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: 5387Z

Calculation Name: 2GEF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GEF

Chain ID: A

ChEMBL ID:

UniProt ID: Q8AZM0

Base Structure: X-ray

Registration Date: 2023-06-19

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2127715.205036
FMO2-HF: Nuclear repulsion 2052732.735748
FMO2-HF: Total energy -74982.469287
FMO2-MP2: Total energy -75201.185058


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:559:ASP)


Summations of interaction energy for fragment #1(A:559: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.
28.44930.6110.018-1.111-1.0690.004
Interaction energy analysis for fragmet #1(A:559:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.962 / q_NPA : -0.985
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].
3A561PRO0-0.029-0.0263.5080.3592.5210.018-1.111-1.0690.004
4A562ILE00.0500.0405.9080.3300.3300.0000.0000.0000.000
5A563SER0-0.019-0.0167.916-1.904-1.9040.0000.0000.0000.000
6A564LEU0-0.024-0.01911.401-0.319-0.3190.0000.0000.0000.000
7A565LEU00.0110.01013.876-0.591-0.5910.0000.0000.0000.000
8A566GLN0-0.023-0.02617.6050.6290.6290.0000.0000.0000.000
9A567THR0-0.001-0.00219.508-0.204-0.2040.0000.0000.0000.000
10A568LEU00.0180.02720.8330.1660.1660.0000.0000.0000.000
11A569ALA0-0.0090.00024.502-0.341-0.3410.0000.0000.0000.000
12A570TYR0-0.049-0.02627.9930.0650.0650.0000.0000.0000.000
13A571LYS10.8620.93129.375-9.515-9.5150.0000.0000.0000.000
14A572GLN00.0520.03031.5050.1430.1430.0000.0000.0000.000
15A573PRO00.0220.00332.000-0.120-0.1200.0000.0000.0000.000
16A574LEU0-0.0400.00334.573-0.162-0.1620.0000.0000.0000.000
17A575GLY00.0200.01437.4280.1490.1490.0000.0000.0000.000
18A576ARG10.8210.86439.117-7.660-7.6600.0000.0000.0000.000
19A577ASN0-0.073-0.04641.848-0.054-0.0540.0000.0000.0000.000
20A578SER0-0.052-0.03843.829-0.033-0.0330.0000.0000.0000.000
21A579ARG10.9620.99144.303-6.765-6.7650.0000.0000.0000.000
22A580ILE00.0330.01844.8070.1220.1220.0000.0000.0000.000
23A581VAL0-0.050-0.01743.421-0.136-0.1360.0000.0000.0000.000
24A582HIS0-0.0120.00045.1730.0360.0360.0000.0000.0000.000
25A583PHE0-0.008-0.01240.9940.0120.0120.0000.0000.0000.000
26A584THR00.023-0.02344.310-0.056-0.0560.0000.0000.0000.000
27A585ASP-1-0.929-0.96340.5817.1937.1930.0000.0000.0000.000
28A586GLY00.0370.01837.441-0.012-0.0120.0000.0000.0000.000
29A587ALA0-0.0180.00033.3270.0110.0110.0000.0000.0000.000
30A588LEU00.0290.02433.2070.1260.1260.0000.0000.0000.000
31A589PHE00.0050.00627.2400.2710.2710.0000.0000.0000.000
32A590PRO0-0.0230.00425.642-0.107-0.1070.0000.0000.0000.000
33A591VAL0-0.007-0.00425.9240.4150.4150.0000.0000.0000.000
34A592VAL0-0.024-0.01521.861-0.205-0.2050.0000.0000.0000.000
35A593ALA0-0.005-0.00323.7590.2310.2310.0000.0000.0000.000
36A594PHE0-0.027-0.02420.154-0.172-0.1720.0000.0000.0000.000
37A595GLY00.0360.02823.8180.0350.0350.0000.0000.0000.000
38A596ASP-1-0.880-0.93125.19711.64911.6490.0000.0000.0000.000
39A597ASN0-0.091-0.05426.550-0.394-0.3940.0000.0000.0000.000
40A598HIS00.0370.00828.218-0.227-0.2270.0000.0000.0000.000
41A599SER00.0410.02724.7640.4480.4480.0000.0000.0000.000
42A600THR00.0130.00026.583-0.327-0.3270.0000.0000.0000.000
43A601SER0-0.040-0.05126.7330.4020.4020.0000.0000.0000.000
44A602GLU-1-0.846-0.91128.5188.7168.7160.0000.0000.0000.000
45A603LEU00.0000.00530.0630.3560.3560.0000.0000.0000.000
46A604TYR00.0770.03230.852-0.103-0.1030.0000.0000.0000.000
47A605ILE0-0.0140.00332.7660.1540.1540.0000.0000.0000.000
48A606ALA0-0.007-0.00431.8280.0270.0270.0000.0000.0000.000
49A607VAL00.0390.01733.952-0.071-0.0710.0000.0000.0000.000
50A608ARG10.8380.90136.991-7.383-7.3830.0000.0000.0000.000
51A609GLY00.0350.02138.209-0.216-0.2160.0000.0000.0000.000
52A610ASP-1-0.963-1.00638.7187.4217.4210.0000.0000.0000.000
53A611HIS00.0660.03339.548-0.229-0.2290.0000.0000.0000.000
54A612ARG10.9460.93437.988-7.633-7.6330.0000.0000.0000.000
55A613ASP-1-0.967-0.97240.4806.8256.8250.0000.0000.0000.000
56A614LEU00.0020.01041.062-0.114-0.1140.0000.0000.0000.000
57A615MET0-0.070-0.00534.8680.0660.0660.0000.0000.0000.000
58A616SER00.011-0.01337.591-0.256-0.2560.0000.0000.0000.000
59A617PRO0-0.044-0.04738.5630.0920.0920.0000.0000.0000.000
60A618ASP-1-0.874-0.90936.2597.8487.8480.0000.0000.0000.000
61A619VAL0-0.008-0.01232.3270.2380.2380.0000.0000.0000.000
62A620ARG10.9100.94634.299-7.047-7.0470.0000.0000.0000.000
63A621ASP-1-0.912-0.93035.8737.7517.7510.0000.0000.0000.000
64A622SER0-0.0240.00429.6800.2200.2200.0000.0000.0000.000
65A623TYR0-0.018-0.02630.662-0.213-0.2130.0000.0000.0000.000
66A624ALA0-0.0320.00426.1150.2510.2510.0000.0000.0000.000
67A625LEU0-0.002-0.01927.387-0.356-0.3560.0000.0000.0000.000
68A626THR00.006-0.00226.8570.4330.4330.0000.0000.0000.000
69A627GLY00.024-0.00226.9740.0550.0550.0000.0000.0000.000
70A628ASP-1-0.872-0.93427.6709.1879.1870.0000.0000.0000.000
71A629ASP-1-0.842-0.89430.2729.5149.5140.0000.0000.0000.000
72A630HIS10.8550.93431.876-8.663-8.6630.0000.0000.0000.000
73A631LYS10.9230.96331.685-8.217-8.2170.0000.0000.0000.000
74A632VAL00.0340.03829.524-0.183-0.1830.0000.0000.0000.000
75A633TRP00.016-0.02131.1500.2640.2640.0000.0000.0000.000
76A634GLY00.0710.02232.082-0.047-0.0470.0000.0000.0000.000
77A635ALA0-0.045-0.00127.1580.1990.1990.0000.0000.0000.000
78A636THR00.022-0.01724.499-0.266-0.2660.0000.0000.0000.000
79A637HIS00.0030.02121.5730.5980.5980.0000.0000.0000.000
80A651LYS10.8120.88322.890-10.524-10.5240.0000.0000.0000.000
81A652PHE0-0.053-0.04322.5030.6360.6360.0000.0000.0000.000
82A653ASN0-0.0040.00520.681-0.662-0.6620.0000.0000.0000.000
83A654VAL00.0260.00223.623-0.306-0.3060.0000.0000.0000.000
84A655LYS10.8760.96626.431-10.975-10.9750.0000.0000.0000.000
85A656THR00.0550.00430.2130.0050.0050.0000.0000.0000.000
86A657ARG10.9000.94832.992-8.269-8.2690.0000.0000.0000.000
87A658THR0-0.047-0.02935.319-0.361-0.3610.0000.0000.0000.000
88A659ASP-1-0.821-0.88934.9398.4828.4820.0000.0000.0000.000
89A660LEU0-0.0110.00232.377-0.087-0.0870.0000.0000.0000.000
90A661THR00.0040.00734.7700.0610.0610.0000.0000.0000.000
91A662ILE0-0.068-0.02129.4320.0010.0010.0000.0000.0000.000
92A663LEU0-0.010-0.00633.691-0.053-0.0530.0000.0000.0000.000
93A664PRO00.0000.02034.0150.1080.1080.0000.0000.0000.000
94A665VAL00.021-0.00835.006-0.226-0.2260.0000.0000.0000.000
95A666ALA0-0.092-0.04136.4480.1990.1990.0000.0000.0000.000
96A667ASP-1-0.844-0.93238.8617.3487.3480.0000.0000.0000.000
97A668VAL0-0.071-0.03638.702-0.003-0.0030.0000.0000.0000.000
98A669PHE0-0.0170.01341.795-0.025-0.0250.0000.0000.0000.000
99A670TRP00.001-0.01338.716-0.023-0.0230.0000.0000.0000.000
100A671ARG10.7860.87545.613-6.321-6.3210.0000.0000.0000.000
101A672ALA0-0.034-0.04747.9020.1010.1010.0000.0000.0000.000
102A673ASP-1-0.835-0.87049.2376.2826.2820.0000.0000.0000.000
103A674GLY00.0160.01745.1350.0460.0460.0000.0000.0000.000
104A675SER0-0.059-0.05543.8880.1800.1800.0000.0000.0000.000
105A676ALA00.027-0.00742.796-0.018-0.0180.0000.0000.0000.000
106A677ASP-1-0.838-0.88144.9506.2796.2790.0000.0000.0000.000
107A678VAL0-0.030-0.02039.8040.1020.1020.0000.0000.0000.000
108A679ASP-1-0.816-0.89042.1706.9166.9160.0000.0000.0000.000
109A680VAL0-0.008-0.00139.4530.2330.2330.0000.0000.0000.000
110A681VAL00.005-0.00137.687-0.147-0.1470.0000.0000.0000.000
111A682TRP0-0.077-0.04738.2340.0460.0460.0000.0000.0000.000
112A683ASN00.052-0.00332.179-0.200-0.2000.0000.0000.0000.000
113A684ASP-1-0.864-0.91235.2617.8247.8240.0000.0000.0000.000
114A685MET0-0.036-0.00628.6690.1270.1270.0000.0000.0000.000
115A686PRO0-0.011-0.00727.275-0.171-0.1710.0000.0000.0000.000
116A687ALA00.0270.01328.515-0.020-0.0200.0000.0000.0000.000
117A688VAL00.0030.01225.3670.3640.3640.0000.0000.0000.000
118A689ALA00.0030.01421.5130.0310.0310.0000.0000.0000.000
119A690GLY00.0130.01019.7850.2030.2030.0000.0000.0000.000
120A691GLN00.040-0.00419.949-0.533-0.5330.0000.0000.0000.000
121A692SER00.0000.01320.677-0.216-0.2160.0000.0000.0000.000
122A693SER00.0990.05522.201-0.041-0.0410.0000.0000.0000.000
123A694SER0-0.057-0.04523.285-0.432-0.4320.0000.0000.0000.000
124A695ILE00.0520.03424.885-0.266-0.2660.0000.0000.0000.000
125A696ALA00.0410.02727.588-0.304-0.3040.0000.0000.0000.000
126A697LEU0-0.051-0.02527.242-0.333-0.3330.0000.0000.0000.000
127A698ALA00.0700.02229.672-0.291-0.2910.0000.0000.0000.000
128A699LEU00.0510.05331.388-0.277-0.2770.0000.0000.0000.000
129A700ALA0-0.0390.01333.485-0.304-0.3040.0000.0000.0000.000
130A701SER0-0.047-0.02633.788-0.251-0.2510.0000.0000.0000.000
131A702SER0-0.111-0.07935.104-0.199-0.1990.0000.0000.0000.000
132A703LEU00.0500.02736.307-0.183-0.1830.0000.0000.0000.000
133A704PRO0-0.060-0.01139.341-0.005-0.0050.0000.0000.0000.000
134A705PHE00.0950.04439.184-0.186-0.1860.0000.0000.0000.000
135A706VAL0-0.0250.00238.7950.2290.2290.0000.0000.0000.000
136A707PRO00.0170.00235.723-0.091-0.0910.0000.0000.0000.000
137A708LYS10.8590.94937.723-7.113-7.1130.0000.0000.0000.000
138A709ALA00.009-0.01533.3130.0770.0770.0000.0000.0000.000
139A710ALA0-0.046-0.00430.784-0.015-0.0150.0000.0000.0000.000
140A711TYR00.034-0.02828.5950.2410.2410.0000.0000.0000.000
141A712THR0-0.044-0.03823.1040.3050.3050.0000.0000.0000.000
142A713GLY00.0550.01221.7310.1670.1670.0000.0000.0000.000
143A714CYS0-0.052-0.01517.783-0.488-0.4880.0000.0000.0000.000
144A715LEU00.0230.01520.950-0.070-0.0700.0000.0000.0000.000
145A716SER00.001-0.00219.4000.5240.5240.0000.0000.0000.000
146A717GLY0-0.019-0.01021.532-0.092-0.0920.0000.0000.0000.000
147A718THR00.0210.01125.064-0.042-0.0420.0000.0000.0000.000
148A719ASN0-0.0270.00221.784-0.436-0.4360.0000.0000.0000.000
149A720VAL00.0430.01221.7400.3260.3260.0000.0000.0000.000
150A721GLN0-0.063-0.04016.5080.3640.3640.0000.0000.0000.000
151A722PRO00.0120.00415.645-0.441-0.4410.0000.0000.0000.000
152A723VAL0-0.028-0.01116.5720.8790.8790.0000.0000.0000.000
153A724GLN00.0380.01613.435-0.293-0.2930.0000.0000.0000.000
154A725PHE00.023-0.00716.942-0.688-0.6880.0000.0000.0000.000
155A726GLY00.0800.03020.394-0.646-0.6460.0000.0000.0000.000
156A727ASN00.0280.00322.405-0.899-0.8990.0000.0000.0000.000
157A728LEU0-0.0050.00023.469-0.417-0.4170.0000.0000.0000.000
158A729LYS10.8500.94721.289-13.041-13.0410.0000.0000.0000.000
159A730ALA00.0610.03526.057-0.391-0.3910.0000.0000.0000.000
160A731ARG10.8200.91927.264-10.861-10.8610.0000.0000.0000.000
161A732ALA00.0100.02329.713-0.304-0.3040.0000.0000.0000.000
162A733ALA00.0210.00830.861-0.275-0.2750.0000.0000.0000.000
163A734HIS10.8280.87631.363-9.720-9.7200.0000.0000.0000.000
164A735LYS10.8490.93534.270-8.490-8.4900.0000.0000.0000.000
165A736ILE00.000-0.01136.195-0.177-0.1770.0000.0000.0000.000
166A737GLY00.0000.01237.726-0.113-0.1130.0000.0000.0000.000
167A738LEU0-0.0070.01035.104-0.039-0.0390.0000.0000.0000.000
168A739PRO0-0.0070.00332.6960.2210.2210.0000.0000.0000.000
169A740LEU0-0.028-0.01625.3340.0530.0530.0000.0000.0000.000
170A741VAL0-0.0030.01428.9060.1310.1310.0000.0000.0000.000
171A742GLY00.0420.01125.6560.0670.0670.0000.0000.0000.000
172A743MET0-0.0180.04019.4530.1480.1480.0000.0000.0000.000
173A744THR0-0.063-0.04419.7170.3090.3090.0000.0000.0000.000
174A745GLN0-0.056-0.06113.4880.6820.6820.0000.0000.0000.000
175A746ASP-1-0.819-0.89416.81914.61214.6120.0000.0000.0000.000
176A747GLY00.0020.01218.811-0.424-0.4240.0000.0000.0000.000
177A748GLY0-0.037-0.02021.865-0.487-0.4870.0000.0000.0000.000
178A749GLU-1-0.827-0.88623.15612.54912.5490.0000.0000.0000.000
179A750ASP-1-0.739-0.84026.3069.7449.7440.0000.0000.0000.000
180A751THR0-0.062-0.03329.195-0.246-0.2460.0000.0000.0000.000
181A752ARG10.8650.91918.944-13.821-13.8210.0000.0000.0000.000
182A753ILE00.0190.01825.820-0.185-0.1850.0000.0000.0000.000
183A754CYS0-0.069-0.08122.7610.4110.4110.0000.0000.0000.000
184A755THR0-0.020-0.03024.4240.2850.2850.0000.0000.0000.000
185A756LEU00.011-0.02127.003-0.127-0.1270.0000.0000.0000.000
186A757ASP-1-0.879-0.93529.2839.2809.2800.0000.0000.0000.000
187A758ASP-1-0.836-0.87329.2489.9119.9110.0000.0000.0000.000
188A759ALA0-0.051-0.03429.335-0.146-0.1460.0000.0000.0000.000
189A760ALA00.002-0.01231.391-0.193-0.1930.0000.0000.0000.000
190A761ASP-1-0.891-0.94834.6248.1268.1260.0000.0000.0000.000
191A762HIS00.0240.01933.210-0.113-0.1130.0000.0000.0000.000
192A763ALA00.004-0.00535.087-0.178-0.1780.0000.0000.0000.000
193A764PHE00.0030.02336.605-0.268-0.2680.0000.0000.0000.000
194A765ASP-1-0.867-0.93637.9477.7297.7290.0000.0000.0000.000
195A766SER0-0.138-0.07537.411-0.182-0.1820.0000.0000.0000.000
196A767MET0-0.060-0.03039.470-0.076-0.0760.0000.0000.0000.000
197A768GLU-1-0.896-0.92242.9156.6506.6500.0000.0000.0000.000
198A769SER0-0.087-0.05443.639-0.051-0.0510.0000.0000.0000.000