FMO DATABASE

FMODB ID: 1N61Z

Calculation Name: 1YUD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YUD

Chain ID: A

ChEMBL ID:

UniProt ID: Q8EIN8

Base Structure: X-ray

Registration Date: 2023-09-22

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	OptH
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	158
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1574736.714323
FMO2-HF: Nuclear repulsion	1510979.075334
FMO2-HF: Total energy	-63757.638989
FMO2-MP2: Total energy	-63941.176605

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.
-7.425	-4.442	1.899	-2.013	-2.87	-0.015

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 : -0.048 / q_NPA : -0.033

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	ASN	0	0.026	0.011	2.437	-6.498	-3.840	1.894	-1.971	-2.581	-0.015
4	A	4	ALA	0	0.019	-0.011	4.681	0.964	1.053	-0.001	-0.013	-0.076	0.000
5	A	5	ASP	-1	-0.903	-0.951	7.722	-1.408	-1.408	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.881	-0.949	7.397	-2.385	-2.385	0.000	0.000	0.000	0.000
7	A	7	PHE	0	0.015	-0.003	6.688	0.366	0.366	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.008	-0.002	10.734	0.176	0.176	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.973	1.006	12.712	0.835	0.835	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.077	-0.048	9.683	0.118	0.118	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.051	-0.021	13.378	0.089	0.089	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.976	-0.987	16.030	-0.188	-0.188	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.115	-0.051	13.751	0.035	0.035	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.899	-0.945	17.591	-0.375	-0.375	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.041	-0.035	20.016	0.043	0.043	0.000	0.000	0.000	0.000
16	A	16	HIS	0	0.034	0.032	20.927	0.020	0.020	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.021	-0.003	22.964	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.856	-0.945	22.873	-0.132	-0.132	0.000	0.000	0.000	0.000
19	A	19	GLY	0	-0.021	-0.009	21.375	0.005	0.005	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.026	0.013	17.142	0.011	0.011	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.046	-0.030	14.567	-0.028	-0.028	0.000	0.000	0.000	0.000
22	A	22	TYR	0	0.037	0.024	17.498	0.023	0.023	0.000	0.000	0.000	0.000
23	A	23	ARG	1	1.021	1.010	19.117	0.148	0.148	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.049	-0.011	20.707	0.017	0.017	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.018	-0.007	20.524	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	26	TYR	0	0.017	0.000	22.366	0.007	0.007	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.919	0.955	26.184	0.047	0.047	0.000	0.000	0.000	0.000
28	A	28	SER	0	0.027	0.028	29.437	0.006	0.006	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.934	-0.973	32.279	-0.012	-0.012	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.045	-0.011	35.094	0.001	0.001	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.025	0.011	36.591	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.063	-0.018	37.660	0.005	0.005	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.874	-0.937	39.559	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	34	PRO	0	-0.067	-0.058	41.111	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.009	0.009	40.606	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.971	0.993	35.962	0.024	0.024	0.000	0.000	0.000	0.000
37	A	37	GLN	0	0.013	-0.005	33.803	0.002	0.002	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.045	-0.032	34.462	0.001	0.001	0.000	0.000	0.000	0.000
39	A	39	TRP	0	0.059	0.045	26.817	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.084	-0.069	27.870	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	41	SER	0	0.031	0.029	22.088	0.012	0.012	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.006	0.016	20.801	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	43	TYR	0	-0.023	-0.002	15.762	0.014	0.014	0.000	0.000	0.000	0.000
44	A	44	PHE	0	0.035	-0.014	16.237	-0.019	-0.019	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.039	-0.011	9.843	-0.018	-0.018	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.003	0.000	12.355	0.025	0.025	0.000	0.000	0.000	0.000
47	A	47	ARG	1	1.009	0.989	10.090	0.727	0.727	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.052	0.018	10.648	0.034	0.034	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.039	-0.008	12.554	0.069	0.069	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.995	-1.001	15.104	-0.323	-0.323	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.013	-0.005	16.119	0.003	0.003	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.059	-0.019	18.682	0.004	0.004	0.000	0.000	0.000	0.000
53	A	53	HIS	0	-0.039	-0.047	21.029	0.024	0.024	0.000	0.000	0.000	0.000
54	A	54	PHE	0	-0.029	-0.015	24.461	0.005	0.005	0.000	0.000	0.000	0.000
55	A	55	HIS	1	0.880	0.953	24.106	0.094	0.094	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.922	0.962	29.046	0.047	0.047	0.000	0.000	0.000	0.000
57	A	57	LEU	0	0.029	0.030	27.253	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.020	-0.007	31.716	0.007	0.007	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.045	-0.042	32.626	0.007	0.007	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.857	-0.915	30.602	0.007	0.007	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.811	-0.926	24.296	-0.061	-0.061	0.000	0.000	0.000	0.000
62	A	62	MET	0	-0.048	-0.019	24.955	0.005	0.005	0.000	0.000	0.000	0.000
63	A	63	TRP	0	-0.036	-0.034	18.425	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.032	-0.032	19.220	0.027	0.027	0.000	0.000	0.000	0.000
65	A	65	PHE	0	0.029	0.009	11.005	-0.032	-0.032	0.000	0.000	0.000	0.000
66	A	66	HIS	0	-0.037	-0.010	12.728	0.101	0.101	0.000	0.000	0.000	0.000
67	A	67	ALA	0	-0.003	-0.021	8.125	0.198	0.198	0.000	0.000	0.000	0.000
68	A	68	GLY	0	-0.012	0.006	6.675	-0.223	-0.223	0.000	0.000	0.000	0.000
69	A	69	GLN	0	0.057	0.001	6.879	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.005	0.032	9.846	-0.020	-0.020	0.000	0.000	0.000	0.000
71	A	71	LEU	0	0.019	0.014	13.455	-0.054	-0.054	0.000	0.000	0.000	0.000
72	A	72	THR	0	-0.023	-0.016	15.895	0.041	0.041	0.000	0.000	0.000	0.000
73	A	73	ILE	0	0.008	0.019	19.531	-0.027	-0.027	0.000	0.000	0.000	0.000
74	A	74	TYR	0	-0.021	-0.012	20.579	0.013	0.013	0.000	0.000	0.000	0.000
75	A	75	MET	0	0.014	-0.003	25.184	-0.010	-0.010	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.015	-0.005	28.436	0.007	0.007	0.000	0.000	0.000	0.000
77	A	77	SER	0	0.015	0.011	31.916	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.031	0.009	34.916	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.935	-0.977	37.769	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	80	GLY	0	-0.046	-0.021	36.408	0.001	0.001	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.986	-0.994	34.899	0.018	0.018	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.043	-0.015	28.248	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	83	THR	0	0.003	0.011	29.589	0.008	0.008	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.027	-0.029	24.312	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.029	0.016	23.644	0.011	0.011	0.000	0.000	0.000	0.000
86	A	86	GLN	0	0.004	-0.002	19.141	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.030	0.038	17.220	0.025	0.025	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.042	0.002	14.617	-0.021	-0.021	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.059	-0.039	12.041	0.010	0.010	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.861	-0.916	15.263	0.436	0.436	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.064	-0.050	16.768	-0.050	-0.050	0.000	0.000	0.000	0.000
92	A	92	ALA	0	-0.055	0.001	19.673	-0.031	-0.031	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.040	0.026	19.459	-0.033	-0.033	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.019	-0.017	21.396	0.006	0.006	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.871	-0.948	15.441	0.234	0.234	0.000	0.000	0.000	0.000
96	A	96	ARG	1	0.839	0.907	19.757	-0.170	-0.170	0.000	0.000	0.000	0.000
97	A	97	PRO	0	0.021	0.006	17.864	-0.026	-0.026	0.000	0.000	0.000	0.000
98	A	98	GLN	0	-0.005	-0.008	19.031	-0.030	-0.030	0.000	0.000	0.000	0.000
99	A	99	PHE	0	-0.009	-0.012	21.908	0.004	0.004	0.000	0.000	0.000	0.000
100	A	100	LEU	0	0.027	0.016	23.880	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	101	VAL	0	-0.003	0.012	25.274	0.002	0.002	0.000	0.000	0.000	0.000
102	A	102	PRO	0	-0.037	-0.017	27.576	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.996	0.991	31.413	-0.006	-0.006	0.000	0.000	0.000	0.000
104	A	104	GLY	0	-0.060	-0.026	33.078	0.003	0.003	0.000	0.000	0.000	0.000
105	A	105	CYS	0	-0.031	0.001	30.540	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	106	ILE	0	-0.018	0.001	30.147	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	107	PHE	0	0.010	-0.007	24.642	0.006	0.006	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.078	0.028	23.824	-0.012	-0.012	0.000	0.000	0.000	0.000
109	A	109	SER	0	-0.088	-0.041	18.815	0.014	0.014	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.044	0.033	17.533	-0.032	-0.032	0.000	0.000	0.000	0.000
111	A	111	MET	0	-0.028	-0.001	10.798	0.000	0.000	0.000	0.000	0.000	0.000
112	A	112	ASN	0	-0.017	-0.006	13.691	-0.024	-0.024	0.000	0.000	0.000	0.000
113	A	113	GLN	0	-0.114	-0.063	10.506	0.119	0.119	0.000	0.000	0.000	0.000
114	A	114	ASP	-1	-0.880	-0.940	10.180	-0.362	-0.362	0.000	0.000	0.000	0.000
115	A	115	GLY	0	-0.007	-0.004	6.677	0.018	0.018	0.000	0.000	0.000	0.000
116	A	116	PHE	0	-0.021	-0.027	3.508	-0.197	0.039	0.006	-0.029	-0.213	0.000
117	A	117	SER	0	0.008	-0.006	7.998	0.126	0.126	0.000	0.000	0.000	0.000
118	A	118	LEU	0	-0.052	0.021	10.443	-0.015	-0.015	0.000	0.000	0.000	0.000
119	A	119	VAL	0	0.025	-0.004	12.096	0.105	0.105	0.000	0.000	0.000	0.000
120	A	120	GLY	0	-0.046	-0.013	15.611	-0.022	-0.022	0.000	0.000	0.000	0.000
121	A	121	CYS	0	0.046	0.035	18.719	0.014	0.014	0.000	0.000	0.000	0.000
122	A	122	MET	0	-0.011	-0.010	22.002	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	123	VAL	0	0.064	0.046	25.373	0.009	0.009	0.000	0.000	0.000	0.000
124	A	124	SER	0	-0.046	-0.038	28.526	0.001	0.001	0.000	0.000	0.000	0.000
125	A	125	PRO	0	-0.024	-0.020	31.679	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	126	GLY	0	-0.037	-0.016	31.672	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	127	PHE	0	0.010	0.009	27.977	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	128	THR	0	-0.043	-0.002	30.968	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	129	PHE	0	-0.004	-0.032	27.907	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.886	-0.937	33.195	-0.058	-0.058	0.000	0.000	0.000	0.000
131	A	131	ASP	-1	-0.933	-0.967	33.290	-0.035	-0.035	0.000	0.000	0.000	0.000
132	A	132	PHE	0	-0.019	-0.015	27.162	0.001	0.001	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.897	-0.952	31.251	-0.052	-0.052	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.015	0.007	26.969	0.001	0.001	0.000	0.000	0.000	0.000
135	A	135	PHE	0	-0.003	-0.004	30.339	0.006	0.006	0.000	0.000	0.000	0.000
136	A	136	SER	0	-0.018	0.006	30.844	-0.006	-0.006	0.000	0.000	0.000	0.000
137	A	137	GLN	0	0.038	-0.009	30.089	0.001	0.001	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.795	-0.908	32.596	-0.077	-0.077	0.000	0.000	0.000	0.000
139	A	139	ALA	0	-0.001	-0.004	36.230	0.005	0.005	0.000	0.000	0.000	0.000
140	A	140	LEU	0	-0.008	-0.011	30.729	0.005	0.005	0.000	0.000	0.000	0.000
141	A	141	LEU	0	-0.032	-0.012	32.816	0.004	0.004	0.000	0.000	0.000	0.000
142	A	142	ALA	0	-0.055	0.005	36.219	0.005	0.005	0.000	0.000	0.000	0.000
143	A	143	MET	0	-0.056	-0.035	37.687	0.004	0.004	0.000	0.000	0.000	0.000
144	A	144	TYR	0	0.038	0.007	34.654	-0.002	-0.002	0.000	0.000	0.000	0.000
145	A	145	PRO	0	0.017	0.023	35.833	-0.003	-0.003	0.000	0.000	0.000	0.000
146	A	146	GLN	0	-0.001	-0.002	35.878	-0.006	-0.006	0.000	0.000	0.000	0.000
147	A	147	HIS	0	0.044	0.020	31.548	0.000	0.000	0.000	0.000	0.000	0.000
148	A	148	LYS	1	0.963	0.979	31.185	0.045	0.045	0.000	0.000	0.000	0.000
149	A	149	ALA	0	-0.067	-0.038	29.004	-0.008	-0.008	0.000	0.000	0.000	0.000
150	A	150	VAL	0	0.084	0.031	25.092	-0.007	-0.007	0.000	0.000	0.000	0.000
151	A	151	VAL	0	0.052	0.031	26.655	-0.012	-0.012	0.000	0.000	0.000	0.000
152	A	152	GLN	0	-0.068	-0.035	28.371	-0.004	-0.004	0.000	0.000	0.000	0.000
153	A	153	LYS	1	0.863	0.942	22.908	0.075	0.075	0.000	0.000	0.000	0.000
154	A	154	LEU	0	0.006	0.032	21.730	-0.019	-0.019	0.000	0.000	0.000	0.000
155	A	155	SER	0	0.058	0.027	24.664	0.006	0.006	0.000	0.000	0.000	0.000
156	A	156	ARG	1	0.986	0.987	23.289	0.190	0.190	0.000	0.000	0.000	0.000
157	A	157	PRO	0	-0.075	-0.030	29.078	0.005	0.005	0.000	0.000	0.000	0.000
158	A	158	GLU	-1	-0.995	-0.982	32.585	-0.100	-0.100	0.000	0.000	0.000	0.000

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