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: 857JY

Calculation Name: 1VE2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VE2

Chain ID: A

ChEMBL ID:

UniProt ID: Q53WA2

Base Structure: X-ray

Registration Date: 2023-06-22

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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2405454.693529
FMO2-HF: Nuclear repulsion 2323676.24185
FMO2-HF: Total energy -81778.45168
FMO2-MP2: Total energy -82022.920584


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-10.494-3.64910.874-6.198-11.519-0.021
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : 0.011
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].
3A3GLY00.0060.0192.127-1.5411.4681.294-1.865-2.439-0.001
4A4LYS10.7970.8753.0000.0471.1820.220-0.563-0.793-0.009
5A5VAL00.0210.0165.679-0.147-0.1470.0000.0000.0000.000
6A6TYR00.0150.0038.886-0.156-0.1560.0000.0000.0000.000
7A7LEU00.0120.00312.4880.0190.0190.0000.0000.0000.000
8A8VAL00.001-0.02415.020-0.055-0.0550.0000.0000.0000.000
9A9GLY0-0.0110.01118.2640.0160.0160.0000.0000.0000.000
10A10ALA0-0.015-0.02821.988-0.018-0.0180.0000.0000.0000.000
11A11GLY00.0440.04224.199-0.013-0.0130.0000.0000.0000.000
12A12PHE0-0.029-0.02927.3270.0110.0110.0000.0000.0000.000
13A13GLY00.0310.01630.2080.0030.0030.0000.0000.0000.000
14A14GLY00.0090.01630.1680.0020.0020.0000.0000.0000.000
15A15PRO00.025-0.00927.8710.0010.0010.0000.0000.0000.000
16A16GLU-1-0.895-0.93228.397-0.013-0.0130.0000.0000.0000.000
17A17HIS0-0.054-0.03029.730-0.004-0.0040.0000.0000.0000.000
18A18LEU0-0.045-0.00923.1870.0060.0060.0000.0000.0000.000
19A19THR00.0180.00822.546-0.016-0.0160.0000.0000.0000.000
20A20LEU00.0650.01323.378-0.002-0.0020.0000.0000.0000.000
21A21LYS10.8030.90115.4600.0810.0810.0000.0000.0000.000
22A22ALA00.0200.00318.743-0.009-0.0090.0000.0000.0000.000
23A23LEU00.0460.02519.6580.0010.0010.0000.0000.0000.000
24A24ARG10.9880.99914.4280.2780.2780.0000.0000.0000.000
25A25VAL0-0.073-0.03714.318-0.034-0.0340.0000.0000.0000.000
26A26LEU00.004-0.00115.9870.0050.0050.0000.0000.0000.000
27A27GLU-1-0.839-0.90218.554-0.136-0.1360.0000.0000.0000.000
28A28VAL0-0.051-0.03313.414-0.032-0.0320.0000.0000.0000.000
29A29ALA0-0.071-0.02012.632-0.042-0.0420.0000.0000.0000.000
30A30GLU-1-0.687-0.8399.872-0.313-0.3130.0000.0000.0000.000
31A31VAL0-0.0010.00412.7930.0280.0280.0000.0000.0000.000
32A32VAL00.0190.00213.8150.0340.0340.0000.0000.0000.000
33A33LEU00.0090.01813.819-0.019-0.0190.0000.0000.0000.000
34A34HIS00.012-0.00217.2180.0020.0020.0000.0000.0000.000
35A35ASP-1-0.757-0.86320.5870.1660.1660.0000.0000.0000.000
36A36ARG10.8200.89023.433-0.144-0.1440.0000.0000.0000.000
37A37LEU00.0150.01026.694-0.009-0.0090.0000.0000.0000.000
38A38VAL0-0.0150.00623.111-0.006-0.0060.0000.0000.0000.000
39A39HIS00.0840.05226.587-0.003-0.0030.0000.0000.0000.000
40A40PRO00.031-0.00227.881-0.001-0.0010.0000.0000.0000.000
41A41GLY00.0160.01028.717-0.004-0.0040.0000.0000.0000.000
42A42VAL0-0.009-0.00423.726-0.008-0.0080.0000.0000.0000.000
43A43LEU0-0.015-0.01723.565-0.003-0.0030.0000.0000.0000.000
44A44ALA0-0.029-0.01424.287-0.003-0.0030.0000.0000.0000.000
45A45LEU0-0.014-0.00324.149-0.011-0.0110.0000.0000.0000.000
46A46ALA0-0.050-0.01519.855-0.013-0.0130.0000.0000.0000.000
47A47LYS10.8270.90019.3450.1110.1110.0000.0000.0000.000
48A48GLY00.0160.02116.778-0.023-0.0230.0000.0000.0000.000
49A49GLU-1-0.983-1.00016.6800.1750.1750.0000.0000.0000.000
50A50LEU00.0010.00617.7480.0390.0390.0000.0000.0000.000
51A51VAL00.0070.00417.3430.0010.0010.0000.0000.0000.000
52A52PRO00.0380.03920.1290.0170.0170.0000.0000.0000.000
53A53VAL0-0.063-0.05919.013-0.010-0.0100.0000.0000.0000.000
54A61LYS11.0081.00325.803-0.128-0.1280.0000.0000.0000.000
55A62THR0-0.029-0.00820.932-0.004-0.0040.0000.0000.0000.000
56A63PRO00.0450.02621.1340.0010.0010.0000.0000.0000.000
57A64GLN00.004-0.01016.751-0.014-0.0140.0000.0000.0000.000
58A65GLU-1-0.851-0.94316.8690.2870.2870.0000.0000.0000.000
59A66ALA00.0080.00815.8150.0550.0550.0000.0000.0000.000
60A67ILE00.0050.01015.7220.0500.0500.0000.0000.0000.000
61A68THR00.030-0.00312.2980.0730.0730.0000.0000.0000.000
62A69ALA00.0040.00811.4660.1580.1580.0000.0000.0000.000
63A70ARG10.8520.91411.311-0.397-0.3970.0000.0000.0000.000
64A71LEU00.0140.0039.9480.0930.0930.0000.0000.0000.000
65A72ILE0-0.002-0.0066.2590.4080.4080.0000.0000.0000.000
66A73ALA0-0.023-0.0126.5040.6580.6580.0000.0000.0000.000
67A74LEU00.0040.0097.9650.1330.1330.0000.0000.0000.000
68A75ALA00.0240.0083.582-0.660-0.2480.162-0.140-0.4340.000
69A76ARG10.8730.9163.630-2.372-0.8060.314-0.654-1.226-0.005
70A77GLU-1-0.811-0.8725.081-0.311-0.2860.0000.003-0.0270.000
71A78GLY0-0.0120.0143.863-0.551-0.4320.001-0.031-0.0890.000
72A79ARG10.8650.9234.945-0.847-0.827-0.001-0.002-0.0160.000
73A80VAL0-0.031-0.0076.1480.2280.2280.0000.0000.0000.000
74A81VAL0-0.0030.0028.2760.0220.0220.0000.0000.0000.000
75A82ALA0-0.002-0.01510.7220.0250.0250.0000.0000.0000.000
76A83ARG10.7480.86213.494-0.233-0.2330.0000.0000.0000.000
77A84LEU0-0.0160.00315.554-0.022-0.0220.0000.0000.0000.000
78A85LYS10.7710.85918.265-0.217-0.2170.0000.0000.0000.000
79A86GLY00.0260.01821.705-0.018-0.0180.0000.0000.0000.000
80A87GLY0-0.0080.00025.3620.0050.0050.0000.0000.0000.000
81A88ASP-1-0.787-0.92323.1260.0660.0660.0000.0000.0000.000
82A89PRO0-0.0370.00218.2180.0120.0120.0000.0000.0000.000
83A90MET0-0.030-0.02417.3420.0440.0440.0000.0000.0000.000
84A91VAL0-0.0160.00121.416-0.003-0.0030.0000.0000.0000.000
85A92PHE00.0240.01524.9610.0010.0010.0000.0000.0000.000
86A93GLY00.0570.02122.8890.0130.0130.0000.0000.0000.000
87A94ARG10.8580.90120.077-0.176-0.1760.0000.0000.0000.000
88A95GLY00.0580.02918.2180.0310.0310.0000.0000.0000.000
89A96GLY0-0.004-0.00216.8770.0310.0310.0000.0000.0000.000
90A97GLU-1-0.816-0.88716.4950.2250.2250.0000.0000.0000.000
91A98GLU-1-0.751-0.84314.1070.3600.3600.0000.0000.0000.000
92A99ALA00.0310.01512.2880.1010.1010.0000.0000.0000.000
93A100LEU0-0.023-0.01411.7030.0450.0450.0000.0000.0000.000
94A101ALA0-0.015-0.00311.566-0.003-0.0030.0000.0000.0000.000
95A102LEU00.0230.0067.8050.0530.0530.0000.0000.0000.000
96A103ARG10.8950.9596.860-0.304-0.3040.0000.0000.0000.000
97A104ARG10.9590.9718.009-0.323-0.3230.0000.0000.0000.000
98A105ALA0-0.0110.0136.262-0.060-0.0600.0000.0000.0000.000
99A106GLY00.0110.0154.313-0.390-0.246-0.001-0.038-0.1050.000
100A107ILE0-0.021-0.0082.448-3.472-1.0501.607-1.252-2.777-0.006
101A108PRO00.0230.0022.259-0.993-3.1207.279-1.634-3.5160.000
102A109PHE0-0.044-0.0245.3110.0710.191-0.001-0.022-0.0970.000
103A110GLU-1-0.805-0.8828.781-0.518-0.5180.0000.0000.0000.000
104A111VAL00.0220.01212.1720.0760.0760.0000.0000.0000.000
105A112VAL0-0.038-0.01915.835-0.064-0.0640.0000.0000.0000.000
106A113PRO00.0330.01018.4830.0160.0160.0000.0000.0000.000
107A114GLY00.0120.01221.942-0.014-0.0140.0000.0000.0000.000
108A115VAL00.0130.02624.7630.0050.0050.0000.0000.0000.000
109A116THR00.0420.00527.2320.0050.0050.0000.0000.0000.000
110A117SER00.031-0.00928.203-0.006-0.0060.0000.0000.0000.000
111A118ALA00.0200.02630.5240.0000.0000.0000.0000.0000.000
112A119VAL00.0330.01432.650-0.003-0.0030.0000.0000.0000.000
113A120GLY00.0130.02131.944-0.005-0.0050.0000.0000.0000.000
114A121ALA00.0330.01632.962-0.004-0.0040.0000.0000.0000.000
115A122LEU00.009-0.00334.990-0.003-0.0030.0000.0000.0000.000
116A123SER0-0.019-0.02335.588-0.004-0.0040.0000.0000.0000.000
117A124ALA0-0.0170.00235.630-0.003-0.0030.0000.0000.0000.000
118A125LEU0-0.032-0.02537.676-0.002-0.0020.0000.0000.0000.000
119A126GLY00.0330.03840.498-0.001-0.0010.0000.0000.0000.000
120A127LEU0-0.039-0.01841.2160.0000.0000.0000.0000.0000.000
121A128PRO00.0100.01540.6840.0020.0020.0000.0000.0000.000
122A129LEU00.0430.01437.1810.0020.0020.0000.0000.0000.000
123A130THR0-0.038-0.01340.9670.0010.0010.0000.0000.0000.000
124A131HIS00.0620.01643.429-0.003-0.0030.0000.0000.0000.000
125A132ARG11.0001.00646.8420.0040.0040.0000.0000.0000.000
126A133GLY00.005-0.00249.6990.0000.0000.0000.0000.0000.000
127A134LEU0-0.077-0.02148.8400.0010.0010.0000.0000.0000.000
128A135ALA00.0300.00044.4680.0020.0020.0000.0000.0000.000
129A136ARG10.8850.94343.888-0.013-0.0130.0000.0000.0000.000
130A137SER0-0.039-0.03739.9450.0000.0000.0000.0000.0000.000
131A138PHE00.016-0.00534.6010.0000.0000.0000.0000.0000.000
132A139ALA00.0100.01236.0800.0010.0010.0000.0000.0000.000
133A140VAL00.006-0.01032.508-0.001-0.0010.0000.0000.0000.000
134A141ALA00.0110.00932.9260.0040.0040.0000.0000.0000.000
135A142THR0-0.027-0.01630.5290.0000.0000.0000.0000.0000.000
136A143GLY00.0590.03433.977-0.002-0.0020.0000.0000.0000.000
137A144HIS0-0.035-0.02132.2560.0010.0010.0000.0000.0000.000
138A145ASP-1-0.905-0.93432.7500.0840.0840.0000.0000.0000.000
139A146PRO00.009-0.00435.900-0.003-0.0030.0000.0000.0000.000
140A147ALA00.0120.01138.511-0.004-0.0040.0000.0000.0000.000
141A148LEU0-0.013-0.00434.355-0.002-0.0020.0000.0000.0000.000
142A149PRO0-0.023-0.01638.684-0.002-0.0020.0000.0000.0000.000
143A150LEU00.0500.04138.3840.0020.0020.0000.0000.0000.000
144A151PRO00.0250.01936.155-0.002-0.0020.0000.0000.0000.000
145A152ARG10.9000.94138.818-0.032-0.0320.0000.0000.0000.000
146A153ALA00.0160.01839.8740.0010.0010.0000.0000.0000.000
147A154ASP-1-0.830-0.88642.0070.0160.0160.0000.0000.0000.000
148A155THR0-0.006-0.01541.604-0.001-0.0010.0000.0000.0000.000
149A156LEU0-0.032-0.01038.3460.0020.0020.0000.0000.0000.000
150A157VAL00.0110.00536.185-0.001-0.0010.0000.0000.0000.000
151A158LEU0-0.018-0.01136.3280.0040.0040.0000.0000.0000.000
152A159LEU00.012-0.00830.250-0.002-0.0020.0000.0000.0000.000
153A160MET0-0.052-0.03732.2630.0060.0060.0000.0000.0000.000
154A161PRO00.0060.02135.7000.0020.0020.0000.0000.0000.000
155A162LEU00.027-0.00438.7670.0000.0000.0000.0000.0000.000
156A163HIS0-0.0300.00239.656-0.002-0.0020.0000.0000.0000.000
157A164THR0-0.022-0.03743.465-0.001-0.0010.0000.0000.0000.000
158A165LEU0-0.002-0.00146.1220.0000.0000.0000.0000.0000.000
159A166GLY00.0170.01045.8980.0010.0010.0000.0000.0000.000
160A167GLY0-0.008-0.00246.340-0.001-0.0010.0000.0000.0000.000
161A168LEU0-0.032-0.01941.6630.0010.0010.0000.0000.0000.000
162A169LYS10.8750.93044.657-0.029-0.0290.0000.0000.0000.000
163A170GLU-1-0.807-0.90247.7980.0300.0300.0000.0000.0000.000
164A171ARG10.8570.90742.361-0.045-0.0450.0000.0000.0000.000
165A172LEU0-0.021-0.00342.8070.0000.0000.0000.0000.0000.000
166A173LEU00.0600.03245.994-0.002-0.0020.0000.0000.0000.000
167A174GLU-1-0.855-0.88945.4200.0370.0370.0000.0000.0000.000
168A175ARG10.6280.78741.693-0.037-0.0370.0000.0000.0000.000
169A176PHE0-0.013-0.01243.620-0.001-0.0010.0000.0000.0000.000
170A177PRO00.0280.03348.9980.0010.0010.0000.0000.0000.000
171A178PRO00.0670.03752.1580.0000.0000.0000.0000.0000.000
172A179GLU-1-0.801-0.90253.4590.0170.0170.0000.0000.0000.000
173A180THR0-0.112-0.05848.837-0.001-0.0010.0000.0000.0000.000
174A181PRO0-0.015-0.01049.7310.0010.0010.0000.0000.0000.000
175A182LEU00.024-0.00145.7140.0010.0010.0000.0000.0000.000
176A183ALA00.0070.00744.160-0.002-0.0020.0000.0000.0000.000
177A184LEU0-0.027-0.00242.6710.0030.0030.0000.0000.0000.000
178A185LEU00.0200.00239.587-0.002-0.0020.0000.0000.0000.000
179A186ALA00.0140.00138.8340.0040.0040.0000.0000.0000.000
180A187ARG10.7940.89435.322-0.040-0.0400.0000.0000.0000.000
181A188VAL00.0480.02336.419-0.002-0.0020.0000.0000.0000.000
182A189GLY00.0120.00935.3100.0030.0030.0000.0000.0000.000
183A190TRP0-0.100-0.05530.368-0.001-0.0010.0000.0000.0000.000
184A191PRO00.0430.01436.578-0.001-0.0010.0000.0000.0000.000
185A192GLY00.0340.00939.0130.0040.0040.0000.0000.0000.000
186A193GLU-1-0.873-0.91739.7760.0170.0170.0000.0000.0000.000
187A194ALA0-0.013-0.00941.081-0.002-0.0020.0000.0000.0000.000
188A195VAL0-0.010-0.00442.5170.0030.0030.0000.0000.0000.000
189A196ARG10.8040.89544.874-0.027-0.0270.0000.0000.0000.000
190A197LEU0-0.002-0.01146.7510.0010.0010.0000.0000.0000.000
191A198GLY00.0510.02249.340-0.001-0.0010.0000.0000.0000.000
192A199ARG10.8420.93251.131-0.015-0.0150.0000.0000.0000.000
193A200VAL0-0.021-0.01448.0860.0010.0010.0000.0000.0000.000
194A201GLU-1-0.885-0.97450.3410.0190.0190.0000.0000.0000.000
195A202ASP-1-0.830-0.89752.0240.0190.0190.0000.0000.0000.000
196A203LEU0-0.070-0.01246.7300.0010.0010.0000.0000.0000.000
197A204PRO00.021-0.01148.094-0.001-0.0010.0000.0000.0000.000
198A205GLY00.0320.02349.0930.0010.0010.0000.0000.0000.000
199A206LEU00.0060.00248.5950.0000.0000.0000.0000.0000.000
200A207GLY0-0.009-0.02046.2300.0000.0000.0000.0000.0000.000
201A208GLU-1-0.809-0.88745.9890.0340.0340.0000.0000.0000.000
202A209GLY00.0320.01546.708-0.002-0.0020.0000.0000.0000.000
203A210LEU0-0.046-0.00742.731-0.002-0.0020.0000.0000.0000.000
204A211PRO00.0180.00840.7250.0030.0030.0000.0000.0000.000
205A212SER0-0.0170.00236.7710.0030.0030.0000.0000.0000.000
206A213PRO00.014-0.00732.386-0.001-0.0010.0000.0000.0000.000
207A214ALA00.0200.00035.397-0.004-0.0040.0000.0000.0000.000
208A215LEU0-0.040-0.00534.1700.0050.0050.0000.0000.0000.000
209A216LEU00.0290.02337.923-0.002-0.0020.0000.0000.0000.000
210A217VAL0-0.004-0.00839.6240.0020.0020.0000.0000.0000.000
211A218VAL00.0180.01741.939-0.002-0.0020.0000.0000.0000.000
212A219GLY00.0930.04044.1530.0010.0010.0000.0000.0000.000
213A220LYS10.9470.97246.641-0.013-0.0130.0000.0000.0000.000
214A221VAL0-0.026-0.00744.045-0.001-0.0010.0000.0000.0000.000
215A222VAL00.0070.01444.820-0.001-0.0010.0000.0000.0000.000
216A223GLY0-0.0090.00247.3520.0000.0000.0000.0000.0000.000
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