FMO DATABASE

FMODB ID: VQZ91

Calculation Name: 5DJN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DJN

Chain ID: A

ChEMBL ID:

UniProt ID: F8VQ75

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	77
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-356650.184662
FMO2-HF: Nuclear repulsion	325115.682151
FMO2-HF: Total energy	-31534.502512
FMO2-MP2: Total energy	-31626.525277

3D Structure

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:363:PRO)

Summations of interaction energy for fragment #1(A:363:PRO)

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.
-2.365	1.13	1.841	-1.917	-3.418	0.001

Interaction energy analysis for fragmet #1(A:363:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.024

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 ES EX CT+mix DI(MP2)

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].
3	A	365	ALA	0	0.000	0.005	2.032	-2.219	0.088	1.727	-1.670	-2.364	0.003
4	A	366	LYS	1	0.807	0.898	2.764	-1.098	-0.048	0.115	-0.232	-0.932	-0.002
5	A	367	VAL	0	0.100	0.061	4.548	0.361	0.499	-0.001	-0.015	-0.122	0.000
6	A	368	ILE	0	0.004	-0.006	6.819	0.156	0.156	0.000	0.000	0.000	0.000
7	A	369	ARG	1	0.731	0.820	7.370	0.174	0.174	0.000	0.000	0.000	0.000
8	A	370	GLU	-1	-0.675	-0.845	8.709	-0.039	-0.039	0.000	0.000	0.000	0.000
9	A	371	LEU	0	0.014	0.022	11.298	0.046	0.046	0.000	0.000	0.000	0.000
10	A	372	ARG	1	0.921	0.953	11.885	0.286	0.286	0.000	0.000	0.000	0.000
11	A	373	GLU	-1	-0.779	-0.852	12.252	-0.064	-0.064	0.000	0.000	0.000	0.000
12	A	374	GLU	-1	-0.868	-0.939	15.056	-0.048	-0.048	0.000	0.000	0.000	0.000
13	A	375	VAL	0	-0.057	-0.039	16.887	0.014	0.014	0.000	0.000	0.000	0.000
14	A	376	GLU	-1	-0.979	-0.984	17.959	-0.088	-0.088	0.000	0.000	0.000	0.000
15	A	377	LYS	1	0.931	0.961	19.420	0.052	0.052	0.000	0.000	0.000	0.000
16	A	378	LEU	0	-0.048	-0.022	20.850	0.009	0.009	0.000	0.000	0.000	0.000
17	A	379	ARG	1	0.922	0.954	20.429	0.117	0.117	0.000	0.000	0.000	0.000
18	A	380	GLU	-1	-0.873	-0.918	23.971	-0.029	-0.029	0.000	0.000	0.000	0.000
19	A	381	GLN	0	0.075	0.036	25.179	0.009	0.009	0.000	0.000	0.000	0.000
20	A	382	LEU	0	-0.030	-0.010	27.105	0.003	0.003	0.000	0.000	0.000	0.000
21	A	383	SER	0	0.011	0.005	28.348	0.002	0.002	0.000	0.000	0.000	0.000
22	A	384	GLN	0	-0.029	-0.018	29.874	0.004	0.004	0.000	0.000	0.000	0.000
23	A	385	ALA	0	-0.020	-0.008	31.621	0.003	0.003	0.000	0.000	0.000	0.000
24	A	386	GLU	-1	-0.827	-0.908	32.639	-0.036	-0.036	0.000	0.000	0.000	0.000
25	A	387	ALA	0	0.012	0.018	34.317	0.002	0.002	0.000	0.000	0.000	0.000
26	A	388	MET	0	0.012	0.001	34.384	0.003	0.003	0.000	0.000	0.000	0.000
27	A	389	LYS	1	0.784	0.880	36.246	0.036	0.036	0.000	0.000	0.000	0.000
28	A	390	ALA	0	-0.013	-0.010	38.636	0.001	0.001	0.000	0.000	0.000	0.000
29	A	391	GLU	-1	-0.843	-0.910	40.357	-0.016	-0.016	0.000	0.000	0.000	0.000
30	A	392	LEU	0	-0.037	-0.021	41.175	0.001	0.001	0.000	0.000	0.000	0.000
31	A	393	LYS	1	0.836	0.904	43.202	0.024	0.024	0.000	0.000	0.000	0.000
32	A	394	GLU	-1	-0.920	-0.951	44.683	-0.019	-0.019	0.000	0.000	0.000	0.000
33	A	395	LYS	1	0.872	0.922	44.739	0.016	0.016	0.000	0.000	0.000	0.000
34	A	396	LEU	0	-0.044	-0.012	47.831	0.001	0.001	0.000	0.000	0.000	0.000
35	A	397	GLU	-1	-0.829	-0.906	47.682	-0.020	-0.020	0.000	0.000	0.000	0.000
36	A	398	GLU	-1	-0.941	-0.974	49.944	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	399	SER	0	0.016	0.003	52.354	0.001	0.001	0.000	0.000	0.000	0.000
38	A	400	GLU	-1	-0.853	-0.922	53.809	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	401	LYS	1	0.795	0.885	55.225	0.014	0.014	0.000	0.000	0.000	0.000
40	A	402	LEU	0	0.034	0.019	56.693	0.001	0.001	0.000	0.000	0.000	0.000
41	A	403	ILE	0	0.013	0.010	57.598	0.001	0.001	0.000	0.000	0.000	0.000
42	A	404	LYS	1	0.840	0.911	56.608	0.015	0.015	0.000	0.000	0.000	0.000
43	A	405	GLU	-1	-0.833	-0.900	59.596	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	406	LEU	0	-0.021	-0.005	61.606	0.001	0.001	0.000	0.000	0.000	0.000
45	A	407	THR	0	-0.022	-0.017	64.244	0.001	0.001	0.000	0.000	0.000	0.000
46	A	408	VAL	0	0.000	0.003	65.956	0.000	0.000	0.000	0.000	0.000	0.000
47	A	409	THR	0	-0.029	-0.025	66.283	0.000	0.000	0.000	0.000	0.000	0.000
48	A	410	TRP	0	-0.028	-0.014	66.781	0.001	0.001	0.000	0.000	0.000	0.000
49	A	411	GLU	-1	-0.912	-0.943	70.252	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	412	GLU	-1	-0.698	-0.810	71.723	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	413	LYS	1	0.876	0.936	72.898	0.006	0.006	0.000	0.000	0.000	0.000
52	A	414	LEU	0	0.033	0.008	73.672	0.000	0.000	0.000	0.000	0.000	0.000
53	A	415	ARG	1	0.954	0.975	76.158	0.007	0.007	0.000	0.000	0.000	0.000
54	A	416	LYS	1	0.773	0.873	74.261	0.007	0.007	0.000	0.000	0.000	0.000
55	A	417	THR	0	-0.056	-0.051	78.026	0.000	0.000	0.000	0.000	0.000	0.000
56	A	418	GLU	-1	-0.909	-0.958	79.184	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	419	ALA	0	-0.021	-0.007	82.016	0.000	0.000	0.000	0.000	0.000	0.000
58	A	420	ILE	0	-0.036	-0.013	82.328	0.000	0.000	0.000	0.000	0.000	0.000
59	A	421	ALA	0	0.000	-0.001	84.807	0.000	0.000	0.000	0.000	0.000	0.000
60	A	422	GLN	0	0.025	0.016	86.382	0.000	0.000	0.000	0.000	0.000	0.000
61	A	423	GLU	-1	-0.971	-1.000	88.029	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	424	ARG	1	0.957	0.971	86.922	0.004	0.004	0.000	0.000	0.000	0.000
63	A	425	GLN	0	-0.054	-0.026	90.730	0.000	0.000	0.000	0.000	0.000	0.000
64	A	426	ARG	1	0.965	0.988	88.712	0.005	0.005	0.000	0.000	0.000	0.000
65	A	427	GLN	0	-0.040	-0.020	92.883	0.000	0.000	0.000	0.000	0.000	0.000
66	A	428	LEU	0	0.009	0.001	94.030	0.000	0.000	0.000	0.000	0.000	0.000
67	A	429	GLU	-1	-0.853	-0.920	94.949	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	430	SER	0	-0.039	-0.009	98.398	0.000	0.000	0.000	0.000	0.000	0.000
69	A	431	MET	0	-0.018	-0.013	100.117	0.000	0.000	0.000	0.000	0.000	0.000
70	A	432	GLY	0	0.019	0.016	101.271	0.000	0.000	0.000	0.000	0.000	0.000
71	A	433	ILE	0	0.035	0.010	102.545	0.000	0.000	0.000	0.000	0.000	0.000
72	A	434	SER	0	-0.049	-0.033	104.161	0.000	0.000	0.000	0.000	0.000	0.000
73	A	435	LEU	0	-0.070	-0.026	105.745	0.000	0.000	0.000	0.000	0.000	0.000
74	A	436	GLU	-1	-0.915	-0.957	106.203	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	437	THR	0	-0.099	-0.036	108.794	0.000	0.000	0.000	0.000	0.000	0.000
76	A	438	SER	0	-0.064	-0.045	110.506	0.000	0.000	0.000	0.000	0.000	0.000
77	A	439	GLY	0	-0.029	0.005	111.650	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:363:PRO)