FMO DATABASE

FMODB ID: 85GGY

Calculation Name: 5JBL-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5JBL

Chain ID: D

ChEMBL ID:

UniProt ID: P06807

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	172
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1698868.884978
FMO2-HF: Nuclear repulsion	1633326.091281
FMO2-HF: Total energy	-65542.793697
FMO2-MP2: Total energy	-65736.870376

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(D:2:ASN)

Summations of interaction energy for fragment #1(D:2:ASN)

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.
-22.787	-14.917	9.902	-7.615	-10.157	0.018

Interaction energy analysis for fragmet #1(D:2:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.002

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	D	4	PRO	0	-0.068	-0.033	3.650	3.650	6.305	0.020	-1.377	-1.298	0.006
4	D	5	GLN	0	-0.004	-0.010	3.557	-3.045	-2.521	0.011	-0.167	-0.367	0.001
5	D	6	LEU	0	-0.013	-0.008	6.989	-0.167	-0.167	0.000	0.000	0.000	0.000
6	D	7	LEU	0	-0.053	-0.017	6.169	0.153	0.153	0.000	0.000	0.000	0.000
7	D	8	ILE	0	0.022	0.007	10.054	-0.236	-0.236	0.000	0.000	0.000	0.000
8	D	9	GLU	-1	-0.775	-0.834	11.277	1.085	1.085	0.000	0.000	0.000	0.000
9	D	10	THR	0	0.015	0.007	15.159	-0.063	-0.063	0.000	0.000	0.000	0.000
10	D	11	TRP	0	0.019	-0.029	15.337	-0.029	-0.029	0.000	0.000	0.000	0.000
11	D	12	GLY	0	-0.029	-0.007	20.552	-0.030	-0.030	0.000	0.000	0.000	0.000
12	D	13	GLN	0	-0.024	-0.022	23.790	0.011	0.011	0.000	0.000	0.000	0.000
13	D	14	PRO	0	-0.046	-0.015	26.485	-0.010	-0.010	0.000	0.000	0.000	0.000
14	D	15	GLY	0	-0.005	-0.004	28.614	-0.007	-0.007	0.000	0.000	0.000	0.000
15	D	16	GLU	-1	-0.900	-0.934	31.765	0.094	0.094	0.000	0.000	0.000	0.000
16	D	17	ILE	0	-0.025	-0.016	33.320	0.012	0.012	0.000	0.000	0.000	0.000
17	D	18	ILE	0	-0.012	0.001	35.519	-0.009	-0.009	0.000	0.000	0.000	0.000
18	D	19	ASP	-1	-0.784	-0.879	38.343	0.107	0.107	0.000	0.000	0.000	0.000
19	D	20	GLY	0	0.004	0.010	40.670	-0.005	-0.005	0.000	0.000	0.000	0.000
20	D	21	VAL	0	0.008	-0.002	41.929	-0.005	-0.005	0.000	0.000	0.000	0.000
21	D	22	PRO	0	-0.032	-0.025	43.169	0.004	0.004	0.000	0.000	0.000	0.000
22	D	23	MET	0	0.012	0.018	39.289	-0.004	-0.004	0.000	0.000	0.000	0.000
23	D	24	LEU	0	-0.015	-0.012	43.745	-0.001	-0.001	0.000	0.000	0.000	0.000
24	D	25	GLU	-1	-0.876	-0.929	43.382	0.095	0.095	0.000	0.000	0.000	0.000
25	D	26	SER	0	-0.044	-0.028	44.511	-0.003	-0.003	0.000	0.000	0.000	0.000
26	D	27	HIS	0	0.010	-0.009	41.563	0.002	0.002	0.000	0.000	0.000	0.000
27	D	28	ASP	-1	-0.887	-0.971	45.409	0.072	0.072	0.000	0.000	0.000	0.000
28	D	29	GLY	0	-0.005	0.004	48.765	-0.004	-0.004	0.000	0.000	0.000	0.000
29	D	30	LYS	1	0.736	0.863	45.223	-0.075	-0.075	0.000	0.000	0.000	0.000
30	D	31	ASP	-1	-0.810	-0.868	49.196	0.061	0.061	0.000	0.000	0.000	0.000
31	D	32	LEU	0	-0.057	-0.033	49.307	0.003	0.003	0.000	0.000	0.000	0.000
32	D	33	GLY	0	0.068	0.042	48.698	-0.003	-0.003	0.000	0.000	0.000	0.000
33	D	34	LEU	0	-0.033	-0.018	46.916	0.002	0.002	0.000	0.000	0.000	0.000
34	D	35	LYS	1	0.884	0.943	40.883	-0.103	-0.103	0.000	0.000	0.000	0.000
35	D	36	PRO	0	0.020	0.019	43.348	0.003	0.003	0.000	0.000	0.000	0.000
36	D	37	GLY	0	-0.004	-0.009	39.423	0.004	0.004	0.000	0.000	0.000	0.000
37	D	38	LEU	0	0.023	0.041	35.874	-0.004	-0.004	0.000	0.000	0.000	0.000
38	D	39	TYR	0	-0.073	-0.061	34.004	0.006	0.006	0.000	0.000	0.000	0.000
39	D	40	ILE	0	0.019	0.009	29.057	-0.004	-0.004	0.000	0.000	0.000	0.000
40	D	41	GLU	-1	-0.917	-0.978	30.646	0.143	0.143	0.000	0.000	0.000	0.000
41	D	42	GLY	0	0.001	-0.004	29.288	-0.010	-0.010	0.000	0.000	0.000	0.000
42	D	43	ILE	0	-0.023	-0.002	23.227	0.012	0.012	0.000	0.000	0.000	0.000
43	D	44	PHE	0	-0.006	-0.008	22.833	0.008	0.008	0.000	0.000	0.000	0.000
44	D	45	LEU	0	-0.022	-0.014	17.023	0.048	0.048	0.000	0.000	0.000	0.000
45	D	46	GLN	0	-0.063	-0.040	18.506	-0.038	-0.038	0.000	0.000	0.000	0.000
46	D	47	ALA	0	-0.008	-0.002	16.915	0.048	0.048	0.000	0.000	0.000	0.000
47	D	48	GLU	-1	-0.888	-0.947	16.460	0.088	0.088	0.000	0.000	0.000	0.000
48	D	49	VAL	0	-0.003	0.004	16.755	-0.041	-0.041	0.000	0.000	0.000	0.000
49	D	50	VAL	0	-0.023	-0.002	13.359	0.045	0.045	0.000	0.000	0.000	0.000
50	D	51	ASN	0	-0.005	-0.006	13.243	-0.060	-0.060	0.000	0.000	0.000	0.000
51	D	52	ARG	1	0.924	0.958	15.213	-0.277	-0.277	0.000	0.000	0.000	0.000
52	D	53	ASN	0	-0.071	-0.031	11.457	-0.118	-0.118	0.000	0.000	0.000	0.000
53	D	54	LYS	1	0.921	0.963	10.996	0.030	0.030	0.000	0.000	0.000	0.000
54	D	55	ARG	1	0.898	0.948	7.850	-1.449	-1.449	0.000	0.000	0.000	0.000
55	D	56	LEU	0	0.026	0.030	10.184	-0.008	-0.008	0.000	0.000	0.000	0.000
56	D	57	TYR	0	0.002	-0.033	10.894	0.103	0.103	0.000	0.000	0.000	0.000
57	D	58	PRO	0	0.025	0.011	11.583	-0.071	-0.071	0.000	0.000	0.000	0.000
58	D	59	LYS	1	0.864	0.928	14.746	-0.084	-0.084	0.000	0.000	0.000	0.000
59	D	60	ARG	1	0.823	0.882	14.339	-0.085	-0.085	0.000	0.000	0.000	0.000
60	D	61	ILE	0	-0.028	-0.011	11.127	-0.009	-0.009	0.000	0.000	0.000	0.000
61	D	62	LEU	0	0.036	0.018	15.162	0.051	0.051	0.000	0.000	0.000	0.000
62	D	63	GLU	-1	-0.889	-0.960	16.573	0.164	0.164	0.000	0.000	0.000	0.000
63	D	64	LYS	1	0.766	0.868	17.142	-0.284	-0.284	0.000	0.000	0.000	0.000
64	D	65	ALA	0	0.024	0.010	15.176	-0.007	-0.007	0.000	0.000	0.000	0.000
65	D	66	VAL	0	0.023	0.005	17.282	-0.007	-0.007	0.000	0.000	0.000	0.000
66	D	67	LYS	1	0.945	0.977	20.382	-0.201	-0.201	0.000	0.000	0.000	0.000
67	D	68	ASP	-1	-0.826	-0.891	19.236	0.286	0.286	0.000	0.000	0.000	0.000
68	D	69	TYR	0	0.015	0.019	19.742	-0.019	-0.019	0.000	0.000	0.000	0.000
69	D	70	ILE	0	0.024	0.000	21.579	-0.021	-0.021	0.000	0.000	0.000	0.000
70	D	71	ASN	0	-0.031	-0.017	24.731	-0.028	-0.028	0.000	0.000	0.000	0.000
71	D	72	GLU	-1	-0.825	-0.889	20.846	0.358	0.358	0.000	0.000	0.000	0.000
72	D	73	GLN	0	-0.009	-0.006	20.883	-0.017	-0.017	0.000	0.000	0.000	0.000
73	D	74	VAL	0	-0.008	0.011	25.015	-0.018	-0.018	0.000	0.000	0.000	0.000
74	D	75	LEU	0	-0.002	-0.010	27.454	-0.018	-0.018	0.000	0.000	0.000	0.000
75	D	76	THR	0	-0.054	-0.031	27.547	-0.014	-0.014	0.000	0.000	0.000	0.000
76	D	77	LYS	1	0.813	0.907	30.228	-0.185	-0.185	0.000	0.000	0.000	0.000
77	D	78	GLN	0	0.056	0.021	26.821	0.000	0.000	0.000	0.000	0.000	0.000
78	D	79	ALA	0	-0.042	0.012	25.090	0.020	0.020	0.000	0.000	0.000	0.000
79	D	80	LEU	0	-0.011	-0.016	26.052	-0.009	-0.009	0.000	0.000	0.000	0.000
80	D	81	GLY	0	0.041	0.024	23.971	0.035	0.035	0.000	0.000	0.000	0.000
81	D	82	GLU	-1	-0.696	-0.809	22.996	0.333	0.333	0.000	0.000	0.000	0.000
82	D	83	LEU	0	0.001	0.008	25.461	0.001	0.001	0.000	0.000	0.000	0.000
83	D	84	ASN	0	-0.056	-0.047	23.753	-0.009	-0.009	0.000	0.000	0.000	0.000
84	D	85	ALA	0	0.035	0.020	18.566	0.007	0.007	0.000	0.000	0.000	0.000
85	D	86	PRO	0	-0.023	0.005	19.575	0.014	0.014	0.000	0.000	0.000	0.000
86	D	87	PRO	0	0.012	-0.003	16.048	0.071	0.071	0.000	0.000	0.000	0.000
87	D	88	ARG	1	0.782	0.851	16.646	-0.369	-0.369	0.000	0.000	0.000	0.000
88	D	89	ALA	0	0.057	0.025	14.579	0.028	0.028	0.000	0.000	0.000	0.000
89	D	90	ASN	0	-0.021	0.000	16.222	0.011	0.011	0.000	0.000	0.000	0.000
90	D	91	VAL	0	0.061	0.032	19.942	0.006	0.006	0.000	0.000	0.000	0.000
91	D	92	ASP	-1	-0.868	-0.914	22.905	0.230	0.230	0.000	0.000	0.000	0.000
92	D	93	PRO	0	0.009	-0.011	25.737	-0.006	-0.006	0.000	0.000	0.000	0.000
93	D	94	MET	0	-0.012	-0.002	28.953	-0.016	-0.016	0.000	0.000	0.000	0.000
94	D	95	GLN	0	-0.103	-0.077	26.326	-0.007	-0.007	0.000	0.000	0.000	0.000
95	D	96	ALA	0	-0.025	-0.001	27.779	0.011	0.011	0.000	0.000	0.000	0.000
96	D	97	ALA	0	0.002	-0.006	28.331	-0.016	-0.016	0.000	0.000	0.000	0.000
97	D	98	ILE	0	-0.027	-0.007	25.789	-0.017	-0.017	0.000	0.000	0.000	0.000
98	D	99	ILE	0	-0.006	-0.001	28.622	0.014	0.014	0.000	0.000	0.000	0.000
99	D	100	ILE	0	-0.006	0.000	23.951	-0.013	-0.013	0.000	0.000	0.000	0.000
100	D	101	GLU	-1	-0.844	-0.909	28.325	0.140	0.140	0.000	0.000	0.000	0.000
101	D	102	ASP	-1	-0.882	-0.941	29.744	0.149	0.149	0.000	0.000	0.000	0.000
102	D	103	MET	0	-0.012	-0.011	21.703	0.018	0.018	0.000	0.000	0.000	0.000
103	D	104	TRP	0	-0.026	0.009	27.171	-0.008	-0.008	0.000	0.000	0.000	0.000
104	D	105	TRP	0	0.012	0.011	19.642	0.006	0.006	0.000	0.000	0.000	0.000
105	D	106	LYS	1	0.943	0.972	26.493	-0.130	-0.130	0.000	0.000	0.000	0.000
106	D	107	GLY	0	0.034	0.022	26.773	0.001	0.001	0.000	0.000	0.000	0.000
107	D	108	ASN	0	0.015	-0.009	21.285	0.007	0.007	0.000	0.000	0.000	0.000
108	D	109	ASP	-1	-0.779	-0.864	21.551	0.195	0.195	0.000	0.000	0.000	0.000
109	D	110	VAL	0	-0.024	-0.023	20.646	-0.012	-0.012	0.000	0.000	0.000	0.000
110	D	111	TYR	0	-0.006	-0.016	23.727	0.004	0.004	0.000	0.000	0.000	0.000
111	D	112	GLY	0	0.033	0.006	26.668	0.011	0.011	0.000	0.000	0.000	0.000
112	D	113	ARG	1	0.837	0.919	27.961	-0.152	-0.152	0.000	0.000	0.000	0.000
113	D	114	ALA	0	-0.013	-0.014	28.197	0.009	0.009	0.000	0.000	0.000	0.000
114	D	115	ARG	1	0.866	0.931	30.309	-0.137	-0.137	0.000	0.000	0.000	0.000
115	D	116	VAL	0	0.003	-0.006	32.174	0.014	0.014	0.000	0.000	0.000	0.000
116	D	117	ILE	0	-0.063	-0.030	31.125	-0.010	-0.010	0.000	0.000	0.000	0.000
117	D	118	GLU	-1	-0.848	-0.904	34.764	0.114	0.114	0.000	0.000	0.000	0.000
118	D	119	GLY	0	-0.034	-0.029	38.173	-0.001	-0.001	0.000	0.000	0.000	0.000
119	D	120	ASP	-1	-0.806	-0.897	34.669	0.148	0.148	0.000	0.000	0.000	0.000
120	D	121	HIS	0	-0.083	-0.041	38.184	-0.001	-0.001	0.000	0.000	0.000	0.000
121	D	122	GLY	0	0.011	0.005	35.112	-0.001	-0.001	0.000	0.000	0.000	0.000
122	D	123	PRO	0	-0.041	-0.027	30.325	-0.004	-0.004	0.000	0.000	0.000	0.000
123	D	124	GLY	0	0.044	0.017	32.471	0.004	0.004	0.000	0.000	0.000	0.000
124	D	125	ASP	-1	-0.750	-0.875	33.841	0.116	0.116	0.000	0.000	0.000	0.000
125	D	126	LYS	1	0.822	0.920	33.531	-0.135	-0.135	0.000	0.000	0.000	0.000
126	D	127	LEU	0	-0.033	-0.016	29.847	-0.003	-0.003	0.000	0.000	0.000	0.000
127	D	128	ALA	0	0.051	0.017	33.367	-0.005	-0.005	0.000	0.000	0.000	0.000
128	D	129	ALA	0	-0.018	-0.005	36.547	-0.007	-0.007	0.000	0.000	0.000	0.000
129	D	130	ASN	0	-0.039	-0.019	32.629	-0.013	-0.013	0.000	0.000	0.000	0.000
130	D	131	ILE	0	0.005	0.005	32.554	-0.004	-0.004	0.000	0.000	0.000	0.000
131	D	132	ARG	1	0.728	0.819	36.306	-0.112	-0.112	0.000	0.000	0.000	0.000
132	D	133	ALA	0	-0.069	-0.017	38.942	-0.007	-0.007	0.000	0.000	0.000	0.000
133	D	134	GLY	0	0.000	-0.002	38.710	-0.005	-0.005	0.000	0.000	0.000	0.000
134	D	135	TRP	0	-0.079	-0.040	28.533	0.004	0.004	0.000	0.000	0.000	0.000
135	D	136	ILE	0	0.072	0.029	30.954	0.002	0.002	0.000	0.000	0.000	0.000
136	D	137	PRO	0	-0.012	0.009	28.394	0.003	0.003	0.000	0.000	0.000	0.000
137	D	138	GLY	0	0.026	0.005	25.304	-0.005	-0.005	0.000	0.000	0.000	0.000
138	D	139	VAL	0	-0.015	-0.003	22.689	0.007	0.007	0.000	0.000	0.000	0.000
139	D	140	ALA	0	-0.017	-0.025	18.548	0.008	0.008	0.000	0.000	0.000	0.000
140	D	141	SER	0	0.063	0.058	15.570	-0.040	-0.040	0.000	0.000	0.000	0.000
141	D	142	ARG	1	0.718	0.798	14.716	-0.437	-0.437	0.000	0.000	0.000	0.000
142	D	143	GLY	0	0.063	0.022	12.930	-0.124	-0.124	0.000	0.000	0.000	0.000
143	D	144	LEU	0	-0.050	-0.010	9.868	0.152	0.152	0.000	0.000	0.000	0.000
144	D	145	GLY	0	0.049	0.012	7.311	-0.633	-0.633	0.000	0.000	0.000	0.000
145	D	146	SER	0	0.058	0.054	2.481	-2.360	-0.476	1.357	-1.206	-2.036	0.014
146	D	147	LEU	0	-0.020	-0.008	2.139	-10.839	-8.940	3.362	-2.204	-3.057	0.032
147	D	148	THR	0	0.003	-0.018	2.126	-8.448	-8.003	5.152	-2.606	-2.991	-0.035
148	D	149	ASP	-1	-0.837	-0.920	4.439	-1.279	-1.198	-0.001	-0.006	-0.074	0.000
149	D	150	THR	0	0.038	-0.004	6.301	0.316	0.316	0.000	0.000	0.000	0.000
150	D	151	ASN	0	-0.085	-0.035	9.993	0.051	0.051	0.000	0.000	0.000	0.000
151	D	152	GLU	-1	-0.862	-0.917	12.033	-0.170	-0.170	0.000	0.000	0.000	0.000
152	D	153	GLY	0	-0.046	-0.018	12.467	0.075	0.075	0.000	0.000	0.000	0.000
153	D	154	TYR	0	-0.084	-0.061	10.577	0.103	0.103	0.000	0.000	0.000	0.000
154	D	155	ARG	1	0.842	0.927	4.181	1.126	1.237	-0.001	-0.005	-0.105	0.000
155	D	156	ILE	0	0.027	0.016	6.969	0.392	0.392	0.000	0.000	0.000	0.000
156	D	157	VAL	0	-0.025	-0.008	6.420	-0.014	-0.014	0.000	0.000	0.000	0.000
157	D	158	ASN	0	-0.006	0.017	3.487	-1.214	-0.943	0.002	-0.044	-0.229	0.000
158	D	159	GLU	-1	-0.794	-0.884	7.591	0.287	0.287	0.000	0.000	0.000	0.000
159	D	160	GLY	0	-0.010	-0.007	9.241	0.031	0.031	0.000	0.000	0.000	0.000
160	D	161	PHE	0	-0.023	-0.002	9.776	0.062	0.062	0.000	0.000	0.000	0.000
161	D	162	LYS	1	0.822	0.895	11.007	-0.722	-0.722	0.000	0.000	0.000	0.000
162	D	163	LEU	0	-0.003	0.005	13.395	0.137	0.137	0.000	0.000	0.000	0.000
163	D	164	THR	0	-0.057	-0.054	14.991	-0.041	-0.041	0.000	0.000	0.000	0.000
164	D	165	VAL	0	0.022	0.024	17.489	-0.070	-0.070	0.000	0.000	0.000	0.000
165	D	166	GLY	0	0.006	0.003	18.713	0.047	0.047	0.000	0.000	0.000	0.000
166	D	167	VAL	0	-0.005	-0.012	20.750	0.006	0.006	0.000	0.000	0.000	0.000
167	D	168	ASP	-1	-0.739	-0.820	20.224	0.440	0.440	0.000	0.000	0.000	0.000
168	D	169	ALA	0	0.012	0.005	23.113	-0.004	-0.004	0.000	0.000	0.000	0.000
169	D	170	VAL	0	-0.011	-0.015	21.324	0.007	0.007	0.000	0.000	0.000	0.000
170	D	171	TRP	0	0.012	0.009	24.731	-0.017	-0.017	0.000	0.000	0.000	0.000
171	D	172	GLY	0	-0.001	0.003	24.012	0.018	0.018	0.000	0.000	0.000	0.000
172	D	173	PRO	0	-0.012	-0.001	20.993	-0.024	-0.024	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:2:ASN)