FMO DATABASE

FMODB ID: 6N25Z

Calculation Name: 5G4D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5G4D

Chain ID: A

ChEMBL ID:

UniProt ID: B6YTB8

Base Structure: X-ray

Registration Date: 2023-09-19

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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-534391.808642
FMO2-HF: Nuclear repulsion	501556.458837
FMO2-HF: Total energy	-32835.349805
FMO2-MP2: Total energy	-32930.075601

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:-2:ALA)

Summations of interaction energy for fragment #1(A:-2:ALA)

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.
-21.24	-20.505	21.141	-10.108	-11.767	-0.069

Interaction energy analysis for fragmet #1(A:-2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.058 / q_NPA : -0.045

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

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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	0	ASP	-1	-0.825	-0.889	3.896	-1.721	-0.297	-0.006	-0.668	-0.749	0.001
4	A	1	MET	0	-0.068	-0.036	2.527	0.081	0.641	0.517	-0.354	-0.723	-0.001
5	A	2	TYR	0	-0.003	-0.037	2.236	-3.005	-0.737	2.802	-1.993	-3.077	-0.016
6	A	3	VAL	0	-0.024	-0.015	4.041	-1.256	-1.170	0.008	-0.025	-0.069	0.000
7	A	4	VAL	0	-0.001	-0.008	7.651	0.310	0.310	0.000	0.000	0.000	0.000
8	A	5	ILE	0	-0.048	-0.019	10.752	-0.153	-0.153	0.000	0.000	0.000	0.000
9	A	6	VAL	0	0.023	0.006	13.833	0.032	0.032	0.000	0.000	0.000	0.000
10	A	7	TYR	0	-0.025	-0.024	17.511	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	8	ASP	-1	-0.910	-0.941	20.651	0.206	0.206	0.000	0.000	0.000	0.000
12	A	9	VAL	0	-0.016	-0.006	23.052	-0.011	-0.011	0.000	0.000	0.000	0.000
13	A	10	ALA	0	0.103	0.068	26.157	0.005	0.005	0.000	0.000	0.000	0.000
14	A	11	VAL	0	0.002	-0.008	28.787	0.005	0.005	0.000	0.000	0.000	0.000
15	A	12	GLU	-1	-0.892	-0.961	30.331	0.091	0.091	0.000	0.000	0.000	0.000
16	A	13	ARG	1	0.728	0.822	26.796	-0.091	-0.091	0.000	0.000	0.000	0.000
17	A	14	VAL	0	0.023	0.024	24.637	0.006	0.006	0.000	0.000	0.000	0.000
18	A	15	ASN	0	0.002	-0.015	23.996	0.031	0.031	0.000	0.000	0.000	0.000
19	A	16	ARG	1	0.892	0.948	24.758	-0.049	-0.049	0.000	0.000	0.000	0.000
20	A	17	VAL	0	0.104	0.066	19.834	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	18	LYS	1	0.932	0.974	19.792	-0.177	-0.177	0.000	0.000	0.000	0.000
22	A	19	LYS	1	0.895	0.934	19.825	-0.061	-0.061	0.000	0.000	0.000	0.000
23	A	20	PHE	0	0.011	0.023	16.353	-0.017	-0.017	0.000	0.000	0.000	0.000
24	A	21	LEU	0	0.062	0.030	14.282	-0.018	-0.018	0.000	0.000	0.000	0.000
25	A	22	ARG	1	0.953	0.970	14.836	-0.194	-0.194	0.000	0.000	0.000	0.000
26	A	23	ARG	1	0.838	0.931	16.323	-0.057	-0.057	0.000	0.000	0.000	0.000
27	A	24	HIS	1	0.808	0.898	11.746	-0.071	-0.071	0.000	0.000	0.000	0.000
28	A	25	LEU	0	-0.003	0.020	8.677	0.027	0.027	0.000	0.000	0.000	0.000
29	A	26	HIS	0	0.030	0.018	8.286	-0.295	-0.295	0.000	0.000	0.000	0.000
30	A	27	TRP	0	-0.050	-0.026	12.786	0.033	0.033	0.000	0.000	0.000	0.000
31	A	28	VAL	0	-0.015	-0.004	13.454	0.001	0.001	0.000	0.000	0.000	0.000
32	A	29	GLN	0	0.014	-0.003	16.356	-0.074	-0.074	0.000	0.000	0.000	0.000
33	A	30	ASN	0	-0.024	-0.019	19.635	0.002	0.002	0.000	0.000	0.000	0.000
34	A	31	SER	0	0.018	0.010	20.199	0.001	0.001	0.000	0.000	0.000	0.000
35	A	32	VAL	0	0.016	0.023	15.194	0.014	0.014	0.000	0.000	0.000	0.000
36	A	33	PHE	0	-0.014	-0.017	13.165	-0.037	-0.037	0.000	0.000	0.000	0.000
37	A	34	GLU	-1	-0.764	-0.813	9.177	2.005	2.005	0.000	0.000	0.000	0.000
38	A	35	GLY	0	0.038	0.010	6.945	-0.346	-0.346	0.000	0.000	0.000	0.000
39	A	36	GLU	-1	-0.860	-0.902	1.866	-11.704	-15.341	14.714	-6.290	-4.788	-0.049
40	A	37	VAL	0	-0.029	-0.017	3.386	-1.013	-0.860	0.005	0.029	-0.186	0.000
41	A	38	THR	0	0.063	0.029	4.594	-0.913	-0.925	-0.001	-0.008	0.021	0.000
42	A	39	LEU	0	-0.010	-0.031	7.260	0.458	0.458	0.000	0.000	0.000	0.000
43	A	40	ALA	0	0.018	0.001	9.596	0.211	0.211	0.000	0.000	0.000	0.000
44	A	41	GLU	-1	-0.800	-0.869	8.864	-0.190	-0.190	0.000	0.000	0.000	0.000
45	A	42	PHE	0	0.064	0.020	9.187	0.188	0.188	0.000	0.000	0.000	0.000
46	A	43	GLU	-1	-0.787	-0.884	10.778	-0.095	-0.095	0.000	0.000	0.000	0.000
47	A	44	ARG	1	0.868	0.920	12.370	0.541	0.541	0.000	0.000	0.000	0.000
48	A	45	ILE	0	-0.053	-0.027	10.313	0.059	0.059	0.000	0.000	0.000	0.000
49	A	46	LYS	1	0.837	0.895	14.370	0.160	0.160	0.000	0.000	0.000	0.000
50	A	47	ALA	0	0.022	0.016	16.250	0.018	0.018	0.000	0.000	0.000	0.000
51	A	48	GLY	0	0.047	0.013	18.214	0.014	0.014	0.000	0.000	0.000	0.000
52	A	49	LEU	0	-0.075	-0.052	15.711	0.031	0.031	0.000	0.000	0.000	0.000
53	A	50	LEU	0	0.030	0.017	19.635	0.007	0.007	0.000	0.000	0.000	0.000
54	A	51	ASP	-1	-0.922	-0.948	22.275	-0.033	-0.033	0.000	0.000	0.000	0.000
55	A	52	LEU	0	-0.183	-0.104	21.473	0.004	0.004	0.000	0.000	0.000	0.000
56	A	53	ILE	0	-0.066	-0.033	21.854	0.019	0.019	0.000	0.000	0.000	0.000
57	A	54	ASP	-1	-0.884	-0.948	25.525	0.038	0.038	0.000	0.000	0.000	0.000
58	A	55	GLU	-1	-0.967	-0.995	24.812	0.041	0.041	0.000	0.000	0.000	0.000
59	A	56	ASP	-1	-0.928	-0.946	27.502	0.049	0.049	0.000	0.000	0.000	0.000
60	A	57	GLU	-1	-0.938	-0.945	29.544	0.081	0.081	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.775	-0.852	25.020	0.122	0.122	0.000	0.000	0.000	0.000
62	A	59	SER	0	-0.021	-0.009	23.574	0.004	0.004	0.000	0.000	0.000	0.000
63	A	60	VAL	0	-0.002	-0.026	17.249	0.024	0.024	0.000	0.000	0.000	0.000
64	A	61	VAL	0	-0.012	0.005	16.011	-0.021	-0.021	0.000	0.000	0.000	0.000
65	A	62	ILE	0	-0.007	-0.011	11.409	0.057	0.057	0.000	0.000	0.000	0.000
66	A	63	TYR	0	0.017	0.011	11.447	-0.071	-0.071	0.000	0.000	0.000	0.000
67	A	64	LYS	1	0.871	0.942	8.010	0.136	0.136	0.000	0.000	0.000	0.000
68	A	65	LEU	0	-0.013	-0.006	5.827	-0.148	-0.148	0.000	0.000	0.000	0.000
69	A	66	ARG	1	0.976	0.970	4.072	-0.241	0.001	0.001	-0.054	-0.189	0.000
70	A	67	SER	0	0.025	0.016	2.130	-1.486	-0.836	3.112	-1.978	-1.784	-0.004
71	A	68	MET	0	0.025	0.019	3.122	-0.110	-1.113	-0.010	1.234	-0.221	0.000
72	A	69	PRO	0	-0.021	0.016	5.281	-0.714	-0.710	-0.001	-0.001	-0.002	0.000
73	A	70	LYS	1	0.892	0.933	8.540	-0.733	-0.733	0.000	0.000	0.000	0.000
74	A	71	ARG	1	0.789	0.849	9.463	-1.709	-1.709	0.000	0.000	0.000	0.000
75	A	72	GLU	-1	-0.881	-0.945	14.305	0.476	0.476	0.000	0.000	0.000	0.000
76	A	73	VAL	0	-0.001	-0.001	17.862	0.022	0.022	0.000	0.000	0.000	0.000
77	A	74	LEU	0	0.025	0.023	20.318	-0.034	-0.034	0.000	0.000	0.000	0.000
78	A	75	GLY	0	0.033	0.028	24.030	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	76	MET	0	-0.042	-0.027	20.851	0.021	0.021	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:ALA)