FMO DATABASE

FMODB ID: G5Y31

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1574392.40192
FMO2-HF: Nuclear repulsion	1510633.269463
FMO2-HF: Total energy	-63759.132457
FMO2-MP2: Total energy	-63942.554374

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.
-6.481	-3.633	1.484	-1.752	-2.578	-0.013

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 : -0.049 / q_NPA : -0.034

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	0.003	-0.015	2.497	-5.439	-3.001	1.467	-1.699	-2.205	-0.013
4	A	4	ALA	0	0.032	0.005	4.851	0.910	0.999	-0.001	-0.010	-0.077	0.000
5	A	5	ASP	-1	-0.877	-0.944	7.980	-1.433	-1.433	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.863	-0.927	6.831	-2.418	-2.418	0.000	0.000	0.000	0.000
7	A	7	PHE	0	0.009	-0.008	6.139	0.366	0.366	0.000	0.000	0.000	0.000
8	A	8	ILE	0	-0.003	0.004	10.788	0.159	0.159	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.960	1.006	12.816	0.807	0.807	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.073	-0.046	9.641	0.108	0.108	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.037	-0.014	13.284	0.083	0.083	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.881	-0.933	16.063	-0.145	-0.145	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.109	-0.057	13.858	0.031	0.031	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.876	-0.934	17.665	-0.352	-0.352	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.044	-0.032	20.031	0.030	0.030	0.000	0.000	0.000	0.000
16	A	16	HIS	0	0.045	0.031	21.058	0.020	0.020	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.022	0.004	23.059	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.814	-0.907	22.791	-0.122	-0.122	0.000	0.000	0.000	0.000
19	A	19	GLY	0	-0.030	-0.006	21.483	0.003	0.003	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.001	-0.006	17.262	0.011	0.011	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.059	-0.034	15.369	-0.022	-0.022	0.000	0.000	0.000	0.000
22	A	22	TYR	0	0.023	0.016	17.532	0.031	0.031	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.905	0.955	19.190	0.130	0.130	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.033	-0.005	20.704	0.018	0.018	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.048	-0.027	20.062	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	26	TYR	0	0.014	-0.002	22.422	0.009	0.009	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.941	0.964	26.138	0.040	0.040	0.000	0.000	0.000	0.000
28	A	28	SER	0	0.026	0.023	29.393	0.006	0.006	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.940	-0.970	32.216	0.000	0.000	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.047	-0.016	35.039	0.000	0.000	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.015	0.006	36.528	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.053	-0.013	37.560	0.005	0.005	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.858	-0.926	39.494	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	34	PRO	0	-0.059	-0.055	41.069	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.013	0.000	40.613	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.871	0.925	35.795	0.019	0.019	0.000	0.000	0.000	0.000
37	A	37	GLN	0	-0.009	-0.024	33.792	0.002	0.002	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.010	-0.008	34.666	0.000	0.000	0.000	0.000	0.000	0.000
39	A	39	TRP	0	0.054	0.039	27.002	0.003	0.003	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.079	-0.050	27.752	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	41	SER	0	0.024	0.024	21.960	0.011	0.011	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.016	0.007	21.034	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	43	TYR	0	0.014	0.015	15.943	0.013	0.013	0.000	0.000	0.000	0.000
44	A	44	PHE	0	0.038	-0.012	16.183	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.046	-0.025	9.757	-0.017	-0.017	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.012	0.006	12.362	0.024	0.024	0.000	0.000	0.000	0.000
47	A	47	ARG	1	1.006	0.987	10.550	0.726	0.726	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.036	-0.021	10.989	0.046	0.046	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.046	-0.012	12.730	0.066	0.066	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.993	-0.992	15.220	-0.315	-0.315	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.006	-0.013	16.218	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.097	-0.047	18.757	0.004	0.004	0.000	0.000	0.000	0.000
53	A	53	HIS	0	-0.042	-0.057	21.066	0.022	0.022	0.000	0.000	0.000	0.000
54	A	54	PHE	0	-0.021	-0.014	24.516	0.005	0.005	0.000	0.000	0.000	0.000
55	A	55	HIS	1	0.853	0.942	24.066	0.090	0.090	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.851	0.918	29.051	0.044	0.044	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.001	0.012	27.577	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	58	THR	0	0.005	-0.003	31.660	0.005	0.005	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.020	-0.016	32.475	0.006	0.006	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.818	-0.898	30.744	0.008	0.008	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.780	-0.905	24.601	-0.053	-0.053	0.000	0.000	0.000	0.000
62	A	62	MET	0	-0.045	-0.014	24.626	0.004	0.004	0.000	0.000	0.000	0.000
63	A	63	TRP	0	-0.036	-0.037	18.269	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.025	-0.028	19.127	0.026	0.026	0.000	0.000	0.000	0.000
65	A	65	PHE	0	0.034	0.010	10.840	-0.029	-0.029	0.000	0.000	0.000	0.000
66	A	66	HIS	0	-0.040	-0.008	12.602	0.103	0.103	0.000	0.000	0.000	0.000
67	A	67	ALA	0	-0.002	-0.018	7.937	0.194	0.194	0.000	0.000	0.000	0.000
68	A	68	GLY	0	-0.002	0.005	6.467	-0.207	-0.207	0.000	0.000	0.000	0.000
69	A	69	GLN	0	0.017	-0.011	6.035	-0.034	-0.034	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.016	0.010	9.675	-0.035	-0.035	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.012	0.000	13.248	-0.051	-0.051	0.000	0.000	0.000	0.000
72	A	72	THR	0	0.001	-0.013	15.757	0.047	0.047	0.000	0.000	0.000	0.000
73	A	73	ILE	0	-0.030	0.021	19.402	-0.025	-0.025	0.000	0.000	0.000	0.000
74	A	74	TYR	0	-0.004	-0.004	20.552	0.019	0.019	0.000	0.000	0.000	0.000
75	A	75	MET	0	0.012	0.004	25.096	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.012	-0.008	28.339	0.006	0.006	0.000	0.000	0.000	0.000
77	A	77	SER	0	0.013	0.014	31.836	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.047	0.015	34.812	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.923	-0.971	37.688	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	80	GLY	0	-0.027	-0.023	36.338	0.001	0.001	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.993	-1.000	34.616	0.017	0.017	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.055	-0.018	27.862	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	83	THR	0	0.021	0.012	29.464	0.006	0.006	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.026	-0.025	24.138	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.017	0.017	23.497	0.011	0.011	0.000	0.000	0.000	0.000
86	A	86	GLN	0	-0.048	-0.037	19.090	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.022	0.035	16.633	0.025	0.025	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.037	-0.002	14.349	-0.023	-0.023	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.059	-0.035	11.574	0.017	0.017	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.820	-0.909	14.920	0.395	0.395	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.073	-0.054	16.426	-0.047	-0.047	0.000	0.000	0.000	0.000
92	A	92	ALA	0	-0.054	-0.008	19.320	-0.030	-0.030	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.022	0.020	19.128	-0.032	-0.032	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.015	-0.017	21.099	0.007	0.007	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.800	-0.893	15.073	0.214	0.214	0.000	0.000	0.000	0.000
96	A	96	ARG	1	0.821	0.901	19.464	-0.167	-0.167	0.000	0.000	0.000	0.000
97	A	97	PRO	0	0.023	0.012	17.711	-0.024	-0.024	0.000	0.000	0.000	0.000
98	A	98	GLN	0	-0.026	-0.019	18.731	-0.030	-0.030	0.000	0.000	0.000	0.000
99	A	99	PHE	0	0.004	-0.005	21.641	0.003	0.003	0.000	0.000	0.000	0.000
100	A	100	LEU	0	0.013	0.008	23.650	-0.007	-0.007	0.000	0.000	0.000	0.000
101	A	101	VAL	0	0.033	0.023	25.271	0.002	0.002	0.000	0.000	0.000	0.000
102	A	102	PRO	0	-0.045	-0.017	27.420	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.888	0.929	31.259	-0.014	-0.014	0.000	0.000	0.000	0.000
104	A	104	GLY	0	-0.037	-0.014	32.959	0.003	0.003	0.000	0.000	0.000	0.000
105	A	105	CYS	0	-0.072	-0.028	30.637	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	106	ILE	0	-0.009	0.008	30.359	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	107	PHE	0	0.005	-0.013	24.068	0.005	0.005	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.090	0.038	23.800	-0.011	-0.011	0.000	0.000	0.000	0.000
109	A	109	SER	0	-0.086	-0.062	18.982	0.016	0.016	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.038	0.021	17.531	-0.030	-0.030	0.000	0.000	0.000	0.000
111	A	111	MET	0	-0.014	0.012	10.933	0.003	0.003	0.000	0.000	0.000	0.000
112	A	112	ASN	0	-0.015	0.017	13.581	-0.020	-0.020	0.000	0.000	0.000	0.000
113	A	113	GLN	0	-0.083	-0.049	10.448	0.099	0.099	0.000	0.000	0.000	0.000
114	A	114	ASP	-1	-0.827	-0.887	10.245	-0.393	-0.393	0.000	0.000	0.000	0.000
115	A	115	GLY	0	-0.010	-0.003	6.793	0.008	0.008	0.000	0.000	0.000	0.000
116	A	116	PHE	0	-0.028	-0.029	3.343	-0.101	0.220	0.018	-0.043	-0.296	0.000
117	A	117	SER	0	0.026	0.003	8.047	0.097	0.097	0.000	0.000	0.000	0.000
118	A	118	LEU	0	-0.048	0.013	10.373	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	119	VAL	0	0.022	-0.008	12.044	0.097	0.097	0.000	0.000	0.000	0.000
120	A	120	GLY	0	-0.046	-0.011	15.486	-0.018	-0.018	0.000	0.000	0.000	0.000
121	A	121	CYS	0	0.042	0.039	18.634	0.012	0.012	0.000	0.000	0.000	0.000
122	A	122	MET	0	0.007	-0.013	21.933	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	123	VAL	0	0.033	0.032	25.293	0.008	0.008	0.000	0.000	0.000	0.000
124	A	124	SER	0	-0.094	-0.068	28.460	0.002	0.002	0.000	0.000	0.000	0.000
125	A	125	PRO	0	0.043	0.019	31.601	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	126	GLY	0	-0.042	-0.014	31.630	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	127	PHE	0	0.014	0.001	28.095	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	128	THR	0	-0.031	-0.009	30.951	-0.008	-0.008	0.000	0.000	0.000	0.000
129	A	129	PHE	0	0.000	-0.027	27.757	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.895	-0.937	33.213	-0.053	-0.053	0.000	0.000	0.000	0.000
131	A	131	ASP	-1	-0.882	-0.902	33.243	-0.029	-0.029	0.000	0.000	0.000	0.000
132	A	132	PHE	0	-0.003	-0.007	27.221	0.000	0.000	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.788	-0.885	31.262	-0.046	-0.046	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.014	0.006	27.218	0.001	0.001	0.000	0.000	0.000	0.000
135	A	135	PHE	0	-0.004	-0.008	30.395	0.006	0.006	0.000	0.000	0.000	0.000
136	A	136	SER	0	-0.011	0.014	30.924	-0.006	-0.006	0.000	0.000	0.000	0.000
137	A	137	GLN	0	0.044	-0.011	30.701	0.004	0.004	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.800	-0.899	32.691	-0.078	-0.078	0.000	0.000	0.000	0.000
139	A	139	ALA	0	0.004	-0.001	36.301	0.005	0.005	0.000	0.000	0.000	0.000
140	A	140	LEU	0	0.003	-0.006	30.845	0.005	0.005	0.000	0.000	0.000	0.000
141	A	141	LEU	0	-0.043	-0.018	33.088	0.003	0.003	0.000	0.000	0.000	0.000
142	A	142	ALA	0	-0.068	-0.007	36.269	0.005	0.005	0.000	0.000	0.000	0.000
143	A	143	MET	0	-0.057	-0.031	37.550	0.004	0.004	0.000	0.000	0.000	0.000
144	A	144	TYR	0	0.018	0.019	34.697	-0.002	-0.002	0.000	0.000	0.000	0.000
145	A	145	PRO	0	0.044	0.033	35.836	-0.003	-0.003	0.000	0.000	0.000	0.000
146	A	146	GLN	0	-0.023	-0.021	35.904	-0.005	-0.005	0.000	0.000	0.000	0.000
147	A	147	HIS	0	0.037	0.013	31.559	0.000	0.000	0.000	0.000	0.000	0.000
148	A	148	LYS	1	0.953	0.972	31.188	0.048	0.048	0.000	0.000	0.000	0.000
149	A	149	ALA	0	-0.043	-0.023	29.074	-0.007	-0.007	0.000	0.000	0.000	0.000
150	A	150	VAL	0	0.089	0.036	25.018	-0.008	-0.008	0.000	0.000	0.000	0.000
151	A	151	VAL	0	0.056	0.034	26.681	-0.011	-0.011	0.000	0.000	0.000	0.000
152	A	152	GLN	0	-0.059	-0.018	28.453	-0.002	-0.002	0.000	0.000	0.000	0.000
153	A	153	LYS	1	0.834	0.920	22.971	0.075	0.075	0.000	0.000	0.000	0.000
154	A	154	LEU	0	-0.006	0.027	21.360	-0.018	-0.018	0.000	0.000	0.000	0.000
155	A	155	SER	0	0.072	0.027	24.717	0.007	0.007	0.000	0.000	0.000	0.000
156	A	156	ARG	1	0.957	0.977	22.946	0.190	0.190	0.000	0.000	0.000	0.000
157	A	157	PRO	0	-0.062	-0.026	29.212	0.005	0.005	0.000	0.000	0.000	0.000
158	A	158	GLU	-1	-1.013	-0.998	32.750	-0.098	-0.098	0.000	0.000	0.000	0.000

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