Manual

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: 2JVMR

Calculation Name: 2YT4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YT4

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WYQ5

Base Structure: X-ray

Registration Date: 2023-09-20

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2298420.268166
FMO2-HF: Nuclear repulsion 2216382.515968
FMO2-HF: Total energy -82037.752198
FMO2-MP2: Total energy -82274.253408


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:489:GLY)


Summations of interaction energy for fragment #1(A:489:GLY)
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.
-1.2150.6092.323-2.169-1.9780.002
Interaction energy analysis for fragmet #1(A:489:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.018
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].
3A491HIS0-0.023-0.0273.798-1.280-0.480-0.011-0.485-0.3040.001
4A492MET00.0060.0206.2450.3590.3590.0000.0000.0000.000
5A493SER00.0390.0148.959-0.123-0.1230.0000.0000.0000.000
6A494VAL0-0.0100.00812.1500.0400.0400.0000.0000.0000.000
7A495GLN00.0380.02314.332-0.027-0.0270.0000.0000.0000.000
8A496ASP-1-0.850-0.92318.0600.0160.0160.0000.0000.0000.000
9A497ALA0-0.024-0.04721.333-0.010-0.0100.0000.0000.0000.000
10A498PRO00.0360.04922.3470.0070.0070.0000.0000.0000.000
11A499THR00.0510.01823.773-0.003-0.0030.0000.0000.0000.000
12A500LYS10.8970.93823.7960.0090.0090.0000.0000.0000.000
13A501LYS10.8420.93121.3220.0070.0070.0000.0000.0000.000
14A502GLU-1-0.836-0.91916.504-0.022-0.0220.0000.0000.0000.000
15A503PHE0-0.092-0.03615.030-0.027-0.0270.0000.0000.0000.000
16A504VAL00.0690.03010.4250.0180.0180.0000.0000.0000.000
17A505ILE0-0.042-0.0118.644-0.030-0.0300.0000.0000.0000.000
18A506ASN00.0780.0406.428-0.401-0.4010.0000.0000.0000.000
19A507PRO0-0.0100.0042.702-0.2140.2240.098-0.127-0.4090.000
20A508ASN00.020-0.0012.1500.5930.9602.233-1.412-1.1880.001
21A509GLY00.0560.0304.1360.0650.1740.003-0.072-0.0400.000
22A510LYS10.7830.8866.8670.6790.6790.0000.0000.0000.000
23A511SER00.003-0.0037.6390.0220.0220.0000.0000.0000.000
24A512GLU-1-0.763-0.8879.0840.3980.3980.0000.0000.0000.000
25A513VAL0-0.022-0.01610.770-0.010-0.0100.0000.0000.0000.000
26A514CYS0-0.044-0.01211.524-0.001-0.0010.0000.0000.0000.000
27A515ILE00.0340.0326.456-0.010-0.0100.0000.0000.0000.000
28A516LEU00.0200.01810.7010.0030.0030.0000.0000.0000.000
29A517HIS0-0.036-0.01913.6220.0090.0090.0000.0000.0000.000
30A518GLU-1-0.806-0.88711.857-0.315-0.3150.0000.0000.0000.000
31A519TYR00.021-0.00112.9250.0070.0070.0000.0000.0000.000
32A520MET00.0190.02214.7330.0070.0070.0000.0000.0000.000
33A521GLN00.0220.02918.1160.0000.0000.0000.0000.0000.000
34A522ARG10.7740.84912.6890.2260.2260.0000.0000.0000.000
35A523VAL0-0.041-0.02116.1930.0010.0010.0000.0000.0000.000
36A524LEU0-0.041-0.01819.0620.0050.0050.0000.0000.0000.000
37A525LYS10.9020.97321.1810.0450.0450.0000.0000.0000.000
38A526VAL00.0260.01022.1090.0030.0030.0000.0000.0000.000
39A527ARG10.9400.97321.5830.0190.0190.0000.0000.0000.000
40A528PRO00.0110.00718.4270.0060.0060.0000.0000.0000.000
41A529VAL0-0.018-0.00321.520-0.009-0.0090.0000.0000.0000.000
42A530TYR00.003-0.01717.1550.0100.0100.0000.0000.0000.000
43A531ASN00.0000.00423.598-0.003-0.0030.0000.0000.0000.000
44A532PHE0-0.015-0.03722.6440.0040.0040.0000.0000.0000.000
45A533PHE00.0210.01725.121-0.003-0.0030.0000.0000.0000.000
46A534GLU-1-0.938-0.96728.0960.0420.0420.0000.0000.0000.000
47A535CYS0-0.025-0.01127.7650.0050.0050.0000.0000.0000.000
48A536GLU-1-0.884-0.93230.1370.0480.0480.0000.0000.0000.000
49A537ASN00.011-0.01427.218-0.002-0.0020.0000.0000.0000.000
50A538PRO00.020-0.00829.3420.0020.0020.0000.0000.0000.000
51A539SER0-0.0050.01425.645-0.001-0.0010.0000.0000.0000.000
52A540GLU-1-0.973-1.00621.3980.1360.1360.0000.0000.0000.000
53A541PRO00.0320.04325.6080.0020.0020.0000.0000.0000.000
54A542PHE0-0.015-0.00923.982-0.004-0.0040.0000.0000.0000.000
55A543GLY00.0980.05524.0680.0110.0110.0000.0000.0000.000
56A544ALA0-0.095-0.06421.122-0.012-0.0120.0000.0000.0000.000
57A545SER00.0410.02722.2720.0140.0140.0000.0000.0000.000
58A546VAL00.0040.00818.625-0.013-0.0130.0000.0000.0000.000
59A547THR0-0.005-0.00222.0930.0050.0050.0000.0000.0000.000
60A548ILE0-0.013-0.03321.140-0.007-0.0070.0000.0000.0000.000
61A549ASP-1-0.890-0.94625.3290.0260.0260.0000.0000.0000.000
62A550GLY00.0110.00929.0050.0010.0010.0000.0000.0000.000
63A551VAL0-0.0080.01326.7800.0030.0030.0000.0000.0000.000
64A552THR00.0090.00024.600-0.002-0.0020.0000.0000.0000.000
65A553TYR0-0.048-0.03920.7530.0030.0030.0000.0000.0000.000
66A554GLY00.0470.04318.9820.0080.0080.0000.0000.0000.000
67A555SER0-0.020-0.03120.054-0.023-0.0230.0000.0000.0000.000
68A556GLY0-0.021-0.02619.6160.0210.0210.0000.0000.0000.000
69A557THR00.0220.00520.342-0.016-0.0160.0000.0000.0000.000
70A558ALA00.008-0.00119.4410.0190.0190.0000.0000.0000.000
71A559SER00.0850.05321.480-0.009-0.0090.0000.0000.0000.000
72A560SER00.0150.00520.166-0.013-0.0130.0000.0000.0000.000
73A561LYS11.0061.01321.240-0.016-0.0160.0000.0000.0000.000
74A562LYS10.9540.97316.1060.0120.0120.0000.0000.0000.000
75A563LEU00.0180.00216.3660.0010.0010.0000.0000.0000.000
76A564ALA00.0400.03616.9430.0210.0210.0000.0000.0000.000
77A565LYS10.9000.96617.986-0.008-0.0080.0000.0000.0000.000
78A566ASN0-0.012-0.03012.904-0.015-0.0150.0000.0000.0000.000
79A567LYS10.8810.96114.098-0.134-0.1340.0000.0000.0000.000
80A568ALA00.0430.03115.8870.0210.0210.0000.0000.0000.000
81A569ALA0-0.0130.00314.1900.0040.0040.0000.0000.0000.000
82A570ARG10.8310.9067.852-0.751-0.7510.0000.0000.0000.000
83A571ALA00.0190.01812.8800.0340.0340.0000.0000.0000.000
84A572THR00.010-0.01816.052-0.007-0.0070.0000.0000.0000.000
85A573LEU0-0.030-0.01710.552-0.024-0.0240.0000.0000.0000.000
86A574GLU-1-0.887-0.93412.6120.5100.5100.0000.0000.0000.000
87A575ILE0-0.034-0.00214.395-0.009-0.0090.0000.0000.0000.000
88A576LEU0-0.041-0.02416.318-0.024-0.0240.0000.0000.0000.000
89A577ILE0-0.075-0.04411.486-0.030-0.0300.0000.0000.0000.000
90A578PRO0-0.023-0.01213.9180.0560.0560.0000.0000.0000.000
91A579ASP-1-0.762-0.86012.7720.4120.4120.0000.0000.0000.000
92A580PHE0-0.0250.0668.0600.2160.2160.0000.0000.0000.000
93A581VAL00.002-0.0499.3310.1530.1530.0000.0000.0000.000
94A582LYS10.8180.9044.245-2.290-2.0980.001-0.068-0.1240.000
95A583GLN00.027-0.0305.2370.5790.497-0.001-0.0050.0870.000
96A592SER0-0.023-0.00820.065-0.002-0.0020.0000.0000.0000.000
97A593GLU-1-0.934-0.99120.5900.1660.1660.0000.0000.0000.000
98A594GLU-1-0.806-0.89422.4660.1070.1070.0000.0000.0000.000
99A595LEU0-0.068-0.02123.911-0.009-0.0090.0000.0000.0000.000
100A596GLU-1-0.929-0.98120.2420.1850.1850.0000.0000.0000.000
101A597TYR00.0390.01622.598-0.006-0.0060.0000.0000.0000.000
102A598PHE0-0.038-0.02725.284-0.013-0.0130.0000.0000.0000.000
103A599ASN00.0480.00720.304-0.006-0.0060.0000.0000.0000.000
104A600HIS0-0.080-0.05120.5230.0010.0010.0000.0000.0000.000
105A601ILE0-0.058-0.01424.864-0.011-0.0110.0000.0000.0000.000
106A602SER0-0.017-0.01227.4400.0050.0050.0000.0000.0000.000
107A603ILE00.0700.04126.8030.0020.0020.0000.0000.0000.000
108A604GLU-1-0.907-0.96130.2040.0300.0300.0000.0000.0000.000
109A605ASP-1-0.818-0.86532.0310.0390.0390.0000.0000.0000.000
110A606SER00.005-0.01433.9550.0020.0020.0000.0000.0000.000
111A607ARG10.8740.90632.318-0.044-0.0440.0000.0000.0000.000
112A608VAL0-0.0010.01131.1450.0020.0020.0000.0000.0000.000
113A609TYR00.0510.02933.8770.0020.0020.0000.0000.0000.000
114A610GLU-1-0.922-0.96136.4070.0460.0460.0000.0000.0000.000
115A611LEU00.0240.01531.4030.0010.0010.0000.0000.0000.000
116A612THR00.0210.00931.1270.0020.0020.0000.0000.0000.000
117A613SER0-0.059-0.02033.5000.0010.0010.0000.0000.0000.000
118A614LYS10.9290.97135.899-0.055-0.0550.0000.0000.0000.000
119A615ALA0-0.042-0.03131.1000.0010.0010.0000.0000.0000.000
120A616GLY00.0310.03132.8090.0050.0050.0000.0000.0000.000
121A617LEU0-0.056-0.03828.6070.0040.0040.0000.0000.0000.000
122A618LEU00.0050.00331.280-0.007-0.0070.0000.0000.0000.000
123A619SER0-0.039-0.03333.1340.0000.0000.0000.0000.0000.000
124A620PRO00.0340.00333.8750.0010.0010.0000.0000.0000.000
125A621TYR00.010-0.01234.949-0.001-0.0010.0000.0000.0000.000
126A622GLN00.0100.01035.2860.0020.0020.0000.0000.0000.000
127A623ILE00.0500.02129.2270.0010.0010.0000.0000.0000.000
128A624LEU00.0020.00732.1100.0010.0010.0000.0000.0000.000
129A625HIS0-0.017-0.01834.3440.0000.0000.0000.0000.0000.000
130A626GLU-1-0.852-0.90630.7700.0780.0780.0000.0000.0000.000
131A627CYS0-0.026-0.00930.5500.0010.0010.0000.0000.0000.000
132A628LEU0-0.027-0.02031.547-0.001-0.0010.0000.0000.0000.000
133A629LYS10.8460.92033.815-0.068-0.0680.0000.0000.0000.000
134A630ARG10.8020.88924.615-0.112-0.1120.0000.0000.0000.000
135A631ASN0-0.010-0.02729.0460.0020.0020.0000.0000.0000.000
136A632HIS00.0350.02332.355-0.002-0.0020.0000.0000.0000.000
137A633GLY00.0090.01434.627-0.002-0.0020.0000.0000.0000.000
138A634MET0-0.008-0.00132.5660.0000.0000.0000.0000.0000.000
139A635GLY0-0.023-0.01036.878-0.001-0.0010.0000.0000.0000.000
140A636ASP-1-0.877-0.92740.5880.0290.0290.0000.0000.0000.000
141A637THR00.001-0.01239.6260.0000.0000.0000.0000.0000.000
142A638SER0-0.059-0.01742.1990.0000.0000.0000.0000.0000.000
143A639ILE0-0.005-0.01743.2340.0000.0000.0000.0000.0000.000
144A640LYS10.8650.94046.076-0.018-0.0180.0000.0000.0000.000
145A641PHE0-0.031-0.04149.0650.0000.0000.0000.0000.0000.000
146A642GLU-1-0.788-0.89550.9830.0170.0170.0000.0000.0000.000
147A643VAL0-0.052-0.02953.7090.0000.0000.0000.0000.0000.000
148A644VAL00.1300.06355.953-0.001-0.0010.0000.0000.0000.000
149A645PRO00.0190.01658.5050.0010.0010.0000.0000.0000.000
150A646GLY00.021-0.00555.1930.0000.0000.0000.0000.0000.000
151A647LYS10.9230.96654.613-0.016-0.0160.0000.0000.0000.000
152A648ASN0-0.029-0.01955.9080.0000.0000.0000.0000.0000.000
153A649GLN00.0010.00155.543-0.001-0.0010.0000.0000.0000.000
154A650LYS10.9210.97846.570-0.018-0.0180.0000.0000.0000.000
155A651SER00.0560.03450.824-0.001-0.0010.0000.0000.0000.000
156A652GLU-1-0.829-0.91049.4000.0170.0170.0000.0000.0000.000
157A653TYR0-0.027-0.01142.5380.0010.0010.0000.0000.0000.000
158A654VAL00.029-0.01146.122-0.001-0.0010.0000.0000.0000.000
159A655MET0-0.034-0.00639.0600.0010.0010.0000.0000.0000.000
160A656ALA00.0130.01142.803-0.001-0.0010.0000.0000.0000.000
161A657CYS00.006-0.01937.9120.0020.0020.0000.0000.0000.000
162A658GLY00.0970.06938.9780.0000.0000.0000.0000.0000.000
163A659LYS10.8210.91833.616-0.025-0.0250.0000.0000.0000.000
164A660HIS0-0.011-0.00335.099-0.001-0.0010.0000.0000.0000.000
165A661THR00.0410.01839.9800.0020.0020.0000.0000.0000.000
166A662VAL0-0.006-0.00439.063-0.001-0.0010.0000.0000.0000.000
167A663ARG10.8940.93242.514-0.015-0.0150.0000.0000.0000.000
168A664GLY0-0.025-0.01044.1520.0000.0000.0000.0000.0000.000
169A665TRP00.0490.03445.3910.0000.0000.0000.0000.0000.000
170A666CYS0-0.114-0.04145.8180.0020.0020.0000.0000.0000.000
171A667LYS11.0200.99947.488-0.023-0.0230.0000.0000.0000.000
172A668ASN00.0670.02047.6810.0010.0010.0000.0000.0000.000
173A669LYS11.0271.02447.435-0.026-0.0260.0000.0000.0000.000
174A670ARG10.9170.96142.985-0.039-0.0390.0000.0000.0000.000
175A671VAL00.0300.00742.1850.0020.0020.0000.0000.0000.000
176A672GLY00.0110.00442.3590.0010.0010.0000.0000.0000.000
177A673LYS10.9320.99041.697-0.037-0.0370.0000.0000.0000.000
178A674GLN00.0330.04538.3420.0040.0040.0000.0000.0000.000
179A675LEU00.0400.02437.9320.0010.0010.0000.0000.0000.000
180A676ALA0-0.011-0.00538.2420.0000.0000.0000.0000.0000.000
181A677SER00.025-0.01836.7000.0000.0000.0000.0000.0000.000
182A678GLN0-0.060-0.03633.9570.0010.0010.0000.0000.0000.000
183A679LYS10.9410.98533.881-0.025-0.0250.0000.0000.0000.000
184A680ILE00.0120.01334.7890.0000.0000.0000.0000.0000.000
185A681LEU00.0190.01330.3260.0010.0010.0000.0000.0000.000
186A682GLN0-0.025-0.01228.1410.0030.0030.0000.0000.0000.000
187A683LEU0-0.038-0.04230.753-0.002-0.0020.0000.0000.0000.000
188A684LEU0-0.012-0.00131.234-0.001-0.0010.0000.0000.0000.000
189A685HIS10.7780.88326.021-0.064-0.0640.0000.0000.0000.000
190A686PRO00.0150.00527.3760.0020.0020.0000.0000.0000.000
191A687HIS00.0110.01223.886-0.005-0.0050.0000.0000.0000.000
192A688VAL00.0120.01422.7840.0050.0050.0000.0000.0000.000
193A689LYS10.9620.98623.639-0.046-0.0460.0000.0000.0000.000
194A690ASN0-0.032-0.02020.7250.0030.0030.0000.0000.0000.000
195A691TRP00.0890.02824.7520.0010.0010.0000.0000.0000.000
196A692GLY00.0530.03022.7180.0030.0030.0000.0000.0000.000
197A693SER0-0.009-0.01421.1220.0170.0170.0000.0000.0000.000
198A694LEU0-0.005-0.00922.0800.0030.0030.0000.0000.0000.000
199A695LEU00.0140.01724.3650.0010.0010.0000.0000.0000.000
200A696ARG10.8410.93817.037-0.205-0.2050.0000.0000.0000.000
201A697MET0-0.048-0.00121.8600.0040.0040.0000.0000.0000.000
202A698TYR00.026-0.00723.814-0.006-0.0060.0000.0000.0000.000
203A699GLY00.0250.01525.657-0.008-0.0080.0000.0000.0000.000
204A700ARG10.9240.97117.373-0.270-0.2700.0000.0000.0000.000
205A701GLU-1-0.868-0.90521.2980.1440.1440.0000.0000.0000.000