FMO DATABASE

FMODB ID: LNMR9

Calculation Name: 2H2Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2H2Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q8IDP1

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1210195.865495
FMO2-HF: Nuclear repulsion	1157621.976159
FMO2-HF: Total energy	-52573.889335
FMO2-MP2: Total energy	-52729.476702

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:3:LYS)

Summations of interaction energy for fragment #1(A:3:LYS)

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.
88.937	94.013	4.575	-4.056	-5.594	-0.024

Interaction energy analysis for fragmet #1(A:3:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.980 / q_NPA : 0.998

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	5	SER	0	0.074	0.033	3.922	-4.316	-2.753	-0.011	-0.876	-0.676	0.003
4	A	6	ARG	1	0.938	0.996	5.917	34.346	34.346	0.000	0.000	0.000	0.000
5	A	7	THR	0	-0.013	-0.020	6.285	-3.269	-3.269	0.000	0.000	0.000	0.000
6	A	8	VAL	0	0.057	0.039	8.997	0.157	0.157	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.818	-0.907	12.745	-19.776	-19.776	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.852	0.906	8.795	28.429	28.429	0.000	0.000	0.000	0.000
9	A	11	HIS	0	0.019	0.005	11.692	1.323	1.323	0.000	0.000	0.000	0.000
10	A	12	ILE	0	-0.025	-0.009	6.253	0.959	0.959	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.937	0.965	10.240	22.450	22.450	0.000	0.000	0.000	0.000
12	A	14	THR	0	-0.005	0.019	12.286	1.375	1.375	0.000	0.000	0.000	0.000
13	A	15	LYS	1	0.992	0.996	15.103	16.069	16.069	0.000	0.000	0.000	0.000
14	A	16	TYR	0	0.047	0.023	15.445	1.144	1.144	0.000	0.000	0.000	0.000
15	A	17	ASN	0	0.006	-0.007	17.920	-0.501	-0.501	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.022	0.002	16.903	-0.246	-0.246	0.000	0.000	0.000	0.000
17	A	19	GLY	0	0.023	0.014	19.611	0.097	0.097	0.000	0.000	0.000	0.000
18	A	20	ASN	0	-0.018	0.010	21.130	0.488	0.488	0.000	0.000	0.000	0.000
19	A	21	ALA	0	0.086	0.042	20.018	-0.842	-0.842	0.000	0.000	0.000	0.000
20	A	22	ASN	0	0.011	0.000	18.168	-0.300	-0.300	0.000	0.000	0.000	0.000
21	A	23	TYR	0	0.037	0.034	14.240	-1.170	-1.170	0.000	0.000	0.000	0.000
22	A	24	ARG	1	0.825	0.895	14.710	16.296	16.296	0.000	0.000	0.000	0.000
23	A	25	ILE	0	0.028	0.012	14.752	-1.300	-1.300	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.027	-0.030	11.279	-1.117	-1.117	0.000	0.000	0.000	0.000
25	A	27	LYS	1	0.855	0.920	10.481	20.598	20.598	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.766	-0.861	10.654	-23.626	-23.626	0.000	0.000	0.000	0.000
27	A	29	LEU	0	0.027	0.024	9.655	-1.414	-1.414	0.000	0.000	0.000	0.000
28	A	30	ASN	0	-0.053	-0.052	5.870	-7.726	-7.726	0.000	0.000	0.000	0.000
29	A	31	ASN	0	-0.037	-0.002	5.762	-6.893	-6.893	0.000	0.000	0.000	0.000
30	A	32	PHE	0	0.040	0.009	6.926	-1.177	-1.177	0.000	0.000	0.000	0.000
31	A	33	LEU	0	-0.018	-0.009	4.936	-0.064	-0.064	0.000	0.000	0.000	0.000
32	A	34	LYS	1	0.865	0.933	2.254	30.935	32.240	3.075	-1.837	-2.543	-0.002
33	A	35	ASN	0	-0.038	-0.037	2.486	-2.981	-0.888	1.510	-1.309	-2.293	-0.025
34	A	36	PRO	0	0.019	0.016	3.714	2.696	2.811	0.001	-0.034	-0.082	0.000
35	A	37	PRO	0	-0.003	-0.004	6.940	0.769	0.769	0.000	0.000	0.000	0.000
36	A	38	ILE	0	0.047	0.019	10.076	-0.919	-0.919	0.000	0.000	0.000	0.000
37	A	39	ASN	0	0.007	0.004	11.549	-0.021	-0.021	0.000	0.000	0.000	0.000
38	A	40	CYS	0	-0.061	-0.002	11.180	1.253	1.253	0.000	0.000	0.000	0.000
39	A	41	THR	0	-0.048	-0.024	10.495	-1.410	-1.410	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.041	-0.035	10.016	0.730	0.730	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.874	-0.919	12.984	-19.320	-19.320	0.000	0.000	0.000	0.000
42	A	44	VAL	0	-0.072	-0.048	13.808	0.216	0.216	0.000	0.000	0.000	0.000
43	A	45	HIS	0	0.014	0.011	16.570	0.678	0.678	0.000	0.000	0.000	0.000
44	A	46	PRO	0	0.079	0.044	18.919	-0.375	-0.375	0.000	0.000	0.000	0.000
45	A	47	SER	0	-0.073	-0.045	19.371	1.072	1.072	0.000	0.000	0.000	0.000
46	A	48	ASN	0	0.035	0.011	19.912	0.226	0.226	0.000	0.000	0.000	0.000
47	A	49	ILE	0	0.040	0.025	13.648	-0.167	-0.167	0.000	0.000	0.000	0.000
48	A	50	ARG	1	0.751	0.862	17.763	13.367	13.367	0.000	0.000	0.000	0.000
49	A	51	ILE	0	-0.003	0.010	20.072	0.475	0.475	0.000	0.000	0.000	0.000
50	A	52	TRP	0	-0.018	-0.015	12.992	-1.281	-1.281	0.000	0.000	0.000	0.000
51	A	53	ILE	0	-0.015	-0.019	17.278	1.170	1.170	0.000	0.000	0.000	0.000
52	A	54	VAL	0	0.031	0.022	13.803	-0.988	-0.988	0.000	0.000	0.000	0.000
53	A	55	GLN	0	-0.008	-0.001	15.057	2.070	2.070	0.000	0.000	0.000	0.000
54	A	56	TYR	0	0.054	0.019	14.872	-1.262	-1.262	0.000	0.000	0.000	0.000
55	A	57	VAL	0	-0.002	0.006	16.137	0.742	0.742	0.000	0.000	0.000	0.000
56	A	58	GLY	0	0.050	0.018	17.532	-0.473	-0.473	0.000	0.000	0.000	0.000
57	A	59	LEU	0	-0.008	-0.005	15.536	-0.052	-0.052	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.837	-0.894	19.159	-12.397	-12.397	0.000	0.000	0.000	0.000
59	A	61	ASN	0	-0.042	-0.014	19.956	0.158	0.158	0.000	0.000	0.000	0.000
60	A	62	THR	0	-0.034	-0.040	21.275	0.173	0.173	0.000	0.000	0.000	0.000
61	A	63	ILE	0	-0.004	-0.009	24.059	0.122	0.122	0.000	0.000	0.000	0.000
62	A	64	TYR	0	-0.036	-0.033	23.042	0.145	0.145	0.000	0.000	0.000	0.000
63	A	65	ALA	0	-0.018	0.009	22.688	-0.437	-0.437	0.000	0.000	0.000	0.000
64	A	66	ASN	0	-0.065	-0.063	21.137	0.586	0.586	0.000	0.000	0.000	0.000
65	A	67	GLU	-1	-0.837	-0.875	22.324	-10.632	-10.632	0.000	0.000	0.000	0.000
66	A	68	VAL	0	-0.068	-0.031	19.479	-0.585	-0.585	0.000	0.000	0.000	0.000
67	A	69	TYR	0	-0.040	-0.037	20.477	0.371	0.371	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.893	0.921	19.634	12.749	12.749	0.000	0.000	0.000	0.000
69	A	71	ILE	0	0.025	0.017	17.857	0.617	0.617	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.923	0.979	19.073	11.827	11.827	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.007	-0.001	16.433	0.157	0.157	0.000	0.000	0.000	0.000
72	A	74	ILE	0	0.012	0.002	20.580	-0.215	-0.215	0.000	0.000	0.000	0.000
73	A	75	PHE	0	0.031	0.003	16.274	0.292	0.292	0.000	0.000	0.000	0.000
74	A	76	PRO	0	0.040	0.035	22.171	0.119	0.119	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-0.761	-0.845	24.837	-11.307	-11.307	0.000	0.000	0.000	0.000
76	A	78	ASN	0	-0.025	-0.031	25.614	-0.466	-0.466	0.000	0.000	0.000	0.000
77	A	79	TYR	0	0.051	0.057	18.134	-0.357	-0.357	0.000	0.000	0.000	0.000
78	A	80	PRO	0	-0.050	-0.046	20.533	-0.234	-0.234	0.000	0.000	0.000	0.000
79	A	81	LEU	0	0.038	0.016	22.586	0.115	0.115	0.000	0.000	0.000	0.000
80	A	82	LYS	1	0.871	0.921	26.310	11.001	11.001	0.000	0.000	0.000	0.000
81	A	83	PRO	0	0.071	0.033	23.951	-0.583	-0.583	0.000	0.000	0.000	0.000
82	A	84	PRO	0	-0.082	-0.040	19.778	0.139	0.139	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.027	0.012	22.603	0.196	0.196	0.000	0.000	0.000	0.000
84	A	86	VAL	0	-0.026	-0.020	19.970	-0.593	-0.593	0.000	0.000	0.000	0.000
85	A	87	TYR	0	0.034	0.022	22.662	0.342	0.342	0.000	0.000	0.000	0.000
86	A	88	PHE	0	0.018	-0.002	21.330	-0.609	-0.609	0.000	0.000	0.000	0.000
87	A	89	LEU	0	-0.039	-0.024	22.662	0.348	0.348	0.000	0.000	0.000	0.000
88	A	90	GLN	0	0.007	-0.022	25.580	0.299	0.299	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.917	0.969	26.964	9.271	9.271	0.000	0.000	0.000	0.000
90	A	92	PRO	0	0.064	0.030	26.207	-0.352	-0.352	0.000	0.000	0.000	0.000
91	A	93	PRO	0	-0.003	0.020	23.653	0.293	0.293	0.000	0.000	0.000	0.000
92	A	94	LYS	1	0.865	0.902	26.682	9.021	9.021	0.000	0.000	0.000	0.000
93	A	95	HIS	0	0.086	0.082	27.178	-0.049	-0.049	0.000	0.000	0.000	0.000
94	A	96	THR	0	-0.008	-0.002	29.391	0.148	0.148	0.000	0.000	0.000	0.000
95	A	97	HIS	0	0.008	0.007	27.588	0.125	0.125	0.000	0.000	0.000	0.000
96	A	98	VAL	0	-0.028	-0.008	25.697	-0.345	-0.345	0.000	0.000	0.000	0.000
97	A	99	TYR	0	0.026	0.019	28.809	0.337	0.337	0.000	0.000	0.000	0.000
98	A	100	SER	0	0.008	-0.017	30.529	-0.285	-0.285	0.000	0.000	0.000	0.000
99	A	101	ASN	0	-0.070	-0.051	32.031	-0.052	-0.052	0.000	0.000	0.000	0.000
100	A	102	GLY	0	0.018	0.009	27.812	-0.194	-0.194	0.000	0.000	0.000	0.000
101	A	103	ASP	-1	-0.870	-0.908	26.726	-10.364	-10.364	0.000	0.000	0.000	0.000
102	A	104	ILE	0	-0.012	-0.015	22.670	0.021	0.021	0.000	0.000	0.000	0.000
103	A	105	CYS	0	-0.039	-0.005	26.778	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	106	LEU	0	0.028	-0.002	21.735	0.000	0.000	0.000	0.000	0.000	0.000
105	A	107	SER	0	0.033	-0.009	26.228	-0.287	-0.287	0.000	0.000	0.000	0.000
106	A	108	VAL	0	0.017	0.007	21.034	-0.074	-0.074	0.000	0.000	0.000	0.000
107	A	109	LEU	0	-0.058	-0.038	21.419	-0.583	-0.583	0.000	0.000	0.000	0.000
108	A	110	GLY	0	-0.030	-0.032	24.676	0.067	0.067	0.000	0.000	0.000	0.000
109	A	111	ASP	-1	-0.922	-0.949	28.132	-9.601	-9.601	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.840	-0.884	26.178	-10.259	-10.259	0.000	0.000	0.000	0.000
111	A	113	TYR	0	-0.112	-0.065	21.345	-0.874	-0.874	0.000	0.000	0.000	0.000
112	A	114	ASN	0	0.062	0.036	23.457	0.029	0.029	0.000	0.000	0.000	0.000
113	A	115	PRO	0	0.034	0.001	22.622	-0.575	-0.575	0.000	0.000	0.000	0.000
114	A	116	SER	0	-0.067	-0.038	19.843	-0.908	-0.908	0.000	0.000	0.000	0.000
115	A	117	LEU	0	-0.002	0.026	18.034	-1.002	-1.002	0.000	0.000	0.000	0.000
116	A	118	SER	0	-0.012	-0.006	13.112	-0.235	-0.235	0.000	0.000	0.000	0.000
117	A	119	ILE	0	0.008	-0.003	13.613	0.454	0.454	0.000	0.000	0.000	0.000
118	A	120	SER	0	0.010	0.007	9.432	1.054	1.054	0.000	0.000	0.000	0.000
119	A	121	GLY	0	0.051	0.031	11.722	0.601	0.601	0.000	0.000	0.000	0.000
120	A	122	LEU	0	0.002	0.014	14.371	0.810	0.810	0.000	0.000	0.000	0.000
121	A	123	ILE	0	0.017	0.005	13.855	0.565	0.565	0.000	0.000	0.000	0.000
122	A	124	LEU	0	0.005	0.003	11.981	0.426	0.426	0.000	0.000	0.000	0.000
123	A	125	SER	0	-0.005	-0.004	14.859	0.800	0.800	0.000	0.000	0.000	0.000
124	A	126	ILE	0	0.012	0.017	18.439	0.600	0.600	0.000	0.000	0.000	0.000
125	A	127	ILE	0	-0.033	-0.016	15.152	0.433	0.433	0.000	0.000	0.000	0.000
126	A	128	SER	0	-0.047	-0.026	18.183	0.588	0.588	0.000	0.000	0.000	0.000
127	A	129	MET	0	-0.005	0.008	19.826	0.485	0.485	0.000	0.000	0.000	0.000
128	A	130	LEU	0	-0.017	0.002	20.740	0.439	0.439	0.000	0.000	0.000	0.000
129	A	131	SER	0	-0.056	-0.025	20.148	0.153	0.153	0.000	0.000	0.000	0.000
130	A	132	SER	0	-0.055	-0.047	22.701	0.320	0.320	0.000	0.000	0.000	0.000
131	A	133	ALA	0	-0.018	-0.010	26.414	0.099	0.099	0.000	0.000	0.000	0.000
132	A	134	LYS	1	0.967	0.976	29.764	7.992	7.992	0.000	0.000	0.000	0.000
133	A	135	GLU	-1	-0.825	-0.898	30.079	-8.632	-8.632	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LYS)