FMO DATABASE

FMODB ID: QVJZY

Calculation Name: 3LYH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LYH

Chain ID: A

ChEMBL ID:

UniProt ID: A1TZQ9

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-919320.906797
FMO2-HF: Nuclear repulsion	872998.044658
FMO2-HF: Total energy	-46322.862139
FMO2-MP2: Total energy	-46458.919042

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:4:PRO)

Summations of interaction energy for fragment #1(A:4:PRO)

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.
-9.206	-2.841	1.868	-3.323	-4.908	-0.005

Interaction energy analysis for fragmet #1(A:4:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : 0.006

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	6	GLN	0	-0.007	0.010	3.843	-1.110	1.225	-0.016	-1.270	-1.048	0.003
4	A	7	ILE	0	-0.038	-0.025	6.481	-0.356	-0.356	0.000	0.000	0.000	0.000
5	A	8	ILE	0	0.035	0.014	10.137	-0.003	-0.003	0.000	0.000	0.000	0.000
6	A	9	LEU	0	0.002	-0.002	13.227	-0.059	-0.059	0.000	0.000	0.000	0.000
7	A	10	LEU	0	0.002	-0.001	16.610	-0.009	-0.009	0.000	0.000	0.000	0.000
8	A	11	ALA	0	0.071	0.042	19.168	-0.022	-0.022	0.000	0.000	0.000	0.000
9	A	12	HIS	0	0.008	-0.016	22.412	0.006	0.006	0.000	0.000	0.000	0.000
10	A	13	GLY	0	0.043	0.029	25.604	0.003	0.003	0.000	0.000	0.000	0.000
11	A	14	SER	0	-0.020	-0.014	26.769	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	15	SER	0	0.058	0.022	28.951	0.003	0.003	0.000	0.000	0.000	0.000
13	A	16	ASP	-1	-0.848	-0.888	31.498	0.061	0.061	0.000	0.000	0.000	0.000
14	A	17	ALA	0	0.076	0.023	30.267	0.006	0.006	0.000	0.000	0.000	0.000
15	A	18	ARG	1	0.869	0.911	30.110	-0.053	-0.053	0.000	0.000	0.000	0.000
16	A	19	TRP	0	-0.047	-0.011	27.312	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	20	CYS	0	-0.021	-0.019	26.324	0.006	0.006	0.000	0.000	0.000	0.000
18	A	21	GLU	-1	-0.858	-0.925	25.742	0.105	0.105	0.000	0.000	0.000	0.000
19	A	22	THR	0	-0.057	-0.042	26.469	0.003	0.003	0.000	0.000	0.000	0.000
20	A	23	PHE	0	-0.038	-0.031	23.352	0.004	0.004	0.000	0.000	0.000	0.000
21	A	24	GLU	-1	-0.823	-0.891	20.984	0.188	0.188	0.000	0.000	0.000	0.000
22	A	25	LYS	1	0.797	0.876	21.890	-0.096	-0.096	0.000	0.000	0.000	0.000
23	A	26	LEU	0	-0.054	-0.022	23.339	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	27	ALA	0	-0.023	-0.008	18.090	0.008	0.008	0.000	0.000	0.000	0.000
25	A	28	GLU	-1	-0.787	-0.867	18.215	0.139	0.139	0.000	0.000	0.000	0.000
26	A	29	PRO	0	0.043	0.021	18.425	0.013	0.013	0.000	0.000	0.000	0.000
27	A	30	THR	0	-0.066	-0.024	14.161	0.003	0.003	0.000	0.000	0.000	0.000
28	A	31	VAL	0	-0.048	-0.032	13.997	0.032	0.032	0.000	0.000	0.000	0.000
29	A	32	GLU	-1	-0.949	-0.966	14.186	0.153	0.153	0.000	0.000	0.000	0.000
30	A	33	SER	0	-0.077	-0.041	15.085	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	34	ILE	0	-0.094	-0.052	9.433	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	35	GLU	-1	-0.825	-0.914	5.878	0.435	0.435	0.000	0.000	0.000	0.000
33	A	36	ASN	0	-0.083	-0.043	5.242	0.106	0.106	0.000	0.000	0.000	0.000
34	A	37	ALA	0	-0.030	0.002	8.343	0.086	0.086	0.000	0.000	0.000	0.000
35	A	38	ALA	0	0.014	0.011	10.726	-0.065	-0.065	0.000	0.000	0.000	0.000
36	A	39	ILE	0	-0.018	0.002	13.461	0.004	0.004	0.000	0.000	0.000	0.000
37	A	40	ALA	0	-0.025	-0.014	16.166	0.023	0.023	0.000	0.000	0.000	0.000
38	A	41	TYR	0	-0.058	-0.052	18.133	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	42	MET	0	-0.076	-0.045	21.121	0.002	0.002	0.000	0.000	0.000	0.000
40	A	43	GLU	-1	-0.912	-0.966	22.988	0.075	0.075	0.000	0.000	0.000	0.000
41	A	44	LEU	0	-0.052	-0.029	25.559	0.006	0.006	0.000	0.000	0.000	0.000
42	A	45	ALA	0	0.010	0.025	24.929	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	46	GLU	-1	-0.784	-0.845	19.624	0.181	0.181	0.000	0.000	0.000	0.000
44	A	47	PRO	0	-0.013	0.001	17.133	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	48	SER	0	0.062	-0.001	19.273	0.005	0.005	0.000	0.000	0.000	0.000
46	A	49	LEU	0	0.060	0.007	14.608	0.029	0.029	0.000	0.000	0.000	0.000
47	A	50	ASP	-1	-0.734	-0.823	14.922	0.183	0.183	0.000	0.000	0.000	0.000
48	A	51	THR	0	-0.053	-0.035	14.976	0.011	0.011	0.000	0.000	0.000	0.000
49	A	52	ILE	0	-0.012	0.013	11.350	0.014	0.014	0.000	0.000	0.000	0.000
50	A	53	VAL	0	0.015	0.005	10.587	0.073	0.073	0.000	0.000	0.000	0.000
51	A	54	ASN	0	-0.044	-0.033	10.246	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	55	ARG	1	0.818	0.907	11.340	-0.276	-0.276	0.000	0.000	0.000	0.000
53	A	56	ALA	0	0.053	0.034	7.180	-0.063	-0.063	0.000	0.000	0.000	0.000
54	A	57	LYS	1	0.818	0.904	6.371	0.195	0.195	0.000	0.000	0.000	0.000
55	A	58	GLY	0	-0.038	-0.013	7.715	-0.206	-0.206	0.000	0.000	0.000	0.000
56	A	59	GLN	0	-0.067	-0.035	5.705	-0.041	-0.041	0.000	0.000	0.000	0.000
57	A	60	GLY	0	0.002	0.011	4.572	-0.281	-0.122	-0.001	-0.024	-0.133	0.000
58	A	61	VAL	0	-0.051	-0.021	2.422	-6.910	-3.448	1.861	-2.178	-3.145	-0.008
59	A	62	GLU	-1	-0.833	-0.917	3.386	-1.200	-1.029	0.025	0.182	-0.378	0.000
60	A	63	GLN	0	-0.056	-0.029	4.954	-0.417	-0.179	-0.001	-0.033	-0.204	0.000
61	A	64	PHE	0	0.031	0.007	6.004	0.550	0.550	0.000	0.000	0.000	0.000
62	A	65	THR	0	-0.036	-0.011	8.687	-0.208	-0.208	0.000	0.000	0.000	0.000
63	A	66	VAL	0	0.032	0.020	11.661	0.058	0.058	0.000	0.000	0.000	0.000
64	A	67	VAL	0	0.008	-0.010	14.884	-0.044	-0.044	0.000	0.000	0.000	0.000
65	A	68	PRO	0	-0.001	0.009	17.470	0.004	0.004	0.000	0.000	0.000	0.000
66	A	69	LEU	0	0.037	0.026	19.528	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	70	PHE	0	-0.011	-0.024	22.452	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	71	LEU	0	0.052	0.013	25.878	0.000	0.000	0.000	0.000	0.000	0.000
69	A	72	ALA	0	-0.003	-0.004	28.593	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	73	ALA	0	0.064	0.030	27.215	0.005	0.005	0.000	0.000	0.000	0.000
71	A	74	GLY	0	0.040	0.027	29.347	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	75	ARG	1	0.860	0.903	30.290	-0.043	-0.043	0.000	0.000	0.000	0.000
73	A	76	HIS	0	0.075	0.046	31.140	0.000	0.000	0.000	0.000	0.000	0.000
74	A	77	LEU	0	0.108	0.066	26.509	0.000	0.000	0.000	0.000	0.000	0.000
75	A	78	ARG	1	0.859	0.919	26.271	-0.051	-0.051	0.000	0.000	0.000	0.000
76	A	79	LYS	1	0.810	0.885	27.552	-0.058	-0.058	0.000	0.000	0.000	0.000
77	A	80	ASP	-1	-0.762	-0.878	26.040	0.059	0.059	0.000	0.000	0.000	0.000
78	A	81	VAL	0	0.024	0.028	21.287	0.004	0.004	0.000	0.000	0.000	0.000
79	A	82	PRO	0	-0.002	-0.013	21.363	0.008	0.008	0.000	0.000	0.000	0.000
80	A	83	ALA	0	0.028	0.021	21.351	0.001	0.001	0.000	0.000	0.000	0.000
81	A	84	MET	0	-0.020	-0.004	19.702	0.003	0.003	0.000	0.000	0.000	0.000
82	A	85	ILE	0	-0.035	-0.015	15.941	0.011	0.011	0.000	0.000	0.000	0.000
83	A	86	GLU	-1	-0.880	-0.939	17.286	0.043	0.043	0.000	0.000	0.000	0.000
84	A	87	ARG	1	0.732	0.824	18.794	-0.113	-0.113	0.000	0.000	0.000	0.000
85	A	88	LEU	0	-0.035	-0.016	15.042	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	89	GLU	-1	-0.816	-0.912	13.627	0.083	0.083	0.000	0.000	0.000	0.000
87	A	90	ALA	0	-0.009	-0.006	14.834	-0.024	-0.024	0.000	0.000	0.000	0.000
88	A	91	GLU	-1	-0.904	-0.940	17.307	0.064	0.064	0.000	0.000	0.000	0.000
89	A	92	HIS	1	0.813	0.891	12.738	-0.113	-0.113	0.000	0.000	0.000	0.000
90	A	93	GLY	0	0.031	0.032	12.348	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	94	VAL	0	-0.057	-0.019	8.801	-0.035	-0.035	0.000	0.000	0.000	0.000
92	A	95	THR	0	-0.001	0.004	9.446	-0.037	-0.037	0.000	0.000	0.000	0.000
93	A	96	ILE	0	-0.043	-0.037	9.855	0.086	0.086	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.935	0.970	11.832	-0.220	-0.220	0.000	0.000	0.000	0.000
95	A	98	LEU	0	0.008	0.008	13.809	0.037	0.037	0.000	0.000	0.000	0.000
96	A	99	ALA	0	-0.047	-0.018	16.251	-0.020	-0.020	0.000	0.000	0.000	0.000
97	A	100	GLU	-1	-0.763	-0.887	18.109	0.075	0.075	0.000	0.000	0.000	0.000
98	A	101	PRO	0	-0.050	-0.010	21.031	0.011	0.011	0.000	0.000	0.000	0.000
99	A	102	ILE	0	0.061	0.017	20.994	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	103	GLY	0	-0.024	-0.003	23.471	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	104	LYS	1	0.748	0.863	25.190	-0.081	-0.081	0.000	0.000	0.000	0.000
102	A	105	ASN	0	-0.005	0.010	21.499	-0.012	-0.012	0.000	0.000	0.000	0.000
103	A	106	PRO	0	0.057	0.018	25.204	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	107	ARG	1	0.944	0.962	22.815	-0.099	-0.099	0.000	0.000	0.000	0.000
105	A	108	LEU	0	0.051	0.032	24.250	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	109	GLY	0	0.030	0.025	27.909	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	110	LEU	0	-0.070	-0.042	28.666	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	111	ALA	0	0.048	0.026	28.198	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	112	ILE	0	0.016	0.010	30.351	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	113	ARG	1	0.819	0.881	33.011	-0.056	-0.056	0.000	0.000	0.000	0.000
111	A	114	ASP	-1	-0.772	-0.857	32.803	0.051	0.051	0.000	0.000	0.000	0.000
112	A	115	VAL	0	0.071	0.036	32.104	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	116	VAL	0	-0.003	-0.006	34.974	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	117	LYS	1	0.815	0.897	36.272	-0.049	-0.049	0.000	0.000	0.000	0.000
115	A	118	GLU	-1	-0.845	-0.903	35.136	0.055	0.055	0.000	0.000	0.000	0.000
116	A	119	GLU	-1	-0.857	-0.926	38.255	0.047	0.047	0.000	0.000	0.000	0.000
117	A	120	LEU	0	-0.092	-0.032	40.749	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	121	GLU	-1	-0.960	-0.971	41.782	0.034	0.034	0.000	0.000	0.000	0.000
119	A	122	ARG	1	0.738	0.850	36.114	-0.052	-0.052	0.000	0.000	0.000	0.000
120	A	123	SER	0	-0.103	-0.046	43.789	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:PRO)