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: 2JRKR

Calculation Name: 1V6Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1V6Z

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SKI6

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 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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2407457.818169
FMO2-HF: Nuclear repulsion 2323342.009381
FMO2-HF: Total energy -84115.808788
FMO2-MP2: Total energy -84367.456599


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:2:ARG)


Summations of interaction energy for fragment #1(A:2:ARG)
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.
-68.527-77.38938.499-10.716-18.923-0.169
Interaction energy analysis for fragmet #1(A:2:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.803 / q_NPA : 0.886
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].
3A4HIS00.0430.0123.846-0.2090.913-0.011-0.410-0.7020.002
4A5ARG10.8320.8866.41721.35121.3510.0000.0000.0000.000
5A6ALA0-0.038-0.0258.5850.4580.4580.0000.0000.0000.000
6A7PHE00.0340.01910.6341.0531.0530.0000.0000.0000.000
7A8SER0-0.022-0.04113.176-0.474-0.4740.0000.0000.0000.000
8A9PRO00.011-0.00215.1410.4530.4530.0000.0000.0000.000
9A10GLY00.0410.02318.9790.1530.1530.0000.0000.0000.000
10A11LEU0-0.087-0.03215.3550.1110.1110.0000.0000.0000.000
11A12THR00.005-0.00417.259-0.183-0.1830.0000.0000.0000.000
12A13GLY00.0380.02014.4900.5120.5120.0000.0000.0000.000
13A14VAL0-0.067-0.02813.837-1.031-1.0310.0000.0000.0000.000
14A15LEU0-0.0190.0078.3920.3710.3710.0000.0000.0000.000
15A16PRO00.0300.01612.8140.8620.8620.0000.0000.0000.000
16A17LEU00.0550.01112.742-1.691-1.6910.0000.0000.0000.000
17A18ARG10.8400.91912.73217.68417.6840.0000.0000.0000.000
18A19GLU-1-0.770-0.89510.173-22.529-22.5290.0000.0000.0000.000
19A20THR0-0.0240.0038.355-3.645-3.6450.0000.0000.0000.000
20A21ARG10.9640.9947.81816.86916.8690.0000.0000.0000.000
21A22HIS00.0210.0227.368-0.186-0.1860.0000.0000.0000.000
22A23LEU00.0220.0142.738-5.772-4.8540.345-0.359-0.9040.002
23A24VAL00.010-0.0033.525-12.929-12.3120.015-0.316-0.317-0.002
24A25GLU-1-0.944-0.9905.797-24.851-24.8510.0000.0000.0000.000
25A26VAL0-0.044-0.0136.8350.4600.4600.0000.0000.0000.000
26A27LEU0-0.035-0.0132.356-3.666-1.5861.425-1.376-2.128-0.001
27A28ARG10.9060.9761.8814.6934.9138.451-4.724-3.947-0.062
28A29ALA00.014-0.0141.831-7.470-9.47211.222-5.103-4.118-0.018
29A30ARG10.8740.9342.31768.45659.2361.0428.829-0.651-0.004
30A31VAL00.0340.0044.825-3.439-3.394-0.001-0.001-0.0420.000
31A32GLY00.0100.0127.3980.1210.1210.0000.0000.0000.000
32A33ASP-1-0.788-0.8701.755-100.748-103.89216.014-7.161-5.709-0.086
33A34ARG10.8220.8914.20333.55633.711-0.001-0.016-0.1380.000
34A35PHE0-0.048-0.0214.038-8.451-8.174-0.001-0.076-0.2010.000
35A36THR0-0.0020.0086.0274.7054.7050.0000.0000.0000.000
36A37VAL0-0.0120.0229.580-1.254-1.2540.0000.0000.0000.000
37A38PHE00.043-0.01312.1701.3151.3150.0000.0000.0000.000
38A39ASP-1-0.804-0.89915.629-15.859-15.8590.0000.0000.0000.000
39A40GLY00.0140.02018.8460.6830.6830.0000.0000.0000.000
40A41GLU-1-0.922-0.95121.445-11.484-11.4840.0000.0000.0000.000
41A42ARG10.7760.85119.62515.44715.4470.0000.0000.0000.000
42A43GLU-1-0.803-0.88414.639-20.105-20.1050.0000.0000.0000.000
43A44ALA00.0150.02014.3300.9200.9200.0000.0000.0000.000
44A45LEU0-0.0380.0088.856-2.032-2.0320.0000.0000.0000.000
45A46ALA00.0300.0029.4561.9101.9100.0000.0000.0000.000
46A47GLU-1-0.759-0.8577.632-28.490-28.4900.0000.0000.0000.000
47A48VAL0-0.021-0.0134.4313.5993.669-0.001-0.003-0.0660.000
48A49VAL0-0.032-0.0197.5010.8360.8360.0000.0000.0000.000
49A50ASP-1-0.818-0.92110.484-20.497-20.4970.0000.0000.0000.000
50A51LEU0-0.024-0.0056.273-1.587-1.5870.0000.0000.0000.000
51A52GLY0-0.0170.0299.557-0.035-0.0350.0000.0000.0000.000
52A53PRO0-0.060-0.01812.2280.1460.1460.0000.0000.0000.000
53A54PRO00.007-0.03913.0041.3871.3870.0000.0000.0000.000
54A55LEU00.0040.0036.086-0.004-0.0040.0000.0000.0000.000
55A56ARG10.9550.97210.57919.18919.1890.0000.0000.0000.000
56A57TYR00.0080.0209.504-2.194-2.1940.0000.0000.0000.000
57A58ARG10.8680.92211.25123.64223.6420.0000.0000.0000.000
58A59VAL00.019-0.00612.264-1.841-1.8410.0000.0000.0000.000
59A60LEU0-0.078-0.03510.4070.9170.9170.0000.0000.0000.000
60A61GLU-1-0.822-0.89414.313-17.970-17.9700.0000.0000.0000.000
61A62GLU-1-0.798-0.87515.600-16.697-16.6970.0000.0000.0000.000
62A63ARG10.8170.87111.08720.76820.7680.0000.0000.0000.000
63A64ARG10.9450.96618.16812.60612.6060.0000.0000.0000.000
64A65PRO00.0300.02518.597-0.396-0.3960.0000.0000.0000.000
65A66GLU-1-0.939-0.95815.453-15.773-15.7730.0000.0000.0000.000
66A67ARG10.8120.89119.70312.86812.8680.0000.0000.0000.000
67A68GLU-1-0.824-0.88522.819-10.356-10.3560.0000.0000.0000.000
68A69VAL00.0300.02022.360-0.395-0.3950.0000.0000.0000.000
69A70GLY00.0110.00622.078-0.358-0.3580.0000.0000.0000.000
70A71VAL0-0.036-0.00222.9470.1000.1000.0000.0000.0000.000
71A72GLU-1-0.823-0.88526.062-8.942-8.9420.0000.0000.0000.000
72A73VAL00.0150.01828.5540.0300.0300.0000.0000.0000.000
73A74VAL0-0.014-0.00931.3420.1210.1210.0000.0000.0000.000
74A75LEU00.0130.00435.1450.0650.0650.0000.0000.0000.000
75A76TYR00.014-0.00137.4400.2260.2260.0000.0000.0000.000
76A77VAL00.005-0.00540.914-0.001-0.0010.0000.0000.0000.000
77A78ALA00.0170.02343.0000.1110.1110.0000.0000.0000.000
78A79LEU0-0.038-0.01846.565-0.073-0.0730.0000.0000.0000.000
79A80LEU00.0420.02345.2060.0740.0740.0000.0000.0000.000
80A81LYS10.9580.96849.3415.5695.5690.0000.0000.0000.000
81A82GLY0-0.004-0.00950.473-0.090-0.0900.0000.0000.0000.000
82A83ASP-1-0.851-0.93047.802-6.331-6.3310.0000.0000.0000.000
83A84LYS10.8230.90746.3016.2596.2590.0000.0000.0000.000
84A85LEU0-0.018-0.01244.339-0.139-0.1390.0000.0000.0000.000
85A86ALA00.0170.00942.933-0.153-0.1530.0000.0000.0000.000
86A87GLU-1-0.919-0.95841.706-7.216-7.2160.0000.0000.0000.000
87A88VAL0-0.020-0.01239.728-0.209-0.2090.0000.0000.0000.000
88A89VAL00.0040.00038.414-0.206-0.2060.0000.0000.0000.000
89A90ARG10.8470.92337.2427.8277.8270.0000.0000.0000.000
90A91ALA00.0470.02335.480-0.245-0.2450.0000.0000.0000.000
91A92ALA0-0.001-0.01433.879-0.277-0.2770.0000.0000.0000.000
92A93THR0-0.064-0.04132.926-0.209-0.2090.0000.0000.0000.000
93A94GLU-1-0.925-0.95630.962-9.538-9.5380.0000.0000.0000.000
94A95LEU0-0.055-0.02129.462-0.353-0.3530.0000.0000.0000.000
95A96GLY00.0450.03228.298-0.164-0.1640.0000.0000.0000.000
96A97ALA0-0.0090.00429.160-0.006-0.0060.0000.0000.0000.000
97A98THR0-0.001-0.03729.297-0.044-0.0440.0000.0000.0000.000
98A99ARG10.7880.89132.3528.3648.3640.0000.0000.0000.000
99A100ILE00.0040.00235.977-0.005-0.0050.0000.0000.0000.000
100A101GLN0-0.031-0.03538.9850.0930.0930.0000.0000.0000.000
101A102PRO0-0.012-0.00642.0440.0340.0340.0000.0000.0000.000
102A103LEU00.0070.00344.2980.0780.0780.0000.0000.0000.000
103A104VAL0-0.0080.00747.3190.0340.0340.0000.0000.0000.000
104A105THR0-0.006-0.02248.3320.0020.0020.0000.0000.0000.000
105A106ARG10.8780.91251.5635.4665.4660.0000.0000.0000.000
106A107HIS00.015-0.00152.8820.1470.1470.0000.0000.0000.000
107A108SER0-0.0270.01150.977-0.014-0.0140.0000.0000.0000.000
108A109VAL00.0170.01052.6550.0980.0980.0000.0000.0000.000
109A110PRO0-0.034-0.00652.0800.0970.0970.0000.0000.0000.000
110A111LYS10.8530.90453.6515.4875.4870.0000.0000.0000.000
111A112GLU-1-0.912-0.94853.560-5.383-5.3830.0000.0000.0000.000
112A113MET0-0.040-0.02046.613-0.073-0.0730.0000.0000.0000.000
113A114GLY00.0390.03352.3190.0250.0250.0000.0000.0000.000
114A115GLU-1-0.754-0.88750.356-6.313-6.3130.0000.0000.0000.000
115A116GLY0-0.003-0.00150.580-0.117-0.1170.0000.0000.0000.000
116A117LYS10.8890.94148.7396.1026.1020.0000.0000.0000.000
117A118LEU00.0550.02845.402-0.154-0.1540.0000.0000.0000.000
118A119ARG10.8790.92245.7766.0146.0140.0000.0000.0000.000
119A120ARG10.9460.98644.0026.8486.8480.0000.0000.0000.000
120A121LEU00.0240.00043.300-0.146-0.1460.0000.0000.0000.000
121A122ARG10.9150.95241.4236.6986.6980.0000.0000.0000.000
122A123ALA0-0.015-0.00240.767-0.180-0.1800.0000.0000.0000.000
123A124VAL0-0.069-0.03339.939-0.141-0.1410.0000.0000.0000.000
124A125ALA00.0630.03637.439-0.190-0.1900.0000.0000.0000.000
125A126LEU00.0050.00136.246-0.247-0.2470.0000.0000.0000.000
126A127GLU-1-0.895-0.93636.095-8.066-8.0660.0000.0000.0000.000
127A128ALA00.0520.02035.486-0.204-0.2040.0000.0000.0000.000
128A129ALA00.0380.03132.322-0.286-0.2860.0000.0000.0000.000
129A130LYS10.9060.95631.2318.1778.1770.0000.0000.0000.000
130A131GLN0-0.049-0.03031.647-0.252-0.2520.0000.0000.0000.000
131A132SER0-0.013-0.00729.506-0.236-0.2360.0000.0000.0000.000
132A133GLY00.0010.00327.163-0.425-0.4250.0000.0000.0000.000
133A134ARG10.7210.82826.8339.7989.7980.0000.0000.0000.000
134A135VAL0-0.033-0.01826.4640.2300.2300.0000.0000.0000.000
135A136VAL0-0.010-0.00227.4420.3750.3750.0000.0000.0000.000
136A137VAL0-0.012-0.00830.1550.0090.0090.0000.0000.0000.000
137A138PRO0-0.018-0.00233.2710.1090.1090.0000.0000.0000.000
138A139GLU-1-0.849-0.89234.902-7.740-7.7400.0000.0000.0000.000
139A140VAL0-0.015-0.00737.7610.0290.0290.0000.0000.0000.000
140A141LEU00.0170.01240.4930.1400.1400.0000.0000.0000.000
141A142PRO00.0260.00443.5030.0310.0310.0000.0000.0000.000
142A143PRO00.0030.00146.496-0.074-0.0740.0000.0000.0000.000
143A144ILE00.0060.02144.8080.1000.1000.0000.0000.0000.000
144A145PRO0-0.008-0.02048.847-0.016-0.0160.0000.0000.0000.000
145A146LEU00.0930.05646.466-0.069-0.0690.0000.0000.0000.000
146A147LYS10.9670.97747.5745.5765.5760.0000.0000.0000.000
147A148ALA0-0.060-0.03047.8160.0050.0050.0000.0000.0000.000
148A149VAL00.0120.02942.201-0.094-0.0940.0000.0000.0000.000
149A150PRO0-0.0030.00940.3630.1260.1260.0000.0000.0000.000
150A151GLN00.003-0.00840.961-0.142-0.1420.0000.0000.0000.000
151A152VAL0-0.040-0.02236.579-0.106-0.1060.0000.0000.0000.000
152A153ALA0-0.010-0.00332.9340.0350.0350.0000.0000.0000.000
153A154GLN00.024-0.00828.635-0.032-0.0320.0000.0000.0000.000
154A155GLY00.0380.02933.940-0.034-0.0340.0000.0000.0000.000
155A156LEU0-0.0110.01332.1180.0360.0360.0000.0000.0000.000
156A157VAL00.0230.00636.7030.0330.0330.0000.0000.0000.000
157A158ALA0-0.0230.00439.737-0.003-0.0030.0000.0000.0000.000
158A159HIS00.0460.00340.7540.1360.1360.0000.0000.0000.000
159A160VAL0-0.003-0.00143.442-0.075-0.0750.0000.0000.0000.000
160A161GLY0-0.0070.00045.375-0.026-0.0260.0000.0000.0000.000
161A162ALA0-0.0140.01540.8260.0000.0000.0000.0000.0000.000
162A163THR0-0.024-0.02940.660-0.054-0.0540.0000.0000.0000.000
163A164ALA00.0190.02535.994-0.155-0.1550.0000.0000.0000.000
164A165ARG10.8950.92633.2628.4448.4440.0000.0000.0000.000
165A166VAL00.0950.03730.149-0.066-0.0660.0000.0000.0000.000
166A167ARG10.9350.95927.7489.5989.5980.0000.0000.0000.000
167A168GLU-1-0.883-0.92128.431-8.968-8.9680.0000.0000.0000.000
168A169VAL0-0.038-0.02830.9850.1240.1240.0000.0000.0000.000
169A170LEU0-0.053-0.01326.5610.0830.0830.0000.0000.0000.000
170A171ASP-1-0.774-0.86226.215-10.304-10.3040.0000.0000.0000.000
171A172PRO0-0.022-0.03322.2250.1800.1800.0000.0000.0000.000
172A173GLU-1-0.916-0.95721.714-12.031-12.0310.0000.0000.0000.000
173A174LYS10.8280.92024.2299.4569.4560.0000.0000.0000.000
174A175PRO0-0.012-0.00927.839-0.088-0.0880.0000.0000.0000.000
175A176LEU0-0.002-0.00929.4860.1370.1370.0000.0000.0000.000
176A177ALA0-0.0210.01031.5690.0840.0840.0000.0000.0000.000
177A178LEU00.018-0.00132.780-0.001-0.0010.0000.0000.0000.000
178A179ALA00.0190.01036.7320.1260.1260.0000.0000.0000.000
179A180VAL0-0.020-0.01939.624-0.022-0.0220.0000.0000.0000.000
180A181GLY00.0310.02242.3280.0870.0870.0000.0000.0000.000
181A182PRO0-0.030-0.02345.943-0.090-0.0900.0000.0000.0000.000
182A183GLU-1-0.820-0.90948.422-6.207-6.2070.0000.0000.0000.000
183A184GLY0-0.039-0.01750.1270.0150.0150.0000.0000.0000.000
184A185GLY0-0.013-0.00448.4990.0430.0430.0000.0000.0000.000
185A186PHE0-0.018-0.02043.5020.0920.0920.0000.0000.0000.000
186A187ALA0-0.026-0.00849.0780.0240.0240.0000.0000.0000.000
187A188GLU-1-0.894-0.94950.642-5.656-5.6560.0000.0000.0000.000
188A189GLU-1-0.759-0.88550.782-5.660-5.6600.0000.0000.0000.000
189A190GLU-1-0.832-0.91849.138-6.008-6.0080.0000.0000.0000.000
190A191VAL0-0.012-0.00345.249-0.129-0.1290.0000.0000.0000.000
191A192ALA00.0660.04546.188-0.104-0.1040.0000.0000.0000.000
192A193LEU0-0.060-0.02346.863-0.047-0.0470.0000.0000.0000.000
193A194LEU0-0.008-0.01942.767-0.086-0.0860.0000.0000.0000.000
194A195GLU-1-0.870-0.94142.722-6.728-6.7280.0000.0000.0000.000
195A196ALA0-0.053-0.02043.207-0.069-0.0690.0000.0000.0000.000
196A197ARG10.7430.87442.4816.3456.3450.0000.0000.0000.000
197A198GLY00.0900.04939.580-0.123-0.1230.0000.0000.0000.000
198A199PHE0-0.111-0.05838.300-0.228-0.2280.0000.0000.0000.000
199A200THR00.0270.00936.6110.1580.1580.0000.0000.0000.000
200A201PRO00.007-0.00338.435-0.138-0.1380.0000.0000.0000.000
201A202VAL0-0.016-0.00235.100-0.124-0.1240.0000.0000.0000.000
202A203SER0-0.007-0.00738.0750.1440.1440.0000.0000.0000.000
203A204LEU00.008-0.00636.642-0.217-0.2170.0000.0000.0000.000
204A205GLY0-0.056-0.02039.2320.0030.0030.0000.0000.0000.000
205A206ARG10.9640.96141.0267.2817.2810.0000.0000.0000.000
206A207ARG10.9550.98640.1977.5577.5570.0000.0000.0000.000
207A208ILE00.0640.03644.823-0.093-0.0930.0000.0000.0000.000
208A209LEU0-0.016-0.00440.728-0.054-0.0540.0000.0000.0000.000
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