FMO DATABASE

FMODB ID: 1NYRZ

Calculation Name: 2A1B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2A1B

Chain ID: A

ChEMBL ID:

UniProt ID: P72761

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-675950.422522
FMO2-HF: Nuclear repulsion	638421.322179
FMO2-HF: Total energy	-37529.100342
FMO2-MP2: Total energy	-37639.467063

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:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-26.792	-20.384	11.597	-8.131	-9.872	-0.061

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : 0.009

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	4	ALA	0	0.035	0.033	3.863	-4.154	-2.678	-0.006	-0.750	-0.720	0.004
4	A	5	VAL	0	0.003	-0.002	6.152	0.128	0.128	0.000	0.000	0.000	0.000
5	A	6	GLY	0	0.005	-0.005	7.628	0.056	0.056	0.000	0.000	0.000	0.000
6	A	7	MET	0	-0.050	-0.016	10.042	0.024	0.024	0.000	0.000	0.000	0.000
7	A	8	ILE	0	0.026	0.015	13.990	0.020	0.020	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.751	-0.817	17.772	-0.432	-0.432	0.000	0.000	0.000	0.000
9	A	10	THR	0	-0.042	-0.051	20.354	0.036	0.036	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.886	0.947	24.092	0.218	0.218	0.000	0.000	0.000	0.000
11	A	12	GLY	0	0.063	0.018	26.449	0.022	0.022	0.000	0.000	0.000	0.000
12	A	13	PHE	0	-0.015	-0.008	23.702	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	14	PRO	0	0.036	0.001	26.293	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.070	0.045	26.602	0.009	0.009	0.000	0.000	0.000	0.000
15	A	16	VAL	0	0.013	0.002	20.822	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	17	VAL	0	-0.035	-0.012	22.163	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.850	-0.906	23.545	-0.063	-0.063	0.000	0.000	0.000	0.000
18	A	19	ALA	0	-0.007	0.001	20.728	0.009	0.009	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.003	-0.008	18.979	0.001	0.001	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.838	-0.896	19.720	0.007	0.007	0.000	0.000	0.000	0.000
21	A	22	SER	0	0.040	-0.007	22.183	0.033	0.033	0.000	0.000	0.000	0.000
22	A	23	MET	0	-0.088	-0.041	15.384	0.017	0.017	0.000	0.000	0.000	0.000
23	A	24	VAL	0	-0.069	-0.038	16.477	0.038	0.038	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.781	0.881	18.217	0.040	0.040	0.000	0.000	0.000	0.000
25	A	26	ALA	0	-0.009	0.005	20.189	0.026	0.026	0.000	0.000	0.000	0.000
26	A	27	ALA	0	-0.042	-0.015	16.208	0.025	0.025	0.000	0.000	0.000	0.000
27	A	28	ARG	1	0.921	0.960	14.605	-0.489	-0.489	0.000	0.000	0.000	0.000
28	A	29	VAL	0	-0.024	-0.007	12.087	0.111	0.111	0.000	0.000	0.000	0.000
29	A	30	THR	0	0.009	0.010	10.729	0.019	0.019	0.000	0.000	0.000	0.000
30	A	31	LEU	0	0.009	-0.004	11.829	-0.121	-0.121	0.000	0.000	0.000	0.000
31	A	32	VAL	0	-0.042	-0.019	9.234	0.063	0.063	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.054	0.031	12.617	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	34	TYR	0	-0.047	-0.025	15.444	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.833	-0.899	16.677	-0.537	-0.537	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.849	0.898	18.759	0.280	0.280	0.000	0.000	0.000	0.000
36	A	37	ILE	0	0.032	0.020	19.323	0.019	0.019	0.000	0.000	0.000	0.000
37	A	38	GLY	0	0.057	0.047	22.523	0.016	0.016	0.000	0.000	0.000	0.000
38	A	39	SER	0	-0.031	-0.037	26.323	0.000	0.000	0.000	0.000	0.000	0.000
39	A	40	GLY	0	0.000	-0.008	28.567	0.002	0.002	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.794	0.880	22.174	0.390	0.390	0.000	0.000	0.000	0.000
41	A	42	VAL	0	-0.034	-0.012	22.095	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	43	THR	0	0.007	0.000	16.007	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	44	VAL	0	0.000	0.009	17.007	0.008	0.008	0.000	0.000	0.000	0.000
44	A	45	ILE	0	-0.007	-0.006	10.884	-0.066	-0.066	0.000	0.000	0.000	0.000
45	A	46	VAL	0	0.030	0.012	11.899	0.095	0.095	0.000	0.000	0.000	0.000
46	A	47	ARG	1	0.730	0.822	2.694	3.026	3.562	0.210	-0.258	-0.488	0.000
47	A	48	GLY	0	0.068	0.022	7.806	0.241	0.241	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.787	-0.866	7.713	1.466	1.466	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.011	-0.018	9.544	-0.287	-0.287	0.000	0.000	0.000	0.000
50	A	51	SER	0	0.026	0.019	10.850	-0.102	-0.102	0.000	0.000	0.000	0.000
51	A	52	GLY	0	0.030	0.017	13.294	-0.057	-0.057	0.000	0.000	0.000	0.000
52	A	53	VAL	0	0.011	0.018	9.521	-0.055	-0.055	0.000	0.000	0.000	0.000
53	A	54	GLN	0	0.014	-0.007	12.871	0.006	0.006	0.000	0.000	0.000	0.000
54	A	55	ALA	0	0.000	0.021	15.380	-0.025	-0.025	0.000	0.000	0.000	0.000
55	A	56	SER	0	0.001	-0.009	15.117	-0.045	-0.045	0.000	0.000	0.000	0.000
56	A	57	VAL	0	0.020	0.001	14.148	-0.023	-0.023	0.000	0.000	0.000	0.000
57	A	58	SER	0	-0.049	-0.038	17.273	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.015	0.005	20.384	0.000	0.000	0.000	0.000	0.000	0.000
59	A	60	GLY	0	0.021	0.016	20.414	0.003	0.003	0.000	0.000	0.000	0.000
60	A	61	ILE	0	0.005	-0.008	19.628	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.857	-0.902	22.881	-0.052	-0.052	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.038	-0.009	24.978	0.009	0.009	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.041	0.019	24.029	0.004	0.004	0.000	0.000	0.000	0.000
64	A	65	ASN	0	-0.054	-0.044	25.563	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	66	ARG	1	0.804	0.884	28.273	0.074	0.074	0.000	0.000	0.000	0.000
66	A	67	VAL	0	0.019	0.028	28.501	0.010	0.010	0.000	0.000	0.000	0.000
67	A	68	ASN	0	-0.008	-0.008	31.412	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	69	GLY	0	-0.053	-0.039	32.793	0.002	0.002	0.000	0.000	0.000	0.000
69	A	70	GLY	0	-0.024	-0.001	28.884	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.831	-0.913	27.918	-0.207	-0.207	0.000	0.000	0.000	0.000
71	A	72	VAL	0	-0.014	0.009	22.159	-0.020	-0.020	0.000	0.000	0.000	0.000
72	A	73	LEU	0	-0.060	-0.012	23.189	0.001	0.001	0.000	0.000	0.000	0.000
73	A	74	SER	0	-0.033	-0.046	19.591	-0.028	-0.028	0.000	0.000	0.000	0.000
74	A	75	THR	0	0.007	-0.019	16.788	0.036	0.036	0.000	0.000	0.000	0.000
75	A	76	HIS	0	0.002	0.018	12.306	0.071	0.071	0.000	0.000	0.000	0.000
76	A	77	ILE	0	0.019	0.001	10.540	0.010	0.010	0.000	0.000	0.000	0.000
77	A	78	ILE	0	-0.031	0.003	6.400	0.012	0.012	0.000	0.000	0.000	0.000
78	A	79	ALA	0	0.037	0.008	6.828	-0.278	-0.278	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.836	0.888	3.368	-2.233	-1.164	0.037	-0.476	-0.629	0.003
80	A	81	PRO	0	-0.015	0.015	2.329	-1.994	-0.461	0.684	-0.726	-1.491	0.000
81	A	82	HIS	0	0.064	0.028	1.909	-13.332	-14.696	7.304	-2.993	-2.947	-0.036
82	A	83	GLU	-1	-0.856	-0.940	3.079	-1.790	-1.177	0.070	-0.197	-0.486	-0.001
83	A	84	ASN	0	-0.063	-0.050	4.223	0.877	0.896	0.000	-0.016	-0.002	0.000
84	A	85	LEU	0	0.007	0.007	6.354	0.444	0.444	0.000	0.000	0.000	0.000
85	A	86	GLU	-1	-0.777	-0.872	2.519	-10.132	-7.606	3.298	-2.715	-3.109	-0.031
86	A	87	TYR	0	-0.007	0.029	6.855	0.568	0.568	0.000	0.000	0.000	0.000
87	A	88	VAL	0	-0.005	-0.001	9.660	0.280	0.280	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.009	-0.006	9.932	0.226	0.226	0.000	0.000	0.000	0.000
89	A	90	PRO	0	0.020	0.012	10.845	-0.103	-0.103	0.000	0.000	0.000	0.000
90	A	91	ILE	0	-0.054	-0.022	6.041	0.095	0.095	0.000	0.000	0.000	0.000
91	A	92	ARG	1	0.865	0.927	7.769	0.767	0.767	0.000	0.000	0.000	0.000
92	A	93	TYR	0	0.056	0.017	6.857	-0.030	-0.030	0.000	0.000	0.000	0.000
93	A	94	THR	0	-0.017	-0.004	11.678	-0.105	-0.105	0.000	0.000	0.000	0.000
94	A	95	GLU	-1	-0.887	-0.960	15.178	-0.086	-0.086	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.975	-0.974	13.740	0.145	0.145	0.000	0.000	0.000	0.000
96	A	97	VAL	0	0.011	-0.001	16.980	0.009	0.009	0.000	0.000	0.000	0.000
97	A	98	GLU	-1	-0.783	-0.850	19.429	-0.177	-0.177	0.000	0.000	0.000	0.000
98	A	99	GLN	0	-0.021	-0.022	21.748	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	100	PHE	0	-0.040	-0.006	22.854	0.005	0.005	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.789	0.872	21.520	0.195	0.195	0.000	0.000	0.000	0.000
101	A	102	THR	0	-0.055	-0.027	24.369	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)