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: JLGY9

Calculation Name: 5DBK-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DBK

Chain ID: B

ChEMBL ID:

UniProt ID: M1Q3P9

Base Structure: X-ray

Registration Date: 2023-09-19

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 352
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5771669.273102
FMO2-HF: Nuclear repulsion 5625110.568274
FMO2-HF: Total energy -146558.704828
FMO2-MP2: Total energy -146986.272524


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:67:ASP)


Summations of interaction energy for fragment #1(B:67: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.
77.756810.049-1.422-1.870.005
Interaction energy analysis for fragmet #1(B:67:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.952 / q_NPA : -0.996
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].
3B69GLU-1-0.887-0.9523.37926.14428.7580.049-1.220-1.4430.005
4B70GLU-1-0.978-0.9844.10833.38134.0110.000-0.202-0.4270.000
5B71ASP-1-0.903-0.9555.78929.78729.7870.0000.0000.0000.000
6B72VAL00.0310.0177.856-4.347-4.3470.0000.0000.0000.000
7B73LYS10.7730.8777.832-24.822-24.8220.0000.0000.0000.000
8B74GLY00.0380.0159.446-2.206-2.2060.0000.0000.0000.000
9B75LYS10.8350.89311.756-22.555-22.5550.0000.0000.0000.000
10B76LEU0-0.035-0.02011.314-1.999-1.9990.0000.0000.0000.000
11B77ASP-1-0.759-0.84513.87418.38318.3830.0000.0000.0000.000
12B78GLU-1-0.925-0.95215.97417.51417.5140.0000.0000.0000.000
13B79TRP0-0.048-0.02917.144-1.099-1.0990.0000.0000.0000.000
14B80LEU0-0.0030.00118.246-0.979-0.9790.0000.0000.0000.000
15B81ASN0-0.026-0.03419.721-1.348-1.3480.0000.0000.0000.000
16B82ALA0-0.0010.00321.761-0.743-0.7430.0000.0000.0000.000
17B83LEU0-0.026-0.02320.874-0.743-0.7430.0000.0000.0000.000
18B84VAL0-0.056-0.02223.848-0.581-0.5810.0000.0000.0000.000
19B85HIS00.006-0.00825.528-0.898-0.8980.0000.0000.0000.000
20B86LEU0-0.061-0.01827.332-0.446-0.4460.0000.0000.0000.000
21B87ASP-1-0.836-0.90826.54610.92910.9290.0000.0000.0000.000
22B88LYS10.9240.92626.618-9.243-9.2430.0000.0000.0000.000
23B89GLN0-0.0290.00727.1230.0750.0750.0000.0000.0000.000
24B90GLN00.0420.01323.2240.7890.7890.0000.0000.0000.000
25B91VAL0-0.007-0.00522.6710.5250.5250.0000.0000.0000.000
26B92GLU-1-0.800-0.88522.57311.58611.5860.0000.0000.0000.000
27B93ARG10.8580.91619.472-14.862-14.8620.0000.0000.0000.000
28B94ILE00.0320.01717.2190.4990.4990.0000.0000.0000.000
29B95TYR0-0.047-0.03118.0720.7320.7320.0000.0000.0000.000
30B96GLU-1-0.953-0.97819.27313.08213.0820.0000.0000.0000.000
31B97GLU-1-0.825-0.88516.72017.09817.0980.0000.0000.0000.000
32B98LEU00.0400.01713.3180.8270.8270.0000.0000.0000.000
33B99GLN0-0.042-0.01315.1540.0250.0250.0000.0000.0000.000
34B100GLY0-0.061-0.01616.256-0.303-0.3030.0000.0000.0000.000
35B101GLU-1-0.822-0.89811.23422.06422.0640.0000.0000.0000.000
36B102MET0-0.024-0.02111.0501.8161.8160.0000.0000.0000.000
37B103LYS10.8790.95612.574-18.069-18.0690.0000.0000.0000.000
38B104HIS0-0.030-0.0179.673-1.211-1.2110.0000.0000.0000.000
39B105VAL00.0360.0326.3800.8750.8750.0000.0000.0000.000
40B106LEU0-0.013-0.0157.600-2.613-2.6130.0000.0000.0000.000
41B107ASP-1-0.817-0.9016.38423.74223.7420.0000.0000.0000.000
42B108PHE00.012-0.0208.449-1.327-1.3270.0000.0000.0000.000
43B109GLU-1-0.985-0.97710.04119.44719.4470.0000.0000.0000.000
44B110ILE00.0530.0216.945-1.243-1.2430.0000.0000.0000.000
45B111ILE00.0010.00610.411-1.386-1.3860.0000.0000.0000.000
46B112ASN0-0.081-0.06412.921-1.741-1.7410.0000.0000.0000.000
47B113TYR0-0.058-0.04412.807-1.506-1.5060.0000.0000.0000.000
48B114TYR00.0730.04413.970-0.878-0.8780.0000.0000.0000.000
49B115LYS10.8720.90215.721-13.989-13.9890.0000.0000.0000.000
50B116LEU0-0.036-0.01818.362-0.804-0.8040.0000.0000.0000.000
51B117LEU00.0070.03016.606-0.788-0.7880.0000.0000.0000.000
52B118TYR00.0180.01119.942-0.646-0.6460.0000.0000.0000.000
53B119THR0-0.091-0.05921.733-0.689-0.6890.0000.0000.0000.000
54B120ARG10.8180.90923.472-11.419-11.4190.0000.0000.0000.000
55B121TYR00.009-0.02123.107-0.449-0.4490.0000.0000.0000.000
56B122LEU00.0090.00125.119-0.409-0.4090.0000.0000.0000.000
57B123ILE0-0.003-0.00427.735-0.385-0.3850.0000.0000.0000.000
58B124MET0-0.0250.02227.005-0.343-0.3430.0000.0000.0000.000
59B125LYS10.7960.88427.360-10.947-10.9470.0000.0000.0000.000
60B126ARG10.8850.94930.877-8.573-8.5730.0000.0000.0000.000
61B127ASP-1-0.862-0.91731.0028.7668.7660.0000.0000.0000.000
62B128ILE0-0.001-0.00431.8660.1990.1990.0000.0000.0000.000
63B129SER00.022-0.00733.1990.0410.0410.0000.0000.0000.000
64B130ALA00.0250.01528.9240.1060.1060.0000.0000.0000.000
65B131LEU0-0.019-0.00227.6930.3550.3550.0000.0000.0000.000
66B132GLU-1-0.837-0.92029.0458.3588.3580.0000.0000.0000.000
67B133GLU-1-0.864-0.90728.68810.00110.0010.0000.0000.0000.000
68B134GLU-1-0.778-0.87522.92212.26912.2690.0000.0000.0000.000
69B135LEU00.0220.01925.2580.3360.3360.0000.0000.0000.000
70B136ASP-1-0.772-0.88627.0489.1269.1260.0000.0000.0000.000
71B137LYS10.7230.84924.157-10.744-10.7440.0000.0000.0000.000
72B138LEU00.0480.03220.4540.1890.1890.0000.0000.0000.000
73B139LYS10.8590.93923.810-8.689-8.6890.0000.0000.0000.000
74B140LYS10.8500.91923.953-11.197-11.1970.0000.0000.0000.000
75B141VAL0-0.043-0.01719.5390.0210.0210.0000.0000.0000.000
76B142TYR00.0390.02621.8140.3500.3500.0000.0000.0000.000
77B143LYS10.9380.95623.028-9.715-9.7150.0000.0000.0000.000
78B144LYS10.9580.97718.244-13.410-13.4100.0000.0000.0000.000
79B145TYR0-0.0060.01718.1690.6770.6770.0000.0000.0000.000
80B146SER00.1250.06216.185-0.823-0.8230.0000.0000.0000.000
81B147PRO00.0320.00318.241-0.426-0.4260.0000.0000.0000.000
82B148PHE00.0920.06217.745-0.533-0.5330.0000.0000.0000.000
83B149GLN00.0320.01114.010-0.821-0.8210.0000.0000.0000.000
84B150LYS10.7770.87319.619-12.728-12.7280.0000.0000.0000.000
85B151LEU00.0090.02023.055-0.462-0.4620.0000.0000.0000.000
86B152LEU00.0490.02019.351-0.450-0.4500.0000.0000.0000.000
87B153TYR00.0070.01723.401-0.460-0.4600.0000.0000.0000.000
88B154MET0-0.072-0.03024.923-0.412-0.4120.0000.0000.0000.000
89B155TYR00.014-0.01426.250-0.525-0.5250.0000.0000.0000.000
90B156GLY00.0530.02826.825-0.275-0.2750.0000.0000.0000.000
91B157ARG10.8060.88927.908-9.670-9.6700.0000.0000.0000.000
92B158GLY00.0390.01730.678-0.319-0.3190.0000.0000.0000.000
93B159LEU00.0150.01429.179-0.288-0.2880.0000.0000.0000.000
94B160LEU00.0140.01231.453-0.210-0.2100.0000.0000.0000.000
95B161CYS0-0.087-0.04233.177-0.280-0.2800.0000.0000.0000.000
96B162CYS0-0.048-0.02235.713-0.258-0.2580.0000.0000.0000.000
97B163LEU0-0.021-0.01734.052-0.194-0.1940.0000.0000.0000.000
98B164GLN0-0.032-0.00236.780-0.192-0.1920.0000.0000.0000.000
99B165TYR0-0.014-0.00739.247-0.228-0.2280.0000.0000.0000.000
100B166ARG10.8930.95938.506-7.674-7.6740.0000.0000.0000.000
101B167TRP00.0650.00738.8180.2140.2140.0000.0000.0000.000
102B168LYS10.8720.93540.535-7.142-7.1420.0000.0000.0000.000
103B169ASP-1-0.878-0.95038.2217.3867.3860.0000.0000.0000.000
104B170GLY0-0.007-0.01835.8580.2160.2160.0000.0000.0000.000
105B171LEU00.0390.02035.7730.2490.2490.0000.0000.0000.000
106B172ASP-1-0.848-0.91836.9677.6687.6680.0000.0000.0000.000
107B173TYR0-0.073-0.04631.4390.2570.2570.0000.0000.0000.000
108B174LEU00.0240.02932.1530.3170.3170.0000.0000.0000.000
109B175LEU00.0350.01533.1840.1700.1700.0000.0000.0000.000
110B176LYS10.9020.94731.679-8.205-8.2050.0000.0000.0000.000
111B177THR0-0.034-0.03027.8670.3500.3500.0000.0000.0000.000
112B178GLU-1-0.814-0.89829.4148.8018.8010.0000.0000.0000.000
113B179VAL0-0.047-0.01931.0720.1660.1660.0000.0000.0000.000
114B180MET00.0260.01425.2180.1630.1630.0000.0000.0000.000
115B181ALA0-0.0150.00726.4620.4410.4410.0000.0000.0000.000
116B182LYS10.9980.99127.244-8.797-8.7970.0000.0000.0000.000
117B183GLU-1-1.011-1.00827.9629.8839.8830.0000.0000.0000.000
118B184GLN0-0.106-0.06721.9560.6990.6990.0000.0000.0000.000
119B185GLY0-0.0060.00824.0070.4530.4530.0000.0000.0000.000
120B186TYR0-0.034-0.02223.0320.2780.2780.0000.0000.0000.000
121B187HIS00.016-0.00925.659-0.677-0.6770.0000.0000.0000.000
122B188GLU-1-0.734-0.83526.58611.19211.1920.0000.0000.0000.000
123B189THR00.019-0.01629.132-0.237-0.2370.0000.0000.0000.000
124B190GLY00.0110.00731.274-0.286-0.2860.0000.0000.0000.000
125B191LEU0-0.0140.00729.604-0.200-0.2000.0000.0000.0000.000
126B192TYR0-0.017-0.02632.142-0.190-0.1900.0000.0000.0000.000
127B193TYR0-0.008-0.01135.252-0.233-0.2330.0000.0000.0000.000
128B194ASN0-0.002-0.01132.146-0.378-0.3780.0000.0000.0000.000
129B195ILE0-0.018-0.00434.202-0.195-0.1950.0000.0000.0000.000
130B196ALA00.0240.01437.481-0.218-0.2180.0000.0000.0000.000
131B197LEU0-0.0070.01538.327-0.223-0.2230.0000.0000.0000.000
132B198ALA00.0090.00138.738-0.168-0.1680.0000.0000.0000.000
133B199TYR00.002-0.01840.440-0.206-0.2060.0000.0000.0000.000
134B200THR0-0.016-0.02043.465-0.193-0.1930.0000.0000.0000.000
135B201HIS0-0.063-0.03742.536-0.219-0.2190.0000.0000.0000.000
136B202LEU0-0.103-0.04443.341-0.049-0.0490.0000.0000.0000.000
137B203ASP-1-0.919-0.94447.0595.8425.8420.0000.0000.0000.000
138B204ILE0-0.033-0.00945.621-0.072-0.0720.0000.0000.0000.000
139B205HIS00.0490.02147.1730.1350.1350.0000.0000.0000.000
140B206HIS00.012-0.00448.1500.1380.1380.0000.0000.0000.000
141B207LEU0-0.0130.00043.6620.0730.0730.0000.0000.0000.000
142B208ALA00.0310.01843.4410.1850.1850.0000.0000.0000.000
143B209ILE00.0070.00043.8240.1500.1500.0000.0000.0000.000
144B210HIS0-0.024-0.00440.648-0.042-0.0420.0000.0000.0000.000
145B211PHE00.029-0.00237.9880.0990.0990.0000.0000.0000.000
146B212VAL0-0.009-0.00539.6630.2130.2130.0000.0000.0000.000
147B213ASN0-0.031-0.00341.5230.0540.0540.0000.0000.0000.000
148B214MET00.0300.02636.9640.0660.0660.0000.0000.0000.000
149B215ALA0-0.017-0.00436.7760.2240.2240.0000.0000.0000.000
150B216LEU0-0.030-0.01937.6660.1320.1320.0000.0000.0000.000
151B217GLU-1-0.940-0.98139.5007.6027.6020.0000.0000.0000.000
152B218GLY00.0330.01635.4540.1030.1030.0000.0000.0000.000
153B219PHE00.004-0.03333.2850.1660.1660.0000.0000.0000.000
154B220ARG10.8700.93036.796-7.221-7.2210.0000.0000.0000.000
155B221SER0-0.0130.00434.531-0.008-0.0080.0000.0000.0000.000
156B222GLU-1-0.858-0.89231.77810.01710.0170.0000.0000.0000.000
157B223ALA0-0.015-0.00334.2820.0910.0910.0000.0000.0000.000
158B224LYS10.8400.92530.578-10.039-10.0390.0000.0000.0000.000
159B225ALA00.0300.00136.996-0.079-0.0790.0000.0000.0000.000
160B226ARG10.8860.94535.988-8.456-8.4560.0000.0000.0000.000
161B227ASN00.003-0.00234.368-0.174-0.1740.0000.0000.0000.000
162B228ILE00.0170.02138.635-0.120-0.1200.0000.0000.0000.000
163B229ILE00.0200.00641.594-0.160-0.1600.0000.0000.0000.000
164B230ASN00.0150.00138.904-0.242-0.2420.0000.0000.0000.000
165B231CYS0-0.0370.00140.0440.0050.0050.0000.0000.0000.000
166B232GLN00.0440.01042.780-0.062-0.0620.0000.0000.0000.000
167B233ILE00.0140.00545.500-0.154-0.1540.0000.0000.0000.000
168B234LEU00.0080.01042.177-0.107-0.1070.0000.0000.0000.000
169B235ILE00.0050.01445.583-0.119-0.1190.0000.0000.0000.000
170B236ALA00.0050.00748.378-0.136-0.1360.0000.0000.0000.000
171B237VAL00.0040.02249.128-0.152-0.1520.0000.0000.0000.000
172B238SER00.0410.02349.122-0.128-0.1280.0000.0000.0000.000
173B239TYR0-0.015-0.03351.178-0.140-0.1400.0000.0000.0000.000
174B240THR0-0.079-0.05254.013-0.174-0.1740.0000.0000.0000.000
175B241GLU-1-0.933-0.97151.2995.9325.9320.0000.0000.0000.000
176B242LYS10.8820.93955.344-5.486-5.4860.0000.0000.0000.000
177B243GLY00.0290.01056.9940.0220.0220.0000.0000.0000.000
178B244GLN0-0.034-0.00657.912-0.076-0.0760.0000.0000.0000.000
179B245TYR00.1100.04958.4260.0130.0130.0000.0000.0000.000
180B246GLU-1-0.831-0.91258.7495.1185.1180.0000.0000.0000.000
181B247GLU-1-0.927-0.95153.0095.9595.9590.0000.0000.0000.000
182B248ALA00.1250.07254.0760.0860.0860.0000.0000.0000.000
183B249LEU0-0.045-0.02754.5960.0700.0700.0000.0000.0000.000
184B250LYS10.7460.85555.932-5.512-5.5120.0000.0000.0000.000
185B251MET00.0250.03148.7880.1120.1120.0000.0000.0000.000
186B252TYR00.046-0.01850.5840.0800.0800.0000.0000.0000.000
187B253GLU-1-0.795-0.86052.7525.5275.5270.0000.0000.0000.000
188B254SER0-0.064-0.04049.7600.0390.0390.0000.0000.0000.000
189B255ILE0-0.032-0.00847.6010.1520.1520.0000.0000.0000.000
190B256LEU0-0.009-0.01049.8090.0550.0550.0000.0000.0000.000
191B257ARG10.8260.89652.630-5.657-5.6570.0000.0000.0000.000
192B258GLU-1-0.760-0.82645.3377.1397.1390.0000.0000.0000.000
193B259ALA00.0180.01947.967-0.040-0.0400.0000.0000.0000.000
194B260THR0-0.048-0.04141.4640.0710.0710.0000.0000.0000.000
195B261SER0-0.028-0.01044.209-0.061-0.0610.0000.0000.0000.000
196B262PHE00.018-0.00239.5090.2240.2240.0000.0000.0000.000
197B263ALA00.0210.00738.646-0.160-0.1600.0000.0000.0000.000
198B264ASP-1-0.773-0.88940.5537.5757.5750.0000.0000.0000.000
199B265LYS10.7810.87742.944-6.957-6.9570.0000.0000.0000.000
200B266ASP-1-0.790-0.88944.7296.7076.7070.0000.0000.0000.000
201B267VAL00.0540.02644.713-0.149-0.1490.0000.0000.0000.000
202B268LEU00.000-0.00342.251-0.094-0.0940.0000.0000.0000.000
203B269LEU0-0.0050.00546.446-0.127-0.1270.0000.0000.0000.000
204B270ALA00.0290.02149.735-0.148-0.1480.0000.0000.0000.000
205B271ILE00.0230.03147.671-0.147-0.1470.0000.0000.0000.000
206B272THR0-0.012-0.01349.207-0.096-0.0960.0000.0000.0000.000
207B273LEU0-0.058-0.03451.672-0.119-0.1190.0000.0000.0000.000
208B274SER00.0180.01553.473-0.096-0.0960.0000.0000.0000.000
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