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: Z65VN

Calculation Name: 1TT7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TT7

Chain ID: A

ChEMBL ID:

UniProt ID: O07615

Base Structure: X-ray

Registration Date: 2023-09-19

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 329
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4617297.206165
FMO2-HF: Nuclear repulsion 4496965.855672
FMO2-HF: Total energy -120331.350492
FMO2-MP2: Total energy -120687.048268


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:2:SER)


Summations of interaction energy for fragment #1(A:2: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.
-4.621-1.9451.817-1.897-2.596-0.014
Interaction energy analysis for fragmet #1(A:2:SER)
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 : -0.016
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].
3A4LEU00.0020.0153.859-1.468-0.302-0.015-0.532-0.6190.001
4A5PHE0-0.0130.0036.1030.9080.9080.0000.0000.0000.000
5A6GLN00.0240.0178.808-0.345-0.3450.0000.0000.0000.000
6A7ALA00.020-0.00412.5760.0780.0780.0000.0000.0000.000
7A8LEU0-0.0260.00114.386-0.050-0.0500.0000.0000.0000.000
8A9GLN0-0.003-0.01516.184-0.001-0.0010.0000.0000.0000.000
9A10ALA00.007-0.00118.7690.0070.0070.0000.0000.0000.000
10A11GLU-1-0.781-0.87620.764-0.081-0.0810.0000.0000.0000.000
11A12LYS10.8270.89423.5280.0780.0780.0000.0000.0000.000
12A13ASN00.0410.02926.152-0.008-0.0080.0000.0000.0000.000
13A14ALA0-0.039-0.04327.8630.0090.0090.0000.0000.0000.000
14A15ASP-1-0.830-0.89230.479-0.065-0.0650.0000.0000.0000.000
15A16ASP-1-0.863-0.92131.019-0.009-0.0090.0000.0000.0000.000
16A17VAL0-0.078-0.04226.664-0.006-0.0060.0000.0000.0000.000
17A18SER0-0.056-0.02825.5650.0120.0120.0000.0000.0000.000
18A19VAL0-0.054-0.01723.0230.0150.0150.0000.0000.0000.000
19A20HIS0-0.068-0.03321.563-0.001-0.0010.0000.0000.0000.000
20A21VAL00.0220.01617.8650.0020.0020.0000.0000.0000.000
21A22LYS10.7830.86615.5060.0190.0190.0000.0000.0000.000
22A23THR0-0.005-0.00310.9360.0480.0480.0000.0000.0000.000
23A24ILE0-0.040-0.0109.683-0.109-0.1090.0000.0000.0000.000
24A25SER00.0330.0066.256-0.136-0.1360.0000.0000.0000.000
25A26THR0-0.044-0.0522.558-3.244-1.8111.833-1.358-1.908-0.015
26A27GLU-1-0.924-0.9554.790-2.318-2.241-0.001-0.007-0.0690.000
27A28ASP-1-0.847-0.9266.001-0.653-0.6530.0000.0000.0000.000
28A29LEU0-0.029-0.0017.1710.2250.2250.0000.0000.0000.000
29A30PRO0-0.0110.00810.204-0.168-0.1680.0000.0000.0000.000
30A31LYS10.8810.9237.7141.6701.6700.0000.0000.0000.000
31A32ASP-1-0.851-0.87711.017-0.271-0.2710.0000.0000.0000.000
32A33GLY0-0.019-0.01612.3660.0670.0670.0000.0000.0000.000
33A34VAL0-0.030-0.01211.480-0.052-0.0520.0000.0000.0000.000
34A35LEU00.0180.0175.2760.0590.0590.0000.0000.0000.000
35A36ILE00.0280.0129.6460.1780.1780.0000.0000.0000.000
36A37LYS10.8590.9218.816-1.967-1.9670.0000.0000.0000.000
37A38VAL0-0.041-0.01010.622-0.127-0.1270.0000.0000.0000.000
38A39ALA0-0.053-0.03813.5160.1040.1040.0000.0000.0000.000
39A40TYR00.025-0.00216.045-0.069-0.0690.0000.0000.0000.000
40A41SER00.0420.00318.322-0.012-0.0120.0000.0000.0000.000
41A42GLY00.008-0.00320.302-0.002-0.0020.0000.0000.0000.000
42A43ILE0-0.0180.01423.363-0.010-0.0100.0000.0000.0000.000
43A44ASN0-0.037-0.02025.485-0.005-0.0050.0000.0000.0000.000
44A45TYR00.038-0.00828.541-0.005-0.0050.0000.0000.0000.000
45A46LYS10.9290.98226.568-0.066-0.0660.0000.0000.0000.000
46A47ASP-1-0.723-0.87424.0430.1170.1170.0000.0000.0000.000
47A48GLY00.0270.01226.646-0.006-0.0060.0000.0000.0000.000
48A49LEU0-0.095-0.04629.412-0.009-0.0090.0000.0000.0000.000
49A50ALA00.0500.02425.059-0.009-0.0090.0000.0000.0000.000
50A51GLY00.0330.02025.872-0.013-0.0130.0000.0000.0000.000
51A52LYS10.9000.94726.555-0.046-0.0460.0000.0000.0000.000
52A53ALA00.1140.06930.176-0.004-0.0040.0000.0000.0000.000
53A54GLY0-0.019-0.01232.3930.0060.0060.0000.0000.0000.000
54A55GLY0-0.008-0.01531.5370.0010.0010.0000.0000.0000.000
55A56ASN0-0.044-0.02830.434-0.008-0.0080.0000.0000.0000.000
56A57ILE0-0.047-0.01626.788-0.005-0.0050.0000.0000.0000.000
57A58VAL00.0370.03524.204-0.001-0.0010.0000.0000.0000.000
58A59ARG10.8260.90726.4500.0410.0410.0000.0000.0000.000
59A60GLU-1-0.930-0.95523.476-0.172-0.1720.0000.0000.0000.000
60A61TYR0-0.026-0.04323.3510.0070.0070.0000.0000.0000.000
61A62PRO0-0.041-0.02819.393-0.006-0.0060.0000.0000.0000.000
62A63LEU00.0250.05718.320-0.024-0.0240.0000.0000.0000.000
63A64ILE00.0020.00212.9900.0260.0260.0000.0000.0000.000
64A65LEU0-0.0020.00517.4090.0020.0020.0000.0000.0000.000
65A66GLY00.0680.00018.7930.0340.0340.0000.0000.0000.000
66A67ILE0-0.069-0.02221.0400.0080.0080.0000.0000.0000.000
67A68ASP-1-0.751-0.81221.2380.1690.1690.0000.0000.0000.000
68A69ALA00.0460.02416.4970.0210.0210.0000.0000.0000.000
69A70ALA00.0190.02218.465-0.037-0.0370.0000.0000.0000.000
70A71GLY00.0270.00914.9870.0530.0530.0000.0000.0000.000
71A72THR00.0210.02213.139-0.040-0.0400.0000.0000.0000.000
72A73VAL0-0.0060.00012.0370.1740.1740.0000.0000.0000.000
73A74VAL0-0.045-0.0245.7180.0890.0890.0000.0000.0000.000
74A75SER00.0280.0076.5830.1560.1560.0000.0000.0000.000
75A76SER00.005-0.0028.590-0.110-0.1100.0000.0000.0000.000
76A77ASN0-0.052-0.02111.006-0.180-0.1800.0000.0000.0000.000
77A78ASP-1-0.794-0.87512.377-0.019-0.0190.0000.0000.0000.000
78A79PRO0-0.008-0.01115.8180.0520.0520.0000.0000.0000.000
79A80ARG10.6760.78418.0400.0010.0010.0000.0000.0000.000
80A81PHE0-0.0120.00815.9630.0140.0140.0000.0000.0000.000
81A82ALA0-0.013-0.01214.887-0.036-0.0360.0000.0000.0000.000
82A83GLU-1-0.952-0.9859.5800.7340.7340.0000.0000.0000.000
83A84GLY0-0.028-0.01313.025-0.035-0.0350.0000.0000.0000.000
84A85ASP-1-0.851-0.91914.6050.3380.3380.0000.0000.0000.000
85A86GLU-1-0.924-0.97216.3490.5340.5340.0000.0000.0000.000
86A87VAL0-0.051-0.01916.384-0.072-0.0720.0000.0000.0000.000
87A88ILE0-0.011-0.01218.6560.0410.0410.0000.0000.0000.000
88A89ALA00.0150.01017.549-0.031-0.0310.0000.0000.0000.000
89A90THR0-0.027-0.04719.5120.0180.0180.0000.0000.0000.000
90A91SER0-0.093-0.03622.550-0.024-0.0240.0000.0000.0000.000
91A92TYR0-0.034-0.01423.0170.0000.0000.0000.0000.0000.000
92A93GLU-1-0.914-0.96122.108-0.063-0.0630.0000.0000.0000.000
93A94LEU00.0390.02917.673-0.014-0.0140.0000.0000.0000.000
94A95GLY0-0.027-0.01920.0370.0150.0150.0000.0000.0000.000
95A96VAL0-0.128-0.06621.6090.0010.0010.0000.0000.0000.000
96A97SER0-0.029-0.02823.008-0.007-0.0070.0000.0000.0000.000
97A98ARG10.8130.88614.4070.0960.0960.0000.0000.0000.000
98A99ASP-1-0.817-0.91614.801-0.085-0.0850.0000.0000.0000.000
99A100GLY0-0.036-0.02416.7440.0140.0140.0000.0000.0000.000
100A101GLY00.0080.00115.7190.0310.0310.0000.0000.0000.000
101A102LEU0-0.049-0.00316.6870.0550.0550.0000.0000.0000.000
102A103SER00.020-0.02512.363-0.087-0.0870.0000.0000.0000.000
103A104GLU-1-0.854-0.9019.8771.4451.4450.0000.0000.0000.000
104A105TYR0-0.016-0.0226.0360.1700.1700.0000.0000.0000.000
105A106ALA00.0540.0449.598-0.211-0.2110.0000.0000.0000.000
106A107SER0-0.012-0.01710.0220.1610.1610.0000.0000.0000.000
107A108VAL00.0180.01411.886-0.097-0.0970.0000.0000.0000.000
108A109PRO00.0650.03915.4500.0280.0280.0000.0000.0000.000
109A110GLY00.0650.02717.5170.0370.0370.0000.0000.0000.000
110A111ASP-1-0.863-0.90618.7060.0090.0090.0000.0000.0000.000
111A112TRP0-0.059-0.03819.938-0.003-0.0030.0000.0000.0000.000
112A113LEU0-0.0420.00216.3580.0210.0210.0000.0000.0000.000
113A114VAL0-0.011-0.01320.948-0.025-0.0250.0000.0000.0000.000
114A115PRO00.021-0.00121.7250.0310.0310.0000.0000.0000.000
115A116LEU0-0.041-0.01321.714-0.022-0.0220.0000.0000.0000.000
116A117PRO00.0020.00623.576-0.006-0.0060.0000.0000.0000.000
117A118GLN0-0.0080.00026.0770.0090.0090.0000.0000.0000.000
118A119ASN0-0.075-0.03528.2450.0160.0160.0000.0000.0000.000
119A120LEU0-0.027-0.01327.207-0.013-0.0130.0000.0000.0000.000
120A121SER00.027-0.01224.2990.0230.0230.0000.0000.0000.000
121A122LEU00.0520.01217.927-0.024-0.0240.0000.0000.0000.000
122A123LYS10.8710.93522.011-0.313-0.3130.0000.0000.0000.000
123A124GLU-1-0.782-0.85624.0750.2290.2290.0000.0000.0000.000
124A125ALA00.0460.02723.318-0.023-0.0230.0000.0000.0000.000
125A126MET0-0.0140.00120.989-0.023-0.0230.0000.0000.0000.000
126A127VAL0-0.0380.00124.395-0.014-0.0140.0000.0000.0000.000
127A128TYR0-0.034-0.03227.958-0.022-0.0220.0000.0000.0000.000
128A129GLY00.0320.01825.239-0.012-0.0120.0000.0000.0000.000
129A130THR00.007-0.04225.347-0.019-0.0190.0000.0000.0000.000
130A131ALA0-0.056-0.02127.671-0.012-0.0120.0000.0000.0000.000
131A132GLY00.0650.00829.981-0.010-0.0100.0000.0000.0000.000
132A133PHE00.0170.00528.849-0.009-0.0090.0000.0000.0000.000
133A134THR0-0.004-0.00430.891-0.010-0.0100.0000.0000.0000.000
134A135ALA00.0050.03033.400-0.009-0.0090.0000.0000.0000.000
135A136ALA00.0590.01933.430-0.007-0.0070.0000.0000.0000.000
136A137LEU0-0.028-0.00933.462-0.006-0.0060.0000.0000.0000.000
137A138SER0-0.032-0.03635.856-0.010-0.0100.0000.0000.0000.000
138A139VAL00.0090.01138.753-0.006-0.0060.0000.0000.0000.000
139A140HIS00.0330.02337.499-0.003-0.0030.0000.0000.0000.000
140A141ARG10.8280.90038.727-0.051-0.0510.0000.0000.0000.000
141A142LEU00.0170.00441.286-0.005-0.0050.0000.0000.0000.000
142A143GLU-1-0.735-0.82242.8330.0720.0720.0000.0000.0000.000
143A144GLN0-0.026-0.00340.099-0.005-0.0050.0000.0000.0000.000
144A145ASN0-0.030-0.01244.920-0.003-0.0030.0000.0000.0000.000
145A146GLY00.0030.01847.564-0.003-0.0030.0000.0000.0000.000
146A147LEU0-0.066-0.02246.874-0.001-0.0010.0000.0000.0000.000
147A148SER0-0.017-0.04948.0070.0030.0030.0000.0000.0000.000
148A149PRO00.0070.01147.995-0.003-0.0030.0000.0000.0000.000
149A150GLU-1-0.813-0.88650.5720.0510.0510.0000.0000.0000.000
150A151LYS10.8210.92152.280-0.048-0.0480.0000.0000.0000.000
151A152GLY0-0.0040.00853.998-0.003-0.0030.0000.0000.0000.000
152A153SER00.002-0.01351.6860.0010.0010.0000.0000.0000.000
153A154VAL0-0.063-0.02946.454-0.003-0.0030.0000.0000.0000.000
154A155LEU0-0.0130.01347.1220.0020.0020.0000.0000.0000.000
155A156VAL00.001-0.00141.6650.0010.0010.0000.0000.0000.000
156A157THR00.001-0.02143.5830.0010.0010.0000.0000.0000.000
157A158GLY0-0.031-0.01241.2790.0030.0030.0000.0000.0000.000
158A159ALA0-0.009-0.00540.0230.0050.0050.0000.0000.0000.000
159A160THR0-0.024-0.02939.8880.0040.0040.0000.0000.0000.000
160A161GLY00.0330.02636.2110.0050.0050.0000.0000.0000.000
161A162GLY0-0.005-0.01233.037-0.002-0.0020.0000.0000.0000.000
162A163VAL0-0.019-0.00333.6840.0020.0020.0000.0000.0000.000
163A164GLY00.0650.02835.459-0.001-0.0010.0000.0000.0000.000
164A165GLY00.0380.01737.715-0.001-0.0010.0000.0000.0000.000
165A166ILE00.006-0.00431.8150.0030.0030.0000.0000.0000.000
166A167ALA00.0010.00236.2430.0000.0000.0000.0000.0000.000
167A168VAL0-0.012-0.00538.982-0.003-0.0030.0000.0000.0000.000
168A169SER0-0.007-0.02137.9390.0000.0000.0000.0000.0000.000
169A170MET0-0.062-0.01233.623-0.002-0.0020.0000.0000.0000.000
170A171LEU0-0.022-0.01439.371-0.003-0.0030.0000.0000.0000.000
171A172ASN00.0120.00942.707-0.006-0.0060.0000.0000.0000.000
172A173LYS10.7580.87138.879-0.128-0.1280.0000.0000.0000.000
173A174ARG10.7910.87741.965-0.081-0.0810.0000.0000.0000.000
174A175GLY00.0080.01143.593-0.004-0.0040.0000.0000.0000.000
175A176TYR0-0.097-0.07044.656-0.006-0.0060.0000.0000.0000.000
176A177ASP-1-0.781-0.83147.9510.0630.0630.0000.0000.0000.000
177A178VAL0-0.038-0.02344.786-0.002-0.0020.0000.0000.0000.000
178A179VAL00.0280.01948.1740.0010.0010.0000.0000.0000.000
179A180ALA00.0160.00545.1820.0000.0000.0000.0000.0000.000
180A181SER0-0.040-0.02045.876-0.003-0.0030.0000.0000.0000.000
181A182THR0-0.023-0.02543.6880.0020.0020.0000.0000.0000.000
182A183GLY0-0.030-0.02045.168-0.003-0.0030.0000.0000.0000.000
183A184ASN00.0070.01043.271-0.002-0.0020.0000.0000.0000.000
184A185ARG10.9220.94146.866-0.052-0.0520.0000.0000.0000.000
185A186GLU-1-0.796-0.88247.0160.0630.0630.0000.0000.0000.000
186A187ALA00.0260.01043.1160.0030.0030.0000.0000.0000.000
187A188ALA00.003-0.00244.6310.0030.0030.0000.0000.0000.000
188A189ASP-1-0.817-0.89546.9000.0770.0770.0000.0000.0000.000
189A190TYR0-0.037-0.04136.7720.0010.0010.0000.0000.0000.000
190A191LEU00.0110.00042.0630.0030.0030.0000.0000.0000.000
191A192LYS10.8740.93043.937-0.071-0.0710.0000.0000.0000.000
192A193GLN0-0.023-0.00442.340-0.001-0.0010.0000.0000.0000.000
193A194LEU0-0.031-0.00337.7330.0050.0050.0000.0000.0000.000
194A195GLY00.0230.01341.3960.0030.0030.0000.0000.0000.000
195A196ALA0-0.044-0.01744.449-0.003-0.0030.0000.0000.0000.000
196A197SER0-0.025-0.03646.6930.0000.0000.0000.0000.0000.000
197A198GLU-1-0.938-0.97050.0380.0500.0500.0000.0000.0000.000
198A199VAL0-0.049-0.03247.7440.0030.0030.0000.0000.0000.000
199A200ILE0-0.035-0.00349.737-0.003-0.0030.0000.0000.0000.000
200A201SER0-0.009-0.03749.6230.0020.0020.0000.0000.0000.000
201A202ARG11.0000.99943.742-0.049-0.0490.0000.0000.0000.000
202A203GLU-1-0.846-0.93150.3120.0410.0410.0000.0000.0000.000
203A204ASP-1-0.815-0.87253.6160.0420.0420.0000.0000.0000.000
204A205VAL0-0.051-0.02549.883-0.002-0.0020.0000.0000.0000.000
205A206TYR0-0.055-0.05851.662-0.004-0.0040.0000.0000.0000.000
206A207ASP-1-0.849-0.88853.6430.0310.0310.0000.0000.0000.000
207A208GLY0-0.0130.00255.170-0.002-0.0020.0000.0000.0000.000
208A209THR0-0.028-0.03156.7820.0000.0000.0000.0000.0000.000
209A210LEU00.0000.01954.1540.0010.0010.0000.0000.0000.000
210A211LYS10.8710.92058.237-0.027-0.0270.0000.0000.0000.000
211A212ALA00.0030.00759.0150.0010.0010.0000.0000.0000.000
212A213LEU00.012-0.00259.5080.0010.0010.0000.0000.0000.000
213A214SER0-0.036-0.02658.557-0.001-0.0010.0000.0000.0000.000
214A215LYS10.9190.94760.700-0.027-0.0270.0000.0000.0000.000
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