Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 5JYYZ

Calculation Name: 1CQ3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1CQ3

Chain ID: A

ChEMBL ID:

UniProt ID: Q85307

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2562743.722729
FMO2-HF: Nuclear repulsion 2474920.797412
FMO2-HF: Total energy -87822.925318
FMO2-MP2: Total energy -88070.515453


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:SER)


Summations of interaction energy for fragment #1(A:1: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.
-6.396-3.115-0.023-1.568-1.69-0.003
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.031
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].
3A3SER00.0000.0193.855-1.8520.965-0.032-1.467-1.318-0.003
4A4SER00.038-0.0056.052-0.642-0.6420.0000.0000.0000.000
5A5SER00.002-0.0208.7580.1010.1010.0000.0000.0000.000
6A6SER0-0.127-0.0703.6310.2670.4780.007-0.044-0.1740.000
7A7SER0-0.036-0.0303.724-0.263-0.0100.002-0.057-0.1980.000
8A8CYS0-0.029-0.0445.7910.3960.3960.0000.0000.0000.000
9A9THR0-0.022-0.0096.392-1.180-1.1800.0000.0000.0000.000
10A10GLU-1-0.939-0.9796.306-2.514-2.5140.0000.0000.0000.000
11A11GLU-1-0.913-0.9419.368-0.584-0.5840.0000.0000.0000.000
12A12GLU-1-0.920-0.96812.175-0.447-0.4470.0000.0000.0000.000
13A13ASN0-0.081-0.07215.5810.0310.0310.0000.0000.0000.000
14A14LYS10.8070.92013.9300.7120.7120.0000.0000.0000.000
15A15HIS0-0.016-0.03115.298-0.044-0.0440.0000.0000.0000.000
16A16HIS00.0090.01010.015-0.223-0.2230.0000.0000.0000.000
17A17MET0-0.0300.01315.0290.0330.0330.0000.0000.0000.000
18A18GLY00.004-0.00918.7950.0200.0200.0000.0000.0000.000
19A19ILE00.0520.02520.192-0.006-0.0060.0000.0000.0000.000
20A20ASP-1-0.791-0.83422.848-0.017-0.0170.0000.0000.0000.000
21A21VAL00.0700.04024.868-0.006-0.0060.0000.0000.0000.000
22A22ILE0-0.054-0.01528.3660.0110.0110.0000.0000.0000.000
23A23ILE00.0710.02430.447-0.004-0.0040.0000.0000.0000.000
24A24LYS10.7980.90433.6600.0060.0060.0000.0000.0000.000
25A25VAL00.0600.03436.584-0.003-0.0030.0000.0000.0000.000
26A26THR0-0.074-0.03539.8910.0030.0030.0000.0000.0000.000
27A27LYS10.8760.94941.550-0.027-0.0270.0000.0000.0000.000
28A28GLN00.000-0.00345.2760.0000.0000.0000.0000.0000.000
29A29ASP-1-0.850-0.90949.0660.0100.0100.0000.0000.0000.000
30A30GLN0-0.076-0.03751.3320.0010.0010.0000.0000.0000.000
31A31THR0-0.013-0.01546.1600.0000.0000.0000.0000.0000.000
32A32PRO0-0.030-0.01948.2680.0010.0010.0000.0000.0000.000
33A33THR0-0.024-0.02046.1240.0000.0000.0000.0000.0000.000
34A34ASN0-0.0050.00442.0050.0040.0040.0000.0000.0000.000
35A35ASP-1-0.897-0.96040.5050.0400.0400.0000.0000.0000.000
36A36LYS10.8080.89738.120-0.040-0.0400.0000.0000.0000.000
37A37ILE00.0180.02932.617-0.002-0.0020.0000.0000.0000.000
38A38CYS00.0250.03025.9540.0110.0110.0000.0000.0000.000
39A39GLN0-0.058-0.02833.0500.0040.0040.0000.0000.0000.000
40A40SER00.000-0.00633.5450.0040.0040.0000.0000.0000.000
41A41VAL00.0010.00328.484-0.005-0.0050.0000.0000.0000.000
42A42THR0-0.073-0.03631.0960.0060.0060.0000.0000.0000.000
43A43GLU-1-0.757-0.83925.2620.0480.0480.0000.0000.0000.000
44A44VAL0-0.0030.00329.6980.0060.0060.0000.0000.0000.000
45A45THR0-0.030-0.00127.941-0.009-0.0090.0000.0000.0000.000
46A46GLU-1-0.798-0.86030.623-0.009-0.0090.0000.0000.0000.000
47A47SER0-0.064-0.07931.783-0.005-0.0050.0000.0000.0000.000
48A48GLU-1-0.906-0.94529.3630.0400.0400.0000.0000.0000.000
49A49ASP-1-0.941-0.96430.8410.0370.0370.0000.0000.0000.000
50A50GLU-1-0.960-0.98633.9450.0290.0290.0000.0000.0000.000
51A51SER0-0.109-0.06134.822-0.004-0.0040.0000.0000.0000.000
52A52GLU-1-0.911-0.94235.9540.0060.0060.0000.0000.0000.000
53A53GLU-1-0.913-0.94235.586-0.013-0.0130.0000.0000.0000.000
54A54VAL00.0240.02334.129-0.001-0.0010.0000.0000.0000.000
55A55VAL0-0.063-0.03136.391-0.005-0.0050.0000.0000.0000.000
56A56LYS10.8770.92038.6140.0310.0310.0000.0000.0000.000
57A57GLY0-0.010-0.00136.7200.0030.0030.0000.0000.0000.000
58A58ASP-1-0.827-0.90831.089-0.067-0.0670.0000.0000.0000.000
59A59PRO0-0.019-0.00229.0880.0020.0020.0000.0000.0000.000
60A60THR0-0.016-0.01230.048-0.006-0.0060.0000.0000.0000.000
61A61THR0-0.038-0.02126.7580.0040.0040.0000.0000.0000.000
62A62TYR0-0.067-0.06129.749-0.005-0.0050.0000.0000.0000.000
63A63TYR0-0.079-0.07725.4730.0050.0050.0000.0000.0000.000
64A64THR0-0.012-0.01431.460-0.005-0.0050.0000.0000.0000.000
65A65VAL0-0.037-0.02631.0940.0080.0080.0000.0000.0000.000
66A66VAL0-0.0060.00933.846-0.005-0.0050.0000.0000.0000.000
67A67GLY00.0360.00635.8330.0060.0060.0000.0000.0000.000
68A68GLY0-0.0090.00037.292-0.004-0.0040.0000.0000.0000.000
69A69GLY00.0350.00939.924-0.003-0.0030.0000.0000.0000.000
70A70LEU0-0.039-0.02139.180-0.004-0.0040.0000.0000.0000.000
71A71THR00.0390.01438.5150.0050.0050.0000.0000.0000.000
72A72MET0-0.065-0.03434.448-0.006-0.0060.0000.0000.0000.000
73A73ASP-1-0.776-0.86135.2300.0210.0210.0000.0000.0000.000
74A74PHE0-0.026-0.03031.857-0.004-0.0040.0000.0000.0000.000
75A75GLY00.0490.01832.8560.0050.0050.0000.0000.0000.000
76A76PHE0-0.034-0.00428.093-0.004-0.0040.0000.0000.0000.000
77A77THR00.0730.03130.1080.0050.0050.0000.0000.0000.000
78A78LYS10.7790.88027.4670.0750.0750.0000.0000.0000.000
79A79CYS0-0.140-0.04626.155-0.003-0.0030.0000.0000.0000.000
80A80PRO0-0.008-0.00420.5350.0080.0080.0000.0000.0000.000
81A81LYS10.8200.89819.807-0.040-0.0400.0000.0000.0000.000
82A82ILE00.0280.03420.779-0.007-0.0070.0000.0000.0000.000
83A83SER0-0.087-0.05718.0590.0250.0250.0000.0000.0000.000
84A84SER0-0.103-0.06119.8620.0350.0350.0000.0000.0000.000
85A85ILE00.0810.03821.885-0.016-0.0160.0000.0000.0000.000
86A86SER0-0.056-0.02825.7040.0130.0130.0000.0000.0000.000
87A87GLU-1-0.737-0.89027.6260.0310.0310.0000.0000.0000.000
88A88TYR0-0.003-0.01031.2010.0060.0060.0000.0000.0000.000
89A89SER00.0740.04333.758-0.006-0.0060.0000.0000.0000.000
90A90ASP-1-0.828-0.91137.6100.0340.0340.0000.0000.0000.000
91A91GLY0-0.0050.02439.539-0.004-0.0040.0000.0000.0000.000
92A92ASN0-0.025-0.01842.9340.0020.0020.0000.0000.0000.000
93A93THR0-0.024-0.02639.578-0.001-0.0010.0000.0000.0000.000
94A94VAL00.0060.00036.2140.0040.0040.0000.0000.0000.000
95A95ASN0-0.057-0.02433.847-0.009-0.0090.0000.0000.0000.000
96A96ALA00.0360.01431.1620.0070.0070.0000.0000.0000.000
97A97ARG10.8280.88023.9060.0090.0090.0000.0000.0000.000
98A98LEU00.0090.01825.7360.0130.0130.0000.0000.0000.000
99A99SER0-0.013-0.02020.818-0.008-0.0080.0000.0000.0000.000
100A100SER00.0600.04018.6010.0130.0130.0000.0000.0000.000
101A101VAL0-0.057-0.02014.5280.0150.0150.0000.0000.0000.000
102A102SER00.0500.04912.6600.0030.0030.0000.0000.0000.000
103A103PRO0-0.010-0.0048.4640.1240.1240.0000.0000.0000.000
104A104GLY0-0.0050.0088.048-0.003-0.0030.0000.0000.0000.000
105A105GLN0-0.037-0.0319.0140.1660.1660.0000.0000.0000.000
106A106GLY0-0.0130.00210.3190.0010.0010.0000.0000.0000.000
107A107LYS10.8910.93011.592-0.304-0.3040.0000.0000.0000.000
108A108ASP-1-0.781-0.84510.6610.3770.3770.0000.0000.0000.000
109A109SER0-0.001-0.00711.823-0.038-0.0380.0000.0000.0000.000
110A110PRO00.0320.00212.926-0.141-0.1410.0000.0000.0000.000
111A111ALA00.0180.01612.186-0.007-0.0070.0000.0000.0000.000
112A112ILE00.0310.03514.303-0.021-0.0210.0000.0000.0000.000
113A113THR0-0.011-0.04217.508-0.053-0.0530.0000.0000.0000.000
114A114ARG10.9290.96219.6890.2990.2990.0000.0000.0000.000
115A115GLU-1-0.839-0.89121.703-0.269-0.2690.0000.0000.0000.000
116A116GLU-1-0.874-0.93921.098-0.208-0.2080.0000.0000.0000.000
117A117ALA00.000-0.00121.2200.0240.0240.0000.0000.0000.000
118A118LEU0-0.021-0.02123.3010.0220.0220.0000.0000.0000.000
119A119SER0-0.044-0.02526.6090.0200.0200.0000.0000.0000.000
120A120MET0-0.0030.01422.6150.0170.0170.0000.0000.0000.000
121A121ILE0-0.059-0.04024.4850.0120.0120.0000.0000.0000.000
122A122LYS10.8020.90327.8820.1320.1320.0000.0000.0000.000
123A123ASP-1-0.859-0.91129.836-0.085-0.0850.0000.0000.0000.000
124A125GLU-1-0.789-0.88730.012-0.033-0.0330.0000.0000.0000.000
125A126MET0-0.044-0.03530.6620.0040.0040.0000.0000.0000.000
126A127SER0-0.0100.00832.5670.0020.0020.0000.0000.0000.000
127A128ILE0-0.008-0.02534.4030.0040.0040.0000.0000.0000.000
128A129ASN0-0.031-0.02736.8630.0000.0000.0000.0000.0000.000
129A130ILE00.0120.01737.5510.0040.0040.0000.0000.0000.000
130A131LYS10.8680.91240.706-0.013-0.0130.0000.0000.0000.000
131A132CYS0-0.050-0.05742.6380.0020.0020.0000.0000.0000.000
132A133SER0-0.045-0.01442.1390.0020.0020.0000.0000.0000.000
133A134GLU-1-0.933-0.96644.1530.0250.0250.0000.0000.0000.000
134A135GLU-1-0.831-0.90840.1110.0450.0450.0000.0000.0000.000
135A136GLU-1-0.833-0.89542.8950.0360.0360.0000.0000.0000.000
136A137LYS10.7670.88235.699-0.063-0.0630.0000.0000.0000.000
137A138ASP-1-0.894-0.94338.0670.0590.0590.0000.0000.0000.000
138A139SER0-0.026-0.03334.0020.0000.0000.0000.0000.0000.000
139A140ASN0-0.062-0.03132.0130.0090.0090.0000.0000.0000.000
140A141ILE0-0.001-0.00128.9560.0000.0000.0000.0000.0000.000
141A142LYS10.8660.93121.859-0.130-0.1300.0000.0000.0000.000
142A143THR00.000-0.00726.052-0.005-0.0050.0000.0000.0000.000
143A144HIS0-0.029-0.02020.282-0.010-0.0100.0000.0000.0000.000
144A145PRO00.0150.00120.310-0.013-0.0130.0000.0000.0000.000
145A146VAL0-0.0010.00220.9950.0140.0140.0000.0000.0000.000
146A147LEU0-0.0220.00916.100-0.001-0.0010.0000.0000.0000.000
147A148GLY00.0480.02517.773-0.013-0.0130.0000.0000.0000.000
148A149SER00.040-0.01717.305-0.008-0.0080.0000.0000.0000.000
149A150ASN0-0.096-0.05315.4390.0020.0020.0000.0000.0000.000
150A151ILE00.0410.03718.404-0.022-0.0220.0000.0000.0000.000
151A152SER0-0.019-0.01121.3940.0280.0280.0000.0000.0000.000
152A153HIS00.002-0.00224.542-0.014-0.0140.0000.0000.0000.000
153A154LYS10.8250.90424.5220.1300.1300.0000.0000.0000.000
154A155LYS10.8470.90729.2360.0480.0480.0000.0000.0000.000
155A156VAL0-0.051-0.02226.595-0.006-0.0060.0000.0000.0000.000
156A157SER0-0.031-0.01829.0250.0100.0100.0000.0000.0000.000
157A158TYR0-0.066-0.04231.245-0.004-0.0040.0000.0000.0000.000
158A159GLU-1-0.855-0.93830.961-0.108-0.1080.0000.0000.0000.000
159A160ASP-1-0.979-0.96233.399-0.049-0.0490.0000.0000.0000.000
160A161ILE00.0210.00029.577-0.005-0.0050.0000.0000.0000.000
161A162ILE0-0.089-0.04433.3460.0060.0060.0000.0000.0000.000
162A163GLY00.0860.06335.4250.0000.0000.0000.0000.0000.000
163A164SER0-0.096-0.04437.6950.0040.0040.0000.0000.0000.000
164A165THR00.0470.00938.8770.0020.0020.0000.0000.0000.000
165A166ILE0-0.077-0.03640.8080.0000.0000.0000.0000.0000.000
166A167VAL00.0220.00541.9940.0020.0020.0000.0000.0000.000
167A168ASP-1-0.762-0.86144.2620.0090.0090.0000.0000.0000.000
168A169THR00.0200.00946.7210.0020.0020.0000.0000.0000.000
169A170LYS10.9040.96448.956-0.013-0.0130.0000.0000.0000.000
170A171CYS0-0.045-0.00945.2600.0010.0010.0000.0000.0000.000
171A172VAL00.0430.00942.8130.0010.0010.0000.0000.0000.000
172A173LYS10.7820.90945.248-0.007-0.0070.0000.0000.0000.000
173A174ASN0-0.008-0.02643.553-0.003-0.0030.0000.0000.0000.000
174A175LEU0-0.0050.00137.7660.0030.0030.0000.0000.0000.000
175A176GLU-1-0.880-0.93238.109-0.010-0.0100.0000.0000.0000.000
176A177ILE0-0.017-0.00532.7210.0040.0040.0000.0000.0000.000
177A178SER0-0.001-0.01330.547-0.006-0.0060.0000.0000.0000.000
178A179VAL00.0170.01028.6750.0050.0050.0000.0000.0000.000
179A180ARG10.7490.85923.6310.1190.1190.0000.0000.0000.000
180A181ILE00.0530.01123.8290.0040.0040.0000.0000.0000.000
181A182GLY00.0550.02021.9470.0020.0020.0000.0000.0000.000
182A183ASP-1-0.765-0.89315.721-0.505-0.5050.0000.0000.0000.000
183A184MET0-0.043-0.00115.4160.0320.0320.0000.0000.0000.000
184A185CYS0-0.094-0.01312.037-0.058-0.0580.0000.0000.0000.000
185A186LYS10.8230.91513.9510.6000.6000.0000.0000.0000.000
186A187GLU-1-0.800-0.86916.402-0.152-0.1520.0000.0000.0000.000
187A188SER0-0.037-0.03018.703-0.022-0.0220.0000.0000.0000.000
188A189SER0-0.011-0.03021.1740.0140.0140.0000.0000.0000.000
189A190GLU-1-0.880-0.92124.328-0.230-0.2300.0000.0000.0000.000
190A191LEU0-0.019-0.01920.5590.0070.0070.0000.0000.0000.000
191A192GLU-1-0.801-0.86821.512-0.199-0.1990.0000.0000.0000.000
192A193VAL00.0370.01625.2390.0110.0110.0000.0000.0000.000
193A194LYS10.7500.85527.5330.0510.0510.0000.0000.0000.000
194A195ASP-1-0.685-0.82230.296-0.051-0.0510.0000.0000.0000.000
195A196GLY0-0.043-0.05132.9650.0020.0020.0000.0000.0000.000
196A197PHE00.0020.01435.5920.0000.0000.0000.0000.0000.000
197A198LYS10.8540.92138.7860.0240.0240.0000.0000.0000.000
198A199TYR0-0.0070.00541.520-0.001-0.0010.0000.0000.0000.000
199A200VAL0-0.029-0.03544.0580.0020.0020.0000.0000.0000.000
200A201ASP-1-0.861-0.94746.7630.0000.0000.0000.0000.0000.000
201A202GLY0-0.0230.00248.7630.0000.0000.0000.0000.0000.000
202A203SER0-0.076-0.03049.322-0.002-0.0020.0000.0000.0000.000
203A204ALA00.0360.00144.9150.0010.0010.0000.0000.0000.000
204A205SER0-0.130-0.08544.1480.0000.0000.0000.0000.0000.000
205A206GLU-1-0.769-0.87839.670-0.040-0.0400.0000.0000.0000.000
206A207ASP-1-0.870-0.90340.276-0.031-0.0310.0000.0000.0000.000
207A208ALA00.0420.03336.0610.0010.0010.0000.0000.0000.000
208A209ALA00.0120.01036.686-0.001-0.0010.0000.0000.0000.000
209A210ASP-1-0.834-0.90631.636-0.057-0.0570.0000.0000.0000.000
210A211ASP-1-0.783-0.88532.057-0.027-0.0270.0000.0000.0000.000
211A212THR0-0.070-0.05927.6730.0020.0020.0000.0000.0000.000
212A213SER0-0.090-0.05829.6400.0070.0070.0000.0000.0000.000
213A214LEU0-0.0140.02132.3590.0050.0050.0000.0000.0000.000
214A215ILE00.0190.01429.8870.0040.0040.0000.0000.0000.000
215A216ASN00.002-0.01031.5940.0000.0000.0000.0000.0000.000
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