FMO DATABASE

FMODB ID: GN1Y1

Calculation Name: 4L9H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4L9H

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y3I1

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	155
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1497996.04526
FMO2-HF: Nuclear repulsion	1437172.529463
FMO2-HF: Total energy	-60823.515797
FMO2-MP2: Total energy	-60999.380747

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:176:GLY)

Summations of interaction energy for fragment #1(A:176: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.
1	2.546	-0.001	-0.745	-0.8	0.004

Interaction energy analysis for fragmet #1(A:176:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / q_NPA : 0.026

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	178	SER	0	0.009	0.001	3.779	0.283	1.829	-0.001	-0.745	-0.800	0.004
4	A	179	SER	0	0.016	0.012	5.969	0.360	0.360	0.000	0.000	0.000	0.000
5	A	180	PRO	0	-0.024	-0.012	8.322	-0.036	-0.036	0.000	0.000	0.000	0.000
6	A	181	HIS	0	0.063	0.016	11.472	0.098	0.098	0.000	0.000	0.000	0.000
7	A	182	SER	0	0.025	0.007	14.074	0.060	0.060	0.000	0.000	0.000	0.000
8	A	183	LEU	0	-0.013	0.011	13.701	0.046	0.046	0.000	0.000	0.000	0.000
9	A	184	GLU	-1	-0.899	-0.946	14.161	-0.167	-0.167	0.000	0.000	0.000	0.000
10	A	185	THR	0	0.016	0.005	16.139	0.036	0.036	0.000	0.000	0.000	0.000
11	A	186	LEU	0	-0.044	-0.025	19.224	0.035	0.035	0.000	0.000	0.000	0.000
12	A	187	TYR	0	0.039	0.000	18.698	0.029	0.029	0.000	0.000	0.000	0.000
13	A	188	GLN	0	-0.029	-0.012	20.344	0.025	0.025	0.000	0.000	0.000	0.000
14	A	189	SER	0	-0.023	-0.010	22.083	0.014	0.014	0.000	0.000	0.000	0.000
15	A	190	ALA	0	-0.065	-0.036	23.836	0.011	0.011	0.000	0.000	0.000	0.000
16	A	191	ASP	-1	-0.934	-0.947	25.009	-0.050	-0.050	0.000	0.000	0.000	0.000
17	A	192	CYS	0	-0.088	-0.041	22.471	0.001	0.001	0.000	0.000	0.000	0.000
18	A	193	SER	0	0.019	-0.002	25.914	0.010	0.010	0.000	0.000	0.000	0.000
19	A	194	ASP	-1	-0.841	-0.915	27.288	-0.031	-0.031	0.000	0.000	0.000	0.000
20	A	195	ALA	0	0.035	0.001	24.207	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	196	ASN	0	-0.057	-0.047	24.483	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	197	ASP	-1	-0.707	-0.803	26.121	-0.082	-0.082	0.000	0.000	0.000	0.000
23	A	198	ALA	0	0.051	0.032	20.856	-0.020	-0.020	0.000	0.000	0.000	0.000
24	A	199	LEU	0	-0.007	0.007	21.129	-0.027	-0.027	0.000	0.000	0.000	0.000
25	A	200	ILE	0	-0.004	-0.007	22.551	-0.024	-0.024	0.000	0.000	0.000	0.000
26	A	201	VAL	0	0.049	0.028	19.853	-0.021	-0.021	0.000	0.000	0.000	0.000
27	A	202	LEU	0	-0.008	0.006	16.065	-0.033	-0.033	0.000	0.000	0.000	0.000
28	A	203	ILE	0	-0.030	-0.021	19.629	-0.033	-0.033	0.000	0.000	0.000	0.000
29	A	204	HIS	0	0.073	0.041	22.410	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	205	LEU	0	0.022	0.009	15.443	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	206	LEU	0	-0.019	-0.009	16.901	-0.031	-0.031	0.000	0.000	0.000	0.000
32	A	207	MET	0	-0.023	0.007	19.925	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	208	LEU	0	-0.025	-0.010	20.797	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	209	GLU	-1	-0.903	-0.944	15.235	-0.613	-0.613	0.000	0.000	0.000	0.000
35	A	210	SER	0	-0.062	-0.034	19.548	-0.023	-0.023	0.000	0.000	0.000	0.000
36	A	211	GLY	0	-0.002	0.004	22.212	0.023	0.023	0.000	0.000	0.000	0.000
37	A	212	TYR	0	-0.016	-0.009	24.494	0.020	0.020	0.000	0.000	0.000	0.000
38	A	213	ILE	0	-0.015	-0.020	25.891	-0.023	-0.023	0.000	0.000	0.000	0.000
39	A	214	PRO	0	0.001	0.006	26.605	0.013	0.013	0.000	0.000	0.000	0.000
40	A	215	GLN	0	0.020	-0.001	29.413	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	216	GLY	0	0.010	-0.010	31.815	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	217	THR	0	0.002	0.001	27.644	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	218	GLU	-1	-0.870	-0.930	29.303	-0.171	-0.171	0.000	0.000	0.000	0.000
44	A	219	ALA	0	0.030	0.022	25.793	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	220	LYS	1	0.895	0.952	23.021	0.311	0.311	0.000	0.000	0.000	0.000
46	A	221	ALA	0	-0.030	-0.020	20.167	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	222	LEU	0	-0.027	-0.022	20.667	-0.024	-0.024	0.000	0.000	0.000	0.000
48	A	223	SER	0	0.045	0.030	23.077	0.014	0.014	0.000	0.000	0.000	0.000
49	A	224	MET	0	-0.018	-0.001	24.366	-0.019	-0.019	0.000	0.000	0.000	0.000
50	A	225	PRO	0	-0.060	-0.028	26.562	0.007	0.007	0.000	0.000	0.000	0.000
51	A	226	GLU	-1	-0.851	-0.940	29.887	-0.096	-0.096	0.000	0.000	0.000	0.000
52	A	227	LYS	1	0.843	0.918	33.086	0.079	0.079	0.000	0.000	0.000	0.000
53	A	228	TRP	0	0.049	0.031	26.881	0.000	0.000	0.000	0.000	0.000	0.000
54	A	229	LYS	1	0.885	0.930	30.070	0.064	0.064	0.000	0.000	0.000	0.000
55	A	230	LEU	0	-0.042	-0.029	32.477	0.004	0.004	0.000	0.000	0.000	0.000
56	A	231	SER	0	0.001	-0.010	36.220	0.000	0.000	0.000	0.000	0.000	0.000
57	A	232	GLY	0	0.001	0.017	35.855	0.003	0.003	0.000	0.000	0.000	0.000
58	A	233	VAL	0	-0.040	-0.010	34.621	0.000	0.000	0.000	0.000	0.000	0.000
59	A	234	TYR	0	-0.016	-0.034	29.378	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	235	LYS	1	0.851	0.916	32.456	0.098	0.098	0.000	0.000	0.000	0.000
61	A	236	LEU	0	0.035	0.033	26.846	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	237	GLN	0	-0.011	-0.015	30.952	0.007	0.007	0.000	0.000	0.000	0.000
63	A	238	TYR	0	0.026	-0.011	25.958	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	239	MET	0	0.037	0.032	31.243	0.016	0.016	0.000	0.000	0.000	0.000
65	A	240	HIS	0	0.035	-0.010	26.108	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	241	PRO	0	0.024	0.026	28.105	0.013	0.013	0.000	0.000	0.000	0.000
67	A	242	LEU	0	-0.018	0.001	28.045	0.007	0.007	0.000	0.000	0.000	0.000
68	A	243	CYS	0	-0.055	-0.031	31.893	0.006	0.006	0.000	0.000	0.000	0.000
69	A	244	GLU	-1	-0.889	-0.931	34.209	-0.133	-0.133	0.000	0.000	0.000	0.000
70	A	245	GLY	0	0.040	0.024	36.789	0.005	0.005	0.000	0.000	0.000	0.000
71	A	246	SER	0	-0.074	-0.039	36.312	0.006	0.006	0.000	0.000	0.000	0.000
72	A	247	SER	0	-0.026	-0.007	35.151	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	248	ALA	0	0.018	0.008	31.790	0.007	0.007	0.000	0.000	0.000	0.000
74	A	249	THR	0	-0.046	-0.025	33.031	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	250	LEU	0	0.012	0.010	27.376	0.004	0.004	0.000	0.000	0.000	0.000
76	A	251	THR	0	0.008	0.000	31.742	0.002	0.002	0.000	0.000	0.000	0.000
77	A	252	CYS	0	-0.045	-0.017	29.774	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	253	VAL	0	0.041	0.009	32.049	0.003	0.003	0.000	0.000	0.000	0.000
79	A	254	PRO	0	0.041	0.028	32.109	0.000	0.000	0.000	0.000	0.000	0.000
80	A	255	LEU	0	-0.006	0.003	33.680	0.002	0.002	0.000	0.000	0.000	0.000
81	A	256	GLY	0	0.001	0.003	34.868	0.001	0.001	0.000	0.000	0.000	0.000
82	A	257	ASN	0	0.011	-0.001	31.265	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	258	LEU	0	-0.040	-0.019	30.051	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	259	ILE	0	0.037	0.022	27.355	0.000	0.000	0.000	0.000	0.000	0.000
85	A	260	VAL	0	-0.050	-0.026	30.024	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	261	VAL	0	0.027	0.002	27.484	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	262	ASN	0	-0.035	-0.025	30.937	0.003	0.003	0.000	0.000	0.000	0.000
88	A	263	ALA	0	0.021	0.009	31.288	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	264	THR	0	-0.026	-0.021	33.211	0.010	0.010	0.000	0.000	0.000	0.000
90	A	265	LEU	0	0.021	0.011	34.995	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	266	LYS	1	0.892	0.964	37.346	0.097	0.097	0.000	0.000	0.000	0.000
92	A	267	ILE	0	0.071	0.018	39.242	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	268	ASN	0	0.031	0.019	41.954	0.003	0.003	0.000	0.000	0.000	0.000
94	A	269	ASN	0	-0.045	-0.043	44.719	0.000	0.000	0.000	0.000	0.000	0.000
95	A	270	GLU	-1	-0.764	-0.816	44.848	-0.074	-0.074	0.000	0.000	0.000	0.000
96	A	271	ILE	0	-0.047	-0.037	40.960	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	272	ARG	1	0.869	0.896	40.162	0.090	0.090	0.000	0.000	0.000	0.000
98	A	273	SER	0	-0.020	-0.006	38.456	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	274	VAL	0	-0.011	0.008	33.609	0.001	0.001	0.000	0.000	0.000	0.000
100	A	275	LYS	1	0.864	0.919	29.857	0.107	0.107	0.000	0.000	0.000	0.000
101	A	276	ARG	1	0.942	0.983	33.554	0.056	0.056	0.000	0.000	0.000	0.000
102	A	277	LEU	0	-0.010	-0.009	25.989	0.002	0.002	0.000	0.000	0.000	0.000
103	A	278	GLN	0	0.010	0.021	30.442	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	279	LEU	0	0.016	0.012	24.419	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	280	LEU	0	0.054	0.025	26.125	0.004	0.004	0.000	0.000	0.000	0.000
106	A	281	PRO	0	0.054	0.022	24.037	0.000	0.000	0.000	0.000	0.000	0.000
107	A	282	GLU	-1	-0.809	-0.893	22.826	0.027	0.027	0.000	0.000	0.000	0.000
108	A	283	SER	0	-0.019	-0.006	21.969	0.022	0.022	0.000	0.000	0.000	0.000
109	A	284	PHE	0	-0.040	-0.032	18.485	0.006	0.006	0.000	0.000	0.000	0.000
110	A	285	ILE	0	-0.023	0.009	18.188	-0.011	-0.011	0.000	0.000	0.000	0.000
111	A	286	CYS	0	-0.027	-0.006	17.210	0.025	0.025	0.000	0.000	0.000	0.000
112	A	287	LYS	1	0.906	0.941	20.427	-0.034	-0.034	0.000	0.000	0.000	0.000
113	A	288	GLU	-1	-0.874	-0.951	23.351	0.063	0.063	0.000	0.000	0.000	0.000
114	A	289	LYS	1	0.772	0.876	16.907	-0.201	-0.201	0.000	0.000	0.000	0.000
115	A	290	LEU	0	-0.010	-0.009	19.777	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	291	GLY	0	-0.015	0.013	22.071	-0.017	-0.017	0.000	0.000	0.000	0.000
117	A	292	GLU	-1	-0.841	-0.911	17.835	0.210	0.210	0.000	0.000	0.000	0.000
118	A	293	ASN	0	0.008	0.007	14.243	-0.057	-0.057	0.000	0.000	0.000	0.000
119	A	294	VAL	0	0.090	0.046	13.319	0.024	0.024	0.000	0.000	0.000	0.000
120	A	295	ALA	0	-0.049	-0.035	10.053	-0.014	-0.014	0.000	0.000	0.000	0.000
121	A	296	ASN	0	-0.048	-0.025	11.665	0.048	0.048	0.000	0.000	0.000	0.000
122	A	297	ILE	0	0.027	0.034	14.588	0.007	0.007	0.000	0.000	0.000	0.000
123	A	298	TYR	0	-0.042	-0.040	14.073	-0.011	-0.011	0.000	0.000	0.000	0.000
124	A	299	LYS	1	0.859	0.922	13.797	-0.024	-0.024	0.000	0.000	0.000	0.000
125	A	300	ASP	-1	-0.908	-0.970	13.880	0.047	0.047	0.000	0.000	0.000	0.000
126	A	301	LEU	0	0.101	0.041	11.420	-0.038	-0.038	0.000	0.000	0.000	0.000
127	A	302	GLN	0	0.015	0.009	10.690	0.075	0.075	0.000	0.000	0.000	0.000
128	A	303	LYS	1	0.926	0.965	13.402	-0.037	-0.037	0.000	0.000	0.000	0.000
129	A	304	LEU	0	0.048	0.042	16.636	0.001	0.001	0.000	0.000	0.000	0.000
130	A	305	SER	0	-0.008	-0.014	15.202	-0.021	-0.021	0.000	0.000	0.000	0.000
131	A	306	ARG	1	0.926	0.957	14.039	0.280	0.280	0.000	0.000	0.000	0.000
132	A	307	LEU	0	0.009	0.026	18.802	0.013	0.013	0.000	0.000	0.000	0.000
133	A	308	PHE	0	0.031	-0.001	21.085	0.013	0.013	0.000	0.000	0.000	0.000
134	A	309	LYS	1	0.868	0.929	16.804	0.481	0.481	0.000	0.000	0.000	0.000
135	A	310	ASP	-1	-0.874	-0.933	21.981	-0.199	-0.199	0.000	0.000	0.000	0.000
136	A	311	GLN	0	-0.044	-0.030	24.175	0.019	0.019	0.000	0.000	0.000	0.000
137	A	312	LEU	0	-0.023	-0.004	25.851	0.017	0.017	0.000	0.000	0.000	0.000
138	A	313	VAL	0	0.018	0.012	23.143	0.005	0.005	0.000	0.000	0.000	0.000
139	A	314	TYR	0	0.035	0.005	20.744	-0.004	-0.004	0.000	0.000	0.000	0.000
140	A	315	PRO	0	0.011	0.011	26.834	0.007	0.007	0.000	0.000	0.000	0.000
141	A	316	LEU	0	-0.003	0.011	29.369	0.010	0.010	0.000	0.000	0.000	0.000
142	A	317	LEU	0	0.007	0.019	26.301	0.007	0.007	0.000	0.000	0.000	0.000
143	A	318	ALA	0	0.024	0.018	30.507	0.006	0.006	0.000	0.000	0.000	0.000
144	A	319	PHE	0	0.013	0.001	32.486	0.008	0.008	0.000	0.000	0.000	0.000
145	A	320	THR	0	-0.040	-0.060	33.383	0.007	0.007	0.000	0.000	0.000	0.000
146	A	321	ARG	1	0.856	0.907	32.489	0.171	0.171	0.000	0.000	0.000	0.000
147	A	322	GLN	0	0.024	0.018	35.571	0.010	0.010	0.000	0.000	0.000	0.000
148	A	323	ALA	0	-0.046	-0.014	38.306	0.006	0.006	0.000	0.000	0.000	0.000
149	A	324	LEU	0	-0.057	-0.023	36.513	0.005	0.005	0.000	0.000	0.000	0.000
150	A	325	ASN	0	-0.084	-0.032	40.185	0.003	0.003	0.000	0.000	0.000	0.000
151	A	326	LEU	0	-0.016	-0.003	36.366	-0.002	-0.002	0.000	0.000	0.000	0.000
152	A	327	PRO	0	0.019	0.005	35.400	0.001	0.001	0.000	0.000	0.000	0.000
153	A	328	ASP	-1	-0.897	-0.938	32.336	-0.144	-0.144	0.000	0.000	0.000	0.000
154	A	329	VAL	0	-0.038	-0.023	27.341	-0.003	-0.003	0.000	0.000	0.000	0.000
155	A	330	PHE	0	-0.012	0.005	24.267	-0.015	-0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:176:GLY)