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: YV5K2

Calculation Name: 1T33-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1T33

Chain ID: A

ChEMBL ID:

UniProt ID: Q8ZQN9

Base Structure: X-ray

Registration Date: 2023-09-24

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 220
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2506182.311342
FMO2-HF: Nuclear repulsion 2419715.068154
FMO2-HF: Total energy -86467.243189
FMO2-MP2: Total energy -86719.253056


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.
-7.676-1.37715.73-6.583-15.448-0.017
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 : 0.087 / q_NPA : 0.038
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].
3A3ILE00.0260.0133.578-2.680-0.572-0.007-1.146-0.9560.001
4A4PRO0-0.013-0.0105.696-0.538-0.5380.0000.0000.0000.000
5A5THR0-0.0260.0016.6060.1720.1720.0000.0000.0000.000
6A6THR00.0340.0178.6040.0430.0430.0000.0000.0000.000
7A7THR0-0.009-0.00312.0270.0500.0500.0000.0000.0000.000
8A8THR00.0980.03311.825-0.069-0.0690.0000.0000.0000.000
9A9LYS10.9570.97212.3240.2410.2410.0000.0000.0000.000
10A10GLY00.0180.01311.183-0.002-0.0020.0000.0000.0000.000
11A11GLU-1-0.896-0.9577.284-0.828-0.8280.0000.0000.0000.000
12A12GLN00.0250.0287.696-0.039-0.0390.0000.0000.0000.000
13A13ALA00.0110.0049.457-0.013-0.0130.0000.0000.0000.000
14A14LYS10.8670.9443.2892.6193.2670.018-0.195-0.4720.001
15A15SER00.023-0.0015.346-0.210-0.2100.0000.0000.0000.000
16A16GLN0-0.020-0.0116.3360.0770.0770.0000.0000.0000.000
17A17LEU0-0.015-0.0167.9070.0800.0800.0000.0000.0000.000
18A18ILE00.0090.0092.2950.957-1.2554.509-0.284-2.0130.000
19A19ALA00.0090.0175.7710.1670.1670.0000.0000.0000.000
20A20ALA00.005-0.0018.7510.0810.0810.0000.0000.0000.000
21A21ALA00.0150.0027.3500.0730.0730.0000.0000.0000.000
22A22LEU00.0090.0086.5660.0980.0980.0000.0000.0000.000
23A23ALA0-0.047-0.0139.5460.0710.0710.0000.0000.0000.000
24A24GLN00.006-0.01212.7180.0450.0450.0000.0000.0000.000
25A25PHE0-0.007-0.0048.4440.0360.0360.0000.0000.0000.000
26A26GLY0-0.0020.00312.6970.0370.0370.0000.0000.0000.000
27A27GLU-1-0.894-0.93414.138-0.030-0.0300.0000.0000.0000.000
28A28TYR0-0.032-0.02716.4960.0090.0090.0000.0000.0000.000
29A29GLY00.0040.00615.2530.0140.0140.0000.0000.0000.000
30A30LEU00.010-0.01212.209-0.028-0.0280.0000.0000.0000.000
31A31HIS0-0.0150.00615.972-0.003-0.0030.0000.0000.0000.000
32A32ALA00.0020.02714.654-0.006-0.0060.0000.0000.0000.000
33A33THR0-0.029-0.04716.222-0.004-0.0040.0000.0000.0000.000
34A34THR00.0820.01813.045-0.013-0.0130.0000.0000.0000.000
35A35ARG10.8580.91315.0840.0830.0830.0000.0000.0000.000
36A36ASP-1-0.791-0.85517.347-0.122-0.1220.0000.0000.0000.000
37A37ILE00.0150.01610.576-0.009-0.0090.0000.0000.0000.000
38A38ALA0-0.013-0.01113.340-0.032-0.0320.0000.0000.0000.000
39A39ALA0-0.019-0.01514.521-0.006-0.0060.0000.0000.0000.000
40A40LEU0-0.044-0.01314.1260.0030.0030.0000.0000.0000.000
41A41ALA0-0.0120.00211.765-0.003-0.0030.0000.0000.0000.000
42A42GLY0-0.0090.01013.571-0.015-0.0150.0000.0000.0000.000
43A43GLN0-0.056-0.02611.868-0.003-0.0030.0000.0000.0000.000
44A44ASN00.0140.00415.2380.0320.0320.0000.0000.0000.000
45A45ILE00.0480.00714.740-0.035-0.0350.0000.0000.0000.000
46A46ALA00.003-0.00214.835-0.008-0.0080.0000.0000.0000.000
47A47ALA0-0.017-0.00812.101-0.007-0.0070.0000.0000.0000.000
48A48ILE00.0100.0079.832-0.077-0.0770.0000.0000.0000.000
49A49THR00.007-0.00110.137-0.042-0.0420.0000.0000.0000.000
50A50TYR0-0.044-0.01611.4390.0480.0480.0000.0000.0000.000
51A51TYR0-0.007-0.0066.8050.0230.0230.0000.0000.0000.000
52A52PHE0-0.027-0.0282.850-0.851-0.3220.091-0.123-0.4980.001
53A53GLY00.0300.0407.5500.2020.2020.0000.0000.0000.000
54A54SER0-0.052-0.0719.2460.0090.0090.0000.0000.0000.000
55A55LYS10.8730.9349.425-0.031-0.0310.0000.0000.0000.000
56A56GLU-1-0.834-0.9449.882-0.043-0.0430.0000.0000.0000.000
57A57ASP-1-0.857-0.8815.7220.4260.4260.0000.0000.0000.000
58A58LEU0-0.053-0.0254.889-0.337-0.247-0.001-0.002-0.0870.000
59A59TYR0-0.019-0.0416.003-0.149-0.1490.0000.0000.0000.000
60A60LEU00.0320.0154.505-0.1060.029-0.001-0.011-0.1230.000
61A61ALA0-0.024-0.0092.342-1.565-0.2001.775-0.980-2.1590.004
62A62CYS0-0.053-0.0182.882-1.8010.0920.741-0.900-1.734-0.014
63A63ALA00.0330.0214.8250.1700.256-0.001-0.008-0.0770.000
64A64GLN0-0.069-0.0561.981-0.846-1.8387.514-2.134-4.388-0.003
65A65TRP00.0260.0002.498-2.0670.2051.042-0.898-2.417-0.006
66A66ILE0-0.034-0.0184.116-0.411-0.5500.0450.248-0.1550.000
67A67ALA0-0.0060.0077.023-0.137-0.1370.0000.0000.0000.000
68A68ASP-1-0.811-0.9084.194-0.450-0.0010.006-0.147-0.307-0.001
69A69PHE0-0.024-0.0177.395-0.239-0.2390.0000.0000.0000.000
70A70LEU00.004-0.0219.340-0.105-0.1050.0000.0000.0000.000
71A71GLY00.0440.02110.805-0.044-0.0440.0000.0000.0000.000
72A72GLU-1-0.893-0.93910.959-0.062-0.0620.0000.0000.0000.000
73A73LYS10.8840.95712.799-0.046-0.0460.0000.0000.0000.000
74A74PHE0-0.029-0.01515.310-0.019-0.0190.0000.0000.0000.000
75A75ARG10.8390.91514.7230.0050.0050.0000.0000.0000.000
76A76PRO0-0.010-0.01716.779-0.002-0.0020.0000.0000.0000.000
77A77HIS0-0.027-0.01720.1790.0030.0030.0000.0000.0000.000
78A78ALA00.0980.05018.749-0.001-0.0010.0000.0000.0000.000
79A79GLU-1-0.824-0.89619.5000.0060.0060.0000.0000.0000.000
80A80LYS10.8500.92122.009-0.015-0.0150.0000.0000.0000.000
81A81ALA00.0630.02624.002-0.003-0.0030.0000.0000.0000.000
82A82GLU-1-0.842-0.91922.4560.0810.0810.0000.0000.0000.000
83A83ARG10.8400.91523.533-0.020-0.0200.0000.0000.0000.000
84A84LEU0-0.053-0.01027.705-0.003-0.0030.0000.0000.0000.000
85A85PHE00.016-0.00826.422-0.002-0.0020.0000.0000.0000.000
86A86SER0-0.092-0.02629.6220.0010.0010.0000.0000.0000.000
87A87GLN0-0.002-0.01331.512-0.005-0.0050.0000.0000.0000.000
88A88PRO0-0.022-0.01734.9790.0020.0020.0000.0000.0000.000
89A89ALA0-0.004-0.00637.7610.0020.0020.0000.0000.0000.000
90A90PRO0-0.029-0.00533.656-0.002-0.0020.0000.0000.0000.000
91A91ASP-1-0.836-0.91635.4790.0180.0180.0000.0000.0000.000
92A92ARG10.9010.94035.458-0.024-0.0240.0000.0000.0000.000
93A93ASP-1-0.877-0.94336.3240.0180.0180.0000.0000.0000.000
94A94ALA00.0140.01432.7920.0000.0000.0000.0000.0000.000
95A95ILE0-0.057-0.02231.5410.0020.0020.0000.0000.0000.000
96A96ARG10.8150.88131.094-0.014-0.0140.0000.0000.0000.000
97A97GLU-1-0.879-0.94631.6180.0140.0140.0000.0000.0000.000
98A98LEU0-0.061-0.01625.242-0.001-0.0010.0000.0000.0000.000
99A99ILE00.0220.00726.8150.0030.0030.0000.0000.0000.000
100A100LEU00.0420.02727.3740.0020.0020.0000.0000.0000.000
101A101LEU0-0.032-0.01324.700-0.003-0.0030.0000.0000.0000.000
102A102ALA00.0080.02222.994-0.001-0.0010.0000.0000.0000.000
103A103CYS00.006-0.00723.1010.0020.0020.0000.0000.0000.000
104A104LYS10.9410.96524.9260.0040.0040.0000.0000.0000.000
105A105ASN0-0.061-0.05520.460-0.009-0.0090.0000.0000.0000.000
106A106MET0-0.0160.00320.0230.0020.0020.0000.0000.0000.000
107A107ILE00.0320.02021.225-0.003-0.0030.0000.0000.0000.000
108A108MET00.0040.03521.752-0.007-0.0070.0000.0000.0000.000
109A109LEU0-0.0130.01215.332-0.005-0.0050.0000.0000.0000.000
110A110LEU0-0.026-0.03118.429-0.006-0.0060.0000.0000.0000.000
111A111THR0-0.045-0.03320.557-0.005-0.0050.0000.0000.0000.000
112A112GLN0-0.0100.00817.6900.0000.0000.0000.0000.0000.000
113A113GLU-1-0.762-0.90418.685-0.039-0.0390.0000.0000.0000.000
114A114ASP-1-0.944-0.95914.803-0.065-0.0650.0000.0000.0000.000
115A115THR00.0440.02513.674-0.006-0.0060.0000.0000.0000.000
116A116VAL0-0.020-0.00514.8200.0160.0160.0000.0000.0000.000
117A117ASN00.032-0.00712.4710.0280.0280.0000.0000.0000.000
118A118LEU00.0450.04410.2950.0000.0000.0000.0000.0000.000
119A119SER00.0240.00712.1890.0230.0230.0000.0000.0000.000
120A120LYS10.8130.93115.0170.0790.0790.0000.0000.0000.000
121A121PHE0-0.005-0.0099.4110.0000.0000.0000.0000.0000.000
122A122ILE00.0170.00211.8750.0200.0200.0000.0000.0000.000
123A123SER00.007-0.01114.6670.0090.0090.0000.0000.0000.000
124A124ARG10.8950.95715.025-0.022-0.0220.0000.0000.0000.000
125A125GLU-1-0.764-0.86112.9840.1700.1700.0000.0000.0000.000
126A126GLN0-0.019-0.00616.4160.0120.0120.0000.0000.0000.000
127A127LEU0-0.047-0.02219.018-0.001-0.0010.0000.0000.0000.000
128A128SER0-0.068-0.02918.692-0.008-0.0080.0000.0000.0000.000
129A129PRO0-0.0110.01316.2690.0020.0020.0000.0000.0000.000
130A130THR0-0.024-0.02812.6750.0070.0070.0000.0000.0000.000
131A131SER00.020-0.00310.049-0.015-0.0150.0000.0000.0000.000
132A132ALA0-0.016-0.0118.7210.0560.0560.0000.0000.0000.000
133A133TYR00.007-0.0039.7860.0350.0350.0000.0000.0000.000
134A134GLN0-0.064-0.03612.096-0.003-0.0030.0000.0000.0000.000
135A135LEU00.0100.0164.578-0.0650.002-0.001-0.003-0.0620.000
136A136VAL00.001-0.0109.105-0.006-0.0060.0000.0000.0000.000
137A137HIS0-0.055-0.02110.550-0.039-0.0390.0000.0000.0000.000
138A138GLU-1-0.866-0.92811.7580.3990.3990.0000.0000.0000.000
139A139GLN0-0.0260.0007.0530.0600.0600.0000.0000.0000.000
140A140VAL0-0.039-0.01611.208-0.041-0.0410.0000.0000.0000.000
141A141ILE0-0.031-0.00814.024-0.031-0.0310.0000.0000.0000.000
142A142ASP-1-0.859-0.92016.0630.1460.1460.0000.0000.0000.000
143A143PRO00.0110.00015.412-0.025-0.0250.0000.0000.0000.000
144A144LEU00.0230.01217.985-0.019-0.0190.0000.0000.0000.000
145A145HIS00.0490.03219.806-0.020-0.0200.0000.0000.0000.000
146A146THR0-0.0050.00621.575-0.017-0.0170.0000.0000.0000.000
147A147HIS0-0.040-0.03021.527-0.010-0.0100.0000.0000.0000.000
148A148LEU00.0060.00522.721-0.010-0.0100.0000.0000.0000.000
149A149THR0-0.031-0.01225.802-0.007-0.0070.0000.0000.0000.000
150A150ARG10.8670.92326.249-0.090-0.0900.0000.0000.0000.000
151A151LEU0-0.027-0.00626.544-0.006-0.0060.0000.0000.0000.000
152A152VAL00.010-0.01129.674-0.005-0.0050.0000.0000.0000.000
153A153ALA0-0.021-0.00331.668-0.003-0.0030.0000.0000.0000.000
154A154ALA0-0.008-0.00532.750-0.003-0.0030.0000.0000.0000.000
155A155TYR0-0.044-0.02434.179-0.004-0.0040.0000.0000.0000.000
156A156THR0-0.039-0.02936.039-0.002-0.0020.0000.0000.0000.000
157A157GLY00.0190.02737.372-0.002-0.0020.0000.0000.0000.000
158A158CYS0-0.079-0.03436.1940.0000.0000.0000.0000.0000.000
159A159ASP-1-0.801-0.90333.9030.0630.0630.0000.0000.0000.000
160A160ALA00.022-0.00429.7320.0010.0010.0000.0000.0000.000
161A161ASN0-0.077-0.04829.7020.0120.0120.0000.0000.0000.000
162A162ASP-1-0.776-0.82831.0660.0560.0560.0000.0000.0000.000
163A163THR00.0690.01030.8570.0020.0020.0000.0000.0000.000
164A164ARG10.8430.87731.723-0.048-0.0480.0000.0000.0000.000
165A165MET00.0250.04131.762-0.004-0.0040.0000.0000.0000.000
166A166ILE00.0330.01826.5160.0000.0000.0000.0000.0000.000
167A167LEU0-0.036-0.02428.6400.0010.0010.0000.0000.0000.000
168A168HIS0-0.031-0.02130.857-0.005-0.0050.0000.0000.0000.000
169A169THR00.009-0.00326.876-0.004-0.0040.0000.0000.0000.000
170A170HIS0-0.027-0.01923.177-0.004-0.0040.0000.0000.0000.000
171A171ALA0-0.023-0.00727.513-0.002-0.0020.0000.0000.0000.000
172A172LEU0-0.002-0.00228.580-0.003-0.0030.0000.0000.0000.000
173A173LEU0-0.0020.00223.493-0.003-0.0030.0000.0000.0000.000
174A174GLY00.0060.00425.796-0.001-0.0010.0000.0000.0000.000
175A175GLU-1-0.865-0.92027.4590.0210.0210.0000.0000.0000.000
176A176VAL0-0.021-0.01023.766-0.005-0.0050.0000.0000.0000.000
177A177LEU00.005-0.01821.056-0.004-0.0040.0000.0000.0000.000
178A178ALA00.0150.02824.207-0.003-0.0030.0000.0000.0000.000
179A179PHE00.0130.00126.140-0.005-0.0050.0000.0000.0000.000
180A180ARG10.8060.90917.265-0.002-0.0020.0000.0000.0000.000
181A181LEU0-0.011-0.02420.470-0.005-0.0050.0000.0000.0000.000
182A182GLY00.0050.01523.619-0.002-0.0020.0000.0000.0000.000
183A183LYS10.8410.91722.2390.0280.0280.0000.0000.0000.000
184A184GLU-1-0.879-0.94326.252-0.020-0.0200.0000.0000.0000.000
185A185THR0-0.062-0.03528.4480.0000.0000.0000.0000.0000.000
186A186ILE00.0340.01428.752-0.001-0.0010.0000.0000.0000.000
187A187LEU0-0.0020.02526.939-0.001-0.0010.0000.0000.0000.000
188A188LEU00.0030.00631.2060.0000.0000.0000.0000.0000.000
189A189ARG10.8460.92733.9700.0000.0000.0000.0000.0000.000
190A190THR0-0.036-0.04233.3030.0000.0000.0000.0000.0000.000
191A191GLY0-0.0200.00435.2670.0000.0000.0000.0000.0000.000
192A192TRP0-0.040-0.02330.857-0.002-0.0020.0000.0000.0000.000
193A193PRO00.0190.01031.4010.0000.0000.0000.0000.0000.000
194A194GLN0-0.010-0.01626.438-0.003-0.0030.0000.0000.0000.000
195A195PHE00.003-0.00224.3790.0020.0020.0000.0000.0000.000
196A196ASP-1-0.794-0.89026.769-0.028-0.0280.0000.0000.0000.000
197A197GLU-1-0.913-0.96727.128-0.020-0.0200.0000.0000.0000.000
198A198GLU-1-0.856-0.92528.619-0.017-0.0170.0000.0000.0000.000
199A199LYS10.7590.86630.0620.0230.0230.0000.0000.0000.000
200A200ALA00.0040.00726.9160.0040.0040.0000.0000.0000.000
201A201GLU-1-0.924-0.96428.734-0.009-0.0090.0000.0000.0000.000
202A202LEU0-0.027-0.01131.7660.0030.0030.0000.0000.0000.000
203A203ILE0-0.0070.00927.8500.0030.0030.0000.0000.0000.000
204A204TYR00.0140.00029.2710.0020.0020.0000.0000.0000.000
205A205GLN0-0.0080.01630.8770.0030.0030.0000.0000.0000.000
206A206THR0-0.045-0.03133.3470.0010.0010.0000.0000.0000.000
207A207VAL00.0300.00729.0350.0020.0020.0000.0000.0000.000
208A208THR0-0.037-0.03232.3660.0030.0030.0000.0000.0000.000
209A209CYS0-0.058-0.01933.6630.0010.0010.0000.0000.0000.000
210A210HIS0-0.051-0.05234.419-0.002-0.0020.0000.0000.0000.000
211A211ILE00.0360.01329.7480.0020.0020.0000.0000.0000.000
212A212ASP-1-0.790-0.86334.2860.0200.0200.0000.0000.0000.000
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