FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: Z6QZN

Calculation Name: 3D7L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D7L

Chain ID: A

ChEMBL ID:

UniProt ID: Q92AH8

Base Structure: X-ray

Registration Date: 2023-09-20

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2104365.079699
FMO2-HF: Nuclear repulsion 2029769.420767
FMO2-HF: Total energy -74595.658932
FMO2-MP2: Total energy -74813.158724


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:SER)


Summations of interaction energy for fragment #1(A:-2:SER)
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.
-3.1730.440.036-1.697-1.949-0.001
Interaction energy analysis for fragmet #1(A:-2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.023
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].
3A0ALA00.0160.0243.869-1.8750.948-0.026-1.441-1.355-0.002
4A1MET00.0020.0055.527-0.823-0.8230.0000.0000.0000.000
5A2LYS10.8520.9193.004-0.4240.3160.063-0.256-0.5460.001
6A3ILE0-0.020-0.0268.069-0.029-0.0290.0000.0000.0000.000
7A4LEU00.0440.03211.6930.1000.1000.0000.0000.0000.000
8A5LEU0-0.048-0.02613.471-0.029-0.0290.0000.0000.0000.000
9A6ILE00.0380.00816.8890.0390.0390.0000.0000.0000.000
10A7GLY00.027-0.01119.693-0.014-0.0140.0000.0000.0000.000
11A8ALA0-0.043-0.01618.9260.0000.0000.0000.0000.0000.000
12A9SER0-0.0010.00721.0340.0030.0030.0000.0000.0000.000
13A10GLY00.0250.02223.9500.0000.0000.0000.0000.0000.000
14A11THR0-0.010-0.01525.836-0.001-0.0010.0000.0000.0000.000
15A12LEU00.0400.01825.6920.0010.0010.0000.0000.0000.000
16A13GLY00.0620.01822.788-0.006-0.0060.0000.0000.0000.000
17A14SER00.0310.02421.6290.0050.0050.0000.0000.0000.000
18A15ALA0-0.015-0.00422.5870.0060.0060.0000.0000.0000.000
19A16VAL0-0.031-0.03019.454-0.004-0.0040.0000.0000.0000.000
20A17LYS10.8480.90116.649-0.161-0.1610.0000.0000.0000.000
21A18GLU-1-0.864-0.91218.2190.0530.0530.0000.0000.0000.000
22A19ARG10.8370.89219.9890.0260.0260.0000.0000.0000.000
23A20LEU0-0.013-0.00615.474-0.007-0.0070.0000.0000.0000.000
24A21GLU-1-0.793-0.87814.2840.1590.1590.0000.0000.0000.000
25A22LYS10.7390.85714.393-0.017-0.0170.0000.0000.0000.000
26A23LYS10.7890.88913.4190.1030.1030.0000.0000.0000.000
27A24ALA00.0060.00910.276-0.077-0.0770.0000.0000.0000.000
28A25GLU-1-0.807-0.8825.1930.7190.769-0.0010.000-0.0480.000
29A26VAL0-0.045-0.0309.167-0.135-0.1350.0000.0000.0000.000
30A27ILE00.0310.0378.2690.0600.0600.0000.0000.0000.000
31A28THR0-0.044-0.06012.416-0.075-0.0750.0000.0000.0000.000
32A29ALA00.0390.01416.2360.0240.0240.0000.0000.0000.000
33A30GLY00.0420.00918.662-0.021-0.0210.0000.0000.0000.000
34A31ARG10.8170.89922.441-0.050-0.0500.0000.0000.0000.000
35A32HIS00.0110.00525.4780.0060.0060.0000.0000.0000.000
36A33SER0-0.042-0.03323.0230.0050.0050.0000.0000.0000.000
37A34GLY00.0050.01219.225-0.021-0.0210.0000.0000.0000.000
38A35ASP-1-0.832-0.86814.0630.2980.2980.0000.0000.0000.000
39A36VAL0-0.0080.00714.8850.0220.0220.0000.0000.0000.000
40A37THR0-0.032-0.02317.693-0.022-0.0220.0000.0000.0000.000
41A38VAL0-0.009-0.01520.3310.0000.0000.0000.0000.0000.000
42A39ASP-1-0.819-0.87922.3390.0290.0290.0000.0000.0000.000
43A40ILE00.021-0.00423.223-0.003-0.0030.0000.0000.0000.000
44A41THR0-0.042-0.02625.520-0.008-0.0080.0000.0000.0000.000
45A42ASN0-0.010-0.00227.049-0.003-0.0030.0000.0000.0000.000
46A43ILE00.0780.02225.0010.0050.0050.0000.0000.0000.000
47A44ASP-1-0.826-0.89423.8420.0580.0580.0000.0000.0000.000
48A45SER00.0030.00922.8730.0130.0130.0000.0000.0000.000
49A46ILE0-0.021-0.00720.1450.0120.0120.0000.0000.0000.000
50A47LYS10.9320.97119.166-0.007-0.0070.0000.0000.0000.000
51A48LYS10.8800.92118.345-0.072-0.0720.0000.0000.0000.000
52A49MET00.0030.02916.3860.0270.0270.0000.0000.0000.000
53A50TYR0-0.026-0.05214.1090.0190.0190.0000.0000.0000.000
54A51GLU-1-0.976-0.97913.4450.1770.1770.0000.0000.0000.000
55A52GLN0-0.058-0.03113.7920.0450.0450.0000.0000.0000.000
56A53VAL0-0.043-0.01310.5530.0880.0880.0000.0000.0000.000
57A54GLY00.0130.0208.9550.1350.1350.0000.0000.0000.000
58A55LYS10.8240.9027.5910.1680.1680.0000.0000.0000.000
59A56VAL0-0.015-0.0026.698-0.193-0.1930.0000.0000.0000.000
60A57ASP-1-0.788-0.8787.322-2.174-2.1740.0000.0000.0000.000
61A58ALA0-0.025-0.0119.9310.1490.1490.0000.0000.0000.000
62A59ILE00.0000.01812.7610.0320.0320.0000.0000.0000.000
63A60VAL0-0.024-0.01715.4790.0070.0070.0000.0000.0000.000
64A61SER00.0170.01218.4150.0310.0310.0000.0000.0000.000
65A62ALA0-0.0340.00621.711-0.005-0.0050.0000.0000.0000.000
66A63THR0-0.026-0.02623.5410.0150.0150.0000.0000.0000.000
67A64GLY00.0400.01225.800-0.009-0.0090.0000.0000.0000.000
68A65SER0-0.071-0.04228.6220.0020.0020.0000.0000.0000.000
69A66ALA00.044-0.01932.285-0.003-0.0030.0000.0000.0000.000
70A67THR0-0.037-0.02535.7040.0030.0030.0000.0000.0000.000
71A68PHE0-0.0030.01137.413-0.003-0.0030.0000.0000.0000.000
72A69SER00.0360.00341.5650.0030.0030.0000.0000.0000.000
73A70PRO00.0140.02245.045-0.002-0.0020.0000.0000.0000.000
74A71LEU00.0460.01946.7650.0000.0000.0000.0000.0000.000
75A72THR0-0.015-0.01748.5430.0000.0000.0000.0000.0000.000
76A73GLU-1-0.880-0.93448.6900.0040.0040.0000.0000.0000.000
77A74LEU0-0.080-0.02842.4200.0010.0010.0000.0000.0000.000
78A75THR0-0.005-0.02646.417-0.001-0.0010.0000.0000.0000.000
79A76PRO00.031-0.00144.125-0.001-0.0010.0000.0000.0000.000
80A77GLU-1-0.828-0.90042.2890.0000.0000.0000.0000.0000.000
81A78LYS10.8790.94041.095-0.002-0.0020.0000.0000.0000.000
82A79ASN00.0520.04240.3240.0000.0000.0000.0000.0000.000
83A80ALA00.0070.00438.292-0.002-0.0020.0000.0000.0000.000
84A81VAL00.0210.02336.0010.0000.0000.0000.0000.0000.000
85A82THR00.0270.00834.6120.0010.0010.0000.0000.0000.000
86A83ILE0-0.030-0.01033.581-0.003-0.0030.0000.0000.0000.000
87A84SER0-0.042-0.03232.398-0.002-0.0020.0000.0000.0000.000
88A85SER00.0010.01529.7420.0000.0000.0000.0000.0000.000
89A86LYS10.7840.89429.0050.0220.0220.0000.0000.0000.000
90A87LEU00.0220.02429.666-0.007-0.0070.0000.0000.0000.000
91A88GLY00.0430.01628.959-0.006-0.0060.0000.0000.0000.000
92A89GLY00.0510.03626.938-0.003-0.0030.0000.0000.0000.000
93A90GLN0-0.021-0.01824.369-0.008-0.0080.0000.0000.0000.000
94A91ILE00.0170.01424.021-0.012-0.0120.0000.0000.0000.000
95A92ASN0-0.027-0.03124.531-0.011-0.0110.0000.0000.0000.000
96A93LEU0-0.0020.00119.715-0.001-0.0010.0000.0000.0000.000
97A94VAL00.0050.02619.612-0.015-0.0150.0000.0000.0000.000
98A95LEU0-0.015-0.01920.414-0.013-0.0130.0000.0000.0000.000
99A96LEU0-0.065-0.03020.7030.0030.0030.0000.0000.0000.000
100A97GLY00.0390.02216.6960.0160.0160.0000.0000.0000.000
101A98ILE00.001-0.00415.719-0.044-0.0440.0000.0000.0000.000
102A99ASP-1-0.929-0.95915.379-0.219-0.2190.0000.0000.0000.000
103A100SER0-0.016-0.00612.352-0.014-0.0140.0000.0000.0000.000
104A101LEU00.0060.02911.207-0.070-0.0700.0000.0000.0000.000
105A102ASN0-0.005-0.0235.9910.3820.3820.0000.0000.0000.000
106A103ASP-1-0.840-0.94210.249-0.423-0.4230.0000.0000.0000.000
107A104LYS10.7840.90112.2740.4160.4160.0000.0000.0000.000
108A105GLY00.0530.04212.8450.0230.0230.0000.0000.0000.000
109A106SER0-0.036-0.02813.5530.0790.0790.0000.0000.0000.000
110A107PHE00.0990.03915.9960.0000.0000.0000.0000.0000.000
111A108THR0-0.082-0.03318.5200.0020.0020.0000.0000.0000.000
112A109LEU00.0330.02720.9750.0120.0120.0000.0000.0000.000
113A110THR00.010-0.01323.8880.0010.0010.0000.0000.0000.000
114A111THR0-0.025-0.01126.9160.0040.0040.0000.0000.0000.000
115A112GLY00.0350.01130.5030.0070.0070.0000.0000.0000.000
116A113ILE00.0460.02033.3220.0000.0000.0000.0000.0000.000
117A114MET0-0.0010.01536.3410.0010.0010.0000.0000.0000.000
118A115MET0-0.082-0.03833.2820.0010.0010.0000.0000.0000.000
119A116GLU-1-0.894-0.90637.369-0.045-0.0450.0000.0000.0000.000
120A117ASP-1-0.885-0.93840.293-0.019-0.0190.0000.0000.0000.000
121A118PRO0-0.058-0.01841.8760.0020.0020.0000.0000.0000.000
122A119ILE00.0480.02441.1170.0010.0010.0000.0000.0000.000
123A120VAL00.028-0.00344.6260.0000.0000.0000.0000.0000.000
124A121GLN0-0.020-0.01644.4660.0010.0010.0000.0000.0000.000
125A122GLY00.0720.04141.1060.0010.0010.0000.0000.0000.000
126A123ALA0-0.002-0.00240.398-0.002-0.0020.0000.0000.0000.000
127A124SER00.0360.01639.373-0.002-0.0020.0000.0000.0000.000
128A125ALA00.0260.00136.251-0.002-0.0020.0000.0000.0000.000
129A126ALA00.0090.01835.965-0.004-0.0040.0000.0000.0000.000
130A127MET0-0.0130.00037.171-0.004-0.0040.0000.0000.0000.000
131A128ALA0-0.010-0.01033.006-0.004-0.0040.0000.0000.0000.000
132A129ASN0-0.015-0.00632.380-0.005-0.0050.0000.0000.0000.000
133A130GLY00.0920.04632.722-0.006-0.0060.0000.0000.0000.000
134A131ALA0-0.022-0.00933.690-0.005-0.0050.0000.0000.0000.000
135A132VAL00.000-0.00327.405-0.006-0.0060.0000.0000.0000.000
136A133THR0-0.009-0.02228.943-0.011-0.0110.0000.0000.0000.000
137A134ALA0-0.028-0.01130.536-0.007-0.0070.0000.0000.0000.000
138A135PHE00.0140.00224.778-0.005-0.0050.0000.0000.0000.000
139A136ALA00.0100.00626.081-0.008-0.0080.0000.0000.0000.000
140A137LYS10.8510.91626.8100.0880.0880.0000.0000.0000.000
141A138SER00.0060.01429.376-0.002-0.0020.0000.0000.0000.000
142A139ALA00.0490.01124.884-0.007-0.0070.0000.0000.0000.000
143A140ALA0-0.024-0.00324.187-0.015-0.0150.0000.0000.0000.000
144A141ILE0-0.072-0.02525.086-0.013-0.0130.0000.0000.0000.000
145A142GLU-1-0.950-0.97525.902-0.103-0.1030.0000.0000.0000.000
146A143MET0-0.067-0.01020.418-0.010-0.0100.0000.0000.0000.000
147A144PRO00.0430.03118.805-0.012-0.0120.0000.0000.0000.000
148A145ARG10.8300.88312.8840.4410.4410.0000.0000.0000.000
149A146GLY00.0060.00916.857-0.062-0.0620.0000.0000.0000.000
150A147ILE0-0.046-0.00814.910-0.022-0.0220.0000.0000.0000.000
151A148ARG10.8110.90916.4330.3710.3710.0000.0000.0000.000
152A149ILE00.0150.00419.157-0.007-0.0070.0000.0000.0000.000
153A150ASN0-0.0320.00121.7490.0180.0180.0000.0000.0000.000
154A151THR00.0190.01423.8220.0020.0020.0000.0000.0000.000
155A152VAL0-0.0030.00624.728-0.003-0.0030.0000.0000.0000.000
156A153SER00.0210.00927.4740.0080.0080.0000.0000.0000.000
157A154PRO00.000-0.00129.6980.0000.0000.0000.0000.0000.000
158A155ASN00.0840.03832.3290.0010.0010.0000.0000.0000.000
159A156VAL0-0.0030.00634.5880.0010.0010.0000.0000.0000.000
160A157LEU0-0.016-0.02230.597-0.001-0.0010.0000.0000.0000.000
161A158GLU-1-0.822-0.92734.7790.0030.0030.0000.0000.0000.000
162A159GLU-1-0.808-0.90231.2590.0110.0110.0000.0000.0000.000
163A160SER0-0.131-0.09334.3990.0040.0040.0000.0000.0000.000
164A161TRP00.0910.05936.540-0.001-0.0010.0000.0000.0000.000
165A162ASP-1-0.872-0.93339.8110.0140.0140.0000.0000.0000.000
166A163LYS10.8120.90935.747-0.016-0.0160.0000.0000.0000.000
167A164LEU0-0.056-0.04136.7220.0000.0000.0000.0000.0000.000
168A165GLU-1-0.881-0.92841.2840.0020.0020.0000.0000.0000.000
169A166PRO00.0370.01144.005-0.002-0.0020.0000.0000.0000.000
170A167PHE0-0.094-0.04142.6270.0000.0000.0000.0000.0000.000
171A168PHE0-0.067-0.04738.785-0.002-0.0020.0000.0000.0000.000
172A169GLU-1-0.880-0.93244.149-0.002-0.0020.0000.0000.0000.000
173A170GLY0-0.019-0.01247.533-0.001-0.0010.0000.0000.0000.000
174A171PHE0-0.032-0.01341.299-0.001-0.0010.0000.0000.0000.000
175A172LEU0-0.019-0.00740.8030.0020.0020.0000.0000.0000.000
176A173PRO0-0.024-0.00137.786-0.003-0.0030.0000.0000.0000.000
177A174VAL0-0.051-0.02933.215-0.003-0.0030.0000.0000.0000.000
178A175PRO00.0370.03831.6540.0020.0020.0000.0000.0000.000
179A176ALA00.037-0.00428.159-0.007-0.0070.0000.0000.0000.000
180A177ALA00.0200.00127.015-0.005-0.0050.0000.0000.0000.000
181A178LYS10.8600.94827.5710.0200.0200.0000.0000.0000.000
182A179VAL00.0380.00827.339-0.008-0.0080.0000.0000.0000.000
183A180ALA00.0260.01623.278-0.011-0.0110.0000.0000.0000.000
184A181ARG10.9300.96823.0980.0120.0120.0000.0000.0000.000
185A182ALA0-0.0030.01524.390-0.014-0.0140.0000.0000.0000.000
186A183PHE00.0470.00420.886-0.015-0.0150.0000.0000.0000.000
187A184GLU-1-0.777-0.84519.515-0.079-0.0790.0000.0000.0000.000
188A185LYS10.8520.92220.0360.0920.0920.0000.0000.0000.000
189A186SER0-0.038-0.02320.838-0.018-0.0180.0000.0000.0000.000
190A187VAL00.0310.02514.778-0.023-0.0230.0000.0000.0000.000
191A188PHE00.003-0.01913.893-0.047-0.0470.0000.0000.0000.000
192A189GLY0-0.0110.01718.0250.0080.0080.0000.0000.0000.000
193A190ALA00.012-0.01219.696-0.025-0.0250.0000.0000.0000.000
194A191GLN0-0.038-0.02421.4200.0000.0000.0000.0000.0000.000
195A192THR00.0470.01922.203-0.020-0.0200.0000.0000.0000.000
196A193GLY00.0610.03023.9500.0110.0110.0000.0000.0000.000
197A194GLU-1-0.882-0.93126.146-0.096-0.0960.0000.0000.0000.000
198A195SER0-0.006-0.01727.3300.0010.0010.0000.0000.0000.000
199A196TYR0-0.034-0.02824.1190.0020.0020.0000.0000.0000.000
200A197GLN0-0.016-0.00529.3740.0030.0030.0000.0000.0000.000
201A198VAL0-0.068-0.03829.440-0.001-0.0010.0000.0000.0000.000
202A199TYR00.029-0.01232.8100.0050.0050.0000.0000.0000.000