Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 89JRY

Calculation Name: 4DEJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DEJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q5R0K1

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2461041.827762
FMO2-HF: Nuclear repulsion 2378626.681741
FMO2-HF: Total energy -82415.146021
FMO2-MP2: Total energy -82654.733008


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:7:LYS)


Summations of interaction energy for fragment #1(A:7:LYS)
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.
-155.724-154.475-0.004-0.572-0.6740.002
Interaction energy analysis for fragmet #1(A:7:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.022 / q_NPA : 0.995
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].
3A9SER00.002-0.0123.8361.8123.061-0.004-0.572-0.6740.002
4A10VAL0-0.0120.0026.0833.6773.6770.0000.0000.0000.000
5A11MET00.0350.0286.439-1.878-1.8780.0000.0000.0000.000
6A12THR00.0020.0026.290-1.680-1.6800.0000.0000.0000.000
7A13LEU0-0.015-0.0098.6720.9960.9960.0000.0000.0000.000
8A14TYR0-0.038-0.0518.848-0.348-0.3480.0000.0000.0000.000
9A15SER00.0340.00813.7541.2131.2130.0000.0000.0000.000
10A16GLY00.0420.01217.277-0.202-0.2020.0000.0000.0000.000
11A17LYS10.8270.88420.51013.87513.8750.0000.0000.0000.000
12A18ASP-1-0.768-0.87022.883-10.400-10.4000.0000.0000.0000.000
13A19ASP-1-0.775-0.83821.881-12.317-12.3170.0000.0000.0000.000
14A20LEU00.0130.01324.027-0.258-0.2580.0000.0000.0000.000
15A21LYS10.8540.89123.14010.76210.7620.0000.0000.0000.000
16A22SER0-0.005-0.05019.705-0.544-0.5440.0000.0000.0000.000
17A23HIS0-0.0120.03020.664-0.192-0.1920.0000.0000.0000.000
18A24GLN00.0220.00723.330-0.310-0.3100.0000.0000.0000.000
19A25VAL0-0.028-0.01116.946-0.041-0.0410.0000.0000.0000.000
20A26ARG10.7560.83818.56513.17113.1710.0000.0000.0000.000
21A27LEU00.0020.00720.141-0.019-0.0190.0000.0000.0000.000
22A28VAL00.014-0.00420.3150.0770.0770.0000.0000.0000.000
23A29LEU0-0.028-0.02015.229-0.106-0.1060.0000.0000.0000.000
24A30ALA00.0220.02218.949-0.152-0.1520.0000.0000.0000.000
25A31GLU-1-0.822-0.86821.648-10.166-10.1660.0000.0000.0000.000
26A32LYS10.7020.83819.54912.03412.0340.0000.0000.0000.000
27A33GLY0-0.0020.01420.656-0.144-0.1440.0000.0000.0000.000
28A34VAL0-0.060-0.02115.338-0.464-0.4640.0000.0000.0000.000
29A35GLY0-0.009-0.00314.562-0.045-0.0450.0000.0000.0000.000
30A36VAL0-0.037-0.03211.480-0.773-0.7730.0000.0000.0000.000
31A37GLU-1-0.835-0.8898.032-35.735-35.7350.0000.0000.0000.000
32A38ILE0-0.003-0.00710.976-0.413-0.4130.0000.0000.0000.000
33A39THR00.0040.01310.463-0.018-0.0180.0000.0000.0000.000
34A40TYR0-0.005-0.01613.3650.7580.7580.0000.0000.0000.000
35A41VAL0-0.024-0.00715.612-0.632-0.6320.0000.0000.0000.000
36A42THR0-0.018-0.02318.3880.5840.5840.0000.0000.0000.000
37A43ASP-1-0.829-0.90521.457-12.964-12.9640.0000.0000.0000.000
38A44GLU-1-0.957-0.96923.318-11.567-11.5670.0000.0000.0000.000
39A45SER0-0.089-0.05119.097-0.402-0.4020.0000.0000.0000.000
40A46THR00.0280.02417.358-0.159-0.1590.0000.0000.0000.000
41A47PRO0-0.001-0.00911.9690.2070.2070.0000.0000.0000.000
42A48GLU-1-0.878-0.93211.501-22.315-22.3150.0000.0000.0000.000
43A49ASP-1-0.827-0.9038.452-27.829-27.8290.0000.0000.0000.000
44A50LEU0-0.010-0.00310.2870.4420.4420.0000.0000.0000.000
45A51LEU0-0.005-0.01212.6260.9800.9800.0000.0000.0000.000
46A52GLN0-0.120-0.05310.370-0.319-0.3190.0000.0000.0000.000
47A53LEU0-0.036-0.0067.6190.3020.3020.0000.0000.0000.000
48A54ASN0-0.030-0.03412.2221.3861.3860.0000.0000.0000.000
49A55PRO00.0010.01615.7360.0830.0830.0000.0000.0000.000
50A56TYR0-0.047-0.02118.8541.0691.0690.0000.0000.0000.000
51A57PRO0-0.030-0.03120.971-0.306-0.3060.0000.0000.0000.000
52A58GLU-1-0.803-0.89022.207-12.767-12.7670.0000.0000.0000.000
53A59ALA0-0.0010.00617.138-0.177-0.1770.0000.0000.0000.000
54A60LYS10.7410.89116.81911.85111.8510.0000.0000.0000.000
55A61PRO0-0.0020.00417.3810.6210.6210.0000.0000.0000.000
56A62THR0-0.025-0.03912.2800.5680.5680.0000.0000.0000.000
57A63LEU0-0.043-0.01411.342-0.816-0.8160.0000.0000.0000.000
58A64VAL00.0400.0106.0860.4230.4230.0000.0000.0000.000
59A65ASP-1-0.790-0.8826.898-23.807-23.8070.0000.0000.0000.000
60A66ARG10.7660.8684.85628.52028.5200.0000.0000.0000.000
61A67GLU-1-0.883-0.9425.446-31.033-31.0330.0000.0000.0000.000
62A68LEU0-0.069-0.0057.6081.5001.5000.0000.0000.0000.000
63A69VAL00.0240.0058.926-1.288-1.2880.0000.0000.0000.000
64A70LEU0-0.036-0.01311.1351.2771.2770.0000.0000.0000.000
65A71TYR00.0750.02514.452-0.112-0.1120.0000.0000.0000.000
66A72ASN00.0150.00817.1570.5180.5180.0000.0000.0000.000
67A73ALA00.0820.03719.825-0.321-0.3210.0000.0000.0000.000
68A74GLN00.0100.00221.1370.0020.0020.0000.0000.0000.000
69A75ILE0-0.018-0.00618.4920.0390.0390.0000.0000.0000.000
70A76ILE0-0.0020.00515.737-0.261-0.2610.0000.0000.0000.000
71A77MET0-0.022-0.00417.992-0.147-0.1470.0000.0000.0000.000
72A78GLU-1-0.754-0.85720.766-10.194-10.1940.0000.0000.0000.000
73A79TYR00.0110.02212.1430.1700.1700.0000.0000.0000.000
74A80LEU0-0.014-0.02115.134-0.167-0.1670.0000.0000.0000.000
75A81ASP-1-0.815-0.90918.497-10.769-10.7690.0000.0000.0000.000
76A82GLU-1-0.914-0.95321.415-10.724-10.7240.0000.0000.0000.000
77A83ARG10.8000.89711.51217.80117.8010.0000.0000.0000.000
78A84PHE0-0.013-0.01913.976-0.489-0.4890.0000.0000.0000.000
79A85PRO00.0080.00820.0480.3200.3200.0000.0000.0000.000
80A86HIS0-0.0460.00223.1970.5770.5770.0000.0000.0000.000
81A87PRO00.0780.04023.418-0.398-0.3980.0000.0000.0000.000
82A88PRO00.0040.00825.578-0.325-0.3250.0000.0000.0000.000
83A89LEU00.0330.01624.1030.2040.2040.0000.0000.0000.000
84A90MET0-0.047-0.01826.9120.2880.2880.0000.0000.0000.000
85A91PRO00.0130.01029.3590.0310.0310.0000.0000.0000.000
86A92VAL00.0390.02431.580-0.160-0.1600.0000.0000.0000.000
87A93TYR00.0170.00633.153-0.056-0.0560.0000.0000.0000.000
88A94PRO00.0510.01234.093-0.045-0.0450.0000.0000.0000.000
89A95VAL00.0380.02235.160-0.098-0.0980.0000.0000.0000.000
90A96ALA00.0470.04235.9930.0040.0040.0000.0000.0000.000
91A97ARG10.8680.94426.5829.6769.6760.0000.0000.0000.000
92A98GLY00.0130.00332.301-0.168-0.1680.0000.0000.0000.000
93A99THR0-0.014-0.02234.4100.0240.0240.0000.0000.0000.000
94A100SER00.015-0.01231.677-0.009-0.0090.0000.0000.0000.000
95A101ARG10.8470.89126.6129.7429.7420.0000.0000.0000.000
96A102LEU0-0.031-0.00331.433-0.073-0.0730.0000.0000.0000.000
97A103MET0-0.010-0.00634.4320.0980.0980.0000.0000.0000.000
98A104MET00.0080.01627.768-0.088-0.0880.0000.0000.0000.000
99A105TYR00.0180.01731.0550.0680.0680.0000.0000.0000.000
100A106ARG10.8520.89532.1257.3797.3790.0000.0000.0000.000
101A107ILE00.0120.02832.0890.0640.0640.0000.0000.0000.000
102A108GLU-1-0.823-0.89627.608-10.220-10.2200.0000.0000.0000.000
103A109ARG10.8980.94331.4447.8617.8610.0000.0000.0000.000
104A110ASP-1-0.827-0.88534.304-7.531-7.5310.0000.0000.0000.000
105A111TRP0-0.007-0.00735.3450.1000.1000.0000.0000.0000.000
106A112TYR00.009-0.02327.451-0.132-0.1320.0000.0000.0000.000
107A113SER0-0.036-0.03132.683-0.059-0.0590.0000.0000.0000.000
108A114LEU0-0.020-0.00934.4470.0890.0890.0000.0000.0000.000
109A115ALA00.0360.01532.8180.0830.0830.0000.0000.0000.000
110A116GLU-1-0.826-0.90231.534-9.576-9.5760.0000.0000.0000.000
111A117LYS10.7890.89733.6017.4627.4620.0000.0000.0000.000
112A118ILE0-0.023-0.01236.9320.0900.0900.0000.0000.0000.000
113A119GLN0-0.022-0.01930.9390.0560.0560.0000.0000.0000.000
114A120LYS10.7870.91632.4469.0589.0580.0000.0000.0000.000
115A121ASN0-0.014-0.03136.9980.1750.1750.0000.0000.0000.000
116A122ASP-1-0.830-0.91240.454-6.961-6.9610.0000.0000.0000.000
117A123ALA00.012-0.00142.250-0.071-0.0710.0000.0000.0000.000
118A124GLN0-0.028-0.01445.0630.1890.1890.0000.0000.0000.000
119A125ALA00.0310.01740.0130.0220.0220.0000.0000.0000.000
120A126ARG10.8550.93440.0747.4277.4270.0000.0000.0000.000
121A127GLN0-0.067-0.03042.6840.0240.0240.0000.0000.0000.000
122A128GLU-1-0.817-0.91342.719-7.152-7.1520.0000.0000.0000.000
123A129LEU00.0230.00637.070-0.012-0.0120.0000.0000.0000.000
124A130LYS10.8210.91041.2666.5716.5710.0000.0000.0000.000
125A131GLU-1-0.872-0.93643.833-6.214-6.2140.0000.0000.0000.000
126A132GLY0-0.0150.01242.0740.0600.0600.0000.0000.0000.000
127A133ILE00.009-0.01138.3450.0090.0090.0000.0000.0000.000
128A134LEU0-0.035-0.02041.9370.0290.0290.0000.0000.0000.000
129A135SER0-0.062-0.04445.4380.0850.0850.0000.0000.0000.000
130A136LEU0-0.009-0.01040.8260.0570.0570.0000.0000.0000.000
131A137ALA0-0.0250.00643.686-0.045-0.0450.0000.0000.0000.000
132A138PRO0-0.019-0.01745.318-0.018-0.0180.0000.0000.0000.000
133A139ILE00.0340.02539.8540.0120.0120.0000.0000.0000.000
134A140PHE0-0.047-0.02938.121-0.112-0.1120.0000.0000.0000.000
135A141ALA0-0.082-0.03943.020-0.003-0.0030.0000.0000.0000.000
136A142ASP-1-0.933-0.95344.705-6.320-6.3200.0000.0000.0000.000
137A143THR0-0.032-0.01740.4860.0300.0300.0000.0000.0000.000
138A144PRO0-0.050-0.00139.354-0.053-0.0530.0000.0000.0000.000
139A145TYR0-0.006-0.00534.470-0.240-0.2400.0000.0000.0000.000
140A146PHE00.030-0.00835.2600.2150.2150.0000.0000.0000.000
141A147MET0-0.037-0.01436.632-0.128-0.1280.0000.0000.0000.000
142A148SER0-0.039-0.02935.0050.0240.0240.0000.0000.0000.000
143A149GLU-1-0.855-0.94637.820-7.081-7.0810.0000.0000.0000.000
144A150GLU-1-0.993-0.99833.726-8.493-8.4930.0000.0000.0000.000
145A151PHE0-0.028-0.00427.5950.0550.0550.0000.0000.0000.000
146A152SER00.020-0.00629.845-0.180-0.1800.0000.0000.0000.000
147A153LEU00.042-0.00624.099-0.139-0.1390.0000.0000.0000.000
148A154VAL00.0020.00227.867-0.085-0.0850.0000.0000.0000.000
149A155ASP-1-0.706-0.81631.165-8.566-8.5660.0000.0000.0000.000
150A156CYS0-0.065-0.01925.876-0.145-0.1450.0000.0000.0000.000
151A157TYR00.002-0.00726.353-0.387-0.3870.0000.0000.0000.000
152A158LEU00.0050.02129.4520.0510.0510.0000.0000.0000.000
153A159ALA00.0140.01229.6130.0710.0710.0000.0000.0000.000
154A160PRO00.002-0.00526.8620.1130.1130.0000.0000.0000.000
155A161LEU0-0.0030.01429.2900.0130.0130.0000.0000.0000.000
156A162LEU00.006-0.02332.4100.1800.1800.0000.0000.0000.000
157A163TRP0-0.035-0.03230.8500.2790.2790.0000.0000.0000.000
158A164ARG10.7610.85526.33310.74610.7460.0000.0000.0000.000
159A165LEU0-0.0180.00633.8580.1340.1340.0000.0000.0000.000
160A166PRO00.0450.01336.7920.1630.1630.0000.0000.0000.000
161A167ALA00.0210.01635.1490.1400.1400.0000.0000.0000.000
162A168TYR0-0.036-0.01731.8240.0160.0160.0000.0000.0000.000
163A169GLY00.0020.01338.0250.1560.1560.0000.0000.0000.000
164A170ILE0-0.063-0.03439.7750.2110.2110.0000.0000.0000.000
165A171ASP-1-0.837-0.90941.716-7.094-7.0940.0000.0000.0000.000
166A172LEU0-0.071-0.04744.2480.0910.0910.0000.0000.0000.000
167A173GLU-1-0.859-0.92445.765-6.115-6.1150.0000.0000.0000.000
168A174GLY00.0240.01549.213-0.009-0.0090.0000.0000.0000.000
169A175GLN0-0.026-0.02151.181-0.057-0.0570.0000.0000.0000.000
170A176GLY00.0540.02748.615-0.053-0.0530.0000.0000.0000.000
171A177ALA00.0400.01046.278-0.153-0.1530.0000.0000.0000.000
172A178LYS10.8170.90745.7456.1546.1540.0000.0000.0000.000
173A179GLU-1-0.805-0.90345.281-6.407-6.4070.0000.0000.0000.000
174A180ILE00.0460.03440.867-0.174-0.1740.0000.0000.0000.000
175A181LYS10.9640.97741.0487.1007.1000.0000.0000.0000.000
176A182GLN0-0.018-0.01441.511-0.060-0.0600.0000.0000.0000.000
177A183TYR0-0.036-0.03834.841-0.107-0.1070.0000.0000.0000.000
178A184MET0-0.022-0.01937.069-0.115-0.1150.0000.0000.0000.000
179A185VAL0-0.029-0.00436.614-0.208-0.2080.0000.0000.0000.000
180A186ARG10.8690.93037.1147.3227.3220.0000.0000.0000.000
181A187LEU0-0.0140.00332.684-0.230-0.2300.0000.0000.0000.000
182A188PHE0-0.041-0.02832.373-0.262-0.2620.0000.0000.0000.000
183A189GLU-1-0.924-0.95433.101-8.158-8.1580.0000.0000.0000.000
184A190ARG10.7780.87029.0649.6089.6080.0000.0000.0000.000
185A191LYS10.9250.95828.8429.1589.1580.0000.0000.0000.000
186A192THR00.037-0.00325.339-0.110-0.1100.0000.0000.0000.000
187A193PHE00.0350.01725.302-0.394-0.3940.0000.0000.0000.000
188A194GLN0-0.013-0.00227.040-0.278-0.2780.0000.0000.0000.000
189A195ASP-1-0.909-0.95923.670-11.870-11.8700.0000.0000.0000.000
190A196SER0-0.102-0.05722.394-0.486-0.4860.0000.0000.0000.000
191A197LEU0-0.0240.01322.940-0.335-0.3350.0000.0000.0000.000
192A198THR0-0.013-0.02922.086-0.222-0.2220.0000.0000.0000.000
193A199GLU-1-0.833-0.92624.291-12.068-12.0680.0000.0000.0000.000
194A200GLU-1-0.779-0.87724.875-12.495-12.4950.0000.0000.0000.000
195A201GLU-1-0.677-0.79425.063-11.679-11.6790.0000.0000.0000.000
196A202LYS10.7900.89025.18312.52612.5260.0000.0000.0000.000
197A203GLU-1-0.899-0.94530.677-9.607-9.6070.0000.0000.0000.000
198A204LEU0-0.011-0.00330.8480.3880.3880.0000.0000.0000.000
199A205ALA0-0.0080.00133.8320.2870.2870.0000.0000.0000.000
200A206ARG10.7590.88031.7199.7859.7850.0000.0000.0000.000
201A207ASN0-0.027-0.00935.1170.3510.3510.0000.0000.0000.000
202A208ALA0-0.0060.01238.3240.1160.1160.0000.0000.0000.000