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About

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: JQRR9

Calculation Name: 1YK9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YK9

Chain ID: A

ChEMBL ID:

UniProt ID: P9WQ35

Base Structure: X-ray

Registration Date: 2023-09-23

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1836033.637298
FMO2-HF: Nuclear repulsion 1765062.066326
FMO2-HF: Total energy -70971.570972
FMO2-MP2: Total energy -71179.14005


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(A:245:ASP)


Summations of interaction energy for fragment #1(A:245: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.
24.87431.7873.823-4.9-5.8340.038
Interaction energy analysis for fragmet #1(A:245:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.931 / q_NPA : -0.966
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].
3A247TYR0-0.021-0.0173.811-1.2581.248-0.029-1.305-1.1720.007
4A248ASP-1-0.885-0.9666.66628.95928.9590.0000.0000.0000.000
5A249GLU-1-0.808-0.85710.13216.30716.3070.0000.0000.0000.000
6A250ALA0-0.019-0.00110.5880.2330.2330.0000.0000.0000.000
7A251SER00.029-0.00112.582-1.039-1.0390.0000.0000.0000.000
8A252VAL0-0.044-0.03514.3511.0841.0840.0000.0000.0000.000
9A253LEU00.0030.00816.055-0.984-0.9840.0000.0000.0000.000
10A254PHE0-0.003-0.01518.7090.8430.8430.0000.0000.0000.000
11A255ALA00.0110.00221.100-0.672-0.6720.0000.0000.0000.000
12A256ASP-1-0.804-0.91123.97112.03112.0310.0000.0000.0000.000
13A257ILE0-0.053-0.00226.707-0.455-0.4550.0000.0000.0000.000
14A258VAL00.0490.02030.414-0.057-0.0570.0000.0000.0000.000
15A259GLY0-0.090-0.04832.929-0.270-0.2700.0000.0000.0000.000
16A260PHE00.0190.00331.264-0.189-0.1890.0000.0000.0000.000
17A261THR0-0.060-0.03933.847-0.079-0.0790.0000.0000.0000.000
18A262GLU-1-0.862-0.92534.8279.0989.0980.0000.0000.0000.000
19A263ARG10.8720.94136.991-8.571-8.5710.0000.0000.0000.000
20A264ALA00.0470.01640.211-0.108-0.1080.0000.0000.0000.000
21A265SER0-0.037-0.01140.244-0.200-0.2000.0000.0000.0000.000
22A266SER00.0340.01142.6490.0140.0140.0000.0000.0000.000
23A267THR0-0.0010.00638.5410.0980.0980.0000.0000.0000.000
24A268ALA0-0.018-0.00740.801-0.161-0.1610.0000.0000.0000.000
25A269PRO00.0150.00739.5020.1780.1780.0000.0000.0000.000
26A270ALA00.0010.00139.6630.1530.1530.0000.0000.0000.000
27A271ASP-1-0.890-0.93640.9057.3987.3980.0000.0000.0000.000
28A272LEU0-0.027-0.04537.9490.1650.1650.0000.0000.0000.000
29A273VAL0-0.030-0.01434.0330.0220.0220.0000.0000.0000.000
30A274ARG10.9891.00234.342-8.552-8.5520.0000.0000.0000.000
31A275PHE0-0.038-0.03035.0810.1060.1060.0000.0000.0000.000
32A276LEU00.0060.01033.0200.0270.0270.0000.0000.0000.000
33A277ASP-1-0.828-0.93030.43910.51910.5190.0000.0000.0000.000
34A278ARG10.8950.95430.421-8.395-8.3950.0000.0000.0000.000
35A279LEU0-0.0280.00131.9380.0120.0120.0000.0000.0000.000
36A280TYR00.011-0.00225.6830.1200.1200.0000.0000.0000.000
37A281SER00.0030.00226.6740.3170.3170.0000.0000.0000.000
38A282ALA00.0100.01328.5300.0550.0550.0000.0000.0000.000
39A283PHE0-0.042-0.02925.0830.0030.0030.0000.0000.0000.000
40A284ASP-1-0.786-0.88622.84914.11714.1170.0000.0000.0000.000
41A285GLU-1-0.965-0.97923.80711.00111.0010.0000.0000.0000.000
42A286LEU0-0.062-0.02726.393-0.098-0.0980.0000.0000.0000.000
43A287VAL0-0.0250.00219.6290.1250.1250.0000.0000.0000.000
44A288ASP-1-0.944-0.97521.76214.33014.3300.0000.0000.0000.000
45A289GLN0-0.032-0.00721.752-0.359-0.3590.0000.0000.0000.000
46A290HIS00.004-0.00719.3700.2780.2780.0000.0000.0000.000
47A291GLY0-0.073-0.04015.5320.4250.4250.0000.0000.0000.000
48A292LEU0-0.033-0.01415.3020.8590.8590.0000.0000.0000.000
49A293GLU-1-0.845-0.93413.48319.13219.1320.0000.0000.0000.000
50A294LYS10.8210.91714.892-14.207-14.2070.0000.0000.0000.000
51A295ILE0-0.041-0.01910.6631.3871.3870.0000.0000.0000.000
52A296GLU-1-0.782-0.87013.11322.76822.7680.0000.0000.0000.000
53A297VAL00.0200.00315.258-0.698-0.6980.0000.0000.0000.000
54A298SER0-0.070-0.02618.9820.0030.0030.0000.0000.0000.000
55A299GLY00.005-0.01321.232-0.334-0.3340.0000.0000.0000.000
56A300ASP-1-0.889-0.93124.54711.75111.7510.0000.0000.0000.000
57A301SER0-0.069-0.01821.9600.1830.1830.0000.0000.0000.000
58A302TYR00.0270.00021.1940.5360.5360.0000.0000.0000.000
59A303MET0-0.028-0.00814.5670.2390.2390.0000.0000.0000.000
60A304VAL00.0350.02516.4230.8390.8390.0000.0000.0000.000
61A305VAL0-0.010-0.00110.837-0.396-0.3960.0000.0000.0000.000
62A306SER00.0750.02113.839-0.422-0.4220.0000.0000.0000.000
63A307GLY0-0.057-0.0279.660-0.225-0.2250.0000.0000.0000.000
64A308VAL00.0010.0128.1723.6213.6210.0000.0000.0000.000
65A309PRO00.0430.0076.956-0.304-0.3040.0000.0000.0000.000
66A310ARG10.8870.9558.014-19.634-19.6340.0000.0000.0000.000
67A311PRO00.0730.0479.365-1.407-1.4070.0000.0000.0000.000
68A312ARG10.9480.95111.956-19.018-19.0180.0000.0000.0000.000
69A313PRO00.0460.00415.6710.3840.3840.0000.0000.0000.000
70A314ASP-1-0.938-0.95917.77114.32314.3230.0000.0000.0000.000
71A315HIS00.0290.02715.109-0.111-0.1110.0000.0000.0000.000
72A316THR00.002-0.00817.060-0.091-0.0910.0000.0000.0000.000
73A317GLN0-0.011-0.01419.512-0.237-0.2370.0000.0000.0000.000
74A318ALA00.0340.03918.553-0.438-0.4380.0000.0000.0000.000
75A319LEU00.0190.00216.823-0.128-0.1280.0000.0000.0000.000
76A320ALA0-0.039-0.00721.027-0.452-0.4520.0000.0000.0000.000
77A321ASP-1-0.839-0.92724.23511.68411.6840.0000.0000.0000.000
78A322PHE00.0530.04322.290-0.249-0.2490.0000.0000.0000.000
79A323ALA00.005-0.00624.461-0.172-0.1720.0000.0000.0000.000
80A324LEU0-0.080-0.03625.898-0.441-0.4410.0000.0000.0000.000
81A325ASP-1-0.815-0.91827.9159.9439.9430.0000.0000.0000.000
82A326MET0-0.052-0.01625.173-0.073-0.0730.0000.0000.0000.000
83A327THR0-0.030-0.02228.351-0.172-0.1720.0000.0000.0000.000
84A328ASN0-0.094-0.03531.882-0.551-0.5510.0000.0000.0000.000
85A329VAL00.0710.03630.220-0.318-0.3180.0000.0000.0000.000
86A330ALA0-0.0120.01231.654-0.262-0.2620.0000.0000.0000.000
87A331ALA0-0.056-0.04433.550-0.157-0.1570.0000.0000.0000.000
88A332GLN0-0.028-0.01136.829-0.440-0.4400.0000.0000.0000.000
89A333LEU00.0070.01635.764-0.242-0.2420.0000.0000.0000.000
90A334LYS10.7980.88838.831-8.073-8.0730.0000.0000.0000.000
91A335ASP-1-0.897-0.91041.9126.7906.7900.0000.0000.0000.000
92A336PRO00.018-0.00742.9420.0930.0930.0000.0000.0000.000
93A337ARG10.9290.93942.755-7.056-7.0560.0000.0000.0000.000
94A338GLY00.0810.05642.8670.1460.1460.0000.0000.0000.000
95A339ASN0-0.068-0.03338.5540.1340.1340.0000.0000.0000.000
96A340PRO00.0060.00539.3590.0210.0210.0000.0000.0000.000
97A341VAL00.0680.02134.4030.1070.1070.0000.0000.0000.000
98A342PRO0-0.066-0.01735.2980.0160.0160.0000.0000.0000.000
99A343LEU00.0370.00328.1120.1330.1330.0000.0000.0000.000
100A344ARG10.8010.90128.538-11.094-11.0940.0000.0000.0000.000
101A345VAL00.0070.00024.5690.4370.4370.0000.0000.0000.000
102A346GLY00.0310.03224.236-0.433-0.4330.0000.0000.0000.000
103A347LEU0-0.012-0.01520.6040.6910.6910.0000.0000.0000.000
104A348ALA00.015-0.01018.581-0.380-0.3800.0000.0000.0000.000
105A349THR0-0.038-0.02616.3830.9640.9640.0000.0000.0000.000
106A350GLY00.0320.01614.938-0.925-0.9250.0000.0000.0000.000
107A351PRO00.0040.01610.8450.8870.8870.0000.0000.0000.000
108A352VAL0-0.035-0.0338.080-0.725-0.7250.0000.0000.0000.000
109A353VAL0-0.0040.0073.6121.1091.2070.008-0.045-0.0610.000
110A354ALA0-0.023-0.0102.504-7.168-5.6842.900-1.933-2.4500.018
111A355GLY0-0.004-0.0043.6131.9862.6070.029-0.352-0.298-0.001
112A356VAL0-0.025-0.0172.745-0.5161.6030.916-1.265-1.7710.014
113A357VAL0-0.0120.0115.4351.0921.177-0.0010.000-0.0820.000
114A358GLY00.0420.0278.208-2.390-2.3900.0000.0000.0000.000
115A359SER0-0.009-0.0209.828-2.953-2.9530.0000.0000.0000.000
116A360ARG10.9941.01611.569-22.863-22.8630.0000.0000.0000.000
117A361ARG10.8770.90213.968-18.632-18.6320.0000.0000.0000.000
118A362PHE00.0380.03512.8721.7741.7740.0000.0000.0000.000
119A363ARG10.8140.88711.307-24.381-24.3810.0000.0000.0000.000
120A364TYR00.0380.0237.4992.7462.7460.0000.0000.0000.000
121A365CYS0-0.070-0.0437.3113.9133.9130.0000.0000.0000.000
122A366VAL00.0710.0258.1983.2003.2000.0000.0000.0000.000
123A367TRP0-0.0160.0008.280-3.583-3.5830.0000.0000.0000.000
124A368GLY00.0640.0288.6562.2752.2750.0000.0000.0000.000
125A369ASP-1-0.901-0.94910.81715.48015.4800.0000.0000.0000.000
126A370ALA00.0280.01413.483-1.200-1.2000.0000.0000.0000.000
127A371VAL00.0360.00611.504-1.021-1.0210.0000.0000.0000.000
128A372ASN0-0.0040.00514.682-1.401-1.4010.0000.0000.0000.000
129A373VAL0-0.054-0.04416.984-1.174-1.1740.0000.0000.0000.000
130A374ALA00.0630.03817.963-0.756-0.7560.0000.0000.0000.000
131A375SER00.0190.02519.800-0.598-0.5980.0000.0000.0000.000
132A376ARG10.8800.94820.273-14.764-14.7640.0000.0000.0000.000
133A377MET0-0.0530.00323.167-0.776-0.7760.0000.0000.0000.000
134A378GLU-1-0.694-0.83024.28711.78911.7890.0000.0000.0000.000
135A379SER0-0.068-0.03825.719-0.460-0.4600.0000.0000.0000.000
136A380THR0-0.129-0.07127.859-0.543-0.5430.0000.0000.0000.000
137A381ASP-1-0.815-0.90329.55910.29110.2910.0000.0000.0000.000
138A382SER0-0.088-0.05031.468-0.336-0.3360.0000.0000.0000.000
139A383VAL0-0.046-0.04534.5370.1420.1420.0000.0000.0000.000
140A384GLY0-0.0060.02333.625-0.097-0.0970.0000.0000.0000.000
141A385GLN0-0.018-0.01632.504-0.070-0.0700.0000.0000.0000.000
142A386ILE00.0410.02326.5320.1940.1940.0000.0000.0000.000
143A387GLN0-0.021-0.01827.257-0.555-0.5550.0000.0000.0000.000
144A388VAL0-0.039-0.03424.9330.6470.6470.0000.0000.0000.000
145A389PRO00.0000.01022.158-0.438-0.4380.0000.0000.0000.000
146A390ASP-1-0.768-0.93225.28910.91010.9100.0000.0000.0000.000
147A391GLU-1-0.899-0.93920.41613.45113.4510.0000.0000.0000.000
148A392VAL0-0.013-0.02620.8340.1470.1470.0000.0000.0000.000
149A393TYR0-0.055-0.00323.128-0.244-0.2440.0000.0000.0000.000
150A394GLU-1-0.903-0.94324.52810.47410.4740.0000.0000.0000.000
151A395ARG10.7070.83717.825-15.209-15.2090.0000.0000.0000.000
152A396LEU0-0.012-0.00924.1040.1810.1810.0000.0000.0000.000
153A397LYS10.8970.92522.275-12.792-12.7920.0000.0000.0000.000
154A398ASP-1-0.878-0.93028.5249.2329.2320.0000.0000.0000.000
155A399ASP-1-0.865-0.92329.0969.8649.8640.0000.0000.0000.000
156A400PHE0-0.061-0.04726.1860.1100.1100.0000.0000.0000.000
157A401VAL0-0.0180.00330.906-0.194-0.1940.0000.0000.0000.000
158A402LEU00.0190.00428.0400.1640.1640.0000.0000.0000.000
159A403ARG10.8900.94532.680-8.347-8.3470.0000.0000.0000.000
160A404GLU-1-0.900-0.95433.9698.7248.7240.0000.0000.0000.000
161A405ARG10.9080.97632.059-9.600-9.6000.0000.0000.0000.000
162A406GLY00.013-0.00433.791-0.293-0.2930.0000.0000.0000.000
163A407HIS0-0.028-0.00832.5170.3560.3560.0000.0000.0000.000
164A408ILE00.026-0.01432.440-0.220-0.2200.0000.0000.0000.000
165A409ASN0-0.014-0.01333.033-0.168-0.1680.0000.0000.0000.000
166A410VAL00.0100.01126.5320.2830.2830.0000.0000.0000.000
167A411LYS10.9660.97028.230-9.953-9.9530.0000.0000.0000.000
168A412GLY0-0.0020.00824.2290.0670.0670.0000.0000.0000.000
169A413LYS10.9090.94919.313-14.364-14.3640.0000.0000.0000.000
170A414GLY00.0190.02725.227-0.045-0.0450.0000.0000.0000.000
171A415VAL0-0.009-0.01027.942-0.391-0.3910.0000.0000.0000.000
172A416MET0-0.077-0.00628.4260.3250.3250.0000.0000.0000.000
173A417ARG10.8660.91423.438-12.141-12.1410.0000.0000.0000.000
174A418THR00.0140.02329.578-0.063-0.0630.0000.0000.0000.000
175A419TRP00.0110.01625.2900.5340.5340.0000.0000.0000.000
176A420TYR00.0430.00228.928-0.521-0.5210.0000.0000.0000.000
177A421LEU00.0110.02029.8080.2520.2520.0000.0000.0000.000
178A422ILE00.0100.01027.488-0.281-0.2810.0000.0000.0000.000
179A423GLY0-0.0100.00630.581-0.094-0.0940.0000.0000.0000.000
180A424ARG10.9210.93532.673-8.537-8.5370.0000.0000.0000.000
181A425LYS10.8960.94526.931-11.064-11.0640.0000.0000.0000.000
182A426VAL0-0.072-0.02931.873-0.301-0.3010.0000.0000.0000.000
183A427ALA00.0290.01433.2300.1970.1970.0000.0000.0000.000
184A428ALA0-0.0130.00435.344-0.315-0.3150.0000.0000.0000.000