FMO DATABASE

FMODB ID: G6741

Calculation Name: 2X89-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2X89

Chain ID: D

ChEMBL ID:

UniProt ID: P61769

Base Structure: X-ray

Registration Date: 2023-06-26

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	91
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-626840.707509
FMO2-HF: Nuclear repulsion	588615.004116
FMO2-HF: Total energy	-38225.703393
FMO2-MP2: Total energy	-38337.203216

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(D:6:MET)

Summations of interaction energy for fragment #1(D:6:MET)

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.
-7.985	-1.027	1.945	-3.658	-5.246	-0.027

Interaction energy analysis for fragmet #1(D:6:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.002

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	D	8	GLN	0	-0.041	-0.009	3.889	1.680	3.185	-0.013	-0.701	-0.791	0.001
4	D	9	VAL	0	0.021	0.004	6.113	-0.617	-0.617	0.000	0.000	0.000	0.000
5	D	10	TYR	0	-0.022	-0.011	8.718	0.140	0.140	0.000	0.000	0.000	0.000
6	D	11	SER	0	0.017	0.011	12.625	-0.084	-0.084	0.000	0.000	0.000	0.000
7	D	12	ARG	1	0.826	0.929	15.927	0.131	0.131	0.000	0.000	0.000	0.000
8	D	13	HIS	0	0.060	0.037	17.131	-0.027	-0.027	0.000	0.000	0.000	0.000
9	D	14	PRO	0	0.058	0.029	19.210	0.024	0.024	0.000	0.000	0.000	0.000
10	D	15	DAL	0	0.053	0.027	19.726	-0.025	-0.025	0.000	0.000	0.000	0.000
11	D	16	GLU	-1	-0.848	-0.922	21.464	0.060	0.060	0.000	0.000	0.000	0.000
12	D	17	ASN	0	-0.069	-0.032	24.532	-0.019	-0.019	0.000	0.000	0.000	0.000
13	D	18	GLY	0	0.073	0.039	26.272	0.000	0.000	0.000	0.000	0.000	0.000
14	D	19	LYS	1	0.752	0.870	26.982	-0.047	-0.047	0.000	0.000	0.000	0.000
15	D	20	SER	0	0.006	-0.009	25.473	-0.006	-0.006	0.000	0.000	0.000	0.000
16	D	21	ASN	0	-0.059	-0.032	19.928	-0.014	-0.014	0.000	0.000	0.000	0.000
17	D	22	PHE	0	0.043	0.011	18.355	-0.014	-0.014	0.000	0.000	0.000	0.000
18	D	23	LEU	0	0.005	0.024	14.956	0.027	0.027	0.000	0.000	0.000	0.000
19	D	24	ASN	0	-0.013	-0.036	12.362	-0.115	-0.115	0.000	0.000	0.000	0.000
20	D	25	CYS	0	-0.053	-0.031	9.252	-0.016	-0.016	0.000	0.000	0.000	0.000
21	D	26	TYR	0	-0.025	-0.003	3.608	-0.833	-0.484	0.003	-0.047	-0.306	0.000
22	D	27	VAL	0	0.027	0.008	4.346	-0.105	0.048	-0.001	-0.060	-0.092	0.000
23	D	28	SER	0	-0.025	-0.028	2.556	-2.317	-0.115	1.238	-1.489	-1.951	-0.014
24	D	29	GLY	0	-0.008	0.001	2.798	-5.464	-3.263	0.678	-1.271	-1.608	-0.014
25	D	30	PHE	0	-0.019	-0.009	3.012	0.311	0.859	0.040	-0.090	-0.498	0.000
26	D	31	HIS	0	0.031	0.016	7.198	0.078	0.078	0.000	0.000	0.000	0.000
27	D	32	PRO	0	0.011	-0.007	10.657	0.005	0.005	0.000	0.000	0.000	0.000
28	D	33	SER	0	-0.061	-0.037	12.431	0.121	0.121	0.000	0.000	0.000	0.000
29	D	34	ASP	-1	-0.831	-0.908	9.868	-1.283	-1.283	0.000	0.000	0.000	0.000
30	D	35	ILE	0	-0.039	-0.023	7.269	-0.002	-0.002	0.000	0.000	0.000	0.000
31	D	36	GLU	-1	-0.860	-0.898	10.954	-0.253	-0.253	0.000	0.000	0.000	0.000
32	D	37	VAL	0	-0.033	-0.039	9.735	-0.041	-0.041	0.000	0.000	0.000	0.000
33	D	38	ASP	-1	-0.733	-0.818	12.324	-0.077	-0.077	0.000	0.000	0.000	0.000
34	D	39	LEU	0	0.003	0.006	13.134	0.028	0.028	0.000	0.000	0.000	0.000
35	D	40	LEU	0	-0.044	-0.019	15.815	-0.001	-0.001	0.000	0.000	0.000	0.000
36	D	41	LYS	1	0.876	0.922	18.090	-0.050	-0.050	0.000	0.000	0.000	0.000
37	D	42	ASN	0	-0.070	-0.050	21.142	0.004	0.004	0.000	0.000	0.000	0.000
38	D	43	GLY	0	0.019	0.019	20.208	0.006	0.006	0.000	0.000	0.000	0.000
39	D	44	GLU	-1	-0.926	-0.963	20.282	0.046	0.046	0.000	0.000	0.000	0.000
40	D	45	ARG	1	0.758	0.839	17.772	0.182	0.182	0.000	0.000	0.000	0.000
41	D	46	ILE	0	-0.022	-0.012	18.582	0.003	0.003	0.000	0.000	0.000	0.000
42	D	47	GLU	-1	-0.850	-0.918	20.823	-0.141	-0.141	0.000	0.000	0.000	0.000
43	D	48	LYS	1	0.781	0.880	22.451	0.116	0.116	0.000	0.000	0.000	0.000
44	D	49	VAL	0	0.021	0.025	15.779	0.019	0.019	0.000	0.000	0.000	0.000
45	D	50	GLU	-1	-0.863	-0.900	18.184	-0.273	-0.273	0.000	0.000	0.000	0.000
46	D	51	HIS	1	0.874	0.899	13.672	0.596	0.596	0.000	0.000	0.000	0.000
47	D	52	SER	0	0.005	0.016	12.921	0.022	0.022	0.000	0.000	0.000	0.000
48	D	53	ASP	-1	-0.892	-0.929	14.563	-0.617	-0.617	0.000	0.000	0.000	0.000
49	D	54	LEU	0	-0.033	-0.019	10.419	-0.044	-0.044	0.000	0.000	0.000	0.000
50	D	55	SER	0	-0.033	0.003	11.428	0.185	0.185	0.000	0.000	0.000	0.000
51	D	56	PHE	0	-0.009	-0.017	10.973	-0.257	-0.257	0.000	0.000	0.000	0.000
52	D	57	SER	0	-0.014	-0.009	9.670	0.219	0.219	0.000	0.000	0.000	0.000
53	D	58	LYS	1	0.913	0.938	11.514	0.420	0.420	0.000	0.000	0.000	0.000
54	D	59	ASP	-1	-0.844	-0.893	9.437	-0.795	-0.795	0.000	0.000	0.000	0.000
55	D	60	TRP	0	-0.024	-0.019	11.319	-0.048	-0.048	0.000	0.000	0.000	0.000
56	D	61	SER	0	-0.016	-0.001	6.173	-0.149	-0.149	0.000	0.000	0.000	0.000
57	D	62	PHE	0	0.007	-0.003	7.455	0.264	0.264	0.000	0.000	0.000	0.000
58	D	63	TYR	0	-0.014	-0.020	6.519	-0.799	-0.799	0.000	0.000	0.000	0.000
59	D	64	LEU	0	0.008	0.020	7.450	0.432	0.432	0.000	0.000	0.000	0.000
60	D	65	LEU	0	0.011	-0.001	8.410	-0.148	-0.148	0.000	0.000	0.000	0.000
61	D	66	TYR	0	0.068	0.029	9.596	0.069	0.069	0.000	0.000	0.000	0.000
62	D	67	TYR	0	-0.080	-0.069	12.803	0.058	0.058	0.000	0.000	0.000	0.000
63	D	68	THR	0	0.004	-0.015	15.719	-0.003	-0.003	0.000	0.000	0.000	0.000
64	D	69	GLU	-1	-0.865	-0.905	19.309	-0.039	-0.039	0.000	0.000	0.000	0.000
65	D	70	PHE	0	-0.025	-0.027	19.118	0.015	0.015	0.000	0.000	0.000	0.000
66	D	71	THR	0	0.034	0.015	22.909	0.003	0.003	0.000	0.000	0.000	0.000
67	D	72	PRO	0	-0.063	-0.017	21.843	0.010	0.010	0.000	0.000	0.000	0.000
68	D	73	THR	0	0.004	-0.031	23.665	-0.005	-0.005	0.000	0.000	0.000	0.000
69	D	74	GLU	-1	-0.842	-0.916	24.926	0.187	0.187	0.000	0.000	0.000	0.000
70	D	75	LYS	1	0.801	0.873	25.618	-0.159	-0.159	0.000	0.000	0.000	0.000
71	D	76	ASP	-1	-0.818	-0.855	23.522	0.109	0.109	0.000	0.000	0.000	0.000
72	D	77	GLU	-1	-0.870	-0.933	19.235	0.383	0.383	0.000	0.000	0.000	0.000
73	D	78	TYR	0	-0.029	-0.019	17.343	-0.065	-0.065	0.000	0.000	0.000	0.000
74	D	79	ALA	0	-0.014	0.004	14.204	0.086	0.086	0.000	0.000	0.000	0.000
75	D	81	ARG	1	0.874	0.933	11.577	0.156	0.156	0.000	0.000	0.000	0.000
76	D	82	VAL	0	0.017	0.010	6.597	-0.116	-0.116	0.000	0.000	0.000	0.000
77	D	83	ASN	0	-0.026	-0.012	9.694	0.178	0.178	0.000	0.000	0.000	0.000
78	D	84	HIS	0	-0.001	0.003	6.821	0.178	0.178	0.000	0.000	0.000	0.000
79	D	85	VAL	0	0.011	0.015	11.406	0.144	0.144	0.000	0.000	0.000	0.000
80	D	86	THR	0	-0.042	-0.035	14.681	-0.014	-0.014	0.000	0.000	0.000	0.000
81	D	87	LEU	0	-0.011	0.007	17.608	0.052	0.052	0.000	0.000	0.000	0.000
82	D	88	SER	0	0.009	-0.002	20.599	0.019	0.019	0.000	0.000	0.000	0.000
83	D	89	GLN	0	-0.037	-0.022	23.964	0.015	0.015	0.000	0.000	0.000	0.000
84	D	90	PRO	0	0.037	0.039	26.369	0.006	0.006	0.000	0.000	0.000	0.000
85	D	91	LYS	1	0.949	0.964	28.001	0.153	0.153	0.000	0.000	0.000	0.000
86	D	92	ILE	0	0.012	0.013	30.976	-0.005	-0.005	0.000	0.000	0.000	0.000
87	D	93	VAL	0	-0.006	-0.020	32.999	0.014	0.014	0.000	0.000	0.000	0.000
88	D	94	LYS	1	0.966	0.984	34.951	0.132	0.132	0.000	0.000	0.000	0.000
89	D	95	TRP	0	0.040	0.015	37.629	0.003	0.003	0.000	0.000	0.000	0.000
90	D	96	ASP	-1	-0.867	-0.920	39.332	-0.101	-0.101	0.000	0.000	0.000	0.000
91	D	97	ARG	1	0.874	0.944	42.958	0.114	0.114	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:6:MET)