FMO DATABASE

FMODB ID: 59KRZ

Calculation Name: 1EM8-B-Xray309

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1EM8

Chain ID: B

ChEMBL ID:

UniProt ID: P28905

Base Structure: X-ray

Registration Date: 2021-09-06

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	112
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-818510.480807
FMO2-HF: Nuclear repulsion	776280.198349
FMO2-HF: Total energy	-42230.282458
FMO2-MP2: Total energy	-42353.034425

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:26:ACE )

Summations of interaction energy for fragment #1(B:26: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.
0.019	1.025	-0.005	-0.422	-0.579	-0.001

Interaction energy analysis for fragmet #1(B:26:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.020

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	B	28	GLU	-1	-0.946	-0.952	3.843	0.503	1.509	-0.005	-0.422	-0.579	-0.001
4	B	29	ILE	0	-0.056	-0.030	6.298	0.230	0.230	0.000	0.000	0.000	0.000
5	B	30	ALA	0	0.026	0.015	8.900	-0.212	-0.212	0.000	0.000	0.000	0.000
6	B	31	ILE	0	-0.074	-0.043	10.931	0.142	0.142	0.000	0.000	0.000	0.000
7	B	32	ALA	0	0.036	0.004	14.479	-0.011	-0.011	0.000	0.000	0.000	0.000
8	B	33	ILE	0	0.020	0.006	16.047	0.020	0.020	0.000	0.000	0.000	0.000
9	B	34	PRO	0	-0.022	-0.009	19.097	0.016	0.016	0.000	0.000	0.000	0.000
10	B	35	ALA	0	0.071	0.027	22.107	0.004	0.004	0.000	0.000	0.000	0.000
11	B	36	HIS	0	-0.005	0.009	23.825	0.007	0.007	0.000	0.000	0.000	0.000
12	B	37	VAL	0	-0.024	-0.004	23.330	0.007	0.007	0.000	0.000	0.000	0.000
13	B	38	ARG	1	0.814	0.893	24.725	0.100	0.100	0.000	0.000	0.000	0.000
14	B	39	LEU	0	-0.010	0.005	25.712	0.003	0.003	0.000	0.000	0.000	0.000
15	B	40	VAL	0	0.030	0.019	20.453	-0.004	-0.004	0.000	0.000	0.000	0.000
16	B	41	MET	0	-0.045	-0.010	23.688	0.009	0.009	0.000	0.000	0.000	0.000
17	B	42	VAL	0	0.030	0.010	21.245	-0.010	-0.010	0.000	0.000	0.000	0.000
18	B	43	ALA	0	0.014	-0.008	24.201	0.016	0.016	0.000	0.000	0.000	0.000
19	B	44	ASN	0	0.034	0.006	24.799	-0.025	-0.025	0.000	0.000	0.000	0.000
20	B	45	ASP	-1	-0.920	-0.942	26.313	-0.115	-0.115	0.000	0.000	0.000	0.000
21	B	46	LEU	0	-0.066	-0.036	24.520	0.004	0.004	0.000	0.000	0.000	0.000
22	B	47	PRO	0	0.006	0.011	28.872	0.007	0.007	0.000	0.000	0.000	0.000
23	B	48	ALA	0	0.066	0.036	31.592	-0.005	-0.005	0.000	0.000	0.000	0.000
24	B	49	LEU	0	0.034	0.005	29.965	0.005	0.005	0.000	0.000	0.000	0.000
25	B	50	THR	0	-0.025	-0.012	33.942	0.002	0.002	0.000	0.000	0.000	0.000
26	B	51	ASP	-1	-0.849	-0.933	36.640	-0.067	-0.067	0.000	0.000	0.000	0.000
27	B	52	PRO	0	-0.002	-0.012	38.320	0.000	0.000	0.000	0.000	0.000	0.000
28	B	53	LEU	0	0.019	0.020	37.700	0.001	0.001	0.000	0.000	0.000	0.000
29	B	54	VAL	0	0.003	-0.004	33.208	-0.001	-0.001	0.000	0.000	0.000	0.000
30	B	55	SER	0	0.037	0.011	35.840	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	56	ASP	-1	-0.948	-0.967	37.765	-0.054	-0.054	0.000	0.000	0.000	0.000
32	B	57	VAL	0	-0.055	-0.025	33.853	0.002	0.002	0.000	0.000	0.000	0.000
33	B	58	LEU	0	0.006	0.004	31.473	-0.001	-0.001	0.000	0.000	0.000	0.000
34	B	59	ARG	1	0.965	0.986	34.870	0.055	0.055	0.000	0.000	0.000	0.000
35	B	60	ALA	0	-0.042	-0.011	37.157	0.003	0.003	0.000	0.000	0.000	0.000
36	B	61	LEU	0	-0.015	-0.008	31.140	0.002	0.002	0.000	0.000	0.000	0.000
37	B	62	THR	0	-0.078	-0.042	33.873	0.000	0.000	0.000	0.000	0.000	0.000
38	B	63	VAL	0	0.002	0.015	30.190	-0.002	-0.002	0.000	0.000	0.000	0.000
39	B	64	SER	0	-0.011	-0.013	33.285	0.002	0.002	0.000	0.000	0.000	0.000
40	B	65	PRO	0	0.064	0.013	32.208	-0.007	-0.007	0.000	0.000	0.000	0.000
41	B	66	ASP	-1	-0.896	-0.947	31.071	-0.088	-0.088	0.000	0.000	0.000	0.000
42	B	67	GLN	0	-0.077	-0.038	28.824	-0.003	-0.003	0.000	0.000	0.000	0.000
43	B	68	VAL	0	0.016	0.004	27.277	-0.007	-0.007	0.000	0.000	0.000	0.000
44	B	69	LEU	0	-0.001	0.014	19.966	0.000	0.000	0.000	0.000	0.000	0.000
45	B	70	GLN	0	-0.062	-0.052	24.162	-0.003	-0.003	0.000	0.000	0.000	0.000
46	B	71	LEU	0	-0.025	-0.024	18.236	-0.014	-0.014	0.000	0.000	0.000	0.000
47	B	72	THR	0	0.049	0.031	21.167	0.005	0.005	0.000	0.000	0.000	0.000
48	B	73	PRO	0	0.036	-0.012	19.867	-0.027	-0.027	0.000	0.000	0.000	0.000
49	B	74	GLU	-1	-0.950	-0.947	17.085	-0.314	-0.314	0.000	0.000	0.000	0.000
50	B	75	LYS	1	1.014	0.984	15.384	0.208	0.208	0.000	0.000	0.000	0.000
51	B	76	ILE	0	-0.025	0.011	14.731	-0.055	-0.055	0.000	0.000	0.000	0.000
52	B	77	ALA	0	0.013	0.008	11.472	-0.019	-0.019	0.000	0.000	0.000	0.000
53	B	78	MET	0	-0.069	-0.045	10.403	-0.145	-0.145	0.000	0.000	0.000	0.000
54	B	79	LEU	0	-0.016	0.026	11.479	-0.016	-0.016	0.000	0.000	0.000	0.000
55	B	80	PRO	0	-0.024	0.006	9.693	-0.109	-0.109	0.000	0.000	0.000	0.000
56	B	81	GLN	0	0.036	0.009	7.829	0.152	0.152	0.000	0.000	0.000	0.000
57	B	82	GLY	0	0.029	0.016	9.923	0.063	0.063	0.000	0.000	0.000	0.000
58	B	83	SER	0	-0.066	-0.034	13.291	0.039	0.039	0.000	0.000	0.000	0.000
59	B	84	HIS	0	0.032	0.014	15.552	0.004	0.004	0.000	0.000	0.000	0.000
60	B	85	CYS	0	-0.079	-0.032	19.196	0.010	0.010	0.000	0.000	0.000	0.000
61	B	86	ASN	0	0.045	0.055	21.938	-0.006	-0.006	0.000	0.000	0.000	0.000
62	B	87	SER	0	0.022	-0.006	22.710	-0.011	-0.011	0.000	0.000	0.000	0.000
63	B	88	TRP	0	0.037	0.001	24.847	0.012	0.012	0.000	0.000	0.000	0.000
64	B	89	ARG	1	0.854	0.930	23.715	0.122	0.122	0.000	0.000	0.000	0.000
65	B	90	LEU	0	-0.033	-0.021	26.668	0.013	0.013	0.000	0.000	0.000	0.000
66	B	91	GLY	0	-0.065	-0.041	27.965	-0.007	-0.007	0.000	0.000	0.000	0.000
67	B	92	THR	0	-0.033	-0.012	22.862	-0.006	-0.006	0.000	0.000	0.000	0.000
68	B	93	ASP	-1	-0.911	-0.951	25.750	-0.096	-0.096	0.000	0.000	0.000	0.000
69	B	94	GLU	-1	-0.913	-0.949	20.879	-0.137	-0.137	0.000	0.000	0.000	0.000
70	B	95	PRO	0	-0.045	-0.029	21.595	-0.011	-0.011	0.000	0.000	0.000	0.000
71	B	96	LEU	0	0.028	0.016	19.011	-0.019	-0.019	0.000	0.000	0.000	0.000
72	B	97	SER	0	-0.009	-0.003	14.235	0.013	0.013	0.000	0.000	0.000	0.000
73	B	98	LEU	0	-0.068	-0.045	15.037	-0.049	-0.049	0.000	0.000	0.000	0.000
74	B	99	GLU	-1	-0.937	-0.951	16.930	-0.095	-0.095	0.000	0.000	0.000	0.000
75	B	100	GLY	0	0.061	0.008	19.271	-0.006	-0.006	0.000	0.000	0.000	0.000
76	B	101	ALA	0	-0.007	0.013	22.905	0.001	0.001	0.000	0.000	0.000	0.000
77	B	102	GLN	0	-0.027	-0.018	20.797	-0.010	-0.010	0.000	0.000	0.000	0.000
78	B	103	VAL	0	0.007	0.012	25.881	0.009	0.009	0.000	0.000	0.000	0.000
79	B	104	ALA	0	0.016	0.002	27.823	-0.010	-0.010	0.000	0.000	0.000	0.000
80	B	105	SER	0	-0.007	0.005	29.440	0.009	0.009	0.000	0.000	0.000	0.000
81	B	106	PRO	0	0.037	0.017	31.062	-0.006	-0.006	0.000	0.000	0.000	0.000
82	B	107	ALA	0	0.105	0.048	31.803	-0.004	-0.004	0.000	0.000	0.000	0.000
83	B	108	LEU	0	0.041	0.018	32.767	0.006	0.006	0.000	0.000	0.000	0.000
84	B	109	THR	0	-0.024	-0.015	34.881	0.006	0.006	0.000	0.000	0.000	0.000
85	B	110	ASP	-1	-0.860	-0.937	36.025	-0.067	-0.067	0.000	0.000	0.000	0.000
86	B	111	LEU	0	-0.052	-0.003	35.079	0.005	0.005	0.000	0.000	0.000	0.000
87	B	112	ARG	1	0.917	0.941	37.951	0.072	0.072	0.000	0.000	0.000	0.000
88	B	113	ALA	0	-0.010	-0.002	40.587	0.004	0.004	0.000	0.000	0.000	0.000
89	B	114	ASN	0	0.045	0.041	40.351	0.004	0.004	0.000	0.000	0.000	0.000
90	B	115	PRO	0	0.027	-0.013	41.578	-0.002	-0.002	0.000	0.000	0.000	0.000
91	B	116	THR	0	0.021	0.009	42.018	0.000	0.000	0.000	0.000	0.000	0.000
92	B	117	ALA	0	-0.010	0.001	37.795	-0.001	-0.001	0.000	0.000	0.000	0.000
93	B	118	ARG	1	0.889	0.940	38.214	0.050	0.050	0.000	0.000	0.000	0.000
94	B	119	ALA	0	-0.010	0.008	39.556	-0.001	-0.001	0.000	0.000	0.000	0.000
95	B	120	ALA	0	0.014	0.004	37.642	0.000	0.000	0.000	0.000	0.000	0.000
96	B	121	LEU	0	0.020	0.010	33.357	-0.001	-0.001	0.000	0.000	0.000	0.000
97	B	122	TRP	0	0.025	0.013	35.648	-0.002	-0.002	0.000	0.000	0.000	0.000
98	B	123	GLN	0	0.006	0.004	37.676	0.000	0.000	0.000	0.000	0.000	0.000
99	B	124	GLN	0	-0.005	-0.014	30.603	-0.004	-0.004	0.000	0.000	0.000	0.000
100	B	125	ILE	0	-0.006	-0.010	33.393	-0.001	-0.001	0.000	0.000	0.000	0.000
101	B	126	CYS	0	-0.063	-0.035	34.531	0.001	0.001	0.000	0.000	0.000	0.000
102	B	127	THR	0	-0.035	0.000	33.072	0.003	0.003	0.000	0.000	0.000	0.000
103	B	128	TYR	0	-0.008	-0.002	28.535	0.001	0.001	0.000	0.000	0.000	0.000
104	B	129	GLU	-1	-0.855	-0.918	32.651	-0.042	-0.042	0.000	0.000	0.000	0.000
105	B	130	HIS	0	-0.037	-0.019	32.918	-0.001	-0.001	0.000	0.000	0.000	0.000
106	B	131	ASP	-1	-0.884	-0.934	28.570	-0.069	-0.069	0.000	0.000	0.000	0.000
107	B	132	PHE	0	-0.043	-0.028	28.779	-0.005	-0.005	0.000	0.000	0.000	0.000
108	B	133	PHE	0	-0.050	-0.015	32.562	0.001	0.001	0.000	0.000	0.000	0.000
109	B	134	PRO	0	0.008	0.016	32.530	0.005	0.005	0.000	0.000	0.000	0.000
110	B	135	ARG	1	0.802	0.866	35.394	0.042	0.042	0.000	0.000	0.000	0.000
111	B	136	ASN	0	-0.008	-0.012	37.842	0.001	0.001	0.000	0.000	0.000	0.000
112	B	137	NME	0	-0.011	0.013	40.176	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:26:ACE )