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: QV67Y

Calculation Name: 3DQP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DQP

Chain ID: A

ChEMBL ID:

UniProt ID: Q9CGI7

Base Structure: X-ray

Registration Date: 2023-09-23

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2627816.280204
FMO2-HF: Nuclear repulsion 2543232.958459
FMO2-HF: Total energy -84583.321745
FMO2-MP2: Total energy -84831.544608


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.
-20.222-9.75815.204-8.294-17.373-0.041
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 : 0.020 / q_NPA : 0.012
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].
3A3ILE00.0490.0282.423-1.4141.2881.792-1.217-3.277-0.001
4A4PHE00.007-0.0034.249-0.527-0.4350.000-0.030-0.0630.000
5A5ILE0-0.0050.0047.9630.2660.2660.0000.0000.0000.000
6A6VAL00.0430.01910.527-0.164-0.1640.0000.0000.0000.000
7A7GLY00.0440.00013.9710.0290.0290.0000.0000.0000.000
8A8SER0-0.004-0.01014.0570.0140.0140.0000.0000.0000.000
9A9THR0-0.037-0.01615.657-0.006-0.0060.0000.0000.0000.000
10A10GLY00.0120.01318.878-0.027-0.0270.0000.0000.0000.000
11A11ARG10.8730.92119.502-0.152-0.1520.0000.0000.0000.000
12A12VAL00.0920.04816.3510.0000.0000.0000.0000.0000.000
13A13GLY00.0470.03015.1090.0430.0430.0000.0000.0000.000
14A14LYS10.9180.95015.070-0.134-0.1340.0000.0000.0000.000
15A15SER00.0130.01816.825-0.020-0.0200.0000.0000.0000.000
16A16LEU00.0270.01610.266-0.014-0.0140.0000.0000.0000.000
17A17LEU0-0.012-0.00911.5110.0630.0630.0000.0000.0000.000
18A18LYS10.9760.99612.813-0.235-0.2350.0000.0000.0000.000
19A19SER0-0.035-0.02612.4570.0330.0330.0000.0000.0000.000
20A20LEU00.034-0.0026.6460.0150.0150.0000.0000.0000.000
21A21SER0-0.082-0.0319.288-0.007-0.0070.0000.0000.0000.000
22A22THR0-0.088-0.03811.636-0.072-0.0720.0000.0000.0000.000
23A23THR0-0.039-0.0186.9980.1480.1480.0000.0000.0000.000
24A24ASP-1-0.886-0.9465.4340.1170.1170.0000.0000.0000.000
25A25TYR0-0.013-0.0122.349-6.048-4.4096.404-2.377-5.665-0.004
26A26GLN0-0.063-0.0333.611-1.139-0.5050.000-0.179-0.4550.000
27A27ILE00.0280.0115.424-0.190-0.1900.0000.0000.0000.000
28A28TYR0-0.008-0.0136.768-0.199-0.1990.0000.0000.0000.000
29A29ALA00.0270.0109.6270.1710.1710.0000.0000.0000.000
30A30GLY00.0400.02412.326-0.068-0.0680.0000.0000.0000.000
31A31ALA0-0.048-0.03514.5240.0370.0370.0000.0000.0000.000
32A32ARG10.9891.01718.164-0.115-0.1150.0000.0000.0000.000
33A33LYS10.9100.95621.641-0.083-0.0830.0000.0000.0000.000
34A34VAL00.0720.03318.4380.0120.0120.0000.0000.0000.000
35A35GLU-1-0.871-0.94519.9550.0400.0400.0000.0000.0000.000
36A36GLN0-0.088-0.05121.9800.0110.0110.0000.0000.0000.000
37A37VAL0-0.038-0.01315.4520.0270.0270.0000.0000.0000.000
38A38PRO0-0.060-0.01516.888-0.022-0.0220.0000.0000.0000.000
39A39GLN00.011-0.00317.053-0.008-0.0080.0000.0000.0000.000
40A40TYR00.0640.01413.8700.0300.0300.0000.0000.0000.000
41A41ASN00.0220.00313.692-0.032-0.0320.0000.0000.0000.000
42A42ASN0-0.0070.0087.605-0.111-0.1110.0000.0000.0000.000
43A43VAL0-0.0030.0119.306-0.060-0.0600.0000.0000.0000.000
44A44LYS10.9120.95810.7250.4430.4430.0000.0000.0000.000
45A45ALA00.0080.01112.7190.0380.0380.0000.0000.0000.000
46A46VAL0-0.010-0.00512.580-0.047-0.0470.0000.0000.0000.000
47A47HIS00.0090.00315.5620.0480.0480.0000.0000.0000.000
48A48PHE00.0430.00515.4550.0020.0020.0000.0000.0000.000
49A49ASP-1-0.873-0.93918.1260.1180.1180.0000.0000.0000.000
50A50VAL0-0.0150.00719.3400.0060.0060.0000.0000.0000.000
51A51ASP-1-0.928-0.98021.2410.1200.1200.0000.0000.0000.000
52A52TRP0-0.051-0.01418.563-0.009-0.0090.0000.0000.0000.000
53A53THR00.0180.00922.9930.0160.0160.0000.0000.0000.000
54A54PRO00.0620.02220.1050.0030.0030.0000.0000.0000.000
55A55GLU-1-0.866-0.95219.4520.1020.1020.0000.0000.0000.000
56A56GLU-1-0.930-0.95820.4810.0590.0590.0000.0000.0000.000
57A57MET0-0.066-0.02116.9630.0030.0030.0000.0000.0000.000
58A58ALA00.0470.01615.7520.0030.0030.0000.0000.0000.000
59A59LYS10.8960.95715.587-0.020-0.0200.0000.0000.0000.000
60A60GLN0-0.067-0.03714.532-0.060-0.0600.0000.0000.0000.000
61A61LEU0-0.038-0.01811.071-0.027-0.0270.0000.0000.0000.000
62A62HIS00.0460.02810.6920.0430.0430.0000.0000.0000.000
63A63GLY0-0.007-0.0049.291-0.088-0.0880.0000.0000.0000.000
64A64MET0-0.083-0.0326.388-0.557-0.5570.0000.0000.0000.000
65A65ASP-1-0.789-0.8852.350-6.696-3.5754.210-3.301-4.030-0.031
66A66ALA00.000-0.0053.2910.4661.3530.787-0.360-1.3140.000
67A67ILE0-0.038-0.0064.960-0.990-0.9870.000-0.0100.0070.000
68A68ILE00.0280.0186.8370.0040.0040.0000.0000.0000.000
69A69ASN00.0590.0859.842-0.207-0.2070.0000.0000.0000.000
70A70VAL00.006-0.00413.481-0.019-0.0190.0000.0000.0000.000
71A71SER0-0.090-0.10215.736-0.069-0.0690.0000.0000.0000.000
72A72GLY00.0300.01918.398-0.001-0.0010.0000.0000.0000.000
73A73SER0-0.073-0.05022.055-0.015-0.0150.0000.0000.0000.000
74A74GLY0-0.003-0.00625.216-0.015-0.0150.0000.0000.0000.000
75A75GLY00.0200.00327.160-0.011-0.0110.0000.0000.0000.000
76A76LYS10.9050.95729.016-0.113-0.1130.0000.0000.0000.000
77A77SER0-0.015-0.02227.654-0.012-0.0120.0000.0000.0000.000
78A78LEU00.0350.03227.2970.0090.0090.0000.0000.0000.000
79A79LEU00.0440.02126.8950.0100.0100.0000.0000.0000.000
80A80LYS10.9680.97627.229-0.090-0.0900.0000.0000.0000.000
81A81VAL00.0060.01122.1350.0050.0050.0000.0000.0000.000
82A82ASP-1-0.797-0.90522.4100.2180.2180.0000.0000.0000.000
83A83LEU00.0040.02222.5020.0140.0140.0000.0000.0000.000
84A84TYR0-0.004-0.00822.9430.0120.0120.0000.0000.0000.000
85A85GLY00.0360.00021.9020.0050.0050.0000.0000.0000.000
86A86ALA0-0.024-0.00718.5460.0230.0230.0000.0000.0000.000
87A87VAL00.0420.00918.2640.0300.0300.0000.0000.0000.000
88A88LYS10.8080.91519.798-0.142-0.1420.0000.0000.0000.000
89A89LEU00.0130.00513.542-0.006-0.0060.0000.0000.0000.000
90A90MET0-0.0420.01415.3200.0230.0230.0000.0000.0000.000
91A91GLN00.012-0.02216.258-0.003-0.0030.0000.0000.0000.000
92A92ALA0-0.038-0.02516.195-0.021-0.0210.0000.0000.0000.000
93A93ALA0-0.0010.00512.155-0.023-0.0230.0000.0000.0000.000
94A94GLU-1-0.828-0.91213.6890.2390.2390.0000.0000.0000.000
95A95LYS10.8550.93215.904-0.150-0.1500.0000.0000.0000.000
96A96ALA0-0.057-0.02713.441-0.038-0.0380.0000.0000.0000.000
97A97GLU-1-0.991-0.97813.0840.0190.0190.0000.0000.0000.000
98A98VAL0-0.038-0.0087.8040.0290.0290.0000.0000.0000.000
99A99LYS10.9160.9399.236-0.263-0.2630.0000.0000.0000.000
100A100ARG10.8840.9564.471-0.742-0.567-0.001-0.018-0.1550.000
101A101PHE00.011-0.0027.4930.3020.3020.0000.0000.0000.000
102A102ILE00.0250.0166.557-0.170-0.1700.0000.0000.0000.000
103A103LEU0-0.015-0.01010.4470.0030.0030.0000.0000.0000.000
104A104LEU0-0.0030.01314.038-0.038-0.0380.0000.0000.0000.000
105A105SER0-0.068-0.07916.321-0.042-0.0420.0000.0000.0000.000
106A106THR0-0.026-0.02219.6870.0010.0010.0000.0000.0000.000
107A107ILE00.0480.02922.529-0.004-0.0040.0000.0000.0000.000
108A108PHE00.0550.02424.217-0.009-0.0090.0000.0000.0000.000
109A109SER0-0.035-0.00221.965-0.015-0.0150.0000.0000.0000.000
110A110LEU00.005-0.00221.307-0.007-0.0070.0000.0000.0000.000
111A111GLN0-0.015-0.01625.3750.0010.0010.0000.0000.0000.000
112A112PRO00.0500.01428.500-0.003-0.0030.0000.0000.0000.000
113A113GLU-1-0.903-0.95230.6340.1040.1040.0000.0000.0000.000
114A114LYS10.8410.90529.589-0.114-0.1140.0000.0000.0000.000
115A115TRP0-0.113-0.03628.202-0.002-0.0020.0000.0000.0000.000
116A116ILE0-0.009-0.00533.043-0.006-0.0060.0000.0000.0000.000
117A117GLY00.0260.00835.7340.0020.0020.0000.0000.0000.000
118A118ALA00.0420.00437.1450.0030.0030.0000.0000.0000.000
119A119GLY0-0.0120.00034.5930.0010.0010.0000.0000.0000.000
120A120PHE00.0310.00728.9010.0050.0050.0000.0000.0000.000
121A121ASP-1-0.950-0.96833.5990.0880.0880.0000.0000.0000.000
122A122ALA0-0.044-0.02235.3000.0000.0000.0000.0000.0000.000
123A123LEU0-0.028-0.00529.4360.0030.0030.0000.0000.0000.000
124A124LYS10.9721.00131.031-0.091-0.0910.0000.0000.0000.000
125A125ASP-1-0.867-0.93831.8520.1080.1080.0000.0000.0000.000
126A126TYR0-0.058-0.04322.8720.0080.0080.0000.0000.0000.000
127A127TYR0-0.005-0.02926.6390.0130.0130.0000.0000.0000.000
128A128ILE00.0040.01327.7190.0070.0070.0000.0000.0000.000
129A129ALA0-0.032-0.01926.3880.0040.0040.0000.0000.0000.000
130A130LYS10.8690.93319.594-0.285-0.2850.0000.0000.0000.000
131A131HIS0-0.003-0.00623.2980.0060.0060.0000.0000.0000.000
132A132PHE0-0.017-0.01824.8620.0030.0030.0000.0000.0000.000
133A133ALA00.0020.00220.8030.0010.0010.0000.0000.0000.000
134A134ASP-1-0.729-0.82419.9500.2980.2980.0000.0000.0000.000
135A135LEU0-0.041-0.01320.9680.0000.0000.0000.0000.0000.000
136A136TYR00.0430.03620.349-0.012-0.0120.0000.0000.0000.000
137A137LEU00.0320.00414.6570.0030.0030.0000.0000.0000.000
138A138THR0-0.065-0.04318.202-0.006-0.0060.0000.0000.0000.000
139A139LYS10.8700.93719.714-0.150-0.1500.0000.0000.0000.000
140A140GLU-1-0.966-0.97921.8120.1150.1150.0000.0000.0000.000
141A141THR0-0.093-0.02417.1840.0230.0230.0000.0000.0000.000
142A142ASN0-0.007-0.01317.273-0.018-0.0180.0000.0000.0000.000
143A143LEU0-0.027-0.01112.0490.0060.0060.0000.0000.0000.000
144A144ASP-1-0.855-0.9269.2270.2600.2600.0000.0000.0000.000
145A145TYR0-0.008-0.0199.5020.1660.1660.0000.0000.0000.000
146A146THR00.0110.00310.175-0.046-0.0460.0000.0000.0000.000
147A147ILE0-0.035-0.00412.0610.0840.0840.0000.0000.0000.000
148A148ILE00.0290.02014.020-0.038-0.0380.0000.0000.0000.000
149A149GLN0-0.049-0.05315.877-0.004-0.0040.0000.0000.0000.000
150A150PRO00.005-0.00118.473-0.023-0.0230.0000.0000.0000.000
151A151GLY00.0590.03821.095-0.012-0.0120.0000.0000.0000.000
152A152ALA0-0.038-0.02424.1350.0130.0130.0000.0000.0000.000
153A153LEU00.0100.00121.2900.0030.0030.0000.0000.0000.000
154A154THR00.0120.00724.909-0.010-0.0100.0000.0000.0000.000
155A155GLU-1-0.916-0.97624.7210.1710.1710.0000.0000.0000.000
156A156GLU-1-0.971-0.96926.2600.1170.1170.0000.0000.0000.000
157A157GLU-1-0.952-0.98624.6910.1700.1700.0000.0000.0000.000
158A158ALA0-0.048-0.01320.181-0.002-0.0020.0000.0000.0000.000
159A159THR0-0.023-0.02122.227-0.015-0.0150.0000.0000.0000.000
160A160GLY0-0.021-0.01119.138-0.011-0.0110.0000.0000.0000.000
161A161LEU0-0.065-0.03119.7060.0010.0010.0000.0000.0000.000
162A162ILE0-0.011-0.00817.1770.0030.0030.0000.0000.0000.000
163A163ASP-1-0.807-0.89521.4490.1170.1170.0000.0000.0000.000
164A164ILE00.005-0.01117.3960.0180.0180.0000.0000.0000.000
165A165ASN00.0050.00418.943-0.001-0.0010.0000.0000.0000.000
166A166ASP-1-0.725-0.83522.2970.1280.1280.0000.0000.0000.000
167A167GLU-1-0.882-0.92825.4530.1180.1180.0000.0000.0000.000
168A168VAL0-0.0260.00126.575-0.008-0.0080.0000.0000.0000.000
169A169SER0-0.040-0.00826.2620.0160.0160.0000.0000.0000.000
170A170ALA00.012-0.01326.765-0.011-0.0110.0000.0000.0000.000
171A171SER0-0.030-0.01226.1330.0120.0120.0000.0000.0000.000
172A172ASN00.0380.00221.6560.0020.0020.0000.0000.0000.000
173A173THR00.0360.03221.9490.0150.0150.0000.0000.0000.000
174A174ILE00.004-0.02419.4670.0260.0260.0000.0000.0000.000
175A175GLY00.0030.00518.4190.0410.0410.0000.0000.0000.000
176A176ASP-1-0.622-0.79317.1000.2740.2740.0000.0000.0000.000
177A177VAL0-0.024-0.00216.5740.0340.0340.0000.0000.0000.000
178A178ALA0-0.071-0.03814.2920.0660.0660.0000.0000.0000.000
179A179ASP-1-0.829-0.90312.5020.5580.5580.0000.0000.0000.000
180A180THR00.007-0.00412.0640.0260.0260.0000.0000.0000.000
181A181ILE0-0.027-0.0189.9670.0310.0310.0000.0000.0000.000
182A182LYS10.8680.9328.054-0.436-0.4360.0000.0000.0000.000
183A183GLU-1-0.911-0.9557.0420.5520.5520.0000.0000.0000.000
184A184LEU0-0.006-0.0017.894-0.138-0.1380.0000.0000.0000.000
185A185VAL0-0.059-0.0192.472-0.434-0.3951.913-0.308-1.644-0.001
186A186MET0-0.031-0.0053.132-3.018-1.8750.100-0.494-0.749-0.004
187A187THR0-0.030-0.0135.178-0.107-0.078-0.0010.000-0.0280.000
188A188ASP-1-0.848-0.9225.503-0.796-0.7960.0000.0000.0000.000
189A189HIS0-0.044-0.0297.7960.1070.1070.0000.0000.0000.000
190A190SER0-0.029-0.0278.9260.0860.0860.0000.0000.0000.000
191A191ILE0-0.0010.0246.9400.1010.1010.0000.0000.0000.000
192A192GLY0-0.013-0.00910.793-0.053-0.0530.0000.0000.0000.000
193A193LYS10.8240.93013.483-0.161-0.1610.0000.0000.0000.000
194A194VAL0-0.005-0.00914.7180.0520.0520.0000.0000.0000.000
195A195ILE00.0030.01013.516-0.027-0.0270.0000.0000.0000.000
196A196SER00.0280.02017.5220.0260.0260.0000.0000.0000.000
197A197MET0-0.0100.00217.8080.0130.0130.0000.0000.0000.000
198A198HIS10.8020.86520.672-0.157-0.1570.0000.0000.0000.000
199A199ASN0-0.006-0.02022.4960.0050.0050.0000.0000.0000.000
200A200GLY0-0.081-0.03524.030-0.012-0.0120.0000.0000.0000.000
201A201LYS10.8800.93125.275-0.109-0.1090.0000.0000.0000.000
202A202THR00.0490.03820.611-0.012-0.0120.0000.0000.0000.000
203A203ALA00.0340.02618.8770.0190.0190.0000.0000.0000.000
204A204ILE00.0230.01013.762-0.006-0.0060.0000.0000.0000.000
205A205LYS10.9520.97312.067-0.188-0.1880.0000.0000.0000.000
206A206GLU-1-0.901-0.94514.7690.0910.0910.0000.0000.0000.000
207A207ALA00.011-0.00117.664-0.013-0.0130.0000.0000.0000.000
208A208LEU0-0.016-0.00411.394-0.004-0.0040.0000.0000.0000.000
209A209GLU-1-0.963-0.98015.0050.0470.0470.0000.0000.0000.000
210A210SER0-0.035-0.03215.936-0.018-0.0180.0000.0000.0000.000
211A211LEU0-0.0180.00014.536-0.003-0.0030.0000.0000.0000.000
212A212LEU0-0.051-0.05714.266-0.010-0.0100.0000.0000.0000.000
213A213GLU-1-0.973-0.96617.3790.0590.0590.0000.0000.0000.000
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