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: 536LZ

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 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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2255327.398989
FMO2-HF: Nuclear repulsion 2178167.955304
FMO2-HF: Total energy -77159.443685
FMO2-MP2: Total energy -77384.391453


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.
-17.394-12.36313.372-8.041-10.361-0.039
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 : 0.018 / q_NPA : 0.002
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].
3A3VAL00.1070.0463.648-2.2290.710-0.001-1.567-1.3700.007
4A4PRO0-0.056-0.0336.1110.2600.2600.0000.0000.0000.000
5A5THR0-0.052-0.0272.254-2.721-1.0252.607-1.385-2.919-0.007
6A6TRP0-0.051-0.0134.876-0.215-0.026-0.001-0.014-0.1740.000
7A7GLN0-0.015-0.0026.2960.3100.3100.0000.0000.0000.000
8A8VAL00.0230.0229.358-0.100-0.1000.0000.0000.0000.000
9A9ARG10.8360.9137.8961.2671.2670.0000.0000.0000.000
10A10ASP-1-0.759-0.86613.928-0.330-0.3300.0000.0000.0000.000
11A11LEU0-0.043-0.02716.7400.0420.0420.0000.0000.0000.000
12A12ARG10.8030.86819.7120.3120.3120.0000.0000.0000.000
13A13ARG10.9350.97022.4760.1930.1930.0000.0000.0000.000
14A14ILE0-0.0210.01020.6560.0220.0220.0000.0000.0000.000
15A15LEU00.0530.01523.895-0.017-0.0170.0000.0000.0000.000
16A16ARG10.8780.94126.9350.1810.1810.0000.0000.0000.000
17A17VAL00.0460.01726.379-0.018-0.0180.0000.0000.0000.000
18A18SER0-0.024-0.02325.959-0.016-0.0160.0000.0000.0000.000
19A19GLU-1-0.843-0.90923.756-0.216-0.2160.0000.0000.0000.000
20A20LEU00.0410.02621.156-0.033-0.0330.0000.0000.0000.000
21A21SER0-0.018-0.00820.992-0.060-0.0600.0000.0000.0000.000
22A22GLN0-0.028-0.02020.653-0.041-0.0410.0000.0000.0000.000
23A23HIS00.0400.01317.143-0.037-0.0370.0000.0000.0000.000
24A24LEU0-0.030-0.00316.208-0.086-0.0860.0000.0000.0000.000
25A25ARG10.9480.97916.1340.3320.3320.0000.0000.0000.000
26A26GLN0-0.033-0.02712.063-0.010-0.0100.0000.0000.0000.000
27A27ALA00.0300.02211.979-0.125-0.1250.0000.0000.0000.000
28A28ARG10.8720.92111.0820.7880.7880.0000.0000.0000.000
29A29THR0-0.048-0.02711.398-0.211-0.2110.0000.0000.0000.000
30A30ASP-1-0.807-0.8938.130-1.152-1.1520.0000.0000.0000.000
31A31PHE00.0130.0066.785-0.722-0.7220.0000.0000.0000.000
32A32ARG10.8660.9316.6560.5210.5210.0000.0000.0000.000
33A33SER0-0.094-0.0576.825-0.205-0.2050.0000.0000.0000.000
34A34THR0-0.057-0.0242.356-1.213-0.0191.195-0.696-1.6930.001
35A35LEU0-0.0040.0121.875-10.994-12.1609.573-4.399-4.008-0.040
36A36SER00.0230.0253.6331.4251.604-0.0010.020-0.1970.000
37A37GLN00.0560.0216.085-0.278-0.2780.0000.0000.0000.000
38A38LEU0-0.029-0.0038.0160.2820.2820.0000.0000.0000.000
39A39VAL0-0.0110.0026.384-0.371-0.3710.0000.0000.0000.000
40A40TYR00.0780.0547.8070.4270.4270.0000.0000.0000.000
41A41PHE0-0.034-0.0448.124-0.580-0.5800.0000.0000.0000.000
42A42ASN0-0.021-0.00710.4450.1140.1140.0000.0000.0000.000
43A43ARG10.8680.9498.5990.6440.6440.0000.0000.0000.000
44A44SER00.002-0.02214.8720.0400.0400.0000.0000.0000.000
45A45VAL0-0.045-0.03718.0260.0380.0380.0000.0000.0000.000
46A46VAL0-0.030-0.00321.2060.0440.0440.0000.0000.0000.000
47A47ASN00.020-0.00618.7090.0510.0510.0000.0000.0000.000
48A48PRO00.0550.02817.633-0.042-0.0420.0000.0000.0000.000
49A49ASN0-0.056-0.02914.761-0.010-0.0100.0000.0000.0000.000
50A50GLU-1-0.990-0.98613.260-0.265-0.2650.0000.0000.0000.000
51A51TYR0-0.089-0.0556.823-0.149-0.1490.0000.0000.0000.000
52A52ASP-1-0.774-0.88213.568-0.659-0.6590.0000.0000.0000.000
53A53ASP-1-0.800-0.90214.966-0.535-0.5350.0000.0000.0000.000
54A54GLU-1-0.824-0.86015.592-0.756-0.7560.0000.0000.0000.000
55A55TYR0-0.022-0.02811.724-0.114-0.1140.0000.0000.0000.000
56A56LEU0-0.038-0.03110.3340.1360.1360.0000.0000.0000.000
57A57LEU00.0020.02411.372-0.140-0.1400.0000.0000.0000.000
58A58SER0-0.005-0.0359.0980.2490.2490.0000.0000.0000.000
59A59ASP-1-0.872-0.92412.114-0.995-0.9950.0000.0000.0000.000
60A60GLN0-0.044-0.01914.5150.2480.2480.0000.0000.0000.000
61A61ARG10.9270.96016.1850.3880.3880.0000.0000.0000.000
62A62LEU00.0110.00715.007-0.035-0.0350.0000.0000.0000.000
63A63THR0-0.028-0.02118.4520.0610.0610.0000.0000.0000.000
64A64TYR0-0.008-0.01420.108-0.056-0.0560.0000.0000.0000.000
65A65VAL00.0580.03121.6140.0290.0290.0000.0000.0000.000
66A66TYR0-0.033-0.03123.670-0.002-0.0020.0000.0000.0000.000
67A67VAL00.0170.03523.9060.0030.0030.0000.0000.0000.000
68A68ASP-1-0.714-0.83827.015-0.248-0.2480.0000.0000.0000.000
69A69GLU-1-0.918-0.98026.094-0.237-0.2370.0000.0000.0000.000
70A70VAL0-0.0010.00425.701-0.011-0.0110.0000.0000.0000.000
71A71THR00.004-0.03224.564-0.012-0.0120.0000.0000.0000.000
72A72ALA0-0.010-0.00122.522-0.036-0.0360.0000.0000.0000.000
73A73GLN00.0160.02620.997-0.043-0.0430.0000.0000.0000.000
74A74LEU00.0120.00720.753-0.015-0.0150.0000.0000.0000.000
75A75CYS00.0080.00519.864-0.016-0.0160.0000.0000.0000.000
76A76GLY00.014-0.00316.985-0.073-0.0730.0000.0000.0000.000
77A77LEU0-0.079-0.04915.686-0.058-0.0580.0000.0000.0000.000
78A78ASN0-0.070-0.03416.3460.0490.0490.0000.0000.0000.000
79A79ARG10.8580.96010.4320.9070.9070.0000.0000.0000.000
80A80LEU00.0440.02015.078-0.014-0.0140.0000.0000.0000.000
81A81LEU0-0.009-0.00718.371-0.020-0.0200.0000.0000.0000.000
82A82PRO00.0240.01520.2030.0220.0220.0000.0000.0000.000
83A83SER0-0.041-0.01824.043-0.022-0.0220.0000.0000.0000.000
84A84ASN0-0.024-0.03326.6820.0120.0120.0000.0000.0000.000
85A85SER00.0490.01629.1240.0240.0240.0000.0000.0000.000
86A86PRO00.0120.01930.948-0.009-0.0090.0000.0000.0000.000
87A87ALA0-0.004-0.01031.751-0.011-0.0110.0000.0000.0000.000
88A88PHE0-0.006-0.00826.983-0.012-0.0120.0000.0000.0000.000
89A89GLY00.0380.03726.564-0.028-0.0280.0000.0000.0000.000
90A90THR0-0.036-0.03322.7330.0070.0070.0000.0000.0000.000
91A91VAL0-0.046-0.02325.067-0.024-0.0240.0000.0000.0000.000
92A92ALA0-0.0050.00122.813-0.007-0.0070.0000.0000.0000.000
93A93THR00.0250.01824.7930.0190.0190.0000.0000.0000.000
94A94ALA00.003-0.01024.197-0.036-0.0360.0000.0000.0000.000
95A95MET0-0.055-0.01125.2430.0050.0050.0000.0000.0000.000
96A96PRO00.0090.02425.048-0.014-0.0140.0000.0000.0000.000
97A97PRO00.0650.01823.8990.0300.0300.0000.0000.0000.000
98A98TRP0-0.024-0.00723.2710.0180.0180.0000.0000.0000.000
99A99LEU0-0.110-0.04429.4450.0200.0200.0000.0000.0000.000
100A100LEU00.029-0.00331.3780.0160.0160.0000.0000.0000.000
101A101ASP-1-0.817-0.89432.743-0.190-0.1900.0000.0000.0000.000
102A102PRO00.023-0.00131.800-0.006-0.0060.0000.0000.0000.000
103A103GLN0-0.009-0.01333.7670.0000.0000.0000.0000.0000.000
104A104GLU-1-0.886-0.93936.558-0.181-0.1810.0000.0000.0000.000
105A105MET0-0.026-0.02030.365-0.005-0.0050.0000.0000.0000.000
106A106ASN0-0.027-0.01934.1020.0060.0060.0000.0000.0000.000
107A107ALA00.0460.03035.3440.0000.0000.0000.0000.0000.000
108A108ILE0-0.013-0.00933.9390.0010.0010.0000.0000.0000.000
109A109LEU0-0.028-0.01929.785-0.007-0.0070.0000.0000.0000.000
110A110GLN0-0.043-0.01833.7230.0010.0010.0000.0000.0000.000
111A111GLN0-0.0110.00736.8050.0050.0050.0000.0000.0000.000
112A112SER0-0.077-0.03232.621-0.003-0.0030.0000.0000.0000.000
113A113CYS0-0.0290.02430.747-0.016-0.0160.0000.0000.0000.000
114A114GLY00.0470.04033.7980.0150.0150.0000.0000.0000.000
115A115GLN00.003-0.00834.729-0.008-0.0080.0000.0000.0000.000
116A116GLY0-0.006-0.02035.2990.0030.0030.0000.0000.0000.000
117A117GLY00.0020.02830.948-0.001-0.0010.0000.0000.0000.000
118A118PHE0-0.034-0.02427.1330.0140.0140.0000.0000.0000.000
119A119VAL0-0.030-0.00327.1640.0130.0130.0000.0000.0000.000
120A120ASN00.023-0.01230.055-0.003-0.0030.0000.0000.0000.000
121A121TYR00.016-0.05027.7540.0030.0030.0000.0000.0000.000
122A122HIS0-0.015-0.02134.3320.0160.0160.0000.0000.0000.000
123A123HIS0-0.0350.00036.1750.0140.0140.0000.0000.0000.000
124A124GLY00.0210.02937.3720.0090.0090.0000.0000.0000.000
125A125PRO00.0250.00135.194-0.012-0.0120.0000.0000.0000.000
126A126SER0-0.0280.00433.665-0.013-0.0130.0000.0000.0000.000
127A127THR0-0.018-0.02931.863-0.016-0.0160.0000.0000.0000.000
128A128ASN0-0.009-0.01129.392-0.011-0.0110.0000.0000.0000.000
129A129GLY00.0220.01829.741-0.005-0.0050.0000.0000.0000.000
130A130PHE0-0.026-0.01624.8320.0020.0020.0000.0000.0000.000
131A131PHE00.0210.00519.988-0.006-0.0060.0000.0000.0000.000
132A132LEU00.0310.02119.097-0.010-0.0100.0000.0000.0000.000
133A133ALA0-0.027-0.01817.2950.0230.0230.0000.0000.0000.000
134A134ILE00.0260.00415.662-0.113-0.1130.0000.0000.0000.000
135A135LEU0-0.020-0.00111.8240.0480.0480.0000.0000.0000.000
136A136MET0-0.0120.03015.232-0.029-0.0290.0000.0000.0000.000
137A137SER00.038-0.00815.399-0.057-0.0570.0000.0000.0000.000
138A138GLN00.011-0.00916.3420.0120.0120.0000.0000.0000.000
139A139LEU0-0.040-0.01018.4990.0710.0710.0000.0000.0000.000
140A140PHE0-0.065-0.03118.8550.0480.0480.0000.0000.0000.000
141A141ILE00.0660.04422.199-0.010-0.0100.0000.0000.0000.000
142A142ARG10.8520.89725.2660.3440.3440.0000.0000.0000.000
143A143ILE00.0090.00627.2540.0200.0200.0000.0000.0000.000
144A144ARG10.8080.87930.4050.2800.2800.0000.0000.0000.000
145A145THR0-0.047-0.03230.735-0.033-0.0330.0000.0000.0000.000
146A146ASP-1-0.759-0.82932.426-0.233-0.2330.0000.0000.0000.000
147A147VAL0-0.002-0.01933.375-0.013-0.0130.0000.0000.0000.000
148A148ILE00.0290.01634.3630.0120.0120.0000.0000.0000.000
149A149ARG10.8580.91633.3030.2060.2060.0000.0000.0000.000
150A150GLY00.0190.01036.863-0.001-0.0010.0000.0000.0000.000
151A151GLN0-0.0220.00531.898-0.011-0.0110.0000.0000.0000.000
152A152GLY00.0220.01932.1970.0040.0040.0000.0000.0000.000
153A153TYR0-0.052-0.04028.039-0.025-0.0250.0000.0000.0000.000
154A154GLY00.0040.00327.3740.0150.0150.0000.0000.0000.000
155A155TRP00.003-0.00427.521-0.025-0.0250.0000.0000.0000.000
156A156TYR00.032-0.00624.0370.0080.0080.0000.0000.0000.000
157A157ALA00.0300.01726.0080.0030.0030.0000.0000.0000.000
158A158ARG10.8120.90419.5070.5750.5750.0000.0000.0000.000
159A159GLN00.0490.00724.0760.0450.0450.0000.0000.0000.000
160A160GLY00.0690.02126.7430.0020.0020.0000.0000.0000.000
161A161ASN0-0.109-0.05030.0740.0100.0100.0000.0000.0000.000
162A162TYR0-0.013-0.01529.9430.0130.0130.0000.0000.0000.000
163A163VAL0-0.009-0.00731.544-0.002-0.0020.0000.0000.0000.000
164A164GLU-1-0.981-0.98127.612-0.345-0.3450.0000.0000.0000.000
165A165GLU-1-0.856-0.92630.640-0.266-0.2660.0000.0000.0000.000
166A166GLY0-0.018-0.00532.3140.0030.0030.0000.0000.0000.000
167A180GLU-1-0.815-0.90524.914-0.359-0.3590.0000.0000.0000.000
168A181THR0-0.018-0.02125.5500.0130.0130.0000.0000.0000.000
169A182ARG10.7840.88720.6490.4270.4270.0000.0000.0000.000
170A183GLU-1-0.771-0.85120.193-0.368-0.3680.0000.0000.0000.000
171A184PHE0-0.014-0.01319.451-0.065-0.0650.0000.0000.0000.000
172A185GLN0-0.0110.00217.4120.0960.0960.0000.0000.0000.000
173A186LEU00.0300.01121.672-0.019-0.0190.0000.0000.0000.000
174A187SER00.0220.00624.2180.0370.0370.0000.0000.0000.000
175A188ASP-1-0.811-0.88325.689-0.296-0.2960.0000.0000.0000.000
176A189LEU0-0.049-0.01822.829-0.010-0.0100.0000.0000.0000.000
177A190ILE0-0.0380.00419.3380.0140.0140.0000.0000.0000.000
178A191HIS00.0020.00112.108-0.105-0.1050.0000.0000.0000.000
179A192TYR00.001-0.03414.942-0.040-0.0400.0000.0000.0000.000
180A193PRO0-0.016-0.00810.2860.0250.0250.0000.0000.0000.000
181A194ILE00.0020.01912.4140.0690.0690.0000.0000.0000.000
182A195VAL0-0.032-0.00711.895-0.097-0.0970.0000.0000.0000.000
183A196ALA0-0.004-0.02512.7750.0210.0210.0000.0000.0000.000
184A197LEU00.0150.03015.5540.0050.0050.0000.0000.0000.000
185A198GLY00.010-0.00618.9530.0140.0140.0000.0000.0000.000
186A199SER00.0290.02222.0330.0080.0080.0000.0000.0000.000
187A200CYS0-0.008-0.01025.809-0.025-0.0250.0000.0000.0000.000
188A201HIS0-0.0220.00428.3540.0170.0170.0000.0000.0000.000
189A202LEU0-0.020-0.00526.2590.0070.0070.0000.0000.0000.000
190A203THR00.0160.00830.2860.0180.0180.0000.0000.0000.000
191A204ARG10.9620.97931.0840.1790.1790.0000.0000.0000.000