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: 53YZZ

Calculation Name: 1TC5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TC5

Chain ID: A

ChEMBL ID:

UniProt ID: P84066

Base Structure: X-ray

Registration Date: 2023-03-13

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2005905.970627
FMO2-HF: Nuclear repulsion 1931983.444028
FMO2-HF: Total energy -73922.526599
FMO2-MP2: Total energy -74135.556032


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:8:HIS)


Summations of interaction energy for fragment #1(A:8:HIS)
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.
-15.922-13.1669.707-6.083-6.38-0.044
Interaction energy analysis for fragmet #1(A:8:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.009
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].
3A10THR0-0.050-0.0042.644-0.4282.5480.086-1.436-1.6260.004
4A11ILE00.011-0.0014.8750.8290.973-0.001-0.015-0.1270.000
5A12ARG10.7840.8518.5922.5802.5800.0000.0000.0000.000
6A13VAL00.003-0.00810.3000.2010.2010.0000.0000.0000.000
7A14MET0-0.024-0.01413.5850.0160.0160.0000.0000.0000.000
8A15LEU0-0.0200.00515.9940.0320.0320.0000.0000.0000.000
9A16GLN0-0.008-0.02418.9400.0100.0100.0000.0000.0000.000
10A17ALA00.0430.03522.5840.0040.0040.0000.0000.0000.000
11A18MET0-0.0090.01925.646-0.020-0.0200.0000.0000.0000.000
12A19ASP-1-0.775-0.90428.157-0.132-0.1320.0000.0000.0000.000
13A20GLN0-0.004-0.01331.9110.0130.0130.0000.0000.0000.000
14A21GLY00.0410.01730.417-0.019-0.0190.0000.0000.0000.000
15A22HIS0-0.018-0.00831.5010.0050.0050.0000.0000.0000.000
16A23LEU0-0.0020.00525.612-0.016-0.0160.0000.0000.0000.000
17A24LEU0-0.060-0.01029.9810.0140.0140.0000.0000.0000.000
18A25VAL0-0.043-0.01828.438-0.034-0.0340.0000.0000.0000.000
19A26ASN00.0530.02930.580-0.012-0.0120.0000.0000.0000.000
20A27ASN00.0190.01330.112-0.013-0.0130.0000.0000.0000.000
21A28VAL0-0.032-0.00432.538-0.003-0.0030.0000.0000.0000.000
22A29ASP-1-0.864-0.93236.090-0.229-0.2290.0000.0000.0000.000
23A30LYS10.8880.95032.8720.2700.2700.0000.0000.0000.000
24A31TYR0-0.008-0.01432.887-0.027-0.0270.0000.0000.0000.000
25A32VAL0-0.0120.00630.1800.0190.0190.0000.0000.0000.000
26A33ARG10.8340.90332.2350.1790.1790.0000.0000.0000.000
27A34ALA0-0.0100.00529.7150.0020.0020.0000.0000.0000.000
28A35GLY00.0260.00631.6900.0060.0060.0000.0000.0000.000
29A36ARG10.7830.90530.5770.1040.1040.0000.0000.0000.000
30A37GLY00.0580.02027.6880.0120.0120.0000.0000.0000.000
31A38VAL0-0.032-0.01321.0120.0010.0010.0000.0000.0000.000
32A39MET00.0000.02223.016-0.007-0.0070.0000.0000.0000.000
33A40VAL0-0.015-0.02117.698-0.015-0.0150.0000.0000.0000.000
34A41TYR00.0200.00518.319-0.031-0.0310.0000.0000.0000.000
35A42ILE00.0130.00713.659-0.061-0.0610.0000.0000.0000.000
36A43ALA0-0.043-0.01312.2990.0700.0700.0000.0000.0000.000
37A44PHE00.0480.0209.697-0.149-0.1490.0000.0000.0000.000
38A45LEU0-0.023-0.0096.6160.5690.5690.0000.0000.0000.000
39A46SER0-0.001-0.0065.003-0.931-0.9310.0000.0000.0000.000
40A47ASP-1-0.760-0.8661.900-18.818-20.7008.496-3.772-2.843-0.047
41A48ARG10.7790.8754.8343.3393.385-0.001-0.004-0.0400.000
42A49ASP-1-0.858-0.9156.012-0.215-0.2150.0000.0000.0000.000
43A50SER0-0.109-0.0642.4930.2480.9131.100-0.568-1.1970.001
44A51DAL00.0410.0103.264-1.608-1.1380.025-0.160-0.336-0.001
45A52PRO0-0.009-0.0173.876-1.504-1.2440.003-0.123-0.140-0.001
46A53ILE0-0.001-0.0086.2860.2390.2390.0000.0000.0000.000
47A54THR00.0240.0147.4470.1680.1680.0000.0000.0000.000
48A55ASP-1-0.728-0.84510.008-0.346-0.3460.0000.0000.0000.000
49A56GLU-1-0.781-0.89111.7800.0220.0220.0000.0000.0000.000
50A57ALA0-0.0130.0077.3720.0760.0760.0000.0000.0000.000
51A58LEU0-0.014-0.0099.337-0.106-0.1060.0000.0000.0000.000
52A59ARG10.8240.88912.0470.0920.0920.0000.0000.0000.000
53A60HIS00.0240.0199.024-0.035-0.0350.0000.0000.0000.000
54A61ALA0-0.008-0.00210.7020.0300.0300.0000.0000.0000.000
55A62VAL0-0.014-0.00712.532-0.015-0.0150.0000.0000.0000.000
56A63GLY00.0630.02715.6480.0190.0190.0000.0000.0000.000
57A64VAL0-0.049-0.02411.7180.0210.0210.0000.0000.0000.000
58A65LEU0-0.038-0.00415.032-0.020-0.0200.0000.0000.0000.000
59A66LEU0-0.015-0.00617.2430.0040.0040.0000.0000.0000.000
60A67HIS0-0.022-0.02317.8550.0210.0210.0000.0000.0000.000
61A68THR0-0.076-0.05316.4800.0610.0610.0000.0000.0000.000
62A69LYS10.7870.87419.137-0.100-0.1000.0000.0000.0000.000
63A70ILE0-0.046-0.01717.7300.0080.0080.0000.0000.0000.000
64A71PHE0-0.043-0.02620.774-0.012-0.0120.0000.0000.0000.000
65A72THR00.0350.01024.5840.0160.0160.0000.0000.0000.000
66A73HIS00.0070.00726.6380.0250.0250.0000.0000.0000.000
67A74PHE00.010-0.00924.354-0.005-0.0050.0000.0000.0000.000
68A75SER0-0.008-0.01830.509-0.003-0.0030.0000.0000.0000.000
69A76PRO0-0.021-0.00733.5530.0090.0090.0000.0000.0000.000
70A77GLU-1-0.762-0.87936.094-0.042-0.0420.0000.0000.0000.000
71A78LYS10.7940.89733.2240.0340.0340.0000.0000.0000.000
72A79MET00.0180.01637.014-0.004-0.0040.0000.0000.0000.000
73A80ILE0-0.004-0.00934.1540.0000.0000.0000.0000.0000.000
74A81ASN0-0.048-0.02431.7060.0100.0100.0000.0000.0000.000
75A82GLN00.003-0.00128.9230.0120.0120.0000.0000.0000.000
76A83PRO0-0.007-0.01123.843-0.015-0.0150.0000.0000.0000.000
77A84GLN0-0.013-0.00725.7080.0140.0140.0000.0000.0000.000
78A85SER00.0320.02222.409-0.030-0.0300.0000.0000.0000.000
79A86LEU00.0430.00421.521-0.007-0.0070.0000.0000.0000.000
80A87GLU-1-0.885-0.90923.5510.0630.0630.0000.0000.0000.000
81A88GLU-1-0.744-0.84325.4200.0270.0270.0000.0000.0000.000
82A89CYS0-0.047-0.00827.7000.0010.0010.0000.0000.0000.000
83A90PRO00.0670.02929.011-0.023-0.0230.0000.0000.0000.000
84A91GLU-1-0.795-0.87030.036-0.098-0.0980.0000.0000.0000.000
85A92MET0-0.0560.00928.011-0.017-0.0170.0000.0000.0000.000
86A93ASP-1-0.691-0.82428.483-0.194-0.1940.0000.0000.0000.000
87A94ILE0-0.035-0.02022.396-0.009-0.0090.0000.0000.0000.000
88A95LEU00.0000.00624.5120.0050.0050.0000.0000.0000.000
89A96ILE00.0130.00919.389-0.041-0.0410.0000.0000.0000.000
90A97VAL00.0200.00120.6840.0280.0280.0000.0000.0000.000
91A98PRO0-0.0230.00918.454-0.097-0.0970.0000.0000.0000.000
92A99GLN0-0.020-0.03117.4620.0670.0670.0000.0000.0000.000
93A100ALA00.0560.02214.651-0.125-0.1250.0000.0000.0000.000
94A101SER00.0130.01214.723-0.214-0.2140.0000.0000.0000.000
95A102LEU00.0390.01314.062-0.016-0.0160.0000.0000.0000.000
96A103GLY00.0250.01011.675-0.190-0.1900.0000.0000.0000.000
97A104GLY0-0.024-0.00712.503-0.135-0.1350.0000.0000.0000.000
98A105LYS10.8790.93410.2762.3682.3680.0000.0000.0000.000
99A106VAL00.0430.02116.0150.0780.0780.0000.0000.0000.000
100A107LYS10.9190.95218.7700.6530.6530.0000.0000.0000.000
101A108GLY00.0210.02120.8860.0520.0520.0000.0000.0000.000
102A109ARG10.9650.98024.3340.3520.3520.0000.0000.0000.000
103A110SER0-0.008-0.00223.5170.0100.0100.0000.0000.0000.000
104A111VAL00.0360.02118.877-0.014-0.0140.0000.0000.0000.000
105A112GLN0-0.048-0.01913.497-0.019-0.0190.0000.0000.0000.000
106A113PHE00.0810.02614.979-0.046-0.0460.0000.0000.0000.000
107A114HIS00.0240.00712.601-0.156-0.1560.0000.0000.0000.000
108A115GLN00.0250.0159.096-0.304-0.3040.0000.0000.0000.000
109A116LEU0-0.0080.0159.057-0.665-0.6650.0000.0000.0000.000
110A117VAL00.0240.0319.0030.0480.0480.0000.0000.0000.000
111A118ALA00.0160.00611.4070.2350.2350.0000.0000.0000.000
112A119LYS10.8760.90814.6600.6020.6020.0000.0000.0000.000
113A120ASP-1-0.793-0.88917.585-0.661-0.6610.0000.0000.0000.000
114A121VAL00.0300.02511.1150.0570.0570.0000.0000.0000.000
115A122GLY00.011-0.00114.100-0.053-0.0530.0000.0000.0000.000
116A123ALA0-0.020-0.01014.9480.0420.0420.0000.0000.0000.000
117A124ALA00.0190.00915.9040.0570.0570.0000.0000.0000.000
118A125LEU0-0.012-0.00910.4470.0430.0430.0000.0000.0000.000
119A126TYR0-0.008-0.02814.5800.0440.0440.0000.0000.0000.000
120A127ASP-1-0.846-0.91117.153-0.366-0.3660.0000.0000.0000.000
121A128ARG10.8550.91916.0300.3580.3580.0000.0000.0000.000
122A129PHE00.014-0.00514.1020.0500.0500.0000.0000.0000.000
123A130CYS0-0.031-0.02416.7810.0730.0730.0000.0000.0000.000
124A131HIS0-0.040-0.03220.3390.0630.0630.0000.0000.0000.000
125A132PHE0-0.049-0.02315.3370.0500.0500.0000.0000.0000.000
126A133VAL00.0030.00318.8660.0490.0490.0000.0000.0000.000
127A134ARG10.8280.89621.2330.3830.3830.0000.0000.0000.000
128A135VAL00.0200.01222.9180.0310.0310.0000.0000.0000.000
129A136ALA0-0.042-0.01521.4820.0300.0300.0000.0000.0000.000
130A137ARG10.7480.85123.5890.1510.1510.0000.0000.0000.000
131A138GLY00.0000.01026.6590.0070.0070.0000.0000.0000.000
132A139VAL0-0.029-0.01327.8040.0040.0040.0000.0000.0000.000
133A140ASP-1-0.747-0.84129.373-0.119-0.1190.0000.0000.0000.000
134A141GLU-1-0.783-0.88925.543-0.249-0.2490.0000.0000.0000.000
135A142SER0-0.078-0.05730.262-0.006-0.0060.0000.0000.0000.000
136A143ARG10.9150.94833.7780.1060.1060.0000.0000.0000.000
137A144VAL0-0.0250.01629.757-0.001-0.0010.0000.0000.0000.000
138A145ASP-1-0.763-0.89331.741-0.260-0.2600.0000.0000.0000.000
139A146ALA0-0.019-0.02027.958-0.006-0.0060.0000.0000.0000.000
140A147ASN0-0.077-0.05027.128-0.011-0.0110.0000.0000.0000.000
141A148GLY00.0450.03228.683-0.011-0.0110.0000.0000.0000.000
142A149ALA0-0.020-0.01329.4200.0160.0160.0000.0000.0000.000
143A150PRO00.001-0.00533.134-0.003-0.0030.0000.0000.0000.000
144A151ARG10.7990.88531.8000.1810.1810.0000.0000.0000.000
145A152SER0-0.033-0.03037.156-0.002-0.0020.0000.0000.0000.000
146A153GLU-1-0.884-0.95240.482-0.139-0.1390.0000.0000.0000.000
147A154GLY0-0.014-0.01041.490-0.001-0.0010.0000.0000.0000.000
148A155ASP-1-0.883-0.90540.198-0.113-0.1130.0000.0000.0000.000
149A156ALA0-0.066-0.02638.357-0.005-0.0050.0000.0000.0000.000
150A157PRO0-0.037-0.02536.0230.0070.0070.0000.0000.0000.000
151A158LYS10.8560.93239.2330.1320.1320.0000.0000.0000.000
152A159ALA00.0430.02939.445-0.006-0.0060.0000.0000.0000.000
153A160GLU-1-0.761-0.88039.342-0.195-0.1950.0000.0000.0000.000
154A161GLY00.0270.01541.3720.0090.0090.0000.0000.0000.000
155A162TRP0-0.011-0.01836.528-0.002-0.0020.0000.0000.0000.000
156A163ILE0-0.032-0.01235.4780.0100.0100.0000.0000.0000.000
157A164LYS10.8860.94336.7220.0860.0860.0000.0000.0000.000
158A165TYR0-0.040-0.00532.394-0.010-0.0100.0000.0000.0000.000
159A166ASN0-0.077-0.06132.9900.0190.0190.0000.0000.0000.000
160A167SER00.0350.00230.3710.0030.0030.0000.0000.0000.000
161A168ARG10.7760.88329.6080.1710.1710.0000.0000.0000.000
162A169VAL00.013-0.00523.715-0.008-0.0080.0000.0000.0000.000
163A170ILE0-0.0080.00926.713-0.009-0.0090.0000.0000.0000.000
164A171SER0-0.007-0.00523.431-0.026-0.0260.0000.0000.0000.000
165A172GLY00.0510.02224.2780.0260.0260.0000.0000.0000.000
166A173THR00.0040.00424.212-0.033-0.0330.0000.0000.0000.000
167A174PHE00.0410.01818.028-0.020-0.0200.0000.0000.0000.000
168A175GLY0-0.022-0.01422.5640.0390.0390.0000.0000.0000.000
169A176ASN0-0.044-0.01324.1310.0530.0530.0000.0000.0000.000
170A177ARG10.8980.93625.6780.3020.3020.0000.0000.0000.000
171A178GLN00.014-0.00323.3580.0470.0470.0000.0000.0000.000
172A179GLY0-0.017-0.00526.811-0.003-0.0030.0000.0000.0000.000
173A180LEU0-0.007-0.01126.0220.0020.0020.0000.0000.0000.000
174A181ARG10.8140.90329.9460.2350.2350.0000.0000.0000.000
175A182PHE0-0.004-0.01826.399-0.009-0.0090.0000.0000.0000.000
176A183GLU-1-0.897-0.94130.583-0.194-0.1940.0000.0000.0000.000
177A184SER0-0.037-0.06228.2550.0050.0050.0000.0000.0000.000
178A185GLU-1-0.876-0.92631.133-0.149-0.1490.0000.0000.0000.000
179A186GLY00.014-0.00529.6240.0110.0110.0000.0000.0000.000
180A187PRO0-0.040-0.01125.4560.0030.0030.0000.0000.0000.000
181A188PHE00.0240.01723.048-0.021-0.0210.0000.0000.0000.000
182A189THR00.0240.01519.2460.0120.0120.0000.0000.0000.000
183A190HIS10.8660.94916.7100.2520.2520.0000.0000.0000.000
184A191MET0-0.045-0.02010.422-0.093-0.0930.0000.0000.0000.000
185A192PHE00.0120.00510.9070.1630.1630.0000.0000.0000.000
186A193ASP-1-0.752-0.8335.707-3.169-3.1690.0000.0000.0000.000
187A194ILE00.0120.0075.2490.0310.108-0.001-0.005-0.0710.000