FMO DATABASE

FMODB ID: 1N4KZ

Calculation Name: 1YOZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YOZ

Chain ID: A

ChEMBL ID:

UniProt ID: O29321

Base Structure: X-ray

Registration Date: 2023-09-21

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	116
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1026068.122791
FMO2-HF: Nuclear repulsion	977845.877273
FMO2-HF: Total energy	-48222.245518
FMO2-MP2: Total energy	-48363.164387

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:9:GLY)

Summations of interaction energy for fragment #1(A:9:GLY)

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.
-5.475	-0.265	5.272	-5.788	-4.696	-0.029

Interaction energy analysis for fragmet #1(A:9:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.011

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	11	MET	0	-0.022	-0.025	3.850	-1.267	0.799	-0.023	-1.150	-0.893	0.000
4	A	12	LEU	0	-0.012	-0.004	5.164	0.008	0.008	0.000	0.000	0.000	0.000
5	A	13	TYR	0	-0.041	-0.040	7.142	-0.260	-0.260	0.000	0.000	0.000	0.000
6	A	14	ILE	0	0.030	0.033	10.206	0.042	0.042	0.000	0.000	0.000	0.000
7	A	15	ASN	0	0.010	-0.020	13.290	-0.016	-0.016	0.000	0.000	0.000	0.000
8	A	16	SER	0	0.058	-0.002	16.052	0.017	0.017	0.000	0.000	0.000	0.000
9	A	17	PHE	0	-0.029	-0.014	19.568	0.011	0.011	0.000	0.000	0.000	0.000
10	A	18	LEU	0	-0.017	-0.007	16.449	0.006	0.006	0.000	0.000	0.000	0.000
11	A	19	ASP	-1	-0.855	-0.929	17.598	-0.072	-0.072	0.000	0.000	0.000	0.000
12	A	20	ARG	1	0.741	0.841	20.758	0.049	0.049	0.000	0.000	0.000	0.000
13	A	21	MET	0	-0.018	-0.007	22.761	0.006	0.006	0.000	0.000	0.000	0.000
14	A	22	GLY	0	0.000	-0.007	22.987	0.005	0.005	0.000	0.000	0.000	0.000
15	A	23	GLU	-1	-0.786	-0.874	23.963	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	24	ILE	0	-0.037	-0.005	26.383	0.005	0.005	0.000	0.000	0.000	0.000
17	A	25	ILE	0	-0.049	-0.028	26.788	0.003	0.003	0.000	0.000	0.000	0.000
18	A	26	ARG	1	0.781	0.861	21.928	0.039	0.039	0.000	0.000	0.000	0.000
19	A	27	GLY	0	-0.014	0.007	28.572	0.005	0.005	0.000	0.000	0.000	0.000
20	A	28	GLU	-1	-0.841	-0.893	26.084	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	29	LYS	1	0.809	0.894	27.246	0.019	0.019	0.000	0.000	0.000	0.000
22	A	30	SER	0	-0.007	-0.002	31.749	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	31	VAL	0	0.054	0.019	33.336	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	32	GLU	-1	-0.905	-0.935	34.256	-0.024	-0.024	0.000	0.000	0.000	0.000
25	A	33	GLU	-1	-0.850	-0.926	29.874	-0.031	-0.031	0.000	0.000	0.000	0.000
26	A	34	ALA	0	0.021	0.015	30.792	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	35	ASP	-1	-0.828	-0.909	31.876	-0.041	-0.041	0.000	0.000	0.000	0.000
28	A	36	LYS	1	0.851	0.912	31.502	0.030	0.030	0.000	0.000	0.000	0.000
29	A	37	LEU	0	0.026	0.014	25.239	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	38	LEU	0	-0.012	-0.002	27.851	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	39	ASP	-1	-0.835	-0.910	30.215	-0.051	-0.051	0.000	0.000	0.000	0.000
32	A	40	GLN	0	0.063	0.005	28.420	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	41	LYS	1	0.888	0.952	27.953	0.044	0.044	0.000	0.000	0.000	0.000
34	A	42	ASN	0	-0.038	-0.032	27.680	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	43	ILE	0	-0.003	0.010	23.757	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	44	PHE	0	0.023	0.011	22.940	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	45	GLU	-1	-0.815	-0.899	23.155	-0.064	-0.064	0.000	0.000	0.000	0.000
38	A	46	MET	0	-0.024	0.002	21.745	0.003	0.003	0.000	0.000	0.000	0.000
39	A	47	PHE	0	0.063	0.025	17.792	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	48	ARG	1	0.788	0.891	18.454	0.067	0.067	0.000	0.000	0.000	0.000
41	A	49	SER	0	0.040	0.019	19.572	0.004	0.004	0.000	0.000	0.000	0.000
42	A	50	ASP	-1	-0.797	-0.871	15.566	-0.106	-0.106	0.000	0.000	0.000	0.000
43	A	51	CYS	0	-0.085	-0.048	14.912	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	52	GLU	-1	-0.884	-0.939	15.351	-0.029	-0.029	0.000	0.000	0.000	0.000
45	A	53	GLU	-1	-0.917	-0.953	14.817	0.017	0.017	0.000	0.000	0.000	0.000
46	A	54	ILE	0	-0.025	-0.014	9.890	0.028	0.028	0.000	0.000	0.000	0.000
47	A	55	LEU	0	-0.033	-0.013	11.936	0.029	0.029	0.000	0.000	0.000	0.000
48	A	56	ASN	0	-0.028	-0.030	14.059	0.019	0.019	0.000	0.000	0.000	0.000
49	A	57	LEU	0	-0.030	-0.001	11.310	0.027	0.027	0.000	0.000	0.000	0.000
50	A	58	TYR	0	0.018	0.011	10.435	0.031	0.031	0.000	0.000	0.000	0.000
51	A	59	LYS	1	0.791	0.883	11.944	0.054	0.054	0.000	0.000	0.000	0.000
52	A	60	SER	0	-0.066	-0.046	14.957	0.006	0.006	0.000	0.000	0.000	0.000
53	A	61	GLY	0	-0.014	-0.009	12.600	0.009	0.009	0.000	0.000	0.000	0.000
54	A	62	LYS	1	0.896	0.959	12.012	-0.059	-0.059	0.000	0.000	0.000	0.000
55	A	63	ALA	0	-0.001	0.005	7.634	0.041	0.041	0.000	0.000	0.000	0.000
56	A	64	GLU	-1	-0.892	-0.941	5.439	1.009	1.009	0.000	0.000	0.000	0.000
57	A	65	LYS	1	0.870	0.924	6.128	0.202	0.202	0.000	0.000	0.000	0.000
58	A	66	GLU	-1	-0.867	-0.940	2.200	-4.483	-3.213	1.985	-1.628	-1.628	-0.004
59	A	67	GLU	-1	-0.732	-0.838	2.659	-1.385	0.307	3.028	-2.881	-1.840	-0.025
60	A	68	VAL	0	0.006	0.004	3.519	-0.605	-0.866	0.029	0.171	0.061	0.000
61	A	69	GLN	0	-0.012	0.001	5.149	-0.139	-0.139	0.000	0.000	0.000	0.000
62	A	70	ARG	1	0.833	0.932	2.745	0.942	1.382	0.254	-0.292	-0.402	0.000
63	A	71	ASN	0	0.006	0.005	4.729	0.174	0.177	-0.001	-0.008	0.006	0.000
64	A	72	PHE	0	0.019	0.005	7.854	0.056	0.056	0.000	0.000	0.000	0.000
65	A	73	TYR	0	0.040	0.025	7.781	0.051	0.051	0.000	0.000	0.000	0.000
66	A	74	LEU	0	-0.010	0.006	7.964	0.101	0.101	0.000	0.000	0.000	0.000
67	A	75	LEU	0	-0.011	0.000	10.585	0.083	0.083	0.000	0.000	0.000	0.000
68	A	76	LYS	1	0.880	0.929	12.885	0.342	0.342	0.000	0.000	0.000	0.000
69	A	77	THR	0	-0.011	-0.013	12.406	0.048	0.048	0.000	0.000	0.000	0.000
70	A	78	TYR	0	0.000	-0.014	14.630	0.044	0.044	0.000	0.000	0.000	0.000
71	A	79	VAL	0	-0.008	-0.013	16.542	0.034	0.034	0.000	0.000	0.000	0.000
72	A	80	VAL	0	-0.024	-0.010	18.172	0.021	0.021	0.000	0.000	0.000	0.000
73	A	81	SER	0	-0.031	-0.020	17.745	0.018	0.018	0.000	0.000	0.000	0.000
74	A	82	GLN	0	-0.059	-0.034	19.471	0.025	0.025	0.000	0.000	0.000	0.000
75	A	83	LEU	0	0.035	0.049	20.728	0.018	0.018	0.000	0.000	0.000	0.000
76	A	84	SER	0	0.028	0.003	22.301	0.016	0.016	0.000	0.000	0.000	0.000
77	A	85	ILE	0	-0.020	-0.009	24.177	0.011	0.011	0.000	0.000	0.000	0.000
78	A	86	HIS	0	-0.004	0.004	20.482	0.009	0.009	0.000	0.000	0.000	0.000
79	A	87	PHE	0	0.038	0.029	25.049	0.008	0.008	0.000	0.000	0.000	0.000
80	A	88	GLU	-1	-0.765	-0.873	27.419	-0.062	-0.062	0.000	0.000	0.000	0.000
81	A	89	ARG	1	0.930	0.964	23.882	0.112	0.112	0.000	0.000	0.000	0.000
82	A	90	LEU	0	0.017	0.010	27.292	0.006	0.006	0.000	0.000	0.000	0.000
83	A	91	LYS	1	0.796	0.895	29.746	0.060	0.060	0.000	0.000	0.000	0.000
84	A	92	GLU	-1	-0.897	-0.948	32.791	-0.056	-0.056	0.000	0.000	0.000	0.000
85	A	93	PHE	0	-0.020	0.014	31.837	0.005	0.005	0.000	0.000	0.000	0.000
86	A	94	ALA	0	0.008	-0.002	33.766	0.005	0.005	0.000	0.000	0.000	0.000
87	A	95	GLU	-1	-0.765	-0.875	35.377	-0.044	-0.044	0.000	0.000	0.000	0.000
88	A	96	SER	0	-0.098	-0.075	36.579	0.004	0.004	0.000	0.000	0.000	0.000
89	A	97	LYS	1	0.782	0.864	35.871	0.037	0.037	0.000	0.000	0.000	0.000
90	A	98	GLY	0	-0.010	0.022	39.803	0.002	0.002	0.000	0.000	0.000	0.000
91	A	99	PHE	0	0.034	-0.001	38.429	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	100	LYS	1	0.709	0.847	34.638	0.044	0.044	0.000	0.000	0.000	0.000
93	A	101	ILE	0	-0.002	-0.019	39.901	0.001	0.001	0.000	0.000	0.000	0.000
94	A	102	GLU	-1	-0.760	-0.855	37.355	-0.044	-0.044	0.000	0.000	0.000	0.000
95	A	103	LYS	1	0.765	0.908	33.662	0.044	0.044	0.000	0.000	0.000	0.000
96	A	104	LYS	1	0.836	0.903	29.792	0.080	0.080	0.000	0.000	0.000	0.000
97	A	105	LEU	0	-0.022	-0.010	25.338	0.001	0.001	0.000	0.000	0.000	0.000
98	A	106	ASP	-1	-0.822	-0.900	30.056	-0.071	-0.071	0.000	0.000	0.000	0.000
99	A	107	PRO	0	-0.002	-0.027	27.887	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	108	GLU	-1	-0.907	-0.950	27.206	-0.086	-0.086	0.000	0.000	0.000	0.000
101	A	109	VAL	0	0.011	0.007	26.810	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	110	ILE	0	-0.013	-0.011	22.705	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	111	ASN	0	-0.046	-0.018	22.863	-0.021	-0.021	0.000	0.000	0.000	0.000
104	A	112	GLU	-1	-0.849	-0.929	23.148	-0.114	-0.114	0.000	0.000	0.000	0.000
105	A	113	ILE	0	-0.040	-0.013	19.894	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	114	ALA	0	0.013	0.002	18.751	-0.013	-0.013	0.000	0.000	0.000	0.000
107	A	115	LEU	0	0.012	-0.003	18.559	-0.019	-0.019	0.000	0.000	0.000	0.000
108	A	116	TYR	0	-0.026	-0.021	19.396	0.004	0.004	0.000	0.000	0.000	0.000
109	A	117	ILE	0	0.034	0.008	14.205	0.003	0.003	0.000	0.000	0.000	0.000
110	A	118	ASP	-1	-0.831	-0.908	15.626	-0.253	-0.253	0.000	0.000	0.000	0.000
111	A	119	ARG	1	0.823	0.930	16.978	0.105	0.105	0.000	0.000	0.000	0.000
112	A	120	VAL	0	0.011	0.016	14.936	0.003	0.003	0.000	0.000	0.000	0.000
113	A	121	GLU	-1	-0.845	-0.927	9.540	-0.468	-0.468	0.000	0.000	0.000	0.000
114	A	122	LYS	1	0.817	0.899	13.122	0.197	0.197	0.000	0.000	0.000	0.000
115	A	123	GLU	-1	-0.814	-0.880	15.779	-0.056	-0.056	0.000	0.000	0.000	0.000
116	A	124	VAL	0	-0.086	-0.028	9.054	0.019	0.019	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:GLY)