0000.0000.000
157B178GLY00.0570.02342.836-0.136-0.1360.0000.0000.0000.000
158B179VAL0-0.0200.00741.284-0.006-0.0060.0000.0000.0000.000
159B180LEU0-0.0180.00136.4250.2040.2040.0000.0000.0000.000
160B181ASN00.0310.01837.017-0.306-0.3060.0000.0000.0000.000
161B182SER0-0.010-0.00233.5860.3670.3670.0000.0000.0000.000
162B183TRP0-0.004-0.00732.629-0.168-0.1680.0000.0000.0000.000
163B184THR00.001-0.01132.0670.1780.1780.0000.0000.0000.000
164B185ASP-1-0.837-0.93126.92311.65211.6520.0000.0000.0000.000
165B186GLN0-0.064-0.03829.887-0.080-0.0800.0000.0000.0000.000
166B187ASP-1-0.790-0.86631.2398.8738.8730.0000.0000.0000.000
167B188SER00.0310.00531.0460.0170.0170.0000.0000.0000.000
168B189LYS10.8060.88432.581-8.291-8.2910.0000.0000.0000.000
169B190ASP-1-0.796-0.88836.1748.0858.0850.0000.0000.0000.000
170B191SER0-0.008-0.00633.481-0.137-0.1370.0000.0000.0000.000
171B192THR0-0.103-0.05034.7350.0490.0490.0000.0000.0000.000
172B193TYR0-0.026-0.02230.3740.3340.3340.0000.0000.0000.000
173B194SER00.0440.03435.856-0.392-0.3920.0000.0000.0000.000
174B195MET0-0.060-0.00436.2450.2890.2890.0000.0000.0000.000
175B196SER00.0130.01937.773-0.210-0.2100.0000.0000.0000.000
176B197SER00.008-0.01238.8680.1230.1230.0000.0000.0000.000
177B198THR00.019-0.00440.350-0.213-0.2130.0000.0000.0000.000
178B199LEU00.0050.01642.3270.1180.1180.0000.0000.0000.000
179B200THR0-0.003-0.00442.727-0.112-0.1120.0000.0000.0000.000
180B201LEU0-0.071-0.03345.239-0.006-0.0060.0000.0000.0000.000
181B202THR00.018-0.01848.4180.0630.0630.0000.0000.0000.000
182B203LYS10.9080.96850.364-5.748-5.7480.0000.0000.0000.000
183B204ASP-1-0.815-0.90053.1235.8435.8430.0000.0000.0000.000
184B205GLU-1-0.857-0.91851.4205.9805.9800.0000.0000.0000.000
185B206TYR00.0290.01152.213-0.077-0.0770.0000.0000.0000.000
186B207GLU-1-0.833-0.94054.0955.5575.5570.0000.0000.0000.000
187B208ARG10.8210.92354.405-5.877-5.8770.0000.0000.0000.000
188B209HIS10.8110.91355.226-5.747-5.7470.0000.0000.0000.000
189B210ASN00.003-0.00458.3190.0390.0390.0000.0000.0000.000
190B211SER00.0520.04756.9690.0200.0200.0000.0000.0000.000
191B212TYR0-0.029-0.01851.7420.1220.1220.0000.0000.0000.000
192B213THR00.008-0.00952.351-0.050-0.0500.0000.0000.0000.000
193B215GLU-1-0.803-0.91048.4846.0216.0210.0000.0000.0000.000
194B216ALA00.0180.01045.3360.1530.1530.0000.0000.0000.000
195B217THR0-0.004-0.00645.322-0.199-0.1990.0000.0000.0000.000
196B218HIS00.0710.03039.916-0.016-0.0160.0000.0000.0000.000
197B219LYS10.9120.94840.717-7.508-7.5080.0000.0000.0000.000
198B220THR0-0.053-0.05043.797-0.149-0.1490.0000.0000.0000.000
199B221SER0-0.040-0.01346.138-0.190-0.1900.0000.0000.0000.000
200B222THR00.0130.00848.6800.0830.0830.0000.0000.0000.000
201B223SER0-0.035-0.00450.968-0.078-0.0780.0000.0000.0000.000
202B224PRO00.0190.00049.5780.0740.0740.0000.0000.0000.000
203B225ILE00.0090.01147.690-0.147-0.1470.0000.0000.0000.000
204B226VAL00.0060.01549.8680.1160.1160.0000.0000.0000.000
205B227LYS10.8730.94450.250-6.233-6.2330.0000.0000.0000.000
206B228SER00.020-0.02252.2020.0520.0520.0000.0000.0000.000
207B229PHE0-0.0100.01451.567-0.020-0.0200.0000.0000.0000.000
208B230ASN00.009-0.00156.3980.0860.0860.0000.0000.0000.000
209B231ARG10.8570.92556.834-5.450-5.4500.0000.0000.0000.000
210B232ASN0-0.021-0.00358.7390.0400.0400.0000.0000.0000.000
211B233GLU-1-0.944-0.96161.5444.8304.8300.0000.0000.0000.000