FMO DATABASE

FMODB ID: 8585Y

Calculation Name: 3LYX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3LYX

Chain ID: A

ChEMBL ID:

UniProt ID: Q486I1

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:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	118
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-953013.212434
FMO2-HF: Nuclear repulsion	905974.412738
FMO2-HF: Total energy	-47038.799696
FMO2-MP2: Total energy	-47174.987593

3D Structure Molmil

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:ASP)

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

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.
-87.515	-81.674	1.924	-3.092	-4.673	0.022

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.870 / q_NPA : -0.950

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	LEU	0	-0.007	-0.007	3.057	-10.917	-8.263	0.079	-1.203	-1.530	0.008
4	A	7	LYS	1	0.981	0.991	2.742	-49.902	-48.061	1.825	-1.335	-2.331	0.012
5	A	8	GLN	0	0.040	0.002	3.692	-17.481	-16.135	0.020	-0.554	-0.812	0.002
6	A	9	ARG	1	0.910	0.957	5.884	-36.200	-36.200	0.000	0.000	0.000	0.000
7	A	10	ALA	0	0.039	0.019	7.568	-3.131	-3.131	0.000	0.000	0.000	0.000
8	A	11	LYS	1	0.937	0.983	8.161	-28.718	-28.718	0.000	0.000	0.000	0.000
9	A	12	ALA	0	0.000	-0.004	9.932	-2.026	-2.026	0.000	0.000	0.000	0.000
10	A	13	PHE	0	0.062	0.039	12.561	-1.504	-1.504	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.841	-0.925	14.572	15.906	15.906	0.000	0.000	0.000	0.000
12	A	15	TYR	0	-0.109	-0.070	12.978	0.120	0.120	0.000	0.000	0.000	0.000
13	A	16	VAL	0	-0.061	-0.016	16.263	-0.617	-0.617	0.000	0.000	0.000	0.000
14	A	17	PHE	0	-0.006	-0.007	18.707	-0.433	-0.433	0.000	0.000	0.000	0.000
15	A	18	ASP	-1	-0.832	-0.914	21.069	13.157	13.157	0.000	0.000	0.000	0.000
16	A	19	ALA	0	-0.001	0.008	21.501	0.542	0.542	0.000	0.000	0.000	0.000
17	A	20	ILE	0	-0.060	-0.032	17.883	-0.121	-0.121	0.000	0.000	0.000	0.000
18	A	21	VAL	0	0.014	0.003	21.003	-0.044	-0.044	0.000	0.000	0.000	0.000
19	A	22	VAL	0	-0.003	0.007	17.553	0.031	0.031	0.000	0.000	0.000	0.000
20	A	23	THR	0	-0.011	-0.005	20.975	-0.474	-0.474	0.000	0.000	0.000	0.000
21	A	24	ASP	-1	-0.779	-0.895	22.598	11.434	11.434	0.000	0.000	0.000	0.000
22	A	25	LEU	0	-0.006	-0.006	24.246	-0.235	-0.235	0.000	0.000	0.000	0.000
23	A	26	GLN	0	-0.080	-0.027	26.940	-0.195	-0.195	0.000	0.000	0.000	0.000
24	A	27	GLY	0	0.017	0.021	27.858	-0.316	-0.316	0.000	0.000	0.000	0.000
25	A	28	PHE	0	-0.043	-0.033	27.489	-0.188	-0.188	0.000	0.000	0.000	0.000
26	A	29	ILE	0	-0.020	-0.006	23.856	0.506	0.506	0.000	0.000	0.000	0.000
27	A	30	ILE	0	-0.020	-0.020	19.594	-0.109	-0.109	0.000	0.000	0.000	0.000
28	A	31	ASP	-1	-0.887	-0.978	16.079	17.371	17.371	0.000	0.000	0.000	0.000
29	A	32	TRP	0	-0.038	-0.026	19.452	-0.479	-0.479	0.000	0.000	0.000	0.000
30	A	33	ASN	0	0.010	0.029	18.288	-0.317	-0.317	0.000	0.000	0.000	0.000
31	A	34	LYS	1	0.974	0.965	18.737	-16.045	-16.045	0.000	0.000	0.000	0.000
32	A	35	GLY	0	0.024	0.030	20.938	-0.597	-0.597	0.000	0.000	0.000	0.000
33	A	36	SER	0	0.015	-0.028	22.695	-0.771	-0.771	0.000	0.000	0.000	0.000
34	A	37	GLU	-1	-0.954	-0.963	24.121	11.706	11.706	0.000	0.000	0.000	0.000
35	A	38	THR	0	-0.084	-0.034	25.172	-0.526	-0.526	0.000	0.000	0.000	0.000
36	A	39	LEU	0	-0.038	-0.012	27.073	-0.423	-0.423	0.000	0.000	0.000	0.000
37	A	40	TYR	0	0.030	-0.009	26.587	-0.313	-0.313	0.000	0.000	0.000	0.000
38	A	41	GLY	0	-0.015	0.002	29.391	-0.402	-0.402	0.000	0.000	0.000	0.000
39	A	42	TYR	0	-0.015	-0.012	28.453	-0.091	-0.091	0.000	0.000	0.000	0.000
40	A	43	SER	0	0.072	0.041	26.444	0.264	0.264	0.000	0.000	0.000	0.000
41	A	44	LYS	1	0.990	0.989	18.546	-15.097	-15.097	0.000	0.000	0.000	0.000
42	A	45	GLU	-1	-0.954	-0.998	23.141	12.421	12.421	0.000	0.000	0.000	0.000
43	A	46	GLN	0	-0.039	-0.008	25.903	-0.334	-0.334	0.000	0.000	0.000	0.000
44	A	47	ALA	0	0.028	0.019	25.556	-0.273	-0.273	0.000	0.000	0.000	0.000
45	A	48	ILE	0	-0.025	0.002	21.514	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	49	GLY	0	-0.026	-0.009	25.370	-0.302	-0.302	0.000	0.000	0.000	0.000
47	A	50	GLN	0	-0.039	-0.011	27.728	-0.631	-0.631	0.000	0.000	0.000	0.000
48	A	51	PRO	0	0.010	0.020	28.921	0.326	0.326	0.000	0.000	0.000	0.000
49	A	52	VAL	0	0.112	0.031	27.600	-0.069	-0.069	0.000	0.000	0.000	0.000
50	A	53	ASN	0	-0.001	0.000	29.743	0.084	0.084	0.000	0.000	0.000	0.000
51	A	54	MET	0	-0.066	-0.015	30.186	-0.304	-0.304	0.000	0.000	0.000	0.000
52	A	55	LEU	0	-0.043	-0.028	28.112	-0.106	-0.106	0.000	0.000	0.000	0.000
53	A	56	HIS	0	0.028	0.020	32.076	-0.210	-0.210	0.000	0.000	0.000	0.000
54	A	57	VAL	0	0.021	0.028	35.593	-0.143	-0.143	0.000	0.000	0.000	0.000
55	A	58	PRO	0	0.008	-0.023	39.185	-0.021	-0.021	0.000	0.000	0.000	0.000
56	A	59	GLY	0	-0.033	-0.017	40.651	-0.032	-0.032	0.000	0.000	0.000	0.000
57	A	60	ASP	-1	-0.787	-0.891	38.608	7.695	7.695	0.000	0.000	0.000	0.000
58	A	61	THR	0	-0.015	-0.012	36.355	0.034	0.034	0.000	0.000	0.000	0.000
59	A	62	GLU	-1	-0.935	-0.950	37.499	7.276	7.276	0.000	0.000	0.000	0.000
60	A	63	HIS	0	0.052	0.002	39.076	0.176	0.176	0.000	0.000	0.000	0.000
61	A	64	ILE	0	0.020	0.025	33.807	0.134	0.134	0.000	0.000	0.000	0.000
62	A	65	THR	0	-0.023	-0.026	33.631	0.317	0.317	0.000	0.000	0.000	0.000
63	A	66	SER	0	-0.024	-0.009	34.364	0.167	0.167	0.000	0.000	0.000	0.000
64	A	67	GLU	-1	-0.881	-0.931	35.428	8.626	8.626	0.000	0.000	0.000	0.000
65	A	68	VAL	0	-0.015	-0.019	29.682	0.221	0.221	0.000	0.000	0.000	0.000
66	A	69	ILE	0	0.004	-0.006	31.098	0.261	0.261	0.000	0.000	0.000	0.000
67	A	70	SER	0	-0.006	0.014	32.148	0.122	0.122	0.000	0.000	0.000	0.000
68	A	71	ALA	0	0.050	0.022	31.176	0.087	0.087	0.000	0.000	0.000	0.000
69	A	72	VAL	0	-0.049	-0.026	26.522	0.275	0.275	0.000	0.000	0.000	0.000
70	A	73	GLU	-1	-0.943	-0.980	28.257	9.605	9.605	0.000	0.000	0.000	0.000
71	A	74	ASN	0	-0.109	-0.048	30.554	-0.143	-0.143	0.000	0.000	0.000	0.000
72	A	75	GLN	0	-0.056	-0.037	30.734	0.024	0.024	0.000	0.000	0.000	0.000
73	A	76	GLY	0	-0.013	0.016	26.773	0.295	0.295	0.000	0.000	0.000	0.000
74	A	77	LYS	1	0.885	0.922	24.700	-11.500	-11.500	0.000	0.000	0.000	0.000
75	A	78	TRP	0	-0.015	0.005	27.173	-0.159	-0.159	0.000	0.000	0.000	0.000
76	A	79	THR	0	-0.068	-0.056	28.134	0.483	0.483	0.000	0.000	0.000	0.000
77	A	80	GLY	0	0.051	0.034	30.451	-0.318	-0.318	0.000	0.000	0.000	0.000
78	A	81	GLU	-1	-0.949	-0.957	32.492	8.966	8.966	0.000	0.000	0.000	0.000
79	A	82	ILE	0	0.005	0.004	31.870	-0.277	-0.277	0.000	0.000	0.000	0.000
80	A	83	ARG	1	0.824	0.900	35.275	-7.463	-7.463	0.000	0.000	0.000	0.000
81	A	84	MET	0	-0.048	-0.013	31.989	0.248	0.248	0.000	0.000	0.000	0.000
82	A	85	LEU	0	-0.010	-0.008	34.760	-0.301	-0.301	0.000	0.000	0.000	0.000
83	A	86	HIS	0	-0.012	0.005	32.443	0.032	0.032	0.000	0.000	0.000	0.000
84	A	87	LYS	1	0.907	0.962	32.473	-9.454	-9.454	0.000	0.000	0.000	0.000
85	A	88	ASP	-1	-0.907	-0.948	34.747	8.145	8.145	0.000	0.000	0.000	0.000
86	A	89	GLY	0	0.037	0.025	37.809	-0.248	-0.248	0.000	0.000	0.000	0.000
87	A	90	HIS	1	0.762	0.874	35.861	-8.660	-8.660	0.000	0.000	0.000	0.000
88	A	91	ILE	0	0.027	0.001	38.205	0.156	0.156	0.000	0.000	0.000	0.000
89	A	92	GLY	0	-0.027	-0.011	36.586	-0.080	-0.080	0.000	0.000	0.000	0.000
90	A	93	TRP	0	-0.012	-0.002	36.208	-0.080	-0.080	0.000	0.000	0.000	0.000
91	A	94	ILE	0	0.002	-0.009	29.889	0.181	0.181	0.000	0.000	0.000	0.000
92	A	95	GLU	-1	-0.865	-0.913	29.744	10.394	10.394	0.000	0.000	0.000	0.000
93	A	96	SER	0	-0.050	-0.046	28.179	0.399	0.399	0.000	0.000	0.000	0.000
94	A	97	MET	0	0.013	-0.002	24.042	0.035	0.035	0.000	0.000	0.000	0.000
95	A	98	CYS	0	-0.040	-0.004	24.869	0.389	0.389	0.000	0.000	0.000	0.000
96	A	99	VAL	0	-0.001	-0.009	20.698	-0.239	-0.239	0.000	0.000	0.000	0.000
97	A	100	PRO	0	0.033	0.033	22.179	0.276	0.276	0.000	0.000	0.000	0.000
98	A	101	ILE	0	-0.017	-0.008	17.170	0.725	0.725	0.000	0.000	0.000	0.000
99	A	102	TYR	0	-0.015	-0.028	18.827	-0.523	-0.523	0.000	0.000	0.000	0.000
100	A	103	GLY	0	0.017	0.015	18.222	0.727	0.727	0.000	0.000	0.000	0.000
101	A	104	GLU	-1	-0.948	-0.988	18.794	13.858	13.858	0.000	0.000	0.000	0.000
102	A	105	ASN	0	-0.069	-0.049	21.150	-0.381	-0.381	0.000	0.000	0.000	0.000
103	A	106	TYR	0	-0.012	-0.015	21.331	-0.143	-0.143	0.000	0.000	0.000	0.000
104	A	107	GLN	0	0.033	0.046	23.198	-0.432	-0.432	0.000	0.000	0.000	0.000
105	A	108	MET	0	0.015	0.012	22.720	0.569	0.569	0.000	0.000	0.000	0.000
106	A	109	VAL	0	0.000	0.000	20.649	-0.362	-0.362	0.000	0.000	0.000	0.000
107	A	110	GLY	0	0.036	0.009	22.212	-0.091	-0.091	0.000	0.000	0.000	0.000
108	A	111	ALA	0	-0.028	0.003	22.352	0.080	0.080	0.000	0.000	0.000	0.000
109	A	112	LEU	0	-0.003	0.001	17.441	0.347	0.347	0.000	0.000	0.000	0.000
110	A	113	GLY	0	0.041	0.022	21.107	-0.389	-0.389	0.000	0.000	0.000	0.000
111	A	114	ILE	0	-0.048	-0.024	20.699	0.529	0.529	0.000	0.000	0.000	0.000
112	A	115	ASN	0	-0.011	0.001	23.370	-0.908	-0.908	0.000	0.000	0.000	0.000
113	A	116	ARG	1	0.843	0.914	24.657	-11.835	-11.835	0.000	0.000	0.000	0.000
114	A	117	ASP	-1	-0.769	-0.857	28.142	9.106	9.106	0.000	0.000	0.000	0.000
115	A	118	ILE	0	-0.061	-0.035	31.414	0.118	0.118	0.000	0.000	0.000	0.000
116	A	119	THR	0	-0.002	-0.017	34.334	-0.339	-0.339	0.000	0.000	0.000	0.000
117	A	120	LYS	1	0.886	0.951	36.728	-8.175	-8.175	0.000	0.000	0.000	0.000
118	A	121	ARG	1	0.940	0.980	31.796	-9.853	-9.853	0.000	0.000	0.000	0.000

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