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: YVQY2

Calculation Name: 3DZB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DZB

Chain ID: A

ChEMBL ID:

UniProt ID: Q5M554

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 OptHSide
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 295
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3952839.790891
FMO2-HF: Nuclear repulsion 3838511.128949
FMO2-HF: Total energy -114328.661942
FMO2-MP2: Total energy -114664.087878


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:4:LYS)


Summations of interaction energy for fragment #1(A:4:LYS)
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.
-250.871-240.64918.645-11.561-17.299-0.112
Interaction energy analysis for fragmet #1(A:4:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.897 / q_NPA : 0.952
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].
3A6ILE0-0.0200.0052.399-2.2470.0611.494-1.274-2.5280.007
4A7TYR0-0.036-0.0375.0473.8043.839-0.001-0.002-0.0310.000
5A8ILE0-0.0050.0048.6940.1860.1860.0000.0000.0000.000
6A9ALA0-0.004-0.00511.6161.3811.3810.0000.0000.0000.000
7A10GLY0-0.0040.00814.9451.0731.0730.0000.0000.0000.000
8A11LEU00.018-0.01115.145-0.565-0.5650.0000.0000.0000.000
9A12GLY00.0140.00618.1290.5800.5800.0000.0000.0000.000
10A13LEU00.0240.03119.324-0.649-0.6490.0000.0000.0000.000
11A14ILE00.0270.01917.059-0.596-0.5960.0000.0000.0000.000
12A15GLY00.0600.01815.292-0.978-0.9780.0000.0000.0000.000
13A16GLY00.0120.01114.486-0.987-0.9870.0000.0000.0000.000
14A17SER0-0.022-0.04315.112-0.484-0.4840.0000.0000.0000.000
15A18LEU0-0.030-0.01012.291-0.513-0.5130.0000.0000.0000.000
16A19ALA00.0240.02110.778-2.002-2.0020.0000.0000.0000.000
17A20LEU0-0.008-0.00510.782-1.250-1.2500.0000.0000.0000.000
18A21GLY00.0200.00212.413-0.514-0.5140.0000.0000.0000.000
19A22ILE0-0.0180.0036.581-0.656-0.6560.0000.0000.0000.000
20A23LYS10.8460.9268.44120.44320.4430.0000.0000.0000.000
21A24ARG10.7260.8599.42919.00219.0020.0000.0000.0000.000
22A25ASP-1-0.818-0.8979.813-23.399-23.3990.0000.0000.0000.000
23A26HIS10.8300.9295.64341.17441.1740.0000.0000.0000.000
24A27PRO00.003-0.0026.847-0.674-0.6740.0000.0000.0000.000
25A28ASP-1-0.916-0.9574.657-35.350-35.202-0.001-0.009-0.1370.000
26A29TYR0-0.032-0.0212.655-17.608-12.1072.740-2.412-5.828-0.028
27A30GLU-1-0.775-0.8633.407-21.330-20.8250.001-0.089-0.4180.000
28A31ILE0-0.038-0.0325.491-2.215-2.2150.0000.0000.0000.000
29A32LEU00.0030.0178.1012.9742.9740.0000.0000.0000.000
30A33GLY00.012-0.00310.308-0.619-0.6190.0000.0000.0000.000
31A34TYR0-0.034-0.02313.3721.0591.0590.0000.0000.0000.000
32A35ASN00.0470.01716.2870.4890.4890.0000.0000.0000.000
33A36ARG10.9560.99119.78611.66811.6680.0000.0000.0000.000
34A37SER0-0.029-0.01122.9010.5970.5970.0000.0000.0000.000
35A38ASP-1-0.776-0.88523.765-11.802-11.8020.0000.0000.0000.000
36A39TYR00.0220.02224.283-0.270-0.2700.0000.0000.0000.000
37A40SER00.011-0.00222.695-0.321-0.3210.0000.0000.0000.000
38A41ARG10.8510.90719.12412.48112.4810.0000.0000.0000.000
39A42ASN0-0.012-0.02819.796-0.580-0.5800.0000.0000.0000.000
40A43ILE0-0.0150.01522.1340.0430.0430.0000.0000.0000.000
41A44ALA0-0.044-0.03016.996-0.212-0.2120.0000.0000.0000.000
42A45LEU00.0330.01216.518-0.770-0.7700.0000.0000.0000.000
43A46GLU-1-0.922-0.93717.871-11.791-11.7910.0000.0000.0000.000
44A47ARG10.8620.92819.75313.62813.6280.0000.0000.0000.000
45A48GLY00.0030.00115.792-0.166-0.1660.0000.0000.0000.000
46A49ILE0-0.081-0.03713.946-0.993-0.9930.0000.0000.0000.000
47A50VAL0-0.034-0.02011.798-1.347-1.3470.0000.0000.0000.000
48A51ASP-1-0.791-0.9039.259-22.602-22.6020.0000.0000.0000.000
49A52ARG10.8530.9139.25021.91121.9110.0000.0000.0000.000
50A53ALA0-0.019-0.00613.335-0.862-0.8620.0000.0000.0000.000
51A54THR00.020-0.02015.7340.8580.8580.0000.0000.0000.000
52A55GLY0-0.022-0.02418.120-0.085-0.0850.0000.0000.0000.000
53A56ASP-1-0.837-0.92119.411-12.708-12.7080.0000.0000.0000.000
54A57PHE00.0050.01515.053-0.780-0.7800.0000.0000.0000.000
55A58LYS10.8840.92415.98311.97611.9760.0000.0000.0000.000
56A59GLU-1-0.911-0.91316.126-15.347-15.3470.0000.0000.0000.000
57A60PHE00.007-0.02211.477-0.448-0.4480.0000.0000.0000.000
58A61ALA00.0070.01511.134-1.527-1.5270.0000.0000.0000.000
59A62PRO00.0350.01111.167-1.573-1.5730.0000.0000.0000.000
60A63LEU0-0.054-0.0168.709-0.690-0.6900.0000.0000.0000.000
61A64ALA0-0.010-0.0036.507-2.208-2.2080.0000.0000.0000.000
62A65ASP-1-0.806-0.8962.835-42.357-39.9690.383-1.273-1.498-0.010
63A66VAL0-0.008-0.0233.694-2.788-2.4340.004-0.047-0.3110.000
64A67ILE0-0.032-0.0066.3241.9901.9900.0000.0000.0000.000
65A68ILE00.0150.0138.4320.8510.8510.0000.0000.0000.000
66A69LEU0-0.020-0.03411.6211.5051.5050.0000.0000.0000.000
67A70ALA0-0.011-0.00315.2470.4760.4760.0000.0000.0000.000
68A71VAL0-0.005-0.00317.1690.8520.8520.0000.0000.0000.000
69A72PRO00.0310.00120.349-0.086-0.0860.0000.0000.0000.000
70A73ILE00.0810.04623.030-0.301-0.3010.0000.0000.0000.000
71A74LYS10.9780.98324.08610.28710.2870.0000.0000.0000.000
72A75GLN0-0.018-0.00421.9990.4510.4510.0000.0000.0000.000
73A76THR0-0.003-0.00419.013-0.586-0.5860.0000.0000.0000.000
74A77MET0-0.011-0.00520.486-0.372-0.3720.0000.0000.0000.000
75A78ALA0-0.048-0.01023.0590.0830.0830.0000.0000.0000.000
76A79TYR00.0510.02318.1340.1090.1090.0000.0000.0000.000
77A80LEU00.0060.01416.950-0.331-0.3310.0000.0000.0000.000
78A81LYS10.9450.97519.50211.19411.1940.0000.0000.0000.000
79A82GLU-1-0.897-0.96020.228-13.693-13.6930.0000.0000.0000.000
80A83LEU0-0.011-0.01114.305-0.049-0.0490.0000.0000.0000.000
81A84ALA00.0160.00817.760-0.599-0.5990.0000.0000.0000.000
82A85ASP-1-0.926-0.94520.186-12.604-12.6040.0000.0000.0000.000
83A86LEU0-0.069-0.01216.9270.1310.1310.0000.0000.0000.000
84A87ASP-1-0.923-0.94716.320-16.849-16.8490.0000.0000.0000.000
85A88LEU0-0.047-0.03212.192-0.571-0.5710.0000.0000.0000.000
86A89LYS10.8820.9415.16932.98432.9840.0000.0000.0000.000
87A90ASP-1-0.822-0.91610.763-22.400-22.4000.0000.0000.0000.000
88A91ASN0-0.026-0.0068.681-0.447-0.4470.0000.0000.0000.000
89A92VAL00.0230.0357.894-3.019-3.0190.0000.0000.0000.000
90A93ILE0-0.0030.0094.4652.9383.013-0.001-0.001-0.0710.000
91A94ILE0-0.0030.0048.464-0.078-0.0780.0000.0000.0000.000
92A95THR00.0180.00810.496-0.026-0.0260.0000.0000.0000.000
93A96ASP-1-0.717-0.84713.201-17.079-17.0790.0000.0000.0000.000
94A97ALA00.006-0.00515.083-0.920-0.9200.0000.0000.0000.000
95A98GLY0-0.047-0.02017.5560.7700.7700.0000.0000.0000.000
96A99SER00.022-0.02820.953-0.495-0.4950.0000.0000.0000.000
97A100THR0-0.078-0.02323.4890.1630.1630.0000.0000.0000.000
98A101LYS10.7460.83618.52515.51515.5150.0000.0000.0000.000
99A102ARG10.7620.85422.69910.90410.9040.0000.0000.0000.000
100A103GLU-1-0.776-0.89524.837-10.879-10.8790.0000.0000.0000.000
101A104ILE0-0.013-0.01320.0380.0000.0000.0000.0000.0000.000
102A105VAL00.0190.01819.371-0.455-0.4550.0000.0000.0000.000
103A106GLU-1-0.747-0.84221.396-11.248-11.2480.0000.0000.0000.000
104A107ALA0-0.094-0.04722.9480.1810.1810.0000.0000.0000.000
105A108ALA00.0060.00118.2090.0590.0590.0000.0000.0000.000
106A109GLU-1-0.812-0.87720.275-14.416-14.4160.0000.0000.0000.000
107A110ARG10.8520.93821.68111.74411.7440.0000.0000.0000.000
108A111TYR0-0.059-0.04521.6920.6280.6280.0000.0000.0000.000
109A112LEU00.0430.01916.0130.0160.0160.0000.0000.0000.000
110A113THR00.018-0.00819.177-0.686-0.6860.0000.0000.0000.000
111A114GLY0-0.065-0.01720.7390.4810.4810.0000.0000.0000.000
112A115LYS10.7770.87016.73816.57616.5760.0000.0000.0000.000
113A116ASN0-0.062-0.05113.983-0.508-0.5080.0000.0000.0000.000
114A117VAL0-0.006-0.00612.446-1.070-1.0700.0000.0000.0000.000
115A118GLN0-0.041-0.0037.0102.0892.0890.0000.0000.0000.000
116A119PHE00.0340.00211.364-1.002-1.0020.0000.0000.0000.000
117A120VAL00.0100.02611.3810.7550.7550.0000.0000.0000.000
118A121GLY00.0150.02414.180-0.355-0.3550.0000.0000.0000.000
119A122SER0-0.006-0.01413.317-1.383-1.3830.0000.0000.0000.000
120A123HIS00.0300.03315.7270.7840.7840.0000.0000.0000.000
121A124PRO0-0.0290.01015.6540.2260.2260.0000.0000.0000.000
122A125MET0-0.0130.00917.6930.6830.6830.0000.0000.0000.000
123A126ALA00.009-0.00320.137-0.584-0.5840.0000.0000.0000.000
124A127GLY00.0600.02822.4470.3750.3750.0000.0000.0000.000
125A128SER0-0.023-0.02423.8100.5680.5680.0000.0000.0000.000
126A129HIS00.0490.02327.0450.2430.2430.0000.0000.0000.000
127A130LYS10.8710.93029.6339.7879.7870.0000.0000.0000.000
128A131SER00.0110.00630.1130.4370.4370.0000.0000.0000.000
129A132GLY00.0210.00828.105-0.176-0.1760.0000.0000.0000.000
130A133ALA00.0000.00428.6220.1120.1120.0000.0000.0000.000
131A134ILE00.0140.02123.6290.2020.2020.0000.0000.0000.000
132A135ALA0-0.0040.00523.780-0.071-0.0710.0000.0000.0000.000
133A136ALA0-0.016-0.03218.386-0.336-0.3360.0000.0000.0000.000
134A137ASP-1-0.808-0.92219.868-13.590-13.5900.0000.0000.0000.000
135A138VAL0-0.0160.01215.345-0.420-0.4200.0000.0000.0000.000
136A139THR0-0.015-0.03217.645-0.530-0.5300.0000.0000.0000.000
137A140LEU0-0.080-0.03219.4460.3540.3540.0000.0000.0000.000
138A141PHE00.021-0.00516.1970.5750.5750.0000.0000.0000.000
139A142GLU-1-0.742-0.81418.477-15.876-15.8760.0000.0000.0000.000
140A143ASN0-0.143-0.09719.3581.2821.2820.0000.0000.0000.000
141A144ALA00.0120.02819.7020.8590.8590.0000.0000.0000.000
142A145TYR00.007-0.01218.840-0.439-0.4390.0000.0000.0000.000
143A146TYR00.0040.00712.1740.2520.2520.0000.0000.0000.000
144A147ILE0-0.049-0.04116.099-0.374-0.3740.0000.0000.0000.000
145A148PHE00.0500.03110.203-0.305-0.3050.0000.0000.0000.000
146A149THR0-0.031-0.03215.8831.0861.0860.0000.0000.0000.000
147A150PRO0-0.0100.00116.194-0.352-0.3520.0000.0000.0000.000
148A151THR0-0.037-0.02716.5161.0091.0090.0000.0000.0000.000
149A152SER0-0.002-0.01717.445-0.725-0.7250.0000.0000.0000.000
150A153LEU0-0.012-0.00315.985-0.104-0.1040.0000.0000.0000.000
151A154THR0-0.082-0.05812.722-1.565-1.5650.0000.0000.0000.000
152A155LYS10.9490.98311.05824.47124.4710.0000.0000.0000.000
153A156GLU-1-0.884-0.95611.900-21.453-21.4530.0000.0000.0000.000
154A157THR0-0.009-0.0066.9700.4640.4640.0000.0000.0000.000
155A158THR0-0.035-0.0317.488-3.305-3.3050.0000.0000.0000.000
156A159ILE00.0350.0177.585-3.531-3.5310.0000.0000.0000.000
157A160PRO0-0.014-0.0098.135-1.538-1.5380.0000.0000.0000.000
158A161GLU-1-0.800-0.8941.751-112.176-114.63811.735-5.319-3.953-0.075
159A162LEU0-0.0070.0074.191-6.605-6.472-0.001-0.029-0.1020.000
160A163LYS10.8020.8966.35025.13825.1380.0000.0000.0000.000
161A164ASP-1-0.881-0.9273.437-62.970-62.3180.010-0.323-0.339-0.002
162A165ILE00.0290.0232.0713.0463.5912.283-0.778-2.050-0.004
163A166LEU0-0.035-0.0324.8965.5975.637-0.001-0.005-0.0330.000
164A167SER0-0.007-0.0228.0612.8282.8280.0000.0000.0000.000
165A168GLY0-0.0240.0019.9942.9872.9870.0000.0000.0000.000
166A169LEU0-0.035-0.02811.7552.3422.3420.0000.0000.0000.000
167A170LYS10.8250.92513.35023.57223.5720.0000.0000.0000.000
168A171SER00.0020.00814.8371.0191.0190.0000.0000.0000.000
169A172ARG10.8560.93216.40813.51813.5180.0000.0000.0000.000
170A173TYR00.008-0.0269.8701.6141.6140.0000.0000.0000.000
171A174VAL0-0.030-0.01015.8740.8740.8740.0000.0000.0000.000
172A175GLU-1-0.837-0.91115.509-20.828-20.8280.0000.0000.0000.000
173A176ILE0-0.042-0.02718.6510.9090.9090.0000.0000.0000.000
174A177ASP-1-0.725-0.86720.972-12.895-12.8950.0000.0000.0000.000
175A178ALA00.0510.01821.8860.1670.1670.0000.0000.0000.000
176A179ALA0-0.004-0.01923.3530.3220.3220.0000.0000.0000.000
177A180GLU-1-0.851-0.91326.128-10.392-10.3920.0000.0000.0000.000
178A181HIS10.7890.88622.43613.80413.8040.0000.0000.0000.000
179A182ASP-1-0.750-0.82625.241-12.349-12.3490.0000.0000.0000.000
180A183ARG10.8860.93527.60510.92910.9290.0000.0000.0000.000
181A184VAL00.0200.00627.5590.3520.3520.0000.0000.0000.000
182A185THR0-0.059-0.05925.0720.2150.2150.0000.0000.0000.000
183A186SER00.0210.01428.3560.3000.3000.0000.0000.0000.000
184A187GLN00.0280.01531.6380.4680.4680.0000.0000.0000.000
185A188ILE0-0.058-0.03028.0270.2810.2810.0000.0000.0000.000
186A189SER0-0.036-0.04628.8980.0650.0650.0000.0000.0000.000
187A190HIS00.0310.01727.0480.6260.6260.0000.0000.0000.000
188A191PHE00.0430.02632.2370.2010.2010.0000.0000.0000.000
189A192PRO0-0.005-0.00233.9920.2180.2180.0000.0000.0000.000
190A193HIS10.8650.93530.95410.12010.1200.0000.0000.0000.000
191A194LEU00.0270.03235.5780.1470.1470.0000.0000.0000.000
192A195LEU0-0.031-0.01338.1180.2340.2340.0000.0000.0000.000
193A196ALA00.0000.01038.1960.1930.1930.0000.0000.0000.000
194A197SER0-0.019-0.03538.2020.1120.1120.0000.0000.0000.000
195A198GLY00.0300.02540.8420.1520.1520.0000.0000.0000.000
196A199LEU0-0.023-0.00443.5240.1960.1960.0000.0000.0000.000
197A200MET0-0.013-0.01342.1900.2360.2360.0000.0000.0000.000
198A201GLU-1-0.941-0.95944.925-7.017-7.0170.0000.0000.0000.000
199A202GLN0-0.007-0.00546.6040.1570.1570.0000.0000.0000.000
200A203ALA0-0.021-0.02048.6820.1670.1670.0000.0000.0000.000
201A204ALA00.0110.01248.3040.1370.1370.0000.0000.0000.000
202A205ASP-1-0.858-0.94050.315-6.210-6.2100.0000.0000.0000.000
203A206TYR0-0.078-0.03852.6500.2010.2010.0000.0000.0000.000
204A207ALA00.012-0.00853.3030.1440.1440.0000.0000.0000.000
205A208GLN0-0.064-0.01753.1990.2100.2100.0000.0000.0000.000
206A209ALA0-0.030-0.00656.9790.1090.1090.0000.0000.0000.000
207A210HIS10.8190.91057.7645.6165.6160.0000.0000.0000.000
208A211GLU-1-0.737-0.84857.516-5.436-5.4360.0000.0000.0000.000
209A212MET0-0.035-0.02057.274-0.096-0.0960.0000.0000.0000.000
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