Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 14QZZ

Calculation Name: 2Z84-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Z84

Chain ID: A

ChEMBL ID:

UniProt ID: Q9CZP0

Base Structure: X-ray

Registration Date: 2023-06-21

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 210
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2378204.770423
FMO2-HF: Nuclear repulsion 2296996.703365
FMO2-HF: Total energy -81208.067058
FMO2-MP2: Total energy -81440.137649


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:7:SER)


Summations of interaction energy for fragment #1(A:7: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.
0.6821.887-0.014-0.575-0.6150.001
Interaction energy analysis for fragmet #1(A:7:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.029
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].
3A9LEU0-0.0070.0093.8692.2313.436-0.014-0.575-0.6150.001
4A10GLU-1-0.845-0.9035.332-2.327-2.3270.0000.0000.0000.000
5A11LEU0-0.0300.0008.1800.2160.2160.0000.0000.0000.000
6A12LEU0-0.019-0.01011.830-0.097-0.0970.0000.0000.0000.000
7A13LYS10.9060.96114.6950.5650.5650.0000.0000.0000.000
8A14ASP-1-0.810-0.87716.528-0.268-0.2680.0000.0000.0000.000
9A15VAL00.0030.00418.5010.0120.0120.0000.0000.0000.000
10A16HIS00.1270.08521.0280.0160.0160.0000.0000.0000.000
11A17LEU0-0.046-0.02222.1210.0100.0100.0000.0000.0000.000
12A18GLY00.0240.00224.564-0.002-0.0020.0000.0000.0000.000
13A19LEU0-0.0250.00727.3170.0100.0100.0000.0000.0000.000
14A20PRO0-0.0060.00829.488-0.004-0.0040.0000.0000.0000.000
15A21VAL00.0320.01233.2280.0000.0000.0000.0000.0000.000
16A22PRO0-0.030-0.01735.2640.0040.0040.0000.0000.0000.000
17A23CYS0-0.048-0.02837.5680.0040.0040.0000.0000.0000.000
18A24HIS00.002-0.00740.604-0.004-0.0040.0000.0000.0000.000
19A25ASP-1-0.905-0.94843.112-0.053-0.0530.0000.0000.0000.000
20A26PRO0-0.052-0.02439.4980.0020.0020.0000.0000.0000.000
21A27ALA00.0340.02941.966-0.002-0.0020.0000.0000.0000.000
22A28ARG10.7700.85641.7050.0600.0600.0000.0000.0000.000
23A29LEU0-0.006-0.01034.5320.0010.0010.0000.0000.0000.000
24A30ALA00.0000.00635.350-0.002-0.0020.0000.0000.0000.000
25A31LEU00.005-0.01628.9830.0040.0040.0000.0000.0000.000
26A32LEU0-0.0420.00425.133-0.002-0.0020.0000.0000.0000.000
27A33SER00.0220.02227.821-0.006-0.0060.0000.0000.0000.000
28A34GLY00.0100.00224.346-0.005-0.0050.0000.0000.0000.000
29A35HIS10.7970.87019.4740.3130.3130.0000.0000.0000.000
30A36TYR00.019-0.01919.073-0.006-0.0060.0000.0000.0000.000
31A37LEU0-0.018-0.00412.598-0.018-0.0180.0000.0000.0000.000
32A38TYR0-0.021-0.03816.4920.0320.0320.0000.0000.0000.000
33A39TYR00.0670.02213.055-0.019-0.0190.0000.0000.0000.000
34A40HIS0-0.053-0.04715.979-0.001-0.0010.0000.0000.0000.000
35A41TYR00.022-0.02717.7140.0190.0190.0000.0000.0000.000
36A42GLY00.005-0.00616.6360.0140.0140.0000.0000.0000.000
37A43CYS0-0.094-0.00713.7270.0540.0540.0000.0000.0000.000
38A44ASP-1-0.805-0.89610.8810.0520.0520.0000.0000.0000.000
39A45GLY0-0.016-0.00111.3710.0610.0610.0000.0000.0000.000
40A46LEU0-0.058-0.02112.975-0.008-0.0080.0000.0000.0000.000
41A47ASP-1-0.797-0.87916.0580.1330.1330.0000.0000.0000.000
42A48ASP-1-0.735-0.86519.1880.0500.0500.0000.0000.0000.000
43A49ARG10.8460.88921.328-0.169-0.1690.0000.0000.0000.000
44A50GLY0-0.018-0.00323.7350.0030.0030.0000.0000.0000.000
45A51TRP0-0.0300.00021.732-0.009-0.0090.0000.0000.0000.000
46A52GLY00.0480.01422.352-0.011-0.0110.0000.0000.0000.000
47A53CYM-1-0.808-0.76322.625-0.022-0.0220.0000.0000.0000.000
48A54GLY00.0450.04624.185-0.016-0.0160.0000.0000.0000.000
49A55TYR0-0.021-0.03620.923-0.018-0.0180.0000.0000.0000.000
50A56ARG10.7330.83415.432-0.053-0.0530.0000.0000.0000.000
51A57THR0-0.008-0.02520.378-0.028-0.0280.0000.0000.0000.000
52A58LEU00.0360.01821.850-0.020-0.0200.0000.0000.0000.000
53A59GLN0-0.030-0.00815.2040.0070.0070.0000.0000.0000.000
54A60THR0-0.013-0.02618.423-0.034-0.0340.0000.0000.0000.000
55A61LEU0-0.054-0.01719.832-0.026-0.0260.0000.0000.0000.000
56A62CYS0-0.020-0.01018.879-0.006-0.0060.0000.0000.0000.000
57A63SER0-0.045-0.01416.540-0.033-0.0330.0000.0000.0000.000
58A64TRP0-0.0490.00318.042-0.040-0.0400.0000.0000.0000.000
59A65PRO00.0240.01221.2590.0030.0030.0000.0000.0000.000
60A66GLY00.0530.01518.3050.0050.0050.0000.0000.0000.000
61A67GLY0-0.019-0.02316.995-0.027-0.0270.0000.0000.0000.000
62A68GLN0-0.041-0.03313.420-0.015-0.0150.0000.0000.0000.000
63A69SER00.0900.0299.6540.0040.0040.0000.0000.0000.000
64A70SER0-0.058-0.0269.8910.0640.0640.0000.0000.0000.000
65A71GLY00.0330.02211.1590.0310.0310.0000.0000.0000.000
66A72VAL0-0.052-0.00313.7140.0970.0970.0000.0000.0000.000
67A73PRO00.0080.02113.965-0.029-0.0290.0000.0000.0000.000
68A74GLY00.0810.03214.6340.0180.0180.0000.0000.0000.000
69A75LEU00.0460.00915.3010.0070.0070.0000.0000.0000.000
70A76PRO00.014-0.00116.621-0.005-0.0050.0000.0000.0000.000
71A77ALA0-0.052-0.01817.4500.0020.0020.0000.0000.0000.000
72A78LEU00.0220.01818.877-0.001-0.0010.0000.0000.0000.000
73A79GLN0-0.001-0.00721.6840.0120.0120.0000.0000.0000.000
74A80GLY0-0.016-0.01222.3920.0040.0040.0000.0000.0000.000
75A81ALA00.0000.01323.3300.0020.0020.0000.0000.0000.000
76A82LEU0-0.008-0.00424.9710.0050.0050.0000.0000.0000.000
77A83GLU-1-0.853-0.93126.2550.0070.0070.0000.0000.0000.000
78A84ALA0-0.065-0.03426.7700.0030.0030.0000.0000.0000.000
79A85MET0-0.050-0.01127.314-0.004-0.0040.0000.0000.0000.000
80A86GLY0-0.0060.01330.9490.0020.0020.0000.0000.0000.000
81A87ASP-1-0.883-0.94530.685-0.051-0.0510.0000.0000.0000.000
82A88LYS10.7860.88129.3480.0290.0290.0000.0000.0000.000
83A89PRO00.0070.01231.972-0.001-0.0010.0000.0000.0000.000
84A90PRO00.021-0.01230.2270.0010.0010.0000.0000.0000.000
85A91GLY0-0.0090.00428.6260.0050.0050.0000.0000.0000.000
86A92PHE00.0070.00626.4900.0070.0070.0000.0000.0000.000
87A93ARG10.9320.97519.0360.0200.0200.0000.0000.0000.000
88A94GLY0-0.025-0.01022.5510.0100.0100.0000.0000.0000.000
89A95SER0-0.077-0.03523.5450.0110.0110.0000.0000.0000.000
90A96ARG10.9540.96723.594-0.105-0.1050.0000.0000.0000.000
91A97ASN0-0.0060.00326.409-0.003-0.0030.0000.0000.0000.000
92A98TRP00.0200.02326.808-0.003-0.0030.0000.0000.0000.000
93A99ILE0-0.040-0.01324.621-0.002-0.0020.0000.0000.0000.000
94A100GLY00.0750.02828.6960.0010.0010.0000.0000.0000.000
95A101CYS0-0.053-0.01829.423-0.007-0.0070.0000.0000.0000.000
96A102VAL00.0230.03330.861-0.008-0.0080.0000.0000.0000.000
97A103GLU-1-0.702-0.84328.069-0.045-0.0450.0000.0000.0000.000
98A104ALA00.0140.01226.358-0.009-0.0090.0000.0000.0000.000
99A105SER0-0.050-0.05027.031-0.012-0.0120.0000.0000.0000.000
100A106LEU00.0540.03229.126-0.009-0.0090.0000.0000.0000.000
101A107CYS0-0.043-0.02323.832-0.005-0.0050.0000.0000.0000.000
102A108LEU0-0.040-0.03423.660-0.018-0.0180.0000.0000.0000.000
103A109GLU-1-0.971-0.97125.513-0.116-0.1160.0000.0000.0000.000
104A110HIS00.000-0.01223.1130.0040.0040.0000.0000.0000.000
105A111PHE0-0.091-0.05719.837-0.005-0.0050.0000.0000.0000.000
106A112GLY0-0.0020.01621.817-0.029-0.0290.0000.0000.0000.000
107A113GLY0-0.0060.00722.944-0.021-0.0210.0000.0000.0000.000
108A114PRO0-0.053-0.02523.2630.0170.0170.0000.0000.0000.000
109A115GLN00.0200.00226.1980.0160.0160.0000.0000.0000.000
110A116GLY00.0700.01929.5000.0000.0000.0000.0000.0000.000
111A117ARG10.9380.96630.1130.0900.0900.0000.0000.0000.000
112A118LEU00.0450.01633.0490.0010.0010.0000.0000.0000.000
113A119CYS0-0.081-0.02435.2310.0010.0010.0000.0000.0000.000
114A120HIS0-0.002-0.01337.1670.0030.0030.0000.0000.0000.000
115A121LEU0-0.0010.01238.721-0.001-0.0010.0000.0000.0000.000
116A122PRO00.0490.02841.4750.0030.0030.0000.0000.0000.000
117A123ARG10.8930.95644.2360.0160.0160.0000.0000.0000.000
118A124GLY00.000-0.00246.498-0.001-0.0010.0000.0000.0000.000
119A125VAL0-0.001-0.00746.0210.0000.0000.0000.0000.0000.000
120A126GLY00.0390.02243.398-0.002-0.0020.0000.0000.0000.000
121A127LEU0-0.023-0.02037.6210.0010.0010.0000.0000.0000.000
122A128ARG10.7080.82041.6750.0330.0330.0000.0000.0000.000
123A129GLY00.0380.02744.5560.0010.0010.0000.0000.0000.000
124A130GLU-1-0.816-0.88639.990-0.062-0.0620.0000.0000.0000.000
125A131GLU-1-0.784-0.89740.174-0.054-0.0540.0000.0000.0000.000
126A132GLU-1-0.765-0.85540.415-0.066-0.0660.0000.0000.0000.000
127A133ARG10.8090.88838.4430.0630.0630.0000.0000.0000.000
128A134LEU0-0.010-0.00733.741-0.007-0.0070.0000.0000.0000.000
129A135TYR00.002-0.04536.059-0.009-0.0090.0000.0000.0000.000
130A136SER0-0.012-0.00437.332-0.006-0.0060.0000.0000.0000.000
131A137HIS0-0.0340.00330.737-0.001-0.0010.0000.0000.0000.000
132A138PHE0-0.0120.00029.788-0.007-0.0070.0000.0000.0000.000
133A139THR0-0.008-0.02033.131-0.008-0.0080.0000.0000.0000.000
134A140THR0-0.084-0.04735.666-0.003-0.0030.0000.0000.0000.000
135A141GLY00.0080.00931.411-0.002-0.0020.0000.0000.0000.000
136A142GLY0-0.044-0.01630.401-0.009-0.0090.0000.0000.0000.000
137A143GLY00.0460.00427.043-0.007-0.0070.0000.0000.0000.000
138A144PRO0-0.006-0.01223.5430.0170.0170.0000.0000.0000.000
139A145VAL0-0.0130.01826.838-0.001-0.0010.0000.0000.0000.000
140A146MET0-0.0070.00727.0780.0010.0010.0000.0000.0000.000
141A147VAL0-0.020-0.02328.8490.0030.0030.0000.0000.0000.000
142A148GLY00.0270.00430.2710.0010.0010.0000.0000.0000.000
143A149GLY00.0450.02231.3380.0010.0010.0000.0000.0000.000
144A150ASP-1-0.882-0.95532.192-0.027-0.0270.0000.0000.0000.000
145A151ALA0-0.047-0.02835.390-0.001-0.0010.0000.0000.0000.000
146A152ASP-1-0.792-0.87634.117-0.021-0.0210.0000.0000.0000.000
147A153ALA0-0.0200.00432.1170.0030.0030.0000.0000.0000.000
148A154GLN0-0.058-0.05129.6360.0020.0020.0000.0000.0000.000
149A155SER0-0.003-0.04426.716-0.007-0.0070.0000.0000.0000.000
150A156LYS10.7770.86427.6040.0370.0370.0000.0000.0000.000
151A157ALA0-0.0100.00425.195-0.007-0.0070.0000.0000.0000.000
152A158LEU0-0.0010.00427.2320.0050.0050.0000.0000.0000.000
153A159LEU0-0.009-0.01624.690-0.010-0.0100.0000.0000.0000.000
154A160GLY00.0370.01128.654-0.009-0.0090.0000.0000.0000.000
155A161ILE0-0.046-0.01032.0540.0060.0060.0000.0000.0000.000
156A162CYS0-0.0020.00935.771-0.004-0.0040.0000.0000.0000.000
157A163GLU-1-0.789-0.83438.479-0.053-0.0530.0000.0000.0000.000
158A164GLY00.0810.04341.997-0.002-0.0020.0000.0000.0000.000
159A165PRO0-0.014-0.02244.3580.0000.0000.0000.0000.0000.000
160A166GLY0-0.0270.00347.6170.0010.0010.0000.0000.0000.000
161A167SER0-0.022-0.02945.8940.0020.0020.0000.0000.0000.000
162A168GLU-1-0.883-0.92943.872-0.043-0.0430.0000.0000.0000.000
163A169VAL00.010-0.00139.451-0.002-0.0020.0000.0000.0000.000
164A170TYR0-0.077-0.07737.1220.0050.0050.0000.0000.0000.000
165A171VAL00.023-0.00333.950-0.004-0.0040.0000.0000.0000.000
166A172LEU0-0.0310.00427.9230.0040.0040.0000.0000.0000.000
167A173ILE00.003-0.01029.335-0.006-0.0060.0000.0000.0000.000
168A174LEU00.0010.00121.717-0.004-0.0040.0000.0000.0000.000
169A175ASP-1-0.755-0.86225.330-0.015-0.0150.0000.0000.0000.000
170A176PRO0-0.0010.02321.7730.0050.0050.0000.0000.0000.000
171A177HIS10.8150.83521.8350.0150.0150.0000.0000.0000.000
172A178TYR00.0070.02018.3250.0050.0050.0000.0000.0000.000
173A179TRP00.0320.00118.9480.0090.0090.0000.0000.0000.000
174A180GLY0-0.0020.01317.404-0.008-0.0080.0000.0000.0000.000
175A181THR00.014-0.01812.4430.0470.0470.0000.0000.0000.000
176A182PRO0-0.0300.01615.135-0.009-0.0090.0000.0000.0000.000
177A183LYS10.8560.89715.451-0.064-0.0640.0000.0000.0000.000
178A184ASN00.002-0.00915.944-0.040-0.0400.0000.0000.0000.000
179A185ARG10.9100.94017.9720.2360.2360.0000.0000.0000.000
180A186CYS00.0170.01420.3600.0050.0050.0000.0000.0000.000
181A187GLU-1-0.786-0.87119.9210.0360.0360.0000.0000.0000.000
182A188LEU0-0.012-0.00118.7930.0080.0080.0000.0000.0000.000
183A189GLN0-0.080-0.05923.0120.0100.0100.0000.0000.0000.000
184A190ALA0-0.035-0.01626.0140.0050.0050.0000.0000.0000.000
185A191ALA0-0.024-0.01025.9420.0060.0060.0000.0000.0000.000
186A192GLY0-0.0030.00827.9150.0050.0050.0000.0000.0000.000
187A193TRP0-0.0110.00223.645-0.001-0.0010.0000.0000.0000.000
188A194VAL0-0.014-0.01723.141-0.012-0.0120.0000.0000.0000.000
189A195GLY00.0360.01126.0920.0050.0050.0000.0000.0000.000
190A196TRP0-0.0050.01129.729-0.002-0.0020.0000.0000.0000.000
191A197GLN00.0130.00531.1230.0080.0080.0000.0000.0000.000
192A198LYS10.9220.96835.4300.0360.0360.0000.0000.0000.000
193A199VAL00.0770.03938.2540.0030.0030.0000.0000.0000.000
194A200LYS10.9230.96139.4390.0250.0250.0000.0000.0000.000
195A201SER0-0.042-0.03238.0400.0030.0030.0000.0000.0000.000
196A202VAL0-0.0260.01134.0810.0020.0020.0000.0000.0000.000
197A203PHE00.0210.00034.7680.0000.0000.0000.0000.0000.000
198A204ASP-1-0.761-0.85139.213-0.018-0.0180.0000.0000.0000.000
199A205SER00.0060.01842.163-0.001-0.0010.0000.0000.0000.000
200A206ASN0-0.058-0.03845.441-0.001-0.0010.0000.0000.0000.000
201A207SER00.000-0.01541.1430.0030.0030.0000.0000.0000.000
202A208PHE0-0.050-0.02541.524-0.002-0.0020.0000.0000.0000.000
203A209TYR00.0290.02336.1840.0010.0010.0000.0000.0000.000
204A210ASN0-0.0080.01034.674-0.003-0.0030.0000.0000.0000.000
205A211LEU00.021-0.01433.320-0.001-0.0010.0000.0000.0000.000
206A212CYS0-0.026-0.00729.556-0.001-0.0010.0000.0000.0000.000
207A213PHE00.0150.00530.128-0.007-0.0070.0000.0000.0000.000
208A214THR00.011-0.00425.782-0.004-0.0040.0000.0000.0000.000
209A215ARG10.8190.89628.8860.1200.1200.0000.0000.0000.000
210A216LEU00.0350.02624.718-0.002-0.0020.0000.0000.0000.000