FMO DATABASE

FMODB ID: LZGK9

Calculation Name: 3LBX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LBX

Chain ID: A

ChEMBL ID:

UniProt ID: P02549

Base Structure: X-ray

Registration Date: 2023-06-22

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	140
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1139715.404452
FMO2-HF: Nuclear repulsion	1081270.654005
FMO2-HF: Total energy	-58444.750447
FMO2-MP2: Total energy	-58616.62374

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:19:GLU)

Summations of interaction energy for fragment #1(A:19:GLU)

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.
28.51	6.438	41.056	-10.1	-8.884	-0.108

Interaction energy analysis for fragmet #1(A:19:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.973 / q_NPA : -1.007

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	21	ALA	0	-0.079	-0.043	3.829	-4.089	-2.716	-0.016	-0.640	-0.717	0.003
4	A	22	GLU	-1	-0.789	-0.888	2.303	47.624	42.030	11.919	-1.477	-4.848	-0.060
5	A	23	GLU	-1	-0.934	-0.958	4.925	20.090	20.196	-0.001	-0.003	-0.102	0.000
6	A	24	ILE	0	-0.019	-0.038	7.481	-0.604	-0.604	0.000	0.000	0.000	0.000
7	A	25	GLN	0	0.097	0.065	1.693	8.242	-9.776	29.155	-7.979	-3.159	-0.051
8	A	26	GLU	-1	-0.906	-0.956	5.070	23.151	23.212	-0.001	-0.001	-0.058	0.000
9	A	27	ARG	1	0.975	0.985	6.778	-30.547	-30.547	0.000	0.000	0.000	0.000
10	A	28	ARG	1	0.876	0.928	5.848	-36.920	-36.920	0.000	0.000	0.000	0.000
11	A	29	GLN	0	0.039	0.019	7.909	-0.066	-0.066	0.000	0.000	0.000	0.000
12	A	30	GLU	-1	-0.832	-0.919	10.759	16.874	16.874	0.000	0.000	0.000	0.000
13	A	31	VAL	0	-0.128	-0.031	9.630	-1.039	-1.039	0.000	0.000	0.000	0.000
14	A	32	LEU	0	0.004	0.010	12.284	-0.707	-0.707	0.000	0.000	0.000	0.000
15	A	33	THR	0	0.017	-0.017	13.987	-1.452	-1.452	0.000	0.000	0.000	0.000
16	A	34	ARG	1	0.969	0.988	16.386	-19.145	-19.145	0.000	0.000	0.000	0.000
17	A	35	TYR	0	-0.020	-0.026	17.744	-1.267	-1.267	0.000	0.000	0.000	0.000
18	A	36	GLN	0	0.010	0.013	19.638	-1.001	-1.001	0.000	0.000	0.000	0.000
19	A	37	SER	0	0.028	0.012	21.280	-0.695	-0.695	0.000	0.000	0.000	0.000
20	A	38	PHE	0	-0.085	-0.052	21.867	-0.473	-0.473	0.000	0.000	0.000	0.000
21	A	39	LYS	1	0.964	0.972	23.671	-12.772	-12.772	0.000	0.000	0.000	0.000
22	A	40	GLU	-1	-0.874	-0.927	25.700	11.342	11.342	0.000	0.000	0.000	0.000
23	A	41	ARG	1	0.969	0.983	24.839	-12.659	-12.659	0.000	0.000	0.000	0.000
24	A	42	VAL	0	-0.064	-0.016	26.955	-0.361	-0.361	0.000	0.000	0.000	0.000
25	A	43	ALA	0	-0.003	-0.006	29.791	-0.379	-0.379	0.000	0.000	0.000	0.000
26	A	44	GLU	-1	-0.916	-0.948	31.493	9.453	9.453	0.000	0.000	0.000	0.000
27	A	45	ARG	1	0.923	0.960	32.546	-9.647	-9.647	0.000	0.000	0.000	0.000
28	A	46	GLY	0	0.021	0.007	34.072	-0.277	-0.277	0.000	0.000	0.000	0.000
29	A	47	GLN	0	0.031	0.028	35.826	-0.134	-0.134	0.000	0.000	0.000	0.000
30	A	48	LYS	1	0.969	0.973	36.332	-8.718	-8.718	0.000	0.000	0.000	0.000
31	A	49	LEU	0	-0.094	-0.048	37.250	-0.196	-0.196	0.000	0.000	0.000	0.000
32	A	50	GLU	-1	-0.907	-0.951	40.098	7.495	7.495	0.000	0.000	0.000	0.000
33	A	51	ASP	-1	-0.919	-0.961	41.416	7.516	7.516	0.000	0.000	0.000	0.000
34	A	52	SER	0	-0.067	-0.044	42.947	-0.267	-0.267	0.000	0.000	0.000	0.000
35	A	53	TYR	0	-0.005	0.007	44.392	-0.198	-0.198	0.000	0.000	0.000	0.000
36	A	54	HIS	0	0.040	0.002	45.559	-0.285	-0.285	0.000	0.000	0.000	0.000
37	A	55	LEU	0	-0.017	0.008	47.682	-0.150	-0.150	0.000	0.000	0.000	0.000
38	A	56	GLN	0	-0.026	-0.028	47.983	-0.232	-0.232	0.000	0.000	0.000	0.000
39	A	57	VAL	0	-0.010	-0.009	49.989	-0.133	-0.133	0.000	0.000	0.000	0.000
40	A	58	PHE	0	-0.015	0.009	52.164	-0.131	-0.131	0.000	0.000	0.000	0.000
41	A	59	LYS	1	0.912	0.955	52.192	-6.273	-6.273	0.000	0.000	0.000	0.000
42	A	60	ARG	1	0.852	0.919	54.056	-6.039	-6.039	0.000	0.000	0.000	0.000
43	A	61	ASP	-1	-0.817	-0.870	56.490	5.681	5.681	0.000	0.000	0.000	0.000
44	A	62	ALA	0	-0.015	-0.015	58.003	-0.126	-0.126	0.000	0.000	0.000	0.000
45	A	63	ASP	-1	-0.882	-0.949	58.025	5.509	5.509	0.000	0.000	0.000	0.000
46	A	64	ASP	-1	-0.970	-0.995	60.092	5.379	5.379	0.000	0.000	0.000	0.000
47	A	65	LEU	0	-0.054	-0.024	62.341	-0.120	-0.120	0.000	0.000	0.000	0.000
48	A	66	GLY	0	0.047	0.010	63.731	-0.102	-0.102	0.000	0.000	0.000	0.000
49	A	67	LYS	1	0.912	0.958	60.968	-5.436	-5.436	0.000	0.000	0.000	0.000
50	A	68	TRP	0	0.027	0.006	66.515	-0.088	-0.088	0.000	0.000	0.000	0.000
51	A	69	ILE	0	0.014	0.007	67.474	-0.091	-0.091	0.000	0.000	0.000	0.000
52	A	70	MET	0	0.000	0.005	69.522	-0.086	-0.086	0.000	0.000	0.000	0.000
53	A	71	GLU	-1	-0.976	-0.980	69.959	4.615	4.615	0.000	0.000	0.000	0.000
54	A	72	LYS	1	0.884	0.951	72.741	-4.544	-4.544	0.000	0.000	0.000	0.000
55	A	73	VAL	0	0.017	-0.002	73.877	-0.081	-0.081	0.000	0.000	0.000	0.000
56	A	74	ASN	0	-0.001	-0.008	73.197	-0.087	-0.087	0.000	0.000	0.000	0.000
57	A	75	ILE	0	0.003	0.003	76.784	-0.066	-0.066	0.000	0.000	0.000	0.000
58	A	76	LEU	0	-0.088	-0.042	78.114	-0.074	-0.074	0.000	0.000	0.000	0.000
59	A	77	THR	0	-0.043	-0.020	78.936	-0.056	-0.056	0.000	0.000	0.000	0.000
60	A	78	ASP	-1	-0.902	-0.905	81.037	4.026	4.026	0.000	0.000	0.000	0.000
61	A	79	LYS	1	0.867	0.912	82.645	-3.725	-3.725	0.000	0.000	0.000	0.000
62	A	80	SER	0	-0.090	-0.068	84.915	-0.071	-0.071	0.000	0.000	0.000	0.000
63	A	81	TYR	0	-0.018	0.016	84.994	0.023	0.023	0.000	0.000	0.000	0.000
64	A	82	GLU	-1	-0.843	-0.917	83.584	3.938	3.938	0.000	0.000	0.000	0.000
65	A	83	ASP	-1	-0.874	-0.962	87.673	3.530	3.530	0.000	0.000	0.000	0.000
66	A	84	PRO	0	-0.102	-0.031	87.995	-0.041	-0.041	0.000	0.000	0.000	0.000
67	A	85	THR	0	0.077	-0.008	91.313	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	86	ASN	0	-0.052	-0.003	93.067	0.005	0.005	0.000	0.000	0.000	0.000
69	A	87	ILE	0	0.071	0.035	92.293	0.050	0.050	0.000	0.000	0.000	0.000
70	A	88	GLN	0	0.039	0.028	91.703	0.077	0.077	0.000	0.000	0.000	0.000
71	A	89	GLY	0	0.074	0.031	90.228	0.039	0.039	0.000	0.000	0.000	0.000
72	A	90	LYS	1	0.774	0.886	88.231	-3.568	-3.568	0.000	0.000	0.000	0.000
73	A	91	TYR	0	0.030	0.025	87.083	0.051	0.051	0.000	0.000	0.000	0.000
74	A	92	GLN	0	0.006	0.015	86.546	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	93	LYS	1	0.915	0.953	83.604	-3.739	-3.739	0.000	0.000	0.000	0.000
76	A	94	HIS	0	0.016	0.017	82.389	0.049	0.049	0.000	0.000	0.000	0.000
77	A	95	GLN	0	0.046	0.014	82.097	0.016	0.016	0.000	0.000	0.000	0.000
78	A	96	SER	0	-0.042	-0.026	79.356	0.047	0.047	0.000	0.000	0.000	0.000
79	A	97	LEU	0	-0.024	-0.004	76.739	0.063	0.063	0.000	0.000	0.000	0.000
80	A	98	GLU	-1	-0.847	-0.938	77.216	4.053	4.053	0.000	0.000	0.000	0.000
81	A	99	ALA	0	-0.029	-0.004	76.899	0.054	0.054	0.000	0.000	0.000	0.000
82	A	100	GLU	-1	-0.929	-0.962	73.923	4.489	4.489	0.000	0.000	0.000	0.000
83	A	101	VAL	0	0.016	0.011	72.539	0.089	0.089	0.000	0.000	0.000	0.000
84	A	102	GLN	0	0.017	0.011	72.125	0.101	0.101	0.000	0.000	0.000	0.000
85	A	103	THR	0	-0.103	-0.066	70.892	0.081	0.081	0.000	0.000	0.000	0.000
86	A	104	LYS	1	0.943	0.983	65.446	-4.878	-4.878	0.000	0.000	0.000	0.000
87	A	105	SER	0	0.033	0.023	67.496	0.105	0.105	0.000	0.000	0.000	0.000
88	A	106	ARG	1	0.922	0.959	65.292	-4.887	-4.887	0.000	0.000	0.000	0.000
89	A	107	LEU	0	0.017	0.000	61.210	0.063	0.063	0.000	0.000	0.000	0.000
90	A	108	MET	0	0.044	0.034	62.741	0.120	0.120	0.000	0.000	0.000	0.000
91	A	109	SER	0	-0.003	-0.007	63.069	0.058	0.058	0.000	0.000	0.000	0.000
92	A	110	GLU	-1	-0.978	-0.971	58.977	5.513	5.513	0.000	0.000	0.000	0.000
93	A	111	LEU	0	0.014	0.013	57.960	0.128	0.128	0.000	0.000	0.000	0.000
94	A	112	GLU	-1	-0.895	-0.956	58.313	5.160	5.160	0.000	0.000	0.000	0.000
95	A	113	LYS	1	0.843	0.912	57.138	-5.532	-5.532	0.000	0.000	0.000	0.000
96	A	114	THR	0	-0.027	-0.024	53.495	0.140	0.140	0.000	0.000	0.000	0.000
97	A	115	ARG	1	0.884	0.958	54.062	-5.653	-5.653	0.000	0.000	0.000	0.000
98	A	116	GLU	-1	-1.019	-1.023	54.266	5.484	5.484	0.000	0.000	0.000	0.000
99	A	117	GLU	-1	-0.870	-0.921	53.237	5.841	5.841	0.000	0.000	0.000	0.000
100	A	118	ARG	1	0.870	0.946	46.260	-6.577	-6.577	0.000	0.000	0.000	0.000
101	A	119	PHE	0	-0.014	-0.007	48.781	0.180	0.180	0.000	0.000	0.000	0.000
102	A	120	THR	0	0.060	0.057	48.914	-0.144	-0.144	0.000	0.000	0.000	0.000
103	A	121	MET	0	0.008	-0.011	50.100	0.084	0.084	0.000	0.000	0.000	0.000
104	A	122	GLY	0	-0.014	-0.011	46.450	0.073	0.073	0.000	0.000	0.000	0.000
105	A	123	HIS	0	0.037	0.031	45.291	0.132	0.132	0.000	0.000	0.000	0.000
106	A	124	SER	0	0.015	-0.009	43.847	-0.108	-0.108	0.000	0.000	0.000	0.000
107	A	125	ALA	0	0.013	0.007	46.731	-0.087	-0.087	0.000	0.000	0.000	0.000
108	A	126	HIS	0	-0.061	0.014	49.730	-0.214	-0.214	0.000	0.000	0.000	0.000
109	A	127	GLU	-1	-0.856	-0.964	51.952	5.710	5.710	0.000	0.000	0.000	0.000
110	A	128	GLU	-1	-0.910	-0.952	50.907	6.284	6.284	0.000	0.000	0.000	0.000
111	A	129	THR	0	-0.034	-0.069	52.052	-0.108	-0.108	0.000	0.000	0.000	0.000
112	A	130	LYS	1	0.917	0.953	54.846	-5.715	-5.715	0.000	0.000	0.000	0.000
113	A	131	ALA	0	-0.019	0.012	57.156	-0.107	-0.107	0.000	0.000	0.000	0.000
114	A	132	HIS	0	0.057	0.029	55.770	0.023	0.023	0.000	0.000	0.000	0.000
115	A	133	ILE	0	-0.012	-0.006	58.880	-0.078	-0.078	0.000	0.000	0.000	0.000
116	A	134	GLU	-1	-0.911	-0.968	61.162	4.869	4.869	0.000	0.000	0.000	0.000
117	A	135	GLU	-1	-0.919	-0.961	60.808	5.292	5.292	0.000	0.000	0.000	0.000
118	A	136	LEU	0	-0.033	-0.016	61.738	-0.097	-0.097	0.000	0.000	0.000	0.000
119	A	137	ARG	1	0.960	0.994	65.257	-4.944	-4.944	0.000	0.000	0.000	0.000
120	A	138	HIS	0	0.023	0.014	66.840	-0.131	-0.131	0.000	0.000	0.000	0.000
121	A	139	LEU	0	-0.029	-0.020	66.525	-0.074	-0.074	0.000	0.000	0.000	0.000
122	A	140	TRP	0	-0.023	-0.025	68.985	-0.051	-0.051	0.000	0.000	0.000	0.000
123	A	141	ASP	-1	-0.889	-0.947	70.825	4.454	4.454	0.000	0.000	0.000	0.000
124	A	142	LEU	0	-0.019	0.006	73.103	-0.074	-0.074	0.000	0.000	0.000	0.000
125	A	143	LEU	0	-0.023	-0.016	72.637	-0.068	-0.068	0.000	0.000	0.000	0.000
126	A	144	LEU	0	-0.034	-0.030	74.220	-0.069	-0.069	0.000	0.000	0.000	0.000
127	A	145	GLU	-1	-0.939	-0.951	76.894	4.045	4.045	0.000	0.000	0.000	0.000
128	A	146	LEU	0	0.050	0.015	77.840	-0.065	-0.065	0.000	0.000	0.000	0.000
129	A	147	THR	0	-0.044	-0.028	77.529	-0.046	-0.046	0.000	0.000	0.000	0.000
130	A	148	LEU	0	0.009	0.017	80.680	-0.055	-0.055	0.000	0.000	0.000	0.000
131	A	149	GLU	-1	-0.902	-0.950	82.662	3.854	3.854	0.000	0.000	0.000	0.000
132	A	150	LYS	1	0.862	0.937	83.718	-3.919	-3.919	0.000	0.000	0.000	0.000
133	A	151	GLY	0	0.017	-0.009	84.457	-0.053	-0.053	0.000	0.000	0.000	0.000
134	A	152	ASP	-1	-0.847	-0.945	85.957	3.705	3.705	0.000	0.000	0.000	0.000
135	A	153	GLN	0	-0.079	-0.032	88.163	-0.067	-0.067	0.000	0.000	0.000	0.000
136	A	154	LEU	0	-0.032	-0.021	87.340	-0.056	-0.056	0.000	0.000	0.000	0.000
137	A	155	LEU	0	0.014	0.008	89.037	-0.049	-0.049	0.000	0.000	0.000	0.000
138	A	156	ARG	1	0.830	0.923	90.296	-3.630	-3.630	0.000	0.000	0.000	0.000
139	A	157	ALA	0	-0.042	-0.003	94.017	-0.045	-0.045	0.000	0.000	0.000	0.000
140	A	158	LEU	0	-0.036	-0.016	93.993	-0.016	-0.016	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:19:GLU)