FMO DATABASE

FMODB ID: 4946N

Calculation Name: 3BJA-A-Xray372

Preferred Name:
Warning: Undefined array key "pref_name" in /home/FMODBwui_src/fmodbwui/detail.php on line 446

Target Type:
Warning: Undefined array key "target_type" in /home/FMODBwui_src/fmodbwui/detail.php on line 447

Ligand Name:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

ligand 3-letter code:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

PDB ID: 3BJA

Chain ID: A

ChEMBL ID:
Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

UniProt ID: Q738D3

Base Structure: X-ray

Registration Date: 2023-09-20

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	139
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1204205.078004
FMO2-HF: Nuclear repulsion	1145808.486021
FMO2-HF: Total energy	-58396.591983
FMO2-MP2: Total energy	-58561.138511

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:0:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

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.
-7.738	-4.492	4.336	-3.295	-4.287	-0.008

Interaction energy analysis for fragmet #1(A:0:GLY)

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 : 0.008

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	2	ASN	0	0.082	0.040	2.645	-3.887	-1.562	0.494	-1.370	-1.449	-0.011
4	A	3	ASN	0	0.007	0.002	2.602	-3.297	-2.666	3.842	-1.838	-2.635	0.003
5	A	4	ARG	1	0.929	0.959	4.001	-0.089	0.201	0.000	-0.087	-0.203	0.000
6	A	5	GLU	-1	-0.908	-0.967	6.083	-0.515	-0.515	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.017	0.018	7.241	0.206	0.206	0.000	0.000	0.000	0.000
8	A	7	TYR	0	-0.040	-0.029	8.139	0.122	0.122	0.000	0.000	0.000	0.000
9	A	8	GLY	0	0.025	0.000	10.012	0.014	0.014	0.000	0.000	0.000	0.000
10	A	9	ASN	0	0.080	0.045	11.691	0.059	0.059	0.000	0.000	0.000	0.000
11	A	10	ILE	0	-0.021	-0.001	12.776	0.025	0.025	0.000	0.000	0.000	0.000
12	A	11	ARG	1	0.892	0.943	13.906	-0.156	-0.156	0.000	0.000	0.000	0.000
13	A	12	ASP	-1	-0.881	-0.931	16.001	-0.071	-0.071	0.000	0.000	0.000	0.000
14	A	13	VAL	0	0.004	-0.002	17.608	0.007	0.007	0.000	0.000	0.000	0.000
15	A	14	TYR	0	-0.027	-0.008	18.925	0.013	0.013	0.000	0.000	0.000	0.000
16	A	15	HIS	0	0.026	-0.010	19.002	0.000	0.000	0.000	0.000	0.000	0.000
17	A	16	LEU	0	-0.049	-0.023	21.451	0.002	0.002	0.000	0.000	0.000	0.000
18	A	17	LEU	0	0.032	0.024	22.641	0.002	0.002	0.000	0.000	0.000	0.000
19	A	18	GLN	0	-0.013	-0.003	24.697	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	19	LYS	1	0.936	0.977	26.426	0.030	0.030	0.000	0.000	0.000	0.000
21	A	20	ASN	0	-0.019	-0.032	27.990	0.003	0.003	0.000	0.000	0.000	0.000
22	A	21	LEU	0	-0.025	0.012	29.488	0.000	0.000	0.000	0.000	0.000	0.000
23	A	22	ASP	-1	-0.802	-0.924	30.998	0.019	0.019	0.000	0.000	0.000	0.000
24	A	23	LYS	1	0.867	0.944	32.580	0.012	0.012	0.000	0.000	0.000	0.000
25	A	24	ALA	0	0.008	0.004	33.954	0.000	0.000	0.000	0.000	0.000	0.000
26	A	25	ILE	0	-0.064	-0.037	34.624	0.000	0.000	0.000	0.000	0.000	0.000
27	A	26	GLU	-1	-0.915	-0.949	37.224	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	27	GLN	0	-0.022	-0.021	38.573	0.000	0.000	0.000	0.000	0.000	0.000
29	A	28	TYR	0	-0.093	-0.082	40.288	0.001	0.001	0.000	0.000	0.000	0.000
30	A	29	ASP	-1	-0.943	-0.961	41.388	0.010	0.010	0.000	0.000	0.000	0.000
31	A	30	ILE	0	-0.096	-0.048	37.900	0.003	0.003	0.000	0.000	0.000	0.000
32	A	31	SER	0	0.016	-0.015	33.379	0.000	0.000	0.000	0.000	0.000	0.000
33	A	32	TYR	0	0.028	-0.011	27.346	0.002	0.002	0.000	0.000	0.000	0.000
34	A	33	VAL	0	-0.019	-0.005	31.409	0.002	0.002	0.000	0.000	0.000	0.000
35	A	34	GLN	0	0.060	0.029	32.669	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	35	PHE	0	0.055	0.039	33.024	0.000	0.000	0.000	0.000	0.000	0.000
37	A	36	GLY	0	0.031	0.010	32.709	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	37	VAL	0	0.012	-0.002	33.552	0.000	0.000	0.000	0.000	0.000	0.000
39	A	38	ILE	0	-0.002	0.003	36.321	0.000	0.000	0.000	0.000	0.000	0.000
40	A	39	GLN	0	-0.002	-0.007	34.620	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	40	VAL	0	-0.020	-0.020	33.638	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	41	LEU	0	-0.042	-0.044	36.355	0.000	0.000	0.000	0.000	0.000	0.000
43	A	42	ALA	0	0.010	0.027	39.775	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	43	LYS	1	0.780	0.917	34.828	-0.018	-0.018	0.000	0.000	0.000	0.000
45	A	44	SER	0	-0.019	0.003	38.925	0.001	0.001	0.000	0.000	0.000	0.000
46	A	45	GLY	0	0.055	0.024	40.760	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	46	LYS	1	0.863	0.935	43.070	-0.021	-0.021	0.000	0.000	0.000	0.000
48	A	47	VAL	0	0.018	0.027	39.214	0.001	0.001	0.000	0.000	0.000	0.000
49	A	48	SER	0	0.058	0.035	40.435	0.000	0.000	0.000	0.000	0.000	0.000
50	A	49	MET	0	0.020	-0.012	38.524	0.000	0.000	0.000	0.000	0.000	0.000
51	A	50	SER	0	0.000	0.010	36.785	0.002	0.002	0.000	0.000	0.000	0.000
52	A	51	LYS	1	1.025	1.005	35.279	-0.045	-0.045	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.025	0.002	35.445	0.001	0.001	0.000	0.000	0.000	0.000
54	A	53	ILE	0	-0.037	-0.038	32.102	0.001	0.001	0.000	0.000	0.000	0.000
55	A	54	GLU	-1	-0.940	-0.972	31.244	0.069	0.069	0.000	0.000	0.000	0.000
56	A	55	ASN	0	-0.045	-0.032	30.493	0.005	0.005	0.000	0.000	0.000	0.000
57	A	56	MET	0	-0.065	-0.011	30.778	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	57	GLY	0	0.001	0.004	27.033	0.006	0.006	0.000	0.000	0.000	0.000
59	A	58	CYS	0	-0.027	-0.016	24.666	0.015	0.015	0.000	0.000	0.000	0.000
60	A	59	VAL	0	0.017	0.021	26.483	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	60	PRO	0	-0.002	0.005	28.185	0.007	0.007	0.000	0.000	0.000	0.000
62	A	61	SER	0	0.018	-0.002	29.373	0.000	0.000	0.000	0.000	0.000	0.000
63	A	62	ASN	0	0.014	-0.012	31.129	0.000	0.000	0.000	0.000	0.000	0.000
64	A	63	MET	0	0.084	0.056	33.409	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	64	THR	0	0.033	0.014	35.904	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	65	THR	0	-0.001	0.003	38.467	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	66	MET	0	-0.045	-0.003	34.728	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	67	ILE	0	0.072	0.014	37.738	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	68	GLN	0	0.025	0.003	40.754	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	69	ARG	1	0.890	0.962	41.153	-0.029	-0.029	0.000	0.000	0.000	0.000
71	A	70	MET	0	0.081	0.033	39.379	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	71	LYS	1	0.901	0.968	43.107	-0.027	-0.027	0.000	0.000	0.000	0.000
73	A	72	ARG	1	0.825	0.911	45.613	-0.023	-0.023	0.000	0.000	0.000	0.000
74	A	73	ASP	-1	-0.839	-0.912	43.917	0.019	0.019	0.000	0.000	0.000	0.000
75	A	74	GLY	0	-0.009	0.018	47.019	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	75	TYR	0	0.013	0.025	43.052	0.000	0.000	0.000	0.000	0.000	0.000
77	A	76	VAL	0	0.021	0.006	41.804	0.000	0.000	0.000	0.000	0.000	0.000
78	A	77	MET	0	-0.021	-0.008	45.251	0.000	0.000	0.000	0.000	0.000	0.000
79	A	78	THR	0	-0.031	-0.036	44.414	0.001	0.001	0.000	0.000	0.000	0.000
80	A	79	GLU	-1	-0.828	-0.919	47.269	0.022	0.022	0.000	0.000	0.000	0.000
81	A	80	LYS	1	0.875	0.952	46.378	-0.036	-0.036	0.000	0.000	0.000	0.000
82	A	81	ASN	0	0.013	-0.012	47.643	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	82	PRO	0	-0.008	-0.009	49.988	0.001	0.001	0.000	0.000	0.000	0.000
84	A	83	ASN	0	-0.041	0.006	50.573	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	84	ASP	-1	-0.821	-0.911	46.277	0.041	0.041	0.000	0.000	0.000	0.000
86	A	85	GLN	0	0.090	0.024	48.922	0.001	0.001	0.000	0.000	0.000	0.000
87	A	86	ARG	1	0.831	0.910	46.057	-0.041	-0.041	0.000	0.000	0.000	0.000
88	A	87	GLU	-1	-0.869	-0.917	43.576	0.042	0.042	0.000	0.000	0.000	0.000
89	A	88	THR	0	-0.065	-0.040	43.702	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	89	LEU	0	0.011	0.010	43.686	0.002	0.002	0.000	0.000	0.000	0.000
91	A	90	VAL	0	-0.014	-0.030	41.646	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	91	TYR	0	-0.009	-0.009	43.862	0.000	0.000	0.000	0.000	0.000	0.000
93	A	92	LEU	0	0.038	0.031	41.953	0.000	0.000	0.000	0.000	0.000	0.000
94	A	93	THR	0	-0.023	-0.019	45.461	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	94	LYS	1	1.015	0.993	48.065	-0.008	-0.008	0.000	0.000	0.000	0.000
96	A	95	LYS	1	0.951	0.974	47.389	-0.014	-0.014	0.000	0.000	0.000	0.000
97	A	96	GLY	0	0.041	0.024	45.100	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	97	GLU	-1	-0.924	-0.960	44.332	0.013	0.013	0.000	0.000	0.000	0.000
99	A	98	GLU	-1	-1.008	-1.018	45.836	0.006	0.006	0.000	0.000	0.000	0.000
100	A	99	THR	0	0.021	-0.005	42.296	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	100	LYS	1	0.828	0.899	39.398	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	101	LYS	1	0.847	0.929	41.836	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	102	GLN	0	-0.006	-0.009	43.821	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	103	VAL	0	0.046	0.038	37.994	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	104	ASP	-1	-0.832	-0.903	38.752	0.003	0.003	0.000	0.000	0.000	0.000
106	A	105	VAL	0	-0.028	-0.006	39.145	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	106	GLN	0	0.142	0.106	38.009	0.000	0.000	0.000	0.000	0.000	0.000
108	A	107	TYR	0	-0.023	-0.006	30.521	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	108	SER	0	-0.013	-0.013	34.545	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	109	ASP	-1	-0.836	-0.917	35.652	-0.021	-0.021	0.000	0.000	0.000	0.000
111	A	110	PHE	0	0.006	0.008	27.956	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	111	LEU	0	0.003	-0.009	29.905	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	112	LYS	1	0.817	0.917	30.849	0.017	0.017	0.000	0.000	0.000	0.000
114	A	113	GLU	-1	-0.944	-0.981	32.102	-0.032	-0.032	0.000	0.000	0.000	0.000
115	A	114	ASN	0	-0.068	-0.026	27.853	-0.006	-0.006	0.000	0.000	0.000	0.000
116	A	115	CYS	0	-0.079	-0.037	26.798	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	116	GLY	0	0.046	0.029	27.821	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	117	CYS	0	-0.063	-0.026	25.226	0.000	0.000	0.000	0.000	0.000	0.000
119	A	118	PHE	0	-0.020	0.005	21.514	-0.007	-0.007	0.000	0.000	0.000	0.000
120	A	119	THR	0	0.017	0.007	26.793	0.010	0.010	0.000	0.000	0.000	0.000
121	A	120	LYS	1	0.941	0.944	27.817	0.050	0.050	0.000	0.000	0.000	0.000
122	A	121	GLU	-1	-0.948	-0.962	26.352	-0.107	-0.107	0.000	0.000	0.000	0.000
123	A	122	GLU	-1	-0.856	-0.941	23.776	-0.134	-0.134	0.000	0.000	0.000	0.000
124	A	123	GLU	-1	-0.916	-0.958	23.374	-0.065	-0.065	0.000	0.000	0.000	0.000
125	A	124	GLY	0	0.038	0.026	24.533	0.003	0.003	0.000	0.000	0.000	0.000
126	A	125	ILE	0	0.009	0.013	19.861	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	126	LEU	0	-0.019	-0.019	18.658	-0.007	-0.007	0.000	0.000	0.000	0.000
128	A	127	GLU	-1	-0.954	-0.974	20.070	-0.038	-0.038	0.000	0.000	0.000	0.000
129	A	128	ASP	-1	-0.873	-0.934	20.999	-0.074	-0.074	0.000	0.000	0.000	0.000
130	A	129	LEU	0	-0.078	-0.046	15.048	0.003	0.003	0.000	0.000	0.000	0.000
131	A	130	LEU	0	-0.004	-0.011	16.569	0.016	0.016	0.000	0.000	0.000	0.000
132	A	131	LEU	0	-0.014	-0.008	18.220	0.031	0.031	0.000	0.000	0.000	0.000
133	A	132	LYS	1	0.927	0.971	14.283	0.185	0.185	0.000	0.000	0.000	0.000
134	A	133	TRP	0	-0.011	-0.011	10.515	-0.010	-0.010	0.000	0.000	0.000	0.000
135	A	134	LYS	1	0.949	0.967	15.428	0.015	0.015	0.000	0.000	0.000	0.000
136	A	135	LYS	1	0.931	0.962	18.473	0.011	0.011	0.000	0.000	0.000	0.000
137	A	136	HIS	0	-0.045	-0.005	10.965	-0.038	-0.038	0.000	0.000	0.000	0.000
138	A	137	LEU	0	-0.027	-0.011	12.686	0.038	0.038	0.000	0.000	0.000	0.000
139	A	138	ASN	0	-0.018	0.010	16.108	0.011	0.011	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)