FMO DATABASE

FMODB ID: N9ZZQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1698914.846655
FMO2-HF: Nuclear repulsion	1633371.921259
FMO2-HF: Total energy	-65542.925396
FMO2-MP2: Total energy	-65736.994228

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.
-29.073	-24.868	16.511	-9.548	-11.167	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 : 0.009 / q_NPA : 0.000

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	-0.069	-0.033	3.486	3.132	5.762	0.023	-1.379	-1.274	0.004
4	D	5	GLN	0	0.011	-0.001	3.005	-4.784	-3.704	0.148	-0.472	-0.756	0.004
5	D	6	LEU	0	-0.004	-0.007	6.895	-0.269	-0.269	0.000	0.000	0.000	0.000
6	D	7	LEU	0	-0.047	-0.010	6.016	0.149	0.149	0.000	0.000	0.000	0.000
7	D	8	ILE	0	0.020	0.012	9.807	-0.389	-0.389	0.000	0.000	0.000	0.000
8	D	9	GLU	-1	-0.787	-0.843	10.923	1.935	1.935	0.000	0.000	0.000	0.000
9	D	10	THR	0	0.023	-0.001	14.721	-0.128	-0.128	0.000	0.000	0.000	0.000
10	D	11	TRP	0	0.019	-0.001	15.070	-0.016	-0.016	0.000	0.000	0.000	0.000
11	D	12	GLY	0	0.009	-0.001	20.311	-0.042	-0.042	0.000	0.000	0.000	0.000
12	D	13	GLN	0	-0.043	-0.016	23.834	0.017	0.017	0.000	0.000	0.000	0.000
13	D	14	PRO	0	-0.028	-0.011	26.448	-0.009	-0.009	0.000	0.000	0.000	0.000
14	D	15	GLY	0	-0.018	-0.005	28.387	-0.010	-0.010	0.000	0.000	0.000	0.000
15	D	16	GLU	-1	-0.893	-0.940	31.456	0.141	0.141	0.000	0.000	0.000	0.000
16	D	17	ILE	0	-0.025	-0.021	32.637	0.017	0.017	0.000	0.000	0.000	0.000
17	D	18	ILE	0	-0.013	0.004	35.255	-0.012	-0.012	0.000	0.000	0.000	0.000
18	D	19	ASP	-1	-0.732	-0.848	37.915	0.154	0.154	0.000	0.000	0.000	0.000
19	D	20	GLY	0	-0.022	-0.008	40.551	-0.007	-0.007	0.000	0.000	0.000	0.000
20	D	21	VAL	0	-0.003	-0.012	41.849	-0.007	-0.007	0.000	0.000	0.000	0.000
21	D	22	PRO	0	-0.029	-0.020	43.173	0.004	0.004	0.000	0.000	0.000	0.000
22	D	23	MET	0	0.023	0.030	38.873	-0.006	-0.006	0.000	0.000	0.000	0.000
23	D	24	LEU	0	-0.015	-0.008	43.417	-0.002	-0.002	0.000	0.000	0.000	0.000
24	D	25	GLU	-1	-0.832	-0.894	43.148	0.116	0.116	0.000	0.000	0.000	0.000
25	D	26	SER	0	-0.031	-0.026	44.345	-0.006	-0.006	0.000	0.000	0.000	0.000
26	D	27	HIS	0	0.025	0.000	41.742	-0.001	-0.001	0.000	0.000	0.000	0.000
27	D	28	ASP	-1	-0.881	-0.968	45.276	0.075	0.075	0.000	0.000	0.000	0.000
28	D	29	GLY	0	-0.004	0.003	48.660	-0.005	-0.005	0.000	0.000	0.000	0.000
29	D	30	LYS	1	0.733	0.861	45.391	-0.077	-0.077	0.000	0.000	0.000	0.000
30	D	31	ASP	-1	-0.815	-0.872	49.385	0.067	0.067	0.000	0.000	0.000	0.000
31	D	32	LEU	0	-0.057	-0.033	49.194	0.003	0.003	0.000	0.000	0.000	0.000
32	D	33	GLY	0	0.050	0.037	48.409	-0.002	-0.002	0.000	0.000	0.000	0.000
33	D	34	LEU	0	-0.036	-0.020	46.815	0.001	0.001	0.000	0.000	0.000	0.000
34	D	35	LYS	1	0.817	0.889	41.065	-0.120	-0.120	0.000	0.000	0.000	0.000
35	D	36	PRO	0	0.017	0.025	43.441	0.002	0.002	0.000	0.000	0.000	0.000
36	D	37	GLY	0	0.011	-0.027	39.412	0.003	0.003	0.000	0.000	0.000	0.000
37	D	38	LEU	0	-0.019	0.026	35.579	-0.003	-0.003	0.000	0.000	0.000	0.000
38	D	39	TYR	0	-0.063	-0.055	34.085	0.008	0.008	0.000	0.000	0.000	0.000
39	D	40	ILE	0	0.016	0.009	29.178	-0.002	-0.002	0.000	0.000	0.000	0.000
40	D	41	GLU	-1	-0.881	-0.957	30.428	0.181	0.181	0.000	0.000	0.000	0.000
41	D	42	GLY	0	-0.010	-0.005	29.065	-0.006	-0.006	0.000	0.000	0.000	0.000
42	D	43	ILE	0	-0.032	-0.009	23.080	0.010	0.010	0.000	0.000	0.000	0.000
43	D	44	PHE	0	-0.019	-0.008	22.670	0.011	0.011	0.000	0.000	0.000	0.000
44	D	45	LEU	0	-0.020	-0.014	16.624	0.066	0.066	0.000	0.000	0.000	0.000
45	D	46	GLN	0	-0.056	-0.041	18.233	-0.040	-0.040	0.000	0.000	0.000	0.000
46	D	47	ALA	0	0.004	-0.001	16.702	0.073	0.073	0.000	0.000	0.000	0.000
47	D	48	GLU	-1	-0.872	-0.935	16.298	0.043	0.043	0.000	0.000	0.000	0.000
48	D	49	VAL	0	-0.009	0.006	16.511	-0.038	-0.038	0.000	0.000	0.000	0.000
49	D	50	VAL	0	-0.020	-0.007	13.569	0.075	0.075	0.000	0.000	0.000	0.000
50	D	51	ASN	0	-0.005	-0.010	13.128	-0.019	-0.019	0.000	0.000	0.000	0.000
51	D	52	ARG	1	0.875	0.925	15.165	-0.481	-0.481	0.000	0.000	0.000	0.000
52	D	53	ASN	0	-0.065	-0.022	11.549	-0.147	-0.147	0.000	0.000	0.000	0.000
53	D	54	LYS	1	0.922	0.963	11.188	-0.171	-0.171	0.000	0.000	0.000	0.000
54	D	55	ARG	1	0.890	0.948	7.645	-2.766	-2.766	0.000	0.000	0.000	0.000
55	D	56	LEU	0	0.021	0.024	9.981	-0.123	-0.123	0.000	0.000	0.000	0.000
56	D	57	TYR	0	0.002	-0.034	10.587	0.042	0.042	0.000	0.000	0.000	0.000
57	D	58	PRO	0	0.034	0.019	11.351	-0.069	-0.069	0.000	0.000	0.000	0.000
58	D	59	LYS	1	0.826	0.901	14.401	-0.070	-0.070	0.000	0.000	0.000	0.000
59	D	60	ARG	1	0.828	0.875	15.090	0.195	0.195	0.000	0.000	0.000	0.000
60	D	61	ILE	0	-0.020	-0.001	11.361	-0.018	-0.018	0.000	0.000	0.000	0.000
61	D	62	LEU	0	0.044	0.027	15.254	0.061	0.061	0.000	0.000	0.000	0.000
62	D	63	GLU	-1	-0.864	-0.939	16.447	0.121	0.121	0.000	0.000	0.000	0.000
63	D	64	LYS	1	0.774	0.874	17.177	-0.164	-0.164	0.000	0.000	0.000	0.000
64	D	65	ALA	0	0.016	0.009	15.039	-0.002	-0.002	0.000	0.000	0.000	0.000
65	D	66	VAL	0	0.028	0.006	17.146	0.007	0.007	0.000	0.000	0.000	0.000
66	D	67	LYS	1	0.951	0.982	20.150	-0.141	-0.141	0.000	0.000	0.000	0.000
67	D	68	ASP	-1	-0.833	-0.893	19.021	0.194	0.194	0.000	0.000	0.000	0.000
68	D	69	TYR	0	-0.008	-0.003	19.571	-0.010	-0.010	0.000	0.000	0.000	0.000
69	D	70	ILE	0	0.016	-0.005	21.454	-0.016	-0.016	0.000	0.000	0.000	0.000
70	D	71	ASN	0	-0.036	-0.018	24.631	-0.021	-0.021	0.000	0.000	0.000	0.000
71	D	72	GLU	-1	-0.811	-0.891	21.029	0.299	0.299	0.000	0.000	0.000	0.000
72	D	73	GLN	0	-0.010	0.008	20.868	-0.003	-0.003	0.000	0.000	0.000	0.000
73	D	74	VAL	0	-0.007	0.015	24.842	-0.012	-0.012	0.000	0.000	0.000	0.000
74	D	75	LEU	0	0.021	0.010	27.338	-0.016	-0.016	0.000	0.000	0.000	0.000
75	D	76	THR	0	-0.058	-0.042	27.341	-0.010	-0.010	0.000	0.000	0.000	0.000
76	D	77	LYS	1	0.775	0.878	30.270	-0.207	-0.207	0.000	0.000	0.000	0.000
77	D	78	GLN	0	0.026	0.016	26.533	0.008	0.008	0.000	0.000	0.000	0.000
78	D	79	ALA	0	-0.035	0.015	24.976	0.026	0.026	0.000	0.000	0.000	0.000
79	D	80	LEU	0	0.003	-0.010	26.003	-0.008	-0.008	0.000	0.000	0.000	0.000
80	D	81	GLY	0	0.042	0.016	24.011	0.038	0.038	0.000	0.000	0.000	0.000
81	D	82	GLU	-1	-0.696	-0.810	22.664	0.441	0.441	0.000	0.000	0.000	0.000
82	D	83	LEU	0	0.003	0.017	25.431	0.002	0.002	0.000	0.000	0.000	0.000
83	D	84	ASN	0	-0.056	-0.042	23.318	0.000	0.000	0.000	0.000	0.000	0.000
84	D	85	ALA	0	0.041	0.016	18.393	-0.002	-0.002	0.000	0.000	0.000	0.000
85	D	86	PRO	0	-0.008	0.011	18.917	0.059	0.059	0.000	0.000	0.000	0.000
86	D	87	PRO	0	0.007	0.000	15.963	0.084	0.084	0.000	0.000	0.000	0.000
87	D	88	ARG	1	0.756	0.837	16.831	-0.507	-0.507	0.000	0.000	0.000	0.000
88	D	89	ALA	0	0.048	0.023	14.617	0.043	0.043	0.000	0.000	0.000	0.000
89	D	90	ASN	0	-0.023	-0.003	16.041	0.021	0.021	0.000	0.000	0.000	0.000
90	D	91	VAL	0	0.084	0.041	19.781	0.026	0.026	0.000	0.000	0.000	0.000
91	D	92	ASP	-1	-0.866	-0.908	22.619	0.297	0.297	0.000	0.000	0.000	0.000
92	D	93	PRO	0	0.008	-0.011	25.481	-0.003	-0.003	0.000	0.000	0.000	0.000
93	D	94	MET	0	-0.024	-0.007	28.904	-0.020	-0.020	0.000	0.000	0.000	0.000
94	D	95	GLN	0	-0.082	-0.066	25.946	0.006	0.006	0.000	0.000	0.000	0.000
95	D	96	ALA	0	-0.028	-0.006	27.436	0.018	0.018	0.000	0.000	0.000	0.000
96	D	97	ALA	0	-0.012	-0.011	28.217	-0.020	-0.020	0.000	0.000	0.000	0.000
97	D	98	ILE	0	-0.027	-0.006	25.603	-0.018	-0.018	0.000	0.000	0.000	0.000
98	D	99	ILE	0	0.007	0.001	28.705	0.011	0.011	0.000	0.000	0.000	0.000
99	D	100	ILE	0	0.000	0.004	23.873	-0.013	-0.013	0.000	0.000	0.000	0.000
100	D	101	GLU	-1	-0.818	-0.888	28.391	0.157	0.157	0.000	0.000	0.000	0.000
101	D	102	ASP	-1	-0.845	-0.931	29.781	0.163	0.163	0.000	0.000	0.000	0.000
102	D	103	MET	0	0.001	-0.009	21.809	0.027	0.027	0.000	0.000	0.000	0.000
103	D	104	TRP	0	-0.065	0.000	27.039	-0.017	-0.017	0.000	0.000	0.000	0.000
104	D	105	TRP	0	0.043	0.018	19.472	0.017	0.017	0.000	0.000	0.000	0.000
105	D	106	LYS	1	0.912	0.951	26.187	-0.159	-0.159	0.000	0.000	0.000	0.000
106	D	107	GLY	0	0.028	0.024	26.454	0.008	0.008	0.000	0.000	0.000	0.000
107	D	108	ASN	0	0.003	-0.019	20.895	-0.018	-0.018	0.000	0.000	0.000	0.000
108	D	109	ASP	-1	-0.786	-0.872	21.394	0.278	0.278	0.000	0.000	0.000	0.000
109	D	110	VAL	0	-0.025	-0.019	20.051	-0.027	-0.027	0.000	0.000	0.000	0.000
110	D	111	TYR	0	-0.011	-0.017	23.194	0.018	0.018	0.000	0.000	0.000	0.000
111	D	112	GLY	0	0.020	0.001	26.175	0.005	0.005	0.000	0.000	0.000	0.000
112	D	113	ARG	1	0.804	0.902	27.892	-0.173	-0.173	0.000	0.000	0.000	0.000
113	D	114	ALA	0	-0.015	-0.018	27.923	0.006	0.006	0.000	0.000	0.000	0.000
114	D	115	ARG	1	0.829	0.940	30.058	-0.170	-0.170	0.000	0.000	0.000	0.000
115	D	116	VAL	0	-0.015	-0.016	31.823	0.018	0.018	0.000	0.000	0.000	0.000
116	D	117	ILE	0	-0.041	-0.020	30.871	-0.015	-0.015	0.000	0.000	0.000	0.000
117	D	118	GLU	-1	-0.782	-0.895	34.430	0.161	0.161	0.000	0.000	0.000	0.000
118	D	119	GLY	0	-0.017	-0.017	38.027	-0.005	-0.005	0.000	0.000	0.000	0.000
119	D	120	ASP	-1	-0.810	-0.899	34.502	0.204	0.204	0.000	0.000	0.000	0.000
120	D	121	HIS	0	-0.084	-0.041	37.908	-0.001	-0.001	0.000	0.000	0.000	0.000
121	D	122	GLY	0	0.020	0.012	35.160	-0.001	-0.001	0.000	0.000	0.000	0.000
122	D	123	PRO	0	-0.037	-0.028	30.079	-0.002	-0.002	0.000	0.000	0.000	0.000
123	D	124	GLY	0	0.029	0.019	32.222	0.009	0.009	0.000	0.000	0.000	0.000
124	D	125	ASP	-1	-0.750	-0.876	33.590	0.166	0.166	0.000	0.000	0.000	0.000
125	D	126	LYS	1	0.836	0.928	33.441	-0.215	-0.215	0.000	0.000	0.000	0.000
126	D	127	LEU	0	-0.032	-0.015	29.542	0.002	0.002	0.000	0.000	0.000	0.000
127	D	128	ALA	0	0.043	0.005	33.099	-0.004	-0.004	0.000	0.000	0.000	0.000
128	D	129	ALA	0	-0.031	-0.014	36.311	-0.008	-0.008	0.000	0.000	0.000	0.000
129	D	130	ASN	0	-0.037	-0.014	32.430	-0.017	-0.017	0.000	0.000	0.000	0.000
130	D	131	ILE	0	0.003	0.007	32.284	-0.004	-0.004	0.000	0.000	0.000	0.000
131	D	132	ARG	1	0.735	0.825	36.082	-0.162	-0.162	0.000	0.000	0.000	0.000
132	D	133	ALA	0	-0.055	-0.011	38.783	-0.009	-0.009	0.000	0.000	0.000	0.000
133	D	134	GLY	0	-0.007	-0.003	38.578	-0.005	-0.005	0.000	0.000	0.000	0.000
134	D	135	TRP	0	-0.088	-0.042	28.469	0.006	0.006	0.000	0.000	0.000	0.000
135	D	136	ILE	0	0.084	0.035	30.877	0.000	0.000	0.000	0.000	0.000	0.000
136	D	137	PRO	0	-0.021	0.007	28.167	0.010	0.010	0.000	0.000	0.000	0.000
137	D	138	GLY	0	0.029	0.006	25.167	-0.007	-0.007	0.000	0.000	0.000	0.000
138	D	139	VAL	0	-0.020	-0.014	22.672	0.001	0.001	0.000	0.000	0.000	0.000
139	D	140	ALA	0	-0.016	-0.021	18.543	0.030	0.030	0.000	0.000	0.000	0.000
140	D	141	SER	0	0.066	0.047	15.690	-0.077	-0.077	0.000	0.000	0.000	0.000
141	D	142	ARG	1	0.722	0.803	14.474	-0.545	-0.545	0.000	0.000	0.000	0.000
142	D	143	GLY	0	0.086	0.044	12.963	-0.189	-0.189	0.000	0.000	0.000	0.000
143	D	144	LEU	0	-0.039	-0.007	9.825	0.256	0.256	0.000	0.000	0.000	0.000
144	D	145	GLY	0	0.060	0.022	7.497	-0.721	-0.721	0.000	0.000	0.000	0.000
145	D	146	SER	0	0.010	0.026	2.416	-1.776	-0.246	1.824	-1.312	-2.042	0.017
146	D	147	LEU	0	0.003	-0.001	1.993	-10.419	-10.146	6.255	-2.915	-3.612	0.037
147	D	148	THR	0	0.001	-0.007	1.947	-13.176	-14.984	8.263	-3.383	-3.072	-0.044
148	D	149	ASP	-1	-0.818	-0.893	4.125	0.862	0.972	-0.001	-0.014	-0.095	0.000
149	D	150	THR	0	0.027	-0.010	6.245	-0.022	-0.022	0.000	0.000	0.000	0.000
150	D	151	ASN	0	-0.085	-0.043	9.978	0.066	0.066	0.000	0.000	0.000	0.000
151	D	152	GLU	-1	-0.867	-0.912	12.054	-0.164	-0.164	0.000	0.000	0.000	0.000
152	D	153	GLY	0	-0.038	-0.016	12.633	0.074	0.074	0.000	0.000	0.000	0.000
153	D	154	TYR	0	-0.105	-0.077	10.900	0.162	0.162	0.000	0.000	0.000	0.000
154	D	155	ARG	1	0.838	0.922	4.679	-0.677	-0.582	-0.001	-0.001	-0.092	0.000
155	D	156	ILE	0	0.043	0.020	6.920	0.395	0.395	0.000	0.000	0.000	0.000
156	D	157	VAL	0	-0.027	-0.013	6.054	-0.077	-0.077	0.000	0.000	0.000	0.000
157	D	158	ASN	0	-0.020	0.002	3.588	-0.716	-0.421	0.000	-0.072	-0.224	0.000
158	D	159	GLU	-1	-0.785	-0.871	7.786	0.159	0.159	0.000	0.000	0.000	0.000
159	D	160	GLY	0	-0.019	-0.010	9.521	-0.144	-0.144	0.000	0.000	0.000	0.000
160	D	161	PHE	0	-0.033	-0.016	9.747	0.110	0.110	0.000	0.000	0.000	0.000
161	D	162	LYS	1	0.797	0.885	10.932	-0.668	-0.668	0.000	0.000	0.000	0.000
162	D	163	LEU	0	0.008	0.010	13.510	0.171	0.171	0.000	0.000	0.000	0.000
163	D	164	THR	0	-0.072	-0.071	14.927	-0.051	-0.051	0.000	0.000	0.000	0.000
164	D	165	VAL	0	0.005	0.012	17.379	-0.083	-0.083	0.000	0.000	0.000	0.000
165	D	166	GLY	0	0.018	0.007	18.585	0.068	0.068	0.000	0.000	0.000	0.000
166	D	167	VAL	0	-0.003	-0.010	20.615	0.011	0.011	0.000	0.000	0.000	0.000
167	D	168	ASP	-1	-0.764	-0.834	20.061	0.588	0.588	0.000	0.000	0.000	0.000
168	D	169	ALA	0	0.035	0.022	22.926	0.008	0.008	0.000	0.000	0.000	0.000
169	D	170	VAL	0	-0.019	-0.023	21.252	0.012	0.012	0.000	0.000	0.000	0.000
170	D	171	TRP	0	0.024	0.010	24.681	-0.024	-0.024	0.000	0.000	0.000	0.000
171	D	172	GLY	0	0.024	0.012	24.140	0.040	0.040	0.000	0.000	0.000	0.000
172	D	173	PRO	0	-0.039	-0.008	21.327	-0.037	-0.037	0.000	0.000	0.000	0.000

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