FMO DATABASE

FMODB ID: ZYZZN

Calculation Name: 3EMF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EMF

Chain ID: A

ChEMBL ID:

UniProt ID: Q48152

Base Structure: X-ray

Registration Date: 2023-03-14

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	OptAll
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	113
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-730980.787668
FMO2-HF: Nuclear repulsion	688582.288581
FMO2-HF: Total energy	-42398.499087
FMO2-MP2: Total energy	-42524.78388

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(A:53:THR)

Summations of interaction energy for fragment #1(A:53:THR)

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.
0.922	3.273	0.45	-0.941	-1.86	-0.001

Interaction energy analysis for fragmet #1(A:53:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.000

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	A	55	VAL	0	0.015	0.003	2.816	-0.750	1.515	0.448	-0.918	-1.795	-0.001
4	A	56	THR	0	-0.047	-0.023	4.042	0.615	0.701	0.002	-0.023	-0.065	0.000
5	A	57	ASN	0	-0.010	-0.030	7.649	0.157	0.157	0.000	0.000	0.000	0.000
6	A	58	LYS	1	0.973	0.979	10.902	0.225	0.225	0.000	0.000	0.000	0.000
7	A	59	LEU	0	-0.010	0.011	14.377	0.047	0.047	0.000	0.000	0.000	0.000
8	A	60	LYS	1	0.861	0.944	16.431	0.150	0.150	0.000	0.000	0.000	0.000
9	A	61	ALA	0	-0.027	-0.016	19.311	-0.030	-0.030	0.000	0.000	0.000	0.000
10	A	62	TYR	0	0.019	-0.002	21.639	0.020	0.020	0.000	0.000	0.000	0.000
11	A	63	GLY	0	0.041	0.012	25.418	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	64	ASP	-1	-0.888	-0.940	21.525	-0.147	-0.147	0.000	0.000	0.000	0.000
13	A	65	ALA	0	0.016	0.002	24.794	0.004	0.004	0.000	0.000	0.000	0.000
14	A	66	ASN	0	-0.047	-0.017	21.546	0.009	0.009	0.000	0.000	0.000	0.000
15	A	67	PHE	0	0.008	0.019	24.896	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	68	ASN	0	-0.023	-0.010	25.816	0.013	0.013	0.000	0.000	0.000	0.000
17	A	69	PHE	0	0.064	0.009	28.094	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	70	THR	0	-0.014	0.004	31.194	0.000	0.000	0.000	0.000	0.000	0.000
19	A	71	ASN	0	-0.035	-0.010	26.901	0.009	0.009	0.000	0.000	0.000	0.000
20	A	72	ASN	0	0.005	0.003	26.259	-0.019	-0.019	0.000	0.000	0.000	0.000
21	A	73	SER	0	0.012	-0.006	29.857	0.009	0.009	0.000	0.000	0.000	0.000
22	A	74	ILE	0	0.052	0.013	32.186	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	75	ALA	0	0.075	0.044	32.599	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	76	ASP	-1	-0.834	-0.873	28.072	-0.162	-0.162	0.000	0.000	0.000	0.000
25	A	77	ALA	0	0.003	-0.004	29.866	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	78	GLU	-1	-0.892	-0.964	32.089	-0.095	-0.095	0.000	0.000	0.000	0.000
27	A	79	LYS	1	0.829	0.931	27.362	0.167	0.167	0.000	0.000	0.000	0.000
28	A	80	GLN	0	-0.008	0.003	26.877	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	81	VAL	0	-0.041	-0.014	29.686	0.003	0.003	0.000	0.000	0.000	0.000
30	A	82	GLN	0	-0.026	-0.017	31.866	0.006	0.006	0.000	0.000	0.000	0.000
31	A	83	GLU	-1	-0.785	-0.895	31.104	-0.111	-0.111	0.000	0.000	0.000	0.000
32	A	84	ALA	0	-0.021	-0.009	30.927	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	85	TYR	0	0.042	0.004	28.098	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	86	LYS	1	0.803	0.904	26.658	0.088	0.088	0.000	0.000	0.000	0.000
35	A	87	GLY	0	-0.005	0.010	23.227	0.001	0.001	0.000	0.000	0.000	0.000
36	A	88	LEU	0	-0.030	-0.012	22.086	-0.032	-0.032	0.000	0.000	0.000	0.000
37	A	89	LEU	0	-0.043	-0.026	16.569	0.001	0.001	0.000	0.000	0.000	0.000
38	A	90	ASN	0	0.017	0.010	20.528	0.014	0.014	0.000	0.000	0.000	0.000
39	A	91	LEU	0	-0.026	-0.032	18.279	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	92	ASN	0	-0.025	-0.026	20.912	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	93	GLU	-1	-0.840	-0.920	21.728	-0.160	-0.160	0.000	0.000	0.000	0.000
42	A	94	LYS	1	0.852	0.945	22.563	0.144	0.144	0.000	0.000	0.000	0.000
43	A	95	ASN	0	-0.010	-0.027	22.426	0.015	0.015	0.000	0.000	0.000	0.000
44	A	96	ALA	0	0.022	0.005	25.685	0.001	0.001	0.000	0.000	0.000	0.000
45	A	97	SER	0	-0.061	-0.037	27.194	0.009	0.009	0.000	0.000	0.000	0.000
46	A	98	ASP	-1	-0.891	-0.940	28.304	-0.113	-0.113	0.000	0.000	0.000	0.000
47	A	99	LYS	1	0.869	0.942	20.833	0.125	0.125	0.000	0.000	0.000	0.000
48	A	100	LEU	0	0.028	0.002	20.646	0.006	0.006	0.000	0.000	0.000	0.000
49	A	101	LEU	0	-0.060	-0.038	18.873	0.013	0.013	0.000	0.000	0.000	0.000
50	A	102	VAL	0	-0.080	-0.044	14.327	-0.015	-0.015	0.000	0.000	0.000	0.000
51	A	103	GLU	-1	-0.804	-0.880	16.866	-0.199	-0.199	0.000	0.000	0.000	0.000
52	A	104	ASP	-1	-0.866	-0.935	15.861	-0.305	-0.305	0.000	0.000	0.000	0.000
53	A	105	ASN	0	-0.068	-0.024	14.734	-0.052	-0.052	0.000	0.000	0.000	0.000
54	A	106	THR	0	-0.052	-0.025	10.974	-0.016	-0.016	0.000	0.000	0.000	0.000
55	A	107	ALA	0	0.002	0.003	7.566	-0.028	-0.028	0.000	0.000	0.000	0.000
56	A	108	ALA	0	0.044	0.033	9.484	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	109	THR	0	0.014	-0.012	7.708	-0.242	-0.242	0.000	0.000	0.000	0.000
58	A	110	VAL	0	0.058	0.010	9.762	0.226	0.226	0.000	0.000	0.000	0.000
59	A	111	GLY	0	0.007	0.006	11.477	0.169	0.169	0.000	0.000	0.000	0.000
60	A	112	ASN	0	0.001	0.021	12.199	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	113	LEU	0	0.079	0.035	13.636	0.078	0.078	0.000	0.000	0.000	0.000
62	A	114	ARG	1	0.945	0.976	13.243	0.578	0.578	0.000	0.000	0.000	0.000
63	A	115	LYS	1	0.887	0.949	16.117	0.471	0.471	0.000	0.000	0.000	0.000
64	A	116	LEU	0	0.011	0.019	17.994	0.025	0.025	0.000	0.000	0.000	0.000
65	A	117	GLY	0	0.022	-0.003	21.158	0.005	0.005	0.000	0.000	0.000	0.000
66	A	118	TRP	0	-0.032	0.002	24.886	0.007	0.007	0.000	0.000	0.000	0.000
67	A	119	VAL	0	0.027	0.005	28.468	0.000	0.000	0.000	0.000	0.000	0.000
68	A	120	LEU	0	0.006	0.024	31.552	0.006	0.006	0.000	0.000	0.000	0.000
69	A	121	SER	0	0.019	-0.023	34.528	0.002	0.002	0.000	0.000	0.000	0.000
70	A	122	SER	0	-0.057	-0.014	37.532	0.002	0.002	0.000	0.000	0.000	0.000
71	A	123	LYS	1	0.957	0.967	41.111	0.072	0.072	0.000	0.000	0.000	0.000
72	A	124	ASN	0	0.004	0.014	44.364	0.003	0.003	0.000	0.000	0.000	0.000
73	A	125	GLY	0	0.064	0.021	48.041	0.003	0.003	0.000	0.000	0.000	0.000
74	A	126	THR	0	0.028	-0.008	48.976	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	127	ARG	1	0.896	0.963	47.639	0.054	0.054	0.000	0.000	0.000	0.000
76	A	128	ASN	0	0.025	0.008	43.505	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	129	GLU	-1	-0.873	-0.909	39.129	-0.095	-0.095	0.000	0.000	0.000	0.000
78	A	130	LYS	1	0.847	0.929	36.764	0.101	0.101	0.000	0.000	0.000	0.000
79	A	131	SER	0	0.012	-0.009	35.086	0.001	0.001	0.000	0.000	0.000	0.000
80	A	132	GLN	0	-0.008	0.003	32.881	0.010	0.010	0.000	0.000	0.000	0.000
81	A	133	GLN	0	-0.023	-0.016	26.428	-0.017	-0.017	0.000	0.000	0.000	0.000
82	A	134	VAL	0	-0.003	0.007	28.637	0.006	0.006	0.000	0.000	0.000	0.000
83	A	135	LYS	1	0.899	0.932	21.842	0.255	0.255	0.000	0.000	0.000	0.000
84	A	136	HIS	0	-0.006	-0.015	20.159	0.012	0.012	0.000	0.000	0.000	0.000
85	A	137	ALA	0	-0.057	-0.034	23.008	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	138	ASP	-1	-0.825	-0.875	24.949	-0.192	-0.192	0.000	0.000	0.000	0.000
87	A	139	GLU	-1	-0.962	-0.988	27.862	-0.138	-0.138	0.000	0.000	0.000	0.000
88	A	140	VAL	0	-0.063	-0.045	31.447	0.005	0.005	0.000	0.000	0.000	0.000
89	A	141	LEU	0	0.026	0.030	34.673	0.002	0.002	0.000	0.000	0.000	0.000
90	A	142	PHE	0	-0.022	-0.018	36.846	0.004	0.004	0.000	0.000	0.000	0.000
91	A	143	GLU	-1	-0.796	-0.889	40.794	-0.076	-0.076	0.000	0.000	0.000	0.000
92	A	144	GLY	0	-0.028	-0.023	43.918	0.001	0.001	0.000	0.000	0.000	0.000
93	A	145	LYS	1	0.876	0.923	45.684	0.074	0.074	0.000	0.000	0.000	0.000
94	A	146	GLY	0	-0.006	-0.008	50.509	0.000	0.000	0.000	0.000	0.000	0.000
95	A	147	GLY	0	0.026	0.021	53.619	0.002	0.002	0.000	0.000	0.000	0.000
96	A	148	VAL	0	-0.035	0.011	48.966	0.000	0.000	0.000	0.000	0.000	0.000
97	A	149	GLN	0	-0.026	-0.007	50.315	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	150	VAL	0	0.016	0.000	43.826	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	151	THR	0	-0.003	0.008	45.513	0.000	0.000	0.000	0.000	0.000	0.000
100	A	152	SER	0	0.037	0.008	40.666	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	153	THR	0	-0.012	0.002	41.683	0.001	0.001	0.000	0.000	0.000	0.000
102	A	154	SER	0	-0.006	-0.020	37.004	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	155	GLU	-1	-0.835	-0.894	38.195	-0.110	-0.110	0.000	0.000	0.000	0.000
104	A	156	ASN	0	-0.040	-0.038	35.250	-0.007	-0.007	0.000	0.000	0.000	0.000
105	A	157	GLY	0	0.042	0.036	33.077	-0.005	-0.005	0.000	0.000	0.000	0.000
106	A	158	LYS	1	0.879	0.953	33.827	0.112	0.112	0.000	0.000	0.000	0.000
107	A	159	HIS	0	-0.057	-0.046	33.203	0.000	0.000	0.000	0.000	0.000	0.000
108	A	160	THR	0	-0.027	-0.025	37.368	0.001	0.001	0.000	0.000	0.000	0.000
109	A	161	ILE	0	0.017	0.028	38.422	0.000	0.000	0.000	0.000	0.000	0.000
110	A	162	THR	0	-0.056	-0.033	41.975	0.002	0.002	0.000	0.000	0.000	0.000
111	A	163	PHE	0	0.028	0.014	42.669	0.000	0.000	0.000	0.000	0.000	0.000
112	A	164	ALA	0	0.014	0.012	48.253	0.002	0.002	0.000	0.000	0.000	0.000
113	A	165	LEU	0	-0.018	-0.027	52.009	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:53:THR)