FMO DATABASE

FMODB ID: Z6KJN

Calculation Name: 2YZ1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YZ1

Chain ID: A

ChEMBL ID:

UniProt ID: P97797

Base Structure: X-ray

Registration Date: 2023-09-19

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	113
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-850755.272033
FMO2-HF: Nuclear repulsion	807048.022175
FMO2-HF: Total energy	-43707.249859
FMO2-MP2: Total energy	-43834.892733

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:7:GLU)

Summations of interaction energy for fragment #1(A:7:GLU)

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.
-123.431	-121.793	18.336	-9.643	-10.331	0.108

Interaction energy analysis for fragmet #1(A:7:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.790 / q_NPA : -0.888

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	9	LYS	1	0.880	0.933	1.834	-123.361	-122.975	18.336	-9.063	-9.659	0.106
4	A	10	VAL	0	0.023	-0.002	4.757	-5.259	-5.250	-0.001	-0.009	0.001	0.000
5	A	11	THR	0	-0.010	-0.002	8.502	0.943	0.943	0.000	0.000	0.000	0.000
6	A	12	GLN	0	0.044	0.004	9.967	-0.793	-0.793	0.000	0.000	0.000	0.000
7	A	13	PRO	0	-0.056	-0.029	13.662	0.464	0.464	0.000	0.000	0.000	0.000
8	A	14	GLU	-1	-0.875	-0.914	13.378	22.079	22.079	0.000	0.000	0.000	0.000
9	A	15	LYS	1	0.893	0.948	16.910	-14.863	-14.863	0.000	0.000	0.000	0.000
10	A	16	SER	0	0.002	-0.018	20.692	0.200	0.200	0.000	0.000	0.000	0.000
11	A	17	VAL	0	-0.074	-0.044	23.873	-0.020	-0.020	0.000	0.000	0.000	0.000
12	A	18	SER	0	0.012	0.009	25.832	-0.208	-0.208	0.000	0.000	0.000	0.000
13	A	19	VAL	0	-0.016	-0.009	29.449	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	20	ALA	0	0.048	0.031	31.502	-0.092	-0.092	0.000	0.000	0.000	0.000
15	A	21	ALA	0	0.035	0.012	34.325	0.174	0.174	0.000	0.000	0.000	0.000
16	A	22	GLY	0	-0.012	0.002	35.358	-0.277	-0.277	0.000	0.000	0.000	0.000
17	A	23	ASP	-1	-0.858	-0.916	32.818	8.946	8.946	0.000	0.000	0.000	0.000
18	A	24	SER	0	-0.055	-0.034	30.820	0.102	0.102	0.000	0.000	0.000	0.000
19	A	25	THR	0	-0.004	0.004	25.957	0.123	0.123	0.000	0.000	0.000	0.000
20	A	26	VAL	0	-0.053	-0.041	21.731	-0.113	-0.113	0.000	0.000	0.000	0.000
21	A	27	LEU	0	0.010	0.031	19.959	0.187	0.187	0.000	0.000	0.000	0.000
22	A	28	ASN	0	-0.007	-0.028	16.765	-0.103	-0.103	0.000	0.000	0.000	0.000
23	A	29	CYS	0	-0.017	-0.004	13.454	0.315	0.315	0.000	0.000	0.000	0.000
24	A	30	THR	0	-0.024	0.004	10.699	-1.478	-1.478	0.000	0.000	0.000	0.000
25	A	31	LEU	0	-0.006	0.006	8.365	1.587	1.587	0.000	0.000	0.000	0.000
26	A	32	THR	0	-0.018	-0.024	3.655	-2.240	-1.233	0.003	-0.544	-0.466	0.002
27	A	33	SER	0	-0.006	-0.017	4.774	-2.809	-2.729	-0.001	-0.013	-0.066	0.000
28	A	34	LEU	0	0.013	-0.004	6.813	0.126	0.126	0.000	0.000	0.000	0.000
29	A	35	LEU	0	-0.035	0.008	7.409	-1.179	-1.179	0.000	0.000	0.000	0.000
30	A	36	PRO	0	0.076	0.031	6.901	2.899	2.899	0.000	0.000	0.000	0.000
31	A	37	VAL	0	0.032	0.013	9.848	0.347	0.347	0.000	0.000	0.000	0.000
32	A	38	GLY	0	0.039	0.014	13.270	-0.175	-0.175	0.000	0.000	0.000	0.000
33	A	39	PRO	0	-0.031	0.012	14.679	0.805	0.805	0.000	0.000	0.000	0.000
34	A	40	ILE	0	0.003	0.016	13.217	1.482	1.482	0.000	0.000	0.000	0.000
35	A	41	LYS	1	0.816	0.902	15.829	-16.828	-16.828	0.000	0.000	0.000	0.000
36	A	42	TRP	0	0.006	-0.006	17.051	1.128	1.128	0.000	0.000	0.000	0.000
37	A	43	TYR	0	0.013	-0.005	18.058	-0.542	-0.542	0.000	0.000	0.000	0.000
38	A	44	ARG	1	0.853	0.929	21.012	-10.905	-10.905	0.000	0.000	0.000	0.000
39	A	45	GLY	0	0.014	0.018	23.361	-0.412	-0.412	0.000	0.000	0.000	0.000
40	A	46	VAL	0	0.002	-0.015	21.420	0.752	0.752	0.000	0.000	0.000	0.000
41	A	47	GLY	0	0.031	0.018	21.780	-0.591	-0.591	0.000	0.000	0.000	0.000
42	A	48	GLN	0	-0.007	-0.023	21.110	0.564	0.564	0.000	0.000	0.000	0.000
43	A	49	SER	0	-0.020	-0.011	23.820	-0.294	-0.294	0.000	0.000	0.000	0.000
44	A	50	ARG	1	0.795	0.907	16.456	-18.080	-18.080	0.000	0.000	0.000	0.000
45	A	51	LEU	0	0.056	0.032	23.827	0.016	0.016	0.000	0.000	0.000	0.000
46	A	52	LEU	0	-0.028	-0.019	21.930	0.496	0.496	0.000	0.000	0.000	0.000
47	A	53	ILE	0	-0.029	-0.008	23.147	-0.494	-0.494	0.000	0.000	0.000	0.000
48	A	54	TYR	0	0.020	0.004	21.414	-0.546	-0.546	0.000	0.000	0.000	0.000
49	A	55	SER	0	-0.022	-0.032	20.702	0.685	0.685	0.000	0.000	0.000	0.000
50	A	56	PHE	0	0.007	0.021	18.373	-0.652	-0.652	0.000	0.000	0.000	0.000
51	A	57	THR	0	0.004	-0.017	18.867	0.906	0.906	0.000	0.000	0.000	0.000
52	A	58	GLY	0	0.028	0.022	18.529	0.542	0.542	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.760	-0.892	17.863	13.722	13.722	0.000	0.000	0.000	0.000
54	A	60	HIS	0	0.007	0.002	20.509	0.651	0.651	0.000	0.000	0.000	0.000
55	A	61	PHE	0	-0.001	0.011	15.560	-0.243	-0.243	0.000	0.000	0.000	0.000
56	A	62	PRO	0	0.000	-0.001	19.103	-0.082	-0.082	0.000	0.000	0.000	0.000
57	A	63	ARG	1	0.891	0.937	20.384	-10.893	-10.893	0.000	0.000	0.000	0.000
58	A	64	VAL	0	-0.054	-0.024	22.196	-0.615	-0.615	0.000	0.000	0.000	0.000
59	A	65	THR	0	-0.014	-0.006	18.134	0.405	0.405	0.000	0.000	0.000	0.000
60	A	66	ASN	0	-0.019	-0.011	18.023	0.326	0.326	0.000	0.000	0.000	0.000
61	A	67	VAL	0	-0.021	-0.006	19.872	-0.486	-0.486	0.000	0.000	0.000	0.000
62	A	68	SER	0	-0.033	-0.023	17.534	0.680	0.680	0.000	0.000	0.000	0.000
63	A	69	ASP	-1	-0.829	-0.906	18.902	13.063	13.063	0.000	0.000	0.000	0.000
64	A	70	ALA	0	-0.005	0.001	19.912	0.415	0.415	0.000	0.000	0.000	0.000
65	A	71	THR	0	-0.062	-0.051	22.492	-0.420	-0.420	0.000	0.000	0.000	0.000
66	A	72	LYS	1	0.778	0.904	16.265	-17.108	-17.108	0.000	0.000	0.000	0.000
67	A	73	ARG	1	0.871	0.912	19.811	-13.857	-13.857	0.000	0.000	0.000	0.000
68	A	74	ASN	0	0.019	0.002	15.199	0.693	0.693	0.000	0.000	0.000	0.000
69	A	75	ASN	0	0.082	0.034	12.987	-0.020	-0.020	0.000	0.000	0.000	0.000
70	A	76	MET	0	-0.004	0.020	9.031	-0.253	-0.253	0.000	0.000	0.000	0.000
71	A	77	ASP	-1	-0.785	-0.846	12.959	16.937	16.937	0.000	0.000	0.000	0.000
72	A	78	PHE	0	0.037	0.007	13.147	-0.497	-0.497	0.000	0.000	0.000	0.000
73	A	79	SER	0	0.003	-0.017	16.555	0.134	0.134	0.000	0.000	0.000	0.000
74	A	80	ILE	0	-0.018	0.009	18.631	-0.528	-0.528	0.000	0.000	0.000	0.000
75	A	81	ARG	1	0.929	0.959	22.041	-10.859	-10.859	0.000	0.000	0.000	0.000
76	A	82	ILE	0	0.017	0.020	24.609	-0.032	-0.032	0.000	0.000	0.000	0.000
77	A	83	SER	0	0.009	-0.026	27.858	0.013	0.013	0.000	0.000	0.000	0.000
78	A	84	ASN	0	-0.097	-0.051	31.363	-0.024	-0.024	0.000	0.000	0.000	0.000
79	A	85	VAL	0	-0.013	0.008	29.697	-0.069	-0.069	0.000	0.000	0.000	0.000
80	A	86	THR	0	0.037	0.001	32.349	-0.308	-0.308	0.000	0.000	0.000	0.000
81	A	87	PRO	0	0.034	-0.004	33.009	0.304	0.304	0.000	0.000	0.000	0.000
82	A	88	GLU	-1	-0.881	-0.944	33.194	9.091	9.091	0.000	0.000	0.000	0.000
83	A	89	ASP	-1	-0.834	-0.884	29.181	10.739	10.739	0.000	0.000	0.000	0.000
84	A	90	ALA	0	0.008	0.026	28.263	0.504	0.504	0.000	0.000	0.000	0.000
85	A	91	GLY	0	0.007	0.004	26.585	0.011	0.011	0.000	0.000	0.000	0.000
86	A	92	THR	0	-0.024	-0.020	20.015	-0.087	-0.087	0.000	0.000	0.000	0.000
87	A	93	TYR	0	-0.024	-0.037	20.656	-0.185	-0.185	0.000	0.000	0.000	0.000
88	A	94	TYR	0	-0.006	0.001	15.762	0.175	0.175	0.000	0.000	0.000	0.000
89	A	96	VAL	0	0.023	0.006	12.920	1.733	1.733	0.000	0.000	0.000	0.000
90	A	97	LYS	1	0.801	0.906	9.450	-25.491	-25.491	0.000	0.000	0.000	0.000
91	A	98	PHE	0	0.026	-0.011	11.864	0.938	0.938	0.000	0.000	0.000	0.000
92	A	99	GLN	0	-0.026	-0.009	12.287	1.933	1.933	0.000	0.000	0.000	0.000
93	A	100	LYS	1	0.836	0.888	14.271	-15.391	-15.391	0.000	0.000	0.000	0.000
94	A	101	GLY	0	0.021	0.014	17.263	0.404	0.404	0.000	0.000	0.000	0.000
95	A	102	PRO	0	-0.031	-0.042	19.146	-0.416	-0.416	0.000	0.000	0.000	0.000
96	A	103	SER	0	-0.043	-0.021	22.037	-0.856	-0.856	0.000	0.000	0.000	0.000
97	A	104	GLU	-1	-0.831	-0.881	22.280	14.563	14.563	0.000	0.000	0.000	0.000
98	A	105	PRO	0	-0.009	-0.005	21.599	-0.466	-0.466	0.000	0.000	0.000	0.000
99	A	106	ASP	-1	-0.765	-0.879	17.992	16.276	16.276	0.000	0.000	0.000	0.000
100	A	107	THR	0	-0.036	-0.006	14.384	-0.235	-0.235	0.000	0.000	0.000	0.000
101	A	108	GLU	-1	-0.818	-0.887	12.929	21.615	21.615	0.000	0.000	0.000	0.000
102	A	109	ILE	0	-0.057	-0.033	8.869	0.172	0.172	0.000	0.000	0.000	0.000
103	A	110	GLN	0	-0.042	-0.024	4.359	-1.570	-1.414	-0.001	-0.014	-0.141	0.000
104	A	111	SER	0	0.027	0.010	8.701	-4.213	-4.213	0.000	0.000	0.000	0.000
105	A	112	GLY	0	0.015	0.022	9.768	2.953	2.953	0.000	0.000	0.000	0.000
106	A	113	GLY	0	0.004	-0.007	11.870	-0.917	-0.917	0.000	0.000	0.000	0.000
107	A	114	GLY	0	0.007	0.004	13.598	-1.291	-1.291	0.000	0.000	0.000	0.000
108	A	115	THR	0	-0.074	-0.044	16.802	0.412	0.412	0.000	0.000	0.000	0.000
109	A	116	GLU	-1	-0.872	-0.906	19.342	12.220	12.220	0.000	0.000	0.000	0.000
110	A	117	VAL	0	-0.010	-0.002	23.083	-0.049	-0.049	0.000	0.000	0.000	0.000
111	A	118	TYR	0	0.015	0.010	26.135	-0.202	-0.202	0.000	0.000	0.000	0.000
112	A	119	VAL	0	-0.004	-0.002	29.392	-0.093	-0.093	0.000	0.000	0.000	0.000
113	A	120	LEU	0	-0.044	-0.019	32.415	-0.301	-0.301	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:GLU)