FMO DATABASE

FMODB ID: J3G89

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1209562.761278
FMO2-HF: Nuclear repulsion	1151875.916079
FMO2-HF: Total energy	-57686.845199
FMO2-MP2: Total energy	-57852.180411

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.
-7.726	-4.31	0.098	-1.447	-2.067	0.008

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 : 0.025 / 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

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	0.042	0.028	3.243	-4.029	-1.495	0.050	-1.150	-1.435	0.006
4	A	7	LYS	1	1.004	0.983	4.812	-0.746	-0.648	-0.001	-0.014	-0.082	0.000
5	A	8	ASN	0	0.014	0.013	7.300	-0.305	-0.305	0.000	0.000	0.000	0.000
6	A	9	VAL	0	0.024	0.015	3.498	-1.119	-0.335	0.049	-0.283	-0.550	0.002
7	A	10	LYS	1	0.853	0.929	6.359	-1.002	-1.002	0.000	0.000	0.000	0.000
8	A	11	GLY	0	0.077	0.029	8.318	-0.213	-0.213	0.000	0.000	0.000	0.000
9	A	12	PHE	0	-0.025	-0.006	9.178	-0.149	-0.149	0.000	0.000	0.000	0.000
10	A	13	LEU	0	0.009	0.011	6.987	-0.202	-0.202	0.000	0.000	0.000	0.000
11	A	14	GLU	-1	-0.828	-0.915	11.191	0.353	0.353	0.000	0.000	0.000	0.000
12	A	15	ASN	0	-0.030	-0.011	13.854	-0.155	-0.155	0.000	0.000	0.000	0.000
13	A	16	THR	0	-0.051	-0.046	13.428	-0.060	-0.060	0.000	0.000	0.000	0.000
14	A	17	LEU	0	-0.036	-0.007	15.123	-0.051	-0.051	0.000	0.000	0.000	0.000
15	A	18	LYS	1	0.860	0.940	17.747	-0.474	-0.474	0.000	0.000	0.000	0.000
16	A	19	PRO	0	0.034	0.012	20.856	0.003	0.003	0.000	0.000	0.000	0.000
17	A	20	TYR	0	-0.016	0.004	23.514	0.027	0.027	0.000	0.000	0.000	0.000
18	A	21	ASP	-1	-0.913	-0.950	25.256	0.207	0.207	0.000	0.000	0.000	0.000
19	A	22	LEU	0	-0.043	-0.035	28.282	0.002	0.002	0.000	0.000	0.000	0.000
20	A	23	HIS	0	0.006	-0.006	28.572	-0.023	-0.023	0.000	0.000	0.000	0.000
21	A	24	SER	0	-0.030	-0.021	33.475	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	25	VAL	0	-0.011	0.013	33.766	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	26	ASP	-1	-0.850	-0.897	37.024	0.083	0.083	0.000	0.000	0.000	0.000
24	A	27	PHE	0	0.014	-0.004	34.098	0.003	0.003	0.000	0.000	0.000	0.000
25	A	28	LYS	1	0.815	0.891	40.314	-0.085	-0.085	0.000	0.000	0.000	0.000
26	A	29	THR	0	-0.011	0.000	41.277	0.003	0.003	0.000	0.000	0.000	0.000
27	A	30	SER	0	0.027	0.018	43.045	0.000	0.000	0.000	0.000	0.000	0.000
28	A	31	SER	0	0.003	0.001	44.454	0.000	0.000	0.000	0.000	0.000	0.000
29	A	32	LEU	0	-0.024	-0.006	47.602	0.001	0.001	0.000	0.000	0.000	0.000
30	A	33	GLN	0	-0.003	-0.004	46.708	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	34	SER	0	-0.053	-0.053	50.910	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	35	SER	0	-0.007	0.004	53.917	0.002	0.002	0.000	0.000	0.000	0.000
33	A	36	MET	0	-0.058	-0.029	56.569	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	37	ILE	0	0.045	0.032	59.703	0.001	0.001	0.000	0.000	0.000	0.000
35	A	38	ILE	0	-0.003	0.001	60.499	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	39	THR	0	0.015	0.005	64.213	0.000	0.000	0.000	0.000	0.000	0.000
37	A	40	ALA	0	0.098	0.046	64.716	0.000	0.000	0.000	0.000	0.000	0.000
38	A	41	THR	0	-0.028	-0.010	65.785	0.000	0.000	0.000	0.000	0.000	0.000
39	A	42	ASN	0	-0.042	-0.034	67.287	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	43	GLY	0	0.063	0.046	63.850	0.000	0.000	0.000	0.000	0.000	0.000
41	A	44	GLY	0	-0.061	-0.030	64.259	0.000	0.000	0.000	0.000	0.000	0.000
42	A	45	ILE	0	-0.034	-0.028	61.588	0.000	0.000	0.000	0.000	0.000	0.000
43	A	46	LEU	0	-0.002	0.017	65.113	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	47	SER	0	-0.024	-0.020	64.679	0.000	0.000	0.000	0.000	0.000	0.000
45	A	48	TYR	0	0.005	-0.010	60.048	0.000	0.000	0.000	0.000	0.000	0.000
46	A	49	ALA	0	0.011	0.021	58.492	0.000	0.000	0.000	0.000	0.000	0.000
47	A	50	THR	0	-0.019	-0.022	55.012	0.001	0.001	0.000	0.000	0.000	0.000
48	A	51	SER	0	0.012	-0.002	51.318	0.000	0.000	0.000	0.000	0.000	0.000
49	A	52	ASN	0	-0.044	-0.003	51.872	0.001	0.001	0.000	0.000	0.000	0.000
50	A	65	SER	0	0.031	0.004	56.948	0.000	0.000	0.000	0.000	0.000	0.000
51	A	66	VAL	0	0.091	0.027	58.299	0.000	0.000	0.000	0.000	0.000	0.000
52	A	67	ASN	0	-0.006	-0.006	60.746	0.000	0.000	0.000	0.000	0.000	0.000
53	A	68	ASN	0	0.057	0.030	53.125	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	69	LEU	0	0.048	0.032	56.075	0.000	0.000	0.000	0.000	0.000	0.000
55	A	70	LYS	1	0.895	0.958	58.241	-0.020	-0.020	0.000	0.000	0.000	0.000
56	A	71	MET	0	-0.002	0.008	57.482	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	72	MET	0	0.030	0.026	53.245	0.000	0.000	0.000	0.000	0.000	0.000
58	A	73	SER	0	-0.014	-0.027	56.540	0.001	0.001	0.000	0.000	0.000	0.000
59	A	74	LEU	0	-0.024	-0.006	59.485	0.000	0.000	0.000	0.000	0.000	0.000
60	A	75	LEU	0	0.047	0.025	53.837	0.000	0.000	0.000	0.000	0.000	0.000
61	A	76	ILE	0	-0.003	-0.006	53.803	0.000	0.000	0.000	0.000	0.000	0.000
62	A	77	LYS	1	0.838	0.930	56.760	-0.021	-0.021	0.000	0.000	0.000	0.000
63	A	78	ASP	-1	-0.886	-0.949	59.628	0.020	0.020	0.000	0.000	0.000	0.000
64	A	79	LYS	1	0.848	0.926	52.803	-0.025	-0.025	0.000	0.000	0.000	0.000
65	A	80	TRP	0	-0.017	-0.010	57.063	0.000	0.000	0.000	0.000	0.000	0.000
66	A	81	SER	0	-0.038	-0.034	58.500	0.000	0.000	0.000	0.000	0.000	0.000
67	A	82	GLU	-1	-0.882	-0.935	57.013	0.021	0.021	0.000	0.000	0.000	0.000
68	A	83	ASP	-1	-0.814	-0.926	54.255	0.029	0.029	0.000	0.000	0.000	0.000
69	A	84	GLU	-1	-0.851	-0.872	57.606	0.029	0.029	0.000	0.000	0.000	0.000
70	A	85	ASN	0	-0.156	-0.096	60.755	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	86	ASP	-1	-0.947	-0.976	59.893	0.018	0.018	0.000	0.000	0.000	0.000
72	A	87	THR	0	-0.104	-0.053	57.655	0.000	0.000	0.000	0.000	0.000	0.000
73	A	88	GLU	-1	-0.845	-0.921	52.368	0.026	0.026	0.000	0.000	0.000	0.000
74	A	89	GLU	-1	-0.779	-0.866	49.862	0.037	0.037	0.000	0.000	0.000	0.000
75	A	90	GLN	0	-0.004	-0.036	49.881	0.000	0.000	0.000	0.000	0.000	0.000
76	A	91	HIS	0	0.016	0.044	53.429	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	92	SER	0	-0.130	-0.074	52.639	0.000	0.000	0.000	0.000	0.000	0.000
78	A	93	ASN	0	-0.144	-0.058	47.431	0.001	0.001	0.000	0.000	0.000	0.000
79	A	94	SER	0	0.055	0.022	48.551	0.004	0.004	0.000	0.000	0.000	0.000
80	A	95	CYS	0	-0.045	-0.012	49.960	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	96	TYR	0	-0.045	-0.025	47.654	0.002	0.002	0.000	0.000	0.000	0.000
82	A	97	PRO	0	-0.009	-0.005	53.863	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	98	VAL	0	-0.022	-0.016	56.333	0.002	0.002	0.000	0.000	0.000	0.000
84	A	99	GLU	-1	-0.888	-0.936	58.917	0.031	0.031	0.000	0.000	0.000	0.000
85	A	100	ILE	0	0.000	-0.002	59.585	0.002	0.002	0.000	0.000	0.000	0.000
86	A	101	ASP	-1	-0.817	-0.909	63.612	0.033	0.033	0.000	0.000	0.000	0.000
87	A	102	SER	0	-0.062	-0.031	66.914	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	103	PHE	0	-0.004	0.012	67.088	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	104	LYS	1	0.841	0.893	61.264	-0.032	-0.032	0.000	0.000	0.000	0.000
90	A	105	THR	0	0.001	0.011	59.844	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	106	LYS	1	0.835	0.903	58.082	-0.027	-0.027	0.000	0.000	0.000	0.000
92	A	107	ILE	0	-0.019	0.000	53.088	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	108	TYR	0	-0.006	-0.034	53.314	0.001	0.001	0.000	0.000	0.000	0.000
94	A	109	THR	0	-0.065	-0.049	48.298	0.002	0.002	0.000	0.000	0.000	0.000
95	A	110	TYR	0	0.059	0.021	49.612	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	111	GLU	-1	-0.785	-0.844	44.120	0.048	0.048	0.000	0.000	0.000	0.000
97	A	112	MET	0	-0.009	-0.005	47.336	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	113	GLU	-1	-0.957	-0.988	47.283	0.028	0.028	0.000	0.000	0.000	0.000
99	A	114	ASP	-1	-0.939	-0.958	42.238	0.037	0.037	0.000	0.000	0.000	0.000
100	A	115	LEU	0	-0.055	-0.016	43.779	0.004	0.004	0.000	0.000	0.000	0.000
101	A	116	HIS	1	0.776	0.897	41.211	-0.054	-0.054	0.000	0.000	0.000	0.000
102	A	117	THR	0	-0.022	-0.027	46.755	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	118	CYS	0	-0.026	-0.022	50.096	0.002	0.002	0.000	0.000	0.000	0.000
104	A	119	VAL	0	0.039	0.015	52.639	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	120	ALA	0	0.027	0.016	56.337	0.001	0.001	0.000	0.000	0.000	0.000
106	A	121	GLN	0	-0.015	-0.004	58.937	0.000	0.000	0.000	0.000	0.000	0.000
107	A	122	ILE	0	0.004	-0.007	62.779	0.001	0.001	0.000	0.000	0.000	0.000
108	A	123	PRO	0	0.024	0.011	65.133	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	124	ASN	0	0.007	-0.002	68.026	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	125	SER	0	-0.086	-0.054	69.403	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	126	ASP	-1	-0.889	-0.920	68.238	0.022	0.022	0.000	0.000	0.000	0.000
112	A	127	LEU	0	-0.035	-0.019	65.943	0.000	0.000	0.000	0.000	0.000	0.000
113	A	128	LEU	0	0.003	0.015	60.882	0.001	0.001	0.000	0.000	0.000	0.000
114	A	129	LEU	0	0.007	0.004	58.177	0.000	0.000	0.000	0.000	0.000	0.000
115	A	130	LEU	0	0.003	0.002	55.167	0.000	0.000	0.000	0.000	0.000	0.000
116	A	131	PHE	0	-0.045	-0.028	52.170	0.001	0.001	0.000	0.000	0.000	0.000
117	A	132	ILE	0	0.064	0.023	50.427	0.000	0.000	0.000	0.000	0.000	0.000
118	A	133	ALA	0	-0.018	-0.021	46.869	0.001	0.001	0.000	0.000	0.000	0.000
119	A	134	GLU	-1	-0.791	-0.884	42.682	0.048	0.048	0.000	0.000	0.000	0.000
120	A	135	GLY	0	0.105	0.059	41.578	0.001	0.001	0.000	0.000	0.000	0.000
121	A	136	SER	0	-0.060	-0.034	38.773	0.001	0.001	0.000	0.000	0.000	0.000
122	A	137	PHE	0	-0.033	-0.016	39.968	0.005	0.005	0.000	0.000	0.000	0.000
123	A	138	PRO	0	0.017	-0.012	39.949	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	139	TYR	0	0.058	-0.005	42.157	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	140	GLY	0	0.014	0.018	43.944	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	141	LEU	0	0.002	-0.009	42.730	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	142	LEU	0	-0.027	-0.002	46.432	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	143	VAL	0	0.047	0.022	48.559	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	144	ILE	0	-0.007	-0.007	48.506	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	145	LYS	1	0.906	0.960	50.298	-0.052	-0.052	0.000	0.000	0.000	0.000
131	A	146	ILE	0	0.001	-0.006	52.128	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	147	GLU	-1	-0.810	-0.896	53.970	0.047	0.047	0.000	0.000	0.000	0.000
133	A	148	ARG	1	0.846	0.917	51.334	-0.056	-0.056	0.000	0.000	0.000	0.000
134	A	149	ALA	0	-0.028	-0.009	56.291	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	150	MET	0	0.018	0.012	58.147	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	151	ARG	1	0.763	0.864	59.765	-0.038	-0.038	0.000	0.000	0.000	0.000
137	A	152	GLU	-1	-0.912	-0.955	60.367	0.038	0.038	0.000	0.000	0.000	0.000
138	A	153	LEU	0	-0.036	-0.027	62.094	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	154	THR	0	-0.044	-0.042	64.006	-0.002	-0.002	0.000	0.000	0.000	0.000
140	A	155	ASP	-1	-0.822	-0.885	64.613	0.035	0.035	0.000	0.000	0.000	0.000
141	A	156	LEU	0	-0.098	-0.040	64.811	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	157	PHE	0	-0.080	-0.029	67.208	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	158	GLY	0	-0.002	0.016	70.454	-0.001	-0.001	0.000	0.000	0.000	0.000

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