FMO DATABASE

FMODB ID: ZNYNN

Calculation Name: 2YZI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YZI

Chain ID: A

ChEMBL ID:

UniProt ID: O57847

Base Structure: X-ray

Registration Date: 2023-09-26

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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1138471.730462
FMO2-HF: Nuclear repulsion	1085933.885303
FMO2-HF: Total energy	-52537.845159
FMO2-MP2: Total energy	-52688.87389

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:4:MET)

Summations of interaction energy for fragment #1(A:4: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.
-26.258	-19.467	23.453	-9.715	-20.529	-0.079

Interaction energy analysis for fragmet #1(A:4:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.057 / q_NPA : -0.020

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	6	MET	0	-0.012	-0.006	2.777	-0.393	1.919	0.651	-0.846	-2.117	0.004
4	A	7	LYS	1	0.903	0.938	6.086	0.980	0.980	0.000	0.000	0.000	0.000
5	A	8	ALA	0	0.055	0.041	5.364	0.239	0.239	0.000	0.000	0.000	0.000
6	A	9	PRO	0	-0.054	-0.020	7.329	0.472	0.472	0.000	0.000	0.000	0.000
7	A	10	ILE	0	0.068	0.024	7.217	0.037	0.037	0.000	0.000	0.000	0.000
8	A	11	LYS	1	0.925	0.941	8.853	0.104	0.104	0.000	0.000	0.000	0.000
9	A	12	VAL	0	-0.083	-0.034	6.438	-0.021	-0.021	0.000	0.000	0.000	0.000
10	A	13	TYR	0	-0.026	-0.022	2.437	-1.697	0.409	1.144	-1.174	-2.077	-0.008
11	A	14	MET	0	-0.054	0.022	7.222	0.214	0.214	0.000	0.000	0.000	0.000
12	A	15	THR	0	0.055	0.036	10.539	-0.228	-0.228	0.000	0.000	0.000	0.000
13	A	16	LYS	1	0.984	0.970	13.624	-0.206	-0.206	0.000	0.000	0.000	0.000
14	A	17	LYS	1	0.874	0.976	16.755	-0.344	-0.344	0.000	0.000	0.000	0.000
15	A	18	LEU	0	-0.016	-0.013	18.405	0.036	0.036	0.000	0.000	0.000	0.000
16	A	19	LEU	0	0.014	0.003	19.992	-0.034	-0.034	0.000	0.000	0.000	0.000
17	A	20	GLY	0	0.042	0.002	23.591	0.021	0.021	0.000	0.000	0.000	0.000
18	A	21	VAL	0	-0.044	-0.011	26.286	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	22	LYS	1	1.018	1.022	29.588	-0.121	-0.121	0.000	0.000	0.000	0.000
20	A	23	PRO	0	0.072	0.029	32.753	0.004	0.004	0.000	0.000	0.000	0.000
21	A	24	SER	0	0.024	-0.001	33.808	0.003	0.003	0.000	0.000	0.000	0.000
22	A	25	THR	0	-0.059	-0.031	31.779	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	26	SER	0	0.077	0.042	33.836	0.007	0.007	0.000	0.000	0.000	0.000
24	A	27	VAL	0	0.023	0.003	30.186	0.009	0.009	0.000	0.000	0.000	0.000
25	A	28	GLN	0	0.008	0.019	30.737	0.008	0.008	0.000	0.000	0.000	0.000
26	A	29	GLU	-1	-0.798	-0.880	31.894	0.144	0.144	0.000	0.000	0.000	0.000
27	A	30	ALA	0	0.006	-0.005	28.210	0.007	0.007	0.000	0.000	0.000	0.000
28	A	31	SER	0	-0.018	-0.030	27.232	0.019	0.019	0.000	0.000	0.000	0.000
29	A	32	ARG	1	0.738	0.835	27.585	-0.131	-0.131	0.000	0.000	0.000	0.000
30	A	33	LEU	0	-0.018	-0.008	28.063	0.003	0.003	0.000	0.000	0.000	0.000
31	A	34	MET	0	-0.052	-0.027	23.507	0.019	0.019	0.000	0.000	0.000	0.000
32	A	35	MET	0	-0.034	-0.010	23.562	0.033	0.033	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.812	-0.867	25.745	0.143	0.143	0.000	0.000	0.000	0.000
34	A	37	PHE	0	-0.057	-0.041	23.811	0.001	0.001	0.000	0.000	0.000	0.000
35	A	38	ASP	-1	-0.930	-0.957	19.988	0.343	0.343	0.000	0.000	0.000	0.000
36	A	39	VAL	0	0.002	0.013	19.119	0.043	0.043	0.000	0.000	0.000	0.000
37	A	40	GLY	0	0.000	-0.015	17.976	-0.030	-0.030	0.000	0.000	0.000	0.000
38	A	41	SER	0	-0.007	-0.026	18.699	0.004	0.004	0.000	0.000	0.000	0.000
39	A	42	LEU	0	-0.001	0.010	20.563	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	43	VAL	0	0.007	-0.001	21.864	0.014	0.014	0.000	0.000	0.000	0.000
41	A	44	VAL	0	-0.043	-0.015	24.529	-0.017	-0.017	0.000	0.000	0.000	0.000
42	A	45	ILE	0	-0.002	-0.002	26.174	0.008	0.008	0.000	0.000	0.000	0.000
43	A	46	ASN	0	-0.022	-0.036	29.833	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	47	ASP	-1	-0.864	-0.939	33.107	0.110	0.110	0.000	0.000	0.000	0.000
45	A	48	ASP	-1	-0.914	-0.933	33.501	0.105	0.105	0.000	0.000	0.000	0.000
46	A	49	GLY	0	-0.013	-0.007	31.105	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	50	ASN	0	-0.025	-0.004	28.487	0.016	0.016	0.000	0.000	0.000	0.000
48	A	51	VAL	0	-0.011	-0.011	24.050	0.000	0.000	0.000	0.000	0.000	0.000
49	A	52	VAL	0	-0.006	-0.003	27.320	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	53	GLY	0	-0.002	-0.022	26.919	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	54	PHE	0	-0.005	-0.005	18.148	0.013	0.013	0.000	0.000	0.000	0.000
52	A	55	PHE	0	-0.002	0.007	23.367	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	56	THR	0	0.025	-0.020	18.482	0.010	0.010	0.000	0.000	0.000	0.000
54	A	57	LYS	1	0.929	0.955	20.773	-0.346	-0.346	0.000	0.000	0.000	0.000
55	A	58	SER	0	0.005	0.002	19.862	-0.021	-0.021	0.000	0.000	0.000	0.000
56	A	59	ASP	-1	-0.853	-0.898	21.978	0.313	0.313	0.000	0.000	0.000	0.000
57	A	60	ILE	0	0.028	0.019	24.276	-0.021	-0.021	0.000	0.000	0.000	0.000
58	A	61	ILE	0	0.014	0.000	23.805	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	62	ARG	1	0.871	0.915	23.848	-0.281	-0.281	0.000	0.000	0.000	0.000
60	A	63	ARG	1	0.848	0.915	25.539	-0.250	-0.250	0.000	0.000	0.000	0.000
61	A	64	VAL	0	0.008	0.012	29.993	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	65	ILE	0	-0.014	-0.005	29.381	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	66	VAL	0	-0.018	-0.009	29.633	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	67	PRO	0	-0.065	-0.013	31.991	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	68	GLY	0	0.036	0.025	34.830	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	69	LEU	0	-0.072	-0.034	35.085	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	70	PRO	0	0.057	0.045	36.218	0.004	0.004	0.000	0.000	0.000	0.000
68	A	71	TYR	0	0.025	-0.006	34.265	0.006	0.006	0.000	0.000	0.000	0.000
69	A	72	ASP	-1	-0.904	-0.965	34.777	0.117	0.117	0.000	0.000	0.000	0.000
70	A	73	ILE	0	-0.010	0.009	33.962	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	74	PRO	0	0.053	0.018	35.067	0.007	0.007	0.000	0.000	0.000	0.000
72	A	75	VAL	0	0.010	0.013	29.636	0.004	0.004	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.868	-0.950	30.721	0.148	0.148	0.000	0.000	0.000	0.000
74	A	77	ARG	1	0.925	0.960	32.839	-0.125	-0.125	0.000	0.000	0.000	0.000
75	A	78	ILE	0	-0.011	0.000	28.236	0.000	0.000	0.000	0.000	0.000	0.000
76	A	79	MET	0	-0.064	0.018	27.222	0.021	0.021	0.000	0.000	0.000	0.000
77	A	80	THR	0	-0.035	-0.022	23.438	-0.023	-0.023	0.000	0.000	0.000	0.000
78	A	81	ARG	1	0.944	0.967	26.226	-0.163	-0.163	0.000	0.000	0.000	0.000
79	A	82	ASN	0	-0.034	-0.012	25.577	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	83	LEU	0	0.008	0.001	22.521	0.024	0.024	0.000	0.000	0.000	0.000
81	A	84	ILE	0	0.003	0.030	18.005	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	85	THR	0	-0.016	-0.011	17.793	0.041	0.041	0.000	0.000	0.000	0.000
83	A	86	ALA	0	-0.005	-0.006	13.867	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	87	ASN	0	0.062	0.023	15.637	-0.030	-0.030	0.000	0.000	0.000	0.000
85	A	88	VAL	0	0.031	0.014	13.827	0.082	0.082	0.000	0.000	0.000	0.000
86	A	89	ASN	0	-0.016	-0.011	12.588	-0.025	-0.025	0.000	0.000	0.000	0.000
87	A	90	THR	0	-0.028	0.001	12.128	-0.079	-0.079	0.000	0.000	0.000	0.000
88	A	91	PRO	0	0.007	0.017	9.306	0.132	0.132	0.000	0.000	0.000	0.000
89	A	92	LEU	0	0.047	0.012	2.957	-0.817	-0.531	1.715	-0.422	-1.579	0.006
90	A	93	GLY	0	0.036	0.010	6.991	0.253	0.253	0.000	0.000	0.000	0.000
91	A	94	GLU	-1	-0.824	-0.880	8.629	0.444	0.444	0.000	0.000	0.000	0.000
92	A	95	VAL	0	-0.010	-0.005	9.377	-0.054	-0.054	0.000	0.000	0.000	0.000
93	A	96	LEU	0	0.024	0.004	4.467	-0.348	-0.173	0.000	-0.030	-0.145	0.000
94	A	97	ARG	1	0.758	0.853	8.964	-0.598	-0.598	0.000	0.000	0.000	0.000
95	A	98	LYS	1	0.926	0.975	12.019	-0.527	-0.527	0.000	0.000	0.000	0.000
96	A	99	MET	0	-0.026	-0.021	10.115	0.023	0.023	0.000	0.000	0.000	0.000
97	A	100	ALA	0	-0.007	0.001	11.336	-0.079	-0.079	0.000	0.000	0.000	0.000
98	A	101	GLU	-1	-0.892	-0.934	13.045	0.276	0.276	0.000	0.000	0.000	0.000
99	A	102	HIS	0	-0.059	-0.052	16.159	-0.055	-0.055	0.000	0.000	0.000	0.000
100	A	103	ARG	1	0.871	0.955	15.405	-0.359	-0.359	0.000	0.000	0.000	0.000
101	A	104	ILE	0	-0.007	0.014	14.370	-0.037	-0.037	0.000	0.000	0.000	0.000
102	A	105	LYS	1	0.934	0.950	12.192	-0.468	-0.468	0.000	0.000	0.000	0.000
103	A	106	HIS	0	0.009	-0.014	12.624	0.077	0.077	0.000	0.000	0.000	0.000
104	A	107	ILE	0	-0.008	0.007	12.236	-0.090	-0.090	0.000	0.000	0.000	0.000
105	A	108	LEU	0	0.029	0.016	14.571	0.058	0.058	0.000	0.000	0.000	0.000
106	A	109	ILE	0	-0.012	-0.018	12.471	0.033	0.033	0.000	0.000	0.000	0.000
107	A	110	GLU	-1	-0.838	-0.905	16.249	0.214	0.214	0.000	0.000	0.000	0.000
108	A	111	GLU	-1	-0.904	-0.966	18.095	0.165	0.165	0.000	0.000	0.000	0.000
109	A	112	GLU	-1	-0.916	-0.946	20.338	0.074	0.074	0.000	0.000	0.000	0.000
110	A	113	GLY	0	-0.019	-0.029	22.521	-0.010	-0.010	0.000	0.000	0.000	0.000
111	A	114	LYS	1	0.860	0.920	23.313	-0.137	-0.137	0.000	0.000	0.000	0.000
112	A	115	ILE	0	-0.029	-0.022	20.040	0.018	0.018	0.000	0.000	0.000	0.000
113	A	116	VAL	0	0.030	0.019	17.446	-0.019	-0.019	0.000	0.000	0.000	0.000
114	A	117	GLY	0	-0.012	-0.007	16.309	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	118	ILE	0	-0.051	-0.014	14.783	-0.020	-0.020	0.000	0.000	0.000	0.000
116	A	119	PHE	0	0.057	0.023	5.534	-0.138	-0.060	-0.001	-0.009	-0.067	0.000
117	A	120	THR	0	-0.021	-0.045	10.811	-0.125	-0.125	0.000	0.000	0.000	0.000
118	A	121	LEU	0	0.025	-0.004	7.613	0.336	0.336	0.000	0.000	0.000	0.000
119	A	122	SER	0	0.018	0.009	7.509	0.173	0.173	0.000	0.000	0.000	0.000
120	A	123	ASP	-1	-0.800	-0.870	8.476	1.249	1.249	0.000	0.000	0.000	0.000
121	A	124	LEU	0	-0.011	0.001	2.427	-0.164	0.108	2.190	-0.484	-1.978	0.002
122	A	125	LEU	0	-0.010	0.019	4.048	1.576	2.309	0.102	-0.307	-0.529	-0.002
123	A	126	GLU	-1	-0.797	-0.898	6.109	0.498	0.498	0.000	0.000	0.000	0.000
124	A	127	ALA	0	-0.035	-0.021	2.812	-2.011	-1.290	1.130	-0.468	-1.382	0.003
125	A	128	SER	0	-0.040	-0.048	2.393	-8.067	-5.652	6.572	-3.475	-5.513	-0.026
126	A	129	ARG	1	0.835	0.906	3.343	-0.583	-2.490	0.047	2.411	-0.550	-0.001
127	A	130	ARG	1	0.836	0.930	3.949	0.126	0.379	-0.001	-0.026	-0.226	0.000
128	A	131	ARG	1	0.955	0.970	4.054	-0.339	-0.113	-0.001	-0.035	-0.190	0.000
129	A	132	LEU	0	-0.013	0.006	6.452	-0.018	-0.018	0.000	0.000	0.000	0.000
130	A	133	GLU	-1	-0.784	-0.897	1.905	-16.874	-17.753	9.905	-4.850	-4.176	-0.057
131	A	134	THR	0	-0.074	-0.047	5.674	0.700	0.700	0.000	0.000	0.000	0.000
132	A	135	ALA	0	0.028	0.024	7.869	0.056	0.056	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:MET)