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: NNJYQ

Calculation Name: 3T5C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3T5C

Chain ID: A

ChEMBL ID:

UniProt ID: P9WQ37

Base Structure: X-ray

Registration Date: 2023-09-23

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 396
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6584831.23097
FMO2-HF: Nuclear repulsion 6433118.437563
FMO2-HF: Total energy -151712.793406
FMO2-MP2: Total energy -152150.734329


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.
-10.678-6.4979.058-1.622-11.618-0.039
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 : -0.015 / q_NPA : 0.003
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].
3A3ASN00.0720.0283.286-1.2201.3720.057-1.166-1.4830.000
4A4ILE00.0370.0085.0170.0140.070-0.001-0.005-0.0490.000
5A5GLY00.0490.0138.3510.0830.0830.0000.0000.0000.000
6A6TRP0-0.048-0.0372.847-0.5360.3840.156-0.243-0.833-0.001
7A7MET00.0070.0278.6820.1880.1880.0000.0000.0000.000
8A8LEU00.0030.01710.3740.1190.1190.0000.0000.0000.000
9A9ARG10.9660.9998.4581.3881.3880.0000.0000.0000.000
10A10GLN0-0.025-0.0327.7840.1550.1550.0000.0000.0000.000
11A11ARG10.8940.97013.3780.0810.0810.0000.0000.0000.000
12A12ALA0-0.010-0.00816.1540.0420.0420.0000.0000.0000.000
13A13THR0-0.067-0.02515.5680.0040.0040.0000.0000.0000.000
14A14VAL0-0.023-0.00715.9300.0340.0340.0000.0000.0000.000
15A15SER0-0.067-0.04118.5820.0360.0360.0000.0000.0000.000
16A16PRO00.0050.03720.9450.0070.0070.0000.0000.0000.000
17A17ARG10.9750.94222.4250.0860.0860.0000.0000.0000.000
18A18LEU0-0.0390.01422.1960.0080.0080.0000.0000.0000.000
19A19GLN00.0570.02524.317-0.010-0.0100.0000.0000.0000.000
20A20ALA00.001-0.00421.3970.0130.0130.0000.0000.0000.000
21A21TYR00.019-0.02023.4200.0100.0100.0000.0000.0000.000
22A22VAL0-0.028-0.01225.377-0.010-0.0100.0000.0000.0000.000
23A23GLU-1-0.788-0.83328.983-0.047-0.0470.0000.0000.0000.000
24A24PRO00.0420.00931.189-0.006-0.0060.0000.0000.0000.000
25A25SER0-0.058-0.01733.926-0.003-0.0030.0000.0000.0000.000
26A26THR00.004-0.01231.289-0.002-0.0020.0000.0000.0000.000
27A27ASP-1-0.927-0.95634.369-0.061-0.0610.0000.0000.0000.000
28A28VAL0-0.0340.01228.219-0.009-0.0090.0000.0000.0000.000
29A29ARG10.8740.93129.4990.0500.0500.0000.0000.0000.000
30A30MET0-0.0040.01324.026-0.006-0.0060.0000.0000.0000.000
31A31THR00.0140.01524.9230.0060.0060.0000.0000.0000.000
32A32TYR00.050-0.01618.484-0.020-0.0200.0000.0000.0000.000
33A33ALA0-0.026-0.00819.883-0.036-0.0360.0000.0000.0000.000
34A34GLN00.0100.00521.190-0.023-0.0230.0000.0000.0000.000
35A35MET00.0230.02318.208-0.007-0.0070.0000.0000.0000.000
36A36ASN00.0570.03215.221-0.047-0.0470.0000.0000.0000.000
37A37ALA0-0.0010.00217.599-0.046-0.0460.0000.0000.0000.000
38A38LEU00.000-0.01520.057-0.019-0.0190.0000.0000.0000.000
39A39ALA00.0200.00416.014-0.001-0.0010.0000.0000.0000.000
40A40ASN0-0.033-0.02614.920-0.068-0.0680.0000.0000.0000.000
41A41ARG10.9641.00016.9320.2480.2480.0000.0000.0000.000
42A42CYS0-0.059-0.01818.5120.0230.0230.0000.0000.0000.000
43A43ALA00.0180.00914.4140.0110.0110.0000.0000.0000.000
44A44ASP-1-0.818-0.89916.381-0.433-0.4330.0000.0000.0000.000
45A45VAL0-0.009-0.01318.5800.0230.0230.0000.0000.0000.000
46A46LEU0-0.035-0.02816.7790.0210.0210.0000.0000.0000.000
47A47THR00.0230.00516.073-0.010-0.0100.0000.0000.0000.000
48A48ALA0-0.033-0.00418.0240.0130.0130.0000.0000.0000.000
49A49LEU0-0.093-0.03821.3650.0270.0270.0000.0000.0000.000
50A50GLY0-0.020-0.00720.3190.0260.0260.0000.0000.0000.000
51A51ILE0-0.102-0.03215.3100.0050.0050.0000.0000.0000.000
52A52ALA00.0220.00214.023-0.069-0.0690.0000.0000.0000.000
53A53LYS10.9740.9806.3361.7471.7470.0000.0000.0000.000
54A54GLY0-0.030-0.01411.1160.0470.0470.0000.0000.0000.000
55A55ASP-1-0.836-0.90212.712-0.248-0.2480.0000.0000.0000.000
56A56ARG10.8400.90215.5480.1170.1170.0000.0000.0000.000
57A57VAL00.0160.00317.476-0.011-0.0110.0000.0000.0000.000
58A58ALA00.0060.00319.8910.0200.0200.0000.0000.0000.000
59A59LEU0-0.033-0.00919.306-0.014-0.0140.0000.0000.0000.000
60A60LEU00.0000.01223.6120.0210.0210.0000.0000.0000.000
61A61MET00.005-0.00525.168-0.008-0.0080.0000.0000.0000.000
62A62PRO00.0130.00127.6700.0080.0080.0000.0000.0000.000
63A63ASN00.0390.01526.403-0.011-0.0110.0000.0000.0000.000
64A64SER00.0590.02425.572-0.007-0.0070.0000.0000.0000.000
65A65VAL00.0580.01422.838-0.002-0.0020.0000.0000.0000.000
66A66GLU-1-0.872-0.94522.265-0.155-0.1550.0000.0000.0000.000
67A67PHE0-0.0220.00620.898-0.020-0.0200.0000.0000.0000.000
68A68CYS0-0.027-0.02119.4760.0010.0010.0000.0000.0000.000
69A69CYS0-0.058-0.02717.846-0.025-0.0250.0000.0000.0000.000
70A70LEU00.0480.02017.546-0.053-0.0530.0000.0000.0000.000
71A71PHE00.0200.01813.997-0.034-0.0340.0000.0000.0000.000
72A72TYR00.004-0.00512.835-0.022-0.0220.0000.0000.0000.000
73A73GLY00.005-0.00512.794-0.105-0.1050.0000.0000.0000.000
74A74ALA00.0310.00713.139-0.094-0.0940.0000.0000.0000.000
75A75ALA0-0.016-0.0069.754-0.067-0.0670.0000.0000.0000.000
76A76LYS10.7200.8328.6700.5370.5370.0000.0000.0000.000
77A77LEU0-0.0140.0098.783-0.244-0.2440.0000.0000.0000.000
78A78GLY00.0290.0098.423-0.144-0.1440.0000.0000.0000.000
79A79ALA0-0.062-0.0129.0510.1280.1280.0000.0000.0000.000
80A80VAL0-0.029-0.01712.4230.0520.0520.0000.0000.0000.000
81A81ALA00.0150.02114.670-0.014-0.0140.0000.0000.0000.000
82A82VAL00.021-0.00717.3520.0440.0440.0000.0000.0000.000
83A83PRO0-0.024-0.00919.175-0.013-0.0130.0000.0000.0000.000
84A84ILE0-0.003-0.00422.2630.0190.0190.0000.0000.0000.000
85A85ASN00.0740.02625.919-0.013-0.0130.0000.0000.0000.000
86A86THR00.0410.00328.7850.0000.0000.0000.0000.0000.000
87A87ARG10.8790.93231.1510.0000.0000.0000.0000.0000.000
88A88LEU0-0.046-0.00629.7780.0050.0050.0000.0000.0000.000
89A89ALA00.0200.02133.895-0.006-0.0060.0000.0000.0000.000
90A90ALA00.0570.00834.9150.0000.0000.0000.0000.0000.000
91A91PRO00.004-0.00234.579-0.003-0.0030.0000.0000.0000.000
92A92GLU-1-0.869-0.94732.4080.0030.0030.0000.0000.0000.000
93A93VAL00.0000.00229.6180.0020.0020.0000.0000.0000.000
94A94SER00.0190.01029.690-0.006-0.0060.0000.0000.0000.000
95A95PHE00.003-0.00628.772-0.003-0.0030.0000.0000.0000.000
96A96ILE0-0.0060.00225.2790.0030.0030.0000.0000.0000.000
97A97LEU00.0080.01425.618-0.003-0.0030.0000.0000.0000.000
98A98SER00.008-0.00625.812-0.011-0.0110.0000.0000.0000.000
99A99ASP-1-0.842-0.85125.0160.0300.0300.0000.0000.0000.000
100A100SER00.016-0.00121.390-0.002-0.0020.0000.0000.0000.000
101A101GLY0-0.0050.00421.380-0.011-0.0110.0000.0000.0000.000
102A102SER0-0.061-0.04021.494-0.022-0.0220.0000.0000.0000.000
103A103LYS10.9520.99519.7170.2650.2650.0000.0000.0000.000
104A104VAL00.0110.01121.6560.0000.0000.0000.0000.0000.000
105A105VAL00.0020.00522.9810.0080.0080.0000.0000.0000.000
106A106ILE00.0100.01122.197-0.002-0.0020.0000.0000.0000.000
107A107TYR0-0.004-0.01026.0310.0120.0120.0000.0000.0000.000
108A108GLY00.015-0.00229.117-0.007-0.0070.0000.0000.0000.000
109A109ALA00.0550.01731.1280.0050.0050.0000.0000.0000.000
110A110PRO0-0.018-0.02033.4710.0020.0020.0000.0000.0000.000
111A111SER0-0.015-0.01832.0360.0060.0060.0000.0000.0000.000
112A112ALA00.0280.01434.050-0.002-0.0020.0000.0000.0000.000
113A113PRO00.0120.01136.0790.0000.0000.0000.0000.0000.000
114A114VAL0-0.0030.01233.9390.0010.0010.0000.0000.0000.000
115A115ILE00.0260.01330.6490.0010.0010.0000.0000.0000.000
116A116ASP-1-0.910-0.96034.580-0.067-0.0670.0000.0000.0000.000
117A117ALA0-0.057-0.03037.7330.0010.0010.0000.0000.0000.000
118A118ILE0-0.0110.00032.3730.0010.0010.0000.0000.0000.000
119A119ARG10.8730.93633.5310.0920.0920.0000.0000.0000.000
120A120ALA0-0.0130.00536.092-0.002-0.0020.0000.0000.0000.000
121A121GLN0-0.093-0.04435.3980.0060.0060.0000.0000.0000.000
122A122ALA0-0.035-0.03939.267-0.003-0.0030.0000.0000.0000.000
123A123ASP-1-0.912-0.95635.902-0.049-0.0490.0000.0000.0000.000
124A124PRO0-0.0210.02033.6580.0040.0040.0000.0000.0000.000
125A125PRO00.0150.00328.732-0.002-0.0020.0000.0000.0000.000
126A126GLY00.0280.00929.816-0.009-0.0090.0000.0000.0000.000
127A127THR0-0.044-0.02024.422-0.003-0.0030.0000.0000.0000.000
128A128VAL0-0.062-0.02125.231-0.018-0.0180.0000.0000.0000.000
129A129THR0-0.051-0.02724.7110.0000.0000.0000.0000.0000.000
130A130ASP-1-0.901-0.94325.549-0.191-0.1910.0000.0000.0000.000
131A131TRP00.029-0.00426.9310.0060.0060.0000.0000.0000.000
132A132ILE0-0.051-0.02325.8270.0010.0010.0000.0000.0000.000
133A133GLY00.0740.04528.6530.0050.0050.0000.0000.0000.000
134A134ALA00.042-0.00329.875-0.010-0.0100.0000.0000.0000.000
135A135ASP-1-0.871-0.93430.509-0.112-0.1120.0000.0000.0000.000
136A136SER00.0080.00630.609-0.010-0.0100.0000.0000.0000.000
137A137LEU00.013-0.00823.882-0.014-0.0140.0000.0000.0000.000
138A138ALA0-0.004-0.00627.259-0.015-0.0150.0000.0000.0000.000
139A139GLU-1-0.981-0.98829.439-0.143-0.1430.0000.0000.0000.000
140A140ARG10.9430.97425.6890.1850.1850.0000.0000.0000.000
141A141LEU00.0260.00123.004-0.020-0.0200.0000.0000.0000.000
142A142ARG10.8450.93025.6730.1340.1340.0000.0000.0000.000
143A143SER0-0.030-0.01827.6500.0030.0030.0000.0000.0000.000
144A144ALA0-0.0510.00422.059-0.009-0.0090.0000.0000.0000.000
145A145ALA00.0090.02320.0120.0180.0180.0000.0000.0000.000
146A146ALA0-0.024-0.04119.732-0.002-0.0020.0000.0000.0000.000
147A147ASP-1-0.959-0.97017.124-0.552-0.5520.0000.0000.0000.000
148A148GLU-1-0.783-0.90011.683-0.741-0.7410.0000.0000.0000.000
149A149PRO00.0230.01610.660-0.049-0.0490.0000.0000.0000.000
150A150ALA0-0.017-0.0079.496-0.127-0.1270.0000.0000.0000.000
151A151VAL0-0.0110.0016.616-0.084-0.0840.0000.0000.0000.000
152A152GLU-1-0.978-0.9952.428-12.169-10.7652.940-1.726-2.618-0.023
153A153CYS0-0.054-0.0122.824-1.596-0.5680.387-0.301-1.1140.000
154A154GLY00.0380.0142.735-0.886-1.1272.884-0.233-2.411-0.006
155A155GLY0-0.006-0.0092.4300.609-0.1882.4671.004-2.675-0.008
156A156ASP-1-0.851-0.9432.9351.5760.6310.1691.071-0.295-0.001
157A157ASP-1-0.883-0.9205.053-0.699-0.535-0.001-0.023-0.1400.000
158A158ASN00.002-0.0177.3620.0570.0570.0000.0000.0000.000
159A159LEU0-0.008-0.0049.775-0.103-0.1030.0000.0000.0000.000
160A160PHE0-0.001-0.01311.764-0.099-0.0990.0000.0000.0000.000
161A161ILE00.0150.02615.2250.0500.0500.0000.0000.0000.000
162A162MET0-0.047-0.02416.203-0.030-0.0300.0000.0000.0000.000
163A163TYR0-0.034-0.05320.6640.0180.0180.0000.0000.0000.000
164A164THR00.0170.01224.033-0.010-0.0100.0000.0000.0000.000
165A165SER00.0230.01526.0760.0000.0000.0000.0000.0000.000
166A166GLY00.0670.04928.424-0.006-0.0060.0000.0000.0000.000
167A167THR0-0.024-0.02729.5780.0010.0010.0000.0000.0000.000
168A168THR0-0.063-0.01232.023-0.001-0.0010.0000.0000.0000.000
169A169GLY00.018-0.00133.706-0.003-0.0030.0000.0000.0000.000
170A170HIS10.9030.95030.725-0.032-0.0320.0000.0000.0000.000
171A171PRO0-0.032-0.00827.8860.0090.0090.0000.0000.0000.000
172A172LYS10.9800.99724.390-0.124-0.1240.0000.0000.0000.000
173A173GLY00.0650.02721.947-0.003-0.0030.0000.0000.0000.000
174A174VAL0-0.016-0.00617.7450.0130.0130.0000.0000.0000.000
175A175VAL0-0.0130.00614.228-0.026-0.0260.0000.0000.0000.000
176A176HIS00.0110.03112.9560.0910.0910.0000.0000.0000.000
177A177THR00.0480.0257.823-0.113-0.1130.0000.0000.0000.000
178A178HIS00.0190.0195.406-0.252-0.2520.0000.0000.0000.000
179A179GLU-1-0.909-0.9695.0231.9061.9060.0000.0000.0000.000
180A180SER00.0440.0196.681-0.050-0.0500.0000.0000.0000.000
181A181VAL00.035-0.00510.204-0.082-0.0820.0000.0000.0000.000
182A182HIS0-0.019-0.0127.608-0.248-0.2480.0000.0000.0000.000
183A183SER00.0340.0119.258-0.015-0.0150.0000.0000.0000.000
184A184ALA00.0150.01411.140-0.058-0.0580.0000.0000.0000.000
185A185ALA0-0.030-0.02013.053-0.048-0.0480.0000.0000.0000.000
186A186SER0-0.001-0.02311.301-0.021-0.0210.0000.0000.0000.000
187A187SER0-0.042-0.01213.956-0.038-0.0380.0000.0000.0000.000
188A188TRP00.0310.01216.518-0.041-0.0410.0000.0000.0000.000
189A189ALA0-0.054-0.03216.652-0.021-0.0210.0000.0000.0000.000
190A190SER0-0.055-0.02716.345-0.002-0.0020.0000.0000.0000.000
191A191THR0-0.022-0.01318.9430.0050.0050.0000.0000.0000.000
192A192ILE0-0.0070.00221.897-0.020-0.0200.0000.0000.0000.000
193A193ASP-1-0.807-0.89623.4790.1490.1490.0000.0000.0000.000
194A194VAL0-0.0160.02721.220-0.025-0.0250.0000.0000.0000.000
195A195ARG10.8560.89123.400-0.094-0.0940.0000.0000.0000.000
196A196TYR0-0.076-0.05221.847-0.017-0.0170.0000.0000.0000.000
197A197ARG10.8870.93423.888-0.027-0.0270.0000.0000.0000.000
198A198ASP-1-0.703-0.80825.5610.0860.0860.0000.0000.0000.000
199A199ARG10.7890.87526.406-0.005-0.0050.0000.0000.0000.000
200A200LEU00.0240.01423.8420.0070.0070.0000.0000.0000.000
201A201LEU00.0220.01327.261-0.011-0.0110.0000.0000.0000.000
202A202LEU0-0.019-0.01724.5920.0130.0130.0000.0000.0000.000
203A203PRO0-0.0150.00027.915-0.011-0.0110.0000.0000.0000.000
204A204LEU0-0.011-0.00427.8770.0000.0000.0000.0000.0000.000
205A205PRO0-0.0040.00227.471-0.005-0.0050.0000.0000.0000.000
206A206MET00.027-0.01222.6730.0060.0060.0000.0000.0000.000
207A207PHE0-0.0320.02122.4890.0020.0020.0000.0000.0000.000
208A208HIS0-0.0020.00823.6050.0140.0140.0000.0000.0000.000
209A209VAL00.0920.04118.657-0.008-0.0080.0000.0000.0000.000
210A210ALA00.0310.02920.1220.0060.0060.0000.0000.0000.000
211A211ALA0-0.0120.00821.7880.0030.0030.0000.0000.0000.000
212A212LEU00.0220.01017.465-0.013-0.0130.0000.0000.0000.000
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