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: VRY51

Calculation Name: 3CUQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CUQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q96H20

Base Structure: X-ray

Registration Date: 2023-03-14

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 OptAll
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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2408241.566942
FMO2-HF: Nuclear repulsion 2322061.956324
FMO2-HF: Total energy -86179.610618
FMO2-MP2: Total energy -86431.494752


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:34:ALA)


Summations of interaction energy for fragment #1(A:34:ALA)
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.
-0.941.2930.438-0.981-1.6890
Interaction energy analysis for fragmet #1(A:34:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.006
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].
3A36MET00.0570.0283.882-2.080-0.780-0.002-0.577-0.7200.001
4A37SER00.0020.0012.570-0.4520.3250.441-0.387-0.831-0.001
5A38LYS10.9470.9744.4931.1181.274-0.001-0.017-0.1380.000
6A39GLN00.046-0.0066.1970.2960.2960.0000.0000.0000.000
7A40LEU0-0.0060.0177.6170.1290.1290.0000.0000.0000.000
8A41ASP-1-0.813-0.9078.300-0.506-0.5060.0000.0000.0000.000
9A42MET0-0.062-0.01310.1030.0460.0460.0000.0000.0000.000
10A43PHE00.0250.02012.2430.0520.0520.0000.0000.0000.000
11A44LYS10.8550.92711.3970.4000.4000.0000.0000.0000.000
12A45THR00.0190.01314.3370.0370.0370.0000.0000.0000.000
13A46ASN0-0.036-0.01916.5410.0270.0270.0000.0000.0000.000
14A47LEU00.0040.00417.9020.0220.0220.0000.0000.0000.000
15A48GLU-1-0.892-0.95716.486-0.204-0.2040.0000.0000.0000.000
16A49GLU-1-0.948-0.96520.543-0.098-0.0980.0000.0000.0000.000
17A50PHE0-0.0050.01322.4590.0140.0140.0000.0000.0000.000
18A51ALA00.0430.01823.4000.0110.0110.0000.0000.0000.000
19A52SER0-0.101-0.06624.8010.0100.0100.0000.0000.0000.000
20A53LYS10.9510.97426.6890.0690.0690.0000.0000.0000.000
21A54HIS0-0.020-0.02527.3470.0090.0090.0000.0000.0000.000
22A55LYS10.9230.97028.4120.0670.0670.0000.0000.0000.000
23A56GLN0-0.052-0.02929.6220.0000.0000.0000.0000.0000.000
24A57GLU-1-0.775-0.87232.988-0.031-0.0310.0000.0000.0000.000
25A58ILE00.0280.01728.2700.0040.0040.0000.0000.0000.000
26A59ARG10.9090.94128.7090.0500.0500.0000.0000.0000.000
27A60LYS10.8580.93134.5230.0310.0310.0000.0000.0000.000
28A61ASN0-0.042-0.02336.1110.0040.0040.0000.0000.0000.000
29A62PRO00.0920.04936.600-0.001-0.0010.0000.0000.0000.000
30A63GLU-1-0.863-0.93736.458-0.002-0.0020.0000.0000.0000.000
31A64PHE0-0.047-0.03030.3390.0010.0010.0000.0000.0000.000
32A65ARG10.7500.85231.9490.0150.0150.0000.0000.0000.000
33A66VAL00.0350.03331.5650.0010.0010.0000.0000.0000.000
34A67GLN0-0.017-0.00932.0290.0040.0040.0000.0000.0000.000
35A68PHE0-0.008-0.00724.3910.0020.0020.0000.0000.0000.000
36A69GLN00.0180.01427.3470.0050.0050.0000.0000.0000.000
37A70ASP-1-0.802-0.88427.8680.0210.0210.0000.0000.0000.000
38A71MET0-0.036-0.01426.9520.0050.0050.0000.0000.0000.000
39A72CYS0-0.082-0.03623.8890.0030.0030.0000.0000.0000.000
40A73ALA00.0300.00623.8700.0100.0100.0000.0000.0000.000
41A74THR0-0.063-0.03325.7890.0100.0100.0000.0000.0000.000
42A75ILE0-0.074-0.03320.2260.0070.0070.0000.0000.0000.000
43A76GLY0-0.0050.01821.0700.0140.0140.0000.0000.0000.000
44A77VAL0-0.078-0.04518.2610.0100.0100.0000.0000.0000.000
45A78ASP-1-0.727-0.86321.0850.0230.0230.0000.0000.0000.000
46A79PRO0-0.046-0.03022.007-0.004-0.0040.0000.0000.0000.000
47A80LEU00.0030.00223.375-0.009-0.0090.0000.0000.0000.000
48A81ALA0-0.0040.02421.0840.0010.0010.0000.0000.0000.000
49A82SER0-0.023-0.02420.0690.0000.0000.0000.0000.0000.000
50A83GLY00.0690.04521.876-0.006-0.0060.0000.0000.0000.000
51A84LYS10.9170.97213.8150.0800.0800.0000.0000.0000.000
52A85GLY00.0430.01017.2490.0040.0040.0000.0000.0000.000
53A86PHE0-0.007-0.01311.8590.0000.0000.0000.0000.0000.000
54A87TRP00.0770.03418.176-0.010-0.0100.0000.0000.0000.000
55A88SER00.0190.01921.5670.0030.0030.0000.0000.0000.000
56A89GLU-1-0.927-0.96717.438-0.125-0.1250.0000.0000.0000.000
57A90MET00.0060.00617.587-0.004-0.0040.0000.0000.0000.000
58A91LEU0-0.016-0.00622.4730.0040.0040.0000.0000.0000.000
59A92GLY0-0.0250.00525.2740.0050.0050.0000.0000.0000.000
60A93VAL0-0.032-0.02225.6170.0050.0050.0000.0000.0000.000
61A94GLY00.0630.02726.3350.0060.0060.0000.0000.0000.000
62A95ASP-1-0.899-0.95726.875-0.038-0.0380.0000.0000.0000.000
63A96PHE0-0.048-0.01429.5510.0020.0020.0000.0000.0000.000
64A97TYR0-0.020-0.04329.9430.0030.0030.0000.0000.0000.000
65A98TYR0-0.079-0.05825.3110.0010.0010.0000.0000.0000.000
66A99GLU-1-0.829-0.88731.667-0.013-0.0130.0000.0000.0000.000
67A100LEU00.0160.01134.7000.0020.0020.0000.0000.0000.000
68A101GLY0-0.006-0.01234.8640.0020.0020.0000.0000.0000.000
69A102VAL0-0.0060.00135.1040.0020.0020.0000.0000.0000.000
70A103GLN00.0580.02637.6440.0020.0020.0000.0000.0000.000
71A104ILE0-0.038-0.01937.9340.0010.0010.0000.0000.0000.000
72A105ILE0-0.0170.00036.9190.0020.0020.0000.0000.0000.000
73A106GLU-1-0.867-0.93841.158-0.007-0.0070.0000.0000.0000.000
74A107VAL0-0.016-0.00743.7260.0000.0000.0000.0000.0000.000
75A108CYS0-0.063-0.03943.5160.0010.0010.0000.0000.0000.000
76A109LEU0-0.038-0.02243.1600.0010.0010.0000.0000.0000.000
77A110ALA00.0410.03546.7470.0000.0000.0000.0000.0000.000
78A111LEU0-0.017-0.02248.7170.0000.0000.0000.0000.0000.000
79A112LYS10.9170.96747.637-0.005-0.0050.0000.0000.0000.000
80A113HIS0-0.058-0.02750.7690.0000.0000.0000.0000.0000.000
81A114ARG10.8020.90854.105-0.001-0.0010.0000.0000.0000.000
82A115ASN00.0440.01250.2640.0010.0010.0000.0000.0000.000
83A116GLY00.0430.02652.7080.0010.0010.0000.0000.0000.000
84A117GLY00.011-0.00448.4740.0010.0010.0000.0000.0000.000
85A118LEU0-0.0390.00247.2940.0010.0010.0000.0000.0000.000
86A119ILE00.0130.01546.041-0.001-0.0010.0000.0000.0000.000
87A120THR00.0610.03347.6760.0010.0010.0000.0000.0000.000
88A121LEU0-0.015-0.02242.494-0.001-0.0010.0000.0000.0000.000
89A122GLU-1-0.944-0.96646.0760.0010.0010.0000.0000.0000.000
90A123GLU-1-0.812-0.92048.8160.0020.0020.0000.0000.0000.000
91A124LEU0-0.001-0.00142.114-0.001-0.0010.0000.0000.0000.000
92A125HIS0-0.045-0.04743.380-0.001-0.0010.0000.0000.0000.000
93A126GLN0-0.036-0.02145.622-0.002-0.0020.0000.0000.0000.000
94A127GLN00.013-0.02148.289-0.001-0.0010.0000.0000.0000.000
95A128VAL00.0120.01341.498-0.001-0.0010.0000.0000.0000.000
96A129LEU0-0.078-0.02943.593-0.002-0.0020.0000.0000.0000.000
97A130LYS10.8250.90245.8570.0030.0030.0000.0000.0000.000
98A131GLY00.0280.02645.695-0.001-0.0010.0000.0000.0000.000
99A132ARG10.7970.88836.4480.0140.0140.0000.0000.0000.000
100A133GLY00.0300.02443.975-0.002-0.0020.0000.0000.0000.000
101A134LYS10.8850.92345.3930.0230.0230.0000.0000.0000.000
102A135PHE0-0.061-0.02640.222-0.002-0.0020.0000.0000.0000.000
103A136ALA00.0450.04843.1340.0010.0010.0000.0000.0000.000
104A137GLN0-0.045-0.04043.7600.0000.0000.0000.0000.0000.000
105A138ASP-1-0.850-0.91338.571-0.017-0.0170.0000.0000.0000.000
106A139VAL00.0490.03938.7660.0000.0000.0000.0000.0000.000
107A140SER0-0.007-0.02338.8430.0010.0010.0000.0000.0000.000
108A141GLN00.0820.01040.5400.0000.0000.0000.0000.0000.000
109A142ASP-1-0.817-0.89736.0470.0090.0090.0000.0000.0000.000
110A143ASP-1-0.787-0.84135.716-0.006-0.0060.0000.0000.0000.000
111A144LEU00.0680.03736.1690.0000.0000.0000.0000.0000.000
112A145ILE00.0000.00836.6300.0020.0020.0000.0000.0000.000
113A146ARG10.7300.82631.286-0.006-0.0060.0000.0000.0000.000
114A147ALA00.0350.02832.9680.0020.0020.0000.0000.0000.000
115A148ILE0-0.003-0.00534.3430.0020.0020.0000.0000.0000.000
116A149LYS10.9090.94632.562-0.021-0.0210.0000.0000.0000.000
117A150LYS10.8290.90026.085-0.021-0.0210.0000.0000.0000.000
118A151LEU00.0080.01531.4690.0030.0030.0000.0000.0000.000
119A152LYS10.8810.93833.828-0.029-0.0290.0000.0000.0000.000
120A153ALA0-0.039-0.01029.1410.0040.0040.0000.0000.0000.000
121A154LEU0-0.033-0.01331.1850.0020.0020.0000.0000.0000.000
122A155GLY0-0.0040.01333.4520.0000.0000.0000.0000.0000.000
123A156THR0-0.067-0.05635.404-0.001-0.0010.0000.0000.0000.000
124A157GLY00.0460.02439.021-0.001-0.0010.0000.0000.0000.000
125A158PHE00.0780.04738.012-0.001-0.0010.0000.0000.0000.000
126A159GLY0-0.076-0.04539.1650.0040.0040.0000.0000.0000.000
127A160ILE0-0.016-0.00137.907-0.002-0.0020.0000.0000.0000.000
128A161ILE00.0190.01442.0240.0020.0020.0000.0000.0000.000
129A162PRO0-0.006-0.00643.447-0.002-0.0020.0000.0000.0000.000
130A163VAL00.0040.01346.1060.0010.0010.0000.0000.0000.000
131A164GLY00.0250.02449.5340.0000.0000.0000.0000.0000.000
132A165GLY0-0.037-0.01450.4250.0000.0000.0000.0000.0000.000
133A166THR0-0.043-0.01947.496-0.001-0.0010.0000.0000.0000.000
134A167TYR0-0.016-0.01442.2920.0020.0020.0000.0000.0000.000
135A168LEU00.0460.02746.207-0.002-0.0020.0000.0000.0000.000
136A169ILE0-0.040-0.02442.0670.0020.0020.0000.0000.0000.000
137A170GLN00.0260.01643.727-0.002-0.0020.0000.0000.0000.000
138A171SER0-0.031-0.03542.8040.0000.0000.0000.0000.0000.000
139A172VAL00.0230.02143.952-0.001-0.0010.0000.0000.0000.000
140A173PRO0-0.047-0.03342.9510.0010.0010.0000.0000.0000.000
141A174ALA00.0280.02444.822-0.001-0.0010.0000.0000.0000.000
142A175GLU-1-0.925-0.96145.3780.0260.0260.0000.0000.0000.000
143A176LEU0-0.030-0.01642.8370.0000.0000.0000.0000.0000.000
144A177ASN00.0340.01146.3440.0010.0010.0000.0000.0000.000
145A178MET00.0330.00847.924-0.001-0.0010.0000.0000.0000.000
146A179ASP-1-0.810-0.87949.5350.0220.0220.0000.0000.0000.000
147A180HIS00.0290.01650.624-0.001-0.0010.0000.0000.0000.000
148A181THR00.0220.01047.435-0.001-0.0010.0000.0000.0000.000
149A182VAL0-0.014-0.00750.258-0.001-0.0010.0000.0000.0000.000
150A183VAL00.0020.00052.996-0.001-0.0010.0000.0000.0000.000
151A184LEU0-0.018-0.00349.966-0.001-0.0010.0000.0000.0000.000
152A185GLN0-0.073-0.05248.526-0.001-0.0010.0000.0000.0000.000
153A186LEU0-0.043-0.00553.206-0.001-0.0010.0000.0000.0000.000
154A187ALA00.0220.00756.131-0.001-0.0010.0000.0000.0000.000
155A188GLU-1-0.851-0.94552.4200.0100.0100.0000.0000.0000.000
156A189LYS10.8430.92055.523-0.010-0.0100.0000.0000.0000.000
157A190ASN0-0.033-0.02058.386-0.001-0.0010.0000.0000.0000.000
158A191GLY00.0050.01558.655-0.001-0.0010.0000.0000.0000.000
159A192TYR0-0.035-0.02259.6910.0000.0000.0000.0000.0000.000
160A193VAL00.0130.01459.8010.0000.0000.0000.0000.0000.000
161A194THR0-0.018-0.04762.039-0.001-0.0010.0000.0000.0000.000
162A195VAL00.0420.01064.5530.0010.0010.0000.0000.0000.000
163A196SER0-0.029-0.05265.6850.0010.0010.0000.0000.0000.000
164A197GLU-1-0.850-0.92162.7450.0110.0110.0000.0000.0000.000
165A198ILE00.0370.03159.7890.0010.0010.0000.0000.0000.000
166A199LYN0-0.044-0.01062.2240.0010.0010.0000.0000.0000.000
167A200ALA0-0.005-0.00264.5870.0010.0010.0000.0000.0000.000
168A201SER0-0.047-0.03260.8690.0000.0000.0000.0000.0000.000
169A202LEU0-0.027-0.01756.7730.0000.0000.0000.0000.0000.000
170A203LYS10.8120.91460.127-0.015-0.0150.0000.0000.0000.000
171A204TRP0-0.016-0.00755.6100.0010.0010.0000.0000.0000.000
172A205GLU-1-0.860-0.94162.4150.0160.0160.0000.0000.0000.000
173A206THR00.0150.00163.9620.0000.0000.0000.0000.0000.000
174A207GLU-1-0.814-0.89763.5170.0150.0150.0000.0000.0000.000
175A208ARG10.8380.90055.263-0.022-0.0220.0000.0000.0000.000
176A209ALA00.012-0.00260.1000.0000.0000.0000.0000.0000.000
177A210ARG10.7910.88261.507-0.014-0.0140.0000.0000.0000.000
178A211GLN00.0150.00159.0780.0000.0000.0000.0000.0000.000
179A212VAL0-0.0120.00455.5290.0000.0000.0000.0000.0000.000
180A213LEU0-0.0080.00057.6550.0000.0000.0000.0000.0000.000
181A214GLU-1-0.872-0.92860.1380.0140.0140.0000.0000.0000.000
182A215HIS0-0.050-0.02452.1740.0000.0000.0000.0000.0000.000
183A216LEU00.005-0.00754.2460.0000.0000.0000.0000.0000.000
184A217LEU0-0.046-0.01356.759-0.001-0.0010.0000.0000.0000.000
185A218LYS10.8040.89855.146-0.017-0.0170.0000.0000.0000.000
186A219GLU-1-0.861-0.92952.2110.0170.0170.0000.0000.0000.000
187A220GLY00.0010.00754.0300.0000.0000.0000.0000.0000.000
188A221LEU0-0.035-0.01550.948-0.001-0.0010.0000.0000.0000.000
189A222ALA0-0.023-0.01655.0640.0000.0000.0000.0000.0000.000
190A223TRP00.0010.00358.6580.0000.0000.0000.0000.0000.000
191A224LEU0-0.023-0.01162.1630.0000.0000.0000.0000.0000.000
192A225ASP-1-0.794-0.89465.4710.0060.0060.0000.0000.0000.000
193A226LEU0-0.035-0.02868.3320.0000.0000.0000.0000.0000.000
194A227GLN0-0.047-0.03071.6590.0000.0000.0000.0000.0000.000
195A228ALA00.0060.03069.6550.0000.0000.0000.0000.0000.000
196A229PRO0-0.011-0.01971.5530.0000.0000.0000.0000.0000.000
197A230GLY0-0.026-0.00572.1860.0000.0000.0000.0000.0000.000
198A231GLU-1-0.787-0.85668.6090.0110.0110.0000.0000.0000.000
199A232ALA00.0120.01868.9260.0000.0000.0000.0000.0000.000
200A233HIS10.8610.94166.090-0.008-0.0080.0000.0000.0000.000
201A234TYR00.0180.00161.7480.0000.0000.0000.0000.0000.000
202A235TRP00.002-0.01861.5890.0000.0000.0000.0000.0000.000
203A236LEU00.0150.00554.8960.0000.0000.0000.0000.0000.000
204A237PRO0-0.0170.00556.6200.0000.0000.0000.0000.0000.000
205A238ALA00.0110.01251.965-0.001-0.0010.0000.0000.0000.000
206A239LEU0-0.076-0.03053.1220.0000.0000.0000.0000.0000.000
207A240PHE0-0.016-0.01055.8880.0000.0000.0000.0000.0000.000
208A241THR00.0140.00456.5000.0000.0000.0000.0000.0000.000
209A242ASP-1-0.796-0.87857.8840.0000.0000.0000.0000.0000.000
210A243LEU0-0.034-0.02555.6060.0000.0000.0000.0000.0000.000
211A244TYR0-0.024-0.01757.441-0.001-0.0010.0000.0000.0000.000
212A245SER0-0.029-0.02357.1900.0000.0000.0000.0000.0000.000
213A246GLN00.0440.04551.030-0.001-0.0010.0000.0000.0000.000
214A247GLU-1-0.886-0.94653.356-0.006-0.0060.0000.0000.0000.000
215A248ILE0-0.076-0.03055.2010.0010.0010.0000.0000.0000.000
216A249THR0-0.037-0.00951.9000.0000.0000.0000.0000.0000.000
217A250ALA00.005-0.00350.0560.0000.0000.0000.0000.0000.000
218A251GLU-1-0.927-0.96149.166-0.002-0.0020.0000.0000.0000.000
219A252GLU-1-1.008-1.00843.8560.0000.0000.0000.0000.0000.000