FMO DATABASE

FMODB ID: VR2J1

Calculation Name: 5D6H-B-Xray323

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D6H

Chain ID: B

ChEMBL ID:

UniProt ID: Q6XBY4

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	114
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-688765.132088
FMO2-HF: Nuclear repulsion	648625.230648
FMO2-HF: Total energy	-40139.901441
FMO2-MP2: Total energy	-40257.836879

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(B:6:ACE )

Summations of interaction energy for fragment #1(B:6:ACE )

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.
0.697	1.568	-0.007	-0.422	-0.442	0

Interaction energy analysis for fragmet #1(B:6:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.013

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].
3	B	8	HIS	0	0.019	0.013	3.820	0.772	1.643	-0.007	-0.422	-0.442
4	B	9	HIS	0	-0.043	-0.010	7.194	-0.024	-0.024	0.000	0.000	0.000
5	B	10	SER	0	-0.032	-0.021	8.263	0.064	0.064	0.000	0.000	0.000
6	B	11	THR	0	-0.006	-0.005	11.514	0.057	0.057	0.000	0.000	0.000
7	B	12	GLY	0	-0.017	0.005	13.878	-0.015	-0.015	0.000	0.000	0.000
8	B	60	CYS	0	-0.039	-0.004	16.185	0.010	0.010	0.000	0.000	0.000
9	B	14	THR	0	-0.025	-0.013	19.354	-0.004	-0.004	0.000	0.000	0.000
10	B	15	VAL	0	-0.001	-0.014	21.784	0.006	0.006	0.000	0.000	0.000
11	B	16	GLY	0	-0.020	0.034	25.301	-0.001	-0.001	0.000	0.000	0.000
12	B	17	GLY	0	0.019	0.006	27.513	-0.002	-0.002	0.000	0.000	0.000
13	B	18	SER	0	-0.028	-0.044	26.820	-0.002	-0.002	0.000	0.000	0.000
14	B	19	NME	0	0.012	0.022	28.483	0.004	0.004	0.000	0.000	0.000
15	B	27	ACE	0	0.004	-0.012	37.414	0.000	0.000	0.000	0.000	0.000
16	B	28	GLY	0	-0.001	-0.008	37.215	0.002	0.002	0.000	0.000	0.000
17	B	29	THR	0	-0.048	-0.012	37.685	-0.002	-0.002	0.000	0.000	0.000
18	B	30	LEU	0	0.038	0.014	39.908	0.002	0.002	0.000	0.000	0.000
19	B	31	ASN	0	-0.014	0.000	42.925	-0.001	-0.001	0.000	0.000	0.000
20	B	32	PHE	0	0.000	0.012	45.995	0.001	0.001	0.000	0.000	0.000
21	B	33	NME	0	0.025	0.026	49.255	0.000	0.000	0.000	0.000	0.000
22	B	42	ACE	0	0.024	0.003	59.438	0.000	0.000	0.000	0.000	0.000
23	B	43	LEU	0	0.019	0.001	57.566	0.001	0.001	0.000	0.000	0.000
24	B	44	THR	0	-0.029	-0.018	61.296	-0.001	-0.001	0.000	0.000	0.000
25	B	45	ALA	0	-0.038	-0.023	60.391	0.000	0.000	0.000	0.000	0.000
26	B	46	GLU	-1	-0.974	-0.971	58.989	0.003	0.003	0.000	0.000	0.000
27	B	47	VAL	0	-0.070	-0.038	59.423	0.000	0.000	0.000	0.000	0.000
28	B	48	ALA	0	0.030	0.005	57.308	0.000	0.000	0.000	0.000	0.000
29	B	49	SER	-1	-0.788	-0.836	52.375	0.004	0.004	0.000	0.000	0.000
30	B	50	ALA	0	-0.066	0.003	51.280	0.001	0.001	0.000	0.000	0.000
31	B	51	ALA	0	0.003	-0.023	46.361	-0.001	-0.001	0.000	0.000	0.000
32	B	52	THR	0	-0.050	-0.031	43.713	0.000	0.000	0.000	0.000	0.000
33	B	53	GLY	0	0.020	0.010	40.338	-0.001	-0.001	0.000	0.000	0.000
34	B	54	GLY	0	0.029	0.022	37.742	0.000	0.000	0.000	0.000	0.000
35	B	55	ASN	0	-0.072	-0.041	32.843	0.000	0.000	0.000	0.000	0.000
36	B	56	ILE	0	0.048	0.033	29.872	0.000	0.000	0.000	0.000	0.000
37	B	57	SER	0	-0.024	-0.012	26.067	0.000	0.000	0.000	0.000	0.000
38	B	58	VAL	0	0.041	0.012	22.817	-0.005	-0.005	0.000	0.000	0.000
39	B	59	THR	0	-0.027	-0.013	19.224	0.009	0.009	0.000	0.000	0.000
40	B	61	ASP	-1	-0.774	-0.898	12.760	-0.029	-0.029	0.000	0.000	0.000
41	B	62	GLY	0	0.071	0.048	12.193	0.003	0.003	0.000	0.000	0.000
42	B	63	THR	0	-0.123	-0.071	9.782	0.029	0.029	0.000	0.000	0.000
43	B	64	ASP	-1	-0.957	-0.986	12.653	-0.037	-0.037	0.000	0.000	0.000
44	B	65	PRO	0	-0.036	-0.010	15.589	-0.004	-0.004	0.000	0.000	0.000
45	B	66	VAL	0	0.015	0.018	17.775	-0.016	-0.016	0.000	0.000	0.000
46	B	67	ASP	-1	-0.884	-0.949	20.394	-0.016	-0.016	0.000	0.000	0.000
47	B	68	PHE	0	-0.020	-0.026	23.738	-0.006	-0.006	0.000	0.000	0.000
48	B	69	THR	0	-0.056	-0.020	26.116	0.007	0.007	0.000	0.000	0.000
49	B	70	VAL	0	0.000	0.001	29.786	-0.002	-0.002	0.000	0.000	0.000
50	B	71	ALA	0	-0.003	-0.004	32.323	0.002	0.002	0.000	0.000	0.000
51	B	72	ILE	0	-0.015	-0.006	35.717	-0.001	-0.001	0.000	0.000	0.000
52	B	73	ASP	-1	-0.843	-0.916	38.427	-0.017	-0.017	0.000	0.000	0.000
53	B	74	NME	0	-0.005	-0.004	41.300	0.002	0.002	0.000	0.000	0.000
54	B	92	ACE	0	0.023	-0.012	48.060	0.000	0.000	0.000	0.000	0.000
55	B	93	TYR	0	-0.168	-0.010	48.572	-0.001	-0.001	0.000	0.000	0.000
56	B	94	ASN	0	0.064	0.024	45.807	-0.002	-0.002	0.000	0.000	0.000
57	B	95	VAL	0	0.003	0.014	40.088	0.002	0.002	0.000	0.000	0.000
58	B	96	TYR	0	0.005	0.002	40.774	-0.001	-0.001	0.000	0.000	0.000
59	B	97	ARG	1	0.848	0.893	31.084	0.002	0.002	0.000	0.000	0.000
60	B	98	ASP	-1	-0.859	-0.921	36.848	0.011	0.011	0.000	0.000	0.000
61	B	99	ALA	0	0.038	0.026	39.133	-0.001	-0.001	0.000	0.000	0.000
62	B	100	ALA	0	-0.033	-0.026	40.743	0.000	0.000	0.000	0.000	0.000
63	B	101	ARG	1	0.887	0.943	42.857	-0.006	-0.006	0.000	0.000	0.000
64	B	102	THR	0	-0.023	-0.018	43.020	-0.001	-0.001	0.000	0.000	0.000
65	B	103	ASN	0	-0.020	-0.019	37.619	-0.002	-0.002	0.000	0.000	0.000
66	B	104	LEU	0	-0.007	-0.002	40.721	0.000	0.000	0.000	0.000	0.000
67	B	105	TYR	0	-0.014	-0.006	35.225	-0.001	-0.001	0.000	0.000	0.000
68	B	106	VAL	0	-0.034	-0.016	40.335	0.000	0.000	0.000	0.000	0.000
69	B	107	VAL	0	0.044	0.021	40.977	-0.001	-0.001	0.000	0.000	0.000
70	B	108	ASN	0	-0.029	-0.027	39.560	-0.001	-0.001	0.000	0.000	0.000
71	B	109	GLN	0	-0.031	-0.008	39.014	-0.003	-0.003	0.000	0.000	0.000
72	B	110	PRO	0	-0.016	-0.009	33.609	0.001	0.001	0.000	0.000	0.000
73	B	111	GLN	0	0.017	0.053	33.944	0.003	0.003	0.000	0.000	0.000
74	B	112	GLN	0	0.041	0.012	28.500	-0.002	-0.002	0.000	0.000	0.000
75	B	113	PHE	0	-0.019	-0.003	27.500	0.007	0.007	0.000	0.000	0.000
76	B	114	THR	0	0.065	0.055	23.173	-0.001	-0.001	0.000	0.000	0.000
77	B	115	THR	0	-0.017	-0.009	20.581	0.007	0.007	0.000	0.000	0.000
78	B	116	VAL	0	0.026	0.001	19.459	0.002	0.002	0.000	0.000	0.000
79	B	117	SER	0	0.071	0.028	15.704	-0.009	-0.009	0.000	0.000	0.000
80	B	118	GLY	0	-0.030	-0.018	17.826	-0.005	-0.005	0.000	0.000	0.000
81	B	119	GLN	0	-0.092	-0.042	20.049	-0.010	-0.010	0.000	0.000	0.000
82	B	120	ALA	0	0.053	0.057	21.275	0.003	0.003	0.000	0.000	0.000
83	B	121	THR	0	0.005	-0.029	22.672	-0.002	-0.002	0.000	0.000	0.000
84	B	122	ALA	0	-0.033	-0.001	25.684	-0.004	-0.004	0.000	0.000	0.000
85	B	123	VAL	0	0.037	0.013	28.741	-0.002	-0.002	0.000	0.000	0.000
86	B	124	PRO	0	-0.048	-0.020	31.188	0.000	0.000	0.000	0.000	0.000
87	B	125	ILE	0	0.037	0.014	34.464	-0.003	-0.003	0.000	0.000	0.000
88	B	126	PHE	0	-0.039	-0.026	37.355	0.002	0.002	0.000	0.000	0.000
89	B	127	GLY	0	0.052	0.027	41.067	-0.002	-0.002	0.000	0.000	0.000
90	B	128	ALA	0	-0.055	-0.052	44.193	0.001	0.001	0.000	0.000	0.000
91	B	129	ILE	0	-0.029	-0.018	47.799	-0.001	-0.001	0.000	0.000	0.000
92	B	130	ALA	0	0.121	0.234	51.372	0.001	0.001	0.000	0.000	0.000
93	B	131	PRO	0	-0.069	-0.183	54.465	0.000	0.000	0.000	0.000	0.000
94	B	132	ASN	0	0.066	0.012	55.887	0.000	0.000	0.000	0.000	0.000
95	B	133	THR	0	-0.111	-0.100	52.006	0.000	0.000	0.000	0.000	0.000
96	B	134	GLY	0	0.113	-0.027	50.894	-0.001	-0.001	0.000	0.000	0.000
97	B	135	THR	0	-0.052	-0.042	48.718	0.000	0.000	0.000	0.000	0.000
98	B	136	PRO	0	0.017	0.030	49.436	-0.001	-0.001	0.000	0.000	0.000
99	B	137	LYS	1	0.955	0.968	51.201	0.008	0.008	0.000	0.000	0.000
100	B	138	ALA	0	-0.024	0.016	53.210	0.000	0.000	0.000	0.000	0.000
101	B	139	GLN	0	-0.031	-0.018	55.906	0.000	0.000	0.000	0.000	0.000
102	B	140	GLY	0	0.033	0.018	56.410	0.000	0.000	0.000	0.000	0.000
103	B	141	ASP	-1	-0.816	-0.912	51.787	-0.004	-0.004	0.000	0.000	0.000
104	B	142	TYR	0	-0.058	-0.040	52.642	0.001	0.001	0.000	0.000	0.000
105	B	143	LYS	1	0.840	0.910	47.855	0.003	0.003	0.000	0.000	0.000
106	B	144	ASP	-1	-0.851	-0.927	46.184	-0.009	-0.009	0.000	0.000	0.000
107	B	145	THR	0	-0.111	-0.057	41.887	0.001	0.001	0.000	0.000	0.000
108	B	146	LEU	0	0.024	0.025	40.572	-0.001	-0.001	0.000	0.000	0.000
109	B	147	LEU	0	-0.017	0.002	37.057	0.000	0.000	0.000	0.000	0.000
110	B	148	VAL	0	-0.020	-0.021	33.217	0.000	0.000	0.000	0.000	0.000
111	B	149	THR	0	-0.026	-0.005	32.092	-0.003	-0.003	0.000	0.000	0.000
112	B	150	VAL	0	-0.017	-0.015	26.978	0.002	0.002	0.000	0.000	0.000
113	B	151	ASN	0	-0.074	-0.045	28.292	-0.006	-0.006	0.000	0.000	0.000
114	B	152	PHE	-1	-0.845	-0.925	22.523	-0.066	-0.066	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:6:ACE )