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: 3JMRL

Calculation Name: 3E7D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E7D

Chain ID: A

ChEMBL ID:

UniProt ID: Q2YRF5

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 OptHSide
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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2066835.224815
FMO2-HF: Nuclear repulsion 1992958.100373
FMO2-HF: Total energy -73877.124442
FMO2-MP2: Total energy -74093.340324


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:4:TYR)


Summations of interaction energy for fragment #1(A:4:TYR)
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.
-18.576-10.6686.656-5.067-9.4980.024
Interaction energy analysis for fragmet #1(A:4:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.023
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].
3A6ARG10.9440.9652.387-19.266-11.6476.657-5.036-9.2400.024
4A7ASP-1-0.832-0.9074.406-1.178-0.9510.000-0.027-0.2000.000
5A8GLY00.0380.0147.654-0.066-0.0660.0000.0000.0000.000
6A9GLN0-0.025-0.0259.2050.0950.0950.0000.0000.0000.000
7A10ALA00.0380.0198.8500.1140.1140.0000.0000.0000.000
8A11ILE0-0.051-0.0314.7040.1070.169-0.001-0.004-0.0580.000
9A12TYR0-0.0050.0168.7410.3040.3040.0000.0000.0000.000
10A13ASP-1-0.792-0.89812.185-0.576-0.5760.0000.0000.0000.000
11A14ARG10.9100.9607.2500.5940.5940.0000.0000.0000.000
12A15SER0-0.025-0.02211.3670.1500.1500.0000.0000.0000.000
13A16PHE00.014-0.00612.7140.1120.1120.0000.0000.0000.000
14A17ALA0-0.027-0.00414.4110.0670.0670.0000.0000.0000.000
15A18ILE0-0.019-0.00410.5940.0360.0360.0000.0000.0000.000
16A19ILE00.0060.01115.1890.0440.0440.0000.0000.0000.000
17A20ARG10.7900.85517.8500.3180.3180.0000.0000.0000.000
18A21ALA0-0.051-0.00817.6710.0220.0220.0000.0000.0000.000
19A22GLU-1-0.943-0.97215.831-0.044-0.0440.0000.0000.0000.000
20A23ALA0-0.020-0.02020.1480.0180.0180.0000.0000.0000.000
21A24ASP-1-0.815-0.87922.736-0.071-0.0710.0000.0000.0000.000
22A25LEU0-0.017-0.02823.581-0.004-0.0040.0000.0000.0000.000
23A26ARG10.8530.91527.7110.0620.0620.0000.0000.0000.000
24A27HIS0-0.028-0.01029.6950.0040.0040.0000.0000.0000.000
25A28ILE0-0.020-0.00628.377-0.002-0.0020.0000.0000.0000.000
26A29PRO00.0580.04131.463-0.003-0.0030.0000.0000.0000.000
27A30ALA00.0620.01931.514-0.011-0.0110.0000.0000.0000.000
28A31ASP-1-0.908-0.95631.026-0.146-0.1460.0000.0000.0000.000
29A32LEU00.020-0.00530.561-0.012-0.0120.0000.0000.0000.000
30A33GLU-1-0.771-0.83824.798-0.244-0.2440.0000.0000.0000.000
31A34LYS10.9900.97924.6930.2390.2390.0000.0000.0000.000
32A35LEU0-0.010-0.00724.233-0.024-0.0240.0000.0000.0000.000
33A36ALA00.0310.01824.949-0.011-0.0110.0000.0000.0000.000
34A37VAL0-0.003-0.00320.032-0.010-0.0100.0000.0000.0000.000
35A38ARG10.8740.93218.8560.4200.4200.0000.0000.0000.000
36A39VAL00.0230.00320.572-0.026-0.0260.0000.0000.0000.000
37A40ILE00.0320.02818.388-0.004-0.0040.0000.0000.0000.000
38A41HIS0-0.053-0.02613.6960.0470.0470.0000.0000.0000.000
39A42ALA0-0.052-0.01716.290-0.037-0.0370.0000.0000.0000.000
40A43CYS0-0.127-0.05418.2050.0030.0030.0000.0000.0000.000
41A44GLY00.0180.02216.2080.0250.0250.0000.0000.0000.000
42A45MET0-0.0080.00216.8350.0490.0490.0000.0000.0000.000
43A46VAL00.0990.04418.455-0.012-0.0120.0000.0000.0000.000
44A47ASP-1-0.834-0.90121.023-0.077-0.0770.0000.0000.0000.000
45A48VAL00.0040.00023.1040.0060.0060.0000.0000.0000.000
46A49ALA0-0.002-0.01224.842-0.001-0.0010.0000.0000.0000.000
47A50ASN0-0.041-0.02626.581-0.001-0.0010.0000.0000.0000.000
48A51ASP-1-0.860-0.91528.663-0.071-0.0710.0000.0000.0000.000
49A52LEU0-0.076-0.01226.785-0.005-0.0050.0000.0000.0000.000
50A53ALA00.0070.00430.7740.0090.0090.0000.0000.0000.000
51A54PHE0-0.018-0.02732.696-0.011-0.0110.0000.0000.0000.000
52A55SER00.0400.04936.2080.0060.0060.0000.0000.0000.000
53A56GLU-1-0.863-0.95238.097-0.098-0.0980.0000.0000.0000.000
54A57GLY0-0.0060.00337.9910.0010.0010.0000.0000.0000.000
55A58ALA00.005-0.00235.688-0.004-0.0040.0000.0000.0000.000
56A59GLY00.0420.01533.497-0.007-0.0070.0000.0000.0000.000
57A60LYS10.8660.91034.1420.1100.1100.0000.0000.0000.000
58A61ALA0-0.0150.00536.610-0.002-0.0020.0000.0000.0000.000
59A62GLY00.0580.01834.647-0.001-0.0010.0000.0000.0000.000
60A63ARG10.8610.93628.7190.1960.1960.0000.0000.0000.000
61A64ASN0-0.016-0.01734.1900.0040.0040.0000.0000.0000.000
62A65ALA00.0780.05337.3450.0010.0010.0000.0000.0000.000
63A66LEU0-0.012-0.00631.321-0.001-0.0010.0000.0000.0000.000
64A67LEU0-0.028-0.01833.768-0.003-0.0030.0000.0000.0000.000
65A68ALA0-0.027-0.00136.3220.0020.0020.0000.0000.0000.000
66A69GLY00.0290.01937.5430.0060.0060.0000.0000.0000.000
67A70ALA0-0.053-0.00737.4360.0010.0010.0000.0000.0000.000
68A71PRO00.0040.01036.500-0.012-0.0120.0000.0000.0000.000
69A72ILE00.016-0.01131.0330.0010.0010.0000.0000.0000.000
70A73LEU0-0.014-0.00434.784-0.005-0.0050.0000.0000.0000.000
71A74CYS0-0.0160.00432.047-0.006-0.0060.0000.0000.0000.000
72A75ASP-1-0.718-0.86232.899-0.142-0.1420.0000.0000.0000.000
73A76ALA0-0.029-0.02430.8620.0070.0070.0000.0000.0000.000
74A77ARG10.8850.93526.9820.2030.2030.0000.0000.0000.000
75A78MET00.016-0.00225.380-0.012-0.0120.0000.0000.0000.000
76A79VAL0-0.043-0.00726.034-0.020-0.0200.0000.0000.0000.000
77A80ALA00.0430.00927.521-0.013-0.0130.0000.0000.0000.000
78A81GLU-1-0.874-0.93125.132-0.255-0.2550.0000.0000.0000.000
79A82GLY00.0020.01923.184-0.028-0.0280.0000.0000.0000.000
80A83ILE0-0.025-0.01423.397-0.024-0.0240.0000.0000.0000.000
81A84THR0-0.038-0.02121.773-0.022-0.0220.0000.0000.0000.000
82A85ARG11.0280.98524.2810.2460.2460.0000.0000.0000.000
83A86SER00.0160.01623.0230.0150.0150.0000.0000.0000.000
84A87ARG10.8060.89922.0110.3580.3580.0000.0000.0000.000
85A88LEU0-0.069-0.02426.1090.0120.0120.0000.0000.0000.000
86A89PRO0-0.033-0.00529.710-0.002-0.0020.0000.0000.0000.000
87A90ALA00.0190.00632.1900.0060.0060.0000.0000.0000.000
88A91ASP-1-0.919-0.93733.835-0.183-0.1830.0000.0000.0000.000
89A92ASN0-0.074-0.04533.127-0.002-0.0020.0000.0000.0000.000
90A93ARG10.9650.97933.7130.1340.1340.0000.0000.0000.000
91A94VAL0-0.012-0.00130.3890.0020.0020.0000.0000.0000.000
92A95ILE0-0.038-0.01833.7670.0010.0010.0000.0000.0000.000
93A96TYR00.005-0.01133.882-0.003-0.0030.0000.0000.0000.000
94A97THR00.0300.00335.979-0.002-0.0020.0000.0000.0000.000
95A98LEU00.0010.01235.3860.0070.0070.0000.0000.0000.000
96A99SER0-0.030-0.02336.0750.0020.0020.0000.0000.0000.000
97A100ASP-1-0.801-0.85938.423-0.096-0.0960.0000.0000.0000.000
98A101PRO00.010-0.00141.8110.0030.0030.0000.0000.0000.000
99A102SER0-0.043-0.04544.1970.0050.0050.0000.0000.0000.000
100A103VAL00.0230.00341.8100.0050.0050.0000.0000.0000.000
101A104PRO0-0.044-0.03443.4550.0030.0030.0000.0000.0000.000
102A105GLU-1-0.790-0.88645.751-0.058-0.0580.0000.0000.0000.000
103A106LEU00.0290.01446.6190.0040.0040.0000.0000.0000.000
104A107ALA0-0.023-0.01645.4440.0010.0010.0000.0000.0000.000
105A108LYS10.7930.87547.4790.0630.0630.0000.0000.0000.000
106A109LYS10.8920.97650.5100.0690.0690.0000.0000.0000.000
107A110ILE0-0.049-0.02046.9060.0020.0020.0000.0000.0000.000
108A111GLY00.0060.02450.5140.0010.0010.0000.0000.0000.000
109A112ASN00.0660.04144.846-0.002-0.0020.0000.0000.0000.000
110A113THR00.002-0.00541.388-0.002-0.0020.0000.0000.0000.000
111A114ARG11.0160.98640.7440.0820.0820.0000.0000.0000.000
112A115SER00.003-0.01137.203-0.001-0.0010.0000.0000.0000.000
113A116ALA00.0020.01739.558-0.004-0.0040.0000.0000.0000.000
114A117ALA00.0560.02042.4540.0000.0000.0000.0000.0000.000
115A118ALA0-0.0140.00040.3560.0000.0000.0000.0000.0000.000
116A119LEU00.0340.01639.747-0.003-0.0030.0000.0000.0000.000
117A120ASP-1-0.822-0.89043.040-0.076-0.0760.0000.0000.0000.000
118A121LEU0-0.054-0.03743.2070.0000.0000.0000.0000.0000.000
119A122TRP0-0.037-0.03137.285-0.004-0.0040.0000.0000.0000.000
120A123LEU00.0250.02143.155-0.002-0.0020.0000.0000.0000.000
121A124PRO0-0.045-0.02545.6100.0010.0010.0000.0000.0000.000
122A125HIS0-0.028-0.02341.737-0.004-0.0040.0000.0000.0000.000
123A126ILE0-0.0120.00642.253-0.006-0.0060.0000.0000.0000.000
124A127GLU-1-0.891-0.92942.843-0.091-0.0910.0000.0000.0000.000
125A128GLY00.0060.00842.902-0.003-0.0030.0000.0000.0000.000
126A129SER0-0.093-0.06438.961-0.008-0.0080.0000.0000.0000.000
127A130ILE0-0.0120.00533.1600.0020.0020.0000.0000.0000.000
128A131VAL00.0180.01936.031-0.004-0.0040.0000.0000.0000.000
129A132ALA00.010-0.00331.267-0.003-0.0030.0000.0000.0000.000
130A133ILE0-0.015-0.01133.327-0.002-0.0020.0000.0000.0000.000
131A134GLY00.0310.00429.9780.0000.0000.0000.0000.0000.000
132A135ASN0-0.118-0.07030.0040.0000.0000.0000.0000.0000.000
133A136ALA00.0120.00032.1150.0080.0080.0000.0000.0000.000
134A137PRO00.0520.02735.416-0.001-0.0010.0000.0000.0000.000
135A138THR0-0.020-0.02037.8350.0010.0010.0000.0000.0000.000
136A139ALA0-0.0100.00337.9010.0030.0030.0000.0000.0000.000
137A140LEU0-0.013-0.00237.1110.0000.0000.0000.0000.0000.000
138A141PHE00.0410.00240.0630.0020.0020.0000.0000.0000.000
139A142ARG10.8110.89943.0840.0750.0750.0000.0000.0000.000
140A143LEU0-0.007-0.01440.2570.0010.0010.0000.0000.0000.000
141A144PHE00.004-0.00141.3230.0010.0010.0000.0000.0000.000
142A145GLU-1-0.835-0.90546.012-0.064-0.0640.0000.0000.0000.000
143A146LEU0-0.052-0.02345.0930.0020.0020.0000.0000.0000.000
144A147LEU0-0.033-0.02143.9780.0010.0010.0000.0000.0000.000
145A148ASP-1-0.825-0.88148.415-0.062-0.0620.0000.0000.0000.000
146A149ALA0-0.066-0.02051.3520.0030.0030.0000.0000.0000.000
147A150GLY0-0.038-0.02151.8150.0010.0010.0000.0000.0000.000
148A151ALA0-0.048-0.01747.823-0.001-0.0010.0000.0000.0000.000
149A152PRO00.0100.00547.2620.0000.0000.0000.0000.0000.000
150A153LYS10.9090.94645.6440.0740.0740.0000.0000.0000.000
151A154PRO0-0.0180.00140.299-0.002-0.0020.0000.0000.0000.000
152A155ALA0-0.004-0.00239.3120.0050.0050.0000.0000.0000.000
153A156LEU0-0.069-0.03533.9630.0000.0000.0000.0000.0000.000
154A157ILE0-0.0020.00837.247-0.004-0.0040.0000.0000.0000.000
155A158ILE0-0.025-0.01530.5440.0000.0000.0000.0000.0000.000
156A159GLY00.0350.00833.870-0.002-0.0020.0000.0000.0000.000
157A160MET0-0.034-0.02728.707-0.002-0.0020.0000.0000.0000.000
158A161PRO0-0.0010.01730.157-0.008-0.0080.0000.0000.0000.000
159A162VAL00.0310.02127.5770.0050.0050.0000.0000.0000.000
160A163GLY00.000-0.01130.7390.0040.0040.0000.0000.0000.000
161A164PHE0-0.038-0.04830.3690.0040.0040.0000.0000.0000.000
162A165VAL00.0080.00035.1760.0060.0060.0000.0000.0000.000
163A166GLY00.0650.04238.163-0.005-0.0050.0000.0000.0000.000
164A167ALA0-0.023-0.00433.876-0.003-0.0030.0000.0000.0000.000
165A168ALA0-0.001-0.00335.576-0.004-0.0040.0000.0000.0000.000
166A169GLU-1-0.828-0.92336.510-0.060-0.0600.0000.0000.0000.000
167A170SER0-0.026-0.01137.805-0.003-0.0030.0000.0000.0000.000
168A171LYS10.8030.89631.7790.1010.1010.0000.0000.0000.000
169A172ASP-1-0.798-0.86537.525-0.067-0.0670.0000.0000.0000.000
170A173GLU-1-0.836-0.90739.774-0.061-0.0610.0000.0000.0000.000
171A174LEU0-0.044-0.01737.4480.0000.0000.0000.0000.0000.000
172A175ALA0-0.029-0.02438.7570.0000.0000.0000.0000.0000.000
173A176ALA0-0.0260.00340.7230.0020.0020.0000.0000.0000.000
174A177ASN00.0250.00244.1900.0010.0010.0000.0000.0000.000
175A178SER00.0120.01842.3770.0010.0010.0000.0000.0000.000
176A179ARG10.7340.82544.0150.0630.0630.0000.0000.0000.000
177A180GLY00.0050.00546.5700.0000.0000.0000.0000.0000.000
178A181VAL0-0.051-0.01741.304-0.002-0.0020.0000.0000.0000.000
179A182PRO00.0230.02139.4030.0010.0010.0000.0000.0000.000
180A183TYR00.0140.00137.026-0.005-0.0050.0000.0000.0000.000
181A184VAL0-0.001-0.00931.108-0.001-0.0010.0000.0000.0000.000
182A185ILE0-0.0160.00232.844-0.004-0.0040.0000.0000.0000.000
183A186VAL00.0160.01227.522-0.004-0.0040.0000.0000.0000.000
184A187ARG10.8290.87530.7620.0700.0700.0000.0000.0000.000
185A188GLY00.0580.03231.337-0.001-0.0010.0000.0000.0000.000
186A189ARG10.9720.97131.0110.0400.0400.0000.0000.0000.000
187A190ARG10.7690.85324.3900.0790.0790.0000.0000.0000.000
188A191GLY00.0710.01426.6840.0040.0040.0000.0000.0000.000
189A192GLY00.0370.01925.915-0.006-0.0060.0000.0000.0000.000
190A193SER00.007-0.01325.356-0.005-0.0050.0000.0000.0000.000
191A194ALA00.0270.02020.838-0.009-0.0090.0000.0000.0000.000
192A195MET00.0270.02822.890-0.013-0.0130.0000.0000.0000.000
193A196THR00.0450.00924.3450.0010.0010.0000.0000.0000.000
194A197ALA00.0230.01324.0080.0020.0020.0000.0000.0000.000
195A198ALA0-0.045-0.00922.030-0.012-0.0120.0000.0000.0000.000
196A199ALA00.0410.01223.665-0.006-0.0060.0000.0000.0000.000
197A200VAL00.0340.01627.0360.0030.0030.0000.0000.0000.000
198A201ASN00.0150.00023.3700.0010.0010.0000.0000.0000.000
199A202ALA0-0.0140.01024.866-0.011-0.0110.0000.0000.0000.000
200A203LEU0-0.056-0.01825.7720.0040.0040.0000.0000.0000.000
201A204ALA00.0040.01627.5100.0110.0110.0000.0000.0000.000
202A205SER0-0.023-0.00725.649-0.006-0.0060.0000.0000.0000.000