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: 53LLZ

Calculation Name: 3C0T-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C0T

Chain ID: A

ChEMBL ID:

UniProt ID: O14198

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2469185.515032
FMO2-HF: Nuclear repulsion 2384719.718842
FMO2-HF: Total energy -84465.79619
FMO2-MP2: Total energy -84711.754951


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.
-19.555-10.7920.833-11.572-18.031-0.085
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 : -0.063 / q_NPA : -0.018
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].
3A3GLU-1-0.788-0.8963.487-3.814-1.4530.013-0.972-1.4030.001
4A4LEU0-0.014-0.0074.9330.5120.602-0.001-0.007-0.0820.000
5A5TYR0-0.035-0.0528.3990.1440.1440.0000.0000.0000.000
6A6LEU0-0.034-0.01610.9950.0790.0790.0000.0000.0000.000
7A7LEU00.0180.00713.774-0.002-0.0020.0000.0000.0000.000
8A8GLY00.0420.01916.4380.0450.0450.0000.0000.0000.000
9A9VAL0-0.0370.00219.484-0.020-0.0200.0000.0000.0000.000
10A10VAL00.008-0.00422.1860.0250.0250.0000.0000.0000.000
11A11PRO0-0.010-0.00724.4510.0000.0000.0000.0000.0000.000
12A12SER00.1310.06327.7090.0120.0120.0000.0000.0000.000
13A13ARG10.9920.99328.6900.1170.1170.0000.0000.0000.000
14A14ARG10.7960.86927.2180.1330.1330.0000.0000.0000.000
15A15PHE00.0440.03523.1770.0070.0070.0000.0000.0000.000
16A16GLU-1-0.891-0.94127.033-0.046-0.0460.0000.0000.0000.000
17A17ALA00.004-0.00429.0090.0070.0070.0000.0000.0000.000
18A18VAL0-0.019-0.01623.6830.0070.0070.0000.0000.0000.000
19A19VAL00.0520.03523.5640.0050.0050.0000.0000.0000.000
20A20ASN00.0220.01025.2470.0200.0200.0000.0000.0000.000
21A21SER0-0.067-0.03226.4930.0140.0140.0000.0000.0000.000
22A22LEU0-0.027-0.02220.4230.0070.0070.0000.0000.0000.000
23A23SER00.0310.01223.2090.0170.0170.0000.0000.0000.000
24A24LYS10.9130.98425.1450.0140.0140.0000.0000.0000.000
25A25THR0-0.122-0.06924.0480.0060.0060.0000.0000.0000.000
26A26LEU0-0.056-0.00718.7680.0050.0050.0000.0000.0000.000
27A27ASP-1-0.835-0.90319.5010.1740.1740.0000.0000.0000.000
28A28GLY0-0.049-0.01119.516-0.003-0.0030.0000.0000.0000.000
29A29PRO0-0.036-0.02419.411-0.007-0.0070.0000.0000.0000.000
30A30LYS10.8970.95211.967-0.255-0.2550.0000.0000.0000.000
31A31THR0-0.006-0.01217.933-0.022-0.0220.0000.0000.0000.000
32A32ILE0-0.032-0.00713.3080.0240.0240.0000.0000.0000.000
33A33LEU00.0460.00616.657-0.026-0.0260.0000.0000.0000.000
34A34GLU-1-0.839-0.90911.592-0.346-0.3460.0000.0000.0000.000
35A35PHE00.0230.01415.748-0.027-0.0270.0000.0000.0000.000
36A36TRP0-0.012-0.0258.445-0.065-0.0650.0000.0000.0000.000
37A37VAL00.008-0.00115.2410.0380.0380.0000.0000.0000.000
38A38VAL0-0.023-0.01814.633-0.078-0.0780.0000.0000.0000.000
39A39TYR0-0.007-0.00615.7930.0820.0820.0000.0000.0000.000
40A40ARG10.8440.92716.4240.2520.2520.0000.0000.0000.000
41A41PRO00.012-0.00217.2940.0450.0450.0000.0000.0000.000
42A42LYS10.9450.99119.8780.2420.2420.0000.0000.0000.000
43A43ASP-1-0.866-0.96123.609-0.228-0.2280.0000.0000.0000.000
44A44VAL0-0.052-0.02926.4300.0170.0170.0000.0000.0000.000
45A45PRO0-0.0350.01026.2350.0120.0120.0000.0000.0000.000
46A46PRO00.0890.04026.737-0.015-0.0150.0000.0000.0000.000
47A47ASN0-0.090-0.03627.457-0.008-0.0080.0000.0000.0000.000
48A48LEU0-0.005-0.00322.1480.0070.0070.0000.0000.0000.000
49A49PRO0-0.028-0.01122.396-0.007-0.0070.0000.0000.0000.000
50A50ARG10.9590.97920.2670.4370.4370.0000.0000.0000.000
51A51GLN00.0710.02516.065-0.010-0.0100.0000.0000.0000.000
52A52PRO00.019-0.01915.793-0.037-0.0370.0000.0000.0000.000
53A53ASP-1-0.898-0.92810.870-1.003-1.0030.0000.0000.0000.000
54A54SER0-0.045-0.02110.743-0.144-0.1440.0000.0000.0000.000
55A55TRP0-0.068-0.03612.9980.1080.1080.0000.0000.0000.000
56A56LEU00.0090.01011.426-0.188-0.1880.0000.0000.0000.000
57A57ARG10.8910.95910.1391.3111.3110.0000.0000.0000.000
58A58LEU0-0.0040.00110.514-0.100-0.1000.0000.0000.0000.000
59A59CYS00.0000.01110.0600.0630.0630.0000.0000.0000.000
60A60SER00.0250.01812.1210.0800.0800.0000.0000.0000.000
61A61ASN00.0380.00913.823-0.064-0.0640.0000.0000.0000.000
62A62ILE00.007-0.01215.3590.0180.0180.0000.0000.0000.000
63A63GLU-1-0.898-0.94718.1070.0020.0020.0000.0000.0000.000
64A64SER0-0.126-0.05518.7510.0230.0230.0000.0000.0000.000
65A65HIS0-0.021-0.02719.2950.0080.0080.0000.0000.0000.000
66A66ASP-1-0.851-0.89423.0820.0000.0000.0000.0000.0000.000
67A67GLU-1-0.947-0.98626.541-0.066-0.0660.0000.0000.0000.000
68A68THR0-0.048-0.04927.429-0.007-0.0070.0000.0000.0000.000
69A69ASP-1-0.888-0.94926.277-0.036-0.0360.0000.0000.0000.000
70A70THR0-0.022-0.02627.660-0.009-0.0090.0000.0000.0000.000
71A71GLU-1-1.038-1.01626.753-0.077-0.0770.0000.0000.0000.000
72A72TRP00.1060.06618.844-0.006-0.0060.0000.0000.0000.000
73A73SER0-0.069-0.00820.7060.0110.0110.0000.0000.0000.000
74A74LYS10.9400.95620.6670.0660.0660.0000.0000.0000.000
75A75ASN0-0.040-0.00122.5370.0260.0260.0000.0000.0000.000
76A76THR00.0400.00716.5160.0160.0160.0000.0000.0000.000
77A77GLN0-0.085-0.03813.1780.0490.0490.0000.0000.0000.000
78A78TRP0-0.0120.00213.315-0.027-0.0270.0000.0000.0000.000
79A79SER0-0.058-0.0327.6500.1320.1320.0000.0000.0000.000
80A80MET0-0.016-0.0078.878-0.043-0.0430.0000.0000.0000.000
81A81TYR00.031-0.0143.734-0.1740.0690.002-0.029-0.2160.000
82A82LEU00.0230.0246.3580.3730.3730.0000.0000.0000.000
83A83GLU-1-0.949-0.9876.575-2.976-2.9760.0000.0000.0000.000
84A84GLY00.0420.0237.4380.5710.5710.0000.0000.0000.000
85A85ASN0-0.027-0.0249.068-0.100-0.1000.0000.0000.0000.000
86A86SER00.0190.00510.749-0.087-0.0870.0000.0000.0000.000
87A87GLU-1-0.931-0.98110.253-0.570-0.5700.0000.0000.0000.000
88A88PRO0-0.100-0.05213.4010.0370.0370.0000.0000.0000.000
89A89LYS10.9470.95817.1910.2990.2990.0000.0000.0000.000
90A90ARG10.8830.94313.7720.5690.5690.0000.0000.0000.000
91A91GLU-1-0.886-0.93817.846-0.413-0.4130.0000.0000.0000.000
92A92ASP-1-0.932-0.95620.322-0.212-0.2120.0000.0000.0000.000
93A93LYS10.8800.94916.5520.2620.2620.0000.0000.0000.000
94A94CYS0-0.0130.01211.9160.0030.0030.0000.0000.0000.000
95A95GLY00.0590.03512.8370.0200.0200.0000.0000.0000.000
96A96ILE00.000-0.0078.105-0.102-0.1020.0000.0000.0000.000
97A97ARG10.8720.9497.2622.7622.7620.0000.0000.0000.000
98A98PRO00.0190.0294.454-1.143-1.068-0.001-0.035-0.0390.000
99A99VAL0-0.006-0.0052.418-0.2061.4271.645-0.941-2.3370.000
100A100ASN00.0060.0051.989-6.093-10.16715.035-5.636-5.326-0.056
101A101ARG10.9620.9702.959-4.546-2.7811.127-0.560-2.3330.000
102A102ALA00.0060.0124.5820.5360.633-0.001-0.005-0.0910.000
103A103LYS10.9330.9757.638-0.883-0.8830.0000.0000.0000.000
104A104LEU00.0010.00910.2310.0500.0500.0000.0000.0000.000
105A105THR00.024-0.00213.805-0.010-0.0100.0000.0000.0000.000
106A106ASN00.0150.00517.2170.0070.0070.0000.0000.0000.000
107A107GLY00.0170.01420.976-0.018-0.0180.0000.0000.0000.000
108A108SER00.0610.02121.640-0.008-0.0080.0000.0000.0000.000
109A109VAL00.0420.02115.371-0.010-0.0100.0000.0000.0000.000
110A110THR00.0200.00418.782-0.032-0.0320.0000.0000.0000.000
111A111GLU-1-0.889-0.94620.007-0.139-0.1390.0000.0000.0000.000
112A112PHE0-0.037-0.01317.6370.0050.0050.0000.0000.0000.000
113A113VAL00.043-0.02315.907-0.009-0.0090.0000.0000.0000.000
114A114GLU-1-0.924-0.95718.737-0.233-0.2330.0000.0000.0000.000
115A115LYS10.8650.93122.0600.1460.1460.0000.0000.0000.000
116A116MET0-0.0840.00115.7950.0040.0040.0000.0000.0000.000
117A117GLY0-0.0050.01320.623-0.010-0.0100.0000.0000.0000.000
118A118TYR0-0.036-0.01214.833-0.012-0.0120.0000.0000.0000.000
119A119GLU-1-0.837-0.93020.697-0.245-0.2450.0000.0000.0000.000
120A120PHE00.018-0.00120.747-0.045-0.0450.0000.0000.0000.000
121A121SER0-0.0580.00419.347-0.001-0.0010.0000.0000.0000.000
122A122HIS0-0.011-0.04117.923-0.012-0.0120.0000.0000.0000.000
123A123GLU-1-0.724-0.86318.809-0.287-0.2870.0000.0000.0000.000
124A124TYR0-0.043-0.00813.5280.0020.0020.0000.0000.0000.000
125A125ILE00.0300.02918.165-0.014-0.0140.0000.0000.0000.000
126A126ILE0-0.070-0.00614.314-0.016-0.0160.0000.0000.0000.000
127A127GLN00.1020.04517.3690.0210.0210.0000.0000.0000.000
128A128GLY00.004-0.01618.351-0.028-0.0280.0000.0000.0000.000
129A129LEU0-0.0220.00918.7120.0300.0300.0000.0000.0000.000
130A130GLU-1-0.816-0.93111.671-0.024-0.0240.0000.0000.0000.000
131A131TYR00.0420.00816.0410.0260.0260.0000.0000.0000.000
132A132PHE0-0.001-0.01812.7080.0090.0090.0000.0000.0000.000
133A133PHE00.0650.02815.735-0.023-0.0230.0000.0000.0000.000
134A134PHE0-0.028-0.01115.845-0.009-0.0090.0000.0000.0000.000
135A135ASP-1-0.907-0.95912.2490.6400.6400.0000.0000.0000.000
136A136THR0-0.108-0.04211.3210.0340.0340.0000.0000.0000.000
137A137THR00.0290.01010.2090.0910.0910.0000.0000.0000.000
138A138VAL0-0.018-0.00512.204-0.143-0.1430.0000.0000.0000.000
139A139ARG10.8090.89810.9550.3710.3710.0000.0000.0000.000
140A140ILE0-0.0150.00314.889-0.056-0.0560.0000.0000.0000.000
141A141TYR0-0.017-0.03414.2490.0250.0250.0000.0000.0000.000
142A142GLN00.0410.03118.489-0.018-0.0180.0000.0000.0000.000
143A143THR0-0.040-0.02517.961-0.013-0.0130.0000.0000.0000.000
144A144LEU00.002-0.01119.9610.0170.0170.0000.0000.0000.000
145A145ILE00.0180.00421.818-0.033-0.0330.0000.0000.0000.000
146A146PRO00.0020.00722.7750.0210.0210.0000.0000.0000.000
147A147SER0-0.0020.00925.450-0.002-0.0020.0000.0000.0000.000
148A148GLN00.010-0.00527.8860.0030.0030.0000.0000.0000.000
149A149GLN0-0.017-0.00924.982-0.012-0.0120.0000.0000.0000.000
150A150ARG10.8070.88721.2720.2550.2550.0000.0000.0000.000
151A151SER0-0.0110.00924.1160.0230.0230.0000.0000.0000.000
152A152ILE00.0500.02121.944-0.017-0.0170.0000.0000.0000.000
153A153LYS10.9190.96524.5880.1000.1000.0000.0000.0000.000
154A154PRO0-0.0130.03327.098-0.012-0.0120.0000.0000.0000.000
155A155PRO0-0.014-0.01628.8730.0060.0060.0000.0000.0000.000
156A156PHE00.027-0.00223.449-0.011-0.0110.0000.0000.0000.000
157A157HIS0-0.002-0.01426.6770.0110.0110.0000.0000.0000.000
158A158PRO00.0190.01825.458-0.020-0.0200.0000.0000.0000.000
159A159MET0-0.032-0.02722.915-0.005-0.0050.0000.0000.0000.000
160A160ASN0-0.033-0.02226.5140.0140.0140.0000.0000.0000.000
161A161GLU-1-0.894-0.95228.671-0.133-0.1330.0000.0000.0000.000
162A162GLU-1-0.963-0.96830.670-0.126-0.1260.0000.0000.0000.000
163A163GLN0-0.077-0.03322.817-0.005-0.0050.0000.0000.0000.000
164A164PRO0-0.060-0.02523.6290.0120.0120.0000.0000.0000.000
165A165TRP00.0780.03221.003-0.021-0.0210.0000.0000.0000.000
166A166ILE0-0.036-0.02616.3920.0000.0000.0000.0000.0000.000
167A167LEU0-0.006-0.01617.5790.0200.0200.0000.0000.0000.000
168A168HIS0-0.040-0.0219.1740.1160.1160.0000.0000.0000.000
169A169VAL00.0110.00513.1320.0610.0610.0000.0000.0000.000
170A170TYR0-0.018-0.0126.694-0.175-0.1750.0000.0000.0000.000
171A171THR00.0260.0137.7860.4110.4110.0000.0000.0000.000
172A172HIS0-0.048-0.0262.784-1.8210.4351.899-1.120-3.036-0.009
173A173VAL0-0.004-0.0023.6930.4841.0350.009-0.110-0.4510.000
174A174ALA0-0.040-0.0252.698-3.625-1.4320.738-1.343-1.588-0.010
175A175ASP-1-0.816-0.9082.8470.7142.2890.368-0.814-1.129-0.011
176A176ALA00.0240.0065.011-0.624-0.6240.0000.0000.0000.000
177A177SER0-0.017-0.0156.310-0.364-0.3640.0000.0000.0000.000
178A178ASN0-0.0050.0108.521-0.244-0.2440.0000.0000.0000.000
179A179GLN00.0760.01610.318-0.029-0.0290.0000.0000.0000.000
180A180VAL0-0.0060.00012.723-0.070-0.0700.0000.0000.0000.000
181A181ALA0-0.021-0.0098.973-0.025-0.0250.0000.0000.0000.000
182A182MET00.0340.0187.712-0.098-0.0980.0000.0000.0000.000
183A183ALA00.0240.01610.414-0.095-0.0950.0000.0000.0000.000
184A184LYS10.9140.95712.529-0.263-0.2630.0000.0000.0000.000
185A185ALA00.0570.0319.3130.0090.0090.0000.0000.0000.000
186A186GLU-1-0.868-0.94211.399-0.342-0.3420.0000.0000.0000.000
187A187ALA0-0.038-0.01713.6000.0030.0030.0000.0000.0000.000
188A188ASN00.001-0.01012.748-0.025-0.0250.0000.0000.0000.000
189A189LEU00.0360.02310.871-0.001-0.0010.0000.0000.0000.000
190A190THR0-0.055-0.02114.813-0.008-0.0080.0000.0000.0000.000
191A191LYS10.8830.94817.884-0.089-0.0890.0000.0000.0000.000
192A192VAL00.0470.02615.7080.0030.0030.0000.0000.0000.000
193A193LYS10.9340.97418.4530.2060.2060.0000.0000.0000.000
194A194THR0-0.053-0.02619.8990.0040.0040.0000.0000.0000.000
195A195LEU00.0200.01721.5850.0050.0050.0000.0000.0000.000
196A196LEU00.0000.00318.9800.0030.0030.0000.0000.0000.000
197A197SER0-0.066-0.03123.224-0.010-0.0100.0000.0000.0000.000
198A198ALA0-0.0140.00325.174-0.002-0.0020.0000.0000.0000.000
199A199PHE0-0.010-0.01223.1190.0020.0020.0000.0000.0000.000
200A200CYS0-0.0350.00122.306-0.018-0.0180.0000.0000.0000.000
201A201ASP-1-0.898-0.92623.561-0.219-0.2190.0000.0000.0000.000
202A202LEU0-0.008-0.00317.769-0.026-0.0260.0000.0000.0000.000
203A203LYS10.9700.96419.0630.3700.3700.0000.0000.0000.000
204A204ASN0-0.0090.01115.644-0.126-0.1260.0000.0000.0000.000
205A205VAL00.0070.01115.9350.0640.0640.0000.0000.0000.000
206A206ARG10.9370.96515.4270.5510.5510.0000.0000.0000.000
207A207LEU00.0660.03910.9980.0470.0470.0000.0000.0000.000