FMO DATABASE

FMODB ID: 5J3JZ

Calculation Name: 5MR1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5MR1

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WWN9

Base Structure: X-ray

Registration Date: 2023-09-20

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-808942.081231
FMO2-HF: Nuclear repulsion	767622.593483
FMO2-HF: Total energy	-41319.487748
FMO2-MP2: Total energy	-41440.174817

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:42:ALA)

Summations of interaction energy for fragment #1(A:42:ALA)

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.
-36.496	-34.05	15.284	-8.937	-8.791	0.038

Interaction energy analysis for fragmet #1(A:42:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.006

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	44	CYS	0	-0.064	-0.038	2.875	-0.113	1.649	0.043	-0.835	-0.970	0.000
4	A	45	GLN	0	-0.001	0.002	3.097	-2.328	-0.521	0.187	-0.838	-1.156	-0.007
5	A	46	GLY	0	0.035	0.019	4.856	0.177	0.169	-0.001	-0.003	0.013	0.000
6	A	47	TRP	0	-0.006	0.000	8.585	0.120	0.120	0.000	0.000	0.000	0.000
7	A	48	LEU	0	0.008	0.013	10.752	0.025	0.025	0.000	0.000	0.000	0.000
8	A	49	TYR	0	-0.092	-0.044	13.524	0.065	0.065	0.000	0.000	0.000	0.000
9	A	50	LYS	1	0.979	0.997	15.735	0.125	0.125	0.000	0.000	0.000	0.000
10	A	51	LYS	1	0.792	0.913	17.793	0.129	0.129	0.000	0.000	0.000	0.000
11	A	52	LYS	1	0.973	0.972	21.176	0.119	0.119	0.000	0.000	0.000	0.000
12	A	53	GLU	-1	-0.823	-0.913	23.351	-0.023	-0.023	0.000	0.000	0.000	0.000
13	A	54	LYS	1	0.997	0.996	24.523	0.030	0.030	0.000	0.000	0.000	0.000
14	A	55	GLY	0	-0.049	-0.016	26.534	0.000	0.000	0.000	0.000	0.000	0.000
15	A	56	SER	0	0.077	0.036	27.637	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	57	PHE	0	0.060	0.024	25.460	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	58	LEU	0	0.043	0.019	28.048	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	59	SER	0	-0.037	-0.006	27.857	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	60	ASN	0	0.069	0.010	25.903	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	61	LYS	1	0.914	0.965	25.237	0.101	0.101	0.000	0.000	0.000	0.000
21	A	62	TRP	0	-0.009	-0.018	19.367	0.011	0.011	0.000	0.000	0.000	0.000
22	A	63	LYS	1	0.965	0.995	18.174	0.154	0.154	0.000	0.000	0.000	0.000
23	A	64	LYS	1	0.947	0.980	15.476	0.399	0.399	0.000	0.000	0.000	0.000
24	A	65	PHE	0	-0.013	-0.008	12.815	0.044	0.044	0.000	0.000	0.000	0.000
25	A	66	TRP	0	0.062	0.040	6.768	-0.021	-0.021	0.000	0.000	0.000	0.000
26	A	67	VAL	0	-0.009	-0.018	7.843	0.144	0.144	0.000	0.000	0.000	0.000
27	A	68	ILE	0	0.052	0.018	2.319	-0.543	-0.702	1.706	-0.502	-1.045	-0.001
28	A	69	LEU	0	-0.011	0.005	3.683	0.599	0.786	0.000	-0.045	-0.142	0.000
29	A	70	LYS	1	0.926	0.938	1.953	-35.871	-37.084	13.341	-6.684	-5.443	0.046
30	A	71	GLY	0	0.027	0.020	3.762	-0.258	-0.188	0.008	-0.030	-0.048	0.000
31	A	72	SER	0	0.009	0.009	6.802	-0.422	-0.422	0.000	0.000	0.000	0.000
32	A	73	SER	0	0.013	0.003	7.885	-0.234	-0.234	0.000	0.000	0.000	0.000
33	A	74	LEU	0	-0.019	-0.003	7.193	0.015	0.015	0.000	0.000	0.000	0.000
34	A	75	TYR	0	0.035	0.013	6.772	0.176	0.176	0.000	0.000	0.000	0.000
35	A	76	TRP	0	-0.006	-0.004	8.559	-0.225	-0.225	0.000	0.000	0.000	0.000
36	A	77	TYR	0	0.069	0.036	7.109	0.095	0.095	0.000	0.000	0.000	0.000
37	A	78	SER	0	-0.056	-0.059	12.058	-0.057	-0.057	0.000	0.000	0.000	0.000
38	A	79	ASN	0	-0.035	-0.033	13.562	-0.025	-0.025	0.000	0.000	0.000	0.000
39	A	80	GLN	0	0.002	-0.016	10.323	0.103	0.103	0.000	0.000	0.000	0.000
40	A	81	MET	0	0.008	0.017	10.809	-0.034	-0.034	0.000	0.000	0.000	0.000
41	A	82	ALA	0	-0.052	-0.003	12.818	0.062	0.062	0.000	0.000	0.000	0.000
42	A	83	GLU	-1	-0.790	-0.880	11.580	0.108	0.108	0.000	0.000	0.000	0.000
43	A	84	LYS	1	0.834	0.901	12.123	-0.065	-0.065	0.000	0.000	0.000	0.000
44	A	85	ALA	0	-0.028	-0.015	10.765	-0.065	-0.065	0.000	0.000	0.000	0.000
45	A	86	ASP	-1	-0.836	-0.908	12.728	-0.082	-0.082	0.000	0.000	0.000	0.000
46	A	87	GLY	0	-0.066	-0.036	13.984	0.012	0.012	0.000	0.000	0.000	0.000
47	A	88	PHE	0	-0.030	-0.017	11.876	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	89	VAL	0	-0.033	-0.004	12.443	-0.026	-0.026	0.000	0.000	0.000	0.000
49	A	90	ASN	0	-0.010	-0.010	12.119	-0.020	-0.020	0.000	0.000	0.000	0.000
50	A	91	LEU	0	0.024	-0.005	10.169	-0.067	-0.067	0.000	0.000	0.000	0.000
51	A	92	PRO	0	0.000	0.005	13.622	-0.045	-0.045	0.000	0.000	0.000	0.000
52	A	93	ASP	-1	-0.822	-0.884	16.349	0.137	0.137	0.000	0.000	0.000	0.000
53	A	94	PHE	0	-0.074	-0.038	16.451	-0.032	-0.032	0.000	0.000	0.000	0.000
54	A	95	THR	0	0.012	0.018	18.561	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	96	VAL	0	-0.005	-0.024	15.130	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	97	GLU	-1	-0.904	-0.942	18.158	-0.099	-0.099	0.000	0.000	0.000	0.000
57	A	98	ARG	1	0.888	0.935	20.046	0.210	0.210	0.000	0.000	0.000	0.000
58	A	99	ALA	0	0.032	0.009	21.440	0.019	0.019	0.000	0.000	0.000	0.000
59	A	100	SER	0	-0.036	-0.034	23.253	-0.013	-0.013	0.000	0.000	0.000	0.000
60	A	101	GLU	-1	-0.834	-0.909	25.682	-0.126	-0.126	0.000	0.000	0.000	0.000
61	A	102	CYS	0	-0.122	-0.051	24.032	0.006	0.006	0.000	0.000	0.000	0.000
62	A	103	LYS	1	1.006	1.008	26.156	0.125	0.125	0.000	0.000	0.000	0.000
63	A	104	LYS	1	0.862	0.950	20.868	0.255	0.255	0.000	0.000	0.000	0.000
64	A	105	LYS	1	0.987	0.987	23.366	0.240	0.240	0.000	0.000	0.000	0.000
65	A	106	HIS	0	-0.016	-0.009	19.051	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	107	ALA	0	0.032	0.019	18.524	-0.038	-0.038	0.000	0.000	0.000	0.000
67	A	108	PHE	0	0.039	0.012	12.909	0.009	0.009	0.000	0.000	0.000	0.000
68	A	109	LYS	1	0.943	0.980	18.505	0.083	0.083	0.000	0.000	0.000	0.000
69	A	110	ILE	0	0.032	0.013	14.007	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	111	SER	0	-0.054	-0.054	17.927	0.014	0.014	0.000	0.000	0.000	0.000
71	A	112	HIS	0	0.132	0.069	19.839	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	113	PRO	0	0.015	0.008	22.009	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	114	GLN	0	-0.014	-0.004	24.236	-0.009	-0.009	0.000	0.000	0.000	0.000
74	A	115	ILE	0	-0.029	0.009	18.957	0.006	0.006	0.000	0.000	0.000	0.000
75	A	116	LYS	1	0.889	0.936	20.338	-0.021	-0.021	0.000	0.000	0.000	0.000
76	A	117	THR	0	0.027	0.041	21.066	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	118	PHE	0	-0.065	-0.028	17.077	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	119	TYR	0	0.038	0.004	18.884	-0.008	-0.008	0.000	0.000	0.000	0.000
79	A	120	PHE	0	0.013	0.001	13.463	0.001	0.001	0.000	0.000	0.000	0.000
80	A	121	ALA	0	-0.006	-0.003	16.414	0.022	0.022	0.000	0.000	0.000	0.000
81	A	122	ALA	0	0.030	0.027	14.636	-0.030	-0.030	0.000	0.000	0.000	0.000
82	A	123	GLU	-1	-0.870	-0.942	16.029	-0.329	-0.329	0.000	0.000	0.000	0.000
83	A	124	ASN	0	0.013	-0.003	17.315	0.018	0.018	0.000	0.000	0.000	0.000
84	A	125	VAL	0	0.016	0.001	17.642	-0.031	-0.031	0.000	0.000	0.000	0.000
85	A	126	GLN	0	0.059	0.026	17.064	-0.023	-0.023	0.000	0.000	0.000	0.000
86	A	127	GLU	-1	-0.885	-0.945	13.108	-0.826	-0.826	0.000	0.000	0.000	0.000
87	A	128	MET	0	-0.052	-0.020	13.061	-0.041	-0.041	0.000	0.000	0.000	0.000
88	A	129	ASN	0	0.017	-0.004	14.687	0.015	0.015	0.000	0.000	0.000	0.000
89	A	130	VAL	0	-0.002	0.013	9.568	0.012	0.012	0.000	0.000	0.000	0.000
90	A	131	TRP	0	0.039	0.007	6.419	-0.085	-0.085	0.000	0.000	0.000	0.000
91	A	132	LEU	0	-0.012	-0.011	11.328	0.068	0.068	0.000	0.000	0.000	0.000
92	A	133	ASN	0	-0.045	-0.008	12.776	0.102	0.102	0.000	0.000	0.000	0.000
93	A	134	LYS	1	0.950	0.967	7.939	1.360	1.360	0.000	0.000	0.000	0.000
94	A	135	LEU	0	0.011	-0.007	10.012	0.135	0.135	0.000	0.000	0.000	0.000
95	A	136	GLY	0	0.012	0.013	11.803	0.107	0.107	0.000	0.000	0.000	0.000
96	A	137	SER	0	-0.013	-0.010	11.740	0.069	0.069	0.000	0.000	0.000	0.000
97	A	138	ALA	0	-0.028	-0.005	9.579	0.099	0.099	0.000	0.000	0.000	0.000
98	A	139	VAL	0	-0.030	-0.003	11.418	0.104	0.104	0.000	0.000	0.000	0.000
99	A	140	ILE	0	-0.003	0.005	14.868	0.023	0.023	0.000	0.000	0.000	0.000
100	A	141	HIS	1	0.800	0.868	15.133	-0.145	-0.145	0.000	0.000	0.000	0.000
101	A	142	GLN	0	0.044	0.038	17.362	-0.059	-0.059	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:42:ALA)