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: 72NJK

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 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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2405856.347655
FMO2-HF: Nuclear repulsion 2321741.243252
FMO2-HF: Total energy -84115.104403
FMO2-MP2: Total energy -84366.81788


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.
-48.935-51.41228.477-10.595-15.405-0.108
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 : 0.868 / q_NPA : 0.928
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].
3A4HIS00.0530.0233.846-0.8910.352-0.011-0.433-0.8000.002
4A5ARG10.9030.9506.06222.27822.2780.0000.0000.0000.000
5A6ALA0-0.047-0.0257.6600.3940.3940.0000.0000.0000.000
6A7PHE00.0410.0289.5901.2131.2130.0000.0000.0000.000
7A8SER0-0.007-0.00812.168-0.658-0.6580.0000.0000.0000.000
8A9PRO00.002-0.00514.1590.4550.4550.0000.0000.0000.000
9A10GLY00.0370.01717.9940.1390.1390.0000.0000.0000.000
10A11LEU0-0.072-0.03214.4310.1790.1790.0000.0000.0000.000
11A12THR0-0.011-0.01316.199-0.152-0.1520.0000.0000.0000.000
12A13GLY00.0460.03313.6390.5910.5910.0000.0000.0000.000
13A14VAL0-0.053-0.01412.948-1.102-1.1020.0000.0000.0000.000
14A15LEU0-0.039-0.0157.4430.5260.5260.0000.0000.0000.000
15A16PRO00.0270.01811.9961.0061.0060.0000.0000.0000.000
16A17LEU00.0660.02012.285-1.761-1.7610.0000.0000.0000.000
17A18ARG10.9220.97312.50617.25317.2530.0000.0000.0000.000
18A19GLU-1-0.821-0.9349.347-23.692-23.6920.0000.0000.0000.000
19A20THR0-0.036-0.0057.833-3.985-3.9850.0000.0000.0000.000
20A21ARG10.9690.9917.83016.95816.9580.0000.0000.0000.000
21A22HIS00.0330.0266.4190.2680.2680.0000.0000.0000.000
22A23LEU00.0280.0152.014-5.272-6.8144.116-0.674-1.900-0.002
23A24VAL00.010-0.0023.699-9.473-9.0730.004-0.188-0.215-0.001
24A25GLU-1-0.958-1.0016.314-23.172-23.1720.0000.0000.0000.000
25A26VAL0-0.048-0.0097.1910.7650.7650.0000.0000.0000.000
26A27LEU0-0.073-0.0372.521-4.469-2.6010.680-0.746-1.802-0.008
27A28ARG10.8920.9623.60424.18625.0920.030-0.362-0.574-0.002
28A29ALA0-0.022-0.0152.031-5.003-6.3675.280-1.473-2.443-0.004
29A30ARG10.8870.9362.92256.01754.8740.2481.627-0.733-0.002
30A31VAL00.0330.0064.480-4.493-4.414-0.001-0.012-0.0650.000
31A32GLY00.0100.0136.9800.0940.0940.0000.0000.0000.000
32A33ASP-1-0.790-0.8771.848-93.203-96.78618.133-8.223-6.327-0.091
33A34ARG10.8650.9273.92834.62134.883-0.001-0.056-0.2060.000
34A35PHE0-0.064-0.0294.456-8.013-7.7210.000-0.042-0.2500.000
35A36THR00.0010.0116.4905.1095.1090.0000.0000.0000.000
36A37VAL0-0.0150.0209.380-1.592-1.5920.0000.0000.0000.000
37A38PHE00.033-0.01411.4321.4631.4630.0000.0000.0000.000
38A39ASP-1-0.797-0.89514.880-16.197-16.1970.0000.0000.0000.000
39A40GLY00.0220.02517.8290.7230.7230.0000.0000.0000.000
40A41GLU-1-0.946-0.95620.586-11.640-11.6400.0000.0000.0000.000
41A42ARG10.8490.91919.41315.61915.6190.0000.0000.0000.000
42A43GLU-1-0.839-0.93414.805-20.346-20.3460.0000.0000.0000.000
43A44ALA00.0200.02414.2460.9410.9410.0000.0000.0000.000
44A45LEU0-0.0470.0049.019-2.217-2.2170.0000.0000.0000.000
45A46ALA00.024-0.0019.1301.9831.9830.0000.0000.0000.000
46A47GLU-1-0.847-0.9387.491-30.432-30.4320.0000.0000.0000.000
47A48VAL0-0.040-0.0204.0733.4373.542-0.001-0.013-0.0900.000
48A49VAL0-0.019-0.0107.3730.9550.9550.0000.0000.0000.000
49A50ASP-1-0.831-0.91810.033-20.519-20.5190.0000.0000.0000.000
50A51LEU0-0.013-0.0086.167-1.705-1.7050.0000.0000.0000.000
51A52GLY0-0.0290.0179.328-0.016-0.0160.0000.0000.0000.000
52A53PRO0-0.072-0.02312.1630.2320.2320.0000.0000.0000.000
53A54PRO00.004-0.03912.6671.4151.4150.0000.0000.0000.000
54A55LEU00.0150.0115.4070.0270.0270.0000.0000.0000.000
55A56ARG10.9560.9709.98619.42319.4230.0000.0000.0000.000
56A57TYR0-0.016-0.0298.784-2.359-2.3590.0000.0000.0000.000
57A58ARG10.9460.98710.69223.96223.9620.0000.0000.0000.000
58A59VAL00.021-0.00412.164-1.973-1.9730.0000.0000.0000.000
59A60LEU0-0.096-0.05010.5861.0591.0590.0000.0000.0000.000
60A61GLU-1-0.881-0.95814.496-17.858-17.8580.0000.0000.0000.000
61A62GLU-1-0.847-0.93116.001-17.411-17.4110.0000.0000.0000.000
62A63ARG10.8750.93310.83921.78421.7840.0000.0000.0000.000
63A64ARG10.9410.96518.26412.89412.8940.0000.0000.0000.000
64A65PRO00.0270.02518.600-0.372-0.3720.0000.0000.0000.000
65A66GLU-1-0.923-0.95715.726-16.160-16.1600.0000.0000.0000.000
66A67ARG10.8110.89119.70313.25213.2520.0000.0000.0000.000
67A68GLU-1-0.814-0.89022.807-10.487-10.4870.0000.0000.0000.000
68A69VAL00.0270.01622.398-0.415-0.4150.0000.0000.0000.000
69A70GLY00.0090.00322.078-0.365-0.3650.0000.0000.0000.000
70A71VAL0-0.0340.00122.9470.1030.1030.0000.0000.0000.000
71A72GLU-1-0.907-0.94626.062-9.215-9.2150.0000.0000.0000.000
72A73VAL00.0220.02428.6260.0340.0340.0000.0000.0000.000
73A74VAL0-0.011-0.00831.3840.1260.1260.0000.0000.0000.000
74A75LEU00.0190.00635.1790.0650.0650.0000.0000.0000.000
75A76TYR00.005-0.00737.4800.2230.2230.0000.0000.0000.000
76A77VAL00.012-0.00240.954-0.001-0.0010.0000.0000.0000.000
77A78ALA00.0140.01943.0370.1120.1120.0000.0000.0000.000
78A79LEU0-0.043-0.01846.600-0.076-0.0760.0000.0000.0000.000
79A80LEU00.0480.02345.1840.0780.0780.0000.0000.0000.000
80A81LYS10.9570.96849.3745.6105.6100.0000.0000.0000.000
81A82GLY0-0.019-0.01850.503-0.090-0.0900.0000.0000.0000.000
82A83ASP-1-0.875-0.94847.807-6.385-6.3850.0000.0000.0000.000
83A84LYS10.9210.98046.3356.1886.1880.0000.0000.0000.000
84A85LEU0-0.003-0.00744.317-0.141-0.1410.0000.0000.0000.000
85A86ALA0-0.0050.00542.965-0.152-0.1520.0000.0000.0000.000
86A87GLU-1-0.904-0.95641.734-7.246-7.2460.0000.0000.0000.000
87A88VAL0-0.013-0.00439.675-0.213-0.2130.0000.0000.0000.000
88A89VAL00.000-0.00238.445-0.210-0.2100.0000.0000.0000.000
89A90ARG10.8670.93937.2737.8837.8830.0000.0000.0000.000
90A91ALA00.0470.02035.516-0.252-0.2520.0000.0000.0000.000
91A92ALA00.002-0.01633.907-0.282-0.2820.0000.0000.0000.000
92A93THR0-0.081-0.05032.959-0.212-0.2120.0000.0000.0000.000
93A94GLU-1-0.922-0.95131.001-9.688-9.6880.0000.0000.0000.000
94A95LEU0-0.062-0.02329.489-0.362-0.3620.0000.0000.0000.000
95A96GLY00.0480.02828.329-0.161-0.1610.0000.0000.0000.000
96A97ALA0-0.0090.00629.194-0.003-0.0030.0000.0000.0000.000
97A98THR00.020-0.00129.306-0.068-0.0680.0000.0000.0000.000
98A99ARG10.8650.93432.3528.3158.3150.0000.0000.0000.000
99A100ILE0-0.0040.00135.977-0.001-0.0010.0000.0000.0000.000
100A101GLN0-0.037-0.03739.0100.0890.0890.0000.0000.0000.000
101A102PRO0-0.020-0.00942.0440.0380.0380.0000.0000.0000.000
102A103LEU00.0080.00144.2930.0820.0820.0000.0000.0000.000
103A104VAL00.0000.01147.3590.0330.0330.0000.0000.0000.000
104A105THR0-0.010-0.02348.3940.0040.0040.0000.0000.0000.000
105A106ARG10.8830.90851.6025.4695.4690.0000.0000.0000.000
106A107HIS00.000-0.01252.9530.1360.1360.0000.0000.0000.000
107A108SER0-0.0270.01051.082-0.012-0.0120.0000.0000.0000.000
108A109VAL00.005-0.00352.6900.0990.0990.0000.0000.0000.000
109A110PRO0-0.043-0.00952.0030.1070.1070.0000.0000.0000.000
110A111LYS10.9100.95153.6885.5025.5020.0000.0000.0000.000
111A112GLU-1-0.912-0.95053.580-5.414-5.4140.0000.0000.0000.000
112A113MET0-0.039-0.01846.721-0.078-0.0780.0000.0000.0000.000
113A114GLY00.0420.03352.3340.0290.0290.0000.0000.0000.000
114A115GLU-1-0.741-0.88350.288-6.344-6.3440.0000.0000.0000.000
115A116GLY0-0.003-0.00750.588-0.123-0.1230.0000.0000.0000.000
116A117LYS10.9170.96648.7576.1396.1390.0000.0000.0000.000
117A118LEU00.0670.03245.391-0.156-0.1560.0000.0000.0000.000
118A119ARG10.8580.91645.7766.0506.0500.0000.0000.0000.000
119A120ARG10.9470.99044.9296.8616.8610.0000.0000.0000.000
120A121LEU00.021-0.00743.345-0.147-0.1470.0000.0000.0000.000
121A122ARG10.9240.96341.4256.7816.7810.0000.0000.0000.000
122A123ALA0-0.0110.00240.789-0.183-0.1830.0000.0000.0000.000
123A124VAL0-0.062-0.03039.891-0.144-0.1440.0000.0000.0000.000
124A125ALA00.0600.03537.401-0.195-0.1950.0000.0000.0000.000
125A126LEU0-0.004-0.00236.246-0.257-0.2570.0000.0000.0000.000
126A127GLU-1-0.905-0.95236.095-8.172-8.1720.0000.0000.0000.000
127A128ALA00.0320.00635.493-0.214-0.2140.0000.0000.0000.000
128A129ALA00.0330.01832.324-0.289-0.2890.0000.0000.0000.000
129A130LYS10.9160.96031.2318.2958.2950.0000.0000.0000.000
130A131GLN0-0.048-0.02531.495-0.272-0.2720.0000.0000.0000.000
131A132SER0-0.0160.00829.610-0.268-0.2680.0000.0000.0000.000
132A133GLY00.0120.00827.157-0.432-0.4320.0000.0000.0000.000
133A134ARG10.7120.83226.8339.9139.9130.0000.0000.0000.000
134A135VAL0-0.030-0.01326.6050.2320.2320.0000.0000.0000.000
135A136VAL0-0.009-0.00527.5330.3820.3820.0000.0000.0000.000
136A137VAL0-0.014-0.00830.1770.0050.0050.0000.0000.0000.000
137A138PRO0-0.018-0.00633.1180.1220.1220.0000.0000.0000.000
138A139GLU-1-0.856-0.91034.902-7.735-7.7350.0000.0000.0000.000
139A140VAL0-0.014-0.00437.7610.0300.0300.0000.0000.0000.000
140A141LEU00.006-0.00240.4460.1270.1270.0000.0000.0000.000
141A142PRO00.012-0.00243.5030.0290.0290.0000.0000.0000.000
142A143PRO00.0070.00646.496-0.080-0.0800.0000.0000.0000.000
143A144ILE00.0180.02644.9180.1020.1020.0000.0000.0000.000
144A145PRO0-0.024-0.02548.847-0.015-0.0150.0000.0000.0000.000
145A146LEU00.1040.05846.451-0.068-0.0680.0000.0000.0000.000
146A147LYS10.9670.97547.6175.6595.6590.0000.0000.0000.000
147A148ALA0-0.064-0.03147.7150.0110.0110.0000.0000.0000.000
148A149VAL00.0160.02842.255-0.090-0.0900.0000.0000.0000.000
149A150PRO0-0.0080.00240.4250.1270.1270.0000.0000.0000.000
150A151GLN00.0160.00140.932-0.162-0.1620.0000.0000.0000.000
151A152VAL0-0.036-0.01836.598-0.109-0.1090.0000.0000.0000.000
152A153ALA0-0.015-0.00632.9080.0370.0370.0000.0000.0000.000
153A154GLN00.0330.00128.877-0.040-0.0400.0000.0000.0000.000
154A155GLY00.0320.02533.985-0.039-0.0390.0000.0000.0000.000
155A156LEU0-0.0100.01332.1770.0410.0410.0000.0000.0000.000
156A157VAL00.0250.01036.7420.0260.0260.0000.0000.0000.000
157A158ALA0-0.0220.00439.790-0.003-0.0030.0000.0000.0000.000
158A159HIS00.0410.00540.7870.1300.1300.0000.0000.0000.000
159A160VAL0-0.005-0.00643.473-0.073-0.0730.0000.0000.0000.000
160A161GLY0-0.007-0.00245.404-0.025-0.0250.0000.0000.0000.000
161A162ALA0-0.0110.01440.8500.0060.0060.0000.0000.0000.000
162A163THR0-0.029-0.02740.688-0.044-0.0440.0000.0000.0000.000
163A164ALA00.0330.03535.969-0.143-0.1430.0000.0000.0000.000
164A165ARG10.8940.92733.2298.4938.4930.0000.0000.0000.000
165A166VAL00.0930.03830.116-0.064-0.0640.0000.0000.0000.000
166A167ARG11.0040.99727.8389.7229.7220.0000.0000.0000.000
167A168GLU-1-0.944-0.96228.462-8.811-8.8110.0000.0000.0000.000
168A169VAL0-0.032-0.02331.0160.1250.1250.0000.0000.0000.000
169A170LEU0-0.049-0.01626.4160.0680.0680.0000.0000.0000.000
170A171ASP-1-0.838-0.90726.000-10.508-10.5080.0000.0000.0000.000
171A172PRO0-0.047-0.04522.2770.1580.1580.0000.0000.0000.000
172A173GLU-1-0.907-0.95621.763-11.985-11.9850.0000.0000.0000.000
173A174LYS10.8960.96624.2359.2559.2550.0000.0000.0000.000
174A175PRO0-0.012-0.00627.839-0.084-0.0840.0000.0000.0000.000
175A176LEU00.003-0.00929.3980.1440.1440.0000.0000.0000.000
176A177ALA0-0.0130.01431.6130.0820.0820.0000.0000.0000.000
177A178LEU00.011-0.00532.808-0.001-0.0010.0000.0000.0000.000
178A179ALA00.0180.01136.7710.1240.1240.0000.0000.0000.000
179A180VAL0-0.016-0.01739.641-0.021-0.0210.0000.0000.0000.000
180A181GLY00.0250.01542.3630.0850.0850.0000.0000.0000.000
181A182PRO0-0.042-0.02745.976-0.094-0.0940.0000.0000.0000.000
182A183GLU-1-0.823-0.93048.454-6.202-6.2020.0000.0000.0000.000
183A184GLY0-0.041-0.01750.1570.0140.0140.0000.0000.0000.000
184A185GLY0-0.014-0.00248.5320.0410.0410.0000.0000.0000.000
185A186PHE0-0.019-0.01843.6110.0910.0910.0000.0000.0000.000
186A187ALA0-0.008-0.00249.1140.0230.0230.0000.0000.0000.000
187A188GLU-1-0.897-0.95050.679-5.664-5.6640.0000.0000.0000.000
188A189GLU-1-0.779-0.89550.821-5.678-5.6780.0000.0000.0000.000
189A190GLU-1-0.841-0.92349.176-6.027-6.0270.0000.0000.0000.000
190A191VAL0-0.0040.00445.405-0.129-0.1290.0000.0000.0000.000
191A192ALA00.0630.04146.228-0.107-0.1070.0000.0000.0000.000
192A193LEU0-0.060-0.02246.855-0.048-0.0480.0000.0000.0000.000
193A194LEU0-0.018-0.02442.987-0.085-0.0850.0000.0000.0000.000
194A195GLU-1-0.871-0.94142.765-6.774-6.7740.0000.0000.0000.000
195A196ALA0-0.054-0.01843.250-0.068-0.0680.0000.0000.0000.000
196A197ARG10.7300.86942.6206.3766.3760.0000.0000.0000.000
197A198GLY00.0930.05239.626-0.125-0.1250.0000.0000.0000.000
198A199PHE0-0.112-0.05838.344-0.230-0.2300.0000.0000.0000.000
199A200THR00.0300.01236.6050.1630.1630.0000.0000.0000.000
200A201PRO00.018-0.00138.473-0.144-0.1440.0000.0000.0000.000
201A202VAL0-0.0110.00235.204-0.124-0.1240.0000.0000.0000.000
202A203SER0-0.014-0.00938.1100.1210.1210.0000.0000.0000.000
203A204LEU00.015-0.00436.656-0.218-0.2180.0000.0000.0000.000
204A205GLY0-0.062-0.02539.2590.0050.0050.0000.0000.0000.000
205A206ARG10.9550.95541.0497.3567.3560.0000.0000.0000.000
206A207ARG10.9540.98440.5217.5567.5560.0000.0000.0000.000
207A208ILE00.0680.04144.846-0.095-0.0950.0000.0000.0000.000
208A209LEU0-0.016-0.00640.728-0.054-0.0540.0000.0000.0000.000
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