FMO DATABASE

FMODB ID: R93R8

Calculation Name: 1JB2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JB2

Chain ID: A

ChEMBL ID:

UniProt ID: P61972

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	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1076288.979295
FMO2-HF: Nuclear repulsion	1026296.410075
FMO2-HF: Total energy	-49992.56922
FMO2-MP2: Total energy	-50136.661569

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:4:LYS)

Summations of interaction energy for fragment #1(A:4:LYS)

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.
-210.239	-207.065	23.466	-13.668	-12.97	-0.137

Interaction energy analysis for fragmet #1(A:4:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.925 / q_NPA : 0.949

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	6	ILE	0	0.041	0.017	3.405	-5.547	-3.444	0.029	-1.044	-1.088	0.003
4	A	7	TRP	0	0.059	0.018	6.012	0.609	0.609	0.000	0.000	0.000	0.000
5	A	8	GLU	-1	-0.803	-0.889	1.638	-136.895	-138.040	22.223	-11.638	-9.440	-0.134
6	A	9	GLN	0	-0.073	-0.039	2.545	-2.806	-0.908	1.217	-0.948	-2.166	-0.006
7	A	10	ILE	0	0.012	0.022	4.662	1.705	1.798	-0.001	-0.016	-0.076	0.000
8	A	11	GLY	0	0.065	0.041	7.539	2.064	2.064	0.000	0.000	0.000	0.000
9	A	12	SER	0	-0.053	-0.042	4.314	0.631	0.782	-0.001	-0.022	-0.127	0.000
10	A	13	SER	0	-0.060	-0.049	6.223	4.769	4.769	0.000	0.000	0.000	0.000
11	A	14	PHE	0	0.014	0.006	8.554	2.950	2.950	0.000	0.000	0.000	0.000
12	A	15	ILE	0	0.013	0.006	8.659	2.014	2.014	0.000	0.000	0.000	0.000
13	A	16	ASN	0	-0.016	-0.010	8.918	2.684	2.684	0.000	0.000	0.000	0.000
14	A	17	HIS	0	0.000	0.003	10.666	1.676	1.676	0.000	0.000	0.000	0.000
15	A	18	TYR	0	0.002	-0.006	13.649	1.730	1.730	0.000	0.000	0.000	0.000
16	A	19	TYR	0	0.003	-0.036	12.458	0.929	0.929	0.000	0.000	0.000	0.000
17	A	20	GLN	0	-0.048	-0.014	13.034	2.296	2.296	0.000	0.000	0.000	0.000
18	A	21	LEU	0	0.025	0.015	16.493	1.121	1.121	0.000	0.000	0.000	0.000
19	A	22	PHE	0	-0.034	-0.025	18.547	0.971	0.971	0.000	0.000	0.000	0.000
20	A	23	ASP	-1	-0.790	-0.887	18.305	-16.007	-16.007	0.000	0.000	0.000	0.000
21	A	24	ASN	0	-0.111	-0.055	18.972	0.910	0.910	0.000	0.000	0.000	0.000
22	A	25	ASP	-1	-0.810	-0.874	22.300	-11.333	-11.333	0.000	0.000	0.000	0.000
23	A	26	ARG	1	0.876	0.948	23.119	11.203	11.203	0.000	0.000	0.000	0.000
24	A	27	THR	0	-0.069	-0.052	24.142	0.100	0.100	0.000	0.000	0.000	0.000
25	A	28	GLN	0	-0.042	-0.041	23.135	-0.215	-0.215	0.000	0.000	0.000	0.000
26	A	29	LEU	0	0.004	0.015	19.709	-0.401	-0.401	0.000	0.000	0.000	0.000
27	A	30	GLY	0	0.002	0.003	22.446	-0.225	-0.225	0.000	0.000	0.000	0.000
28	A	31	ALA	0	-0.050	-0.036	22.274	0.242	0.242	0.000	0.000	0.000	0.000
29	A	32	ILE	0	-0.012	0.004	17.874	-0.276	-0.276	0.000	0.000	0.000	0.000
30	A	33	TYR	0	-0.025	-0.020	20.290	-0.411	-0.411	0.000	0.000	0.000	0.000
31	A	34	ILE	0	0.026	0.006	23.077	0.485	0.485	0.000	0.000	0.000	0.000
32	A	35	ASP	-1	-0.866	-0.955	25.683	-10.804	-10.804	0.000	0.000	0.000	0.000
33	A	36	ALA	0	-0.019	-0.013	27.063	0.263	0.263	0.000	0.000	0.000	0.000
34	A	37	SER	0	-0.025	-0.023	22.872	0.012	0.012	0.000	0.000	0.000	0.000
35	A	38	CYS	0	-0.101	-0.045	24.200	0.760	0.760	0.000	0.000	0.000	0.000
36	A	39	LEU	0	0.030	0.032	22.355	-0.613	-0.613	0.000	0.000	0.000	0.000
37	A	40	THR	0	-0.065	-0.038	23.526	0.746	0.746	0.000	0.000	0.000	0.000
38	A	41	TRP	0	0.024	0.006	21.351	-0.685	-0.685	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.787	-0.896	24.685	-11.039	-11.039	0.000	0.000	0.000	0.000
40	A	43	GLY	0	-0.079	-0.056	26.493	0.176	0.176	0.000	0.000	0.000	0.000
41	A	44	GLN	0	-0.005	0.026	28.088	0.182	0.182	0.000	0.000	0.000	0.000
42	A	45	GLN	0	-0.028	-0.024	28.237	-0.394	-0.394	0.000	0.000	0.000	0.000
43	A	46	PHE	0	0.020	-0.006	27.730	0.397	0.397	0.000	0.000	0.000	0.000
44	A	47	GLN	0	0.026	0.009	27.795	-0.382	-0.382	0.000	0.000	0.000	0.000
45	A	48	GLY	0	0.066	0.040	28.720	0.424	0.424	0.000	0.000	0.000	0.000
46	A	49	LYS	1	0.838	0.921	26.103	12.117	12.117	0.000	0.000	0.000	0.000
47	A	50	ALA	0	0.004	0.004	28.780	-0.121	-0.121	0.000	0.000	0.000	0.000
48	A	51	ALA	0	0.072	0.037	30.912	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	52	ILE	0	-0.046	-0.009	24.532	-0.089	-0.089	0.000	0.000	0.000	0.000
50	A	53	VAL	0	0.028	0.005	27.029	-0.191	-0.191	0.000	0.000	0.000	0.000
51	A	54	GLU	-1	-0.942	-0.945	28.470	-9.141	-9.141	0.000	0.000	0.000	0.000
52	A	55	LYS	1	0.833	0.931	27.596	11.232	11.232	0.000	0.000	0.000	0.000
53	A	56	LEU	0	0.007	-0.002	23.280	0.008	0.008	0.000	0.000	0.000	0.000
54	A	57	SER	0	-0.047	-0.039	27.056	-0.042	-0.042	0.000	0.000	0.000	0.000
55	A	58	SER	0	-0.106	-0.060	30.009	0.203	0.203	0.000	0.000	0.000	0.000
56	A	59	LEU	0	-0.031	-0.006	25.388	0.181	0.181	0.000	0.000	0.000	0.000
57	A	60	PRO	0	0.017	0.000	29.586	0.000	0.000	0.000	0.000	0.000	0.000
58	A	61	PHE	0	-0.011	0.013	24.502	0.167	0.167	0.000	0.000	0.000	0.000
59	A	62	GLN	0	-0.060	-0.056	29.552	0.161	0.161	0.000	0.000	0.000	0.000
60	A	63	LYS	1	0.848	0.918	26.002	10.814	10.814	0.000	0.000	0.000	0.000
61	A	64	ILE	0	-0.050	-0.023	21.852	0.164	0.164	0.000	0.000	0.000	0.000
62	A	65	GLN	0	-0.016	0.006	18.978	-0.134	-0.134	0.000	0.000	0.000	0.000
63	A	66	HIS	1	0.833	0.897	15.956	17.337	17.337	0.000	0.000	0.000	0.000
64	A	67	SER	0	-0.017	-0.014	14.531	-0.027	-0.027	0.000	0.000	0.000	0.000
65	A	68	ILE	0	-0.032	-0.009	9.361	0.698	0.698	0.000	0.000	0.000	0.000
66	A	69	THR	0	-0.042	-0.027	11.247	-0.617	-0.617	0.000	0.000	0.000	0.000
67	A	70	ALA	0	0.006	0.003	8.642	-1.271	-1.271	0.000	0.000	0.000	0.000
68	A	71	GLN	0	0.028	0.025	5.242	-2.766	-2.766	0.000	0.000	0.000	0.000
69	A	72	ASP	-1	-0.893	-0.923	6.400	-40.118	-40.118	0.000	0.000	0.000	0.000
70	A	73	HIS	0	0.016	0.004	4.692	6.128	6.202	-0.001	0.000	-0.073	0.000
71	A	74	GLN	0	-0.027	-0.012	8.119	-0.067	-0.067	0.000	0.000	0.000	0.000
72	A	75	PRO	0	0.016	0.016	9.664	0.689	0.689	0.000	0.000	0.000	0.000
73	A	76	THR	0	-0.024	-0.037	11.916	0.575	0.575	0.000	0.000	0.000	0.000
74	A	77	PRO	0	0.030	0.001	15.782	-0.096	-0.096	0.000	0.000	0.000	0.000
75	A	78	ASP	-1	-0.894	-0.920	18.479	-14.637	-14.637	0.000	0.000	0.000	0.000
76	A	79	SER	0	-0.046	-0.032	15.505	0.270	0.270	0.000	0.000	0.000	0.000
77	A	80	CYS	0	-0.038	0.010	15.566	0.231	0.231	0.000	0.000	0.000	0.000
78	A	81	ILE	0	-0.021	-0.014	9.405	-0.867	-0.867	0.000	0.000	0.000	0.000
79	A	82	ILE	0	-0.006	0.010	12.618	1.149	1.149	0.000	0.000	0.000	0.000
80	A	83	SER	0	-0.012	-0.035	9.291	-1.622	-1.622	0.000	0.000	0.000	0.000
81	A	84	GLU	-1	-0.878	-0.921	10.189	-18.925	-18.925	0.000	0.000	0.000	0.000
82	A	85	VAL	0	-0.022	-0.013	9.919	-3.727	-3.727	0.000	0.000	0.000	0.000
83	A	86	VAL	0	0.014	0.009	11.780	2.507	2.507	0.000	0.000	0.000	0.000
84	A	87	GLY	0	0.048	0.020	12.496	-2.115	-2.115	0.000	0.000	0.000	0.000
85	A	88	GLN	0	-0.047	-0.017	14.891	1.945	1.945	0.000	0.000	0.000	0.000
86	A	89	LEU	0	0.010	0.003	17.605	-0.869	-0.869	0.000	0.000	0.000	0.000
87	A	90	LYS	1	0.827	0.925	20.361	11.916	11.916	0.000	0.000	0.000	0.000
88	A	91	ALA	0	0.054	0.033	23.780	-0.303	-0.303	0.000	0.000	0.000	0.000
89	A	92	ASP	-1	-0.732	-0.874	26.292	-10.244	-10.244	0.000	0.000	0.000	0.000
90	A	93	GLU	-1	-0.899	-0.954	28.999	-10.688	-10.688	0.000	0.000	0.000	0.000
91	A	94	ASP	-1	-0.890	-0.914	28.173	-10.393	-10.393	0.000	0.000	0.000	0.000
92	A	95	PRO	0	-0.028	-0.026	28.112	-0.201	-0.201	0.000	0.000	0.000	0.000
93	A	96	ILE	0	-0.016	-0.011	21.885	-0.238	-0.238	0.000	0.000	0.000	0.000
94	A	97	MET	0	-0.022	-0.004	22.981	0.455	0.455	0.000	0.000	0.000	0.000
95	A	98	GLY	0	0.068	0.033	19.733	-0.729	-0.729	0.000	0.000	0.000	0.000
96	A	99	PHE	0	-0.072	-0.039	14.817	0.781	0.781	0.000	0.000	0.000	0.000
97	A	100	HIS	0	-0.036	-0.032	15.844	-0.389	-0.389	0.000	0.000	0.000	0.000
98	A	101	GLN	0	-0.003	-0.019	15.433	0.753	0.753	0.000	0.000	0.000	0.000
99	A	102	MET	0	-0.015	0.004	14.443	-1.428	-1.428	0.000	0.000	0.000	0.000
100	A	103	PHE	0	0.021	-0.010	13.451	1.097	1.097	0.000	0.000	0.000	0.000
101	A	104	LEU	0	-0.037	-0.006	14.833	-1.061	-1.061	0.000	0.000	0.000	0.000
102	A	105	LEU	0	0.029	0.013	11.854	0.958	0.958	0.000	0.000	0.000	0.000
103	A	106	LYS	1	0.891	0.916	15.584	14.816	14.816	0.000	0.000	0.000	0.000
104	A	107	ASN	0	-0.044	-0.015	16.098	0.913	0.913	0.000	0.000	0.000	0.000
105	A	108	ILE	0	0.012	-0.013	17.750	0.744	0.744	0.000	0.000	0.000	0.000
106	A	109	ASN	0	-0.056	-0.035	21.538	0.033	0.033	0.000	0.000	0.000	0.000
107	A	110	ASP	-1	-0.870	-0.915	18.294	-15.421	-15.421	0.000	0.000	0.000	0.000
108	A	111	ALA	0	0.013	0.024	18.473	-0.461	-0.461	0.000	0.000	0.000	0.000
109	A	112	TRP	0	-0.020	-0.018	13.222	-0.160	-0.160	0.000	0.000	0.000	0.000
110	A	113	VAL	0	0.007	0.008	16.516	-0.128	-0.128	0.000	0.000	0.000	0.000
111	A	114	CYS	0	-0.033	0.002	17.599	-0.381	-0.381	0.000	0.000	0.000	0.000
112	A	115	THR	0	0.006	0.002	18.832	0.772	0.772	0.000	0.000	0.000	0.000
113	A	116	ASN	0	-0.005	-0.005	19.793	0.640	0.640	0.000	0.000	0.000	0.000
114	A	117	ASP	-1	-0.692	-0.809	18.796	-17.603	-17.603	0.000	0.000	0.000	0.000
115	A	118	MET	0	-0.019	-0.013	18.935	1.050	1.050	0.000	0.000	0.000	0.000
116	A	119	PHE	0	0.040	0.032	19.001	-0.848	-0.848	0.000	0.000	0.000	0.000
117	A	120	ARG	1	0.910	0.946	20.420	13.612	13.612	0.000	0.000	0.000	0.000
118	A	121	LEU	0	0.062	0.040	20.996	-0.677	-0.677	0.000	0.000	0.000	0.000
119	A	122	ALA	0	-0.042	-0.028	20.569	0.283	0.283	0.000	0.000	0.000	0.000
120	A	123	LEU	0	-0.026	-0.016	22.667	-0.050	-0.050	0.000	0.000	0.000	0.000
121	A	124	HIS	0	-0.004	0.001	22.224	0.064	0.064	0.000	0.000	0.000	0.000
122	A	125	ASN	0	-0.013	-0.002	16.372	-0.703	-0.703	0.000	0.000	0.000	0.000
123	A	126	PHE	0	0.040	0.023	14.203	-0.164	-0.164	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:LYS)