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: N1QKQ

Calculation Name: 2V0X-A-Xray372

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: 2023-06-20

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 OptH
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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1755811.572723
FMO2-HF: Nuclear repulsion 1680309.690891
FMO2-HF: Total energy -75501.881832
FMO2-MP2: Total energy -75718.516847


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:465:HIS)


Summations of interaction energy for fragment #1(A:465:HIS)
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.
-2.8-0.1580.12-0.912-1.850.005
Interaction energy analysis for fragmet #1(A:465:HIS)
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 : -0.004
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].
3A467LEU0-0.045-0.0073.597-2.867-0.7720.079-0.768-1.4060.005
4A468THR0-0.021-0.0195.2050.0380.084-0.001-0.004-0.0410.000
5A469THR0-0.009-0.0178.924-0.187-0.1870.0000.0000.0000.000
6A470LEU0-0.038-0.01312.3560.0270.0270.0000.0000.0000.000
7A471GLY00.0050.01415.629-0.071-0.0710.0000.0000.0000.000
8A472VAL00.0280.00715.7230.0650.0650.0000.0000.0000.000
9A473GLU-1-0.969-0.96510.9630.6030.6030.0000.0000.0000.000
10A489PRO0-0.022-0.00931.030-0.002-0.0020.0000.0000.0000.000
11A490SER0-0.012-0.02130.2160.0090.0090.0000.0000.0000.000
12A491PHE00.0260.01824.422-0.014-0.0140.0000.0000.0000.000
13A492PRO0-0.020-0.00526.1480.0130.0130.0000.0000.0000.000
14A493LEU00.0140.00327.3050.0020.0020.0000.0000.0000.000
15A494HIS00.0850.03420.848-0.001-0.0010.0000.0000.0000.000
16A495GLU-1-0.856-0.94225.683-0.041-0.0410.0000.0000.0000.000
17A496SER0-0.020-0.01924.1520.0160.0160.0000.0000.0000.000
18A497ILE00.0010.01225.9860.0120.0120.0000.0000.0000.000
19A498LEU0-0.0070.00128.3830.0080.0080.0000.0000.0000.000
20A499LYS10.9540.98928.975-0.032-0.0320.0000.0000.0000.000
21A500VAL00.0060.00828.1490.0060.0060.0000.0000.0000.000
22A501VAL00.003-0.01031.1410.0030.0030.0000.0000.0000.000
23A502GLU-1-0.966-0.98334.0580.0090.0090.0000.0000.0000.000
24A503GLU-1-0.951-0.99431.4450.0750.0750.0000.0000.0000.000
25A504GLU-1-0.855-0.93234.6810.0770.0770.0000.0000.0000.000
26A505TRP0-0.080-0.05937.166-0.004-0.0040.0000.0000.0000.000
27A506GLN0-0.053-0.01538.358-0.004-0.0040.0000.0000.0000.000
28A507GLN0-0.061-0.04440.840-0.004-0.0040.0000.0000.0000.000
29A508ILE00.0050.01042.1120.0040.0040.0000.0000.0000.000
30A509ASP-1-0.887-0.92443.5180.0450.0450.0000.0000.0000.000
31A510ARG10.9050.96537.174-0.064-0.0640.0000.0000.0000.000
32A511GLN0-0.042-0.03041.873-0.002-0.0020.0000.0000.0000.000
33A512LEU00.0110.01638.8390.0010.0010.0000.0000.0000.000
34A513PRO00.0030.00134.4660.0040.0040.0000.0000.0000.000
35A514SER00.0270.02035.8880.0010.0010.0000.0000.0000.000
36A515VAL00.0750.03031.5780.0090.0090.0000.0000.0000.000
37A516ALA0-0.025-0.01831.7940.0090.0090.0000.0000.0000.000
38A517CYS0-0.048-0.03630.7880.0040.0040.0000.0000.0000.000
39A518ARG10.9670.98926.801-0.199-0.1990.0000.0000.0000.000
40A519TYR0-0.007-0.01825.2390.0130.0130.0000.0000.0000.000
41A520PRO00.0150.02728.699-0.018-0.0180.0000.0000.0000.000
42A521VAL00.0510.03631.3870.0000.0000.0000.0000.0000.000
43A522SER0-0.014-0.00931.2750.0050.0050.0000.0000.0000.000
44A523SER00.000-0.00833.708-0.007-0.0070.0000.0000.0000.000
45A524ILE00.0430.01537.4400.0000.0000.0000.0000.0000.000
46A525GLU-1-0.937-0.97040.4590.0720.0720.0000.0000.0000.000
47A526ALA00.0360.01537.039-0.004-0.0040.0000.0000.0000.000
48A527ALA00.0130.00439.033-0.003-0.0030.0000.0000.0000.000
49A528ARG10.9500.97040.235-0.063-0.0630.0000.0000.0000.000
50A529ILE0-0.038-0.01440.485-0.004-0.0040.0000.0000.0000.000
51A530LEU0-0.024-0.00136.299-0.003-0.0030.0000.0000.0000.000
52A531SER0-0.064-0.01840.6130.0000.0000.0000.0000.0000.000
53A532VAL00.0310.00543.316-0.003-0.0030.0000.0000.0000.000
54A533PRO0-0.048-0.00745.7560.0010.0010.0000.0000.0000.000
55A534LYS10.9570.95948.621-0.061-0.0610.0000.0000.0000.000
56A535VAL00.0030.00951.854-0.001-0.0010.0000.0000.0000.000
57A536ASP-1-0.890-0.94055.2790.0410.0410.0000.0000.0000.000
58A537ASP-1-0.869-0.95057.1210.0430.0430.0000.0000.0000.000
59A538GLU-1-0.939-0.97559.6190.0360.0360.0000.0000.0000.000
60A539ILE0-0.026-0.01759.281-0.002-0.0020.0000.0000.0000.000
61A540LEU00.001-0.00358.147-0.002-0.0020.0000.0000.0000.000
62A541GLY00.0120.00962.149-0.001-0.0010.0000.0000.0000.000
63A542PHE0-0.108-0.04865.105-0.001-0.0010.0000.0000.0000.000
64A543ILE0-0.049-0.01061.894-0.001-0.0010.0000.0000.0000.000
65A544SER0-0.073-0.02764.594-0.001-0.0010.0000.0000.0000.000
66A556SER00.027-0.01067.1570.0000.0000.0000.0000.0000.000
67A557THR0-0.009-0.01062.5780.0000.0000.0000.0000.0000.000
68A558GLU-1-0.809-0.89761.4070.0310.0310.0000.0000.0000.000
69A559SER0-0.033-0.00960.1390.0010.0010.0000.0000.0000.000
70A560CYS0-0.070-0.03758.2080.0010.0010.0000.0000.0000.000
71A561ASP-1-0.830-0.92156.9840.0250.0250.0000.0000.0000.000
72A562LYS10.9750.99756.226-0.036-0.0360.0000.0000.0000.000
73A563HIS10.8470.92853.512-0.031-0.0310.0000.0000.0000.000
74A564LEU0-0.012-0.01752.2660.0010.0010.0000.0000.0000.000
75A565ASP-1-0.865-0.92151.8080.0410.0410.0000.0000.0000.000
76A566LEU00.0070.00948.2240.0020.0020.0000.0000.0000.000
77A567ALA0-0.027-0.01347.8800.0020.0020.0000.0000.0000.000
78A568LEU00.008-0.00146.8450.0010.0010.0000.0000.0000.000
79A569CYS00.0040.01546.7140.0020.0020.0000.0000.0000.000
80A570ARG10.9010.94043.695-0.050-0.0500.0000.0000.0000.000
81A571SER0-0.033-0.02942.3210.0020.0020.0000.0000.0000.000
82A572TYR0-0.058-0.01841.762-0.001-0.0010.0000.0000.0000.000
83A573GLU-1-0.903-0.96040.2000.0790.0790.0000.0000.0000.000
84A574ALA0-0.040-0.02238.0960.0060.0060.0000.0000.0000.000
85A575ALA00.0230.00036.7790.0040.0040.0000.0000.0000.000
86A576ALA0-0.0050.00936.8890.0020.0020.0000.0000.0000.000
87A577SER0-0.006-0.01434.5590.0080.0080.0000.0000.0000.000
88A578ALA00.0000.01132.5220.0090.0090.0000.0000.0000.000
89A579LEU00.0100.01632.0060.0030.0030.0000.0000.0000.000
90A580GLN0-0.072-0.06132.417-0.003-0.0030.0000.0000.0000.000
91A581ILE00.0240.01227.2360.0110.0110.0000.0000.0000.000
92A582ALA00.0210.01627.7630.0100.0100.0000.0000.0000.000
93A583ALA0-0.035-0.02228.1950.0010.0010.0000.0000.0000.000
94A584HIS0-0.035-0.03625.7230.0130.0130.0000.0000.0000.000
95A585THR00.0140.00723.6750.0160.0160.0000.0000.0000.000
96A586ALA0-0.040-0.00923.6820.0010.0010.0000.0000.0000.000
97A587PHE0-0.033-0.01423.076-0.004-0.0040.0000.0000.0000.000
98A588VAL00.0530.02619.1330.0050.0050.0000.0000.0000.000
99A589ALA00.0170.01519.8590.0080.0080.0000.0000.0000.000
100A590LYS10.9080.94720.348-0.082-0.0820.0000.0000.0000.000
101A591SER0-0.041-0.01019.5250.0050.0050.0000.0000.0000.000
102A592LEU00.0530.03414.3000.0090.0090.0000.0000.0000.000
103A593GLN0-0.017-0.01416.232-0.006-0.0060.0000.0000.0000.000
104A594ALA0-0.029-0.02218.242-0.018-0.0180.0000.0000.0000.000
105A595ASP-1-0.849-0.94013.9100.3200.3200.0000.0000.0000.000
106A596ILE0-0.014-0.00913.282-0.003-0.0030.0000.0000.0000.000
107A597SER0-0.027-0.00514.628-0.036-0.0360.0000.0000.0000.000
108A598GLN00.0100.01415.482-0.008-0.0080.0000.0000.0000.000
109A599ALA00.012-0.00910.8960.0040.0040.0000.0000.0000.000
110A600ALA0-0.0090.00212.931-0.031-0.0310.0000.0000.0000.000
111A601GLN0-0.033-0.03514.756-0.015-0.0150.0000.0000.0000.000
112A602ILE0-0.064-0.02212.7790.0060.0060.0000.0000.0000.000
113A603ILE0-0.004-0.0069.461-0.012-0.0120.0000.0000.0000.000
114A604ASN0-0.039-0.01613.000-0.061-0.0610.0000.0000.0000.000
115A605SER0-0.089-0.02916.588-0.018-0.0180.0000.0000.0000.000
116A606ASP-1-0.859-0.90416.8690.0170.0170.0000.0000.0000.000
117A607PRO00.0190.01712.2800.0350.0350.0000.0000.0000.000
118A608SER0-0.036-0.04512.347-0.037-0.0370.0000.0000.0000.000
119A609ASP-1-0.932-0.96011.9680.3240.3240.0000.0000.0000.000
120A610ALA0-0.003-0.0176.7870.0610.0610.0000.0000.0000.000
121A611GLN00.027-0.0046.8740.0450.0450.0000.0000.0000.000
122A612GLN0-0.0310.0018.8640.1090.1090.0000.0000.0000.000
123A613ALA00.0640.0229.0520.0570.0570.0000.0000.0000.000
124A614LEU00.013-0.0083.253-0.666-0.1650.042-0.140-0.4030.000
125A615ARG10.9651.0016.264-0.508-0.5080.0000.0000.0000.000
126A616ILE0-0.083-0.0508.877-0.018-0.0180.0000.0000.0000.000
127A617LEU00.0520.0226.101-0.031-0.0310.0000.0000.0000.000
128A618ASN00.0210.0316.9730.1970.1970.0000.0000.0000.000
129A619ARG10.9200.9647.947-0.477-0.4770.0000.0000.0000.000
130A620THR0-0.043-0.0269.795-0.083-0.0830.0000.0000.0000.000
131A621TYR00.007-0.0018.275-0.069-0.0690.0000.0000.0000.000
132A622ASP-1-0.861-0.92210.3790.5700.5700.0000.0000.0000.000
133A623ALA00.0240.00813.025-0.070-0.0700.0000.0000.0000.000
134A624ALA0-0.032-0.02313.268-0.056-0.0560.0000.0000.0000.000
135A625SER00.006-0.00813.976-0.040-0.0400.0000.0000.0000.000
136A626TYR00.0270.02015.858-0.053-0.0530.0000.0000.0000.000
137A627LEU0-0.040-0.02018.089-0.042-0.0420.0000.0000.0000.000
138A628CYS0-0.045-0.01418.494-0.047-0.0470.0000.0000.0000.000
139A629ASP-1-0.864-0.93820.0820.2700.2700.0000.0000.0000.000
140A630ALA00.008-0.00422.106-0.021-0.0210.0000.0000.0000.000
141A631ALA0-0.034-0.01123.457-0.021-0.0210.0000.0000.0000.000
142A632PHE0-0.035-0.03622.174-0.025-0.0250.0000.0000.0000.000
143A633ASP-1-0.844-0.88726.4420.1570.1570.0000.0000.0000.000
144A634GLU-1-0.887-0.94928.0940.0640.0640.0000.0000.0000.000
145A635VAL0-0.043-0.02028.460-0.012-0.0120.0000.0000.0000.000
146A636ARG10.8840.94529.012-0.108-0.1080.0000.0000.0000.000
147A637MET00.0040.00432.558-0.006-0.0060.0000.0000.0000.000
148A638SER00.0380.01433.801-0.009-0.0090.0000.0000.0000.000
149A639ALA0-0.0190.00034.861-0.007-0.0070.0000.0000.0000.000
150A640CYS00.0120.01136.468-0.003-0.0030.0000.0000.0000.000
151A641ALA00.0510.02538.532-0.004-0.0040.0000.0000.0000.000
152A642MET0-0.051-0.02638.532-0.005-0.0050.0000.0000.0000.000
153A643GLY00.0160.01140.983-0.004-0.0040.0000.0000.0000.000
154A644SER00.0240.00142.666-0.001-0.0010.0000.0000.0000.000
155A645SER00.0030.01344.409-0.003-0.0030.0000.0000.0000.000
156A646THR0-0.041-0.03044.431-0.004-0.0040.0000.0000.0000.000
157A647MET00.0130.00746.829-0.002-0.0020.0000.0000.0000.000
158A648GLY00.0400.01348.722-0.001-0.0010.0000.0000.0000.000
159A649ARG10.9440.96248.322-0.009-0.0090.0000.0000.0000.000
160A650ARG10.7790.87846.931-0.019-0.0190.0000.0000.0000.000
161A651TYR00.0270.00451.946-0.002-0.0020.0000.0000.0000.000
162A652LEU00.0120.00054.808-0.001-0.0010.0000.0000.0000.000
163A653TRP0-0.044-0.02354.338-0.002-0.0020.0000.0000.0000.000
164A654LEU0-0.044-0.01355.805-0.002-0.0020.0000.0000.0000.000
165A655LYS10.8780.92859.063-0.014-0.0140.0000.0000.0000.000
166A656ASP-1-0.827-0.89861.1630.0130.0130.0000.0000.0000.000
167A657CYS0-0.0530.01161.5610.0000.0000.0000.0000.0000.000
168A658LYS10.9550.95264.618-0.011-0.0110.0000.0000.0000.000
169A659ILE00.0440.01861.073-0.001-0.0010.0000.0000.0000.000
170A660SER00.0340.01363.6680.0010.0010.0000.0000.0000.000
171A661PRO00.0450.00261.4100.0000.0000.0000.0000.0000.000
172A662ALA00.0210.02259.4620.0010.0010.0000.0000.0000.000
173A663SER00.0670.02458.0680.0010.0010.0000.0000.0000.000
174A664LYS10.8680.95257.294-0.015-0.0150.0000.0000.0000.000
175A665ASN00.0260.02454.2470.0020.0020.0000.0000.0000.000
176A666LYS10.9460.96552.680-0.018-0.0180.0000.0000.0000.000
177A667LEU0-0.002-0.00652.3400.0000.0000.0000.0000.0000.000
178A668THR0-0.034-0.03651.656-0.001-0.0010.0000.0000.0000.000
179A669VAL00.0060.00649.0930.0010.0010.0000.0000.0000.000
180A670ALA0-0.0310.00947.7210.0020.0020.0000.0000.0000.000
181A671PRO00.0620.04743.0470.0000.0000.0000.0000.0000.000
182A672PHE0-0.074-0.01741.822-0.005-0.0050.0000.0000.0000.000
183A673LYS10.9840.98940.743-0.001-0.0010.0000.0000.0000.000
184A674GLY00.0770.04740.794-0.004-0.0040.0000.0000.0000.000
185A675GLY0-0.011-0.00342.086-0.002-0.0020.0000.0000.0000.000
186A676THR0-0.030-0.02644.4360.0010.0010.0000.0000.0000.000
187A677LEU0-0.0030.00347.0260.0020.0020.0000.0000.0000.000
188A678PHE00.0580.01948.6500.0030.0030.0000.0000.0000.000
189A679GLY0-0.0140.01247.1700.0010.0010.0000.0000.0000.000
190A680GLY0-0.028-0.03148.029-0.003-0.0030.0000.0000.0000.000
191A681GLU-1-0.901-0.93651.1150.0070.0070.0000.0000.0000.000
192A682VAL00.008-0.01652.6600.0000.0000.0000.0000.0000.000
193A683HIS0-0.018-0.01255.1960.0000.0000.0000.0000.0000.000
194A684LYS10.9050.97057.3180.0030.0030.0000.0000.0000.000
195A685VAL0-0.0050.00358.7140.0010.0010.0000.0000.0000.000