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: K36M3

Calculation Name: 4YTE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YTE

Chain ID: A

ChEMBL ID:

UniProt ID: Q58125

Base Structure: X-ray

Registration Date: 2023-06-20

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2116777.220629
FMO2-HF: Nuclear repulsion 2042659.793685
FMO2-HF: Total energy -74117.426944
FMO2-MP2: Total energy -74334.319336


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.
-45.154-37.8524.442-10.813-20.929-0.01
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 : -0.009 / 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].
3A3ILE0-0.024-0.0042.7940.3522.5210.173-0.708-1.6340.000
4A4SER00.0290.0025.190-0.394-0.369-0.001-0.005-0.0190.000
5A5ILE0-0.046-0.0088.4050.2760.2760.0000.0000.0000.000
6A6TYR0-0.053-0.06711.304-0.126-0.1260.0000.0000.0000.000
7A7GLY00.0270.02014.9070.0380.0380.0000.0000.0000.000
8A8ALA00.014-0.00316.3200.0560.0560.0000.0000.0000.000
9A9GLY0-0.027-0.01217.8360.0340.0340.0000.0000.0000.000
10A10ASN00.019-0.00520.597-0.018-0.0180.0000.0000.0000.000
11A11GLN00.0730.02620.0700.0120.0120.0000.0000.0000.000
12A12ARG10.9090.94124.549-0.068-0.0680.0000.0000.0000.000
13A13LEU0-0.0260.00625.925-0.002-0.0020.0000.0000.0000.000
14A14TYR00.025-0.00521.1550.0070.0070.0000.0000.0000.000
15A15LEU00.0120.00926.1970.0010.0010.0000.0000.0000.000
16A16GLU-1-0.875-0.91628.8170.0730.0730.0000.0000.0000.000
17A17GLN0-0.018-0.02431.024-0.001-0.0010.0000.0000.0000.000
18A18LEU0-0.053-0.02626.2100.0010.0010.0000.0000.0000.000
19A19LYS10.8960.97829.563-0.092-0.0920.0000.0000.0000.000
20A20VAL00.0340.01223.2740.0020.0020.0000.0000.0000.000
21A21PRO00.0330.01626.1190.0070.0070.0000.0000.0000.000
22A22GLU-1-0.906-0.95527.1980.1140.1140.0000.0000.0000.000
23A23LYS10.8650.94128.576-0.122-0.1220.0000.0000.0000.000
24A24PHE0-0.041-0.02923.9590.0050.0050.0000.0000.0000.000
25A25GLY00.0280.03824.5540.0140.0140.0000.0000.0000.000
26A26GLY0-0.004-0.01821.9870.0130.0130.0000.0000.0000.000
27A27GLU-1-0.929-0.96821.4100.1360.1360.0000.0000.0000.000
28A28PRO0-0.0130.03820.9190.0260.0260.0000.0000.0000.000
29A29PRO00.0300.01718.131-0.011-0.0110.0000.0000.0000.000
30A30TYR0-0.003-0.03418.8410.0260.0260.0000.0000.0000.000
31A31GLY0-0.029-0.01417.540-0.021-0.0210.0000.0000.0000.000
32A32GLY00.0490.01814.4650.0620.0620.0000.0000.0000.000
33A33ALA00.0610.01913.6670.0480.0480.0000.0000.0000.000
34A34GLY00.0090.01714.8510.0060.0060.0000.0000.0000.000
35A35MET0-0.053-0.03810.6550.0070.0070.0000.0000.0000.000
36A36ALA00.0080.01310.0700.2060.2060.0000.0000.0000.000
37A37ILE00.0550.02510.4630.0590.0590.0000.0000.0000.000
38A38GLU-1-0.997-1.00310.9430.6890.6890.0000.0000.0000.000
39A39PHE00.002-0.0116.4070.2810.2810.0000.0000.0000.000
40A40ALA00.0380.0267.0230.6230.6230.0000.0000.0000.000
41A41LYS10.9170.9568.305-0.572-0.5720.0000.0000.0000.000
42A42ALA0-0.050-0.0107.149-0.148-0.1480.0000.0000.0000.000
43A43GLY0-0.020-0.0076.1880.4470.4470.0000.0000.0000.000
44A44HIS10.7450.8471.987-25.934-27.35912.568-4.691-6.4520.042
45A45ASP-1-0.825-0.9202.767-4.132-3.0460.042-0.287-0.8410.000
46A46VAL0-0.015-0.0014.786-0.263-0.265-0.001-0.0160.0200.000
47A47VAL00.0220.0177.6650.0070.0070.0000.0000.0000.000
48A48LEU0-0.043-0.02710.6850.1660.1660.0000.0000.0000.000
49A49SER0-0.053-0.07513.145-0.061-0.0610.0000.0000.0000.000
50A50GLU-1-0.816-0.94315.8750.1570.1570.0000.0000.0000.000
51A51PRO0-0.0070.01019.197-0.024-0.0240.0000.0000.0000.000
52A52ASN0-0.018-0.01522.607-0.019-0.0190.0000.0000.0000.000
53A53ARG10.9880.96723.2570.0330.0330.0000.0000.0000.000
54A54ASP-1-0.897-0.93824.9130.0270.0270.0000.0000.0000.000
55A55VAL0-0.122-0.04121.6130.0110.0110.0000.0000.0000.000
56A56MET0-0.054-0.04019.3210.0270.0270.0000.0000.0000.000
57A57SER00.0420.02924.962-0.010-0.0100.0000.0000.0000.000
58A58ASP-1-0.778-0.89624.9920.0030.0030.0000.0000.0000.000
59A59ASP-1-0.913-0.95124.4130.0290.0290.0000.0000.0000.000
60A60LEU0-0.071-0.04522.5020.0100.0100.0000.0000.0000.000
61A61TRP00.011-0.01818.2050.0170.0170.0000.0000.0000.000
62A62LYS10.9350.98219.4910.0170.0170.0000.0000.0000.000
63A63LYS10.8440.92119.237-0.200-0.2000.0000.0000.0000.000
64A64VAL0-0.037-0.03015.0560.0320.0320.0000.0000.0000.000
65A65GLU-1-0.949-0.98414.868-0.105-0.1050.0000.0000.0000.000
66A66ASP-1-0.898-0.95015.514-0.048-0.0480.0000.0000.0000.000
67A67ALA0-0.121-0.05212.8110.0080.0080.0000.0000.0000.000
68A68GLY00.0020.00111.1650.0420.0420.0000.0000.0000.000
69A69VAL0-0.091-0.03310.744-0.125-0.1250.0000.0000.0000.000
70A70LYS10.9270.96911.2220.5390.5390.0000.0000.0000.000
71A71VAL00.0220.00313.1650.0160.0160.0000.0000.0000.000
72A72VAL0-0.030-0.00715.355-0.034-0.0340.0000.0000.0000.000
73A73SER00.0350.00817.6600.0380.0380.0000.0000.0000.000
74A74ASP-1-0.897-0.94819.095-0.128-0.1280.0000.0000.0000.000
75A75ASP-1-0.790-0.86816.908-0.022-0.0220.0000.0000.0000.000
76A76ILE0-0.007-0.00515.983-0.022-0.0220.0000.0000.0000.000
77A77GLU-1-0.876-0.93815.682-0.411-0.4110.0000.0000.0000.000
78A78ALA00.0050.00512.963-0.105-0.1050.0000.0000.0000.000
79A79ALA0-0.002-0.00711.601-0.089-0.0890.0000.0000.0000.000
80A80LYS10.9260.95912.0280.2790.2790.0000.0000.0000.000
81A81HIS0-0.075-0.0296.923-0.028-0.0280.0000.0000.0000.000
82A82GLY0-0.0200.0036.324-0.471-0.4710.0000.0000.0000.000
83A83GLU-1-0.813-0.9142.486-9.309-5.9172.835-2.807-3.419-0.035
84A84ILE0-0.037-0.0223.2920.3930.7731.211-0.292-1.2990.001
85A85HIS00.0090.0506.272-0.226-0.2260.0000.0000.0000.000
86A86VAL00.019-0.0038.2960.0480.0480.0000.0000.0000.000
87A87LEU00.002-0.01011.022-0.124-0.1240.0000.0000.0000.000
88A88PHE00.0140.01614.7710.0230.0230.0000.0000.0000.000
89A89THR00.0200.03116.132-0.057-0.0570.0000.0000.0000.000
90A90PRO00.0270.01519.391-0.006-0.0060.0000.0000.0000.000
91A91PHE00.012-0.00821.283-0.011-0.0110.0000.0000.0000.000
92A92GLY0-0.033-0.01522.543-0.013-0.0130.0000.0000.0000.000
93A93ARG10.9000.95023.546-0.127-0.1270.0000.0000.0000.000
94A94ILE00.0700.02821.309-0.008-0.0080.0000.0000.0000.000
95A95THR0-0.011-0.02618.807-0.011-0.0110.0000.0000.0000.000
96A96LEU00.0440.00320.0650.0070.0070.0000.0000.0000.000
97A97ASN00.0110.01422.132-0.008-0.0080.0000.0000.0000.000
98A98ILE00.0400.01916.951-0.015-0.0150.0000.0000.0000.000
99A99ALA00.0180.01017.256-0.019-0.0190.0000.0000.0000.000
100A100ASN0-0.001-0.01018.321-0.007-0.0070.0000.0000.0000.000
101A101THR0-0.053-0.01319.601-0.023-0.0230.0000.0000.0000.000
102A102ILE00.013-0.00713.514-0.024-0.0240.0000.0000.0000.000
103A103ILE0-0.0140.00816.037-0.031-0.0310.0000.0000.0000.000
104A104GLU-1-0.987-1.00416.801-0.043-0.0430.0000.0000.0000.000
105A105HIS0-0.051-0.02416.666-0.051-0.0510.0000.0000.0000.000
106A106VAL0-0.047-0.00111.590-0.066-0.0660.0000.0000.0000.000
107A107PRO00.0220.0219.1950.0630.0630.0000.0000.0000.000
108A108GLU-1-0.909-0.97111.735-0.065-0.0650.0000.0000.0000.000
109A109ASN0-0.086-0.05510.393-0.012-0.0120.0000.0000.0000.000
110A110ALA0-0.0170.0178.3020.2080.2080.0000.0000.0000.000
111A111ILE0-0.021-0.0166.4780.0830.0830.0000.0000.0000.000
112A112ILE00.0200.0199.6020.0140.0140.0000.0000.0000.000
113A113CYS0-0.062-0.01310.3940.0710.0710.0000.0000.0000.000
114A114ASN00.0320.01512.9300.0220.0220.0000.0000.0000.000
115A115THR00.0310.02313.4250.0220.0220.0000.0000.0000.000
116A116CYS0-0.0370.02015.733-0.014-0.0140.0000.0000.0000.000
117A117THR00.0510.01718.2970.0230.0230.0000.0000.0000.000
118A118ILE0-0.009-0.00420.785-0.022-0.0220.0000.0000.0000.000
119A119PRO00.0340.01720.0180.0300.0300.0000.0000.0000.000
120A120THR00.1050.04816.590-0.006-0.0060.0000.0000.0000.000
121A121PRO00.006-0.00319.148-0.014-0.0140.0000.0000.0000.000
122A122VAL0-0.041-0.01322.299-0.021-0.0210.0000.0000.0000.000
123A123LEU00.0360.01816.968-0.020-0.0200.0000.0000.0000.000
124A124TYR00.0210.01719.382-0.018-0.0180.0000.0000.0000.000
125A125ARG10.9720.96521.210-0.171-0.1710.0000.0000.0000.000
126A126SER0-0.087-0.03522.553-0.017-0.0170.0000.0000.0000.000
127A127LEU00.0620.02518.939-0.014-0.0140.0000.0000.0000.000
128A128GLU-1-0.922-0.94922.5260.1050.1050.0000.0000.0000.000
129A129GLY0-0.009-0.01624.464-0.005-0.0050.0000.0000.0000.000
130A130ILE00.0680.02220.917-0.008-0.0080.0000.0000.0000.000
131A131LEU00.0280.03017.552-0.010-0.0100.0000.0000.0000.000
132A132ARG10.8820.96120.940-0.086-0.0860.0000.0000.0000.000
133A133LEU0-0.039-0.01023.793-0.008-0.0080.0000.0000.0000.000
134A134LYS10.9280.95322.4660.0120.0120.0000.0000.0000.000
135A135ARG10.7850.87913.9020.0630.0630.0000.0000.0000.000
136A136ARG10.8900.92618.337-0.043-0.0430.0000.0000.0000.000
137A137ASP-1-0.736-0.82714.4250.0230.0230.0000.0000.0000.000
138A138VAL0-0.0030.00913.1210.0610.0610.0000.0000.0000.000
139A139GLY0-0.0050.01712.492-0.011-0.0110.0000.0000.0000.000
140A140ILE0-0.064-0.05312.9780.0350.0350.0000.0000.0000.000
141A141SER0-0.003-0.02011.4010.0260.0260.0000.0000.0000.000
142A142SER0-0.020-0.02612.450-0.067-0.0670.0000.0000.0000.000
143A143MET00.0100.0046.7040.0360.0360.0000.0000.0000.000
144A144HIS0-0.044-0.04611.615-0.043-0.0430.0000.0000.0000.000
145A145PRO0-0.067-0.00414.3140.0060.0060.0000.0000.0000.000
146A146THR00.0140.00615.583-0.032-0.0320.0000.0000.0000.000
147A147GLY00.0010.00218.029-0.040-0.0400.0000.0000.0000.000
148A148VAL00.0220.00718.4780.0260.0260.0000.0000.0000.000
149A149PRO00.0100.03314.472-0.007-0.0070.0000.0000.0000.000
150A150GLY00.1200.06016.165-0.041-0.0410.0000.0000.0000.000
151A151THR0-0.078-0.07717.679-0.035-0.0350.0000.0000.0000.000
152A152PRO00.0400.01818.5240.0370.0370.0000.0000.0000.000
153A153SER0-0.055-0.03419.4400.0160.0160.0000.0000.0000.000
154A154GLN0-0.0060.01613.659-0.051-0.0510.0000.0000.0000.000
155A155LYS10.9640.96515.493-0.255-0.2550.0000.0000.0000.000
156A156TYR00.0450.02914.3220.0270.0270.0000.0000.0000.000
157A157TYR00.0680.02310.8160.0290.0290.0000.0000.0000.000
158A158THR0-0.031-0.01412.638-0.026-0.0260.0000.0000.0000.000
159A159ILE0-0.024-0.0158.2760.0310.0310.0000.0000.0000.000
160A160ALA00.0080.01112.370-0.057-0.0570.0000.0000.0000.000
161A161GLY00.0540.01913.8460.0550.0550.0000.0000.0000.000
162A162LYS10.9320.96615.067-0.238-0.2380.0000.0000.0000.000
163A163ALA0-0.010-0.00718.004-0.007-0.0070.0000.0000.0000.000
164A164LEU00.0300.00121.310-0.006-0.0060.0000.0000.0000.000
165A165GLU-1-0.957-0.96724.0130.1290.1290.0000.0000.0000.000
166A166GLY0-0.013-0.00923.756-0.011-0.0110.0000.0000.0000.000
167A167LYS10.9010.96121.291-0.181-0.1810.0000.0000.0000.000
168A168GLU-1-0.896-0.95517.6160.2630.2630.0000.0000.0000.000
169A169TYR0-0.056-0.03817.029-0.036-0.0360.0000.0000.0000.000
170A170ALA00.0640.03712.2300.0170.0170.0000.0000.0000.000
171A171THR00.0380.03112.1490.0110.0110.0000.0000.0000.000
172A172GLU-1-0.859-0.94112.0240.4270.4270.0000.0000.0000.000
173A173ASP-1-0.879-0.9319.7420.5400.5400.0000.0000.0000.000
174A174GLN0-0.063-0.0377.8900.3760.3760.0000.0000.0000.000
175A175ILE00.007-0.0037.4330.3420.3420.0000.0000.0000.000
176A176ASN00.019-0.0087.5950.0070.0070.0000.0000.0000.000
177A177LYS10.8860.9522.895-2.665-3.4624.292-0.943-2.5510.003
178A178LEU0-0.004-0.0062.655-3.978-2.3030.517-0.951-1.241-0.013
179A179VAL00.001-0.0065.145-0.220-0.201-0.001-0.004-0.0140.000
180A180GLU-1-0.843-0.9413.4220.1200.3690.011-0.047-0.2120.000
181A181LEU0-0.0260.0032.297-1.803-0.5662.665-0.957-2.945-0.008
182A182VAL0-0.0180.0153.1591.3530.5500.1320.907-0.2350.000
183A183LYS10.8900.9416.511-0.414-0.4140.0000.0000.0000.000
184A184SER0-0.065-0.0204.5640.2980.397-0.001-0.012-0.0870.000
185A185VAL00.0110.0106.472-0.003-0.0030.0000.0000.0000.000
186A186GLY0-0.033-0.0158.741-0.164-0.1640.0000.0000.0000.000
187A187LYS10.8560.94510.144-0.702-0.7020.0000.0000.0000.000
188A188ILE0-0.009-0.01710.975-0.006-0.0060.0000.0000.0000.000
189A189PRO0-0.017-0.0028.9990.0070.0070.0000.0000.0000.000
190A190TYR00.000-0.01211.135-0.059-0.0590.0000.0000.0000.000
191A191VAL00.0290.01811.6090.0190.0190.0000.0000.0000.000
192A192THR0-0.013-0.00214.158-0.044-0.0440.0000.0000.0000.000
193A193PRO00.0070.01116.8910.0270.0270.0000.0000.0000.000
194A194ALA0-0.030-0.00518.112-0.023-0.0230.0000.0000.0000.000