FMO DATABASE

FMODB ID: 94712

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
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	-1140559.400577
FMO2-HF: Nuclear repulsion	1082113.186498
FMO2-HF: Total energy	-58446.214078
FMO2-MP2: Total energy	-58618.002734

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.
-0.57500000000001	-6.626	29.203	-12.964	-10.187	-0.047

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 : -0.923 / q_NPA : -0.946

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	-0.064	-0.040	3.711	-3.467	-2.074	-0.016	-0.641	-0.735	0.003
4	A	22	GLU	-1	-0.808	-0.903	2.354	41.997	44.983	5.293	-4.304	-3.975	-0.045
5	A	23	GLU	-1	-0.945	-0.960	4.915	20.065	20.168	-0.001	-0.003	-0.099	0.000
6	A	24	ILE	0	-0.033	-0.049	7.715	-0.544	-0.544	0.000	0.000	0.000	0.000
7	A	25	GLN	0	0.072	0.031	1.864	-15.172	-25.758	23.928	-8.016	-5.326	-0.005
8	A	26	GLU	-1	-0.921	-0.961	5.152	22.863	22.916	-0.001	0.000	-0.052	0.000
9	A	27	ARG	1	0.983	0.989	6.744	-30.464	-30.464	0.000	0.000	0.000	0.000
10	A	28	ARG	1	0.900	0.940	5.888	-36.490	-36.490	0.000	0.000	0.000	0.000
11	A	29	GLN	0	0.054	0.023	7.958	0.614	0.614	0.000	0.000	0.000	0.000
12	A	30	GLU	-1	-0.854	-0.927	10.859	16.542	16.542	0.000	0.000	0.000	0.000
13	A	31	VAL	0	-0.123	-0.038	10.043	-1.009	-1.009	0.000	0.000	0.000	0.000
14	A	32	LEU	0	-0.013	-0.003	12.303	-0.724	-0.724	0.000	0.000	0.000	0.000
15	A	33	THR	0	0.022	0.001	14.056	-1.445	-1.445	0.000	0.000	0.000	0.000
16	A	34	ARG	1	0.967	0.996	16.422	-18.936	-18.936	0.000	0.000	0.000	0.000
17	A	35	TYR	0	0.010	-0.005	17.805	-1.346	-1.346	0.000	0.000	0.000	0.000
18	A	36	GLN	0	0.030	0.023	19.708	-0.742	-0.742	0.000	0.000	0.000	0.000
19	A	37	SER	0	-0.006	-0.019	21.225	-0.594	-0.594	0.000	0.000	0.000	0.000
20	A	38	PHE	0	-0.082	-0.054	21.960	-0.500	-0.500	0.000	0.000	0.000	0.000
21	A	39	LYS	1	0.965	0.978	23.719	-12.981	-12.981	0.000	0.000	0.000	0.000
22	A	40	GLU	-1	-0.876	-0.930	25.584	11.257	11.257	0.000	0.000	0.000	0.000
23	A	41	ARG	1	0.955	0.976	24.811	-12.608	-12.608	0.000	0.000	0.000	0.000
24	A	42	VAL	0	-0.053	-0.015	27.479	-0.371	-0.371	0.000	0.000	0.000	0.000
25	A	43	ALA	0	0.003	0.001	29.848	-0.379	-0.379	0.000	0.000	0.000	0.000
26	A	44	GLU	-1	-0.864	-0.922	31.540	9.420	9.420	0.000	0.000	0.000	0.000
27	A	45	ARG	1	0.946	0.973	32.590	-9.672	-9.672	0.000	0.000	0.000	0.000
28	A	46	GLY	0	0.020	0.009	34.127	-0.274	-0.274	0.000	0.000	0.000	0.000
29	A	47	GLN	0	-0.004	-0.003	35.883	-0.184	-0.184	0.000	0.000	0.000	0.000
30	A	48	LYS	1	0.901	0.933	35.334	-9.190	-9.190	0.000	0.000	0.000	0.000
31	A	49	LEU	0	-0.084	-0.040	37.166	-0.187	-0.187	0.000	0.000	0.000	0.000
32	A	50	GLU	-1	-0.854	-0.923	40.173	7.315	7.315	0.000	0.000	0.000	0.000
33	A	51	ASP	-1	-0.860	-0.916	41.577	7.387	7.387	0.000	0.000	0.000	0.000
34	A	52	SER	0	-0.054	-0.031	42.988	-0.266	-0.266	0.000	0.000	0.000	0.000
35	A	53	TYR	0	-0.011	0.000	44.441	-0.206	-0.206	0.000	0.000	0.000	0.000
36	A	54	HIS	0	-0.003	-0.024	45.185	-0.326	-0.326	0.000	0.000	0.000	0.000
37	A	55	LEU	0	-0.016	0.007	47.726	-0.154	-0.154	0.000	0.000	0.000	0.000
38	A	56	GLN	0	-0.025	-0.024	47.517	-0.262	-0.262	0.000	0.000	0.000	0.000
39	A	57	VAL	0	-0.025	-0.014	50.188	-0.137	-0.137	0.000	0.000	0.000	0.000
40	A	58	PHE	0	-0.011	0.007	52.213	-0.137	-0.137	0.000	0.000	0.000	0.000
41	A	59	LYS	1	0.869	0.917	52.163	-6.307	-6.307	0.000	0.000	0.000	0.000
42	A	60	ARG	1	0.856	0.920	53.839	-6.053	-6.053	0.000	0.000	0.000	0.000
43	A	61	ASP	-1	-0.818	-0.877	56.538	5.682	5.682	0.000	0.000	0.000	0.000
44	A	62	ALA	0	-0.005	-0.010	58.046	-0.126	-0.126	0.000	0.000	0.000	0.000
45	A	63	ASP	-1	-0.880	-0.944	58.159	5.502	5.502	0.000	0.000	0.000	0.000
46	A	64	ASP	-1	-0.907	-0.951	60.294	5.346	5.346	0.000	0.000	0.000	0.000
47	A	65	LEU	0	-0.058	-0.023	62.386	-0.120	-0.120	0.000	0.000	0.000	0.000
48	A	66	GLY	0	0.043	0.009	63.767	-0.099	-0.099	0.000	0.000	0.000	0.000
49	A	67	LYS	1	0.829	0.906	60.456	-5.479	-5.479	0.000	0.000	0.000	0.000
50	A	68	TRP	0	0.056	0.013	66.556	-0.078	-0.078	0.000	0.000	0.000	0.000
51	A	69	ILE	0	-0.001	0.005	67.446	-0.091	-0.091	0.000	0.000	0.000	0.000
52	A	70	MET	0	0.003	0.004	69.404	-0.085	-0.085	0.000	0.000	0.000	0.000
53	A	71	GLU	-1	-0.967	-0.972	70.256	4.651	4.651	0.000	0.000	0.000	0.000
54	A	72	LYS	1	0.818	0.897	72.735	-4.548	-4.548	0.000	0.000	0.000	0.000
55	A	73	VAL	0	0.001	-0.010	73.937	-0.081	-0.081	0.000	0.000	0.000	0.000
56	A	74	ASN	0	0.009	-0.002	73.300	-0.074	-0.074	0.000	0.000	0.000	0.000
57	A	75	ILE	0	0.009	0.008	76.452	-0.067	-0.067	0.000	0.000	0.000	0.000
58	A	76	LEU	0	-0.093	-0.037	77.840	-0.081	-0.081	0.000	0.000	0.000	0.000
59	A	77	THR	0	0.055	0.018	79.538	-0.057	-0.057	0.000	0.000	0.000	0.000
60	A	78	ASP	-1	-0.913	-0.899	80.494	4.072	4.072	0.000	0.000	0.000	0.000
61	A	79	LYS	1	0.846	0.896	82.727	-3.725	-3.725	0.000	0.000	0.000	0.000
62	A	80	SER	0	-0.073	-0.051	84.868	-0.071	-0.071	0.000	0.000	0.000	0.000
63	A	81	TYR	0	0.003	0.028	85.191	0.028	0.028	0.000	0.000	0.000	0.000
64	A	82	GLU	-1	-0.873	-0.936	83.672	3.951	3.951	0.000	0.000	0.000	0.000
65	A	83	ASP	-1	-0.902	-0.967	87.869	3.561	3.561	0.000	0.000	0.000	0.000
66	A	84	PRO	0	-0.079	-0.035	88.314	-0.041	-0.041	0.000	0.000	0.000	0.000
67	A	85	THR	0	0.053	0.005	91.514	0.002	0.002	0.000	0.000	0.000	0.000
68	A	86	ASN	0	-0.048	-0.008	93.186	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	87	ILE	0	0.087	0.039	92.350	0.049	0.049	0.000	0.000	0.000	0.000
70	A	88	GLN	0	0.052	0.038	91.762	0.066	0.066	0.000	0.000	0.000	0.000
71	A	89	GLY	0	0.065	0.021	90.294	0.038	0.038	0.000	0.000	0.000	0.000
72	A	90	LYS	1	0.783	0.889	88.296	-3.580	-3.580	0.000	0.000	0.000	0.000
73	A	91	TYR	0	0.044	0.021	86.869	0.048	0.048	0.000	0.000	0.000	0.000
74	A	92	GLN	0	0.027	0.018	86.609	0.006	0.006	0.000	0.000	0.000	0.000
75	A	93	LYS	1	0.912	0.953	83.668	-3.738	-3.738	0.000	0.000	0.000	0.000
76	A	94	HIS	0	-0.029	-0.019	82.450	0.044	0.044	0.000	0.000	0.000	0.000
77	A	95	GLN	0	0.013	0.007	82.158	0.030	0.030	0.000	0.000	0.000	0.000
78	A	96	SER	0	-0.033	-0.024	79.356	0.044	0.044	0.000	0.000	0.000	0.000
79	A	97	LEU	0	-0.009	-0.001	76.746	0.061	0.061	0.000	0.000	0.000	0.000
80	A	98	GLU	-1	-0.817	-0.911	77.277	4.046	4.046	0.000	0.000	0.000	0.000
81	A	99	ALA	0	-0.022	-0.002	76.964	0.053	0.053	0.000	0.000	0.000	0.000
82	A	100	GLU	-1	-0.844	-0.906	73.692	4.507	4.507	0.000	0.000	0.000	0.000
83	A	101	VAL	0	0.005	0.008	72.605	0.088	0.088	0.000	0.000	0.000	0.000
84	A	102	GLN	0	0.023	0.013	72.187	0.098	0.098	0.000	0.000	0.000	0.000
85	A	103	THR	0	-0.089	-0.059	70.904	0.078	0.078	0.000	0.000	0.000	0.000
86	A	104	LYS	1	0.905	0.970	65.986	-4.843	-4.843	0.000	0.000	0.000	0.000
87	A	105	SER	0	0.041	0.021	67.559	0.101	0.101	0.000	0.000	0.000	0.000
88	A	106	ARG	1	0.841	0.915	63.022	-5.013	-5.013	0.000	0.000	0.000	0.000
89	A	107	LEU	0	0.002	-0.010	61.275	0.074	0.074	0.000	0.000	0.000	0.000
90	A	108	MET	0	0.049	0.039	62.802	0.124	0.124	0.000	0.000	0.000	0.000
91	A	109	SER	0	0.012	0.001	63.126	0.050	0.050	0.000	0.000	0.000	0.000
92	A	110	GLU	-1	-0.901	-0.934	59.141	5.437	5.437	0.000	0.000	0.000	0.000
93	A	111	LEU	0	0.016	0.027	57.992	0.133	0.133	0.000	0.000	0.000	0.000
94	A	112	GLU	-1	-0.876	-0.944	58.366	5.135	5.135	0.000	0.000	0.000	0.000
95	A	113	LYS	1	0.822	0.895	56.930	-5.548	-5.548	0.000	0.000	0.000	0.000
96	A	114	THR	0	-0.042	-0.042	53.700	0.136	0.136	0.000	0.000	0.000	0.000
97	A	115	ARG	1	0.900	0.972	54.119	-5.622	-5.622	0.000	0.000	0.000	0.000
98	A	116	GLU	-1	-1.009	-1.026	54.314	5.475	5.475	0.000	0.000	0.000	0.000
99	A	117	GLU	-1	-0.864	-0.914	53.346	5.832	5.832	0.000	0.000	0.000	0.000
100	A	118	ARG	1	0.864	0.941	46.355	-6.577	-6.577	0.000	0.000	0.000	0.000
101	A	119	PHE	0	-0.014	0.000	48.725	0.171	0.171	0.000	0.000	0.000	0.000
102	A	120	THR	0	0.051	0.043	49.172	-0.133	-0.133	0.000	0.000	0.000	0.000
103	A	121	MET	0	0.010	-0.004	50.134	0.092	0.092	0.000	0.000	0.000	0.000
104	A	122	GLY	0	-0.013	-0.010	46.473	0.071	0.071	0.000	0.000	0.000	0.000
105	A	123	HIS	0	0.011	0.003	45.274	0.067	0.067	0.000	0.000	0.000	0.000
106	A	124	SER	0	-0.001	-0.016	43.749	-0.107	-0.107	0.000	0.000	0.000	0.000
107	A	125	ALA	0	0.017	0.014	46.746	-0.093	-0.093	0.000	0.000	0.000	0.000
108	A	126	HIS	0	-0.024	0.016	49.751	-0.220	-0.220	0.000	0.000	0.000	0.000
109	A	127	GLU	-1	-0.777	-0.911	51.976	5.717	5.717	0.000	0.000	0.000	0.000
110	A	128	GLU	-1	-0.874	-0.913	50.702	6.303	6.303	0.000	0.000	0.000	0.000
111	A	129	THR	0	-0.022	-0.046	52.221	-0.113	-0.113	0.000	0.000	0.000	0.000
112	A	130	LYS	1	0.799	0.880	54.873	-5.839	-5.839	0.000	0.000	0.000	0.000
113	A	131	ALA	0	-0.026	0.011	57.169	-0.109	-0.109	0.000	0.000	0.000	0.000
114	A	132	HIS	0	0.013	-0.001	56.027	0.030	0.030	0.000	0.000	0.000	0.000
115	A	133	ILE	0	-0.009	-0.002	58.770	-0.077	-0.077	0.000	0.000	0.000	0.000
116	A	134	GLU	-1	-0.833	-0.910	61.195	4.864	4.864	0.000	0.000	0.000	0.000
117	A	135	GLU	-1	-0.889	-0.941	60.892	5.304	5.304	0.000	0.000	0.000	0.000
118	A	136	LEU	0	-0.034	-0.016	61.840	-0.094	-0.094	0.000	0.000	0.000	0.000
119	A	137	ARG	1	0.914	0.957	64.891	-4.950	-4.950	0.000	0.000	0.000	0.000
120	A	138	HIS	0	-0.028	-0.018	66.534	-0.144	-0.144	0.000	0.000	0.000	0.000
121	A	139	LEU	0	-0.030	-0.019	66.404	-0.073	-0.073	0.000	0.000	0.000	0.000
122	A	140	TRP	0	-0.021	-0.025	69.018	-0.050	-0.050	0.000	0.000	0.000	0.000
123	A	141	ASP	-1	-0.885	-0.947	70.862	4.442	4.442	0.000	0.000	0.000	0.000
124	A	142	LEU	0	-0.017	0.009	73.130	-0.074	-0.074	0.000	0.000	0.000	0.000
125	A	143	LEU	0	-0.016	-0.017	72.601	-0.069	-0.069	0.000	0.000	0.000	0.000
126	A	144	LEU	0	-0.017	-0.014	73.977	-0.070	-0.070	0.000	0.000	0.000	0.000
127	A	145	GLU	-1	-0.954	-0.966	76.936	4.058	4.058	0.000	0.000	0.000	0.000
128	A	146	LEU	0	0.045	0.013	77.517	-0.069	-0.069	0.000	0.000	0.000	0.000
129	A	147	THR	0	-0.028	-0.017	77.879	-0.041	-0.041	0.000	0.000	0.000	0.000
130	A	148	LEU	0	0.005	0.013	80.724	-0.057	-0.057	0.000	0.000	0.000	0.000
131	A	149	GLU	-1	-0.933	-0.962	82.707	3.815	3.815	0.000	0.000	0.000	0.000
132	A	150	LYS	1	0.808	0.896	83.437	-3.966	-3.966	0.000	0.000	0.000	0.000
133	A	151	GLY	0	0.040	0.007	84.492	-0.052	-0.052	0.000	0.000	0.000	0.000
134	A	152	ASP	-1	-0.781	-0.896	86.006	3.652	3.652	0.000	0.000	0.000	0.000
135	A	153	GLN	0	-0.076	-0.023	87.422	-0.075	-0.075	0.000	0.000	0.000	0.000
136	A	154	LEU	0	-0.023	-0.019	87.217	-0.056	-0.056	0.000	0.000	0.000	0.000
137	A	155	LEU	0	-0.015	-0.003	88.409	-0.048	-0.048	0.000	0.000	0.000	0.000
138	A	156	ARG	1	0.743	0.861	90.177	-3.650	-3.650	0.000	0.000	0.000	0.000
139	A	157	ALA	0	-0.056	-0.014	94.066	-0.045	-0.045	0.000	0.000	0.000	0.000
140	A	158	LEU	0	-0.038	-0.010	94.053	-0.017	-0.017	0.000	0.000	0.000	0.000

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