FMO DATABASE

FMODB ID: 145KZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-813885.856204
FMO2-HF: Nuclear repulsion	771826.518768
FMO2-HF: Total energy	-42059.337435
FMO2-MP2: Total energy	-42181.5609

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.
-0.428	0.44	-0.01	-0.327	-0.531	0

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 : -0.016 / q_NPA : -0.029

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].
3	B	29	ILE	0	-0.057	-0.031	3.809	-0.160	0.609	-0.009	-0.318	-0.443
4	B	30	ALA	0	0.022	0.013	4.790	-0.248	-0.149	-0.001	-0.009	-0.088
5	B	31	ILE	0	-0.073	-0.042	6.808	0.287	0.287	0.000	0.000	0.000
6	B	32	ALA	0	0.037	0.005	10.259	-0.048	-0.048	0.000	0.000	0.000
7	B	33	ILE	0	0.019	0.006	12.073	0.096	0.096	0.000	0.000	0.000
8	B	34	PRO	0	-0.022	-0.008	15.196	-0.010	-0.010	0.000	0.000	0.000
9	B	35	ALA	0	0.069	0.026	18.259	0.010	0.010	0.000	0.000	0.000
10	B	36	HIS	0	-0.004	0.009	20.347	-0.002	-0.002	0.000	0.000	0.000
11	B	37	VAL	0	-0.023	-0.004	19.367	0.022	0.022	0.000	0.000	0.000
12	B	38	ARG	1	0.816	0.894	21.136	0.225	0.225	0.000	0.000	0.000
13	B	39	LEU	0	-0.012	0.005	22.087	0.007	0.007	0.000	0.000	0.000
14	B	40	VAL	0	0.033	0.020	16.668	-0.003	-0.003	0.000	0.000	0.000
15	B	41	MET	0	-0.048	-0.011	19.820	0.019	0.019	0.000	0.000	0.000
16	B	42	VAL	0	0.030	0.009	17.650	-0.004	-0.004	0.000	0.000	0.000
17	B	43	ALA	0	0.014	-0.007	20.532	0.011	0.011	0.000	0.000	0.000
18	B	44	ASN	0	0.034	0.006	21.839	-0.003	-0.003	0.000	0.000	0.000
19	B	45	ASP	-1	-0.919	-0.942	23.078	-0.006	-0.006	0.000	0.000	0.000
20	B	46	LEU	0	-0.066	-0.036	20.643	-0.007	-0.007	0.000	0.000	0.000
21	B	47	PRO	0	0.005	0.012	25.087	0.004	0.004	0.000	0.000	0.000
22	B	48	ALA	0	0.065	0.036	27.611	-0.008	-0.008	0.000	0.000	0.000
23	B	49	LEU	0	0.035	0.005	25.840	0.004	0.004	0.000	0.000	0.000
24	B	50	THR	0	-0.025	-0.012	29.826	-0.001	-0.001	0.000	0.000	0.000
25	B	51	ASP	-1	-0.849	-0.933	32.606	-0.041	-0.041	0.000	0.000	0.000
26	B	52	PRO	0	-0.003	-0.012	34.315	-0.003	-0.003	0.000	0.000	0.000
27	B	53	LEU	0	0.021	0.021	33.971	-0.001	-0.001	0.000	0.000	0.000
28	B	54	VAL	0	-0.002	-0.005	29.215	-0.003	-0.003	0.000	0.000	0.000
29	B	55	SER	0	0.040	0.011	31.887	-0.007	-0.007	0.000	0.000	0.000
30	B	56	ASP	-1	-0.950	-0.967	33.729	-0.060	-0.060	0.000	0.000	0.000
31	B	57	VAL	0	-0.053	-0.024	30.175	-0.001	-0.001	0.000	0.000	0.000
32	B	58	LEU	0	0.006	0.004	27.520	-0.005	-0.005	0.000	0.000	0.000
33	B	59	ARG	1	0.963	0.985	31.039	0.067	0.067	0.000	0.000	0.000
34	B	60	ALA	0	-0.042	-0.011	33.609	-0.001	-0.001	0.000	0.000	0.000
35	B	61	LEU	0	-0.013	-0.007	27.583	0.000	0.000	0.000	0.000	0.000
36	B	62	THR	0	-0.078	-0.042	30.426	-0.009	-0.009	0.000	0.000	0.000
37	B	63	VAL	0	0.001	0.015	26.401	-0.008	-0.008	0.000	0.000	0.000
38	B	64	SER	0	-0.010	-0.012	29.566	0.011	0.011	0.000	0.000	0.000
39	B	65	PRO	0	0.063	0.013	28.232	-0.011	-0.011	0.000	0.000	0.000
40	B	66	ASP	-1	-0.897	-0.949	26.921	-0.130	-0.130	0.000	0.000	0.000
41	B	67	GLN	0	-0.076	-0.037	24.888	-0.007	-0.007	0.000	0.000	0.000
42	B	68	VAL	0	0.018	0.003	23.260	-0.014	-0.014	0.000	0.000	0.000
43	B	69	LEU	0	-0.003	0.015	15.747	-0.001	-0.001	0.000	0.000	0.000
44	B	70	GLN	0	-0.063	-0.052	20.063	0.002	0.002	0.000	0.000	0.000
45	B	71	LEU	0	-0.027	-0.023	14.208	-0.014	-0.014	0.000	0.000	0.000
46	B	72	THR	0	0.054	0.033	17.541	0.001	0.001	0.000	0.000	0.000
47	B	73	PRO	0	0.031	-0.014	16.295	-0.021	-0.021	0.000	0.000	0.000
48	B	74	GLU	-1	-0.948	-0.946	13.784	0.003	0.003	0.000	0.000	0.000
49	B	75	LYS	1	1.012	0.985	11.807	0.132	0.132	0.000	0.000	0.000
50	B	76	ILE	0	-0.025	0.009	10.908	-0.084	-0.084	0.000	0.000	0.000
51	B	77	ALA	0	0.012	0.007	8.891	-0.083	-0.083	0.000	0.000	0.000
52	B	78	MET	0	-0.070	-0.044	6.785	0.066	0.066	0.000	0.000	0.000
53	B	79	LEU	0	-0.015	0.026	7.279	-0.326	-0.326	0.000	0.000	0.000
54	B	80	PRO	0	-0.023	0.007	6.187	-0.116	-0.116	0.000	0.000	0.000
55	B	81	GLN	0	0.030	0.006	6.051	0.326	0.326	0.000	0.000	0.000
56	B	82	GLY	0	0.031	0.017	7.758	-0.063	-0.063	0.000	0.000	0.000
57	B	83	SER	0	-0.064	-0.034	10.409	0.055	0.055	0.000	0.000	0.000
58	B	84	HIS	0	0.031	0.014	12.742	0.041	0.041	0.000	0.000	0.000
59	B	85	CYS	0	-0.077	-0.030	16.500	0.004	0.004	0.000	0.000	0.000
60	B	86	ASN	0	0.047	0.055	18.779	0.003	0.003	0.000	0.000	0.000
61	B	87	SER	0	0.020	-0.007	19.288	-0.005	-0.005	0.000	0.000	0.000
62	B	88	TRP	0	0.036	0.001	21.432	0.012	0.012	0.000	0.000	0.000
63	B	89	ARG	1	0.854	0.930	20.758	0.066	0.066	0.000	0.000	0.000
64	B	90	LEU	0	-0.033	-0.021	23.274	0.008	0.008	0.000	0.000	0.000
65	B	91	GLY	0	-0.064	-0.040	24.815	0.004	0.004	0.000	0.000	0.000
66	B	92	THR	0	-0.032	-0.012	20.118	0.012	0.012	0.000	0.000	0.000
67	B	93	ASP	-1	-0.910	-0.950	23.175	-0.022	-0.022	0.000	0.000	0.000
68	B	94	GLU	-1	-0.915	-0.950	19.147	0.019	0.019	0.000	0.000	0.000
69	B	95	PRO	0	-0.042	-0.028	19.685	-0.012	-0.012	0.000	0.000	0.000
70	B	96	LEU	0	0.026	0.016	15.923	0.008	0.008	0.000	0.000	0.000
71	B	97	SER	0	-0.009	-0.004	11.497	0.024	0.024	0.000	0.000	0.000
72	B	98	LEU	0	-0.070	-0.045	12.399	-0.077	-0.077	0.000	0.000	0.000
73	B	99	GLU	-1	-0.935	-0.950	14.708	-0.233	-0.233	0.000	0.000	0.000
74	B	100	GLY	0	0.060	0.007	16.959	-0.015	-0.015	0.000	0.000	0.000
75	B	101	ALA	0	-0.005	0.014	20.352	0.016	0.016	0.000	0.000	0.000
76	B	102	GLN	0	-0.031	-0.020	18.386	0.012	0.012	0.000	0.000	0.000
77	B	103	VAL	0	0.010	0.014	23.056	0.014	0.014	0.000	0.000	0.000
78	B	104	ALA	0	0.011	0.000	24.731	-0.004	-0.004	0.000	0.000	0.000
79	B	105	SER	0	-0.007	0.006	26.417	0.002	0.002	0.000	0.000	0.000
80	B	106	PRO	0	0.038	0.017	28.053	0.002	0.002	0.000	0.000	0.000
81	B	107	ALA	0	0.107	0.048	28.607	-0.006	-0.006	0.000	0.000	0.000
82	B	108	LEU	0	0.037	0.017	29.584	0.001	0.001	0.000	0.000	0.000
83	B	109	THR	0	-0.021	-0.015	31.396	0.000	0.000	0.000	0.000	0.000
84	B	110	ASP	-1	-0.864	-0.938	33.239	-0.010	-0.010	0.000	0.000	0.000
85	B	111	LEU	0	-0.051	-0.003	31.605	0.000	0.000	0.000	0.000	0.000
86	B	112	ARG	1	0.917	0.941	34.311	0.035	0.035	0.000	0.000	0.000
87	B	113	ALA	0	-0.010	-0.003	37.086	0.000	0.000	0.000	0.000	0.000
88	B	114	ASN	0	0.045	0.042	37.334	0.000	0.000	0.000	0.000	0.000
89	B	115	PRO	0	0.027	-0.013	38.410	-0.003	-0.003	0.000	0.000	0.000
90	B	116	THR	0	0.019	0.008	39.342	-0.003	-0.003	0.000	0.000	0.000
91	B	117	ALA	0	-0.009	0.001	34.803	-0.002	-0.002	0.000	0.000	0.000
92	B	118	ARG	1	0.893	0.942	35.111	0.030	0.030	0.000	0.000	0.000
93	B	119	ALA	0	-0.013	0.007	36.321	-0.004	-0.004	0.000	0.000	0.000
94	B	120	ALA	0	0.013	0.004	34.917	-0.003	-0.003	0.000	0.000	0.000
95	B	121	LEU	0	0.019	0.010	30.012	-0.003	-0.003	0.000	0.000	0.000
96	B	122	TRP	0	0.026	0.013	32.594	-0.006	-0.006	0.000	0.000	0.000
97	B	123	GLN	0	0.005	0.003	34.723	-0.003	-0.003	0.000	0.000	0.000
98	B	124	GLN	0	-0.005	-0.015	27.865	-0.007	-0.007	0.000	0.000	0.000
99	B	125	ILE	0	-0.003	-0.008	30.205	-0.005	-0.005	0.000	0.000	0.000
100	B	126	CYS	0	-0.064	-0.035	31.582	-0.004	-0.004	0.000	0.000	0.000
101	B	127	THR	0	-0.037	-0.002	30.878	0.000	0.000	0.000	0.000	0.000
102	B	128	TYR	0	-0.004	0.000	26.248	-0.004	-0.004	0.000	0.000	0.000
103	B	129	GLU	-1	-0.858	-0.919	29.975	-0.084	-0.084	0.000	0.000	0.000
104	B	130	HIS	0	-0.037	-0.020	30.714	-0.004	-0.004	0.000	0.000	0.000
105	B	131	ASP	-1	-0.885	-0.934	25.994	-0.149	-0.149	0.000	0.000	0.000
106	B	132	PHE	0	-0.044	-0.029	25.645	-0.011	-0.011	0.000	0.000	0.000
107	B	133	PHE	0	-0.050	-0.015	29.554	0.002	0.002	0.000	0.000	0.000
108	B	134	PRO	0	0.005	0.012	29.771	0.007	0.007	0.000	0.000	0.000
109	B	135	ARG	1	0.815	0.877	32.754	0.094	0.094	0.000	0.000	0.000
110	B	136	ASN	0	-0.022	-0.002	35.438	-0.004	-0.004	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:27:GLY)