FMO DATABASE

FMODB ID: 6Y41Z

Calculation Name: 3ERS-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ERS

Chain ID: X

ChEMBL ID:

UniProt ID: P42589

Base Structure: X-ray

Registration Date: 2023-09-23

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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-847106.418608
FMO2-HF: Nuclear repulsion	801237.220347
FMO2-HF: Total energy	-45869.198261
FMO2-MP2: Total energy	-45995.937358

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(X:1:MET)

Summations of interaction energy for fragment #1(X: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.
-3.969	-0.116	0.595	-2.195	-2.251	-0.009

Interaction energy analysis for fragmet #1(X: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 : 0.002

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	X	3	THR	0	-0.019	-0.002	2.644	-4.532	-0.922	0.594	-2.163	-2.040	-0.009
4	X	4	VAL	0	-0.001	-0.005	3.943	0.201	0.444	0.001	-0.032	-0.211	0.000
5	X	5	ALA	0	0.016	0.006	6.403	-0.057	-0.057	0.000	0.000	0.000	0.000
6	X	6	TYR	0	0.063	0.017	10.237	0.204	0.204	0.000	0.000	0.000	0.000
7	X	7	ALA	0	-0.003	-0.016	12.705	0.093	0.093	0.000	0.000	0.000	0.000
8	X	8	ASP	-1	-0.802	-0.901	8.634	0.323	0.323	0.000	0.000	0.000	0.000
9	X	9	PHE	0	0.029	0.022	10.304	0.196	0.196	0.000	0.000	0.000	0.000
10	X	10	ALA	0	-0.022	-0.021	11.577	0.001	0.001	0.000	0.000	0.000	0.000
11	X	11	ARG	1	0.811	0.906	11.387	-0.467	-0.467	0.000	0.000	0.000	0.000
12	X	12	LEU	0	0.032	0.037	9.983	0.012	0.012	0.000	0.000	0.000	0.000
13	X	13	GLU	-1	-0.806	-0.899	14.696	0.139	0.139	0.000	0.000	0.000	0.000
14	X	14	MET	0	0.005	0.008	12.128	0.015	0.015	0.000	0.000	0.000	0.000
15	X	15	ARG	1	0.788	0.868	16.747	-0.195	-0.195	0.000	0.000	0.000	0.000
16	X	16	VAL	0	0.050	0.031	19.518	0.015	0.015	0.000	0.000	0.000	0.000
17	X	17	GLY	0	0.003	-0.007	21.790	-0.002	-0.002	0.000	0.000	0.000	0.000
18	X	18	LYS	1	0.840	0.912	23.832	-0.096	-0.096	0.000	0.000	0.000	0.000
19	X	19	ILE	0	0.018	0.027	23.224	0.006	0.006	0.000	0.000	0.000	0.000
20	X	20	VAL	0	-0.019	-0.019	26.796	-0.010	-0.010	0.000	0.000	0.000	0.000
21	X	21	GLU	-1	-0.893	-0.950	29.202	0.117	0.117	0.000	0.000	0.000	0.000
22	X	22	VAL	0	0.026	0.008	27.596	0.012	0.012	0.000	0.000	0.000	0.000
23	X	23	LYS	1	0.871	0.934	29.194	-0.133	-0.133	0.000	0.000	0.000	0.000
24	X	24	ARG	1	0.901	0.956	29.100	-0.125	-0.125	0.000	0.000	0.000	0.000
25	X	25	HIS	0	-0.055	-0.034	30.834	-0.005	-0.005	0.000	0.000	0.000	0.000
26	X	26	GLU	-1	-0.876	-0.931	32.991	0.096	0.096	0.000	0.000	0.000	0.000
27	X	27	ASN	0	-0.077	-0.051	35.358	-0.003	-0.003	0.000	0.000	0.000	0.000
28	X	28	ALA	0	0.055	0.027	32.592	0.005	0.005	0.000	0.000	0.000	0.000
29	X	29	ASP	-1	-0.885	-0.941	28.758	0.144	0.144	0.000	0.000	0.000	0.000
30	X	30	LYS	1	0.936	0.985	22.111	-0.210	-0.210	0.000	0.000	0.000	0.000
31	X	31	LEU	0	-0.034	-0.030	22.743	0.009	0.009	0.000	0.000	0.000	0.000
32	X	32	TYR	0	-0.088	-0.060	25.046	-0.011	-0.011	0.000	0.000	0.000	0.000
33	X	33	ILE	0	-0.040	-0.019	25.105	0.017	0.017	0.000	0.000	0.000	0.000
34	X	34	VAL	0	0.026	0.009	24.010	-0.011	-0.011	0.000	0.000	0.000	0.000
35	X	35	GLN	0	-0.020	-0.004	25.241	0.021	0.021	0.000	0.000	0.000	0.000
36	X	36	VAL	0	-0.003	-0.011	22.151	-0.009	-0.009	0.000	0.000	0.000	0.000
37	X	37	ASP	-1	-0.845	-0.920	25.334	0.110	0.110	0.000	0.000	0.000	0.000
38	X	38	VAL	0	-0.007	-0.026	22.652	0.006	0.006	0.000	0.000	0.000	0.000
39	X	39	GLY	0	-0.009	0.001	25.948	-0.001	-0.001	0.000	0.000	0.000	0.000
40	X	40	GLN	0	-0.059	-0.044	28.881	-0.007	-0.007	0.000	0.000	0.000	0.000
41	X	41	LYS	1	0.863	0.936	23.195	-0.190	-0.190	0.000	0.000	0.000	0.000
42	X	42	THR	0	0.014	0.003	27.584	-0.002	-0.002	0.000	0.000	0.000	0.000
43	X	43	LEU	0	-0.038	-0.010	22.301	0.001	0.001	0.000	0.000	0.000	0.000
44	X	44	GLN	0	0.050	0.025	24.886	-0.010	-0.010	0.000	0.000	0.000	0.000
45	X	45	THR	0	-0.020	-0.052	19.501	0.024	0.024	0.000	0.000	0.000	0.000
46	X	46	VAL	0	-0.019	-0.017	20.837	-0.020	-0.020	0.000	0.000	0.000	0.000
47	X	47	THR	0	0.010	0.016	20.136	0.025	0.025	0.000	0.000	0.000	0.000
48	X	48	SER	0	-0.012	-0.011	17.943	-0.018	-0.018	0.000	0.000	0.000	0.000
49	X	49	LEU	0	0.076	0.011	17.713	-0.007	-0.007	0.000	0.000	0.000	0.000
50	X	50	VAL	0	-0.005	0.006	21.653	-0.012	-0.012	0.000	0.000	0.000	0.000
51	X	51	PRO	0	-0.043	-0.009	24.094	-0.009	-0.009	0.000	0.000	0.000	0.000
52	X	52	TYR	0	-0.106	-0.067	21.222	-0.004	-0.004	0.000	0.000	0.000	0.000
53	X	53	TYR	0	0.040	0.020	20.467	-0.001	-0.001	0.000	0.000	0.000	0.000
54	X	54	SER	0	0.031	0.014	25.816	0.005	0.005	0.000	0.000	0.000	0.000
55	X	55	GLU	-1	-0.792	-0.899	28.683	0.115	0.115	0.000	0.000	0.000	0.000
56	X	56	GLU	-1	-0.956	-0.987	30.190	0.073	0.073	0.000	0.000	0.000	0.000
57	X	57	GLU	-1	-0.815	-0.884	27.035	0.097	0.097	0.000	0.000	0.000	0.000
58	X	58	LEU	0	-0.022	-0.017	23.746	0.003	0.003	0.000	0.000	0.000	0.000
59	X	59	MET	0	-0.028	-0.006	27.351	0.006	0.006	0.000	0.000	0.000	0.000
60	X	60	GLY	0	-0.006	0.008	29.875	-0.006	-0.006	0.000	0.000	0.000	0.000
61	X	61	LYS	1	0.765	0.880	23.695	-0.111	-0.111	0.000	0.000	0.000	0.000
62	X	62	THR	0	-0.030	-0.021	23.929	0.006	0.006	0.000	0.000	0.000	0.000
63	X	63	VAL	0	0.026	0.020	20.250	-0.001	-0.001	0.000	0.000	0.000	0.000
64	X	64	VAL	0	0.017	0.009	16.160	-0.010	-0.010	0.000	0.000	0.000	0.000
65	X	65	VAL	0	0.037	0.016	17.032	0.021	0.021	0.000	0.000	0.000	0.000
66	X	66	LEU	0	0.004	0.015	12.250	-0.012	-0.012	0.000	0.000	0.000	0.000
67	X	67	CYS	0	-0.071	-0.042	15.941	-0.018	-0.018	0.000	0.000	0.000	0.000
68	X	68	ASN	0	0.012	0.004	16.704	0.001	0.001	0.000	0.000	0.000	0.000
69	X	69	LEU	0	0.018	0.024	13.343	0.027	0.027	0.000	0.000	0.000	0.000
70	X	70	GLN	0	-0.008	-0.009	16.461	-0.036	-0.036	0.000	0.000	0.000	0.000
71	X	71	LYS	1	0.862	0.914	18.476	-0.216	-0.216	0.000	0.000	0.000	0.000
72	X	72	ALA	0	0.060	0.044	18.464	0.000	0.000	0.000	0.000	0.000	0.000
73	X	73	LYS	1	0.816	0.883	20.591	-0.232	-0.232	0.000	0.000	0.000	0.000
74	X	74	MET	0	0.033	0.017	19.699	0.010	0.010	0.000	0.000	0.000	0.000
75	X	75	ARG	1	0.963	0.983	23.274	-0.196	-0.196	0.000	0.000	0.000	0.000
76	X	76	GLY	0	0.020	0.023	26.591	-0.013	-0.013	0.000	0.000	0.000	0.000
77	X	77	GLU	-1	-0.821	-0.907	26.236	0.157	0.157	0.000	0.000	0.000	0.000
78	X	78	THR	0	-0.035	-0.022	24.625	0.017	0.017	0.000	0.000	0.000	0.000
79	X	79	SER	0	0.021	0.019	19.245	-0.018	-0.018	0.000	0.000	0.000	0.000
80	X	80	GLU	-1	-0.858	-0.920	20.820	0.212	0.212	0.000	0.000	0.000	0.000
81	X	81	CYS	0	-0.039	0.018	18.756	0.002	0.002	0.000	0.000	0.000	0.000
82	X	82	MET	0	0.004	0.015	14.818	-0.013	-0.013	0.000	0.000	0.000	0.000
83	X	83	LEU	0	0.029	0.010	15.970	0.009	0.009	0.000	0.000	0.000	0.000
84	X	84	LEU	0	-0.006	-0.002	12.162	0.030	0.030	0.000	0.000	0.000	0.000
85	X	85	CYS	0	-0.039	-0.017	12.708	-0.052	-0.052	0.000	0.000	0.000	0.000
86	X	86	ALA	0	-0.020	-0.007	11.928	0.030	0.030	0.000	0.000	0.000	0.000
87	X	87	GLU	-1	-0.886	-0.931	11.399	0.351	0.351	0.000	0.000	0.000	0.000
88	X	88	THR	0	-0.013	-0.006	12.921	-0.010	-0.010	0.000	0.000	0.000	0.000
89	X	89	ASP	-1	-0.927	-0.965	12.057	0.181	0.181	0.000	0.000	0.000	0.000
90	X	90	ASP	-1	-0.886	-0.917	13.283	0.235	0.235	0.000	0.000	0.000	0.000
91	X	91	GLY	0	-0.028	-0.012	14.767	0.010	0.010	0.000	0.000	0.000	0.000
92	X	92	SER	0	-0.117	-0.068	15.538	-0.013	-0.013	0.000	0.000	0.000	0.000
93	X	93	GLU	-1	-0.885	-0.922	17.703	0.095	0.095	0.000	0.000	0.000	0.000
94	X	94	SER	0	-0.034	-0.040	14.266	0.008	0.008	0.000	0.000	0.000	0.000
95	X	95	VAL	0	-0.018	0.000	16.178	-0.011	-0.011	0.000	0.000	0.000	0.000
96	X	96	LEU	0	-0.013	-0.020	16.413	0.016	0.016	0.000	0.000	0.000	0.000
97	X	97	LEU	0	-0.014	0.002	12.852	-0.024	-0.024	0.000	0.000	0.000	0.000
98	X	98	THR	0	-0.006	-0.027	17.414	0.010	0.010	0.000	0.000	0.000	0.000
99	X	99	PRO	0	-0.041	-0.014	20.150	-0.009	-0.009	0.000	0.000	0.000	0.000
100	X	100	GLU	-1	-0.809	-0.893	22.139	-0.008	-0.008	0.000	0.000	0.000	0.000
101	X	101	ARG	1	0.841	0.911	24.067	-0.011	-0.011	0.000	0.000	0.000	0.000
102	X	102	MET	0	0.017	0.006	26.460	0.008	0.008	0.000	0.000	0.000	0.000
103	X	103	MET	0	0.018	0.014	25.239	-0.010	-0.010	0.000	0.000	0.000	0.000
104	X	104	PRO	0	0.010	-0.005	27.971	0.006	0.006	0.000	0.000	0.000	0.000
105	X	105	ALA	0	0.003	0.024	26.202	0.006	0.006	0.000	0.000	0.000	0.000
106	X	106	GLY	0	0.028	0.008	24.970	-0.008	-0.008	0.000	0.000	0.000	0.000
107	X	107	VAL	0	-0.044	-0.013	23.658	0.005	0.005	0.000	0.000	0.000	0.000
108	X	108	ARG	1	0.854	0.927	16.649	-0.207	-0.207	0.000	0.000	0.000	0.000
109	X	109	VAL	0	0.031	0.025	15.471	-0.022	-0.022	0.000	0.000	0.000	0.000
110	X	110	VAL	0	-0.036	-0.025	17.403	0.028	0.028	0.000	0.000	0.000	0.000
111	X	111	LEU	0	-0.016	-0.005	12.314	0.003	0.003	0.000	0.000	0.000	0.000
112	X	112	ASP	-1	-0.933	-0.958	16.524	-0.130	-0.130	0.000	0.000	0.000	0.000

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