Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 3QR3L

Calculation Name: 1VAJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VAJ

Chain ID: A

ChEMBL ID:

UniProt ID: O57770

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2412582.144709
FMO2-HF: Nuclear repulsion 2331877.34401
FMO2-HF: Total energy -80704.800699
FMO2-MP2: Total energy -80943.404933


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:PHE)


Summations of interaction energy for fragment #1(A:3:PHE)
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.
-17.257-6.3869.869-6.499-14.241-0.032
Interaction energy analysis for fragmet #1(A:3:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.061 / q_NPA : -0.044
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].
3A5ILE0-0.037-0.0193.285-0.1571.7400.012-0.792-1.1180.001
4A6LYS10.8620.9082.889-0.8850.7470.273-0.840-1.064-0.010
5A7ASP-1-0.761-0.8683.805-0.653-0.0900.008-0.112-0.4600.000
6A8GLU-1-0.772-0.8606.447-1.179-1.1790.0000.0000.0000.000
7A9TRP0-0.005-0.0157.0470.0350.0350.0000.0000.0000.000
8A10GLY00.0660.0387.6530.1360.1360.0000.0000.0000.000
9A11GLU-1-0.841-0.9198.740-0.331-0.3310.0000.0000.0000.000
10A12PHE0-0.070-0.02811.7940.0740.0740.0000.0000.0000.000
11A13LEU00.0300.00510.1200.0720.0720.0000.0000.0000.000
12A14VAL00.0170.01612.3340.0600.0600.0000.0000.0000.000
13A15ARG10.8520.90114.2690.4090.4090.0000.0000.0000.000
14A16LEU0-0.059-0.02016.5320.0340.0340.0000.0000.0000.000
15A17ALA00.0420.01616.9120.0270.0270.0000.0000.0000.000
16A18ARG10.7230.81418.6760.1350.1350.0000.0000.0000.000
17A19ARG10.9180.96620.8110.2250.2250.0000.0000.0000.000
18A20ALA00.001-0.00821.6840.0130.0130.0000.0000.0000.000
19A21ILE00.0230.02021.9310.0140.0140.0000.0000.0000.000
20A22GLU-1-0.767-0.88324.923-0.105-0.1050.0000.0000.0000.000
21A23GLU-1-0.866-0.91526.344-0.107-0.1070.0000.0000.0000.000
22A24TYR00.0370.02427.4790.0090.0090.0000.0000.0000.000
23A25LEU0-0.018-0.01928.5360.0080.0080.0000.0000.0000.000
24A26LYS10.7720.90029.5120.1160.1160.0000.0000.0000.000
25A27THR0-0.084-0.06931.7010.0050.0050.0000.0000.0000.000
26A28GLY00.0070.01932.8440.0020.0020.0000.0000.0000.000
27A29LYS10.8700.93730.5230.0920.0920.0000.0000.0000.000
28A30GLU-1-0.764-0.86624.653-0.142-0.1420.0000.0000.0000.000
29A31ILE0-0.077-0.02921.7030.0010.0010.0000.0000.0000.000
30A32GLU-1-0.884-0.94624.418-0.153-0.1530.0000.0000.0000.000
31A33PRO0-0.006-0.01619.933-0.010-0.0100.0000.0000.0000.000
32A34PRO0-0.0330.01019.3350.0180.0180.0000.0000.0000.000
33A35LYS10.8930.92820.6980.2140.2140.0000.0000.0000.000
34A36ASP-1-0.872-0.92919.087-0.298-0.2980.0000.0000.0000.000
35A37THR0-0.004-0.02215.969-0.042-0.0420.0000.0000.0000.000
36A38PRO0-0.0020.01312.2870.0270.0270.0000.0000.0000.000
37A39PRO00.0180.00114.4450.0140.0140.0000.0000.0000.000
38A40GLU-1-0.853-0.93910.692-0.763-0.7630.0000.0000.0000.000
39A41LEU0-0.030-0.0149.512-0.002-0.0020.0000.0000.0000.000
40A42TRP0-0.018-0.01013.0540.0950.0950.0000.0000.0000.000
41A43GLU-1-0.852-0.88911.588-0.460-0.4600.0000.0000.0000.000
42A44LYS10.8120.90414.7820.1330.1330.0000.0000.0000.000
43A45MET0-0.005-0.0018.054-0.061-0.0610.0000.0000.0000.000
44A46GLY00.0270.03113.2400.0180.0180.0000.0000.0000.000
45A47VAL0-0.014-0.01812.476-0.067-0.0670.0000.0000.0000.000
46A48PHE00.0200.00614.1040.0380.0380.0000.0000.0000.000
47A49VAL0-0.033-0.00515.057-0.032-0.0320.0000.0000.0000.000
48A50THR0-0.004-0.01616.2540.0160.0160.0000.0000.0000.000
49A51LEU0-0.0060.01218.825-0.014-0.0140.0000.0000.0000.000
50A52ASN00.009-0.00617.5340.0140.0140.0000.0000.0000.000
51A53ARG10.8790.91921.5450.0000.0000.0000.0000.0000.000
52A54TYR00.018-0.01619.5970.0070.0070.0000.0000.0000.000
53A55ASN0-0.069-0.03823.0110.0040.0040.0000.0000.0000.000
54A56VAL0-0.0180.00424.0520.0010.0010.0000.0000.0000.000
55A57PRO00.0220.00423.4530.0030.0030.0000.0000.0000.000
56A58PRO00.0590.04019.472-0.005-0.0050.0000.0000.0000.000
57A59GLN00.0410.01821.425-0.011-0.0110.0000.0000.0000.000
58A60THR0-0.100-0.05223.437-0.005-0.0050.0000.0000.0000.000
59A61ALA00.0000.00421.596-0.007-0.0070.0000.0000.0000.000
60A62LEU00.0140.02020.153-0.010-0.0100.0000.0000.0000.000
61A63ARG10.7210.82622.9940.0360.0360.0000.0000.0000.000
62A64GLY00.0430.03023.423-0.003-0.0030.0000.0000.0000.000
63A65CYS0-0.114-0.05918.5330.0010.0010.0000.0000.0000.000
64A66ILE00.0230.01720.7390.0120.0120.0000.0000.0000.000
65A67GLY00.0440.00218.466-0.017-0.0170.0000.0000.0000.000
66A68PHE0-0.0420.00017.9550.0180.0180.0000.0000.0000.000
67A69PRO00.0450.01916.878-0.017-0.0170.0000.0000.0000.000
68A70THR00.0110.00316.8970.0110.0110.0000.0000.0000.000
69A71PRO00.0290.03315.671-0.019-0.0190.0000.0000.0000.000
70A72ILE0-0.009-0.01417.491-0.003-0.0030.0000.0000.0000.000
71A73TYR0-0.0020.00919.2960.0050.0050.0000.0000.0000.000
72A74PRO00.0070.00317.379-0.013-0.0130.0000.0000.0000.000
73A75LEU00.0310.02010.1680.0180.0180.0000.0000.0000.000
74A76VAL00.0250.01314.7640.0210.0210.0000.0000.0000.000
75A77GLU-1-0.874-0.95816.417-0.163-0.1630.0000.0000.0000.000
76A78ALA0-0.024-0.00916.4960.0270.0270.0000.0000.0000.000
77A79THR00.018-0.00614.6450.0210.0210.0000.0000.0000.000
78A80ILE0-0.041-0.01516.9840.0250.0250.0000.0000.0000.000
79A81LYS10.8310.89720.3180.1590.1590.0000.0000.0000.000
80A82ALA00.0150.01618.6460.0170.0170.0000.0000.0000.000
81A83ALA00.0060.01219.2450.0170.0170.0000.0000.0000.000
82A84ILE00.0120.01720.8900.0150.0150.0000.0000.0000.000
83A85TYR00.0220.00023.8340.0080.0080.0000.0000.0000.000
84A86SER0-0.086-0.05421.6470.0110.0110.0000.0000.0000.000
85A87ALA00.0240.00923.7660.0090.0090.0000.0000.0000.000
86A88VAL0-0.071-0.04326.2390.0070.0070.0000.0000.0000.000
87A89ASP-1-0.883-0.93527.877-0.057-0.0570.0000.0000.0000.000
88A90ASP-1-0.738-0.84425.290-0.017-0.0170.0000.0000.0000.000
89A91PRO0-0.020-0.01728.0120.0020.0020.0000.0000.0000.000
90A92ARG10.7680.86023.2440.0100.0100.0000.0000.0000.000
91A93PHE0-0.024-0.00425.6130.0030.0030.0000.0000.0000.000
92A94PRO0-0.0100.00831.104-0.002-0.0020.0000.0000.0000.000
93A95PRO00.0370.00830.965-0.001-0.0010.0000.0000.0000.000
94A96VAL0-0.021-0.00226.6420.0030.0030.0000.0000.0000.000
95A97LYS10.8480.93029.9220.0380.0380.0000.0000.0000.000
96A98LEU00.0150.00029.410-0.003-0.0030.0000.0000.0000.000
97A99GLU-1-0.824-0.93130.483-0.053-0.0530.0000.0000.0000.000
98A100GLU-1-0.786-0.86628.907-0.038-0.0380.0000.0000.0000.000
99A101MET00.0320.02623.0860.0030.0030.0000.0000.0000.000
100A102ASP-1-0.840-0.87425.978-0.084-0.0840.0000.0000.0000.000
101A103ASN0-0.119-0.06627.0340.0060.0060.0000.0000.0000.000
102A104LEU00.0060.01923.6810.0080.0080.0000.0000.0000.000
103A105VAL0-0.026-0.00418.588-0.010-0.0100.0000.0000.0000.000
104A106VAL0-0.004-0.01017.2330.0090.0090.0000.0000.0000.000
105A107GLU-1-0.794-0.88813.1400.0110.0110.0000.0000.0000.000
106A108VAL0-0.014-0.00611.867-0.010-0.0100.0000.0000.0000.000
107A109SER00.0180.00710.7390.0210.0210.0000.0000.0000.000
108A110VAL00.0210.0068.1250.0210.0210.0000.0000.0000.000
109A111LEU0-0.031-0.0128.7750.0280.0280.0000.0000.0000.000
110A112THR0-0.031-0.0307.320-0.046-0.0460.0000.0000.0000.000
111A113PRO0-0.028-0.0369.872-0.012-0.0120.0000.0000.0000.000
112A114PRO00.0060.00613.3370.0670.0670.0000.0000.0000.000
113A115GLU-1-0.913-0.94914.6270.4610.4610.0000.0000.0000.000
114A116LEU0-0.016-0.01917.300-0.008-0.0080.0000.0000.0000.000
115A117ILE0-0.041-0.01919.7270.0230.0230.0000.0000.0000.000
116A118GLU-1-0.927-0.95721.9520.1870.1870.0000.0000.0000.000
117A119GLY0-0.026-0.03124.6630.0090.0090.0000.0000.0000.000
118A120PRO00.0080.00227.696-0.006-0.0060.0000.0000.0000.000
119A121PRO00.0250.02428.4660.0120.0120.0000.0000.0000.000
120A122GLU-1-0.833-0.94528.0780.1240.1240.0000.0000.0000.000
121A123GLU-1-0.843-0.90526.8330.1920.1920.0000.0000.0000.000
122A124ARG10.7890.90023.877-0.106-0.1060.0000.0000.0000.000
123A125PRO00.0730.02822.2410.0230.0230.0000.0000.0000.000
124A126ARG10.8270.90421.068-0.150-0.1500.0000.0000.0000.000
125A127LYS10.7940.90019.570-0.182-0.1820.0000.0000.0000.000
126A128ILE0-0.033-0.00916.5060.0400.0400.0000.0000.0000.000
127A129LYS10.9030.94612.312-0.423-0.4230.0000.0000.0000.000
128A130VAL00.0650.03413.5400.0230.0230.0000.0000.0000.000
129A131GLY0-0.015-0.01411.4240.0180.0180.0000.0000.0000.000
130A132ARG10.6870.8068.603-0.512-0.5120.0000.0000.0000.000
131A133ASP-1-0.745-0.8479.7070.4880.4880.0000.0000.0000.000
132A134GLY00.0130.01612.523-0.038-0.0380.0000.0000.0000.000
133A135LEU00.002-0.00114.6900.0300.0300.0000.0000.0000.000
134A136ILE0-0.014-0.02417.750-0.026-0.0260.0000.0000.0000.000
135A137VAL00.0300.01320.9250.0150.0150.0000.0000.0000.000
136A138GLU-1-0.809-0.88024.6380.0460.0460.0000.0000.0000.000
137A139LYS10.8030.88627.361-0.059-0.0590.0000.0000.0000.000
138A140GLY00.0070.00631.068-0.005-0.0050.0000.0000.0000.000
139A141ILE0-0.046-0.03031.7770.0000.0000.0000.0000.0000.000
140A142TYR0-0.0390.00530.747-0.005-0.0050.0000.0000.0000.000
141A143SER0-0.016-0.04325.0360.0050.0050.0000.0000.0000.000
142A144GLY00.0080.01024.749-0.009-0.0090.0000.0000.0000.000
143A145LEU0-0.027-0.00617.3290.0090.0090.0000.0000.0000.000
144A146LEU0-0.020-0.00619.127-0.015-0.0150.0000.0000.0000.000
145A147LEU00.0210.00714.2180.0180.0180.0000.0000.0000.000
146A148PRO00.0250.00310.567-0.001-0.0010.0000.0000.0000.000
147A149GLN00.002-0.01212.4540.0390.0390.0000.0000.0000.000
148A150VAL0-0.0110.00913.693-0.005-0.0050.0000.0000.0000.000
149A151PRO00.0300.01615.474-0.006-0.0060.0000.0000.0000.000
150A152VAL0-0.033-0.02312.6820.0010.0010.0000.0000.0000.000
151A153GLU-1-0.947-0.96116.1240.0450.0450.0000.0000.0000.000
152A154TRP0-0.064-0.04818.412-0.013-0.0130.0000.0000.0000.000
153A155GLY0-0.055-0.01019.867-0.005-0.0050.0000.0000.0000.000
154A156TRP0-0.0050.00820.3950.0040.0040.0000.0000.0000.000
155A157ASP-1-0.834-0.90419.8330.1530.1530.0000.0000.0000.000
156A158GLU-1-0.827-0.94417.4860.2320.2320.0000.0000.0000.000
157A159GLU-1-0.955-0.97820.6440.1160.1160.0000.0000.0000.000
158A160GLU-1-0.860-0.93423.6430.0970.0970.0000.0000.0000.000
159A161PHE0-0.002-0.00516.094-0.009-0.0090.0000.0000.0000.000
160A162LEU00.0030.01321.677-0.007-0.0070.0000.0000.0000.000
161A163ALA00.0080.02123.359-0.010-0.0100.0000.0000.0000.000
162A164GLU-1-0.845-0.93923.6280.0570.0570.0000.0000.0000.000
163A165THR0-0.096-0.07021.487-0.008-0.0080.0000.0000.0000.000
164A166CYS0-0.085-0.03023.746-0.006-0.0060.0000.0000.0000.000
165A167TRP0-0.0100.01327.294-0.010-0.0100.0000.0000.0000.000
166A168LYS10.9130.96123.368-0.034-0.0340.0000.0000.0000.000
167A169ALA0-0.039-0.01826.474-0.008-0.0080.0000.0000.0000.000
168A170GLY0-0.044-0.02027.937-0.005-0.0050.0000.0000.0000.000
169A171LEU0-0.048-0.02629.522-0.002-0.0020.0000.0000.0000.000
170A172PRO00.010-0.00231.6520.0000.0000.0000.0000.0000.000
171A173PRO00.0250.00729.7780.0040.0040.0000.0000.0000.000
172A174ASP-1-0.856-0.92929.4330.0740.0740.0000.0000.0000.000
173A175CYS0-0.034-0.01830.5420.0020.0020.0000.0000.0000.000
174A176TRP00.0650.02426.5000.0050.0050.0000.0000.0000.000
175A177LEU0-0.0200.01128.4070.0090.0090.0000.0000.0000.000
176A178ASP-1-0.835-0.91131.1800.0690.0690.0000.0000.0000.000
177A179GLU-1-0.939-0.99331.1060.0860.0860.0000.0000.0000.000
178A180ASP-1-0.900-0.93230.8350.0670.0670.0000.0000.0000.000
179A181THR0-0.087-0.03727.774-0.007-0.0070.0000.0000.0000.000
180A182LYS10.8600.95125.518-0.061-0.0610.0000.0000.0000.000
181A183VAL00.0370.01022.004-0.007-0.0070.0000.0000.0000.000
182A184TYR0-0.056-0.05319.0770.0130.0130.0000.0000.0000.000
183A185LYS10.8620.96315.323-0.431-0.4310.0000.0000.0000.000
184A186PHE0-0.0060.00412.2050.0030.0030.0000.0000.0000.000
185A187THR00.0450.0308.0270.0810.0810.0000.0000.0000.000
186A188ALA00.0210.0068.010-0.084-0.0840.0000.0000.0000.000
187A189GLU-1-0.817-0.8862.547-9.641-6.5973.099-2.688-3.455-0.029
188A190ILE00.0050.0125.898-0.146-0.1460.0000.0000.0000.000
189A191PHE0-0.027-0.0034.5940.1660.318-0.001-0.003-0.1480.000
190A192GLU-1-0.785-0.88110.468-0.032-0.0320.0000.0000.0000.000
191A193GLU-1-0.721-0.83313.544-0.130-0.1300.0000.0000.0000.000
192A194GLU-1-0.789-0.88414.155-0.075-0.0750.0000.0000.0000.000
193A195TYR0-0.020-0.00116.6500.0100.0100.0000.0000.0000.000
194A196PRO00.0010.00520.265-0.015-0.0150.0000.0000.0000.000
195A197ARG10.7180.81921.5070.1010.1010.0000.0000.0000.000
196A198GLY00.0020.00819.763-0.006-0.0060.0000.0000.0000.000
197A199PRO0-0.068-0.03215.517-0.021-0.0210.0000.0000.0000.000
198A200ILE0-0.0180.00411.9270.0200.0200.0000.0000.0000.000
199A201LYS10.7910.8789.3390.0680.0680.0000.0000.0000.000
200A202ARG10.7770.8462.403-4.681-1.0986.478-2.064-7.9960.006
201A203LYS10.7900.8687.326-0.136-0.1360.0000.0000.0000.000
202A204PRO0-0.040-0.0144.9690.0310.0310.0000.0000.0000.000
203A205LEU00.0100.0186.789-0.057-0.0570.0000.0000.0000.000