FMO DATABASE

FMODB ID: 2N56R

Calculation Name: 2HY5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HY5

Chain ID: A

ChEMBL ID:

UniProt ID: O87896

Base Structure: X-ray

Registration Date: 2023-09-23

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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1143639.938535
FMO2-HF: Nuclear repulsion	1092644.340076
FMO2-HF: Total energy	-50995.598459
FMO2-MP2: Total energy	-51145.570735

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.
-41.817	-40.404	27.953	-12.512	-16.854	-0.062

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 : -0.043 / q_NPA : -0.016

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	PHE	0	-0.034	-0.037	2.412	0.691	3.822	0.768	-1.542	-2.357	-0.001
4	A	4	ALA	0	0.014	0.011	5.894	-0.035	-0.035	0.000	0.000	0.000	0.000
5	A	5	LEU	0	-0.009	-0.003	8.830	0.393	0.393	0.000	0.000	0.000	0.000
6	A	6	GLN	0	-0.017	-0.017	11.818	-0.018	-0.018	0.000	0.000	0.000	0.000
7	A	7	ILE	0	0.002	0.003	15.347	0.088	0.088	0.000	0.000	0.000	0.000
8	A	8	ASN	0	0.054	0.020	18.211	-0.060	-0.060	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.814	-0.911	21.490	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.028	0.019	23.209	-0.032	-0.032	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.014	0.011	25.041	0.018	0.018	0.000	0.000	0.000	0.000
12	A	12	TYR	0	-0.009	-0.031	26.004	0.009	0.009	0.000	0.000	0.000	0.000
13	A	13	GLN	0	-0.041	-0.012	27.925	0.012	0.012	0.000	0.000	0.000	0.000
14	A	14	HIS	1	0.861	0.911	24.605	0.024	0.024	0.000	0.000	0.000	0.000
15	A	15	GLN	0	0.038	0.028	21.155	-0.019	-0.019	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.044	0.023	19.791	-0.025	-0.025	0.000	0.000	0.000	0.000
17	A	17	SER	0	0.028	0.005	18.526	-0.041	-0.041	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.746	-0.850	18.769	-0.206	-0.206	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.043	-0.037	17.515	-0.029	-0.029	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.017	0.011	14.333	0.001	0.001	0.000	0.000	0.000	0.000
21	A	21	TYR	0	0.009	0.006	13.912	-0.100	-0.100	0.000	0.000	0.000	0.000
22	A	22	GLN	0	0.010	-0.010	14.999	-0.134	-0.134	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.042	-0.010	7.736	-0.032	-0.032	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.023	-0.001	10.461	-0.170	-0.170	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.829	0.900	10.623	0.167	0.167	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.015	0.010	11.469	-0.114	-0.114	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.033	-0.014	6.572	0.023	0.023	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.014	0.008	6.826	-0.594	-0.594	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.820	-0.895	8.992	-0.560	-0.560	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.846	0.922	6.878	0.373	0.373	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.003	0.009	6.239	0.102	0.102	0.000	0.000	0.000	0.000
32	A	32	HIS	0	-0.036	-0.002	1.987	-10.092	-12.819	11.015	-3.962	-4.325	-0.031
33	A	33	GLU	-1	-0.773	-0.868	3.892	-2.338	-1.844	0.000	-0.110	-0.384	0.000
34	A	34	ILE	0	-0.031	-0.021	5.955	-0.412	-0.412	0.000	0.000	0.000	0.000
35	A	35	PHE	0	-0.007	0.016	8.256	0.521	0.521	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.758	0.848	10.001	1.393	1.393	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.012	0.009	11.876	-0.033	-0.033	0.000	0.000	0.000	0.000
38	A	38	PHE	0	0.013	-0.002	14.476	0.078	0.078	0.000	0.000	0.000	0.000
39	A	39	PHE	0	0.041	0.013	17.085	0.084	0.084	0.000	0.000	0.000	0.000
40	A	40	TYR	0	0.019	-0.008	20.150	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	41	HIS	0	-0.004	-0.015	22.192	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.755	-0.879	25.111	-0.107	-0.107	0.000	0.000	0.000	0.000
43	A	43	GLY	0	-0.015	0.017	22.292	-0.008	-0.008	0.000	0.000	0.000	0.000
44	A	44	VAL	0	-0.011	-0.006	23.256	-0.036	-0.036	0.000	0.000	0.000	0.000
45	A	45	ASN	0	0.014	0.007	24.909	-0.028	-0.028	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.088	-0.038	22.589	0.015	0.015	0.000	0.000	0.000	0.000
47	A	47	SER	0	0.038	0.012	23.861	-0.024	-0.024	0.000	0.000	0.000	0.000
48	A	48	THR	0	-0.006	0.005	25.473	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.865	0.896	29.290	0.235	0.235	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.010	-0.001	30.713	0.007	0.007	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.057	-0.011	29.255	0.009	0.009	0.000	0.000	0.000	0.000
52	A	52	THR	0	0.007	-0.005	32.232	-0.013	-0.013	0.000	0.000	0.000	0.000
53	A	53	PRO	0	-0.023	-0.006	30.092	0.013	0.013	0.000	0.000	0.000	0.000
54	A	54	PRO	0	0.023	0.010	32.813	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	55	GLN	0	-0.022	-0.014	33.070	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.921	-0.954	33.470	-0.088	-0.088	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.815	-0.894	28.827	-0.097	-0.097	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.730	0.840	24.297	0.096	0.096	0.000	0.000	0.000	0.000
59	A	59	HIS	0	0.078	0.040	27.210	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.026	-0.013	22.483	-0.032	-0.032	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.007	0.005	23.106	-0.039	-0.039	0.000	0.000	0.000	0.000
62	A	62	ASN	0	0.008	0.002	23.975	-0.054	-0.054	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.922	0.973	20.808	0.222	0.222	0.000	0.000	0.000	0.000
64	A	64	TRP	0	-0.023	-0.028	14.942	-0.083	-0.083	0.000	0.000	0.000	0.000
65	A	65	ALA	0	-0.016	-0.004	19.382	-0.078	-0.078	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.894	-0.958	21.071	-0.399	-0.399	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.048	-0.017	14.042	-0.039	-0.039	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.004	-0.021	16.325	-0.122	-0.122	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.862	-0.912	17.746	-0.595	-0.595	0.000	0.000	0.000	0.000
70	A	70	GLN	0	-0.053	-0.022	16.182	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	71	TYR	0	-0.031	-0.028	12.247	-0.060	-0.060	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.940	-0.957	13.432	-1.179	-1.179	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.025	-0.001	12.031	-0.080	-0.080	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.718	-0.828	14.478	-0.743	-0.743	0.000	0.000	0.000	0.000
75	A	75	MET	0	-0.040	-0.004	15.983	0.002	0.002	0.000	0.000	0.000	0.000
76	A	76	VAL	0	-0.026	-0.018	17.742	0.078	0.078	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.017	0.009	19.842	0.025	0.025	0.000	0.000	0.000	0.000
78	A	78	CYS	0	-0.037	-0.009	22.516	0.011	0.011	0.000	0.000	0.000	0.000
79	A	79	VAL	0	0.086	0.034	23.900	0.033	0.033	0.000	0.000	0.000	0.000
80	A	80	ALA	0	0.021	0.019	27.194	0.020	0.020	0.000	0.000	0.000	0.000
81	A	81	ALA	0	-0.062	-0.037	26.098	0.028	0.028	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.043	0.020	27.179	0.015	0.015	0.000	0.000	0.000	0.000
83	A	83	GLN	0	0.006	-0.021	28.944	0.019	0.019	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.808	0.899	30.524	0.120	0.120	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.807	0.896	28.861	0.125	0.125	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.022	0.039	32.653	0.003	0.003	0.000	0.000	0.000	0.000
87	A	87	ILE	0	-0.040	-0.001	27.543	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	88	VAL	0	-0.014	-0.017	30.943	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.788	-0.888	29.628	-0.289	-0.289	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.756	-0.882	32.080	-0.231	-0.231	0.000	0.000	0.000	0.000
91	A	91	GLY	0	-0.013	0.010	33.320	0.013	0.013	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.825	-0.916	31.312	-0.196	-0.196	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.018	0.011	34.387	0.016	0.016	0.000	0.000	0.000	0.000
94	A	94	SER	0	-0.051	-0.005	37.348	0.012	0.012	0.000	0.000	0.000	0.000
95	A	95	ARG	1	0.879	0.930	31.744	0.232	0.232	0.000	0.000	0.000	0.000
96	A	96	ASN	0	-0.077	-0.040	34.836	0.018	0.018	0.000	0.000	0.000	0.000
97	A	97	GLY	0	0.023	0.023	39.078	0.008	0.008	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.765	0.869	37.795	0.139	0.139	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.862	-0.929	40.973	-0.132	-0.132	0.000	0.000	0.000	0.000
100	A	100	ALA	0	-0.014	-0.002	39.321	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	101	THR	0	-0.062	-0.052	34.218	0.001	0.001	0.000	0.000	0.000	0.000
102	A	102	ASN	0	-0.058	-0.047	32.097	-0.007	-0.007	0.000	0.000	0.000	0.000
103	A	103	ILE	0	0.026	0.037	26.007	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	104	HIS	0	0.030	0.002	26.131	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	105	PRO	0	0.006	-0.009	26.364	-0.023	-0.023	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.815	0.906	20.443	0.586	0.586	0.000	0.000	0.000	0.000
107	A	107	PHE	0	-0.026	-0.002	21.313	-0.062	-0.062	0.000	0.000	0.000	0.000
108	A	108	ARG	1	0.823	0.884	18.322	0.737	0.737	0.000	0.000	0.000	0.000
109	A	109	ILE	0	0.027	0.020	23.148	-0.011	-0.011	0.000	0.000	0.000	0.000
110	A	110	SER	0	0.001	-0.009	22.184	-0.025	-0.025	0.000	0.000	0.000	0.000
111	A	111	GLY	0	0.024	0.020	24.043	0.033	0.033	0.000	0.000	0.000	0.000
112	A	112	LEU	0	0.038	0.001	20.582	-0.042	-0.042	0.000	0.000	0.000	0.000
113	A	113	GLY	0	-0.001	0.005	19.958	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	114	GLN	0	0.042	0.029	18.030	-0.062	-0.062	0.000	0.000	0.000	0.000
115	A	115	LEU	0	0.022	0.032	14.910	-0.113	-0.113	0.000	0.000	0.000	0.000
116	A	116	VAL	0	-0.012	-0.014	14.657	-0.037	-0.037	0.000	0.000	0.000	0.000
117	A	117	GLU	-1	-0.812	-0.896	14.815	-1.019	-1.019	0.000	0.000	0.000	0.000
118	A	118	ALA	0	0.036	0.004	11.753	-0.113	-0.113	0.000	0.000	0.000	0.000
119	A	119	ALA	0	-0.055	-0.035	10.290	-0.192	-0.192	0.000	0.000	0.000	0.000
120	A	120	ILE	0	-0.061	-0.019	10.798	0.131	0.131	0.000	0.000	0.000	0.000
121	A	121	GLN	0	-0.044	-0.021	10.130	-0.153	-0.153	0.000	0.000	0.000	0.000
122	A	122	ALA	0	-0.031	-0.006	6.227	-0.730	-0.730	0.000	0.000	0.000	0.000
123	A	123	ASP	-1	-0.829	-0.905	2.367	-13.845	-9.529	4.480	-3.735	-5.061	-0.043
124	A	124	ARG	1	0.826	0.895	2.353	-11.903	-15.704	11.690	-3.163	-4.727	0.013
125	A	125	LEU	0	0.053	0.039	5.869	-0.904	-0.904	0.000	0.000	0.000	0.000
126	A	126	VAL	0	-0.045	-0.023	8.054	0.413	0.413	0.000	0.000	0.000	0.000
127	A	127	VAL	0	-0.011	-0.008	10.891	-0.234	-0.234	0.000	0.000	0.000	0.000
128	A	128	PHE	0	0.002	0.005	12.136	0.096	0.096	0.000	0.000	0.000	0.000
129	A	129	GLY	0	-0.020	-0.028	17.109	-0.064	-0.064	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.897	-0.921	20.777	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)