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: YVGZ2

Calculation Name: 1ZD8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZD8

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UIJ7

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 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 212
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2405986.528777
FMO2-HF: Nuclear repulsion 2323116.390841
FMO2-HF: Total energy -82870.137936
FMO2-MP2: Total energy -83116.892499


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:6:LEU)


Summations of interaction energy for fragment #1(A:6:LEU)
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.
-9.7240.395.944-4.86-11.198-0.03
Interaction energy analysis for fragmet #1(A:6:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : 0.005
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].
3A8ARG10.8620.9362.588-0.6563.1770.614-1.720-2.7270.006
4A9ALA00.0250.0096.1970.2180.2180.0000.0000.0000.000
5A10VAL00.0040.0179.2690.1210.1210.0000.0000.0000.000
6A11ILE0-0.027-0.00412.6500.0090.0090.0000.0000.0000.000
7A12MET0-0.037-0.02215.4810.0240.0240.0000.0000.0000.000
8A13GLY00.0650.01519.0450.0070.0070.0000.0000.0000.000
9A14ALA00.0230.02622.4430.0050.0050.0000.0000.0000.000
10A15PRO0-0.0180.00125.6130.0030.0030.0000.0000.0000.000
11A16GLY00.0790.03427.2500.0030.0030.0000.0000.0000.000
12A17SER0-0.039-0.03024.2040.0030.0030.0000.0000.0000.000
13A18GLY00.0210.00524.543-0.001-0.0010.0000.0000.0000.000
14A19LYS10.8610.92918.3760.2300.2300.0000.0000.0000.000
15A20GLY00.0430.03319.598-0.005-0.0050.0000.0000.0000.000
16A21THR00.003-0.00620.2550.0040.0040.0000.0000.0000.000
17A22VAL00.011-0.00217.3510.0140.0140.0000.0000.0000.000
18A23SER00.029-0.01315.820-0.008-0.0080.0000.0000.0000.000
19A24SER0-0.0210.02315.6160.0150.0150.0000.0000.0000.000
20A25ARG10.8450.91716.9130.0790.0790.0000.0000.0000.000
21A26ILE00.0170.00111.7770.0240.0240.0000.0000.0000.000
22A27THR0-0.014-0.02912.0900.0210.0210.0000.0000.0000.000
23A28THR0-0.076-0.03412.7910.0480.0480.0000.0000.0000.000
24A29HIS0-0.026-0.01214.4540.0430.0430.0000.0000.0000.000
25A30PHE0-0.044-0.0079.074-0.013-0.0130.0000.0000.0000.000
26A31GLU-1-0.876-0.9125.7000.6110.6110.0000.0000.0000.000
27A32LEU0-0.047-0.0415.6030.2560.2560.0000.0000.0000.000
28A33LYS10.8560.9306.829-0.404-0.4040.0000.0000.0000.000
29A34HIS0-0.036-0.0298.830-0.101-0.1010.0000.0000.0000.000
30A35LEU0-0.0040.0049.1550.0320.0320.0000.0000.0000.000
31A36SER00.006-0.01812.905-0.042-0.0420.0000.0000.0000.000
32A37SER00.0200.00116.4910.0240.0240.0000.0000.0000.000
33A38GLY0-0.013-0.00518.5380.0180.0180.0000.0000.0000.000
34A39ASP-1-0.780-0.86718.889-0.079-0.0790.0000.0000.0000.000
35A40LEU00.0370.04216.4280.0170.0170.0000.0000.0000.000
36A41LEU0-0.036-0.03019.5090.0140.0140.0000.0000.0000.000
37A42ARG10.8590.90422.5470.0960.0960.0000.0000.0000.000
38A43ASP-1-0.800-0.86920.776-0.030-0.0300.0000.0000.0000.000
39A44ASN0-0.018-0.01720.4860.0150.0150.0000.0000.0000.000
40A45MET0-0.059-0.01724.1980.0060.0060.0000.0000.0000.000
41A46LEU0-0.051-0.01125.8320.0050.0050.0000.0000.0000.000
42A47ARG10.8000.87121.0770.0430.0430.0000.0000.0000.000
43A48GLY00.0100.02527.1550.0030.0030.0000.0000.0000.000
44A49THR0-0.035-0.02224.2710.0000.0000.0000.0000.0000.000
45A50GLU-1-0.854-0.93727.535-0.047-0.0470.0000.0000.0000.000
46A51ILE0-0.025-0.01823.352-0.004-0.0040.0000.0000.0000.000
47A52GLY00.0350.02126.397-0.006-0.0060.0000.0000.0000.000
48A53VAL00.0130.00727.286-0.002-0.0020.0000.0000.0000.000
49A54LEU00.000-0.00127.726-0.002-0.0020.0000.0000.0000.000
50A55ALA0-0.006-0.02226.361-0.003-0.0030.0000.0000.0000.000
51A56LYS10.8750.90828.4390.0460.0460.0000.0000.0000.000
52A57ALA0-0.0060.01531.3760.0010.0010.0000.0000.0000.000
53A58PHE0-0.025-0.02030.221-0.001-0.0010.0000.0000.0000.000
54A59ILE00.010-0.00726.809-0.001-0.0010.0000.0000.0000.000
55A60ASP-1-0.816-0.88831.253-0.052-0.0520.0000.0000.0000.000
56A61GLN0-0.049-0.00734.5630.0030.0030.0000.0000.0000.000
57A62GLY0-0.0020.00133.426-0.001-0.0010.0000.0000.0000.000
58A63LYS10.7950.89832.2660.0690.0690.0000.0000.0000.000
59A64LEU0-0.014-0.00826.882-0.002-0.0020.0000.0000.0000.000
60A65ILE00.0230.01124.7930.0060.0060.0000.0000.0000.000
61A66PRO00.0250.02226.424-0.010-0.0100.0000.0000.0000.000
62A67ASP-1-0.751-0.85824.314-0.180-0.1800.0000.0000.0000.000
63A68ASP-1-0.786-0.87023.359-0.134-0.1340.0000.0000.0000.000
64A69VAL0-0.019-0.01223.564-0.005-0.0050.0000.0000.0000.000
65A70MET0-0.0060.00320.4370.0010.0010.0000.0000.0000.000
66A71THR00.002-0.01818.753-0.021-0.0210.0000.0000.0000.000
67A72ARG10.8240.89718.4350.1080.1080.0000.0000.0000.000
68A73LEU0-0.017-0.00218.6830.0010.0010.0000.0000.0000.000
69A74ALA00.0150.00715.5790.0040.0040.0000.0000.0000.000
70A75LEU00.0350.00714.007-0.018-0.0180.0000.0000.0000.000
71A76HIS00.0030.00413.712-0.010-0.0100.0000.0000.0000.000
72A77GLU-1-0.888-0.95812.686-0.170-0.1700.0000.0000.0000.000
73A78LEU00.0220.0029.3060.0160.0160.0000.0000.0000.000
74A79LYS10.8640.9428.9680.1250.1250.0000.0000.0000.000
75A80ASN0-0.075-0.03210.0600.0470.0470.0000.0000.0000.000
76A81LEU00.0270.0137.3850.0640.0640.0000.0000.0000.000
77A82THR0-0.0050.0114.771-0.196-0.091-0.001-0.011-0.0930.000
78A83GLN00.0220.0192.954-1.3380.0450.708-0.665-1.426-0.007
79A84TYR00.0130.0072.856-1.568-0.0051.801-0.912-2.453-0.010
80A85SER00.0600.0482.518-4.164-0.9242.775-1.974-4.040-0.019
81A86TRP0-0.071-0.0543.2750.1210.0800.0480.429-0.4360.000
82A87LEU00.0110.0086.376-0.206-0.2060.0000.0000.0000.000
83A88LEU00.0150.0089.7440.1210.1210.0000.0000.0000.000
84A89ASP-1-0.746-0.84112.076-0.222-0.2220.0000.0000.0000.000
85A90GLY0-0.023-0.02215.6000.0350.0350.0000.0000.0000.000
86A91PHE0-0.0050.01114.8980.0330.0330.0000.0000.0000.000
87A92PRO00.0270.02215.283-0.035-0.0350.0000.0000.0000.000
88A93ARG10.8560.90118.2140.1590.1590.0000.0000.0000.000
89A94THR0-0.013-0.03321.7010.0080.0080.0000.0000.0000.000
90A95LEU00.0590.02121.926-0.021-0.0210.0000.0000.0000.000
91A96PRO00.0580.02222.188-0.021-0.0210.0000.0000.0000.000
92A97GLN0-0.029-0.01619.507-0.026-0.0260.0000.0000.0000.000
93A98ALA00.0260.00417.791-0.030-0.0300.0000.0000.0000.000
94A99GLU-1-0.870-0.92217.489-0.272-0.2720.0000.0000.0000.000
95A100ALA0-0.071-0.05018.582-0.013-0.0130.0000.0000.0000.000
96A101LEU0-0.002-0.00111.904-0.003-0.0030.0000.0000.0000.000
97A102ASP-1-0.872-0.93113.718-0.573-0.5730.0000.0000.0000.000
98A103ARG10.8300.92214.9160.2450.2450.0000.0000.0000.000
99A104ALA0-0.061-0.01013.5250.0340.0340.0000.0000.0000.000
100A105TYR0-0.016-0.0288.557-0.006-0.0060.0000.0000.0000.000
101A106GLN00.0200.0278.2690.2200.2200.0000.0000.0000.000
102A107ILE0-0.035-0.0258.054-0.357-0.3570.0000.0000.0000.000
103A108ASP-1-0.834-0.9226.063-2.634-2.6340.0000.0000.0000.000
104A109THR0-0.078-0.0449.4840.2130.2130.0000.0000.0000.000
105A110VAL00.0160.01711.442-0.016-0.0160.0000.0000.0000.000
106A111ILE00.0210.02812.8700.0540.0540.0000.0000.0000.000
107A112ASN00.012-0.00716.2620.0250.0250.0000.0000.0000.000
108A113LEU0-0.027-0.01019.4200.0160.0160.0000.0000.0000.000
109A114ASN0-0.030-0.02522.3390.0120.0120.0000.0000.0000.000
110A115VAL0-0.004-0.00425.6760.0110.0110.0000.0000.0000.000
111A116PRO00.0250.00928.467-0.001-0.0010.0000.0000.0000.000
112A117PHE00.0520.01331.9910.0030.0030.0000.0000.0000.000
113A118GLU-1-0.775-0.88633.443-0.069-0.0690.0000.0000.0000.000
114A119VAL0-0.0020.01032.1890.0040.0040.0000.0000.0000.000
115A120ILE0-0.026-0.01228.6190.0040.0040.0000.0000.0000.000
116A121LYS10.8730.91832.3090.0720.0720.0000.0000.0000.000
117A122GLN0-0.060-0.02035.5390.0040.0040.0000.0000.0000.000
118A123ARG10.8760.92927.9360.0920.0920.0000.0000.0000.000
119A124LEU0-0.102-0.06430.6580.0020.0020.0000.0000.0000.000
120A125THR0-0.040-0.01334.5690.0030.0030.0000.0000.0000.000
121A126ALA00.0150.02637.3680.0040.0040.0000.0000.0000.000
122A127ARG10.8840.95636.3080.0420.0420.0000.0000.0000.000
123A128TRP00.0170.01539.7920.0000.0000.0000.0000.0000.000
124A129ILE0-0.027-0.02540.6440.0010.0010.0000.0000.0000.000
125A130HIS00.0650.04144.7060.0000.0000.0000.0000.0000.000
126A131PRO0-0.033-0.02847.3130.0010.0010.0000.0000.0000.000
127A132ALA00.0100.01648.2630.0010.0010.0000.0000.0000.000
128A133SER0-0.038-0.04448.6680.0010.0010.0000.0000.0000.000
129A134GLY00.0200.01844.8800.0010.0010.0000.0000.0000.000
130A135ARG10.8100.87843.5360.0150.0150.0000.0000.0000.000
131A136VAL0-0.032-0.01739.002-0.002-0.0020.0000.0000.0000.000
132A137TYR00.008-0.01342.4590.0020.0020.0000.0000.0000.000
133A138ASN00.0260.01436.474-0.003-0.0030.0000.0000.0000.000
134A139ILE00.015-0.01540.5480.0020.0020.0000.0000.0000.000
135A140GLU-1-0.846-0.91636.115-0.058-0.0580.0000.0000.0000.000
136A141PHE0-0.098-0.04734.0810.0010.0010.0000.0000.0000.000
137A142ASN0-0.069-0.04139.5470.0010.0010.0000.0000.0000.000
138A143PRO00.0490.03342.6200.0000.0000.0000.0000.0000.000
139A144PRO0-0.0130.00945.1240.0020.0020.0000.0000.0000.000
140A145LYS10.8390.89448.3900.0160.0160.0000.0000.0000.000
141A146THR0-0.0060.00351.3980.0000.0000.0000.0000.0000.000
142A147VAL00.018-0.00449.802-0.001-0.0010.0000.0000.0000.000
143A148GLY00.0070.00449.7300.0010.0010.0000.0000.0000.000
144A149ILE0-0.0080.00050.8440.0000.0000.0000.0000.0000.000
145A150ASP-1-0.717-0.80450.031-0.018-0.0180.0000.0000.0000.000
146A151ASP-1-0.817-0.89450.070-0.018-0.0180.0000.0000.0000.000
147A152LEU0-0.080-0.03152.1780.0010.0010.0000.0000.0000.000
148A153THR0-0.017-0.04353.4960.0010.0010.0000.0000.0000.000
149A154GLY00.0090.02054.9820.0000.0000.0000.0000.0000.000
150A155GLU-1-0.897-0.92553.962-0.018-0.0180.0000.0000.0000.000
151A156PRO00.005-0.01052.966-0.001-0.0010.0000.0000.0000.000
152A157LEU0-0.053-0.00446.9480.0000.0000.0000.0000.0000.000
153A158ILE0-0.016-0.00845.016-0.001-0.0010.0000.0000.0000.000
154A159GLN0-0.007-0.01541.295-0.001-0.0010.0000.0000.0000.000
155A160ARG10.8340.87634.5530.0500.0500.0000.0000.0000.000
156A161GLU-1-0.743-0.88040.953-0.046-0.0460.0000.0000.0000.000
157A162ASP-1-0.979-0.98135.676-0.060-0.0600.0000.0000.0000.000
158A163ASP-1-0.812-0.87936.506-0.055-0.0550.0000.0000.0000.000
159A164LYS10.8540.94038.4820.0440.0440.0000.0000.0000.000
160A165PRO00.028-0.00239.697-0.004-0.0040.0000.0000.0000.000
161A166GLU-1-0.865-0.93639.800-0.056-0.0560.0000.0000.0000.000
162A167THR0-0.027-0.02436.942-0.004-0.0040.0000.0000.0000.000
163A168VAL0-0.004-0.00434.620-0.007-0.0070.0000.0000.0000.000
164A169ILE0-0.004-0.00635.051-0.008-0.0080.0000.0000.0000.000
165A170LYS10.9881.00136.0270.0660.0660.0000.0000.0000.000
166A171ARG10.9460.97628.6730.0850.0850.0000.0000.0000.000
167A172LEU0-0.017-0.01830.531-0.010-0.0100.0000.0000.0000.000
168A173LYS10.9060.95231.5220.0940.0940.0000.0000.0000.000
169A174ALA00.0470.03431.772-0.006-0.0060.0000.0000.0000.000
170A175TYR00.007-0.00523.441-0.008-0.0080.0000.0000.0000.000
171A176GLU-1-0.839-0.90927.560-0.136-0.1360.0000.0000.0000.000
172A177ASP-1-0.920-0.95829.095-0.126-0.1260.0000.0000.0000.000
173A178GLN0-0.020-0.00526.231-0.012-0.0120.0000.0000.0000.000
174A179THR00.008-0.02023.318-0.014-0.0140.0000.0000.0000.000
175A180LYS10.9020.96824.5580.1250.1250.0000.0000.0000.000
176A181PRO00.0260.00026.163-0.011-0.0110.0000.0000.0000.000
177A182VAL00.0060.01620.070-0.014-0.0140.0000.0000.0000.000
178A183LEU0-0.011-0.01220.969-0.031-0.0310.0000.0000.0000.000
179A184GLU-1-0.868-0.91822.435-0.242-0.2420.0000.0000.0000.000
180A185TYR00.0390.02117.935-0.001-0.0010.0000.0000.0000.000
181A186TYR00.051-0.00415.388-0.007-0.0070.0000.0000.0000.000
182A187GLN0-0.026-0.01218.778-0.027-0.0270.0000.0000.0000.000
183A188LYS10.8280.91521.2030.2280.2280.0000.0000.0000.000
184A189LYS10.7950.88916.4440.4620.4620.0000.0000.0000.000
185A190GLY00.0030.01917.153-0.036-0.0360.0000.0000.0000.000
186A191VAL0-0.0060.00113.110-0.013-0.0130.0000.0000.0000.000
187A192LEU0-0.095-0.03915.005-0.035-0.0350.0000.0000.0000.000
188A193GLU-1-0.883-0.93615.929-0.328-0.3280.0000.0000.0000.000
189A194THR0-0.027-0.02617.8620.0130.0130.0000.0000.0000.000
190A195PHE00.0300.01616.8040.0260.0260.0000.0000.0000.000
191A196SER00.0140.01022.2240.0050.0050.0000.0000.0000.000
192A197GLY0-0.004-0.00725.9430.0070.0070.0000.0000.0000.000
193A198THR00.029-0.02028.067-0.005-0.0050.0000.0000.0000.000
194A199GLU-1-0.779-0.85628.968-0.062-0.0620.0000.0000.0000.000
195A200THR00.0390.00823.781-0.006-0.0060.0000.0000.0000.000
196A201ASN00.0340.00824.546-0.009-0.0090.0000.0000.0000.000
197A202LYS10.8690.94026.0890.0750.0750.0000.0000.0000.000
198A203ILE00.0130.02421.634-0.002-0.0020.0000.0000.0000.000
199A204TRP00.0370.00216.201-0.019-0.0190.0000.0000.0000.000
200A205PRO00.0190.01519.707-0.009-0.0090.0000.0000.0000.000
201A206TYR00.0310.02019.804-0.001-0.0010.0000.0000.0000.000
202A207VAL0-0.0090.00415.525-0.021-0.0210.0000.0000.0000.000
203A208TYR0-0.030-0.02415.344-0.035-0.0350.0000.0000.0000.000
204A209ALA00.0400.00715.1730.0070.0070.0000.0000.0000.000
205A210PHE0-0.002-0.00613.084-0.020-0.0200.0000.0000.0000.000
206A211LEU0-0.010-0.0139.815-0.071-0.0710.0000.0000.0000.000
207A212GLN0-0.0260.00110.3570.0380.0380.0000.0000.0000.000
208A213THR0-0.023-0.00810.8090.0340.0340.0000.0000.0000.000
209A214LYS10.8530.9327.4010.8470.8470.0000.0000.0000.000
210A215VAL0-0.017-0.0074.727-0.579-0.548-0.001-0.007-0.0230.000
211A216PRO00.0170.0195.107-0.011-0.0110.0000.0000.0000.000
212A217GLN00.0190.0168.0660.0310.0310.0000.0000.0000.000