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: 59LKZ

Calculation Name: 2V0X-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2V0X

Chain ID: A

ChEMBL ID:

UniProt ID: Q61033

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 201
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1775534.654977
FMO2-HF: Nuclear repulsion 1699519.968833
FMO2-HF: Total energy -76014.686143
FMO2-MP2: Total energy -76232.958411


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:464:ACE )


Summations of interaction energy for fragment #1(A:464:ACE )
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.
6.232-0.97414.865-5.134-2.526-0.008
Interaction energy analysis for fragmet #1(A:464:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.060
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].
3A466SER 0-0.044-0.0013.6030.9021.450-0.0080.092-0.633-0.001
4A467LEU 0-0.0220.0094.3760.3400.4880.000-0.013-0.1350.000
5A468THR 0-0.019-0.0176.443-0.002-0.0020.0000.0000.0000.000
6A469THR 0-0.009-0.0159.7570.0230.0230.0000.0000.0000.000
7A470LEU 0-0.041-0.01513.1820.0070.0070.0000.0000.0000.000
8A471GLY 00.0080.01516.608-0.001-0.0010.0000.0000.0000.000
9A472VAL 00.0260.00217.185-0.002-0.0020.0000.0000.0000.000
10A473GLU -1-0.939-0.95413.451-0.129-0.1290.0000.0000.0000.000
11A474NME 0-0.038-0.01613.694-0.007-0.0070.0000.0000.0000.000
12A488ACE 00.0380.00734.7420.0000.0000.0000.0000.0000.000
13A489PRO 0-0.034-0.00334.200-0.004-0.0040.0000.0000.0000.000
14A490SER 0-0.032-0.02634.5990.0050.0050.0000.0000.0000.000
15A491PHE 00.0200.01127.818-0.006-0.0060.0000.0000.0000.000
16A492PRO 0-0.016-0.00331.1280.0050.0050.0000.0000.0000.000
17A493LEU 00.0130.00231.722-0.004-0.0040.0000.0000.0000.000
18A494HIS 00.0850.03425.3720.0070.0070.0000.0000.0000.000
19A495GLU -1-0.853-0.94130.502-0.052-0.0520.0000.0000.0000.000
20A496SER 0-0.020-0.02028.4140.0050.0050.0000.0000.0000.000
21A497ILE 00.0000.01229.0560.0050.0050.0000.0000.0000.000
22A498LEU 0-0.0070.00131.9730.0050.0050.0000.0000.0000.000
23A499LYS 10.9530.98933.1630.0380.0380.0000.0000.0000.000
24A500VAL 00.0090.00831.1530.0040.0040.0000.0000.0000.000
25A501VAL 0-0.004-0.01234.4010.0040.0040.0000.0000.0000.000
26A502GLU -1-0.961-0.98137.378-0.029-0.0290.0000.0000.0000.000
27A503GLU -1-0.951-0.99434.863-0.025-0.0250.0000.0000.0000.000
28A504GLU -1-0.854-0.93237.023-0.017-0.0170.0000.0000.0000.000
29A505TRP 0-0.086-0.06139.8730.0020.0020.0000.0000.0000.000
30A506GLN 0-0.050-0.01442.1210.0020.0020.0000.0000.0000.000
31A507GLN 0-0.059-0.04343.7980.0010.0010.0000.0000.0000.000
32A508ILE 00.0090.01244.4920.0000.0000.0000.0000.0000.000
33A509ASP -1-0.896-0.92745.903-0.009-0.0090.0000.0000.0000.000
34A510ARG 10.9080.96539.4860.0170.0170.0000.0000.0000.000
35A511GLN 0-0.044-0.03143.1030.0000.0000.0000.0000.0000.000
36A512LEU 00.0110.01740.216-0.001-0.0010.0000.0000.0000.000
37A513PRO 00.0040.00235.7710.0020.0020.0000.0000.0000.000
38A514SER 00.0260.02036.8920.0000.0000.0000.0000.0000.000
39A515VAL 00.0750.03032.6810.0000.0000.0000.0000.0000.000
40A516ALA 0-0.026-0.01832.7040.0010.0010.0000.0000.0000.000
41A517CYS 0-0.045-0.03531.3380.0030.0030.0000.0000.0000.000
42A518ARG 10.9660.98927.7380.0020.0020.0000.0000.0000.000
43A519TYR 0-0.006-0.01826.4310.0010.0010.0000.0000.0000.000
44A520PRO 00.0150.02829.311-0.001-0.0010.0000.0000.0000.000
45A521VAL 00.0540.03632.036-0.001-0.0010.0000.0000.0000.000
46A522SER 0-0.016-0.00831.7850.0030.0030.0000.0000.0000.000
47A523SER 0-0.001-0.00934.206-0.001-0.0010.0000.0000.0000.000
48A524ILE 00.0440.01537.879-0.001-0.0010.0000.0000.0000.000
49A525GLU -1-0.936-0.96941.0570.0010.0010.0000.0000.0000.000
50A526ALA 00.0370.01537.868-0.001-0.0010.0000.0000.0000.000
51A527ALA 00.0100.00439.812-0.001-0.0010.0000.0000.0000.000
52A528ARG 10.9550.97240.9610.0010.0010.0000.0000.0000.000
53A529ILE 0-0.040-0.01541.529-0.001-0.0010.0000.0000.0000.000
54A530LEU 0-0.023-0.00137.238-0.001-0.0010.0000.0000.0000.000
55A531SER 0-0.064-0.01841.6530.0000.0000.0000.0000.0000.000
56A532VAL 00.0250.00344.317-0.001-0.0010.0000.0000.0000.000
57A533PRO 0-0.042-0.00546.9010.0010.0010.0000.0000.0000.000
58A534LYS 10.9570.95949.7300.0000.0000.0000.0000.0000.000
59A535VAL 00.0020.00952.9070.0000.0000.0000.0000.0000.000
60A536ASP -1-0.889-0.94056.396-0.003-0.0030.0000.0000.0000.000
61A537ASP -1-0.868-0.94958.1340.0000.0000.0000.0000.0000.000
62A538GLU -1-0.937-0.97460.532-0.001-0.0010.0000.0000.0000.000
63A539ILE 0-0.026-0.01760.4570.0000.0000.0000.0000.0000.000
64A540LEU 00.003-0.00259.1700.0000.0000.0000.0000.0000.000
65A541GLY 00.0230.01563.2350.0000.0000.0000.0000.0000.000
66A542PHE 0-0.106-0.05166.2090.0000.0000.0000.0000.0000.000
67A543ILE 0-0.049-0.01563.1100.0000.0000.0000.0000.0000.000
68A544SER 0-0.061-0.03165.6630.0000.0000.0000.0000.0000.000
69A545NME 0-0.0340.00168.1440.0000.0000.0000.0000.0000.000
70A555ACE 00.0510.01970.6860.0000.0000.0000.0000.0000.000
71A556SER 0-0.032-0.04268.7390.0000.0000.0000.0000.0000.000
72A557THR 0-0.010-0.00564.2280.0000.0000.0000.0000.0000.000
73A558GLU -1-0.804-0.89062.802-0.005-0.0050.0000.0000.0000.000
74A559SER 0-0.027-0.00661.6250.0000.0000.0000.0000.0000.000
75A560CYS 0-0.071-0.03959.764-0.001-0.0010.0000.0000.0000.000
76A561ASP -1-0.830-0.92158.580-0.008-0.0080.0000.0000.0000.000
77A562LYS 10.9770.99857.6200.0040.0040.0000.0000.0000.000
78A563HIS 10.8480.92855.0410.0080.0080.0000.0000.0000.000
79A564LEU 0-0.011-0.01753.846-0.001-0.0010.0000.0000.0000.000
80A565ASP -1-0.867-0.92253.383-0.007-0.0070.0000.0000.0000.000
81A566LEU 00.0060.01049.5940.0000.0000.0000.0000.0000.000
82A567ALA 0-0.027-0.01349.4750.0000.0000.0000.0000.0000.000
83A568LEU 00.0090.00048.437-0.001-0.0010.0000.0000.0000.000
84A569CYS 00.0050.01448.2150.0000.0000.0000.0000.0000.000
85A570ARG 10.9020.94045.2160.0090.0090.0000.0000.0000.000
86A571SER 0-0.035-0.02943.821-0.001-0.0010.0000.0000.0000.000
87A572TYR 0-0.054-0.01743.319-0.002-0.0020.0000.0000.0000.000
88A573GLU -1-0.909-0.96141.457-0.007-0.0070.0000.0000.0000.000
89A574ALA 0-0.034-0.02139.5580.0000.0000.0000.0000.0000.000
90A575ALA 00.018-0.00138.280-0.002-0.0020.0000.0000.0000.000
91A576ALA 0-0.0010.01038.338-0.001-0.0010.0000.0000.0000.000
92A577SER 0-0.009-0.01535.8670.0010.0010.0000.0000.0000.000
93A578ALA 0-0.0020.01034.0160.0000.0000.0000.0000.0000.000
94A579LEU 00.0140.01833.454-0.002-0.0020.0000.0000.0000.000
95A580GLN 0-0.076-0.06233.547-0.001-0.0010.0000.0000.0000.000
96A581ILE 00.0250.01228.5910.0020.0020.0000.0000.0000.000
97A582ALA 00.0200.01629.036-0.002-0.0020.0000.0000.0000.000
98A583ALA 0-0.032-0.02129.497-0.002-0.0020.0000.0000.0000.000
99A584HIS 0-0.035-0.03626.7300.0000.0000.0000.0000.0000.000
100A585THR 00.0120.00625.081-0.002-0.0020.0000.0000.0000.000
101A586ALA 0-0.038-0.00824.929-0.005-0.0050.0000.0000.0000.000
102A587PHE 0-0.033-0.01423.496-0.002-0.0020.0000.0000.0000.000
103A588VAL 00.0510.02620.0860.0020.0020.0000.0000.0000.000
104A589ALA 00.0190.01520.849-0.006-0.0060.0000.0000.0000.000
105A590LYS 10.9100.94821.4770.0300.0300.0000.0000.0000.000
106A591SER 0-0.043-0.01220.0360.0010.0010.0000.0000.0000.000
107A592LEU 00.0510.03315.6590.0020.0020.0000.0000.0000.000
108A593GLN 0-0.016-0.01317.135-0.006-0.0060.0000.0000.0000.000
109A594ALA 0-0.029-0.02219.000-0.005-0.0050.0000.0000.0000.000
110A595ASP -1-0.850-0.94114.2660.0320.0320.0000.0000.0000.000
111A596ILE 0-0.015-0.01014.309-0.003-0.0030.0000.0000.0000.000
112A597SER 0-0.026-0.00415.275-0.012-0.0120.0000.0000.0000.000
113A598GLN 00.0110.01415.374-0.005-0.0050.0000.0000.0000.000
114A599ALA 00.012-0.01011.0980.0190.0190.0000.0000.0000.000
115A600ALA 0-0.0100.00312.936-0.012-0.0120.0000.0000.0000.000
116A601GLN 0-0.031-0.03415.083-0.001-0.0010.0000.0000.0000.000
117A602ILE 0-0.070-0.02511.7900.0180.0180.0000.0000.0000.000
118A603ILE 0-0.004-0.0069.811-0.001-0.0010.0000.0000.0000.000
119A604ASN 0-0.036-0.01412.601-0.025-0.0250.0000.0000.0000.000
120A605SER 0-0.086-0.02916.1910.0000.0000.0000.0000.0000.000
121A606ASP -1-0.862-0.90515.6510.0470.0470.0000.0000.0000.000
122A607PRO 00.0260.02111.5610.0210.0210.0000.0000.0000.000
123A608SER 0-0.037-0.04710.705-0.013-0.0130.0000.0000.0000.000
124A609ASP -1-0.933-0.96010.0290.2810.2810.0000.0000.0000.000
125A610ALA 0-0.003-0.0175.2550.0480.0480.0000.0000.0000.000
126A611GLN 00.023-0.0064.430-0.172-0.1210.000-0.015-0.0360.000
127A612GLN 0-0.0300.0016.856-0.018-0.0180.0000.0000.0000.000
128A613ALA 00.0620.0228.361-0.013-0.0130.0000.0000.0000.000
129A614LEU 00.0070.0322.0095.873-2.08014.873-5.198-1.722-0.007
130A615ARG 10.9610.9995.435-0.513-0.5130.0000.0000.0000.000
131A616ILE 0-0.081-0.0497.793-0.112-0.1120.0000.0000.0000.000
132A617LEU 00.0560.0236.774-0.053-0.0530.0000.0000.0000.000
133A618ASN 00.0180.0286.740-0.137-0.1370.0000.0000.0000.000
134A619ARG 10.9210.9658.307-0.115-0.1150.0000.0000.0000.000
135A620THR 0-0.044-0.02610.852-0.045-0.0450.0000.0000.0000.000
136A621TYR 00.0210.0089.803-0.015-0.0150.0000.0000.0000.000
137A622ASP -1-0.864-0.92311.8300.0160.0160.0000.0000.0000.000
138A623ALA 00.0260.00814.078-0.001-0.0010.0000.0000.0000.000
139A624ALA 0-0.031-0.02315.0500.0020.0020.0000.0000.0000.000
140A625SER 00.002-0.01015.614-0.005-0.0050.0000.0000.0000.000
141A626TYR 00.0280.02017.4980.0080.0080.0000.0000.0000.000
142A627LEU 0-0.039-0.01919.6490.0040.0040.0000.0000.0000.000
143A628CYS 0-0.046-0.01520.4750.0040.0040.0000.0000.0000.000
144A629ASP -1-0.863-0.93721.494-0.044-0.0440.0000.0000.0000.000
145A630ALA 0-0.003-0.00723.7430.0050.0050.0000.0000.0000.000
146A631ALA 0-0.025-0.00825.1940.0030.0030.0000.0000.0000.000
147A632PHE 0-0.031-0.03524.8800.0030.0030.0000.0000.0000.000
148A633ASP -1-0.846-0.88828.111-0.021-0.0210.0000.0000.0000.000
149A634GLU -1-0.889-0.95029.776-0.027-0.0270.0000.0000.0000.000
150A635VAL 0-0.039-0.01930.7530.0020.0020.0000.0000.0000.000
151A636ARG 10.8810.94431.2190.0290.0290.0000.0000.0000.000
152A637MET 00.0110.00634.0810.0020.0020.0000.0000.0000.000
153A638SER 00.0320.01235.6340.0020.0020.0000.0000.0000.000
154A639ALA 0-0.0130.00237.0600.0010.0010.0000.0000.0000.000
155A640CYS 00.0040.00938.1500.0020.0020.0000.0000.0000.000
156A641ALA 00.0550.02640.2670.0020.0020.0000.0000.0000.000
157A642MET 0-0.048-0.02440.9240.0000.0000.0000.0000.0000.000
158A643GLY 00.0170.01242.9930.0010.0010.0000.0000.0000.000
159A644SER 00.0250.00044.5290.0020.0020.0000.0000.0000.000
160A645SER 0-0.0010.01246.2090.0010.0010.0000.0000.0000.000
161A646THR 0-0.040-0.02946.9080.0010.0010.0000.0000.0000.000
162A647MET 00.0100.00648.9670.0010.0010.0000.0000.0000.000
163A648GLY 00.0460.01550.6850.0010.0010.0000.0000.0000.000
164A649ARG 10.9400.96150.7610.0190.0190.0000.0000.0000.000
165A650ARG 10.7830.88050.3450.0170.0170.0000.0000.0000.000
166A651TYR 00.0220.00253.7780.0010.0010.0000.0000.0000.000
167A652LEU 00.0120.00056.7520.0000.0000.0000.0000.0000.000
168A653TRP 0-0.043-0.02156.6990.0000.0000.0000.0000.0000.000
169A654LEU 0-0.045-0.01358.7080.0000.0000.0000.0000.0000.000
170A655LYS 10.8770.92861.6110.0100.0100.0000.0000.0000.000
171A656ASP -1-0.833-0.90163.274-0.008-0.0080.0000.0000.0000.000
172A657CYS 0-0.0480.01364.6060.0000.0000.0000.0000.0000.000
173A658LYS 10.9560.95467.3590.0080.0080.0000.0000.0000.000
174A659ILE 00.0440.01964.2580.0000.0000.0000.0000.0000.000
175A660SER 00.0310.01566.8760.0000.0000.0000.0000.0000.000
176A661PRO 00.0540.00764.0200.0000.0000.0000.0000.0000.000
177A662ALA 00.0190.02262.2230.0000.0000.0000.0000.0000.000
178A663SER 00.0630.01661.2540.0000.0000.0000.0000.0000.000
179A664LYS 10.8640.95060.6070.0080.0080.0000.0000.0000.000
180A665ASN 00.0240.02356.9680.0000.0000.0000.0000.0000.000
181A666LYS 10.9490.96756.3060.0110.0110.0000.0000.0000.000
182A667LEU 0-0.002-0.00555.721-0.001-0.0010.0000.0000.0000.000
183A668THR 0-0.036-0.03754.088-0.001-0.0010.0000.0000.0000.000
184A669VAL 00.0030.00451.8340.0000.0000.0000.0000.0000.000
185A670ALA 0-0.0280.01050.8250.0000.0000.0000.0000.0000.000
186A671PRO 00.0670.04946.8820.0000.0000.0000.0000.0000.000
187A672PHE 0-0.082-0.01944.7780.0000.0000.0000.0000.0000.000
188A673LYS 10.9890.99044.7630.0210.0210.0000.0000.0000.000
189A674GLY 00.0750.04644.868-0.002-0.0020.0000.0000.0000.000
190A675GLY 0-0.009-0.00245.8080.0010.0010.0000.0000.0000.000
191A676THR 0-0.031-0.02648.4240.0010.0010.0000.0000.0000.000
192A677LEU 0-0.0040.00350.6750.0000.0000.0000.0000.0000.000
193A678PHE 00.0600.01951.9390.0000.0000.0000.0000.0000.000
194A679GLY 0-0.0140.01251.3050.0000.0000.0000.0000.0000.000
195A680GLY 0-0.028-0.03152.130-0.001-0.0010.0000.0000.0000.000
196A681GLU -1-0.901-0.93755.507-0.013-0.0130.0000.0000.0000.000
197A682VAL 00.005-0.01757.5700.0010.0010.0000.0000.0000.000
198A683HIS 0-0.019-0.01259.9660.0010.0010.0000.0000.0000.000
199A684LYS 10.9060.96661.3960.0140.0140.0000.0000.0000.000
200A685VAL 0-0.033-0.01762.9670.0010.0010.0000.0000.0000.000
201A686NME 00.0270.02565.5210.0000.0000.0000.0000.0000.000