FMO DATABASE

FMODB ID: N1ZQQ

Calculation Name: 1EM8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1EM8

Chain ID: A

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	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	147
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1433566.364116
FMO2-HF: Nuclear repulsion	1375692.800256
FMO2-HF: Total energy	-57873.56386
FMO2-MP2: Total energy	-58044.383977

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:1:MET)

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

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.
-8.362	-2.574	3.907	-3.679	-6.014	-0.014

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : 0.003

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	3	ASN	0	-0.018	-0.024	2.709	-2.931	2.018	0.887	-2.510	-3.326	-0.013
4	A	4	ALA	0	0.008	0.004	4.508	-0.022	0.034	-0.001	-0.014	-0.040	0.000
5	A	5	THR	0	-0.023	-0.011	8.061	0.395	0.395	0.000	0.000	0.000	0.000
6	A	6	PHE	0	0.005	-0.007	10.696	-0.076	-0.076	0.000	0.000	0.000	0.000
7	A	7	TYR	0	0.005	-0.006	13.942	0.090	0.090	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.008	-0.013	16.853	-0.024	-0.024	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.030	-0.009	19.771	0.001	0.001	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.893	-0.946	23.204	0.007	0.007	0.000	0.000	0.000	0.000
11	A	11	ASN	0	-0.014	-0.011	26.300	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.884	-0.977	27.404	-0.067	-0.067	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.022	-0.020	29.588	0.000	0.000	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.030	-0.013	31.259	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.013	-0.004	32.423	0.006	0.006	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.813	-0.893	33.126	-0.068	-0.068	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.019	0.000	34.827	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.041	-0.019	29.382	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	19	SER	0	0.051	-0.004	27.418	0.006	0.006	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.033	0.023	26.966	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.009	-0.014	21.521	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.747	-0.829	23.178	-0.134	-0.134	0.000	0.000	0.000	0.000
23	A	23	GLN	0	0.020	0.013	25.279	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.005	0.010	19.956	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.007	-0.014	19.916	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	26	CYS	0	-0.039	-0.007	21.405	-0.021	-0.021	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.863	-0.942	22.554	-0.090	-0.090	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.028	-0.014	16.234	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.014	0.001	18.588	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.033	0.018	20.083	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	31	GLU	-1	-0.842	-0.886	17.168	-0.146	-0.146	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.838	0.876	12.583	0.230	0.230	0.000	0.000	0.000	0.000
33	A	33	TRP	0	0.010	0.019	17.368	-0.019	-0.019	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.968	0.993	20.066	0.108	0.108	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.093	-0.046	16.221	0.002	0.002	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.000	-0.001	16.989	-0.017	-0.017	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.844	0.926	12.799	0.438	0.438	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.754	0.872	16.745	0.428	0.428	0.000	0.000	0.000	0.000
39	A	39	VAL	0	0.041	0.022	16.723	-0.086	-0.086	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.045	-0.019	16.957	0.033	0.033	0.000	0.000	0.000	0.000
41	A	41	ILE	0	0.027	0.017	17.554	-0.030	-0.030	0.000	0.000	0.000	0.000
42	A	42	ALA	0	-0.036	-0.021	18.510	0.010	0.010	0.000	0.000	0.000	0.000
43	A	43	CYS	0	0.008	0.022	20.465	0.009	0.009	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.772	-0.853	23.603	-0.214	-0.214	0.000	0.000	0.000	0.000
45	A	45	ASP	-1	-0.854	-0.940	25.174	-0.132	-0.132	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.840	-0.933	28.255	-0.149	-0.149	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.987	0.989	30.483	0.094	0.094	0.000	0.000	0.000	0.000
48	A	48	GLN	0	-0.043	-0.045	25.166	-0.010	-0.010	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.045	0.005	27.033	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	50	TYR	0	0.002	-0.011	27.979	0.003	0.003	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.804	0.918	29.060	0.123	0.123	0.000	0.000	0.000	0.000
52	A	52	LEU	0	0.013	-0.006	24.160	0.004	0.004	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.837	-0.936	28.042	-0.161	-0.161	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.932	-0.963	29.496	-0.088	-0.088	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.008	0.007	28.674	0.005	0.005	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.008	-0.014	23.998	0.003	0.003	0.000	0.000	0.000	0.000
57	A	57	TRP	0	-0.102	-0.044	28.428	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.034	-0.008	31.334	0.008	0.008	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.777	0.888	27.823	0.086	0.086	0.000	0.000	0.000	0.000
60	A	60	PRO	0	0.043	0.003	25.450	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	61	ALA	0	0.003	0.012	28.304	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.966	-0.982	30.843	-0.042	-0.042	0.000	0.000	0.000	0.000
63	A	63	SER	0	-0.087	-0.041	28.438	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	64	PHE	0	0.041	0.014	29.728	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.036	0.017	24.664	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	66	PRO	0	-0.021	0.008	26.248	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	HIS	1	0.748	0.853	25.860	0.132	0.132	0.000	0.000	0.000	0.000
68	A	68	ASN	0	0.004	-0.002	26.732	0.014	0.014	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.100	0.064	26.714	-0.024	-0.024	0.000	0.000	0.000	0.000
70	A	70	ALA	0	-0.009	-0.007	24.997	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.112	-0.083	26.779	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.898	-0.927	29.476	-0.135	-0.135	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.054	0.028	29.324	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	74	PRO	0	-0.022	-0.020	27.836	0.005	0.005	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.995	0.997	25.280	0.213	0.213	0.000	0.000	0.000	0.000
76	A	76	GLY	0	-0.045	-0.028	24.800	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.097	0.072	23.744	-0.033	-0.033	0.000	0.000	0.000	0.000
78	A	78	ALA	0	0.000	0.013	25.047	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	79	PRO	0	-0.008	-0.013	22.510	-0.032	-0.032	0.000	0.000	0.000	0.000
80	A	80	VAL	0	0.040	0.029	21.294	-0.043	-0.043	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.747	-0.845	21.681	-0.309	-0.309	0.000	0.000	0.000	0.000
82	A	82	ILE	0	0.030	0.027	22.049	-0.029	-0.029	0.000	0.000	0.000	0.000
83	A	83	ALA	0	0.031	0.001	22.252	0.016	0.016	0.000	0.000	0.000	0.000
84	A	84	TRP	0	0.004	0.000	24.082	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	85	PRO	0	-0.001	0.001	24.795	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	86	GLN	0	-0.014	0.001	25.741	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.904	0.969	26.980	0.194	0.194	0.000	0.000	0.000	0.000
88	A	88	ARG	1	0.875	0.927	19.376	0.364	0.364	0.000	0.000	0.000	0.000
89	A	89	SER	0	0.055	0.046	19.588	0.014	0.014	0.000	0.000	0.000	0.000
90	A	90	SER	0	-0.044	-0.046	22.054	0.002	0.002	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.016	-0.016	18.365	-0.049	-0.049	0.000	0.000	0.000	0.000
92	A	92	ARG	1	0.845	0.899	15.578	0.550	0.550	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.775	0.881	15.614	0.444	0.444	0.000	0.000	0.000	0.000
94	A	94	ASP	-1	-0.792	-0.869	12.392	-0.729	-0.729	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.027	-0.012	11.339	-0.203	-0.203	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.026	0.004	12.251	0.131	0.131	0.000	0.000	0.000	0.000
97	A	97	ILE	0	0.003	-0.001	13.527	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	98	SER	0	-0.026	-0.017	15.490	0.031	0.031	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.018	-0.005	17.174	0.035	0.035	0.000	0.000	0.000	0.000
100	A	100	ARG	1	0.805	0.908	19.333	0.282	0.282	0.000	0.000	0.000	0.000
101	A	101	THR	0	0.017	-0.022	20.307	0.003	0.003	0.000	0.000	0.000	0.000
102	A	102	SER	0	-0.005	0.007	20.826	0.019	0.019	0.000	0.000	0.000	0.000
103	A	103	PHE	0	0.006	-0.014	12.472	-0.005	-0.005	0.000	0.000	0.000	0.000
104	A	104	ALA	0	0.020	0.012	16.506	0.034	0.034	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.856	-0.917	15.887	-0.439	-0.439	0.000	0.000	0.000	0.000
106	A	106	PHE	0	-0.023	-0.019	14.771	-0.083	-0.083	0.000	0.000	0.000	0.000
107	A	107	ALA	0	0.030	0.008	12.629	-0.089	-0.089	0.000	0.000	0.000	0.000
108	A	108	THR	0	-0.043	-0.033	10.375	-0.241	-0.241	0.000	0.000	0.000	0.000
109	A	109	ALA	0	-0.008	0.000	9.519	-0.233	-0.233	0.000	0.000	0.000	0.000
110	A	110	PHE	0	-0.024	-0.001	9.671	-0.071	-0.071	0.000	0.000	0.000	0.000
111	A	111	THR	0	0.016	0.008	4.586	-0.058	0.041	-0.001	-0.024	-0.074	0.000
112	A	112	GLU	-1	-0.852	-0.914	5.680	-2.038	-2.038	0.000	0.000	0.000	0.000
113	A	113	VAL	0	0.000	-0.007	8.124	0.237	0.237	0.000	0.000	0.000	0.000
114	A	114	VAL	0	-0.013	0.009	10.108	0.120	0.120	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.727	-0.819	12.973	-0.323	-0.323	0.000	0.000	0.000	0.000
116	A	116	PHE	0	0.018	-0.003	15.001	0.051	0.051	0.000	0.000	0.000	0.000
117	A	117	VAL	0	-0.018	-0.023	17.527	-0.006	-0.006	0.000	0.000	0.000	0.000
118	A	118	PRO	0	0.036	0.017	20.026	0.014	0.014	0.000	0.000	0.000	0.000
119	A	119	TYR	0	0.029	0.043	23.543	0.009	0.009	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.732	-0.838	26.300	-0.025	-0.025	0.000	0.000	0.000	0.000
121	A	121	ASP	-1	-0.835	-0.922	26.962	-0.015	-0.015	0.000	0.000	0.000	0.000
122	A	122	SER	0	-0.071	-0.070	27.246	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	123	LEU	0	0.005	-0.004	25.249	-0.009	-0.009	0.000	0.000	0.000	0.000
124	A	124	LYS	1	0.776	0.895	22.879	0.001	0.001	0.000	0.000	0.000	0.000
125	A	125	GLN	0	0.004	0.005	22.212	0.007	0.007	0.000	0.000	0.000	0.000
126	A	126	LEU	0	0.043	0.018	22.376	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	127	ALA	0	0.015	0.019	18.758	-0.021	-0.021	0.000	0.000	0.000	0.000
128	A	128	ARG	1	0.815	0.888	17.763	0.004	0.004	0.000	0.000	0.000	0.000
129	A	129	GLU	-1	-0.797	-0.874	18.413	-0.058	-0.058	0.000	0.000	0.000	0.000
130	A	130	ARG	1	0.820	0.887	16.053	0.183	0.183	0.000	0.000	0.000	0.000
131	A	131	TYR	0	-0.002	0.009	12.087	-0.047	-0.047	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.804	0.880	13.077	0.048	0.048	0.000	0.000	0.000	0.000
133	A	133	ALA	0	0.022	0.017	13.757	-0.008	-0.008	0.000	0.000	0.000	0.000
134	A	134	TYR	0	-0.019	-0.037	9.809	-0.073	-0.073	0.000	0.000	0.000	0.000
135	A	135	ARG	1	0.933	0.964	9.233	-0.270	-0.270	0.000	0.000	0.000	0.000
136	A	136	VAL	0	-0.029	-0.010	9.735	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	137	ALA	0	-0.017	0.004	10.515	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	138	GLY	0	-0.010	-0.007	6.820	-0.243	-0.243	0.000	0.000	0.000	0.000
139	A	139	PHE	0	-0.080	-0.038	4.910	-0.741	-0.637	-0.001	-0.005	-0.098	0.000
140	A	140	ASN	0	-0.030	-0.017	2.777	-1.166	-0.690	3.023	-1.068	-2.430	-0.001
141	A	141	LEU	0	-0.034	-0.024	4.566	-0.907	-0.803	0.000	-0.058	-0.046	0.000
142	A	142	ASN	0	-0.003	0.007	7.983	0.059	0.059	0.000	0.000	0.000	0.000
143	A	143	THR	0	-0.016	-0.004	10.259	-0.163	-0.163	0.000	0.000	0.000	0.000
144	A	144	ALA	0	0.010	0.011	13.942	0.048	0.048	0.000	0.000	0.000	0.000
145	A	145	THR	0	0.015	-0.006	15.809	-0.028	-0.028	0.000	0.000	0.000	0.000
146	A	146	TRP	0	0.040	0.019	16.803	0.020	0.020	0.000	0.000	0.000	0.000
147	A	147	LYS	1	0.939	0.990	20.205	-0.051	-0.051	0.000	0.000	0.000	0.000

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