FMO DATABASE

FMODB ID: R5ZQ8

Calculation Name: 4M1A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4M1A

Chain ID: A

ChEMBL ID:

UniProt ID: D1AJN4

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	108
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-870164.545907
FMO2-HF: Nuclear repulsion	825968.793424
FMO2-HF: Total energy	-44195.752483
FMO2-MP2: Total energy	-44325.787255

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.
-29.778	-35.307	33.732	-3.214	-24.99	-0.018

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 : -0.019 / q_NPA : 0.042

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	HIS	0	-0.023	-0.015	2.243	2.191	-4.443	4.798	6.048	-4.211	-0.007
4	A	4	ILE	0	-0.040	-0.008	4.420	-0.557	-0.468	-0.001	-0.014	-0.074	0.000
5	A	5	ARG	1	0.825	0.880	7.772	-1.565	-1.565	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.009	0.000	10.948	-0.010	-0.010	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.821	0.888	14.389	-0.781	-0.781	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.078	0.039	17.926	0.011	0.011	0.000	0.000	0.000	0.000
9	A	9	ALA	0	-0.001	0.010	19.641	-0.025	-0.025	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.865	-0.939	20.625	0.378	0.378	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.851	0.908	19.353	-0.298	-0.298	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.832	-0.895	19.810	0.291	0.291	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.843	0.901	21.357	-0.309	-0.309	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.023	0.009	15.168	0.030	0.030	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.770	0.864	16.280	-0.247	-0.247	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.808	-0.871	17.625	0.345	0.345	0.000	0.000	0.000	0.000
17	A	17	PHE	0	-0.007	-0.001	13.200	-0.014	-0.014	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.018	-0.029	13.186	0.023	0.023	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.010	0.003	15.155	-0.026	-0.026	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.004	0.001	16.965	0.013	0.013	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.053	-0.018	12.693	0.007	0.007	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.024	0.008	10.517	0.146	0.146	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.876	-0.944	11.258	0.190	0.190	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.899	-0.937	13.481	0.512	0.512	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.019	-0.018	9.448	0.039	0.039	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.038	0.024	9.126	0.171	0.171	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.042	-0.022	10.194	-0.098	-0.098	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.061	-0.032	12.072	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.017	-0.007	7.229	0.168	0.168	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.957	-0.964	7.424	0.308	0.308	0.000	0.000	0.000	0.000
31	A	31	CYS	0	-0.088	-0.033	5.598	-0.028	-0.028	0.000	0.000	0.000	0.000
32	A	32	PRO	0	-0.005	0.001	6.551	0.385	0.385	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.065	0.030	7.592	-0.030	-0.030	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.941	-0.988	8.260	-0.428	-0.428	0.000	0.000	0.000	0.000
35	A	35	TRP	0	-0.035	-0.022	3.141	-1.616	-0.600	0.069	-0.256	-0.830	-0.001
36	A	36	PHE	0	-0.011	0.013	3.421	0.834	1.302	0.045	-0.306	-0.206	-0.002
37	A	37	THR	0	0.003	0.010	4.336	-0.351	-0.101	0.000	-0.053	-0.197	0.000
38	A	38	PHE	0	0.032	-0.007	6.673	0.075	0.075	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.839	-0.881	8.255	1.309	1.309	0.000	0.000	0.000	0.000
40	A	40	TYR	0	-0.045	-0.043	11.803	0.017	0.017	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.017	-0.017	13.508	-0.039	-0.039	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.788	-0.865	16.141	0.300	0.300	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.057	-0.037	19.278	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	44	THR	0	-0.003	0.018	21.530	0.020	0.020	0.000	0.000	0.000	0.000
45	A	45	PHE	0	-0.006	0.004	20.732	0.017	0.017	0.000	0.000	0.000	0.000
46	A	46	PHE	0	0.016	-0.005	26.068	-0.023	-0.023	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.021	0.007	29.235	0.008	0.008	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.910	-0.951	31.832	0.160	0.160	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.005	0.006	34.472	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.789	0.889	34.390	-0.187	-0.187	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.869	-0.958	29.914	0.247	0.247	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.914	-0.961	28.577	0.291	0.291	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.849	-0.912	27.995	0.336	0.336	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.017	0.001	25.453	0.028	0.028	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.092	-0.051	21.420	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.025	0.018	18.368	0.013	0.013	0.000	0.000	0.000	0.000
57	A	57	PHE	0	-0.019	-0.009	15.631	0.036	0.036	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.010	-0.004	12.355	0.007	0.007	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.844	-0.894	10.614	0.937	0.937	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.015	0.002	7.250	0.066	0.066	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.012	0.005	4.868	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	62	TRP	0	0.010	-0.021	2.311	-0.826	0.308	2.651	-1.462	-2.323	0.002
63	A	63	PHE	0	0.010	-0.004	2.302	-7.210	-13.108	17.972	-3.563	-8.512	0.025
64	A	64	ASP	-1	-0.840	-0.907	4.313	2.721	2.466	-0.011	0.531	-0.265	0.002
65	A	65	ARG	1	0.872	0.941	3.695	-4.781	-4.365	0.017	-0.093	-0.340	0.001
66	A	66	ASP	-1	-0.823	-0.910	9.572	0.884	0.884	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.002	-0.017	12.855	0.153	0.153	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.873	-0.904	15.496	0.545	0.545	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.031	0.006	10.880	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.829	0.902	11.347	-1.522	-1.522	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.877	-0.962	12.568	0.869	0.869	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.830	0.911	14.897	-0.692	-0.692	0.000	0.000	0.000	0.000
73	A	73	ILE	0	0.018	0.015	9.623	-0.059	-0.059	0.000	0.000	0.000	0.000
74	A	74	ALA	0	0.000	0.001	13.907	-0.066	-0.066	0.000	0.000	0.000	0.000
75	A	75	ALA	0	-0.001	0.008	16.274	-0.090	-0.090	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.011	0.019	14.433	-0.063	-0.063	0.000	0.000	0.000	0.000
77	A	77	PHE	0	0.026	-0.012	10.851	-0.071	-0.071	0.000	0.000	0.000	0.000
78	A	78	THR	0	-0.013	-0.016	17.107	-0.078	-0.078	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.875	-0.935	20.520	0.374	0.374	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.770	0.879	17.856	-0.606	-0.606	0.000	0.000	0.000	0.000
81	A	81	TRP	0	0.056	0.022	16.547	-0.086	-0.086	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.859	0.923	21.579	-0.451	-0.451	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.786	0.899	23.751	-0.439	-0.439	0.000	0.000	0.000	0.000
84	A	84	ILE	0	-0.069	-0.021	21.953	-0.028	-0.028	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.007	-0.006	24.019	-0.018	-0.018	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.892	-0.952	26.554	0.314	0.314	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.843	0.928	24.119	-0.368	-0.368	0.000	0.000	0.000	0.000
88	A	88	ILE	0	-0.012	0.001	23.558	0.016	0.016	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.031	0.019	19.239	0.008	0.008	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.064	-0.041	18.407	-0.037	-0.037	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.022	0.019	13.324	0.021	0.021	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.029	-0.006	12.809	-0.048	-0.048	0.000	0.000	0.000	0.000
93	A	93	PHE	0	0.032	0.011	9.405	0.074	0.074	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.060	-0.034	8.233	-0.525	-0.525	0.000	0.000	0.000	0.000
95	A	95	PRO	0	-0.001	0.006	6.781	0.636	0.636	0.000	0.000	0.000	0.000
96	A	96	LEU	0	0.012	0.004	2.239	-1.315	-1.286	1.555	-0.278	-1.306	0.000
97	A	97	ILE	0	0.007	-0.016	6.076	0.288	0.288	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.821	-0.886	5.488	-1.905	-1.905	0.000	0.000	0.000	0.000
99	A	99	ASN	0	-0.033	-0.029	7.096	-0.250	-0.250	0.000	0.000	0.000	0.000
100	A	100	MET	0	-0.095	-0.044	8.799	0.178	0.178	0.000	0.000	0.000	0.000
101	A	101	TYR	0	-0.042	-0.025	2.094	-5.044	-3.970	5.938	-2.545	-4.467	-0.026
102	A	102	TYR	0	-0.059	-0.033	6.898	0.159	0.159	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.829	-0.900	3.565	-9.994	-9.266	0.012	-0.333	-0.407	-0.002
104	A	104	ASP	-1	-0.912	-0.957	7.315	-1.169	-1.169	0.000	0.000	0.000	0.000
105	A	105	GLY	0	-0.056	-0.019	10.696	0.200	0.200	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.063	-0.031	10.363	0.249	0.249	0.000	0.000	0.000	0.000
107	A	107	HIS	0	-0.049	-0.028	8.775	0.007	0.007	0.000	0.000	0.000	0.000
108	A	108	PHE	0	-0.034	-0.031	3.198	-2.972	-0.918	0.687	-0.890	-1.852	-0.010

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