FMO DATABASE

FMODB ID: YZZ32

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1009533.33733
FMO2-HF: Nuclear repulsion	958972.087029
FMO2-HF: Total energy	-50561.250301
FMO2-MP2: Total energy	-50707.428837

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.
-10.155	-6.932	6.665	-4.668	-5.218	-0.04

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 : 0.022 / q_NPA : 0.000

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	-0.007	-0.007	3.839	-0.916	-0.190	-0.006	-0.420	-0.300	0.001
4	A	8	PRO	0	-0.023	-0.002	6.450	0.195	0.195	0.000	0.000	0.000	0.000
5	A	9	ILE	0	0.013	0.017	9.123	0.178	0.178	0.000	0.000	0.000	0.000
6	A	10	PRO	0	0.044	0.034	10.399	-0.043	-0.043	0.000	0.000	0.000	0.000
7	A	11	THR	0	0.073	0.022	9.550	0.031	0.031	0.000	0.000	0.000	0.000
8	A	12	ASN	0	-0.014	-0.015	12.225	0.053	0.053	0.000	0.000	0.000	0.000
9	A	13	ARG	1	0.824	0.897	15.128	0.161	0.161	0.000	0.000	0.000	0.000
10	A	14	LEU	0	0.031	0.015	10.396	0.024	0.024	0.000	0.000	0.000	0.000
11	A	15	LYS	1	0.959	0.974	15.066	0.006	0.006	0.000	0.000	0.000	0.000
12	A	16	GLN	0	-0.081	-0.045	17.326	0.016	0.016	0.000	0.000	0.000	0.000
13	A	17	ILE	0	0.010	0.019	16.436	0.005	0.005	0.000	0.000	0.000	0.000
14	A	18	ALA	0	-0.006	-0.013	17.246	0.009	0.009	0.000	0.000	0.000	0.000
15	A	19	ALA	0	-0.002	0.003	19.293	0.010	0.010	0.000	0.000	0.000	0.000
16	A	20	ASP	-1	-0.849	-0.922	22.424	-0.050	-0.050	0.000	0.000	0.000	0.000
17	A	21	ALA	0	0.032	0.020	21.665	0.003	0.003	0.000	0.000	0.000	0.000
18	A	22	CYS	0	-0.077	-0.033	21.974	0.008	0.008	0.000	0.000	0.000	0.000
19	A	23	ASN	0	-0.019	-0.014	24.879	0.009	0.009	0.000	0.000	0.000	0.000
20	A	24	ASP	-1	-0.888	-0.939	26.775	-0.047	-0.047	0.000	0.000	0.000	0.000
21	A	25	ALA	0	-0.082	-0.021	27.070	0.001	0.001	0.000	0.000	0.000	0.000
22	A	26	ILE	0	-0.012	-0.032	27.929	0.003	0.003	0.000	0.000	0.000	0.000
23	A	27	GLY	0	0.045	0.029	30.582	0.004	0.004	0.000	0.000	0.000	0.000
24	A	28	SER	0	-0.058	-0.035	31.822	0.003	0.003	0.000	0.000	0.000	0.000
25	A	29	ALA	0	-0.047	-0.012	33.718	0.000	0.000	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.879	-0.934	35.602	0.001	0.001	0.000	0.000	0.000	0.000
27	A	31	PHE	0	-0.019	-0.004	36.746	0.002	0.002	0.000	0.000	0.000	0.000
28	A	32	TYR	0	0.013	-0.010	30.832	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	33	ASP	-1	-0.800	-0.902	34.480	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	34	HIS	0	0.025	0.003	34.032	0.000	0.000	0.000	0.000	0.000	0.000
31	A	35	ALA	0	-0.013	-0.003	34.421	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.896	0.941	33.997	0.006	0.006	0.000	0.000	0.000	0.000
33	A	37	THR	0	-0.027	-0.008	29.656	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	38	GLU	-1	-0.936	-0.952	28.805	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	39	GLN	0	0.035	0.001	28.708	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	40	TRP	0	0.006	0.002	28.474	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	41	ASN	0	0.059	0.025	24.499	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	42	HIS	0	0.004	0.018	24.064	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	43	GLN	0	0.039	0.016	24.657	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	44	ILE	0	0.019	0.028	21.124	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	45	ILE	0	-0.005	-0.011	19.659	-0.011	-0.011	0.000	0.000	0.000	0.000
42	A	46	ASN	0	-0.085	-0.059	20.234	-0.024	-0.024	0.000	0.000	0.000	0.000
43	A	47	THR	0	-0.017	-0.017	21.888	-0.015	-0.015	0.000	0.000	0.000	0.000
44	A	48	ILE	0	0.004	0.005	16.222	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	49	LEU	0	0.005	0.005	16.017	-0.030	-0.030	0.000	0.000	0.000	0.000
46	A	50	LYS	1	0.947	0.969	17.863	0.074	0.074	0.000	0.000	0.000	0.000
47	A	51	ALA	0	0.032	0.026	18.973	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	52	VAL	0	0.001	-0.009	13.444	-0.016	-0.016	0.000	0.000	0.000	0.000
49	A	53	ILE	0	-0.020	0.006	14.831	-0.052	-0.052	0.000	0.000	0.000	0.000
50	A	54	ALA	0	-0.018	-0.010	16.738	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	55	GLU	-1	-0.824	-0.891	16.383	-0.189	-0.189	0.000	0.000	0.000	0.000
52	A	56	SER	0	-0.034	-0.029	12.956	-0.069	-0.069	0.000	0.000	0.000	0.000
53	A	57	GLN	0	-0.050	-0.012	14.541	-0.048	-0.048	0.000	0.000	0.000	0.000
54	A	58	PRO	0	-0.011	0.006	16.205	0.016	0.016	0.000	0.000	0.000	0.000
55	A	59	SER	0	0.016	-0.009	18.497	0.013	0.013	0.000	0.000	0.000	0.000
56	A	60	ASP	-1	-0.878	-0.902	21.437	-0.145	-0.145	0.000	0.000	0.000	0.000
57	A	61	SER	0	0.048	0.009	21.654	-0.014	-0.014	0.000	0.000	0.000	0.000
58	A	62	THR	0	-0.137	-0.076	23.546	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	63	THR	0	-0.038	-0.014	17.406	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	64	PRO	0	-0.017	-0.017	18.979	0.000	0.000	0.000	0.000	0.000	0.000
61	A	65	PRO	0	0.007	-0.010	16.680	-0.027	-0.027	0.000	0.000	0.000	0.000
62	A	66	GLN	0	0.037	0.028	12.217	-0.045	-0.045	0.000	0.000	0.000	0.000
63	A	67	PHE	0	-0.013	0.003	6.539	-0.083	-0.083	0.000	0.000	0.000	0.000
64	A	68	LYS	1	0.886	0.937	11.259	0.450	0.450	0.000	0.000	0.000	0.000
65	A	69	PHE	0	0.039	0.004	10.309	-0.082	-0.082	0.000	0.000	0.000	0.000
66	A	70	ALA	0	-0.014	0.004	12.467	0.043	0.043	0.000	0.000	0.000	0.000
67	A	71	VAL	0	0.019	0.001	13.504	0.005	0.005	0.000	0.000	0.000	0.000
68	A	72	ASN	0	-0.022	0.003	16.032	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	73	SER	0	0.008	-0.011	17.960	0.011	0.011	0.000	0.000	0.000	0.000
70	A	74	THR	0	-0.055	-0.027	20.696	0.004	0.004	0.000	0.000	0.000	0.000
71	A	75	ILE	0	0.034	0.017	23.209	0.002	0.002	0.000	0.000	0.000	0.000
72	A	76	VAL	0	-0.067	-0.033	25.665	0.001	0.001	0.000	0.000	0.000	0.000
73	A	77	GLN	0	0.000	0.006	28.429	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	78	HIS	0	-0.058	-0.032	29.902	0.003	0.003	0.000	0.000	0.000	0.000
75	A	79	LEU	0	-0.078	-0.046	33.273	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	80	VAL	0	0.042	0.029	36.051	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	81	PRO	0	0.050	0.036	39.434	0.001	0.001	0.000	0.000	0.000	0.000
78	A	82	SER	0	0.021	-0.004	42.423	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	83	SER	0	0.034	0.015	45.269	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	84	LYS	1	0.861	0.939	43.804	-0.019	-0.019	0.000	0.000	0.000	0.000
81	A	104	ASP	-1	-0.921	-0.957	44.511	0.017	0.017	0.000	0.000	0.000	0.000
82	A	105	GLY	0	-0.055	-0.031	44.245	0.002	0.002	0.000	0.000	0.000	0.000
83	A	106	LYS	1	0.873	0.920	39.469	-0.029	-0.029	0.000	0.000	0.000	0.000
84	A	107	PRO	0	0.071	0.045	37.059	0.001	0.001	0.000	0.000	0.000	0.000
85	A	108	HIS	0	-0.047	-0.034	34.299	0.004	0.004	0.000	0.000	0.000	0.000
86	A	109	VAL	0	0.035	0.035	31.630	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	110	GLY	0	-0.014	0.003	33.586	0.004	0.004	0.000	0.000	0.000	0.000
88	A	111	ARG	1	0.800	0.842	27.664	-0.059	-0.059	0.000	0.000	0.000	0.000
89	A	112	ARG	1	0.979	0.992	29.396	-0.038	-0.038	0.000	0.000	0.000	0.000
90	A	113	GLY	0	0.011	0.007	28.553	0.004	0.004	0.000	0.000	0.000	0.000
91	A	114	MET	0	-0.037	-0.030	23.015	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	115	HIS	0	0.004	-0.003	18.722	0.001	0.001	0.000	0.000	0.000	0.000
93	A	116	SER	0	0.025	0.023	17.726	-0.021	-0.021	0.000	0.000	0.000	0.000
94	A	117	ALA	0	-0.023	-0.013	15.907	0.027	0.027	0.000	0.000	0.000	0.000
95	A	118	THR	0	0.007	-0.012	12.068	-0.052	-0.052	0.000	0.000	0.000	0.000
96	A	119	GLY	0	0.013	0.019	11.941	0.091	0.091	0.000	0.000	0.000	0.000
97	A	120	ALA	0	-0.015	-0.014	8.789	-0.044	-0.044	0.000	0.000	0.000	0.000
98	A	121	PHE	0	-0.028	-0.004	10.721	0.022	0.022	0.000	0.000	0.000	0.000
99	A	122	TRP	0	0.016	-0.004	5.696	-0.063	-0.063	0.000	0.000	0.000	0.000
100	A	123	ASN	0	0.018	0.020	6.705	0.070	0.070	0.000	0.000	0.000	0.000
101	A	124	ASP	-1	-0.829	-0.917	4.019	-0.412	-0.120	-0.001	-0.121	-0.170	0.000
102	A	125	LYS	1	0.856	0.913	1.995	-6.296	-6.703	5.062	-2.225	-2.429	-0.025
103	A	126	THR	0	-0.059	-0.042	3.343	-0.259	0.675	0.081	-0.510	-0.505	-0.003
104	A	127	ASP	-1	-0.798	-0.887	3.587	-2.053	-1.744	0.022	-0.127	-0.204	-0.001
105	A	128	GLY	0	0.029	0.001	2.502	-0.801	0.274	1.507	-1.165	-1.417	-0.012
106	A	129	MET	0	-0.031	-0.019	4.235	-0.782	-0.684	0.000	-0.031	-0.067	0.000
107	A	130	TRP	0	0.001	0.010	7.621	0.168	0.168	0.000	0.000	0.000	0.000
108	A	131	THR	0	-0.039	-0.030	10.112	-0.022	-0.022	0.000	0.000	0.000	0.000
109	A	132	TYR	0	-0.041	-0.036	13.781	0.000	0.000	0.000	0.000	0.000	0.000
110	A	133	LYS	1	0.944	0.966	16.488	-0.172	-0.172	0.000	0.000	0.000	0.000
111	A	134	HIS	0	0.043	0.029	20.585	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	135	GLU	-1	-0.897	-0.936	23.771	0.071	0.071	0.000	0.000	0.000	0.000
113	A	136	GLY	0	0.019	0.022	26.361	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	137	ASP	-1	-0.833	-0.902	29.962	0.023	0.023	0.000	0.000	0.000	0.000
115	A	138	GLU	-1	-0.872	-0.962	32.776	0.025	0.025	0.000	0.000	0.000	0.000
116	A	139	SER	0	-0.082	-0.059	35.808	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	140	LYS	1	0.837	0.930	31.544	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	141	GLY	0	0.058	0.025	34.173	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	142	MET	0	-0.071	-0.038	30.133	0.000	0.000	0.000	0.000	0.000	0.000
120	A	143	ASP	-1	-0.776	-0.824	25.765	0.045	0.045	0.000	0.000	0.000	0.000
121	A	144	VAL	0	0.020	0.005	22.444	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	145	VAL	0	-0.051	-0.017	18.606	0.010	0.010	0.000	0.000	0.000	0.000
123	A	146	VAL	0	0.019	0.006	16.165	-0.011	-0.011	0.000	0.000	0.000	0.000
124	A	147	MET	0	-0.036	-0.006	12.511	0.053	0.053	0.000	0.000	0.000	0.000
125	A	148	LEU	0	-0.007	0.008	10.484	-0.034	-0.034	0.000	0.000	0.000	0.000
126	A	149	ILE	0	0.017	-0.003	8.777	0.086	0.086	0.000	0.000	0.000	0.000
127	A	150	TRP	0	0.008	0.018	3.559	0.791	0.987	0.000	-0.069	-0.126	0.000
128	A	151	ILE	0	-0.019	-0.010	6.624	-0.179	-0.179	0.000	0.000	0.000	0.000
129	A	152	ALA	0	0.051	0.043	7.154	0.142	0.142	0.000	0.000	0.000	0.000
130	A	153	VAL	0	-0.065	-0.034	8.831	0.246	0.246	0.000	0.000	0.000	0.000

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