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: 667LZ

Calculation Name: 1TII-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TII

Chain ID: A

ChEMBL ID:

UniProt ID: P43528

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 -2033468.083126
FMO2-HF: Nuclear repulsion 1960483.063109
FMO2-HF: Total energy -72985.020017
FMO2-MP2: Total energy -73200.846383


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:ASN)


Summations of interaction energy for fragment #1(A:1:ASN)
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.
-8.875-3.3833.502-3.315-5.679-0.009
Interaction energy analysis for fragmet #1(A:1:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.006
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].
3A3TYR0-0.029-0.0142.365-7.009-2.8492.632-2.551-4.242-0.006
4A4PHE0-0.018-0.0145.9930.6800.6800.0000.0000.0000.000
5A5ARG10.8240.8839.5191.0191.0190.0000.0000.0000.000
6A6ALA0-0.0110.02012.9120.1100.1100.0000.0000.0000.000
7A7ASP-1-0.753-0.83116.285-0.858-0.8580.0000.0000.0000.000
8A8SER00.052-0.00118.9730.0330.0330.0000.0000.0000.000
9A9ARG10.7650.89119.2410.8000.8000.0000.0000.0000.000
10A10THR00.007-0.02221.759-0.035-0.0350.0000.0000.0000.000
11A11PRO00.022-0.00720.193-0.029-0.0290.0000.0000.0000.000
12A12ASP-1-0.815-0.87921.639-0.384-0.3840.0000.0000.0000.000
13A13GLU-1-0.801-0.87424.462-0.429-0.4290.0000.0000.0000.000
14A14VAL00.0020.02118.183-0.022-0.0220.0000.0000.0000.000
15A15ARG10.8640.91621.3430.4000.4000.0000.0000.0000.000
16A16ARG10.8360.90522.6710.3700.3700.0000.0000.0000.000
17A17SER0-0.0050.00722.1800.0230.0230.0000.0000.0000.000
18A18GLY00.0070.00921.285-0.035-0.0350.0000.0000.0000.000
19A19GLY00.008-0.00217.720-0.086-0.0860.0000.0000.0000.000
20A20LEU0-0.061-0.02414.6750.0990.0990.0000.0000.0000.000
21A21ILE00.0570.04117.090-0.142-0.1420.0000.0000.0000.000
22A22PRO00.049-0.00118.7090.0300.0300.0000.0000.0000.000
23A23ARG10.8240.90620.5980.5430.5430.0000.0000.0000.000
24A24GLY0-0.0090.00623.7310.0480.0480.0000.0000.0000.000
25A25GLN0-0.010-0.02022.834-0.029-0.0290.0000.0000.0000.000
26A26ASP-1-0.916-0.94325.777-0.447-0.4470.0000.0000.0000.000
27A27GLU-1-0.933-0.96727.049-0.403-0.4030.0000.0000.0000.000
28A28ALA00.010-0.00824.016-0.047-0.0470.0000.0000.0000.000
29A29TYR00.004-0.01116.463-0.032-0.0320.0000.0000.0000.000
30A30GLU-1-0.938-0.96819.307-0.784-0.7840.0000.0000.0000.000
31A31ARG10.8010.90722.6060.5390.5390.0000.0000.0000.000
32A32GLY00.0720.04725.4540.0300.0300.0000.0000.0000.000
33A33THR0-0.009-0.00723.931-0.033-0.0330.0000.0000.0000.000
34A34PRO0-0.053-0.02521.0220.0330.0330.0000.0000.0000.000
35A35ILE0-0.0020.00124.2530.0100.0100.0000.0000.0000.000
36A36ASN0-0.042-0.03125.5420.0340.0340.0000.0000.0000.000
37A37ILE0-0.032-0.02519.909-0.056-0.0560.0000.0000.0000.000
38A38ASN0-0.004-0.00721.427-0.015-0.0150.0000.0000.0000.000
39A39LEU00.0390.02914.414-0.018-0.0180.0000.0000.0000.000
40A40TYR00.0530.03318.456-0.011-0.0110.0000.0000.0000.000
41A41ASP-1-0.814-0.89520.723-0.483-0.4830.0000.0000.0000.000
42A42HIS10.7270.85215.3581.0971.0970.0000.0000.0000.000
43A43ALA0-0.010-0.00117.1700.0000.0000.0000.0000.0000.000
44A44ARG10.8490.90518.4790.5020.5020.0000.0000.0000.000
45A45GLY00.0070.00921.6450.0460.0460.0000.0000.0000.000
46A46THR0-0.0090.00121.597-0.035-0.0350.0000.0000.0000.000
47A47ALA0-0.057-0.01721.3290.0220.0220.0000.0000.0000.000
48A48THR00.0260.00823.2940.0260.0260.0000.0000.0000.000
49A49GLY00.0380.03525.926-0.006-0.0060.0000.0000.0000.000
50A50ASN00.024-0.00120.091-0.045-0.0450.0000.0000.0000.000
51A51THR00.0420.00916.760-0.016-0.0160.0000.0000.0000.000
52A52ARG10.8440.88416.6970.6620.6620.0000.0000.0000.000
53A53TYR00.002-0.00816.920-0.111-0.1110.0000.0000.0000.000
54A54ASN00.0240.01419.1200.0520.0520.0000.0000.0000.000
55A55ASP-1-0.804-0.88320.187-0.655-0.6550.0000.0000.0000.000
56A56GLY00.0840.03920.455-0.034-0.0340.0000.0000.0000.000
57A57TYR00.0150.01914.145-0.028-0.0280.0000.0000.0000.000
58A58VAL0-0.061-0.03314.4370.1360.1360.0000.0000.0000.000
59A59SER0-0.050-0.03412.912-0.260-0.2600.0000.0000.0000.000
60A60THR0-0.046-0.0268.229-0.189-0.1890.0000.0000.0000.000
61A61THR00.0380.0138.3330.0220.0220.0000.0000.0000.000
62A62THR00.0650.0214.528-0.162-0.112-0.001-0.006-0.0430.000
63A63THR0-0.003-0.0025.3461.1531.1530.0000.0000.0000.000
64A64LEU00.0380.0308.062-0.275-0.2750.0000.0000.0000.000
65A65ARG10.9840.98911.165-0.299-0.2990.0000.0000.0000.000
66A66GLN0-0.0030.01010.482-0.033-0.0330.0000.0000.0000.000
67A67ALA00.0490.01411.347-0.056-0.0560.0000.0000.0000.000
68A68HIS0-0.041-0.02813.0260.0310.0310.0000.0000.0000.000
69A69LEU0-0.042-0.02115.3920.0110.0110.0000.0000.0000.000
70A70LEU00.0270.00613.2110.0140.0140.0000.0000.0000.000
71A71GLY00.0370.01517.000-0.011-0.0110.0000.0000.0000.000
72A72GLN0-0.014-0.00918.8660.0050.0050.0000.0000.0000.000
73A73ASN0-0.029-0.00319.9280.0560.0560.0000.0000.0000.000
74A74MET0-0.038-0.00819.650-0.028-0.0280.0000.0000.0000.000
75A75LEU0-0.055-0.01919.978-0.011-0.0110.0000.0000.0000.000
76A76GLY00.0270.02123.3030.0280.0280.0000.0000.0000.000
77A77GLY0-0.016-0.00525.4110.0060.0060.0000.0000.0000.000
78A78TYR0-0.094-0.05125.4350.0140.0140.0000.0000.0000.000
79A79ASN0-0.012-0.01026.9950.0150.0150.0000.0000.0000.000
80A80GLU-1-0.823-0.88125.258-0.215-0.2150.0000.0000.0000.000
81A81TYR0-0.034-0.02618.527-0.041-0.0410.0000.0000.0000.000
82A82TYR00.001-0.03019.1610.0350.0350.0000.0000.0000.000
83A83ILE0-0.033-0.00813.427-0.061-0.0610.0000.0000.0000.000
84A84TYR0-0.007-0.03113.9960.0770.0770.0000.0000.0000.000
85A85VAL0-0.004-0.0078.453-0.030-0.0300.0000.0000.0000.000
86A86VAL0-0.026-0.0088.2580.2930.2930.0000.0000.0000.000
87A87ALA00.0470.0334.999-0.951-0.9510.0000.0000.0000.000
88A88ALA0-0.001-0.0032.3090.4031.2170.872-0.629-1.057-0.003
89A89ALA00.010-0.0014.4651.2771.455-0.001-0.033-0.1440.000
90A90PRO00.0490.0147.676-0.236-0.2360.0000.0000.0000.000
91A91ASN00.0170.01810.235-0.153-0.1530.0000.0000.0000.000
92A92LEU0-0.067-0.0145.9540.1490.1490.0000.0000.0000.000
93A93PHE00.0610.0228.689-0.186-0.1860.0000.0000.0000.000
94A94ASP-1-0.792-0.8638.097-2.046-2.0460.0000.0000.0000.000
95A95VAL00.028-0.0039.4430.3790.3790.0000.0000.0000.000
96A96ASN0-0.024-0.01011.4970.2850.2850.0000.0000.0000.000
97A97GLY0-0.019-0.00111.7070.2020.2020.0000.0000.0000.000
98A98VAL0-0.0030.00712.6210.1610.1610.0000.0000.0000.000
99A99LEU00.0030.00114.9540.1280.1280.0000.0000.0000.000
100A100GLY00.0470.02916.3580.1030.1030.0000.0000.0000.000
101A101ARG10.7840.87217.9440.2380.2380.0000.0000.0000.000
102A102TYR0-0.044-0.05120.3610.0440.0440.0000.0000.0000.000
103A103SER0-0.026-0.01615.270-0.034-0.0340.0000.0000.0000.000
104A104PRO0-0.006-0.01018.2180.0550.0550.0000.0000.0000.000
105A105TYR0-0.024-0.00917.4890.0960.0960.0000.0000.0000.000
106A106PRO00.0560.04115.253-0.072-0.0720.0000.0000.0000.000
107A107SER00.0020.00213.800-0.064-0.0640.0000.0000.0000.000
108A108GLU-1-0.871-0.90913.625-0.648-0.6480.0000.0000.0000.000
109A109ASN0-0.072-0.0378.418-0.118-0.1180.0000.0000.0000.000
110A110GLU-1-0.743-0.8418.787-1.709-1.7090.0000.0000.0000.000
111A111TYR0-0.026-0.0415.418-0.973-0.9730.0000.0000.0000.000
112A112ALA00.0100.0158.5630.0330.0330.0000.0000.0000.000
113A113ALA00.001-0.00611.098-0.119-0.1190.0000.0000.0000.000
114A114LEU00.0290.00712.1300.2630.2630.0000.0000.0000.000
115A115GLY00.0030.00315.195-0.044-0.0440.0000.0000.0000.000
116A116GLY0-0.003-0.02115.8200.1360.1360.0000.0000.0000.000
117A117ILE0-0.045-0.00811.565-0.189-0.1890.0000.0000.0000.000
118A118PRO00.0500.04413.3630.1730.1730.0000.0000.0000.000
119A119LEU00.010-0.02014.184-0.153-0.1530.0000.0000.0000.000
120A120SER0-0.005-0.00314.204-0.062-0.0620.0000.0000.0000.000
121A121GLN00.0300.0138.0160.5820.5820.0000.0000.0000.000
122A122ILE0-0.052-0.0109.698-0.382-0.3820.0000.0000.0000.000
123A123ILE00.0290.0086.2840.4000.4000.0000.0000.0000.000
124A124GLY0-0.005-0.02010.9230.3100.3100.0000.0000.0000.000
125A125TRP00.0070.00813.778-0.169-0.1690.0000.0000.0000.000
126A126TYR0-0.012-0.00512.4640.1490.1490.0000.0000.0000.000
127A127ARG10.8140.89717.5340.1100.1100.0000.0000.0000.000
128A128VAL0-0.026-0.01119.0220.0510.0510.0000.0000.0000.000
129A129SER00.0300.02422.204-0.031-0.0310.0000.0000.0000.000
130A130PHE00.012-0.01825.9300.0230.0230.0000.0000.0000.000
131A131GLY00.0120.02223.3090.0140.0140.0000.0000.0000.000
132A132ALA0-0.0050.01122.5610.0170.0170.0000.0000.0000.000
133A133ILE00.006-0.00717.064-0.036-0.0360.0000.0000.0000.000
134A134GLU-1-0.840-0.90621.301-0.041-0.0410.0000.0000.0000.000
135A135GLY0-0.036-0.01621.677-0.017-0.0170.0000.0000.0000.000
136A136GLY0-0.013-0.01917.7940.0180.0180.0000.0000.0000.000
137A137MET0-0.048-0.01611.268-0.060-0.0600.0000.0000.0000.000
138A138HIS00.000-0.00115.9560.0230.0230.0000.0000.0000.000
139A139ARG10.9080.95513.574-0.114-0.1140.0000.0000.0000.000
140A140ASN00.0260.00614.4440.1920.1920.0000.0000.0000.000
141A141ARG10.9210.95015.6100.2170.2170.0000.0000.0000.000
142A142ASP-1-0.846-0.91717.533-0.492-0.4920.0000.0000.0000.000
143A143TYR0-0.0140.0127.0610.2200.2200.0000.0000.0000.000
144A144ARG10.7960.89112.8980.8030.8030.0000.0000.0000.000
145A145ARG10.9690.9819.7570.1820.1820.0000.0000.0000.000
146A146ASP-1-0.898-0.9699.845-0.719-0.7190.0000.0000.0000.000
147A147LEU00.0020.00511.8610.0580.0580.0000.0000.0000.000
148A148PHE00.0400.0136.693-0.099-0.0990.0000.0000.0000.000
149A149ARG10.8820.9445.962-0.517-0.5170.0000.0000.0000.000
150A150GLY0-0.004-0.0065.5170.4490.4490.0000.0000.0000.000
151A151LEU0-0.0280.0165.7310.3440.3440.0000.0000.0000.000
152A152SER0-0.010-0.0213.875-0.498-0.2560.001-0.092-0.1510.000
153A153ALA0-0.021-0.0094.673-0.085-0.037-0.001-0.004-0.0420.000
154A154ALA00.0210.0206.4730.7280.7280.0000.0000.0000.000
155A155PRO0-0.0090.0159.513-0.191-0.1910.0000.0000.0000.000
156A156ASN00.014-0.01311.238-0.223-0.2230.0000.0000.0000.000
157A157GLU-1-0.895-0.96113.547-0.638-0.6380.0000.0000.0000.000
158A158ASP-1-0.897-0.95014.912-0.847-0.8470.0000.0000.0000.000
159A159GLY0-0.004-0.01215.0190.0130.0130.0000.0000.0000.000
160A160TYR0-0.075-0.04315.8690.0830.0830.0000.0000.0000.000
161A161ARG10.8570.91718.9190.4830.4830.0000.0000.0000.000
162A162ILE0-0.059-0.03016.2280.0450.0450.0000.0000.0000.000
163A163ALA00.0030.01218.595-0.040-0.0400.0000.0000.0000.000
164A164GLY00.0110.00019.592-0.005-0.0050.0000.0000.0000.000
165A165PHE0-0.004-0.00120.5860.0130.0130.0000.0000.0000.000
166A166PRO0-0.0020.00424.7360.0080.0080.0000.0000.0000.000
167A167ASP-1-0.832-0.93328.416-0.269-0.2690.0000.0000.0000.000
168A168GLY0-0.019-0.00731.3080.0050.0050.0000.0000.0000.000
169A169PHE0-0.059-0.01824.7950.0120.0120.0000.0000.0000.000
170A170PRO00.0520.00728.552-0.008-0.0080.0000.0000.0000.000
171A171ALA00.0240.02523.7750.0110.0110.0000.0000.0000.000
172A172TRP0-0.048-0.03023.184-0.020-0.0200.0000.0000.0000.000
173A173GLU-1-0.945-0.97927.688-0.187-0.1870.0000.0000.0000.000
174A174GLU-1-0.847-0.88225.751-0.252-0.2520.0000.0000.0000.000
175A175VAL0-0.0310.00924.077-0.025-0.0250.0000.0000.0000.000
176A176PRO0-0.006-0.01019.6130.0170.0170.0000.0000.0000.000
177A177TRP0-0.004-0.02918.9430.0340.0340.0000.0000.0000.000
178A178ARG10.8710.92123.1250.2050.2050.0000.0000.0000.000
179A179GLU-1-0.863-0.91124.499-0.210-0.2100.0000.0000.0000.000
180A180PHE0-0.024-0.02320.472-0.007-0.0070.0000.0000.0000.000
181A181ALA00.0340.04323.919-0.033-0.0330.0000.0000.0000.000
182A182PRO0-0.0010.00824.6970.0210.0210.0000.0000.0000.000
183A183ASN00.002-0.01527.5500.0010.0010.0000.0000.0000.000
184A184SER0-0.038-0.01930.6160.0130.0130.0000.0000.0000.000
185A185CYS0-0.024-0.00828.382-0.012-0.0120.0000.0000.0000.000
186A186LEU0-0.0060.02029.1550.0000.0000.0000.0000.0000.000
187A187PRO0-0.0070.00731.8640.0140.0140.0000.0000.0000.000