FMO DATABASE

FMODB ID: YV742

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

Total energy (hartree)

FMO2-HF: Electronic energy	-356100.538077
FMO2-HF: Nuclear repulsion	324567.150495
FMO2-HF: Total energy	-31533.387582
FMO2-MP2: Total energy	-31625.415674

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.
-1.266	1.336	3.915	-2.49	-4.026	0

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 : 0.008 / q_NPA : -0.027

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	0.010	0.015	1.800	-1.126	-0.035	3.795	-2.224	-2.662	0.001
4	A	366	LYS	1	0.886	0.942	2.842	-1.020	0.337	0.121	-0.249	-1.228	-0.001
5	A	367	VAL	0	0.135	0.067	4.565	0.295	0.449	-0.001	-0.017	-0.136	0.000
6	A	368	ILE	0	0.001	-0.004	6.959	0.220	0.220	0.000	0.000	0.000	0.000
7	A	369	ARG	1	0.869	0.924	7.039	0.277	0.277	0.000	0.000	0.000	0.000
8	A	370	GLU	-1	-0.847	-0.931	9.256	-0.235	-0.235	0.000	0.000	0.000	0.000
9	A	371	LEU	0	0.018	0.024	11.299	0.069	0.069	0.000	0.000	0.000	0.000
10	A	372	ARG	1	0.875	0.929	11.374	0.390	0.390	0.000	0.000	0.000	0.000
11	A	373	GLU	-1	-0.820	-0.906	12.315	-0.164	-0.164	0.000	0.000	0.000	0.000
12	A	374	GLU	-1	-0.889	-0.941	15.070	-0.110	-0.110	0.000	0.000	0.000	0.000
13	A	375	VAL	0	-0.082	-0.045	16.920	0.024	0.024	0.000	0.000	0.000	0.000
14	A	376	GLU	-1	-0.979	-0.985	17.986	-0.110	-0.110	0.000	0.000	0.000	0.000
15	A	377	LYS	1	1.003	1.005	19.433	0.101	0.101	0.000	0.000	0.000	0.000
16	A	378	LEU	0	-0.052	-0.031	21.090	0.015	0.015	0.000	0.000	0.000	0.000
17	A	379	ARG	1	0.921	0.955	19.983	0.157	0.157	0.000	0.000	0.000	0.000
18	A	380	GLU	-1	-0.905	-0.939	24.006	-0.054	-0.054	0.000	0.000	0.000	0.000
19	A	381	GLN	0	0.035	0.001	24.564	0.014	0.014	0.000	0.000	0.000	0.000
20	A	382	LEU	0	-0.046	-0.014	27.134	0.005	0.005	0.000	0.000	0.000	0.000
21	A	383	SER	0	-0.013	-0.002	28.376	0.006	0.006	0.000	0.000	0.000	0.000
22	A	384	GLN	0	0.040	0.018	30.074	0.003	0.003	0.000	0.000	0.000	0.000
23	A	385	ALA	0	-0.010	-0.011	31.644	0.004	0.004	0.000	0.000	0.000	0.000
24	A	386	GLU	-1	-0.897	-0.966	32.293	-0.057	-0.057	0.000	0.000	0.000	0.000
25	A	387	ALA	0	-0.009	0.011	34.360	0.003	0.003	0.000	0.000	0.000	0.000
26	A	388	MET	0	0.010	0.005	34.196	0.004	0.004	0.000	0.000	0.000	0.000
27	A	389	LYS	1	0.896	0.958	37.130	0.053	0.053	0.000	0.000	0.000	0.000
28	A	390	ALA	0	-0.040	-0.026	38.687	0.002	0.002	0.000	0.000	0.000	0.000
29	A	391	GLU	-1	-0.910	-0.961	40.402	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	392	LEU	0	-0.057	-0.023	41.166	0.002	0.002	0.000	0.000	0.000	0.000
31	A	393	LYS	1	0.903	0.957	42.740	0.039	0.039	0.000	0.000	0.000	0.000
32	A	394	GLU	-1	-0.884	-0.931	44.737	-0.027	-0.027	0.000	0.000	0.000	0.000
33	A	395	LYS	1	0.949	0.975	45.163	0.026	0.026	0.000	0.000	0.000	0.000
34	A	396	LEU	0	-0.068	-0.024	47.876	0.001	0.001	0.000	0.000	0.000	0.000
35	A	397	GLU	-1	-0.891	-0.952	47.417	-0.029	-0.029	0.000	0.000	0.000	0.000
36	A	398	GLU	-1	-0.932	-0.978	49.516	-0.022	-0.022	0.000	0.000	0.000	0.000
37	A	399	SER	0	-0.030	-0.010	52.398	0.002	0.002	0.000	0.000	0.000	0.000
38	A	400	GLU	-1	-0.905	-0.963	52.632	-0.025	-0.025	0.000	0.000	0.000	0.000
39	A	401	LYS	1	0.863	0.933	54.974	0.022	0.022	0.000	0.000	0.000	0.000
40	A	402	LEU	0	0.045	0.025	56.744	0.001	0.001	0.000	0.000	0.000	0.000
41	A	403	ILE	0	0.025	0.016	58.129	0.001	0.001	0.000	0.000	0.000	0.000
42	A	404	LYS	1	0.927	0.957	56.763	0.022	0.022	0.000	0.000	0.000	0.000
43	A	405	GLU	-1	-0.910	-0.956	59.468	-0.017	-0.017	0.000	0.000	0.000	0.000
44	A	406	LEU	0	-0.020	-0.005	62.017	0.001	0.001	0.000	0.000	0.000	0.000
45	A	407	THR	0	-0.026	-0.013	64.402	0.001	0.001	0.000	0.000	0.000	0.000
46	A	408	VAL	0	-0.003	0.004	65.895	0.001	0.001	0.000	0.000	0.000	0.000
47	A	409	THR	0	-0.029	-0.025	66.374	0.001	0.001	0.000	0.000	0.000	0.000
48	A	410	TRP	0	-0.028	-0.015	66.542	0.001	0.001	0.000	0.000	0.000	0.000
49	A	411	GLU	-1	-0.923	-0.952	70.301	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	412	GLU	-1	-0.737	-0.842	71.763	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	413	LYS	1	0.848	0.918	72.872	0.010	0.010	0.000	0.000	0.000	0.000
52	A	414	LEU	0	0.028	-0.005	74.127	0.001	0.001	0.000	0.000	0.000	0.000
53	A	415	ARG	1	0.941	0.980	76.213	0.011	0.011	0.000	0.000	0.000	0.000
54	A	416	LYS	1	0.851	0.921	74.507	0.011	0.011	0.000	0.000	0.000	0.000
55	A	417	THR	0	-0.052	-0.034	78.167	0.000	0.000	0.000	0.000	0.000	0.000
56	A	418	GLU	-1	-0.886	-0.954	79.393	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	419	ALA	0	-0.026	-0.011	82.066	0.000	0.000	0.000	0.000	0.000	0.000
58	A	420	ILE	0	-0.027	-0.003	82.299	0.000	0.000	0.000	0.000	0.000	0.000
59	A	421	ALA	0	-0.019	-0.011	84.848	0.000	0.000	0.000	0.000	0.000	0.000
60	A	422	GLN	0	0.032	0.018	86.420	0.000	0.000	0.000	0.000	0.000	0.000
61	A	423	GLU	-1	-0.990	-0.995	88.079	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	424	ARG	1	0.956	0.965	86.803	0.007	0.007	0.000	0.000	0.000	0.000
63	A	425	GLN	0	0.023	0.024	90.769	0.000	0.000	0.000	0.000	0.000	0.000
64	A	426	ARG	1	0.964	0.981	88.964	0.008	0.008	0.000	0.000	0.000	0.000
65	A	427	GLN	0	-0.032	-0.018	92.881	0.000	0.000	0.000	0.000	0.000	0.000
66	A	428	LEU	0	-0.003	-0.004	93.871	0.000	0.000	0.000	0.000	0.000	0.000
67	A	429	GLU	-1	-0.900	-0.955	95.301	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	430	SER	0	-0.063	-0.018	98.444	0.000	0.000	0.000	0.000	0.000	0.000
69	A	431	MET	0	-0.005	-0.020	100.158	0.000	0.000	0.000	0.000	0.000	0.000
70	A	432	GLY	0	0.021	0.020	101.307	0.000	0.000	0.000	0.000	0.000	0.000
71	A	433	ILE	0	0.051	0.021	102.789	0.000	0.000	0.000	0.000	0.000	0.000
72	A	434	SER	0	-0.048	-0.034	104.434	0.000	0.000	0.000	0.000	0.000	0.000
73	A	435	LEU	0	-0.067	-0.019	105.671	0.000	0.000	0.000	0.000	0.000	0.000
74	A	436	GLU	-1	-0.922	-0.961	106.778	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	437	THR	0	-0.143	-0.054	108.629	0.000	0.000	0.000	0.000	0.000	0.000
76	A	438	SER	0	-0.021	-0.024	110.815	0.000	0.000	0.000	0.000	0.000	0.000
77	A	439	GLY	0	-0.040	-0.001	111.677	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)