FMO DATABASE

FMODB ID: 1NVMZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-357115.831086
FMO2-HF: Nuclear repulsion	325580.835868
FMO2-HF: Total energy	-31534.995219
FMO2-MP2: Total energy	-31626.935083

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.
0.253	4.137	0.369	-1.589	-2.662	-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 : 0.066 / q_NPA : 0.011

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	0.027	0.011	2.475	-1.795	0.618	0.312	-1.121	-1.604	0.000
4	A	366	LYS	1	0.832	0.905	2.828	0.757	2.013	0.058	-0.442	-0.871	-0.001
5	A	367	VAL	0	0.043	0.034	4.662	0.560	0.775	-0.001	-0.026	-0.187	0.000
6	A	368	ILE	0	0.013	0.005	7.062	0.308	0.308	0.000	0.000	0.000	0.000
7	A	369	ARG	1	0.707	0.801	7.550	0.865	0.865	0.000	0.000	0.000	0.000
8	A	370	GLU	-1	-0.700	-0.836	8.255	-0.694	-0.694	0.000	0.000	0.000	0.000
9	A	371	LEU	0	-0.012	-0.003	11.431	0.114	0.114	0.000	0.000	0.000	0.000
10	A	372	ARG	1	0.858	0.913	11.964	0.551	0.551	0.000	0.000	0.000	0.000
11	A	373	GLU	-1	-0.769	-0.844	12.606	-0.400	-0.400	0.000	0.000	0.000	0.000
12	A	374	GLU	-1	-0.795	-0.886	15.651	-0.147	-0.147	0.000	0.000	0.000	0.000
13	A	375	VAL	0	-0.026	-0.021	17.495	0.034	0.034	0.000	0.000	0.000	0.000
14	A	376	GLU	-1	-0.912	-0.940	17.631	-0.281	-0.281	0.000	0.000	0.000	0.000
15	A	377	LYS	1	0.877	0.932	19.877	0.195	0.195	0.000	0.000	0.000	0.000
16	A	378	LEU	0	-0.036	-0.013	21.303	0.021	0.021	0.000	0.000	0.000	0.000
17	A	379	ARG	1	0.922	0.956	19.784	0.266	0.266	0.000	0.000	0.000	0.000
18	A	380	GLU	-1	-0.884	-0.918	24.342	-0.102	-0.102	0.000	0.000	0.000	0.000
19	A	381	GLN	0	0.055	0.009	24.970	0.008	0.008	0.000	0.000	0.000	0.000
20	A	382	LEU	0	-0.031	-0.004	27.471	0.010	0.010	0.000	0.000	0.000	0.000
21	A	383	SER	0	0.006	0.001	28.656	0.007	0.007	0.000	0.000	0.000	0.000
22	A	384	GLN	0	-0.040	-0.026	30.194	0.013	0.013	0.000	0.000	0.000	0.000
23	A	385	ALA	0	-0.021	-0.008	31.964	0.007	0.007	0.000	0.000	0.000	0.000
24	A	386	GLU	-1	-0.826	-0.903	32.607	-0.088	-0.088	0.000	0.000	0.000	0.000
25	A	387	ALA	0	0.003	0.012	34.587	0.005	0.005	0.000	0.000	0.000	0.000
26	A	388	MET	0	0.015	0.002	34.688	0.007	0.007	0.000	0.000	0.000	0.000
27	A	389	LYS	1	0.790	0.878	36.023	0.090	0.090	0.000	0.000	0.000	0.000
28	A	390	ALA	0	-0.009	-0.006	38.883	0.004	0.004	0.000	0.000	0.000	0.000
29	A	391	GLU	-1	-0.838	-0.910	40.668	-0.049	-0.049	0.000	0.000	0.000	0.000
30	A	392	LEU	0	-0.038	-0.025	41.328	0.004	0.004	0.000	0.000	0.000	0.000
31	A	393	LYS	1	0.771	0.875	43.074	0.058	0.058	0.000	0.000	0.000	0.000
32	A	394	GLU	-1	-0.866	-0.917	44.831	-0.051	-0.051	0.000	0.000	0.000	0.000
33	A	395	LYS	1	0.878	0.927	45.186	0.049	0.049	0.000	0.000	0.000	0.000
34	A	396	LEU	0	-0.036	-0.003	48.201	0.003	0.003	0.000	0.000	0.000	0.000
35	A	397	GLU	-1	-0.823	-0.915	47.820	-0.050	-0.050	0.000	0.000	0.000	0.000
36	A	398	GLU	-1	-0.941	-0.975	49.713	-0.040	-0.040	0.000	0.000	0.000	0.000
37	A	399	SER	0	0.003	-0.001	52.626	0.002	0.002	0.000	0.000	0.000	0.000
38	A	400	GLU	-1	-0.897	-0.938	53.996	-0.037	-0.037	0.000	0.000	0.000	0.000
39	A	401	LYS	1	0.790	0.875	55.252	0.036	0.036	0.000	0.000	0.000	0.000
40	A	402	LEU	0	0.037	0.021	56.834	0.002	0.002	0.000	0.000	0.000	0.000
41	A	403	ILE	0	0.019	0.010	57.616	0.002	0.002	0.000	0.000	0.000	0.000
42	A	404	LYS	1	0.844	0.928	56.754	0.037	0.037	0.000	0.000	0.000	0.000
43	A	405	GLU	-1	-0.797	-0.886	59.439	-0.031	-0.031	0.000	0.000	0.000	0.000
44	A	406	LEU	0	-0.012	0.005	61.732	0.001	0.001	0.000	0.000	0.000	0.000
45	A	407	THR	0	-0.028	-0.026	64.320	0.001	0.001	0.000	0.000	0.000	0.000
46	A	408	VAL	0	-0.009	-0.003	66.045	0.001	0.001	0.000	0.000	0.000	0.000
47	A	409	THR	0	-0.048	-0.046	66.271	0.001	0.001	0.000	0.000	0.000	0.000
48	A	410	TRP	0	-0.026	-0.017	67.469	0.001	0.001	0.000	0.000	0.000	0.000
49	A	411	GLU	-1	-0.890	-0.931	70.574	-0.020	-0.020	0.000	0.000	0.000	0.000
50	A	412	GLU	-1	-0.706	-0.819	72.022	-0.019	-0.019	0.000	0.000	0.000	0.000
51	A	413	LYS	1	0.892	0.950	73.101	0.019	0.019	0.000	0.000	0.000	0.000
52	A	414	LEU	0	0.017	0.016	73.924	0.001	0.001	0.000	0.000	0.000	0.000
53	A	415	ARG	1	0.929	0.958	76.227	0.020	0.020	0.000	0.000	0.000	0.000
54	A	416	LYS	1	0.784	0.878	74.820	0.020	0.020	0.000	0.000	0.000	0.000
55	A	417	THR	0	-0.043	-0.041	78.277	0.001	0.001	0.000	0.000	0.000	0.000
56	A	418	GLU	-1	-0.893	-0.956	79.083	-0.017	-0.017	0.000	0.000	0.000	0.000
57	A	419	ALA	0	-0.027	-0.010	82.302	0.000	0.000	0.000	0.000	0.000	0.000
58	A	420	ILE	0	-0.030	-0.013	82.422	0.000	0.000	0.000	0.000	0.000	0.000
59	A	421	ALA	0	0.003	0.001	84.995	0.000	0.000	0.000	0.000	0.000	0.000
60	A	422	GLN	0	0.036	0.008	86.582	0.000	0.000	0.000	0.000	0.000	0.000
61	A	423	GLU	-1	-0.893	-0.946	88.205	-0.013	-0.013	0.000	0.000	0.000	0.000
62	A	424	ARG	1	0.851	0.916	87.888	0.014	0.014	0.000	0.000	0.000	0.000
63	A	425	GLN	0	-0.054	-0.024	91.030	0.000	0.000	0.000	0.000	0.000	0.000
64	A	426	ARG	1	0.965	0.989	88.857	0.014	0.014	0.000	0.000	0.000	0.000
65	A	427	GLN	0	-0.041	-0.019	93.463	0.000	0.000	0.000	0.000	0.000	0.000
66	A	428	LEU	0	0.006	0.001	94.268	0.000	0.000	0.000	0.000	0.000	0.000
67	A	429	GLU	-1	-0.847	-0.913	94.898	-0.012	-0.012	0.000	0.000	0.000	0.000
68	A	430	SER	0	-0.008	-0.003	98.523	0.000	0.000	0.000	0.000	0.000	0.000
69	A	431	MET	0	-0.047	-0.017	100.244	0.000	0.000	0.000	0.000	0.000	0.000
70	A	432	GLY	0	0.010	0.012	101.423	0.000	0.000	0.000	0.000	0.000	0.000
71	A	433	ILE	0	0.031	0.013	102.475	0.000	0.000	0.000	0.000	0.000	0.000
72	A	434	SER	0	-0.029	-0.027	104.229	0.000	0.000	0.000	0.000	0.000	0.000
73	A	435	LEU	0	-0.033	0.001	106.135	0.000	0.000	0.000	0.000	0.000	0.000
74	A	436	GLU	-1	-0.910	-0.959	105.981	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	437	THR	0	-0.096	-0.046	108.809	0.000	0.000	0.000	0.000	0.000	0.000
76	A	438	SER	0	-0.084	-0.042	110.343	0.000	0.000	0.000	0.000	0.000	0.000
77	A	439	GLY	0	-0.055	-0.023	111.693	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)