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: 14Z9Z

Calculation Name: 3WVZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WVZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q53FT3

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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1861246.288141
FMO2-HF: Nuclear repulsion 1784147.895889
FMO2-HF: Total energy -77098.392252
FMO2-MP2: Total energy -77319.804274


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:-3:ALA)


Summations of interaction energy for fragment #1(A:-3: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.
-8.87-4.1570.539-2.529-2.7230.006
Interaction energy analysis for fragmet #1(A:-3:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : 0.003
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].
3A-1GLY0-0.0170.0012.839-5.514-2.3130.256-1.821-1.6360.011
4A0SER00.011-0.0024.504-0.0090.078-0.001-0.020-0.0660.000
5A1MET00.0080.0277.432-0.388-0.3880.0000.0000.0000.000
6A2PHE00.000-0.0118.664-0.300-0.3000.0000.0000.0000.000
7A3GLY00.0320.01212.3670.0600.0600.0000.0000.0000.000
8A4CYS0-0.055-0.01715.705-0.046-0.0460.0000.0000.0000.000
9A5LEU00.0110.00518.472-0.006-0.0060.0000.0000.0000.000
10A6VAL00.0630.03622.128-0.011-0.0110.0000.0000.0000.000
11A7ALA00.009-0.00525.320-0.003-0.0030.0000.0000.0000.000
12A8GLY00.0130.00628.482-0.005-0.0050.0000.0000.0000.000
13A9ARG10.8260.91625.368-0.179-0.1790.0000.0000.0000.000
14A10LEU00.0160.00122.963-0.003-0.0030.0000.0000.0000.000
15A11VAL0-0.036-0.01218.4570.0100.0100.0000.0000.0000.000
16A12GLN0-0.025-0.01317.2690.0340.0340.0000.0000.0000.000
17A13THR00.025-0.01113.6180.0030.0030.0000.0000.0000.000
18A14ALA0-0.020-0.00311.9140.1430.1430.0000.0000.0000.000
19A15ALA0-0.0090.01010.883-0.092-0.0920.0000.0000.0000.000
20A16GLN00.0280.01010.6980.1590.1590.0000.0000.0000.000
21A17GLN0-0.033-0.0224.475-0.382-0.325-0.001-0.010-0.0460.000
22A18VAL0-0.041-0.0168.761-0.136-0.1360.0000.0000.0000.000
23A19ALA00.015-0.0018.171-0.219-0.2190.0000.0000.0000.000
24A20GLU-1-0.962-0.9702.794-1.662-0.9570.261-0.289-0.677-0.002
25A21ASP-1-0.868-0.9343.4410.1080.7710.024-0.389-0.298-0.003
26A22LYS10.8590.9376.086-0.415-0.4150.0000.0000.0000.000
27A23PHE0-0.006-0.0065.2310.0570.0570.0000.0000.0000.000
28A24VAL00.0220.00610.391-0.178-0.1780.0000.0000.0000.000
29A25PHE0-0.028-0.01013.4950.0590.0590.0000.0000.0000.000
30A26ASP-1-0.794-0.90016.6320.2780.2780.0000.0000.0000.000
31A27LEU0-0.089-0.05519.849-0.001-0.0010.0000.0000.0000.000
32A28PRO00.0370.01222.806-0.019-0.0190.0000.0000.0000.000
33A29ASP-1-0.842-0.90725.9280.1400.1400.0000.0000.0000.000
34A30TYR00.045-0.00626.819-0.003-0.0030.0000.0000.0000.000
35A31GLU-1-0.885-0.95328.5520.1200.1200.0000.0000.0000.000
36A32SER0-0.121-0.04631.310-0.007-0.0070.0000.0000.0000.000
37A33ILE0-0.0170.00126.0880.0050.0050.0000.0000.0000.000
38A34ASN00.0180.00429.927-0.005-0.0050.0000.0000.0000.000
39A35HIS0-0.025-0.02527.761-0.001-0.0010.0000.0000.0000.000
40A36VAL00.0170.01421.3650.0060.0060.0000.0000.0000.000
41A37VAL0-0.033-0.00821.644-0.012-0.0120.0000.0000.0000.000
42A38VAL00.0240.01316.2420.0260.0260.0000.0000.0000.000
43A39PHE0-0.013-0.02416.989-0.037-0.0370.0000.0000.0000.000
44A40MET0-0.0130.01311.9680.0530.0530.0000.0000.0000.000
45A41LEU0-0.048-0.02511.583-0.066-0.0660.0000.0000.0000.000
46A42GLY0-0.017-0.00113.969-0.044-0.0440.0000.0000.0000.000
47A43THR0-0.039-0.0169.866-0.079-0.0790.0000.0000.0000.000
48A44ILE00.0180.0066.820-0.117-0.1170.0000.0000.0000.000
49A45PRO0-0.022-0.01010.5770.0950.0950.0000.0000.0000.000
50A46PHE00.008-0.0099.693-0.034-0.0340.0000.0000.0000.000
51A47PRO00.0300.0037.032-0.027-0.0270.0000.0000.0000.000
52A48GLU-1-0.919-0.9669.876-0.108-0.1080.0000.0000.0000.000
53A49GLY00.0240.01512.862-0.013-0.0130.0000.0000.0000.000
54A50MET0-0.045-0.0148.8600.0180.0180.0000.0000.0000.000
55A51GLY0-0.002-0.01512.8770.0000.0000.0000.0000.0000.000
56A52GLY00.0280.01912.2440.0300.0300.0000.0000.0000.000
57A53SER00.006-0.00613.500-0.031-0.0310.0000.0000.0000.000
58A54VAL0-0.018-0.01115.0550.0490.0490.0000.0000.0000.000
59A55TYR00.0200.00516.305-0.042-0.0420.0000.0000.0000.000
60A56PHE00.0280.00519.0270.0310.0310.0000.0000.0000.000
61A57SER00.0840.07221.163-0.021-0.0210.0000.0000.0000.000
62A58TYR0-0.044-0.01923.0370.0050.0050.0000.0000.0000.000
63A59PRO00.0230.01226.559-0.003-0.0030.0000.0000.0000.000
64A60ASP-1-0.822-0.87229.4790.0810.0810.0000.0000.0000.000
65A61SER0-0.041-0.06531.941-0.003-0.0030.0000.0000.0000.000
66A62ASN0-0.105-0.05829.8610.0020.0020.0000.0000.0000.000
67A63GLY00.0400.02727.2740.0040.0040.0000.0000.0000.000
68A64MET0-0.097-0.10023.929-0.001-0.0010.0000.0000.0000.000
69A65PRO00.0550.04921.3690.0230.0230.0000.0000.0000.000
70A66VAL0-0.0220.02722.061-0.011-0.0110.0000.0000.0000.000
71A67TRP00.0840.01217.6160.0200.0200.0000.0000.0000.000
72A68GLN00.1060.08222.051-0.015-0.0150.0000.0000.0000.000
73A69LEU0-0.056-0.02319.4610.0200.0200.0000.0000.0000.000
74A70LEU0-0.026-0.01621.183-0.016-0.0160.0000.0000.0000.000
75A71GLY00.007-0.00520.908-0.018-0.0180.0000.0000.0000.000
76A72PHE00.0160.01418.1180.0160.0160.0000.0000.0000.000
77A73VAL0-0.0220.00914.500-0.008-0.0080.0000.0000.0000.000
78A74THR00.0360.00915.6480.0020.0020.0000.0000.0000.000
79A75ASN00.0930.03013.4570.0450.0450.0000.0000.0000.000
80A76GLY0-0.0160.01016.746-0.004-0.0040.0000.0000.0000.000
81A77LYS10.8460.91819.403-0.123-0.1230.0000.0000.0000.000
82A78PRO00.0520.03417.1960.0150.0150.0000.0000.0000.000
83A79SER0-0.011-0.00817.4620.0380.0380.0000.0000.0000.000
84A80ALA0-0.013-0.00819.926-0.026-0.0260.0000.0000.0000.000
85A81ILE00.0030.00722.0930.0170.0170.0000.0000.0000.000
86A82PHE00.0060.00320.080-0.014-0.0140.0000.0000.0000.000
87A83LYS10.9020.94525.410-0.090-0.0900.0000.0000.0000.000
88A84ILE00.0160.00524.5700.0000.0000.0000.0000.0000.000
89A85SER0-0.031-0.00327.747-0.002-0.0020.0000.0000.0000.000
90A86GLY0-0.013-0.01431.420-0.004-0.0040.0000.0000.0000.000
91A87LEU0-0.055-0.01627.057-0.005-0.0050.0000.0000.0000.000
92A88LYS10.9680.98131.347-0.064-0.0640.0000.0000.0000.000
93A89SER00.037-0.04230.6370.0020.0020.0000.0000.0000.000
94A90GLY0-0.015-0.00529.976-0.006-0.0060.0000.0000.0000.000
95A91GLU-1-0.940-0.97130.1430.0660.0660.0000.0000.0000.000
96A92GLY0-0.010-0.00426.5540.0080.0080.0000.0000.0000.000
97A93SER0-0.039-0.01422.663-0.004-0.0040.0000.0000.0000.000
98A94GLN00.0380.02122.9050.0070.0070.0000.0000.0000.000
99A95HIS0-0.028-0.01118.8140.0160.0160.0000.0000.0000.000
100A96PRO00.0390.02714.425-0.015-0.0150.0000.0000.0000.000
101A97PHE0-0.030-0.01812.6620.0100.0100.0000.0000.0000.000
102A98GLY00.0240.01515.228-0.020-0.0200.0000.0000.0000.000
103A99ALA0-0.0170.00014.406-0.013-0.0130.0000.0000.0000.000
104A100MET00.006-0.01215.993-0.015-0.0150.0000.0000.0000.000
105A101ASN0-0.048-0.02015.8320.0170.0170.0000.0000.0000.000
106A102ILE00.0590.03415.9490.0360.0360.0000.0000.0000.000
107A103VAL0-0.017-0.01318.724-0.031-0.0310.0000.0000.0000.000
108A104ARG10.7530.88421.476-0.184-0.1840.0000.0000.0000.000
109A105THR0-0.011-0.01623.983-0.015-0.0150.0000.0000.0000.000
110A106PRO00.030-0.00727.3260.0080.0080.0000.0000.0000.000
111A107SER00.0650.04229.701-0.001-0.0010.0000.0000.0000.000
112A108VAL0-0.0350.00223.1520.0050.0050.0000.0000.0000.000
113A109ALA0-0.024-0.00524.086-0.002-0.0020.0000.0000.0000.000
114A110GLN00.0340.03518.560-0.003-0.0030.0000.0000.0000.000
115A111ILE0-0.0230.00016.587-0.030-0.0300.0000.0000.0000.000
116A112GLY00.0170.01114.8860.0590.0590.0000.0000.0000.000
117A113ILE0-0.056-0.02811.579-0.072-0.0720.0000.0000.0000.000
118A114SER00.0120.00710.7530.1350.1350.0000.0000.0000.000
119A115VAL0-0.024-0.0177.033-0.043-0.0430.0000.0000.0000.000
120A116GLU-1-0.895-0.9519.9220.0810.0810.0000.0000.0000.000
121A117LEU00.0460.01612.799-0.017-0.0170.0000.0000.0000.000
122A118LEU00.007-0.01714.9420.0250.0250.0000.0000.0000.000
123A119ASP-1-0.904-0.94717.496-0.028-0.0280.0000.0000.0000.000
124A120SER0-0.047-0.03417.2700.0000.0000.0000.0000.0000.000
125A121MET0-0.049-0.00215.9980.0090.0090.0000.0000.0000.000
126A122ALA0-0.038-0.00819.3160.0070.0070.0000.0000.0000.000
127A123GLN0-0.040-0.01922.268-0.002-0.0020.0000.0000.0000.000
128A124GLN0-0.023-0.00318.7110.0070.0070.0000.0000.0000.000
129A125THR0-0.025-0.02723.270-0.005-0.0050.0000.0000.0000.000
130A126PRO0-0.038-0.01923.4130.0040.0040.0000.0000.0000.000
131A127VAL00.0080.02225.329-0.009-0.0090.0000.0000.0000.000
132A128GLY00.0320.02028.0430.0010.0010.0000.0000.0000.000
133A129ASN0-0.082-0.06130.6850.0010.0010.0000.0000.0000.000
134A130ALA00.0760.05825.7930.0030.0030.0000.0000.0000.000
135A131ALA00.0190.01226.8420.0080.0080.0000.0000.0000.000
136A132VAL0-0.048-0.02027.744-0.008-0.0080.0000.0000.0000.000
137A133SER00.026-0.00229.503-0.001-0.0010.0000.0000.0000.000
138A134SER0-0.018-0.00132.2950.0000.0000.0000.0000.0000.000
139A135VAL00.0550.00234.9440.0000.0000.0000.0000.0000.000
140A136ASP-1-0.884-0.94336.2340.0520.0520.0000.0000.0000.000
141A137SER0-0.018-0.00136.458-0.001-0.0010.0000.0000.0000.000
142A138PHE00.0180.00138.350-0.001-0.0010.0000.0000.0000.000
143A139THR00.0400.01941.208-0.003-0.0030.0000.0000.0000.000
144A140GLN00.0150.01438.428-0.002-0.0020.0000.0000.0000.000
145A141PHE0-0.013-0.00642.542-0.002-0.0020.0000.0000.0000.000
146A142THR0-0.003-0.00844.492-0.003-0.0030.0000.0000.0000.000
147A143GLN00.0140.00144.4600.0000.0000.0000.0000.0000.000
148A144LYS10.9670.98942.893-0.052-0.0520.0000.0000.0000.000
149A145MET0-0.022-0.00647.323-0.001-0.0010.0000.0000.0000.000
150A146LEU0-0.0240.00750.275-0.002-0.0020.0000.0000.0000.000
151A147ASP-1-0.828-0.90350.1590.0330.0330.0000.0000.0000.000
152A148ASN0-0.103-0.04550.877-0.002-0.0020.0000.0000.0000.000
153A149PHE00.0360.01452.991-0.001-0.0010.0000.0000.0000.000
154A150TYR00.0410.02655.820-0.002-0.0020.0000.0000.0000.000
155A151ASN0-0.008-0.00453.823-0.002-0.0020.0000.0000.0000.000
156A152PHE00.0060.01556.972-0.001-0.0010.0000.0000.0000.000
157A153ALA00.0040.00058.655-0.001-0.0010.0000.0000.0000.000
158A154SER0-0.038-0.04160.572-0.001-0.0010.0000.0000.0000.000
159A155SER0-0.104-0.04460.691-0.001-0.0010.0000.0000.0000.000
160A156PHE0-0.007-0.00661.7000.0000.0000.0000.0000.0000.000
161A157ALA0-0.061-0.01465.715-0.001-0.0010.0000.0000.0000.000
162A158VAL00.0290.01367.6120.0000.0000.0000.0000.0000.000
163A159SER0-0.049-0.03271.224-0.001-0.0010.0000.0000.0000.000
164A160GLN00.064-0.01174.3350.0000.0000.0000.0000.0000.000
165A161ALA0-0.018-0.00677.6560.0000.0000.0000.0000.0000.000
166A162GLN0-0.0230.00272.2070.0000.0000.0000.0000.0000.000
167A163MET0-0.0260.01374.1210.0000.0000.0000.0000.0000.000
168A164THR00.0160.01775.6890.0000.0000.0000.0000.0000.000
169A165PRO0-0.043-0.03777.4760.0000.0000.0000.0000.0000.000
170A166SER00.0060.00175.1370.0000.0000.0000.0000.0000.000
171A167PRO0-0.003-0.00477.7780.0000.0000.0000.0000.0000.000
172A168SER0-0.006-0.00676.0930.0000.0000.0000.0000.0000.000
173A169GLU-1-0.920-0.94071.6040.0210.0210.0000.0000.0000.000
174A170MET0-0.042-0.01672.241-0.001-0.0010.0000.0000.0000.000
175A171PHE00.0460.01871.2780.0010.0010.0000.0000.0000.000
176A172ILE0-0.022-0.01266.664-0.001-0.0010.0000.0000.0000.000
177A173PRO00.0090.00669.6740.0000.0000.0000.0000.0000.000
178A174ALA00.1110.03966.9980.0000.0000.0000.0000.0000.000
179A175ASN00.006-0.00566.1650.0010.0010.0000.0000.0000.000
180A176VAL0-0.0010.00466.4720.0000.0000.0000.0000.0000.000
181A177VAL00.0250.01062.1540.0000.0000.0000.0000.0000.000
182A178LEU00.0230.02360.9060.0010.0010.0000.0000.0000.000
183A179LYS10.9590.98561.430-0.018-0.0180.0000.0000.0000.000
184A180TRP0-0.042-0.02256.7900.0000.0000.0000.0000.0000.000
185A181TYR0-0.012-0.02753.5910.0000.0000.0000.0000.0000.000
186A182GLU-1-0.865-0.93656.8750.0220.0220.0000.0000.0000.000
187A183ASN0-0.045-0.02957.1630.0000.0000.0000.0000.0000.000
188A184PHE0-0.0120.00152.6280.0000.0000.0000.0000.0000.000
189A185GLN00.0390.01452.3080.0000.0000.0000.0000.0000.000
190A186ARG10.8970.94352.242-0.020-0.0200.0000.0000.0000.000
191A187ARG10.9320.95653.145-0.023-0.0230.0000.0000.0000.000
192A188LEU00.004-0.00848.6950.0000.0000.0000.0000.0000.000
193A189ALA0-0.021-0.00448.2290.0010.0010.0000.0000.0000.000
194A190GLN0-0.047-0.02548.464-0.001-0.0010.0000.0000.0000.000
195A191ASN0-0.005-0.00348.7470.0010.0010.0000.0000.0000.000
196A192PRO00.0610.03544.8680.0000.0000.0000.0000.0000.000
197A193LEU00.0010.00144.3570.0020.0020.0000.0000.0000.000
198A194PHE0-0.079-0.02148.511-0.001-0.0010.0000.0000.0000.000
199A195TRP0-0.040-0.00647.312-0.001-0.0010.0000.0000.0000.000