FMO DATABASE

FMODB ID: V55M1

Calculation Name: 5HYC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5HYC

Chain ID: A

ChEMBL ID:

UniProt ID: G4NCW2

Base Structure: X-ray

Registration Date: 2023-06-21

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	-1011202.282435
FMO2-HF: Nuclear repulsion	960640.802539
FMO2-HF: Total energy	-50561.479896
FMO2-MP2: Total energy	-50707.774726

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:5:GLY)

Summations of interaction energy for fragment #1(A:5:GLY)

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.
-13.199	-12.491	11.605	-6.158	-6.155	-0.058

Interaction energy analysis for fragmet #1(A:5:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / 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

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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	7	SER	0	-0.006	-0.004	3.885	-0.991	-0.249	-0.002	-0.429	-0.310	0.001
4	A	8	PRO	0	-0.032	-0.008	6.702	0.223	0.223	0.000	0.000	0.000	0.000
5	A	9	ILE	0	0.026	0.030	9.092	0.189	0.189	0.000	0.000	0.000	0.000
6	A	10	PRO	0	0.025	0.012	10.744	-0.037	-0.037	0.000	0.000	0.000	0.000
7	A	11	THR	0	0.067	0.027	9.816	0.010	0.010	0.000	0.000	0.000	0.000
8	A	12	ASN	0	-0.010	-0.014	12.455	0.035	0.035	0.000	0.000	0.000	0.000
9	A	13	ARG	1	0.810	0.896	15.503	0.164	0.164	0.000	0.000	0.000	0.000
10	A	14	LEU	0	0.027	0.017	10.573	0.013	0.013	0.000	0.000	0.000	0.000
11	A	15	LYS	1	0.946	0.961	15.121	-0.015	-0.015	0.000	0.000	0.000	0.000
12	A	16	GLN	0	-0.082	-0.044	17.323	0.016	0.016	0.000	0.000	0.000	0.000
13	A	17	ILE	0	0.025	0.021	16.564	0.005	0.005	0.000	0.000	0.000	0.000
14	A	18	ALA	0	0.003	-0.008	17.279	0.004	0.004	0.000	0.000	0.000	0.000
15	A	19	ALA	0	-0.002	0.005	19.344	0.011	0.011	0.000	0.000	0.000	0.000
16	A	20	ASP	-1	-0.847	-0.920	22.449	-0.074	-0.074	0.000	0.000	0.000	0.000
17	A	21	ALA	0	0.043	0.018	21.625	0.005	0.005	0.000	0.000	0.000	0.000
18	A	22	CYS	0	-0.078	-0.038	21.798	0.007	0.007	0.000	0.000	0.000	0.000
19	A	23	ASN	0	-0.017	-0.007	24.736	0.012	0.012	0.000	0.000	0.000	0.000
20	A	24	ASP	-1	-0.899	-0.946	27.098	-0.064	-0.064	0.000	0.000	0.000	0.000
21	A	25	ALA	0	-0.073	-0.023	26.683	0.002	0.002	0.000	0.000	0.000	0.000
22	A	26	ILE	0	-0.008	-0.019	27.553	0.004	0.004	0.000	0.000	0.000	0.000
23	A	27	GLY	0	0.046	0.031	30.270	0.006	0.006	0.000	0.000	0.000	0.000
24	A	28	SER	0	-0.046	-0.033	31.801	0.004	0.004	0.000	0.000	0.000	0.000
25	A	29	ALA	0	-0.037	-0.010	33.049	0.001	0.001	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.884	-0.937	35.006	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	31	PHE	0	-0.029	-0.011	36.353	0.003	0.003	0.000	0.000	0.000	0.000
28	A	32	TYR	0	0.020	-0.004	30.354	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	33	ASP	-1	-0.803	-0.909	33.825	-0.021	-0.021	0.000	0.000	0.000	0.000
30	A	34	HIS	0	0.044	0.022	33.149	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	35	ALA	0	-0.004	0.005	33.330	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.882	0.938	33.409	0.023	0.023	0.000	0.000	0.000	0.000
33	A	37	THR	0	-0.038	-0.021	28.943	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	38	GLU	-1	-0.933	-0.949	28.197	-0.060	-0.060	0.000	0.000	0.000	0.000
35	A	39	GLN	0	0.044	0.008	28.107	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	40	TRP	0	0.009	0.012	27.979	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	41	ASN	0	0.036	0.015	23.957	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	42	HIS	0	0.038	0.029	23.580	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	43	GLN	0	-0.005	-0.010	24.570	-0.013	-0.013	0.000	0.000	0.000	0.000
40	A	44	ILE	0	0.037	0.030	20.615	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	45	ILE	0	-0.016	-0.012	19.253	-0.016	-0.016	0.000	0.000	0.000	0.000
42	A	46	ASN	0	-0.059	-0.039	19.924	-0.029	-0.029	0.000	0.000	0.000	0.000
43	A	47	THR	0	-0.033	-0.026	21.740	-0.015	-0.015	0.000	0.000	0.000	0.000
44	A	48	ILE	0	0.025	0.010	16.076	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	49	LEU	0	-0.014	0.000	15.795	-0.036	-0.036	0.000	0.000	0.000	0.000
46	A	50	LYS	1	0.943	0.965	17.966	0.111	0.111	0.000	0.000	0.000	0.000
47	A	51	ALA	0	0.018	0.020	18.998	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	52	VAL	0	0.002	-0.012	13.711	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	53	ILE	0	-0.016	0.006	15.306	-0.047	-0.047	0.000	0.000	0.000	0.000
50	A	54	ALA	0	-0.030	-0.011	17.141	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	55	GLU	-1	-0.824	-0.896	16.938	-0.195	-0.195	0.000	0.000	0.000	0.000
52	A	56	SER	0	-0.027	-0.027	12.913	-0.064	-0.064	0.000	0.000	0.000	0.000
53	A	57	GLN	0	-0.039	-0.009	14.549	-0.059	-0.059	0.000	0.000	0.000	0.000
54	A	58	PRO	0	-0.016	0.003	16.038	0.021	0.021	0.000	0.000	0.000	0.000
55	A	59	SER	0	0.015	-0.011	18.230	0.010	0.010	0.000	0.000	0.000	0.000
56	A	60	ASP	-1	-0.869	-0.892	21.069	-0.148	-0.148	0.000	0.000	0.000	0.000
57	A	61	SER	0	0.040	0.008	21.425	-0.016	-0.016	0.000	0.000	0.000	0.000
58	A	62	THR	0	-0.102	-0.063	23.578	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	63	THR	0	-0.057	-0.029	17.003	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	64	PRO	0	-0.013	-0.016	18.382	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	65	PRO	0	0.002	-0.001	16.785	-0.022	-0.022	0.000	0.000	0.000	0.000
62	A	66	GLN	0	0.013	0.010	12.023	-0.066	-0.066	0.000	0.000	0.000	0.000
63	A	67	PHE	0	-0.005	0.003	6.676	-0.091	-0.091	0.000	0.000	0.000	0.000
64	A	68	LYS	1	0.867	0.936	11.848	0.574	0.574	0.000	0.000	0.000	0.000
65	A	69	PHE	0	0.035	-0.004	10.564	-0.139	-0.139	0.000	0.000	0.000	0.000
66	A	70	ALA	0	-0.012	-0.003	12.331	0.072	0.072	0.000	0.000	0.000	0.000
67	A	71	VAL	0	0.020	-0.002	13.076	-0.029	-0.029	0.000	0.000	0.000	0.000
68	A	72	ASN	0	-0.020	0.008	15.504	0.011	0.011	0.000	0.000	0.000	0.000
69	A	73	SER	0	0.018	-0.016	17.425	0.007	0.007	0.000	0.000	0.000	0.000
70	A	74	THR	0	-0.037	-0.019	20.252	0.003	0.003	0.000	0.000	0.000	0.000
71	A	75	ILE	0	0.019	0.015	22.769	0.006	0.006	0.000	0.000	0.000	0.000
72	A	76	VAL	0	-0.056	-0.029	25.112	0.000	0.000	0.000	0.000	0.000	0.000
73	A	77	GLN	0	-0.016	-0.004	27.899	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	78	HIS	0	-0.034	-0.022	29.699	0.003	0.003	0.000	0.000	0.000	0.000
75	A	79	LEU	0	-0.083	-0.045	32.764	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	80	VAL	0	0.031	0.026	35.590	0.000	0.000	0.000	0.000	0.000	0.000
77	A	81	PRO	0	0.062	0.041	38.685	0.001	0.001	0.000	0.000	0.000	0.000
78	A	82	SER	0	0.003	-0.012	41.687	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	83	SER	0	0.030	0.017	44.536	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	84	LYS	1	0.866	0.939	43.213	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	104	ASP	-1	-0.893	-0.948	44.538	0.016	0.016	0.000	0.000	0.000	0.000
82	A	105	GLY	0	-0.051	-0.026	44.361	0.002	0.002	0.000	0.000	0.000	0.000
83	A	106	LYS	1	0.867	0.907	40.079	-0.032	-0.032	0.000	0.000	0.000	0.000
84	A	107	PRO	0	0.035	0.046	37.139	0.001	0.001	0.000	0.000	0.000	0.000
85	A	108	HIS	0	-0.034	-0.029	34.404	0.005	0.005	0.000	0.000	0.000	0.000
86	A	109	VAL	0	0.024	0.016	30.802	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	110	GLY	0	0.009	0.020	32.629	0.005	0.005	0.000	0.000	0.000	0.000
88	A	111	ARG	1	0.782	0.832	27.023	-0.057	-0.057	0.000	0.000	0.000	0.000
89	A	112	ARG	1	0.963	0.983	28.330	-0.019	-0.019	0.000	0.000	0.000	0.000
90	A	113	GLY	0	0.021	0.013	28.262	0.005	0.005	0.000	0.000	0.000	0.000
91	A	114	MET	0	-0.035	-0.027	22.555	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	115	HIS	0	0.000	-0.004	18.296	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	116	SER	0	0.032	0.015	16.740	-0.031	-0.031	0.000	0.000	0.000	0.000
94	A	117	ALA	0	-0.039	-0.014	14.784	0.038	0.038	0.000	0.000	0.000	0.000
95	A	118	THR	0	0.022	-0.003	10.937	-0.047	-0.047	0.000	0.000	0.000	0.000
96	A	119	GLY	0	0.017	0.020	11.164	0.101	0.101	0.000	0.000	0.000	0.000
97	A	120	ALA	0	-0.014	-0.015	8.491	-0.057	-0.057	0.000	0.000	0.000	0.000
98	A	121	PHE	0	-0.023	-0.011	10.560	0.063	0.063	0.000	0.000	0.000	0.000
99	A	122	TRP	0	0.011	0.003	5.010	-0.032	-0.032	0.000	0.000	0.000	0.000
100	A	123	ASN	0	0.035	0.017	6.849	0.283	0.283	0.000	0.000	0.000	0.000
101	A	124	ASP	-1	-0.833	-0.913	3.384	-0.348	-0.031	0.007	-0.122	-0.203	0.000
102	A	125	LYS	1	0.843	0.909	2.013	-5.331	-5.598	5.013	-2.138	-2.608	-0.025
103	A	126	THR	0	-0.061	-0.049	3.314	-0.028	0.681	0.146	-0.382	-0.474	-0.003
104	A	127	ASP	-1	-0.784	-0.872	3.814	-1.865	-1.522	0.005	-0.162	-0.185	0.000
105	A	128	GLY	0	0.026	0.003	1.969	-6.568	-8.045	6.432	-2.813	-2.143	-0.031
106	A	129	MET	0	-0.034	-0.011	3.686	0.277	0.464	0.005	-0.058	-0.133	0.000
107	A	130	TRP	0	0.009	0.013	6.930	0.311	0.311	0.000	0.000	0.000	0.000
108	A	131	THR	0	-0.039	-0.030	9.642	-0.022	-0.022	0.000	0.000	0.000	0.000
109	A	132	TYR	0	-0.049	-0.040	13.275	0.038	0.038	0.000	0.000	0.000	0.000
110	A	133	LYS	1	0.951	0.965	16.316	-0.168	-0.168	0.000	0.000	0.000	0.000
111	A	134	HIS	0	0.034	0.033	20.382	0.001	0.001	0.000	0.000	0.000	0.000
112	A	135	GLU	-1	-0.885	-0.925	23.625	0.070	0.070	0.000	0.000	0.000	0.000
113	A	136	GLY	0	0.024	0.022	26.017	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	137	ASP	-1	-0.839	-0.909	29.701	0.020	0.020	0.000	0.000	0.000	0.000
115	A	138	GLU	-1	-0.867	-0.956	32.787	0.021	0.021	0.000	0.000	0.000	0.000
116	A	139	SER	0	-0.080	-0.054	35.687	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	140	LYS	1	0.848	0.930	31.388	0.008	0.008	0.000	0.000	0.000	0.000
118	A	141	GLY	0	0.029	0.014	33.932	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	142	MET	0	-0.081	-0.039	29.762	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	143	ASP	-1	-0.764	-0.819	25.535	0.035	0.035	0.000	0.000	0.000	0.000
121	A	144	VAL	0	0.013	-0.001	22.122	-0.006	-0.006	0.000	0.000	0.000	0.000
122	A	145	VAL	0	-0.046	-0.021	18.326	0.014	0.014	0.000	0.000	0.000	0.000
123	A	146	VAL	0	0.008	0.003	16.187	-0.017	-0.017	0.000	0.000	0.000	0.000
124	A	147	MET	0	-0.040	-0.008	11.860	0.058	0.058	0.000	0.000	0.000	0.000
125	A	148	LEU	0	-0.005	0.015	10.350	-0.021	-0.021	0.000	0.000	0.000	0.000
126	A	149	ILE	0	0.016	-0.009	8.263	0.060	0.060	0.000	0.000	0.000	0.000
127	A	150	TRP	0	-0.009	0.009	4.225	0.808	0.962	-0.001	-0.054	-0.099	0.000
128	A	151	ILE	0	-0.003	0.003	6.567	-0.392	-0.392	0.000	0.000	0.000	0.000
129	A	152	ALA	0	0.055	0.037	7.389	0.232	0.232	0.000	0.000	0.000	0.000
130	A	153	VAL	0	-0.050	-0.019	9.261	0.226	0.226	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:GLY)