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: 17YJZ

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 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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2400521.543419
FMO2-HF: Nuclear repulsion 2318744.232278
FMO2-HF: Total energy -81777.311141
FMO2-MP2: Total energy -82021.781838


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.
-9.252-1.7385.608-4.358-8.763-0.02
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 : -0.003 / q_NPA : -0.019
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].
3A3GLY00.0290.0193.009-1.0361.2130.105-0.948-1.4060.000
4A4LYS10.7710.8682.985-1.4140.3420.181-0.975-0.961-0.010
5A5VAL00.0230.0215.693-0.005-0.0050.0000.0000.0000.000
6A6TYR0-0.019-0.0079.104-0.167-0.1670.0000.0000.0000.000
7A7LEU0-0.020-0.00812.2670.0450.0450.0000.0000.0000.000
8A8VAL00.019-0.01815.354-0.039-0.0390.0000.0000.0000.000
9A9GLY00.0060.02118.0780.0180.0180.0000.0000.0000.000
10A10ALA0-0.008-0.02921.782-0.008-0.0080.0000.0000.0000.000
11A11GLY00.0010.01924.158-0.001-0.0010.0000.0000.0000.000
12A12PHE00.003-0.01727.1570.0060.0060.0000.0000.0000.000
13A13GLY00.0180.00030.3480.0050.0050.0000.0000.0000.000
14A14GLY00.0250.03030.0160.0010.0010.0000.0000.0000.000
15A15PRO00.023-0.01328.036-0.003-0.0030.0000.0000.0000.000
16A16GLU-1-0.948-0.95728.396-0.043-0.0430.0000.0000.0000.000
17A17HIS0-0.008-0.00429.726-0.007-0.0070.0000.0000.0000.000
18A18LEU0-0.052-0.00523.234-0.004-0.0040.0000.0000.0000.000
19A19THR00.0200.01022.324-0.008-0.0080.0000.0000.0000.000
20A20LEU00.0920.01823.432-0.002-0.0020.0000.0000.0000.000
21A21LYS10.8730.94814.9380.2780.2780.0000.0000.0000.000
22A22ALA00.0110.00018.631-0.013-0.0130.0000.0000.0000.000
23A23LEU00.0430.02419.6460.0030.0030.0000.0000.0000.000
24A24ARG10.9961.01113.7740.3250.3250.0000.0000.0000.000
25A25VAL0-0.078-0.04914.199-0.014-0.0140.0000.0000.0000.000
26A26LEU0-0.009-0.00916.0020.0080.0080.0000.0000.0000.000
27A27GLU-1-0.915-0.94418.605-0.102-0.1020.0000.0000.0000.000
28A28VAL0-0.065-0.04113.457-0.008-0.0080.0000.0000.0000.000
29A29ALA0-0.067-0.02512.994-0.014-0.0140.0000.0000.0000.000
30A30GLU-1-0.790-0.89210.584-0.108-0.1080.0000.0000.0000.000
31A31VAL00.0030.00913.7650.0300.0300.0000.0000.0000.000
32A32VAL00.0150.00114.5170.0010.0010.0000.0000.0000.000
33A33LEU0-0.0090.00514.9990.0000.0000.0000.0000.0000.000
34A34HIS00.018-0.00718.003-0.008-0.0080.0000.0000.0000.000
35A35ASP-1-0.802-0.90021.2280.0300.0300.0000.0000.0000.000
36A36ARG10.9320.95123.992-0.052-0.0520.0000.0000.0000.000
37A37LEU0-0.026-0.00927.134-0.002-0.0020.0000.0000.0000.000
38A38VAL00.0160.02524.002-0.005-0.0050.0000.0000.0000.000
39A39HIS00.0720.05027.4070.0030.0030.0000.0000.0000.000
40A40PRO00.0520.00428.261-0.001-0.0010.0000.0000.0000.000
41A41GLY00.0130.00029.0370.0000.0000.0000.0000.0000.000
42A42VAL0-0.0080.00224.129-0.005-0.0050.0000.0000.0000.000
43A43LEU0-0.008-0.01323.859-0.003-0.0030.0000.0000.0000.000
44A44ALA0-0.025-0.00924.5530.0000.0000.0000.0000.0000.000
45A45LEU0-0.024-0.01224.082-0.002-0.0020.0000.0000.0000.000
46A46ALA0-0.055-0.01720.289-0.011-0.0110.0000.0000.0000.000
47A47LYS10.9310.96520.1940.0720.0720.0000.0000.0000.000
48A48GLY00.0240.03117.657-0.001-0.0010.0000.0000.0000.000
49A49GLU-1-0.992-1.00017.8870.1240.1240.0000.0000.0000.000
50A50LEU0-0.023-0.01218.7770.0120.0120.0000.0000.0000.000
51A51VAL00.0110.00418.2840.0060.0060.0000.0000.0000.000
52A52PRO0-0.0130.00220.6940.0010.0010.0000.0000.0000.000
53A53VAL0-0.038-0.01319.2710.0020.0020.0000.0000.0000.000
54A61LYS10.9630.96226.013-0.019-0.0190.0000.0000.0000.000
55A62THR0-0.012-0.01721.4260.0010.0010.0000.0000.0000.000
56A63PRO00.0310.02421.634-0.004-0.0040.0000.0000.0000.000
57A64GLN00.017-0.00816.5890.0000.0000.0000.0000.0000.000
58A65GLU-1-0.861-0.94517.1260.0820.0820.0000.0000.0000.000
59A66ALA0-0.0070.00116.1220.0290.0290.0000.0000.0000.000
60A67ILE0-0.0060.00315.9480.0400.0400.0000.0000.0000.000
61A68THR00.028-0.00312.0710.0460.0460.0000.0000.0000.000
62A69ALA00.0060.01411.6020.0830.0830.0000.0000.0000.000
63A70ARG10.9480.99011.358-0.236-0.2360.0000.0000.0000.000
64A71LEU00.0130.00510.6810.0900.0900.0000.0000.0000.000
65A72ILE0-0.005-0.0076.1460.2480.2480.0000.0000.0000.000
66A73ALA0-0.036-0.0236.9330.5560.5560.0000.0000.0000.000
67A74LEU00.0300.0068.3190.1880.1880.0000.0000.0000.000
68A75ALA00.0170.0174.540-0.215-0.0660.004-0.040-0.1130.000
69A76ARG10.9110.9433.956-0.7150.3930.135-0.378-0.865-0.001
70A77GLU-1-0.947-0.9574.957-0.154-0.1430.0000.017-0.0290.000
71A78GLY0-0.055-0.0194.381-0.441-0.382-0.001-0.011-0.0470.000
72A79ARG10.9040.9425.390-0.665-0.663-0.001-0.0010.0010.000
73A80VAL0-0.037-0.0087.0100.1420.1420.0000.0000.0000.000
74A81VAL00.001-0.0058.7920.0470.0470.0000.0000.0000.000
75A82ALA00.007-0.00911.229-0.031-0.0310.0000.0000.0000.000
76A83ARG10.7860.91613.904-0.039-0.0390.0000.0000.0000.000
77A84LEU0-0.019-0.00916.166-0.027-0.0270.0000.0000.0000.000
78A85LYS10.7940.90818.4440.0020.0020.0000.0000.0000.000
79A86GLY00.0120.02922.211-0.010-0.0100.0000.0000.0000.000
80A87GLY0-0.031-0.01025.3300.0000.0000.0000.0000.0000.000
81A88ASP-1-0.787-0.91423.145-0.082-0.0820.0000.0000.0000.000
82A89PRO0-0.012-0.01218.9120.0090.0090.0000.0000.0000.000
83A90MET00.005-0.01817.5990.0130.0130.0000.0000.0000.000
84A91VAL0-0.0320.00021.4290.0000.0000.0000.0000.0000.000
85A92PHE00.0350.01324.9890.0070.0070.0000.0000.0000.000
86A93GLY00.0530.01423.3290.0000.0000.0000.0000.0000.000
87A94ARG10.9480.97019.772-0.006-0.0060.0000.0000.0000.000
88A95GLY00.0670.02318.1070.0090.0090.0000.0000.0000.000
89A96GLY0-0.010-0.00216.798-0.001-0.0010.0000.0000.0000.000
90A97GLU-1-0.924-0.97116.524-0.017-0.0170.0000.0000.0000.000
91A98GLU-1-0.761-0.86414.0760.0650.0650.0000.0000.0000.000
92A99ALA00.0300.01112.2480.0230.0230.0000.0000.0000.000
93A100LEU0-0.019-0.01511.659-0.032-0.0320.0000.0000.0000.000
94A101ALA0-0.0060.00111.483-0.048-0.0480.0000.0000.0000.000
95A102LEU00.0120.0077.870-0.028-0.0280.0000.0000.0000.000
96A103ARG10.9370.9726.8010.3290.3290.0000.0000.0000.000
97A104ARG10.9450.9627.963-0.017-0.0170.0000.0000.0000.000
98A105ALA0-0.0170.0196.081-0.028-0.0280.0000.0000.0000.000
99A106GLY0-0.003-0.0014.219-0.547-0.3870.000-0.051-0.1090.000
100A107ILE0-0.025-0.0152.296-3.562-2.0212.613-1.262-2.892-0.011
101A108PRO0-0.003-0.0042.772-1.867-1.3882.572-0.709-2.3420.002
102A109PHE0-0.009-0.0145.7840.2620.2620.0000.0000.0000.000
103A110GLU-1-0.837-0.9008.999-0.711-0.7110.0000.0000.0000.000
104A111VAL00.0240.00812.1720.0600.0600.0000.0000.0000.000
105A112VAL0-0.052-0.03115.581-0.033-0.0330.0000.0000.0000.000
106A113PRO00.010-0.00418.0570.0190.0190.0000.0000.0000.000
107A114GLY00.0160.01721.696-0.002-0.0020.0000.0000.0000.000
108A115VAL00.0190.04224.4020.0010.0010.0000.0000.0000.000
109A116THR00.021-0.00927.5810.0070.0070.0000.0000.0000.000
110A117SER00.0630.00329.1490.0000.0000.0000.0000.0000.000
111A118ALA00.0290.02431.1420.0020.0020.0000.0000.0000.000
112A119VAL00.017-0.00132.6760.0010.0010.0000.0000.0000.000
113A120GLY00.007-0.00732.0740.0000.0000.0000.0000.0000.000
114A121ALA00.0320.02633.0370.0000.0000.0000.0000.0000.000
115A122LEU00.015-0.00435.3560.0010.0010.0000.0000.0000.000
116A123SER00.0140.00835.7020.0000.0000.0000.0000.0000.000
117A124ALA0-0.0170.01535.6080.0000.0000.0000.0000.0000.000
118A125LEU0-0.053-0.04137.5490.0010.0010.0000.0000.0000.000
119A126GLY00.0140.02040.3400.0010.0010.0000.0000.0000.000
120A127LEU0-0.035-0.01741.2060.0010.0010.0000.0000.0000.000
121A128PRO0-0.0140.01040.807-0.002-0.0020.0000.0000.0000.000
122A129LEU00.0460.01937.2420.0020.0020.0000.0000.0000.000
123A130THR0-0.039-0.00540.8620.0010.0010.0000.0000.0000.000
124A131HIS00.0700.02143.4440.0000.0000.0000.0000.0000.000
125A132ARG10.9910.99946.6950.0300.0300.0000.0000.0000.000
126A133GLY0-0.010-0.01249.4070.0010.0010.0000.0000.0000.000
127A134LEU0-0.059-0.00948.7400.0010.0010.0000.0000.0000.000
128A135ALA00.0170.00344.3580.0010.0010.0000.0000.0000.000
129A136ARG10.9150.96044.1280.0320.0320.0000.0000.0000.000
130A137SER0-0.012-0.00640.068-0.002-0.0020.0000.0000.0000.000
131A138PHE00.0350.00834.3090.0020.0020.0000.0000.0000.000
132A139ALA00.0100.01435.950-0.003-0.0030.0000.0000.0000.000
133A140VAL0-0.003-0.00832.3100.0020.0020.0000.0000.0000.000
134A141ALA0-0.0070.00233.027-0.002-0.0020.0000.0000.0000.000
135A142THR0-0.0020.00030.4680.0010.0010.0000.0000.0000.000
136A143GLY00.0570.02633.844-0.001-0.0010.0000.0000.0000.000
137A144HIS0-0.046-0.03431.5160.0020.0020.0000.0000.0000.000
138A145ASP-1-0.906-0.93532.557-0.011-0.0110.0000.0000.0000.000
139A146PRO0-0.018-0.02335.728-0.002-0.0020.0000.0000.0000.000
140A147ALA0-0.0100.00638.7590.0000.0000.0000.0000.0000.000
141A148LEU0-0.038-0.01634.357-0.001-0.0010.0000.0000.0000.000
142A149PRO0-0.014-0.01138.5270.0000.0000.0000.0000.0000.000
143A150LEU00.0600.04638.197-0.001-0.0010.0000.0000.0000.000
144A151PRO00.0210.02436.427-0.001-0.0010.0000.0000.0000.000
145A152ARG10.9550.96538.7150.0270.0270.0000.0000.0000.000
146A153ALA0-0.0050.00439.639-0.002-0.0020.0000.0000.0000.000
147A154ASP-1-0.854-0.91841.778-0.030-0.0300.0000.0000.0000.000
148A155THR0-0.030-0.03141.0720.0020.0020.0000.0000.0000.000
149A156LEU0-0.024-0.00438.413-0.002-0.0020.0000.0000.0000.000
150A157VAL00.004-0.00236.1730.0010.0010.0000.0000.0000.000
151A158LEU0-0.010-0.01536.470-0.001-0.0010.0000.0000.0000.000
152A159LEU0-0.018-0.02430.8070.0010.0010.0000.0000.0000.000
153A160MET0-0.063-0.03532.2470.0020.0020.0000.0000.0000.000
154A161PRO00.0130.02236.0290.0010.0010.0000.0000.0000.000
155A162LEU00.019-0.00638.4300.0010.0010.0000.0000.0000.000
156A163HIS0-0.0110.01339.943-0.001-0.0010.0000.0000.0000.000
157A164THR00.0440.00543.7100.0010.0010.0000.0000.0000.000
158A165LEU00.0270.01946.223-0.001-0.0010.0000.0000.0000.000
159A166GLY00.0050.00445.7420.0000.0000.0000.0000.0000.000
160A167GLY00.029-0.01745.843-0.001-0.0010.0000.0000.0000.000
161A168LEU0-0.017-0.00841.981-0.001-0.0010.0000.0000.0000.000
162A169LYS10.9350.97044.8920.0090.0090.0000.0000.0000.000
163A170GLU-1-0.879-0.93547.779-0.011-0.0110.0000.0000.0000.000
164A171ARG10.9780.98642.8820.0130.0130.0000.0000.0000.000
165A172LEU0-0.035-0.00542.946-0.001-0.0010.0000.0000.0000.000
166A173LEU00.0570.03645.989-0.001-0.0010.0000.0000.0000.000
167A174GLU-1-0.975-0.96945.545-0.017-0.0170.0000.0000.0000.000
168A175ARG10.6590.80041.6010.0220.0220.0000.0000.0000.000
169A176PHE0-0.040-0.02643.704-0.001-0.0010.0000.0000.0000.000
170A177PRO00.0420.04849.0040.0010.0010.0000.0000.0000.000
171A178PRO00.0600.01251.9240.0000.0000.0000.0000.0000.000
172A179GLU-1-0.807-0.91453.724-0.016-0.0160.0000.0000.0000.000
173A180THR0-0.109-0.03048.652-0.001-0.0010.0000.0000.0000.000
174A181PRO0-0.010-0.00249.8070.0010.0010.0000.0000.0000.000
175A182LEU00.0450.00645.594-0.001-0.0010.0000.0000.0000.000
176A183ALA00.0090.00744.5390.0010.0010.0000.0000.0000.000
177A184LEU0-0.030-0.01043.1380.0000.0000.0000.0000.0000.000
178A185LEU00.0230.00340.2130.0000.0000.0000.0000.0000.000
179A186ALA00.013-0.00139.3190.0000.0000.0000.0000.0000.000
180A187ARG10.8600.93836.4260.0060.0060.0000.0000.0000.000
181A188VAL00.0700.03736.7030.0000.0000.0000.0000.0000.000
182A189GLY0-0.016-0.00535.682-0.001-0.0010.0000.0000.0000.000
183A190TRP0-0.124-0.05930.6510.0020.0020.0000.0000.0000.000
184A191PRO00.0430.01536.8980.0000.0000.0000.0000.0000.000
185A192GLY00.018-0.00539.7530.0010.0010.0000.0000.0000.000
186A193GLU-1-0.880-0.92040.241-0.020-0.0200.0000.0000.0000.000
187A194ALA0-0.008-0.00841.6840.0010.0010.0000.0000.0000.000
188A195VAL00.0060.00443.191-0.001-0.0010.0000.0000.0000.000
189A196ARG10.8550.94545.4810.0100.0100.0000.0000.0000.000
190A197LEU0-0.013-0.01447.225-0.001-0.0010.0000.0000.0000.000
191A198GLY00.0470.02349.9070.0010.0010.0000.0000.0000.000
192A199ARG10.8680.92451.3360.0140.0140.0000.0000.0000.000
193A200VAL0-0.018-0.00848.1610.0010.0010.0000.0000.0000.000
194A201GLU-1-0.937-0.98650.350-0.012-0.0120.0000.0000.0000.000
195A202ASP-1-0.819-0.88752.077-0.012-0.0120.0000.0000.0000.000
196A203LEU0-0.091-0.02046.6490.0010.0010.0000.0000.0000.000
197A204PRO00.020-0.02148.4770.0000.0000.0000.0000.0000.000
198A205GLY00.0680.04249.4210.0000.0000.0000.0000.0000.000
199A206LEU0-0.004-0.00348.9070.0000.0000.0000.0000.0000.000
200A207GLY0-0.019-0.01846.749-0.001-0.0010.0000.0000.0000.000
201A208GLU-1-0.919-0.95947.188-0.004-0.0040.0000.0000.0000.000
202A209GLY00.0440.02046.7990.0000.0000.0000.0000.0000.000
203A210LEU0-0.109-0.06843.4620.0000.0000.0000.0000.0000.000
204A211PRO0-0.0020.00641.3780.0010.0010.0000.0000.0000.000
205A212SER0-0.0090.01637.4310.0000.0000.0000.0000.0000.000
206A213PRO0-0.018-0.02533.1840.0010.0010.0000.0000.0000.000
207A214ALA00.035-0.00336.221-0.001-0.0010.0000.0000.0000.000
208A215LEU0-0.053-0.02134.5180.0000.0000.0000.0000.0000.000
209A216LEU00.0300.03238.2960.0010.0010.0000.0000.0000.000
210A217VAL00.007-0.00139.874-0.002-0.0020.0000.0000.0000.000
211A218VAL00.0100.01542.1060.0010.0010.0000.0000.0000.000
212A219GLY00.0900.03044.277-0.002-0.0020.0000.0000.0000.000
213A220LYS10.9710.97146.8540.0230.0230.0000.0000.0000.000
214A221VAL00.0000.00844.2020.0010.0010.0000.0000.0000.000
215A222VAL0-0.0020.00445.1920.0000.0000.0000.0000.0000.000
216A223GLY0-0.030-0.01547.6700.0010.0010.0000.0000.0000.000
217A224LEU00.007-0.00548.2270.0010.0010.0000.0000.0000.000
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219A226GLY00.0040.01648.4620.0000.0000.0000.0000.0000.000
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