FMO DATABASE

FMODB ID: YZK92

Calculation Name: 3BJA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BJA

Chain ID: A

ChEMBL ID:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1210300.970695
FMO2-HF: Nuclear repulsion	1151903.298904
FMO2-HF: Total energy	-58397.671791
FMO2-MP2: Total energy	-58562.206533

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.
-13.329	-18.89	17.903	-6.6	-5.743	-0.009

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 : 0.041 / q_NPA : 0.018

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	0.087	0.040	2.001	-5.674	-5.886	5.381	-2.601	-2.568	-0.030
4	A	3	ASN	0	0.006	-0.008	1.991	-7.495	-13.077	12.523	-3.929	-3.013	0.021
5	A	4	ARG	1	0.937	0.968	4.449	0.502	0.735	-0.001	-0.070	-0.162	0.000
6	A	5	GLU	-1	-0.875	-0.939	6.380	-0.422	-0.422	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.025	0.013	7.641	0.199	0.199	0.000	0.000	0.000	0.000
8	A	7	TYR	0	-0.007	-0.011	8.701	0.002	0.002	0.000	0.000	0.000	0.000
9	A	8	GLY	0	0.012	0.003	10.426	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	9	ASN	0	0.019	-0.003	11.817	0.051	0.051	0.000	0.000	0.000	0.000
11	A	10	ILE	0	-0.006	0.005	13.280	0.011	0.011	0.000	0.000	0.000	0.000
12	A	11	ARG	1	0.893	0.944	14.530	-0.179	-0.179	0.000	0.000	0.000	0.000
13	A	12	ASP	-1	-0.852	-0.933	16.519	-0.068	-0.068	0.000	0.000	0.000	0.000
14	A	13	VAL	0	0.001	0.001	18.096	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	14	TYR	0	-0.007	0.000	19.524	0.005	0.005	0.000	0.000	0.000	0.000
16	A	15	HIS	0	-0.020	-0.017	18.450	0.004	0.004	0.000	0.000	0.000	0.000
17	A	16	LEU	0	-0.042	-0.023	21.793	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	17	LEU	0	0.021	0.018	23.027	0.000	0.000	0.000	0.000	0.000	0.000
19	A	18	GLN	0	-0.013	-0.010	25.243	0.001	0.001	0.000	0.000	0.000	0.000
20	A	19	LYS	1	0.962	0.991	26.809	0.022	0.022	0.000	0.000	0.000	0.000
21	A	20	ASN	0	-0.031	-0.031	28.544	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	21	LEU	0	-0.030	0.007	29.902	0.000	0.000	0.000	0.000	0.000	0.000
23	A	22	ASP	-1	-0.792	-0.919	30.740	0.032	0.032	0.000	0.000	0.000	0.000
24	A	23	LYS	1	0.772	0.857	32.996	0.001	0.001	0.000	0.000	0.000	0.000
25	A	24	ALA	0	-0.004	0.008	34.402	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	25	ILE	0	-0.064	-0.032	34.969	0.001	0.001	0.000	0.000	0.000	0.000
27	A	26	GLU	-1	-0.797	-0.874	37.529	0.002	0.002	0.000	0.000	0.000	0.000
28	A	27	GLN	0	-0.038	-0.014	38.982	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	28	TYR	0	-0.041	-0.030	40.873	0.000	0.000	0.000	0.000	0.000	0.000
30	A	29	ASP	-1	-0.944	-0.963	41.829	0.017	0.017	0.000	0.000	0.000	0.000
31	A	30	ILE	0	-0.112	-0.060	38.471	0.003	0.003	0.000	0.000	0.000	0.000
32	A	31	SER	0	0.038	0.006	33.509	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	32	TYR	0	0.017	-0.020	27.747	0.003	0.003	0.000	0.000	0.000	0.000
34	A	33	VAL	0	-0.006	0.000	31.401	0.005	0.005	0.000	0.000	0.000	0.000
35	A	34	GLN	0	0.029	-0.007	32.971	0.000	0.000	0.000	0.000	0.000	0.000
36	A	35	PHE	0	0.037	0.025	33.817	0.001	0.001	0.000	0.000	0.000	0.000
37	A	36	GLY	0	0.039	0.023	33.372	0.001	0.001	0.000	0.000	0.000	0.000
38	A	37	VAL	0	0.025	-0.007	34.210	0.001	0.001	0.000	0.000	0.000	0.000
39	A	38	ILE	0	-0.038	-0.017	37.018	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	39	GLN	0	-0.030	-0.025	35.527	0.001	0.001	0.000	0.000	0.000	0.000
41	A	40	VAL	0	-0.011	0.004	34.520	0.001	0.001	0.000	0.000	0.000	0.000
42	A	41	LEU	0	-0.049	-0.031	37.269	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	42	ALA	0	0.026	0.024	40.355	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	43	LYS	1	0.801	0.905	35.768	-0.052	-0.052	0.000	0.000	0.000	0.000
45	A	44	SER	0	-0.017	0.005	39.490	0.002	0.002	0.000	0.000	0.000	0.000
46	A	45	GLY	0	0.046	0.014	41.091	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	46	LYS	1	0.789	0.882	43.429	-0.035	-0.035	0.000	0.000	0.000	0.000
48	A	47	VAL	0	0.013	0.023	39.962	0.001	0.001	0.000	0.000	0.000	0.000
49	A	48	SER	0	0.008	-0.002	41.461	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	49	MET	0	0.009	-0.010	38.384	0.002	0.002	0.000	0.000	0.000	0.000
51	A	50	SER	0	-0.003	0.017	37.039	0.003	0.003	0.000	0.000	0.000	0.000
52	A	51	LYS	1	0.910	0.942	34.935	-0.082	-0.082	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.009	-0.007	36.247	0.002	0.002	0.000	0.000	0.000	0.000
54	A	53	ILE	0	-0.031	-0.032	32.230	0.002	0.002	0.000	0.000	0.000	0.000
55	A	54	GLU	-1	-0.860	-0.926	31.856	0.094	0.094	0.000	0.000	0.000	0.000
56	A	55	ASN	0	-0.020	-0.006	31.382	0.010	0.010	0.000	0.000	0.000	0.000
57	A	56	MET	0	-0.052	-0.009	31.391	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	57	GLY	0	0.003	-0.001	27.755	0.005	0.005	0.000	0.000	0.000	0.000
59	A	58	CYS	0	-0.034	-0.019	24.673	0.015	0.015	0.000	0.000	0.000	0.000
60	A	59	VAL	0	0.021	0.026	26.877	-0.012	-0.012	0.000	0.000	0.000	0.000
61	A	60	PRO	0	0.008	0.020	28.180	0.004	0.004	0.000	0.000	0.000	0.000
62	A	61	SER	0	0.027	-0.008	29.061	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	62	ASN	0	0.011	-0.006	30.846	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	63	MET	0	0.063	0.040	33.294	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	64	THR	0	0.024	0.012	35.759	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	65	THR	0	0.013	0.003	38.298	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	66	MET	0	-0.028	0.032	34.976	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	67	ILE	0	0.073	0.023	37.903	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	68	GLN	0	0.010	-0.005	40.776	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	69	ARG	1	0.887	0.959	40.673	-0.029	-0.029	0.000	0.000	0.000	0.000
71	A	70	MET	0	0.056	0.028	39.435	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	71	LYS	1	0.878	0.956	42.970	-0.034	-0.034	0.000	0.000	0.000	0.000
73	A	72	ARG	1	0.761	0.855	44.982	-0.026	-0.026	0.000	0.000	0.000	0.000
74	A	73	ASP	-1	-0.782	-0.859	43.987	0.024	0.024	0.000	0.000	0.000	0.000
75	A	74	GLY	0	0.026	0.022	46.782	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	75	TYR	0	0.014	0.017	43.575	0.000	0.000	0.000	0.000	0.000	0.000
77	A	76	VAL	0	0.008	-0.003	42.159	0.001	0.001	0.000	0.000	0.000	0.000
78	A	77	MET	0	-0.015	-0.003	45.594	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	78	THR	0	-0.006	-0.023	44.517	0.002	0.002	0.000	0.000	0.000	0.000
80	A	79	GLU	-1	-0.785	-0.857	47.560	0.034	0.034	0.000	0.000	0.000	0.000
81	A	80	LYS	1	0.881	0.942	46.652	-0.043	-0.043	0.000	0.000	0.000	0.000
82	A	81	ASN	0	0.027	0.010	47.044	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	82	PRO	0	0.006	-0.007	49.950	0.000	0.000	0.000	0.000	0.000	0.000
84	A	83	ASN	0	-0.045	-0.017	50.758	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	84	ASP	-1	-0.792	-0.864	47.707	0.051	0.051	0.000	0.000	0.000	0.000
86	A	85	GLN	0	0.075	0.028	48.914	0.002	0.002	0.000	0.000	0.000	0.000
87	A	86	ARG	1	0.829	0.885	45.785	-0.051	-0.051	0.000	0.000	0.000	0.000
88	A	87	GLU	-1	-0.856	-0.912	43.237	0.059	0.059	0.000	0.000	0.000	0.000
89	A	88	THR	0	-0.038	-0.032	44.032	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	89	LEU	0	-0.008	0.004	43.786	0.003	0.003	0.000	0.000	0.000	0.000
91	A	90	VAL	0	0.002	-0.022	41.435	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	91	TYR	0	-0.009	-0.023	44.265	0.001	0.001	0.000	0.000	0.000	0.000
93	A	92	LEU	0	0.049	0.035	42.435	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	93	THR	0	-0.055	-0.036	45.998	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	94	LYS	1	0.938	0.965	48.651	-0.018	-0.018	0.000	0.000	0.000	0.000
96	A	95	LYS	1	0.951	0.994	46.981	-0.023	-0.023	0.000	0.000	0.000	0.000
97	A	96	GLY	0	0.036	0.026	45.405	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	97	GLU	-1	-0.880	-0.930	45.091	0.031	0.031	0.000	0.000	0.000	0.000
99	A	98	GLU	-1	-0.898	-0.965	46.689	0.019	0.019	0.000	0.000	0.000	0.000
100	A	99	THR	0	-0.001	-0.021	43.161	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	100	LYS	1	0.785	0.875	39.826	-0.036	-0.036	0.000	0.000	0.000	0.000
102	A	101	LYS	1	0.841	0.906	42.204	-0.026	-0.026	0.000	0.000	0.000	0.000
103	A	102	GLN	0	-0.005	0.009	44.416	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	103	VAL	0	0.029	0.015	38.432	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	104	ASP	-1	-0.788	-0.872	39.127	0.032	0.032	0.000	0.000	0.000	0.000
106	A	105	VAL	0	-0.035	-0.002	39.360	0.000	0.000	0.000	0.000	0.000	0.000
107	A	106	GLN	0	0.078	0.039	38.504	0.000	0.000	0.000	0.000	0.000	0.000
108	A	107	TYR	0	-0.027	-0.004	31.240	0.000	0.000	0.000	0.000	0.000	0.000
109	A	108	SER	0	0.014	-0.002	34.834	0.000	0.000	0.000	0.000	0.000	0.000
110	A	109	ASP	-1	-0.837	-0.918	35.966	0.006	0.006	0.000	0.000	0.000	0.000
111	A	110	PHE	0	0.045	0.019	28.375	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	111	LEU	0	0.012	0.001	30.181	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	112	LYS	1	0.816	0.908	31.373	-0.009	-0.009	0.000	0.000	0.000	0.000
114	A	113	GLU	-1	-0.949	-0.977	32.595	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	114	ASN	0	-0.071	-0.033	28.386	-0.009	-0.009	0.000	0.000	0.000	0.000
116	A	115	CYS	0	-0.063	-0.036	26.864	0.005	0.005	0.000	0.000	0.000	0.000
117	A	116	GLY	0	0.001	0.025	28.166	0.002	0.002	0.000	0.000	0.000	0.000
118	A	117	CYS	0	-0.061	-0.028	25.497	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	118	PHE	0	-0.011	0.005	21.932	-0.006	-0.006	0.000	0.000	0.000	0.000
120	A	119	THR	0	-0.010	-0.041	27.138	0.006	0.006	0.000	0.000	0.000	0.000
121	A	120	LYS	1	0.801	0.850	27.757	0.000	0.000	0.000	0.000	0.000	0.000
122	A	121	GLU	-1	-0.938	-0.952	26.066	-0.029	-0.029	0.000	0.000	0.000	0.000
123	A	122	GLU	-1	-0.812	-0.884	23.373	-0.046	-0.046	0.000	0.000	0.000	0.000
124	A	123	GLU	-1	-0.807	-0.884	23.357	0.013	0.013	0.000	0.000	0.000	0.000
125	A	124	GLY	0	0.043	0.032	24.597	0.011	0.011	0.000	0.000	0.000	0.000
126	A	125	ILE	0	0.023	0.012	19.852	0.011	0.011	0.000	0.000	0.000	0.000
127	A	126	LEU	0	-0.024	-0.015	18.969	0.016	0.016	0.000	0.000	0.000	0.000
128	A	127	GLU	-1	-0.939	-0.967	20.353	0.081	0.081	0.000	0.000	0.000	0.000
129	A	128	ASP	-1	-0.882	-0.943	20.886	0.077	0.077	0.000	0.000	0.000	0.000
130	A	129	LEU	0	-0.079	-0.039	15.058	0.033	0.033	0.000	0.000	0.000	0.000
131	A	130	LEU	0	0.005	-0.003	16.891	0.056	0.056	0.000	0.000	0.000	0.000
132	A	131	LEU	0	-0.026	-0.014	18.737	0.035	0.035	0.000	0.000	0.000	0.000
133	A	132	LYS	1	0.947	0.977	14.498	-0.163	-0.163	0.000	0.000	0.000	0.000
134	A	133	TRP	0	-0.005	-0.009	11.607	0.028	0.028	0.000	0.000	0.000	0.000
135	A	134	LYS	1	0.942	0.958	15.784	-0.099	-0.099	0.000	0.000	0.000	0.000
136	A	135	LYS	1	0.935	0.965	18.923	-0.165	-0.165	0.000	0.000	0.000	0.000
137	A	136	HIS	0	-0.030	0.006	11.947	-0.055	-0.055	0.000	0.000	0.000	0.000
138	A	137	LEU	0	-0.045	-0.029	13.475	0.036	0.036	0.000	0.000	0.000	0.000
139	A	138	ASN	0	-0.050	-0.003	16.638	-0.031	-0.031	0.000	0.000	0.000	0.000

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