FMO DATABASE

FMODB ID: J36M9

Calculation Name: 3LGO-A-Xray317

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	147
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1218154.618108
FMO2-HF: Nuclear repulsion	1160129.418498
FMO2-HF: Total energy	-58025.19961
FMO2-MP2: Total energy	-58191.992043

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:3:ACE )

Summations of interaction energy for fragment #1(A:3:ACE )

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.
0.658	1.69	0.01	-0.45	-0.591	0

Interaction energy analysis for fragmet #1(A:3:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.005

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].
3	A	5	HIS	0	0.028	0.015	3.849	1.156	1.942	-0.005	-0.362	-0.418
4	A	6	SER	0	0.005	0.006	3.412	0.137	0.355	0.015	-0.072	-0.161
5	A	7	LYS	1	1.040	0.999	5.431	-0.445	-0.445	0.000	0.000	0.000
6	A	8	ASN	0	-0.020	-0.011	6.117	-0.187	-0.187	0.000	0.000	0.000
7	A	9	VAL	0	0.038	0.016	4.410	-0.101	-0.073	0.000	-0.016	-0.012
8	A	10	LYS	1	0.932	0.992	7.470	0.233	0.233	0.000	0.000	0.000
9	A	11	GLY	0	0.066	0.020	10.520	0.015	0.015	0.000	0.000	0.000
10	A	12	PHE	0	-0.030	0.001	10.248	0.026	0.026	0.000	0.000	0.000
11	A	13	LEU	0	0.003	0.009	11.290	0.011	0.011	0.000	0.000	0.000
12	A	14	GLU	-1	-0.877	-0.949	13.755	-0.099	-0.099	0.000	0.000	0.000
13	A	15	ASN	0	-0.084	-0.034	15.236	0.027	0.027	0.000	0.000	0.000
14	A	16	THR	0	-0.047	-0.058	15.024	0.007	0.007	0.000	0.000	0.000
15	A	17	LEU	0	-0.041	-0.010	17.642	-0.001	-0.001	0.000	0.000	0.000
16	A	18	LYS	1	0.890	0.955	20.241	0.021	0.021	0.000	0.000	0.000
17	A	19	PRO	0	0.041	0.028	22.536	-0.006	-0.006	0.000	0.000	0.000
18	A	20	TYR	0	-0.005	0.013	24.953	0.001	0.001	0.000	0.000	0.000
19	A	21	ASP	-1	-0.927	-0.963	26.799	-0.021	-0.021	0.000	0.000	0.000
20	A	22	LEU	0	-0.044	-0.023	29.380	0.001	0.001	0.000	0.000	0.000
21	A	23	HIS	0	0.004	-0.012	29.125	0.003	0.003	0.000	0.000	0.000
22	A	24	SER	0	-0.048	-0.023	34.358	0.000	0.000	0.000	0.000	0.000
23	A	25	VAL	0	0.007	0.014	35.466	0.000	0.000	0.000	0.000	0.000
24	A	26	ASP	-1	-0.871	-0.919	38.435	-0.012	-0.012	0.000	0.000	0.000
25	A	27	PHE	0	-0.045	-0.049	36.125	-0.002	-0.002	0.000	0.000	0.000
26	A	28	LYS	1	0.887	0.954	42.102	0.019	0.019	0.000	0.000	0.000
27	A	29	THR	0	0.031	0.020	43.922	-0.001	-0.001	0.000	0.000	0.000
28	A	30	SER	0	0.006	0.008	45.557	0.001	0.001	0.000	0.000	0.000
29	A	31	SER	0	-0.008	-0.017	47.414	0.001	0.001	0.000	0.000	0.000
30	A	32	LEU	0	-0.053	-0.027	51.171	-0.001	-0.001	0.000	0.000	0.000
31	A	33	GLN	0	0.023	0.032	52.206	0.000	0.000	0.000	0.000	0.000
32	A	34	SER	0	0.018	-0.010	54.997	0.001	0.001	0.000	0.000	0.000
33	A	35	SER	0	-0.035	-0.009	57.735	0.000	0.000	0.000	0.000	0.000
34	A	36	MET	0	-0.040	-0.039	60.117	0.001	0.001	0.000	0.000	0.000
35	A	37	ILE	0	0.092	0.055	63.258	0.000	0.000	0.000	0.000	0.000
36	A	38	ILE	0	-0.020	0.016	65.144	0.000	0.000	0.000	0.000	0.000
37	A	39	THR	0	0.034	0.020	68.035	0.000	0.000	0.000	0.000	0.000
38	A	40	ALA	0	0.119	0.055	68.684	0.000	0.000	0.000	0.000	0.000
39	A	41	THR	0	-0.035	-0.023	69.734	0.000	0.000	0.000	0.000	0.000
40	A	42	ASN	0	0.004	-0.031	71.678	0.000	0.000	0.000	0.000	0.000
41	A	43	GLY	0	0.072	0.024	68.424	0.000	0.000	0.000	0.000	0.000
42	A	44	GLY	0	-0.085	-0.051	69.066	0.000	0.000	0.000	0.000	0.000
43	A	45	ILE	0	-0.034	-0.030	65.707	0.000	0.000	0.000	0.000	0.000
44	A	46	LEU	0	-0.010	0.018	69.071	0.000	0.000	0.000	0.000	0.000
45	A	47	SER	0	-0.015	-0.016	68.005	0.000	0.000	0.000	0.000	0.000
46	A	48	TYR	0	-0.011	-0.016	63.808	-0.001	-0.001	0.000	0.000	0.000
47	A	49	ALA	0	0.004	0.018	61.582	0.000	0.000	0.000	0.000	0.000
48	A	50	THR	0	-0.016	-0.019	59.003	0.000	0.000	0.000	0.000	0.000
49	A	51	SER	0	0.010	-0.008	55.083	0.000	0.000	0.000	0.000	0.000
50	A	52	ASN	0	-0.032	-0.016	55.814	0.000	0.000	0.000	0.000	0.000
51	A	53	NME	0	0.012	0.030	57.705	0.000	0.000	0.000	0.000	0.000
52	A	64	ACE	0	0.059	0.021	59.845	0.000	0.000	0.000	0.000	0.000
53	A	65	SER	0	-0.011	-0.015	60.597	0.001	0.001	0.000	0.000	0.000
54	A	66	VAL	0	0.078	0.025	62.929	0.000	0.000	0.000	0.000	0.000
55	A	67	ASN	0	-0.042	-0.023	64.980	0.001	0.001	0.000	0.000	0.000
56	A	68	ASN	0	0.060	0.011	58.128	0.000	0.000	0.000	0.000	0.000
57	A	69	LEU	0	0.008	0.009	60.204	0.000	0.000	0.000	0.000	0.000
58	A	70	LYS	1	0.970	0.978	62.415	0.015	0.015	0.000	0.000	0.000
59	A	71	MET	0	-0.034	0.001	61.854	0.001	0.001	0.000	0.000	0.000
60	A	72	MET	0	0.054	0.034	58.325	0.000	0.000	0.000	0.000	0.000
61	A	73	SER	0	-0.016	-0.010	61.486	0.000	0.000	0.000	0.000	0.000
62	A	74	LEU	0	-0.018	0.001	64.085	0.001	0.001	0.000	0.000	0.000
63	A	75	LEU	0	0.048	0.033	58.872	0.000	0.000	0.000	0.000	0.000
64	A	76	ILE	0	-0.018	-0.029	58.480	0.000	0.000	0.000	0.000	0.000
65	A	77	LYS	1	0.859	0.967	61.154	0.014	0.014	0.000	0.000	0.000
66	A	78	ASP	-1	-0.938	-0.963	63.845	-0.015	-0.015	0.000	0.000	0.000
67	A	79	LYS	1	0.969	0.976	56.739	0.021	0.021	0.000	0.000	0.000
68	A	80	TRP	0	0.012	0.010	61.162	0.000	0.000	0.000	0.000	0.000
69	A	81	SER	0	-0.021	-0.013	62.721	0.000	0.000	0.000	0.000	0.000
70	A	82	GLU	-1	-0.955	-0.974	62.463	-0.017	-0.017	0.000	0.000	0.000
71	A	83	ASP	-1	-0.856	-0.941	59.386	-0.017	-0.017	0.000	0.000	0.000
72	A	84	GLU	-1	-0.984	-0.976	62.160	-0.011	-0.011	0.000	0.000	0.000
73	A	85	ASN	0	-0.112	-0.070	64.719	0.001	0.001	0.000	0.000	0.000
74	A	86	ASP	-1	-0.877	-0.931	63.151	-0.015	-0.015	0.000	0.000	0.000
75	A	87	THR	0	-0.163	0.006	60.396	0.000	0.000	0.000	0.000	0.000
76	A	88	GLU	-1	-0.769	-0.827	58.051	-0.020	-0.020	0.000	0.000	0.000
77	A	89	GLU	-1	-1.071	-1.087	58.633	-0.013	-0.013	0.000	0.000	0.000
78	A	90	GLN	0	-0.023	-0.086	59.701	0.001	0.001	0.000	0.000	0.000
79	A	91	HIS	0	0.007	0.006	56.519	0.000	0.000	0.000	0.000	0.000
80	A	92	SER	0	-0.094	-0.060	55.980	0.001	0.001	0.000	0.000	0.000
81	A	93	ASN	0	-0.045	-0.024	51.099	0.001	0.001	0.000	0.000	0.000
82	A	94	SER	0	0.000	-0.038	52.486	0.000	0.000	0.000	0.000	0.000
83	A	95	CYS	0	-0.014	0.050	53.545	0.000	0.000	0.000	0.000	0.000
84	A	96	TYR	0	-0.026	-0.018	50.064	0.000	0.000	0.000	0.000	0.000
85	A	97	PRO	0	-0.046	-0.025	56.835	0.000	0.000	0.000	0.000	0.000
86	A	98	VAL	0	0.017	0.009	58.856	0.000	0.000	0.000	0.000	0.000
87	A	99	GLU	-1	-0.884	-0.950	61.520	-0.007	-0.007	0.000	0.000	0.000
88	A	100	ILE	0	-0.003	0.015	62.108	0.000	0.000	0.000	0.000	0.000
89	A	101	ASP	-1	-0.770	-0.891	65.904	-0.007	-0.007	0.000	0.000	0.000
90	A	102	SER	0	-0.083	-0.067	68.723	0.000	0.000	0.000	0.000	0.000
91	A	103	PHE	0	0.009	0.045	69.239	0.000	0.000	0.000	0.000	0.000
92	A	104	LYS	1	0.820	0.892	64.270	0.008	0.008	0.000	0.000	0.000
93	A	105	THR	0	-0.011	0.004	63.301	0.000	0.000	0.000	0.000	0.000
94	A	106	LYS	1	0.931	0.977	61.506	0.011	0.011	0.000	0.000	0.000
95	A	107	ILE	0	0.024	0.019	56.391	0.000	0.000	0.000	0.000	0.000
96	A	108	TYR	0	0.006	-0.026	56.787	0.000	0.000	0.000	0.000	0.000
97	A	109	THR	0	-0.037	-0.024	51.648	-0.001	-0.001	0.000	0.000	0.000
98	A	110	TYR	0	0.083	0.011	53.502	0.000	0.000	0.000	0.000	0.000
99	A	111	GLU	-1	-0.968	-0.942	47.773	-0.030	-0.030	0.000	0.000	0.000
100	A	112	MET	0	-0.060	-0.013	51.867	0.001	0.001	0.000	0.000	0.000
101	A	113	GLU	-1	-0.978	-0.996	52.304	-0.026	-0.026	0.000	0.000	0.000
102	A	114	ASP	-1	-0.909	-0.961	47.432	-0.034	-0.034	0.000	0.000	0.000
103	A	115	LEU	0	-0.004	0.001	48.765	0.000	0.000	0.000	0.000	0.000
104	A	116	HIS	1	0.732	0.893	45.391	0.028	0.028	0.000	0.000	0.000
105	A	117	THR	0	-0.029	-0.032	50.987	0.001	0.001	0.000	0.000	0.000
106	A	118	CYS	0	-0.046	-0.033	54.472	0.000	0.000	0.000	0.000	0.000
107	A	119	VAL	0	0.056	0.043	56.695	0.000	0.000	0.000	0.000	0.000
108	A	120	ALA	0	0.057	0.027	60.220	0.000	0.000	0.000	0.000	0.000
109	A	121	GLN	0	0.032	0.011	62.243	0.000	0.000	0.000	0.000	0.000
110	A	122	ILE	0	-0.013	-0.003	66.026	0.000	0.000	0.000	0.000	0.000
111	A	123	PRO	0	0.005	0.009	68.293	0.000	0.000	0.000	0.000	0.000
112	A	124	ASN	0	-0.002	-0.010	71.055	0.000	0.000	0.000	0.000	0.000
113	A	125	SER	0	0.010	-0.007	72.174	0.000	0.000	0.000	0.000	0.000
114	A	126	ASP	-1	-0.875	-0.916	71.599	-0.009	-0.009	0.000	0.000	0.000
115	A	127	LEU	0	-0.085	-0.045	69.521	-0.001	-0.001	0.000	0.000	0.000
116	A	128	LEU	0	-0.027	0.008	64.661	0.000	0.000	0.000	0.000	0.000
117	A	129	LEU	0	-0.011	-0.006	61.456	0.000	0.000	0.000	0.000	0.000
118	A	130	LEU	0	-0.012	-0.009	58.650	0.000	0.000	0.000	0.000	0.000
119	A	131	PHE	0	-0.082	-0.017	55.342	0.000	0.000	0.000	0.000	0.000
120	A	132	ILE	0	0.074	0.023	54.343	0.000	0.000	0.000	0.000	0.000
121	A	133	ALA	0	-0.032	-0.032	50.422	0.000	0.000	0.000	0.000	0.000
122	A	134	GLU	-1	-0.777	-0.883	46.865	-0.029	-0.029	0.000	0.000	0.000
123	A	135	GLY	0	0.084	0.022	46.174	0.001	0.001	0.000	0.000	0.000
124	A	136	SER	0	-0.027	-0.027	42.848	-0.001	-0.001	0.000	0.000	0.000
125	A	137	PHE	0	-0.031	-0.012	43.791	0.001	0.001	0.000	0.000	0.000
126	A	138	PRO	0	0.015	-0.010	43.182	0.000	0.000	0.000	0.000	0.000
127	A	139	TYR	0	0.136	0.061	45.468	0.001	0.001	0.000	0.000	0.000
128	A	140	GLY	0	0.007	0.022	46.785	0.001	0.001	0.000	0.000	0.000
129	A	141	LEU	0	0.017	-0.007	44.710	0.001	0.001	0.000	0.000	0.000
130	A	142	LEU	0	-0.003	0.006	48.865	0.001	0.001	0.000	0.000	0.000
131	A	143	VAL	0	0.036	0.019	51.452	0.001	0.001	0.000	0.000	0.000
132	A	144	ILE	0	-0.010	-0.003	50.772	0.001	0.001	0.000	0.000	0.000
133	A	145	LYS	1	0.896	0.941	52.504	0.017	0.017	0.000	0.000	0.000
134	A	146	ILE	0	0.013	-0.014	54.379	0.001	0.001	0.000	0.000	0.000
135	A	147	GLU	-1	-0.928	-0.951	56.587	-0.009	-0.009	0.000	0.000	0.000
136	A	148	ARG	1	0.964	0.970	52.519	0.011	0.011	0.000	0.000	0.000
137	A	149	ALA	0	-0.027	-0.001	58.777	0.000	0.000	0.000	0.000	0.000
138	A	150	MET	0	0.020	0.011	60.580	0.000	0.000	0.000	0.000	0.000
139	A	151	ARG	1	0.834	0.922	62.109	0.007	0.007	0.000	0.000	0.000
140	A	152	GLU	-1	-0.865	-0.944	62.553	-0.008	-0.008	0.000	0.000	0.000
141	A	153	LEU	0	-0.055	-0.020	64.307	0.000	0.000	0.000	0.000	0.000
142	A	154	THR	0	-0.060	-0.047	66.292	0.000	0.000	0.000	0.000	0.000
143	A	155	ASP	-1	-0.868	-0.931	65.838	-0.007	-0.007	0.000	0.000	0.000
144	A	156	LEU	0	-0.150	-0.056	67.199	0.000	0.000	0.000	0.000	0.000
145	A	157	PHE	0	-0.133	-0.068	69.241	0.000	0.000	0.000	0.000	0.000
146	A	158	GLY	0	0.077	0.049	72.746	0.000	0.000	0.000	0.000	0.000
147	A	159	NME	0	-0.068	-0.029	75.005	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ACE )