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: VRL11

Calculation Name: 3AQ2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3AQ2

Chain ID: A

ChEMBL ID:

UniProt ID: Q44522

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2257894.90102
FMO2-HF: Nuclear repulsion 2180734.976722
FMO2-HF: Total energy -77159.924298
FMO2-MP2: Total energy -77384.72869


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.
-17.107-11.54112.795-7.806-10.557-0.049
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 : 0.012 / q_NPA : 0.003
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].
3A3VAL00.0980.0403.782-1.3071.136-0.002-1.250-1.1910.005
4A4PRO0-0.040-0.0286.2000.2670.2670.0000.0000.0000.000
5A5THR0-0.040-0.0242.448-3.845-1.6382.248-1.343-3.113-0.009
6A6TRP0-0.057-0.0214.590-0.230-0.030-0.001-0.012-0.1870.000
7A7GLN00.0000.0005.9740.4220.4220.0000.0000.0000.000
8A8VAL00.0020.0178.711-0.064-0.0640.0000.0000.0000.000
9A9ARG10.8230.8907.0101.3531.3530.0000.0000.0000.000
10A10ASP-1-0.787-0.88913.376-0.345-0.3450.0000.0000.0000.000
11A11LEU0-0.030-0.01616.1630.0480.0480.0000.0000.0000.000
12A12ARG10.7300.83219.2550.3210.3210.0000.0000.0000.000
13A13ARG10.9450.96821.9270.1930.1930.0000.0000.0000.000
14A14ILE0-0.0160.01319.7630.0260.0260.0000.0000.0000.000
15A15LEU00.0360.01123.122-0.017-0.0170.0000.0000.0000.000
16A16ARG10.8900.94526.1130.1490.1490.0000.0000.0000.000
17A17VAL00.0300.00825.715-0.014-0.0140.0000.0000.0000.000
18A18SER0-0.013-0.00925.522-0.018-0.0180.0000.0000.0000.000
19A19GLU-1-0.824-0.90023.001-0.176-0.1760.0000.0000.0000.000
20A20LEU00.0370.03120.806-0.030-0.0300.0000.0000.0000.000
21A21SER0-0.021-0.00220.538-0.047-0.0470.0000.0000.0000.000
22A22GLN0-0.037-0.02920.171-0.035-0.0350.0000.0000.0000.000
23A23HIS00.022-0.00416.609-0.021-0.0210.0000.0000.0000.000
24A24LEU0-0.0090.00415.753-0.083-0.0830.0000.0000.0000.000
25A25ARG10.9470.97515.8290.2520.2520.0000.0000.0000.000
26A26GLN0-0.034-0.01711.4280.0040.0040.0000.0000.0000.000
27A27ALA00.0330.02211.653-0.117-0.1170.0000.0000.0000.000
28A28ARG10.9010.92610.9100.7320.7320.0000.0000.0000.000
29A29THR0-0.039-0.03211.562-0.180-0.1800.0000.0000.0000.000
30A30ASP-1-0.796-0.8637.707-0.928-0.9280.0000.0000.0000.000
31A31PHE00.0220.0266.512-0.655-0.6550.0000.0000.0000.000
32A32ARG10.8260.9126.5230.3750.3750.0000.0000.0000.000
33A33SER0-0.063-0.0537.027-0.031-0.0310.0000.0000.0000.000
34A34THR0-0.052-0.0432.412-0.8060.4971.067-0.679-1.6910.000
35A35LEU0-0.0070.0111.892-11.341-12.0799.484-4.556-4.191-0.045
36A36SER0-0.0050.0133.5811.4761.627-0.0010.034-0.1840.000
37A37GLN00.0670.0306.207-0.108-0.1080.0000.0000.0000.000
38A38LEU0-0.056-0.0168.2460.2310.2310.0000.0000.0000.000
39A39VAL00.0000.0016.521-0.374-0.3740.0000.0000.0000.000
40A40TYR00.0700.0448.3620.3010.3010.0000.0000.0000.000
41A41PHE0-0.056-0.0368.651-0.554-0.5540.0000.0000.0000.000
42A42ASN0-0.020-0.01310.9210.0570.0570.0000.0000.0000.000
43A43ARG10.8640.9519.3180.8280.8280.0000.0000.0000.000
44A44SER0-0.037-0.03615.4710.0550.0550.0000.0000.0000.000
45A45VAL0-0.018-0.02518.6700.0310.0310.0000.0000.0000.000
46A46VAL0-0.037-0.01221.9170.0460.0460.0000.0000.0000.000
47A47ASN0-0.005-0.03018.9110.0630.0630.0000.0000.0000.000
48A48PRO00.0310.02617.952-0.048-0.0480.0000.0000.0000.000
49A49ASN0-0.081-0.04315.393-0.014-0.0140.0000.0000.0000.000
50A50GLU-1-0.919-0.94113.847-0.400-0.4000.0000.0000.0000.000
51A51TYR0-0.062-0.0517.310-0.113-0.1130.0000.0000.0000.000
52A52ASP-1-0.782-0.87314.014-0.719-0.7190.0000.0000.0000.000
53A53ASP-1-0.813-0.92515.432-0.618-0.6180.0000.0000.0000.000
54A54GLU-1-0.835-0.83916.143-0.794-0.7940.0000.0000.0000.000
55A55TYR00.009-0.01911.928-0.142-0.1420.0000.0000.0000.000
56A56LEU0-0.053-0.02411.2980.1460.1460.0000.0000.0000.000
57A57LEU00.0160.02811.625-0.164-0.1640.0000.0000.0000.000
58A58SER00.008-0.0319.1810.2230.2230.0000.0000.0000.000
59A59ASP-1-0.848-0.89812.054-0.928-0.9280.0000.0000.0000.000
60A60GLN0-0.034-0.01814.4760.2140.2140.0000.0000.0000.000
61A61ARG10.9210.94616.4250.3790.3790.0000.0000.0000.000
62A62LEU00.0030.00515.224-0.040-0.0400.0000.0000.0000.000
63A63THR0-0.036-0.03018.5790.0610.0610.0000.0000.0000.000
64A64TYR0-0.010-0.01220.064-0.065-0.0650.0000.0000.0000.000
65A65VAL00.0470.02321.8500.0280.0280.0000.0000.0000.000
66A66TYR0-0.024-0.02523.286-0.004-0.0040.0000.0000.0000.000
67A67VAL00.0190.03123.339-0.001-0.0010.0000.0000.0000.000
68A68ASP-1-0.712-0.82626.576-0.254-0.2540.0000.0000.0000.000
69A69GLU-1-0.846-0.92825.075-0.248-0.2480.0000.0000.0000.000
70A70VAL0-0.023-0.00624.777-0.013-0.0130.0000.0000.0000.000
71A71THR00.012-0.03124.143-0.017-0.0170.0000.0000.0000.000
72A72ALA0-0.0020.00521.894-0.040-0.0400.0000.0000.0000.000
73A73GLN00.0150.00920.301-0.039-0.0390.0000.0000.0000.000
74A74LEU0-0.0110.00219.949-0.017-0.0170.0000.0000.0000.000
75A75CYS00.0070.00519.479-0.020-0.0200.0000.0000.0000.000
76A76GLY00.0200.00716.138-0.080-0.0800.0000.0000.0000.000
77A77LEU0-0.057-0.03014.939-0.073-0.0730.0000.0000.0000.000
78A78ASN0-0.068-0.03515.4250.0320.0320.0000.0000.0000.000
79A79ARG10.8590.94110.0161.0851.0850.0000.0000.0000.000
80A80LEU00.0220.00814.641-0.041-0.0410.0000.0000.0000.000
81A81LEU0-0.004-0.00717.968-0.018-0.0180.0000.0000.0000.000
82A82PRO00.0170.01020.0660.0180.0180.0000.0000.0000.000
83A83SER0-0.034-0.02223.927-0.022-0.0220.0000.0000.0000.000
84A84ASN0-0.057-0.05426.6430.0140.0140.0000.0000.0000.000
85A85SER00.0490.01929.0800.0260.0260.0000.0000.0000.000
86A86PRO00.0090.01130.700-0.013-0.0130.0000.0000.0000.000
87A87ALA0-0.003-0.01032.006-0.010-0.0100.0000.0000.0000.000
88A88PHE0-0.009-0.00627.054-0.014-0.0140.0000.0000.0000.000
89A89GLY00.0500.04426.762-0.031-0.0310.0000.0000.0000.000
90A90THR0-0.042-0.04722.7240.0110.0110.0000.0000.0000.000
91A91VAL0-0.026-0.00625.060-0.029-0.0290.0000.0000.0000.000
92A92ALA00.0040.00422.921-0.013-0.0130.0000.0000.0000.000
93A93THR00.0000.00624.8150.0240.0240.0000.0000.0000.000
94A94ALA00.0270.00524.167-0.035-0.0350.0000.0000.0000.000
95A95MET0-0.055-0.01425.2250.0120.0120.0000.0000.0000.000
96A96PRO0-0.0030.01424.693-0.019-0.0190.0000.0000.0000.000
97A97PRO00.0430.01123.3870.0310.0310.0000.0000.0000.000
98A98TRP00.0040.00622.7760.0150.0150.0000.0000.0000.000
99A99LEU0-0.094-0.03529.2400.0190.0190.0000.0000.0000.000
100A100LEU00.0130.00331.1320.0160.0160.0000.0000.0000.000
101A101ASP-1-0.788-0.87332.412-0.185-0.1850.0000.0000.0000.000
102A102PRO00.016-0.00631.444-0.007-0.0070.0000.0000.0000.000
103A103GLN0-0.036-0.03133.3810.0010.0010.0000.0000.0000.000
104A104GLU-1-0.871-0.93236.041-0.178-0.1780.0000.0000.0000.000
105A105MET0-0.015-0.01229.469-0.007-0.0070.0000.0000.0000.000
106A106ASN0-0.022-0.01233.5900.0030.0030.0000.0000.0000.000
107A107ALA00.0270.02635.044-0.001-0.0010.0000.0000.0000.000
108A108ILE0-0.007-0.00633.8790.0000.0000.0000.0000.0000.000
109A109LEU0-0.0240.00529.494-0.010-0.0100.0000.0000.0000.000
110A110GLN0-0.030-0.02633.5760.0010.0010.0000.0000.0000.000
111A111GLN0-0.059-0.01636.7200.0100.0100.0000.0000.0000.000
112A112SER0-0.037-0.02932.6440.0000.0000.0000.0000.0000.000
113A113CYS0-0.0300.02030.722-0.019-0.0190.0000.0000.0000.000
114A114GLY00.0220.02733.7990.0170.0170.0000.0000.0000.000
115A115GLN00.000-0.01234.607-0.009-0.0090.0000.0000.0000.000
116A116GLY0-0.006-0.02235.2050.0050.0050.0000.0000.0000.000
117A117GLY00.0010.02730.821-0.002-0.0020.0000.0000.0000.000
118A118PHE0-0.040-0.02526.9730.0140.0140.0000.0000.0000.000
119A119VAL0-0.039-0.01726.9450.0150.0150.0000.0000.0000.000
120A120ASN00.024-0.01630.052-0.003-0.0030.0000.0000.0000.000
121A121TYR00.027-0.02327.5640.0070.0070.0000.0000.0000.000
122A122HIS00.0130.00634.1750.0180.0180.0000.0000.0000.000
123A123HIS0-0.0160.00635.2310.0150.0150.0000.0000.0000.000
124A124GLY00.0260.02836.8980.0100.0100.0000.0000.0000.000
125A125PRO0-0.003-0.01034.767-0.012-0.0120.0000.0000.0000.000
126A126SER00.0030.01533.054-0.013-0.0130.0000.0000.0000.000
127A127THR0-0.024-0.03231.044-0.016-0.0160.0000.0000.0000.000
128A128ASN0-0.004-0.01428.850-0.015-0.0150.0000.0000.0000.000
129A129GLY00.0390.02929.509-0.002-0.0020.0000.0000.0000.000
130A130PHE0-0.038-0.02924.3720.0060.0060.0000.0000.0000.000
131A131PHE00.015-0.00119.574-0.004-0.0040.0000.0000.0000.000
132A132LEU00.0350.03018.632-0.008-0.0080.0000.0000.0000.000
133A133ALA0-0.029-0.02017.1980.0350.0350.0000.0000.0000.000
134A134ILE00.0100.00115.654-0.113-0.1130.0000.0000.0000.000
135A135LEU0-0.0160.00611.8160.0560.0560.0000.0000.0000.000
136A136MET00.0090.04415.275-0.028-0.0280.0000.0000.0000.000
137A137SER00.038-0.01815.869-0.060-0.0600.0000.0000.0000.000
138A138GLN0-0.014-0.02216.8570.0330.0330.0000.0000.0000.000
139A139LEU0-0.022-0.00518.8340.0730.0730.0000.0000.0000.000
140A140PHE0-0.069-0.04019.1950.0460.0460.0000.0000.0000.000
141A141ILE00.0530.05422.596-0.008-0.0080.0000.0000.0000.000
142A142ARG10.7970.85925.7130.3320.3320.0000.0000.0000.000
143A143ILE0-0.019-0.00927.4800.0200.0200.0000.0000.0000.000
144A144ARG10.8150.87530.5960.2770.2770.0000.0000.0000.000
145A145THR0-0.028-0.02730.797-0.031-0.0310.0000.0000.0000.000
146A146ASP-1-0.760-0.82832.417-0.233-0.2330.0000.0000.0000.000
147A147VAL0-0.009-0.02433.496-0.009-0.0090.0000.0000.0000.000
148A148ILE00.0160.01334.0500.0110.0110.0000.0000.0000.000
149A149ARG10.8500.89633.4160.1920.1920.0000.0000.0000.000
150A150GLY00.0260.02336.9530.0020.0020.0000.0000.0000.000
151A151GLN0-0.036-0.00631.656-0.014-0.0140.0000.0000.0000.000
152A152GLY00.0400.02131.8720.0060.0060.0000.0000.0000.000
153A153TYR0-0.062-0.05128.194-0.024-0.0240.0000.0000.0000.000
154A154GLY00.0140.01627.6930.0130.0130.0000.0000.0000.000
155A155TRP0-0.014-0.02727.079-0.034-0.0340.0000.0000.0000.000
156A156TYR00.0390.00123.9740.0170.0170.0000.0000.0000.000
157A157ALA00.0170.00626.1030.0080.0080.0000.0000.0000.000
158A158ARG10.7960.88720.0440.6090.6090.0000.0000.0000.000
159A159GLN00.0340.00424.3060.0470.0470.0000.0000.0000.000
160A160GLY00.0640.02127.0400.0060.0060.0000.0000.0000.000
161A161ASN0-0.119-0.05730.4130.0060.0060.0000.0000.0000.000
162A162TYR0-0.0060.00530.1530.0160.0160.0000.0000.0000.000
163A163VAL0-0.003-0.00931.9890.0000.0000.0000.0000.0000.000
164A164GLU-1-0.827-0.91627.655-0.379-0.3790.0000.0000.0000.000
165A165GLU-1-0.823-0.87530.824-0.261-0.2610.0000.0000.0000.000
166A166GLY0-0.080-0.03932.6600.0100.0100.0000.0000.0000.000
167A180GLU-1-0.805-0.89025.419-0.399-0.3990.0000.0000.0000.000
168A181THR0-0.040-0.03426.0200.0230.0230.0000.0000.0000.000
169A182ARG10.8000.89221.0250.4710.4710.0000.0000.0000.000
170A183GLU-1-0.759-0.83820.690-0.409-0.4090.0000.0000.0000.000
171A184PHE0-0.015-0.01819.958-0.071-0.0710.0000.0000.0000.000
172A185GLN0-0.009-0.00117.2500.1000.1000.0000.0000.0000.000
173A186LEU00.0210.01422.057-0.013-0.0130.0000.0000.0000.000
174A187SER00.022-0.01024.4000.0390.0390.0000.0000.0000.000
175A188ASP-1-0.806-0.87825.503-0.328-0.3280.0000.0000.0000.000
176A189LEU0-0.057-0.01822.427-0.005-0.0050.0000.0000.0000.000
177A190ILE0-0.0190.02319.3670.0140.0140.0000.0000.0000.000
178A191HIS00.0050.00512.440-0.107-0.1070.0000.0000.0000.000
179A192TYR00.019-0.02714.718-0.040-0.0400.0000.0000.0000.000
180A193PRO0-0.011-0.01310.1730.0260.0260.0000.0000.0000.000
181A194ILE0-0.0040.02912.2400.0550.0550.0000.0000.0000.000
182A195VAL0-0.028-0.00411.556-0.110-0.1100.0000.0000.0000.000
183A196ALA00.003-0.02212.4170.0220.0220.0000.0000.0000.000
184A197LEU00.0050.02115.2260.0010.0010.0000.0000.0000.000
185A198GLY00.018-0.00518.6290.0210.0210.0000.0000.0000.000
186A199SER00.0300.02621.8420.0040.0040.0000.0000.0000.000
187A200CYS0-0.017-0.01625.671-0.022-0.0220.0000.0000.0000.000
188A201HIS0-0.0320.00428.0730.0190.0190.0000.0000.0000.000
189A202LEU0-0.036-0.00625.8130.0100.0100.0000.0000.0000.000
190A203THR00.0350.01829.8470.0170.0170.0000.0000.0000.000
191A204ARG10.9390.96330.5080.1610.1610.0000.0000.0000.000