FMO DATABASE

FMODB ID: V5Z61

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

Total energy (hartree)

FMO2-HF: Electronic energy	-626205.959451
FMO2-HF: Nuclear repulsion	587981.971002
FMO2-HF: Total energy	-38223.988449
FMO2-MP2: Total energy	-38335.504897

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.
-11.568	-4.114	3.638	-4.945	-6.148	-0.03

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 : -0.020 / q_NPA : -0.016

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	D	8	GLN	0	-0.029	-0.006	3.860	0.621	2.597	-0.021	-0.966	-0.990	0.001
4	D	9	VAL	0	0.026	0.009	6.361	-0.541	-0.541	0.000	0.000	0.000	0.000
5	D	10	TYR	0	-0.039	-0.012	9.551	0.117	0.117	0.000	0.000	0.000	0.000
6	D	11	SER	0	0.005	-0.006	12.901	-0.085	-0.085	0.000	0.000	0.000	0.000
7	D	12	ARG	1	0.898	0.955	16.241	0.013	0.013	0.000	0.000	0.000	0.000
8	D	13	HIS	0	0.021	0.009	17.456	-0.013	-0.013	0.000	0.000	0.000	0.000
9	D	14	PRO	0	0.030	0.025	19.828	0.020	0.020	0.000	0.000	0.000	0.000
10	D	15	DAL	0	0.004	-0.017	20.000	-0.035	-0.035	0.000	0.000	0.000	0.000
11	D	16	GLU	-1	-0.856	-0.899	21.880	0.105	0.105	0.000	0.000	0.000	0.000
12	D	17	ASN	0	0.010	-0.011	25.332	-0.007	-0.007	0.000	0.000	0.000	0.000
13	D	18	GLY	0	0.071	0.024	26.711	-0.007	-0.007	0.000	0.000	0.000	0.000
14	D	19	LYS	1	0.777	0.898	27.099	-0.104	-0.104	0.000	0.000	0.000	0.000
15	D	20	SER	0	-0.040	-0.035	25.781	-0.011	-0.011	0.000	0.000	0.000	0.000
16	D	21	ASN	0	-0.005	0.015	20.544	0.007	0.007	0.000	0.000	0.000	0.000
17	D	22	PHE	0	0.045	0.018	18.076	-0.021	-0.021	0.000	0.000	0.000	0.000
18	D	23	LEU	0	0.011	0.015	14.820	0.057	0.057	0.000	0.000	0.000	0.000
19	D	24	ASN	0	-0.017	-0.020	11.807	-0.158	-0.158	0.000	0.000	0.000	0.000
20	D	25	CYS	0	-0.039	-0.015	9.103	0.005	0.005	0.000	0.000	0.000	0.000
21	D	26	TYR	0	-0.017	-0.021	3.919	-0.989	-0.629	0.001	-0.058	-0.303	0.000
22	D	27	VAL	0	0.051	0.024	4.273	-0.206	-0.047	-0.001	-0.088	-0.070	0.000
23	D	28	SER	0	-0.025	-0.030	2.393	-3.708	-1.291	2.799	-2.512	-2.704	-0.017
24	D	29	GLY	0	-0.008	-0.008	2.683	-6.287	-4.073	0.857	-1.289	-1.782	-0.014
25	D	30	PHE	0	-0.003	-0.017	3.591	0.349	0.677	0.003	-0.032	-0.299	0.000
26	D	31	HIS	0	0.006	0.004	7.094	0.304	0.304	0.000	0.000	0.000	0.000
27	D	32	PRO	0	0.050	0.002	10.698	-0.005	-0.005	0.000	0.000	0.000	0.000
28	D	33	SER	0	-0.039	-0.006	12.188	0.062	0.062	0.000	0.000	0.000	0.000
29	D	34	ASP	-1	-0.888	-0.932	10.024	-1.109	-1.109	0.000	0.000	0.000	0.000
30	D	35	ILE	0	-0.066	-0.039	7.683	-0.022	-0.022	0.000	0.000	0.000	0.000
31	D	36	GLU	-1	-0.918	-0.955	11.315	-0.262	-0.262	0.000	0.000	0.000	0.000
32	D	37	VAL	0	-0.037	-0.031	9.882	-0.048	-0.048	0.000	0.000	0.000	0.000
33	D	38	ASP	-1	-0.783	-0.867	12.490	-0.191	-0.191	0.000	0.000	0.000	0.000
34	D	39	LEU	0	-0.029	-0.014	13.121	0.005	0.005	0.000	0.000	0.000	0.000
35	D	40	LEU	0	-0.028	-0.024	15.403	-0.003	-0.003	0.000	0.000	0.000	0.000
36	D	41	LYS	1	0.949	0.966	18.182	-0.017	-0.017	0.000	0.000	0.000	0.000
37	D	42	ASN	0	-0.046	-0.047	21.055	0.005	0.005	0.000	0.000	0.000	0.000
38	D	43	GLY	0	0.005	0.007	19.708	-0.004	-0.004	0.000	0.000	0.000	0.000
39	D	44	GLU	-1	-0.916	-0.939	20.760	-0.016	-0.016	0.000	0.000	0.000	0.000
40	D	45	ARG	1	0.862	0.932	18.482	0.199	0.199	0.000	0.000	0.000	0.000
41	D	46	ILE	0	0.005	0.008	18.686	0.012	0.012	0.000	0.000	0.000	0.000
42	D	47	GLU	-1	-0.956	-0.984	20.761	-0.109	-0.109	0.000	0.000	0.000	0.000
43	D	48	LYS	1	0.909	0.949	22.316	0.074	0.074	0.000	0.000	0.000	0.000
44	D	49	VAL	0	0.027	0.033	15.766	0.015	0.015	0.000	0.000	0.000	0.000
45	D	50	GLU	-1	-0.924	-0.948	18.139	-0.178	-0.178	0.000	0.000	0.000	0.000
46	D	51	HIS	1	0.907	0.920	13.345	0.488	0.488	0.000	0.000	0.000	0.000
47	D	52	SER	0	-0.024	0.008	12.888	0.013	0.013	0.000	0.000	0.000	0.000
48	D	53	ASP	-1	-0.885	-0.933	14.555	-0.448	-0.448	0.000	0.000	0.000	0.000
49	D	54	LEU	0	-0.006	-0.020	10.128	-0.003	-0.003	0.000	0.000	0.000	0.000
50	D	55	SER	0	-0.064	-0.018	11.485	0.151	0.151	0.000	0.000	0.000	0.000
51	D	56	PHE	0	0.003	-0.015	11.345	-0.187	-0.187	0.000	0.000	0.000	0.000
52	D	57	SER	0	-0.019	-0.010	9.508	0.208	0.208	0.000	0.000	0.000	0.000
53	D	58	LYS	1	0.988	0.965	12.096	0.097	0.097	0.000	0.000	0.000	0.000
54	D	59	ASP	-1	-0.975	-0.985	10.200	-0.712	-0.712	0.000	0.000	0.000	0.000
55	D	60	TRP	0	-0.018	0.008	11.890	-0.047	-0.047	0.000	0.000	0.000	0.000
56	D	61	SER	0	0.037	0.045	6.921	-0.081	-0.081	0.000	0.000	0.000	0.000
57	D	62	PHE	0	0.012	0.014	7.648	0.262	0.262	0.000	0.000	0.000	0.000
58	D	63	TYR	0	-0.012	-0.012	6.211	-0.708	-0.708	0.000	0.000	0.000	0.000
59	D	64	LEU	0	-0.021	0.003	7.085	0.231	0.231	0.000	0.000	0.000	0.000
60	D	65	LEU	0	0.004	0.000	8.362	0.076	0.076	0.000	0.000	0.000	0.000
61	D	66	TYR	0	0.039	0.031	9.448	0.072	0.072	0.000	0.000	0.000	0.000
62	D	67	TYR	0	-0.024	-0.019	12.729	0.084	0.084	0.000	0.000	0.000	0.000
63	D	68	THR	0	-0.011	-0.028	15.538	-0.024	-0.024	0.000	0.000	0.000	0.000
64	D	69	GLU	-1	-0.939	-0.943	18.908	0.033	0.033	0.000	0.000	0.000	0.000
65	D	70	PHE	0	-0.042	-0.040	19.287	0.005	0.005	0.000	0.000	0.000	0.000
66	D	71	THR	0	0.057	0.013	22.906	0.003	0.003	0.000	0.000	0.000	0.000
67	D	72	PRO	0	-0.073	-0.001	22.011	-0.002	-0.002	0.000	0.000	0.000	0.000
68	D	73	THR	0	-0.010	-0.057	23.926	-0.004	-0.004	0.000	0.000	0.000	0.000
69	D	74	GLU	-1	-0.958	-1.001	24.938	0.159	0.159	0.000	0.000	0.000	0.000
70	D	75	LYS	1	0.928	0.953	25.224	-0.119	-0.119	0.000	0.000	0.000	0.000
71	D	76	ASP	-1	-0.850	-0.850	23.371	0.087	0.087	0.000	0.000	0.000	0.000
72	D	77	GLU	-1	-0.908	-0.948	19.449	0.265	0.265	0.000	0.000	0.000	0.000
73	D	78	TYR	0	-0.012	-0.019	16.991	-0.048	-0.048	0.000	0.000	0.000	0.000
74	D	79	ALA	0	-0.015	0.005	13.868	0.063	0.063	0.000	0.000	0.000	0.000
75	D	81	ARG	1	0.860	0.923	11.570	0.207	0.207	0.000	0.000	0.000	0.000
76	D	82	VAL	0	0.030	0.021	6.751	-0.059	-0.059	0.000	0.000	0.000	0.000
77	D	83	ASN	0	-0.035	-0.015	9.769	0.097	0.097	0.000	0.000	0.000	0.000
78	D	84	HIS	0	0.018	0.003	7.226	-0.013	-0.013	0.000	0.000	0.000	0.000
79	D	85	VAL	0	-0.001	0.008	11.517	0.130	0.130	0.000	0.000	0.000	0.000
80	D	86	THR	0	-0.023	-0.015	14.783	-0.011	-0.011	0.000	0.000	0.000	0.000
81	D	87	LEU	0	-0.008	0.003	17.788	0.037	0.037	0.000	0.000	0.000	0.000
82	D	88	SER	0	-0.013	-0.025	20.934	0.019	0.019	0.000	0.000	0.000	0.000
83	D	89	GLN	0	-0.039	-0.015	24.424	0.011	0.011	0.000	0.000	0.000	0.000
84	D	90	PRO	0	0.039	0.038	26.871	0.004	0.004	0.000	0.000	0.000	0.000
85	D	91	LYS	1	0.997	0.989	28.405	0.135	0.135	0.000	0.000	0.000	0.000
86	D	92	ILE	0	0.002	0.001	30.848	-0.007	-0.007	0.000	0.000	0.000	0.000
87	D	93	VAL	0	-0.027	-0.022	33.118	0.010	0.010	0.000	0.000	0.000	0.000
88	D	94	LYS	1	0.959	0.980	35.284	0.114	0.114	0.000	0.000	0.000	0.000
89	D	95	TRP	0	0.033	0.009	37.693	0.002	0.002	0.000	0.000	0.000	0.000
90	D	96	ASP	-1	-0.945	-0.960	39.231	-0.085	-0.085	0.000	0.000	0.000	0.000
91	D	97	ARG	1	0.963	0.985	42.935	0.093	0.093	0.000	0.000	0.000	0.000

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