FMO DATABASE

FMODB ID: 82M1Y

Calculation Name: 3LGO-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3LGO

Chain ID: A

ChEMBL ID:
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UniProt ID: P38247

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	OptH
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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1213353.470852
FMO2-HF: Nuclear repulsion	1155669.454765
FMO2-HF: Total energy	-57684.016087
FMO2-MP2: Total energy	-57849.747033

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:LEU)

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

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.
-8.948	-5.016	0.063	-1.664	-2.33	0.007

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / 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

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	6	SER	0	0.019	0.013	3.164	-5.783	-2.450	0.050	-1.510	-1.872	0.007
4	A	7	LYS	1	1.034	0.996	4.816	-1.106	-0.987	-0.001	-0.022	-0.096	0.000
5	A	8	ASN	0	-0.015	-0.008	7.305	-0.575	-0.575	0.000	0.000	0.000	0.000
6	A	9	VAL	0	0.032	0.012	3.587	-0.533	-0.053	0.014	-0.132	-0.362	0.000
7	A	10	LYS	1	0.931	0.992	6.487	-0.663	-0.663	0.000	0.000	0.000	0.000
8	A	11	GLY	0	0.066	0.020	8.762	-0.143	-0.143	0.000	0.000	0.000	0.000
9	A	12	PHE	0	-0.029	0.002	9.278	-0.089	-0.089	0.000	0.000	0.000	0.000
10	A	13	LEU	0	0.003	0.008	7.683	-0.181	-0.181	0.000	0.000	0.000	0.000
11	A	14	GLU	-1	-0.879	-0.949	11.651	0.369	0.369	0.000	0.000	0.000	0.000
12	A	15	ASN	0	-0.084	-0.034	14.307	-0.146	-0.146	0.000	0.000	0.000	0.000
13	A	16	THR	0	-0.044	-0.057	13.723	-0.025	-0.025	0.000	0.000	0.000	0.000
14	A	17	LEU	0	-0.044	-0.011	15.777	-0.047	-0.047	0.000	0.000	0.000	0.000
15	A	18	LYS	1	0.891	0.955	18.020	-0.413	-0.413	0.000	0.000	0.000	0.000
16	A	19	PRO	0	0.041	0.029	21.064	0.003	0.003	0.000	0.000	0.000	0.000
17	A	20	TYR	0	-0.006	0.012	23.797	0.025	0.025	0.000	0.000	0.000	0.000
18	A	21	ASP	-1	-0.927	-0.963	25.486	0.196	0.196	0.000	0.000	0.000	0.000
19	A	22	LEU	0	-0.044	-0.023	28.524	0.003	0.003	0.000	0.000	0.000	0.000
20	A	23	HIS	0	0.003	-0.013	28.962	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	24	SER	0	-0.047	-0.023	33.947	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	25	VAL	0	0.006	0.013	34.534	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	26	ASP	-1	-0.873	-0.919	37.675	0.084	0.084	0.000	0.000	0.000	0.000
24	A	27	PHE	0	-0.044	-0.049	34.403	0.002	0.002	0.000	0.000	0.000	0.000
25	A	28	LYS	1	0.886	0.954	40.497	-0.079	-0.079	0.000	0.000	0.000	0.000
26	A	29	THR	0	0.034	0.022	41.677	0.002	0.002	0.000	0.000	0.000	0.000
27	A	30	SER	0	0.004	0.008	43.092	0.000	0.000	0.000	0.000	0.000	0.000
28	A	31	SER	0	-0.010	-0.019	44.608	0.000	0.000	0.000	0.000	0.000	0.000
29	A	32	LEU	0	-0.044	-0.023	48.101	0.000	0.000	0.000	0.000	0.000	0.000
30	A	33	GLN	0	0.020	0.030	48.274	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	34	SER	0	0.015	-0.012	51.534	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	35	SER	0	-0.036	-0.009	54.384	0.001	0.001	0.000	0.000	0.000	0.000
33	A	36	MET	0	-0.039	-0.039	56.909	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	37	ILE	0	0.089	0.055	59.876	0.001	0.001	0.000	0.000	0.000	0.000
35	A	38	ILE	0	-0.017	0.017	61.316	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	39	THR	0	0.035	0.020	64.435	0.000	0.000	0.000	0.000	0.000	0.000
37	A	40	ALA	0	0.120	0.055	65.032	0.000	0.000	0.000	0.000	0.000	0.000
38	A	41	THR	0	-0.037	-0.025	66.089	0.000	0.000	0.000	0.000	0.000	0.000
39	A	42	ASN	0	0.001	-0.031	67.555	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	43	GLY	0	0.075	0.027	64.407	0.000	0.000	0.000	0.000	0.000	0.000
41	A	44	GLY	0	-0.086	-0.053	65.085	0.000	0.000	0.000	0.000	0.000	0.000
42	A	45	ILE	0	-0.030	-0.028	61.787	0.001	0.001	0.000	0.000	0.000	0.000
43	A	46	LEU	0	-0.012	0.017	65.316	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	47	SER	0	-0.019	-0.018	64.841	0.000	0.000	0.000	0.000	0.000	0.000
45	A	48	TYR	0	-0.009	-0.014	60.286	0.000	0.000	0.000	0.000	0.000	0.000
46	A	49	ALA	0	0.000	0.016	58.507	0.000	0.000	0.000	0.000	0.000	0.000
47	A	50	THR	0	-0.016	-0.019	55.552	0.000	0.000	0.000	0.000	0.000	0.000
48	A	51	SER	0	0.030	0.004	51.727	0.001	0.001	0.000	0.000	0.000	0.000
49	A	52	ASN	0	-0.038	0.005	52.106	0.001	0.001	0.000	0.000	0.000	0.000
50	A	65	SER	0	0.046	0.015	57.272	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	66	VAL	0	0.075	0.016	58.690	0.000	0.000	0.000	0.000	0.000	0.000
52	A	67	ASN	0	-0.048	-0.026	60.464	0.000	0.000	0.000	0.000	0.000	0.000
53	A	68	ASN	0	0.074	0.018	53.802	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	69	LEU	0	-0.001	0.002	56.153	0.000	0.000	0.000	0.000	0.000	0.000
55	A	70	LYS	1	0.965	0.976	58.261	-0.018	-0.018	0.000	0.000	0.000	0.000
56	A	71	MET	0	-0.033	0.000	57.070	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	72	MET	0	0.058	0.037	54.122	0.000	0.000	0.000	0.000	0.000	0.000
58	A	73	SER	0	-0.018	-0.011	57.223	0.001	0.001	0.000	0.000	0.000	0.000
59	A	74	LEU	0	-0.023	-0.002	60.048	0.000	0.000	0.000	0.000	0.000	0.000
60	A	75	LEU	0	0.047	0.033	54.267	0.000	0.000	0.000	0.000	0.000	0.000
61	A	76	ILE	0	-0.010	-0.025	54.512	0.000	0.000	0.000	0.000	0.000	0.000
62	A	77	LYS	1	0.856	0.966	57.053	-0.019	-0.019	0.000	0.000	0.000	0.000
63	A	78	ASP	-1	-0.945	-0.968	59.466	0.017	0.017	0.000	0.000	0.000	0.000
64	A	79	LYS	1	0.885	0.933	52.398	-0.022	-0.022	0.000	0.000	0.000	0.000
65	A	80	TRP	0	0.015	0.011	57.150	0.000	0.000	0.000	0.000	0.000	0.000
66	A	81	SER	0	-0.035	-0.019	58.863	0.000	0.000	0.000	0.000	0.000	0.000
67	A	82	GLU	-1	-0.939	-0.967	58.055	0.017	0.017	0.000	0.000	0.000	0.000
68	A	83	ASP	-1	-0.823	-0.925	55.448	0.024	0.024	0.000	0.000	0.000	0.000
69	A	84	GLU	-1	-0.971	-0.971	58.315	0.025	0.025	0.000	0.000	0.000	0.000
70	A	85	ASN	0	-0.122	-0.075	61.115	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	86	ASP	-1	-0.966	-0.987	58.930	0.016	0.016	0.000	0.000	0.000	0.000
72	A	87	THR	0	-0.048	0.071	56.635	0.000	0.000	0.000	0.000	0.000	0.000
73	A	88	GLU	-1	-0.807	-0.908	52.454	0.021	0.021	0.000	0.000	0.000	0.000
74	A	89	GLU	-1	-0.909	-0.957	49.397	0.033	0.033	0.000	0.000	0.000	0.000
75	A	90	GLN	0	0.053	-0.078	50.056	0.000	0.000	0.000	0.000	0.000	0.000
76	A	91	HIS	0	0.016	0.042	52.615	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	92	SER	0	-0.146	-0.080	52.721	0.000	0.000	0.000	0.000	0.000	0.000
78	A	93	ASN	0	-0.090	-0.035	47.822	0.001	0.001	0.000	0.000	0.000	0.000
79	A	94	SER	0	0.000	-0.034	48.982	0.002	0.002	0.000	0.000	0.000	0.000
80	A	95	CYS	0	-0.056	0.024	50.239	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	96	TYR	0	-0.032	-0.022	47.198	0.002	0.002	0.000	0.000	0.000	0.000
82	A	97	PRO	0	-0.053	-0.030	54.105	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	98	VAL	0	0.016	0.008	56.595	0.002	0.002	0.000	0.000	0.000	0.000
84	A	99	GLU	-1	-0.888	-0.952	59.226	0.030	0.030	0.000	0.000	0.000	0.000
85	A	100	ILE	0	-0.002	0.017	59.872	0.001	0.001	0.000	0.000	0.000	0.000
86	A	101	ASP	-1	-0.769	-0.890	63.839	0.031	0.031	0.000	0.000	0.000	0.000
87	A	102	SER	0	-0.084	-0.069	66.872	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	103	PHE	0	0.005	0.043	67.108	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	104	LYS	1	0.819	0.890	62.071	-0.029	-0.029	0.000	0.000	0.000	0.000
90	A	105	THR	0	-0.016	0.003	60.444	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	106	LYS	1	0.930	0.976	58.442	-0.027	-0.027	0.000	0.000	0.000	0.000
92	A	107	ILE	0	0.021	0.016	53.400	0.000	0.000	0.000	0.000	0.000	0.000
93	A	108	TYR	0	0.010	-0.024	53.488	0.001	0.001	0.000	0.000	0.000	0.000
94	A	109	THR	0	-0.040	-0.027	48.442	0.001	0.001	0.000	0.000	0.000	0.000
95	A	110	TYR	0	0.080	0.015	49.591	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	111	GLU	-1	-0.946	-0.935	43.493	0.039	0.039	0.000	0.000	0.000	0.000
97	A	112	MET	0	-0.057	-0.011	47.721	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	113	GLU	-1	-0.983	-0.999	47.564	0.023	0.023	0.000	0.000	0.000	0.000
99	A	114	ASP	-1	-0.915	-0.964	42.954	0.031	0.031	0.000	0.000	0.000	0.000
100	A	115	LEU	0	-0.009	-0.003	44.514	0.003	0.003	0.000	0.000	0.000	0.000
101	A	116	HIS	1	0.733	0.898	41.734	-0.048	-0.048	0.000	0.000	0.000	0.000
102	A	117	THR	0	-0.027	-0.034	47.247	0.000	0.000	0.000	0.000	0.000	0.000
103	A	118	CYS	0	-0.043	-0.031	50.954	0.001	0.001	0.000	0.000	0.000	0.000
104	A	119	VAL	0	0.051	0.040	53.334	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	120	ALA	0	0.056	0.027	56.863	0.001	0.001	0.000	0.000	0.000	0.000
106	A	121	GLN	0	0.030	0.011	59.141	0.000	0.000	0.000	0.000	0.000	0.000
107	A	122	ILE	0	-0.012	-0.003	62.942	0.001	0.001	0.000	0.000	0.000	0.000
108	A	123	PRO	0	0.002	0.007	65.524	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	124	ASN	0	-0.001	-0.011	68.306	0.000	0.000	0.000	0.000	0.000	0.000
110	A	125	SER	0	0.007	-0.008	69.314	0.000	0.000	0.000	0.000	0.000	0.000
111	A	126	ASP	-1	-0.880	-0.917	68.448	0.020	0.020	0.000	0.000	0.000	0.000
112	A	127	LEU	0	-0.082	-0.045	66.222	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	128	LEU	0	-0.021	0.011	61.196	0.001	0.001	0.000	0.000	0.000	0.000
114	A	129	LEU	0	-0.016	-0.009	58.471	0.000	0.000	0.000	0.000	0.000	0.000
115	A	130	LEU	0	-0.015	-0.008	54.976	0.000	0.000	0.000	0.000	0.000	0.000
116	A	131	PHE	0	-0.081	-0.017	52.377	0.001	0.001	0.000	0.000	0.000	0.000
117	A	132	ILE	0	0.075	0.025	50.497	0.000	0.000	0.000	0.000	0.000	0.000
118	A	133	ALA	0	-0.034	-0.033	47.073	0.001	0.001	0.000	0.000	0.000	0.000
119	A	134	GLU	-1	-0.777	-0.882	43.083	0.042	0.042	0.000	0.000	0.000	0.000
120	A	135	GLY	0	0.087	0.023	42.165	0.001	0.001	0.000	0.000	0.000	0.000
121	A	136	SER	0	-0.032	-0.030	39.401	0.002	0.002	0.000	0.000	0.000	0.000
122	A	137	PHE	0	-0.032	-0.012	40.519	0.005	0.005	0.000	0.000	0.000	0.000
123	A	138	PRO	0	0.017	-0.009	40.356	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	139	TYR	0	0.145	0.066	42.529	0.000	0.000	0.000	0.000	0.000	0.000
125	A	140	GLY	0	0.007	0.022	43.986	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	141	LEU	0	0.012	-0.010	42.456	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	142	LEU	0	-0.001	0.007	46.468	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	143	VAL	0	0.041	0.023	48.691	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	144	ILE	0	-0.013	-0.006	48.816	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	145	LYS	1	0.892	0.939	50.002	-0.048	-0.048	0.000	0.000	0.000	0.000
131	A	146	ILE	0	0.017	-0.012	52.033	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	147	GLU	-1	-0.928	-0.951	54.196	0.042	0.042	0.000	0.000	0.000	0.000
133	A	148	ARG	1	0.961	0.968	51.048	-0.054	-0.054	0.000	0.000	0.000	0.000
134	A	149	ALA	0	-0.028	-0.001	56.499	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	150	MET	0	0.024	0.012	58.254	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	151	ARG	1	0.831	0.921	60.122	-0.036	-0.036	0.000	0.000	0.000	0.000
137	A	152	GLU	-1	-0.867	-0.946	60.531	0.035	0.035	0.000	0.000	0.000	0.000
138	A	153	LEU	0	-0.054	-0.019	62.232	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	154	THR	0	-0.062	-0.047	63.991	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	155	ASP	-1	-0.867	-0.931	64.095	0.034	0.034	0.000	0.000	0.000	0.000
141	A	156	LEU	0	-0.150	-0.056	65.181	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	157	PHE	0	-0.126	-0.063	66.858	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	158	GLY	0	0.007	0.018	70.501	0.000	0.000	0.000	0.000	0.000	0.000

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