FMO DATABASE

FMODB ID: 17V3Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-626483.580807
FMO2-HF: Nuclear repulsion	588258.618332
FMO2-HF: Total energy	-38224.962474
FMO2-MP2: Total energy	-38336.480199

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.
-8.338	-1.085	1.989	-3.99	-5.253	-0.022

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 : 0.006 / q_NPA : -0.004

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	-0.034	-0.010	3.860	1.180	3.169	-0.021	-0.980	-0.989	0.001
4	D	9	VAL	0	0.025	0.007	6.110	-0.732	-0.732	0.000	0.000	0.000	0.000
5	D	10	TYR	0	-0.041	-0.012	8.603	0.140	0.140	0.000	0.000	0.000	0.000
6	D	11	SER	0	0.019	0.013	12.361	-0.091	-0.091	0.000	0.000	0.000	0.000
7	D	12	ARG	1	0.857	0.933	15.485	0.091	0.091	0.000	0.000	0.000	0.000
8	D	13	HIS	0	0.031	0.019	16.809	-0.028	-0.028	0.000	0.000	0.000	0.000
9	D	14	PRO	0	0.034	0.021	19.089	0.025	0.025	0.000	0.000	0.000	0.000
10	D	15	DAL	0	0.013	-0.013	19.678	-0.034	-0.034	0.000	0.000	0.000	0.000
11	D	16	GLU	-1	-0.869	-0.897	21.333	0.094	0.094	0.000	0.000	0.000	0.000
12	D	17	ASN	0	-0.006	-0.017	24.916	-0.007	-0.007	0.000	0.000	0.000	0.000
13	D	18	GLY	0	0.069	0.023	26.415	-0.004	-0.004	0.000	0.000	0.000	0.000
14	D	19	LYS	1	0.776	0.882	26.703	-0.087	-0.087	0.000	0.000	0.000	0.000
15	D	20	SER	0	-0.007	-0.003	25.295	-0.009	-0.009	0.000	0.000	0.000	0.000
16	D	21	ASN	0	-0.037	-0.009	19.685	-0.004	-0.004	0.000	0.000	0.000	0.000
17	D	22	PHE	0	0.050	0.015	18.002	-0.022	-0.022	0.000	0.000	0.000	0.000
18	D	23	LEU	0	0.012	0.023	14.865	0.047	0.047	0.000	0.000	0.000	0.000
19	D	24	ASN	0	-0.015	-0.026	11.959	-0.133	-0.133	0.000	0.000	0.000	0.000
20	D	25	CYS	0	-0.037	-0.013	8.961	-0.013	-0.013	0.000	0.000	0.000	0.000
21	D	26	TYR	0	-0.023	-0.020	3.274	-0.741	-0.307	0.007	-0.068	-0.373	0.000
22	D	27	VAL	0	0.048	0.021	4.374	-0.241	-0.111	-0.001	-0.078	-0.051	0.000
23	D	28	SER	0	-0.031	-0.033	2.533	-1.990	0.118	1.490	-1.585	-2.013	-0.010
24	D	29	GLY	0	-0.014	-0.008	2.833	-5.219	-3.017	0.506	-1.235	-1.473	-0.013
25	D	30	PHE	0	-0.020	-0.013	3.364	0.256	0.646	0.008	-0.044	-0.354	0.000
26	D	31	HIS	0	0.035	0.017	7.627	0.214	0.214	0.000	0.000	0.000	0.000
27	D	32	PRO	0	0.036	0.006	11.147	0.005	0.005	0.000	0.000	0.000	0.000
28	D	33	SER	0	-0.045	-0.012	12.641	0.085	0.085	0.000	0.000	0.000	0.000
29	D	34	ASP	-1	-0.862	-0.932	10.469	-1.269	-1.269	0.000	0.000	0.000	0.000
30	D	35	ILE	0	-0.060	-0.034	7.978	-0.007	-0.007	0.000	0.000	0.000	0.000
31	D	36	GLU	-1	-0.875	-0.920	11.441	-0.253	-0.253	0.000	0.000	0.000	0.000
32	D	37	VAL	0	-0.040	-0.035	9.865	-0.020	-0.020	0.000	0.000	0.000	0.000
33	D	38	ASP	-1	-0.751	-0.840	12.426	-0.138	-0.138	0.000	0.000	0.000	0.000
34	D	39	LEU	0	-0.030	-0.023	13.020	0.030	0.030	0.000	0.000	0.000	0.000
35	D	40	LEU	0	-0.028	-0.024	15.805	-0.011	-0.011	0.000	0.000	0.000	0.000
36	D	41	LYS	1	0.882	0.927	18.132	-0.060	-0.060	0.000	0.000	0.000	0.000
37	D	42	ASN	0	-0.053	-0.050	21.055	0.006	0.006	0.000	0.000	0.000	0.000
38	D	43	GLY	0	0.005	0.007	19.475	-0.006	-0.006	0.000	0.000	0.000	0.000
39	D	44	GLU	-1	-0.915	-0.940	20.510	0.032	0.032	0.000	0.000	0.000	0.000
40	D	45	ARG	1	0.752	0.862	18.022	0.204	0.204	0.000	0.000	0.000	0.000
41	D	46	ILE	0	-0.002	0.005	18.633	0.007	0.007	0.000	0.000	0.000	0.000
42	D	47	GLU	-1	-0.902	-0.958	20.630	-0.131	-0.131	0.000	0.000	0.000	0.000
43	D	48	LYS	1	0.850	0.921	22.303	0.087	0.087	0.000	0.000	0.000	0.000
44	D	49	VAL	0	0.029	0.029	15.821	0.014	0.014	0.000	0.000	0.000	0.000
45	D	50	GLU	-1	-0.859	-0.893	18.242	-0.257	-0.257	0.000	0.000	0.000	0.000
46	D	51	HIS	1	0.889	0.906	13.418	0.604	0.604	0.000	0.000	0.000	0.000
47	D	52	SER	0	-0.012	0.007	13.050	0.015	0.015	0.000	0.000	0.000	0.000
48	D	53	ASP	-1	-0.894	-0.928	14.624	-0.584	-0.584	0.000	0.000	0.000	0.000
49	D	54	LEU	0	-0.023	-0.015	10.466	-0.029	-0.029	0.000	0.000	0.000	0.000
50	D	55	SER	0	-0.059	-0.012	11.529	0.182	0.182	0.000	0.000	0.000	0.000
51	D	56	PHE	0	0.011	-0.015	11.365	-0.218	-0.218	0.000	0.000	0.000	0.000
52	D	57	SER	0	-0.021	-0.015	9.328	0.227	0.227	0.000	0.000	0.000	0.000
53	D	58	LYS	1	0.980	0.965	12.014	0.316	0.316	0.000	0.000	0.000	0.000
54	D	59	ASP	-1	-0.916	-0.943	8.991	-1.042	-1.042	0.000	0.000	0.000	0.000
55	D	60	TRP	0	-0.033	-0.004	11.510	-0.030	-0.030	0.000	0.000	0.000	0.000
56	D	61	SER	0	0.017	0.026	6.503	-0.111	-0.111	0.000	0.000	0.000	0.000
57	D	62	PHE	0	0.005	-0.002	7.777	0.250	0.250	0.000	0.000	0.000	0.000
58	D	63	TYR	0	-0.004	-0.009	6.344	-0.772	-0.772	0.000	0.000	0.000	0.000
59	D	64	LEU	0	-0.009	0.004	7.172	0.378	0.378	0.000	0.000	0.000	0.000
60	D	65	LEU	0	-0.001	-0.005	8.490	-0.064	-0.064	0.000	0.000	0.000	0.000
61	D	66	TYR	0	0.052	0.035	9.814	0.023	0.023	0.000	0.000	0.000	0.000
62	D	67	TYR	0	-0.070	-0.070	12.850	0.071	0.071	0.000	0.000	0.000	0.000
63	D	68	THR	0	-0.017	-0.025	15.686	-0.008	-0.008	0.000	0.000	0.000	0.000
64	D	69	GLU	-1	-0.911	-0.936	19.056	-0.009	-0.009	0.000	0.000	0.000	0.000
65	D	70	PHE	0	-0.037	-0.035	19.002	0.015	0.015	0.000	0.000	0.000	0.000
66	D	71	THR	0	0.056	0.015	22.773	-0.002	-0.002	0.000	0.000	0.000	0.000
67	D	72	PRO	0	-0.079	-0.001	21.725	0.004	0.004	0.000	0.000	0.000	0.000
68	D	73	THR	0	0.011	-0.023	23.663	-0.006	-0.006	0.000	0.000	0.000	0.000
69	D	74	GLU	-1	-0.846	-0.929	24.914	0.221	0.221	0.000	0.000	0.000	0.000
70	D	75	LYS	1	0.823	0.886	25.420	-0.186	-0.186	0.000	0.000	0.000	0.000
71	D	76	ASP	-1	-0.816	-0.855	23.528	0.130	0.130	0.000	0.000	0.000	0.000
72	D	77	GLU	-1	-0.880	-0.937	19.724	0.415	0.415	0.000	0.000	0.000	0.000
73	D	78	TYR	0	-0.027	-0.024	17.125	-0.069	-0.069	0.000	0.000	0.000	0.000
74	D	79	ALA	0	-0.010	0.008	13.986	0.099	0.099	0.000	0.000	0.000	0.000
75	D	81	ARG	1	0.872	0.933	11.300	0.186	0.186	0.000	0.000	0.000	0.000
76	D	82	VAL	0	0.032	0.017	6.683	-0.107	-0.107	0.000	0.000	0.000	0.000
77	D	83	ASN	0	-0.035	-0.012	9.422	0.140	0.140	0.000	0.000	0.000	0.000
78	D	84	HIS	0	0.008	0.004	6.879	0.087	0.087	0.000	0.000	0.000	0.000
79	D	85	VAL	0	0.005	0.009	11.423	0.147	0.147	0.000	0.000	0.000	0.000
80	D	86	THR	0	-0.025	-0.014	14.795	-0.028	-0.028	0.000	0.000	0.000	0.000
81	D	87	LEU	0	-0.009	0.001	17.812	0.047	0.047	0.000	0.000	0.000	0.000
82	D	88	SER	0	0.000	-0.012	21.038	0.019	0.019	0.000	0.000	0.000	0.000
83	D	89	GLN	0	-0.046	-0.022	24.480	0.018	0.018	0.000	0.000	0.000	0.000
84	D	90	PRO	0	0.036	0.035	27.076	0.006	0.006	0.000	0.000	0.000	0.000
85	D	91	LYS	1	0.995	0.986	28.554	0.161	0.161	0.000	0.000	0.000	0.000
86	D	92	ILE	0	0.000	0.001	31.055	-0.008	-0.008	0.000	0.000	0.000	0.000
87	D	93	VAL	0	-0.022	-0.017	33.360	0.012	0.012	0.000	0.000	0.000	0.000
88	D	94	LYS	1	0.961	0.981	35.577	0.138	0.138	0.000	0.000	0.000	0.000
89	D	95	TRP	0	0.029	0.005	38.008	0.003	0.003	0.000	0.000	0.000	0.000
90	D	96	ASP	-1	-0.932	-0.957	39.567	-0.106	-0.106	0.000	0.000	0.000	0.000
91	D	97	ARG	1	0.952	0.986	43.260	0.117	0.117	0.000	0.000	0.000	0.000

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