FMO DATABASE

FMODB ID: 2JVKR

Calculation Name: 1Y9W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y9W

Chain ID: A

ChEMBL ID:

UniProt ID: Q81CG1

Base Structure: X-ray

Registration Date: 2023-09-20

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	140
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1207632.865111
FMO2-HF: Nuclear repulsion	1149663.218359
FMO2-HF: Total energy	-57969.646752
FMO2-MP2: Total energy	-58137.858734

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.
-5.175	-1.567	0.01	-1.938	-1.679	0.006

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 : 0.003 / q_NPA : -0.003

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	MET	0	-0.007	0.010	3.422	-4.740	-1.139	0.011	-1.932	-1.680	0.006
4	A	4	LYS	1	0.899	0.935	5.421	-0.859	-0.852	-0.001	-0.006	0.001	0.000
5	A	5	HIS	0	-0.043	-0.023	9.110	0.259	0.259	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.007	0.001	12.266	-0.095	-0.095	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.869	-0.924	15.380	0.288	0.288	0.000	0.000	0.000	0.000
8	A	8	ASN	0	-0.032	-0.019	18.422	-0.025	-0.025	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.027	0.032	21.276	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.025	-0.054	22.017	-0.011	-0.011	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.973	0.968	24.893	-0.042	-0.042	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.024	0.009	24.761	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.797	-0.857	19.891	0.065	0.065	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.016	0.011	23.812	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.789	-0.880	26.308	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	16	TYR	0	0.001	0.008	19.598	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.006	-0.002	20.939	-0.011	-0.011	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.875	0.926	24.899	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.035	-0.042	28.146	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.849	0.935	22.232	0.079	0.079	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.020	0.013	25.970	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.012	0.010	28.006	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	23	GLN	0	0.023	0.007	25.703	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	24	TYR	0	-0.015	0.000	26.063	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	25	ASN	0	0.051	0.022	28.288	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	26	MET	0	-0.005	-0.003	31.875	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.112	-0.063	29.005	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.030	-0.008	29.805	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.005	0.007	32.620	0.004	0.004	0.000	0.000	0.000	0.000
30	A	30	THR	0	0.011	-0.021	36.315	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.836	-0.936	38.435	-0.047	-0.047	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.916	-0.925	40.733	-0.032	-0.032	0.000	0.000	0.000	0.000
33	A	33	VAL	0	0.008	-0.002	40.062	0.003	0.003	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.748	0.878	35.583	0.052	0.052	0.000	0.000	0.000	0.000
35	A	35	GLN	0	-0.004	0.007	41.171	0.000	0.000	0.000	0.000	0.000	0.000
36	A	36	PRO	0	-0.037	-0.014	42.164	0.000	0.000	0.000	0.000	0.000	0.000
37	A	37	MET	0	-0.009	-0.013	39.689	0.002	0.002	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.814	-0.883	42.676	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.948	-0.963	44.061	0.000	0.000	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.012	-0.008	46.765	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	SER	0	-0.019	-0.021	50.441	0.002	0.002	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.009	0.004	52.992	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.001	-0.012	56.318	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.024	0.029	58.923	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.826	0.902	61.237	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	46	ASN	0	0.010	-0.004	63.809	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.861	-0.944	65.484	0.001	0.001	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.921	-0.947	65.770	0.005	0.005	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.012	0.010	62.566	0.000	0.000	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.799	0.914	61.598	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	51	ILE	0	0.017	0.000	57.433	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	52	PHE	0	-0.009	-0.028	61.518	0.001	0.001	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.041	0.022	59.783	0.000	0.000	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.011	-0.011	56.760	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.031	-0.004	53.288	0.001	0.001	0.000	0.000	0.000	0.000
56	A	56	THR	0	0.000	-0.017	49.473	0.000	0.000	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.005	0.008	47.813	0.001	0.001	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.017	-0.011	43.115	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	59	MET	0	-0.040	-0.001	45.710	0.000	0.000	0.000	0.000	0.000	0.000
60	A	60	TYR	0	0.059	0.016	40.067	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	61	PHE	0	-0.007	0.004	36.581	0.001	0.001	0.000	0.000	0.000	0.000
62	A	62	TYR	0	0.009	0.013	42.868	0.001	0.001	0.000	0.000	0.000	0.000
63	A	63	HIS	0	-0.071	-0.044	43.271	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.048	0.020	46.820	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	65	HIS	0	-0.021	-0.016	44.524	0.001	0.001	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.022	-0.025	46.626	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.802	-0.876	44.529	0.005	0.005	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.017	-0.014	45.475	0.002	0.002	0.000	0.000	0.000	0.000
69	A	69	LEU	0	-0.014	-0.003	50.302	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	70	TRP	0	-0.017	-0.006	54.142	0.001	0.001	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.018	-0.016	56.713	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.817	-0.860	60.494	0.009	0.009	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.918	-0.981	62.249	0.009	0.009	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.037	-0.032	63.900	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.010	-0.002	65.173	0.000	0.000	0.000	0.000	0.000	0.000
76	A	76	ARG	1	0.863	0.933	63.448	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	77	HIS	0	-0.023	-0.018	65.268	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.827	-0.892	67.699	0.004	0.004	0.000	0.000	0.000	0.000
79	A	79	GLY	0	-0.003	0.005	66.056	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	80	TYR	0	-0.004	-0.033	63.769	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.061	0.027	60.405	0.000	0.000	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.074	-0.049	60.111	0.000	0.000	0.000	0.000	0.000	0.000
83	A	83	GLN	0	-0.023	-0.014	61.831	0.000	0.000	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.001	0.007	58.416	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.011	0.007	55.496	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	86	HIS	0	-0.011	-0.005	57.758	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.843	-0.938	59.547	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	88	ILE	0	-0.020	-0.007	52.188	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.771	-0.865	55.125	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	90	GLY	0	-0.043	-0.003	56.543	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.020	0.007	53.768	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	92	ALA	0	0.054	0.013	51.970	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.844	0.921	52.942	0.006	0.006	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.925	-0.947	55.413	-0.012	-0.012	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.749	0.854	51.077	0.010	0.010	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.031	0.012	50.811	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	97	CYS	0	-0.102	-0.027	49.817	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.889	0.925	44.560	0.019	0.019	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.076	-0.040	46.374	0.000	0.000	0.000	0.000	0.000	0.000
100	A	100	ILE	0	0.007	0.020	49.781	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.022	-0.018	44.379	0.000	0.000	0.000	0.000	0.000	0.000
102	A	102	LEU	0	0.039	0.032	47.545	0.000	0.000	0.000	0.000	0.000	0.000
103	A	103	ASP	-1	-0.890	-0.931	45.330	0.014	0.014	0.000	0.000	0.000	0.000
104	A	104	SER	0	0.010	0.007	48.098	0.000	0.000	0.000	0.000	0.000	0.000
105	A	105	PHE	0	0.049	0.010	44.204	0.001	0.001	0.000	0.000	0.000	0.000
106	A	106	SER	0	-0.019	-0.032	50.135	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	107	PHE	0	-0.081	-0.036	48.644	0.000	0.000	0.000	0.000	0.000	0.000
108	A	108	GLN	0	-0.009	-0.007	49.151	0.000	0.000	0.000	0.000	0.000	0.000
109	A	109	ALA	0	0.011	0.022	54.234	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	110	PRO	0	0.079	0.041	53.372	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.861	-0.952	55.235	0.008	0.008	0.000	0.000	0.000	0.000
112	A	112	PHE	0	0.016	0.004	57.532	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	113	TYR	0	0.069	0.040	54.305	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.982	1.008	56.982	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.817	0.901	58.065	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	116	HIS	0	-0.031	0.001	59.173	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	117	GLY	0	-0.009	0.002	59.471	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	118	TYR	0	-0.021	-0.029	52.492	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	119	ARG	1	0.786	0.881	49.188	0.001	0.001	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.833	-0.910	50.886	0.009	0.009	0.000	0.000	0.000	0.000
121	A	121	TYR	0	-0.098	-0.066	44.074	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	122	GLY	0	0.012	0.004	46.027	0.000	0.000	0.000	0.000	0.000	0.000
123	A	123	VAL	0	0.003	0.015	46.575	0.000	0.000	0.000	0.000	0.000	0.000
124	A	124	VAL	0	-0.034	-0.008	42.201	0.001	0.001	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.864	-0.951	45.131	0.018	0.018	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.879	-0.951	45.524	0.032	0.032	0.000	0.000	0.000	0.000
127	A	127	HIS	0	-0.047	0.006	41.876	0.005	0.005	0.000	0.000	0.000	0.000
128	A	128	PRO	0	0.025	-0.001	44.715	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.948	0.959	45.439	-0.034	-0.034	0.000	0.000	0.000	0.000
130	A	130	GLY	0	-0.082	-0.036	47.169	0.000	0.000	0.000	0.000	0.000	0.000
131	A	131	HIS	1	0.836	0.917	49.335	-0.025	-0.025	0.000	0.000	0.000	0.000
132	A	132	SER	0	0.043	0.047	48.195	0.001	0.001	0.000	0.000	0.000	0.000
133	A	133	GLN	0	-0.013	-0.017	43.484	0.002	0.002	0.000	0.000	0.000	0.000
134	A	134	HIS	0	0.005	0.006	47.340	0.001	0.001	0.000	0.000	0.000	0.000
135	A	135	PHE	0	0.016	0.008	43.071	0.000	0.000	0.000	0.000	0.000	0.000
136	A	136	PHE	0	0.004	-0.010	47.878	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.756	-0.850	49.025	-0.005	-0.005	0.000	0.000	0.000	0.000
138	A	138	LYS	1	0.798	0.891	50.772	0.002	0.002	0.000	0.000	0.000	0.000
139	A	139	ARG	1	0.843	0.908	47.642	0.007	0.007	0.000	0.000	0.000	0.000
140	A	140	LEU	0	-0.017	-0.004	52.918	0.000	0.000	0.000	0.000	0.000	0.000

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