FMO DATABASE

FMODB ID: GN8G1

Calculation Name: 1EM8-B-Xray372

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: 2023-03-13

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	110
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-814377.917723
FMO2-HF: Nuclear repulsion	772318.100858
FMO2-HF: Total energy	-42059.816865
FMO2-MP2: Total energy	-42181.970849

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:27:GLY)

Summations of interaction energy for fragment #1(B:27:GLY)

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.
1.42	2.667	-0.012	-0.581	-0.653	0.002

Interaction energy analysis for fragmet #1(B:27:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : 0.001

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	29	ILE	0	-0.046	-0.025	3.809	0.579	1.718	-0.011	-0.572	-0.556	0.002
4	B	30	ALA	0	0.022	0.016	4.791	-0.064	0.044	-0.001	-0.009	-0.097	0.000
5	B	31	ILE	0	-0.067	-0.042	6.813	0.195	0.195	0.000	0.000	0.000	0.000
6	B	32	ALA	0	0.035	0.007	10.263	0.027	0.027	0.000	0.000	0.000	0.000
7	B	33	ILE	0	0.024	0.006	12.083	0.083	0.083	0.000	0.000	0.000	0.000
8	B	34	PRO	0	-0.012	-0.004	15.205	-0.022	-0.022	0.000	0.000	0.000	0.000
9	B	35	ALA	0	0.061	0.023	18.269	0.025	0.025	0.000	0.000	0.000	0.000
10	B	36	HIS	0	-0.012	0.003	20.361	0.003	0.003	0.000	0.000	0.000	0.000
11	B	37	VAL	0	-0.036	-0.002	19.226	0.024	0.024	0.000	0.000	0.000	0.000
12	B	38	ARG	1	0.824	0.895	21.145	0.178	0.178	0.000	0.000	0.000	0.000
13	B	39	LEU	0	-0.001	0.008	22.108	0.016	0.016	0.000	0.000	0.000	0.000
14	B	40	VAL	0	0.031	0.016	16.577	-0.015	-0.015	0.000	0.000	0.000	0.000
15	B	41	MET	0	-0.049	-0.009	19.820	0.024	0.024	0.000	0.000	0.000	0.000
16	B	42	VAL	0	0.027	0.007	17.672	-0.007	-0.007	0.000	0.000	0.000	0.000
17	B	43	ALA	0	0.020	-0.001	20.526	0.009	0.009	0.000	0.000	0.000	0.000
18	B	44	ASN	0	0.012	-0.004	21.828	0.007	0.007	0.000	0.000	0.000	0.000
19	B	45	ASP	-1	-0.914	-0.946	23.066	0.056	0.056	0.000	0.000	0.000	0.000
20	B	46	LEU	0	-0.050	-0.024	20.580	-0.005	-0.005	0.000	0.000	0.000	0.000
21	B	47	PRO	0	0.005	0.012	25.079	-0.005	-0.005	0.000	0.000	0.000	0.000
22	B	48	ALA	0	0.050	0.029	27.607	-0.009	-0.009	0.000	0.000	0.000	0.000
23	B	49	LEU	0	0.041	0.007	25.857	0.007	0.007	0.000	0.000	0.000	0.000
24	B	50	THR	0	-0.001	-0.001	29.825	-0.001	-0.001	0.000	0.000	0.000	0.000
25	B	51	ASP	-1	-0.821	-0.898	32.553	0.001	0.001	0.000	0.000	0.000	0.000
26	B	52	PRO	0	-0.003	-0.011	34.312	-0.001	-0.001	0.000	0.000	0.000	0.000
27	B	53	LEU	0	0.004	0.014	33.920	0.000	0.000	0.000	0.000	0.000	0.000
28	B	54	VAL	0	-0.006	-0.013	29.229	0.001	0.001	0.000	0.000	0.000	0.000
29	B	55	SER	0	0.026	0.008	31.885	-0.005	-0.005	0.000	0.000	0.000	0.000
30	B	56	ASP	-1	-0.898	-0.947	33.729	-0.022	-0.022	0.000	0.000	0.000	0.000
31	B	57	VAL	0	-0.050	-0.019	30.230	0.000	0.000	0.000	0.000	0.000	0.000
32	B	58	LEU	0	0.005	0.005	27.382	-0.001	-0.001	0.000	0.000	0.000	0.000
33	B	59	ARG	1	0.925	0.963	31.040	0.029	0.029	0.000	0.000	0.000	0.000
34	B	60	ALA	0	-0.044	-0.012	33.732	-0.001	-0.001	0.000	0.000	0.000	0.000
35	B	61	LEU	0	-0.009	-0.011	27.614	0.002	0.002	0.000	0.000	0.000	0.000
36	B	62	THR	0	-0.061	-0.031	30.430	-0.006	-0.006	0.000	0.000	0.000	0.000
37	B	63	VAL	0	-0.019	0.001	26.461	-0.009	-0.009	0.000	0.000	0.000	0.000
38	B	64	SER	0	-0.012	-0.020	29.570	0.010	0.010	0.000	0.000	0.000	0.000
39	B	65	PRO	0	0.044	0.001	28.236	-0.007	-0.007	0.000	0.000	0.000	0.000
40	B	66	ASP	-1	-0.865	-0.921	26.925	-0.109	-0.109	0.000	0.000	0.000	0.000
41	B	67	GLN	0	-0.061	-0.032	24.892	-0.009	-0.009	0.000	0.000	0.000	0.000
42	B	68	VAL	0	0.008	0.000	23.265	-0.002	-0.002	0.000	0.000	0.000	0.000
43	B	69	LEU	0	-0.003	0.013	15.760	-0.014	-0.014	0.000	0.000	0.000	0.000
44	B	70	GLN	0	-0.057	-0.050	20.063	0.012	0.012	0.000	0.000	0.000	0.000
45	B	71	LEU	0	-0.010	-0.013	14.264	-0.027	-0.027	0.000	0.000	0.000	0.000
46	B	72	THR	0	0.020	-0.006	17.519	0.006	0.006	0.000	0.000	0.000	0.000
47	B	73	PRO	0	0.025	-0.016	16.285	-0.004	-0.004	0.000	0.000	0.000	0.000
48	B	74	GLU	-1	-0.883	-0.881	13.886	0.142	0.142	0.000	0.000	0.000	0.000
49	B	75	LYS	1	0.964	0.942	11.817	0.111	0.111	0.000	0.000	0.000	0.000
50	B	76	ILE	0	-0.015	0.015	10.900	-0.063	-0.063	0.000	0.000	0.000	0.000
51	B	77	ALA	0	0.018	0.011	8.954	-0.030	-0.030	0.000	0.000	0.000	0.000
52	B	78	MET	0	-0.067	-0.042	6.777	0.251	0.251	0.000	0.000	0.000	0.000
53	B	79	LEU	0	-0.010	0.028	7.279	-0.464	-0.464	0.000	0.000	0.000	0.000
54	B	80	PRO	0	-0.010	0.011	6.194	0.056	0.056	0.000	0.000	0.000	0.000
55	B	81	GLN	0	0.020	0.004	6.070	0.211	0.211	0.000	0.000	0.000	0.000
56	B	82	GLY	0	0.026	0.013	7.766	-0.176	-0.176	0.000	0.000	0.000	0.000
57	B	83	SER	0	-0.062	-0.033	10.410	-0.057	-0.057	0.000	0.000	0.000	0.000
58	B	84	HIS	0	0.020	0.000	12.751	0.078	0.078	0.000	0.000	0.000	0.000
59	B	85	CYS	0	-0.071	-0.030	16.508	-0.038	-0.038	0.000	0.000	0.000	0.000
60	B	86	ASN	0	0.040	0.057	18.785	0.028	0.028	0.000	0.000	0.000	0.000
61	B	87	SER	0	0.021	-0.003	19.286	-0.006	-0.006	0.000	0.000	0.000	0.000
62	B	88	TRP	0	0.025	-0.002	21.432	0.004	0.004	0.000	0.000	0.000	0.000
63	B	89	ARG	1	0.858	0.932	20.937	-0.141	-0.141	0.000	0.000	0.000	0.000
64	B	90	LEU	0	-0.030	-0.017	23.267	0.000	0.000	0.000	0.000	0.000	0.000
65	B	91	GLY	0	-0.062	-0.037	24.805	0.008	0.008	0.000	0.000	0.000	0.000
66	B	92	THR	0	-0.037	-0.020	20.109	0.013	0.013	0.000	0.000	0.000	0.000
67	B	93	ASP	-1	-0.917	-0.958	23.164	0.154	0.154	0.000	0.000	0.000	0.000
68	B	94	GLU	-1	-0.903	-0.940	19.158	0.312	0.312	0.000	0.000	0.000	0.000
69	B	95	PRO	0	-0.036	-0.021	19.581	-0.014	-0.014	0.000	0.000	0.000	0.000
70	B	96	LEU	0	0.007	0.010	15.941	0.038	0.038	0.000	0.000	0.000	0.000
71	B	97	SER	0	0.000	0.011	11.497	0.017	0.017	0.000	0.000	0.000	0.000
72	B	98	LEU	0	-0.072	-0.047	12.396	-0.015	-0.015	0.000	0.000	0.000	0.000
73	B	99	GLU	-1	-0.918	-0.945	14.708	0.094	0.094	0.000	0.000	0.000	0.000
74	B	100	GLY	0	0.062	0.017	16.962	-0.036	-0.036	0.000	0.000	0.000	0.000
75	B	101	ALA	0	-0.018	0.007	20.356	0.025	0.025	0.000	0.000	0.000	0.000
76	B	102	GLN	0	-0.031	-0.028	18.091	0.001	0.001	0.000	0.000	0.000	0.000
77	B	103	VAL	0	0.007	0.010	23.054	0.009	0.009	0.000	0.000	0.000	0.000
78	B	104	ALA	0	0.003	-0.003	24.727	0.003	0.003	0.000	0.000	0.000	0.000
79	B	105	SER	0	-0.003	0.006	26.410	-0.008	-0.008	0.000	0.000	0.000	0.000
80	B	106	PRO	0	0.037	0.013	28.044	0.007	0.007	0.000	0.000	0.000	0.000
81	B	107	ALA	0	0.096	0.046	28.603	-0.006	-0.006	0.000	0.000	0.000	0.000
82	B	108	LEU	0	0.040	0.013	29.582	-0.004	-0.004	0.000	0.000	0.000	0.000
83	B	109	THR	0	-0.027	-0.019	31.388	-0.006	-0.006	0.000	0.000	0.000	0.000
84	B	110	ASP	-1	-0.864	-0.934	32.811	0.060	0.060	0.000	0.000	0.000	0.000
85	B	111	LEU	0	-0.047	-0.006	31.529	-0.003	-0.003	0.000	0.000	0.000	0.000
86	B	112	ARG	1	0.890	0.909	33.989	-0.016	-0.016	0.000	0.000	0.000	0.000
87	B	113	ALA	0	-0.005	0.002	37.078	-0.003	-0.003	0.000	0.000	0.000	0.000
88	B	114	ASN	0	0.032	0.028	37.319	-0.002	-0.002	0.000	0.000	0.000	0.000
89	B	115	PRO	0	0.021	-0.007	38.402	0.000	0.000	0.000	0.000	0.000	0.000
90	B	116	THR	0	0.023	0.011	39.656	-0.003	-0.003	0.000	0.000	0.000	0.000
91	B	117	ALA	0	0.009	0.011	34.739	0.001	0.001	0.000	0.000	0.000	0.000
92	B	118	ARG	1	0.886	0.935	35.104	-0.019	-0.019	0.000	0.000	0.000	0.000
93	B	119	ALA	0	-0.013	0.006	36.316	-0.003	-0.003	0.000	0.000	0.000	0.000
94	B	120	ALA	0	0.010	0.002	34.970	-0.001	-0.001	0.000	0.000	0.000	0.000
95	B	121	LEU	0	0.016	0.012	30.348	0.002	0.002	0.000	0.000	0.000	0.000
96	B	122	TRP	0	0.029	0.011	32.591	-0.001	-0.001	0.000	0.000	0.000	0.000
97	B	123	GLN	0	0.011	0.010	34.722	0.001	0.001	0.000	0.000	0.000	0.000
98	B	124	GLN	0	0.010	-0.004	27.988	0.003	0.003	0.000	0.000	0.000	0.000
99	B	125	ILE	0	0.007	-0.002	30.074	-0.001	-0.001	0.000	0.000	0.000	0.000
100	B	126	CYS	0	-0.071	-0.036	31.581	-0.005	-0.005	0.000	0.000	0.000	0.000
101	B	127	THR	0	-0.051	-0.018	31.220	-0.001	-0.001	0.000	0.000	0.000	0.000
102	B	128	TYR	0	-0.014	-0.001	25.875	0.002	0.002	0.000	0.000	0.000	0.000
103	B	129	GLU	-1	-0.854	-0.913	29.978	-0.015	-0.015	0.000	0.000	0.000	0.000
104	B	130	HIS	0	-0.024	-0.013	30.636	-0.011	-0.011	0.000	0.000	0.000	0.000
105	B	131	ASP	-1	-0.901	-0.945	26.002	-0.020	-0.020	0.000	0.000	0.000	0.000
106	B	132	PHE	0	-0.044	-0.030	25.434	-0.012	-0.012	0.000	0.000	0.000	0.000
107	B	133	PHE	0	-0.049	-0.013	29.559	-0.004	-0.004	0.000	0.000	0.000	0.000
108	B	134	PRO	0	0.026	0.020	29.919	0.004	0.004	0.000	0.000	0.000	0.000
109	B	135	ARG	1	0.789	0.863	32.762	0.022	0.022	0.000	0.000	0.000	0.000
110	B	136	ASN	0	-0.012	0.004	35.448	-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:27:GLY)