FMO DATABASE

FMODB ID: ZYJ7N

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	OptHSide
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	-869697.704079
FMO2-HF: Nuclear repulsion	825502.477776
FMO2-HF: Total energy	-44195.226303
FMO2-MP2: Total energy	-44325.320532

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.
-29.771	-37.163	37.904	-3.708	-26.804	-0.012

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 : -0.024 / q_NPA : 0.051

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	0.007	-0.011	2.286	0.770	-5.618	6.047	5.318	-4.978	-0.010
4	A	4	ILE	0	-0.020	0.002	4.261	-0.578	-0.484	0.000	-0.015	-0.079	0.000
5	A	5	ARG	1	0.795	0.870	7.876	-1.201	-1.201	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.018	0.009	10.812	-0.002	-0.002	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.848	0.900	14.285	-0.731	-0.731	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.063	0.023	17.543	0.023	0.023	0.000	0.000	0.000	0.000
9	A	9	ALA	0	-0.011	0.012	19.299	-0.024	-0.024	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.861	-0.939	20.860	0.335	0.335	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.870	0.917	19.270	-0.256	-0.256	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.878	-0.924	19.654	0.274	0.274	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.908	0.944	21.278	-0.290	-0.290	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.040	0.017	15.033	0.033	0.033	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.776	0.875	16.402	-0.234	-0.234	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.830	-0.898	17.683	0.332	0.332	0.000	0.000	0.000	0.000
17	A	17	PHE	0	-0.018	0.002	13.183	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.040	-0.044	12.827	0.039	0.039	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.024	0.005	15.107	-0.019	-0.019	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.003	-0.004	17.090	0.017	0.017	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.058	-0.011	12.412	0.009	0.009	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.020	0.001	10.115	0.130	0.130	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.889	-0.942	11.032	0.174	0.174	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.939	-0.976	13.164	0.580	0.580	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.048	-0.031	9.312	0.072	0.072	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.047	0.024	8.410	0.223	0.223	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.028	-0.010	9.476	-0.092	-0.092	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.069	-0.026	11.741	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.034	-0.028	6.706	0.148	0.148	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.949	-0.954	7.392	0.419	0.419	0.000	0.000	0.000	0.000
31	A	31	CYS	0	-0.099	-0.041	4.931	-0.047	-0.047	0.000	0.000	0.000	0.000
32	A	32	PRO	0	0.003	0.005	5.987	0.438	0.438	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.062	0.029	7.039	-0.124	-0.124	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.937	-0.985	8.085	-0.299	-0.299	0.000	0.000	0.000	0.000
35	A	35	TRP	0	-0.048	-0.027	2.648	-1.639	-0.426	0.243	-0.351	-1.104	-0.001
36	A	36	PHE	0	0.013	0.017	3.318	0.608	1.223	0.091	-0.402	-0.304	-0.003
37	A	37	THR	0	-0.001	0.013	4.569	-0.166	0.029	-0.001	-0.027	-0.167	0.000
38	A	38	PHE	0	0.033	-0.007	6.757	0.183	0.183	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.856	-0.885	8.699	0.851	0.851	0.000	0.000	0.000	0.000
40	A	40	TYR	0	-0.058	-0.060	11.860	0.045	0.045	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.010	-0.014	13.464	-0.044	-0.044	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.803	-0.866	16.051	0.273	0.273	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.071	-0.042	18.875	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	44	THR	0	0.016	0.007	21.522	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	PHE	0	0.020	0.032	20.600	0.003	0.003	0.000	0.000	0.000	0.000
46	A	46	PHE	0	0.010	-0.002	25.976	-0.022	-0.022	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.002	-0.004	29.026	0.010	0.010	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.902	-0.954	31.593	0.153	0.153	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.008	-0.005	34.177	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.806	0.903	34.371	-0.178	-0.178	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.903	-0.957	29.507	0.230	0.230	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.922	-0.964	28.606	0.276	0.276	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.826	-0.913	27.884	0.321	0.321	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.004	0.009	25.009	0.028	0.028	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.103	-0.048	21.349	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.029	0.020	18.084	0.004	0.004	0.000	0.000	0.000	0.000
57	A	57	PHE	0	-0.031	-0.027	15.392	0.019	0.019	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.009	-0.007	11.976	0.005	0.005	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.842	-0.886	10.560	0.855	0.855	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.012	0.008	6.745	0.065	0.065	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.023	-0.015	4.710	-0.241	-0.108	-0.001	-0.014	-0.118	0.000
62	A	62	TRP	0	0.018	-0.013	2.131	-0.321	0.371	4.078	-1.988	-2.781	0.003
63	A	63	PHE	0	0.016	-0.008	2.245	-6.678	-14.631	19.893	-3.189	-8.751	0.029
64	A	64	ASP	-1	-0.835	-0.919	4.256	2.997	2.554	-0.015	0.730	-0.273	0.003
65	A	65	ARG	1	0.889	0.947	3.002	-5.994	-5.073	0.217	-0.278	-0.860	0.001
66	A	66	ASP	-1	-0.854	-0.920	8.905	0.974	0.974	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.027	-0.021	12.152	0.177	0.177	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.871	-0.898	14.793	0.597	0.597	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.039	0.011	10.519	-0.023	-0.023	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.842	0.923	11.020	-1.651	-1.651	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.895	-0.954	12.450	0.861	0.861	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.824	0.902	14.627	-0.758	-0.758	0.000	0.000	0.000	0.000
73	A	73	ILE	0	0.016	0.010	9.282	-0.062	-0.062	0.000	0.000	0.000	0.000
74	A	74	ALA	0	0.024	0.006	13.524	-0.090	-0.090	0.000	0.000	0.000	0.000
75	A	75	ALA	0	-0.010	0.007	15.807	-0.111	-0.111	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.021	0.020	14.343	-0.084	-0.084	0.000	0.000	0.000	0.000
77	A	77	PHE	0	0.024	-0.015	10.624	-0.079	-0.079	0.000	0.000	0.000	0.000
78	A	78	THR	0	-0.035	-0.032	16.862	-0.092	-0.092	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.947	-0.972	20.153	0.434	0.434	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.876	0.938	18.064	-0.637	-0.637	0.000	0.000	0.000	0.000
81	A	81	TRP	0	0.036	0.006	16.417	-0.096	-0.096	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.845	0.918	21.430	-0.466	-0.466	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.886	0.955	23.911	-0.428	-0.428	0.000	0.000	0.000	0.000
84	A	84	ILE	0	-0.060	-0.014	22.118	-0.032	-0.032	0.000	0.000	0.000	0.000
85	A	85	THR	0	0.016	0.010	23.700	-0.019	-0.019	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.916	-0.960	26.581	0.309	0.309	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.845	0.935	24.081	-0.358	-0.358	0.000	0.000	0.000	0.000
88	A	88	ILE	0	-0.019	-0.008	23.226	0.023	0.023	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.019	0.014	18.730	0.004	0.004	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.041	-0.021	18.057	-0.016	-0.016	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.006	0.004	13.257	0.029	0.029	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.041	-0.007	12.596	-0.070	-0.070	0.000	0.000	0.000	0.000
93	A	93	PHE	0	0.021	-0.001	8.954	0.059	0.059	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.058	-0.030	8.103	-0.505	-0.505	0.000	0.000	0.000	0.000
95	A	95	PRO	0	0.009	0.011	6.612	0.598	0.598	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.018	-0.006	2.199	-1.118	-1.576	2.474	-0.397	-1.619	-0.001
97	A	97	ILE	0	0.029	-0.004	5.971	0.262	0.262	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.884	-0.944	5.981	-1.319	-1.319	0.000	0.000	0.000	0.000
99	A	99	ASN	0	-0.038	-0.026	7.372	-0.309	-0.309	0.000	0.000	0.000	0.000
100	A	100	MET	0	-0.083	-0.043	9.027	0.149	0.149	0.000	0.000	0.000	0.000
101	A	101	TYR	0	-0.040	-0.014	2.164	-5.217	-3.591	4.346	-2.131	-3.841	-0.023
102	A	102	TYR	0	-0.043	-0.025	7.095	0.031	0.031	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.853	-0.927	3.770	-8.978	-8.489	0.005	-0.184	-0.310	-0.001
104	A	104	ASP	-1	-0.897	-0.952	7.470	-1.187	-1.187	0.000	0.000	0.000	0.000
105	A	105	GLY	0	-0.069	-0.032	10.770	0.170	0.170	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.048	-0.021	10.825	0.250	0.250	0.000	0.000	0.000	0.000
107	A	107	HIS	0	-0.072	-0.035	8.924	-0.020	-0.020	0.000	0.000	0.000	0.000
108	A	108	PHE	0	0.032	0.030	3.012	-2.705	-0.833	0.527	-0.780	-1.619	-0.009

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