FMO DATABASE

FMODB ID: Z6M3N

Calculation Name: 1JB2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	123
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1077548.790958
FMO2-HF: Nuclear repulsion	1027556.508007
FMO2-HF: Total energy	-49992.282952
FMO2-MP2: Total energy	-50136.415812

3D Structure Molmil

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.
-204.385	-199.692	21.735	-13.348	-13.079	-0.13

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 : 0.916 / q_NPA : 0.947

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	0.066	0.018	3.127	-6.954	-4.441	0.108	-1.288	-1.333	0.002
4	A	7	TRP	0	0.069	0.022	5.789	0.406	0.406	0.000	0.000	0.000	0.000
5	A	8	GLU	-1	-0.818	-0.902	1.664	-129.594	-130.056	20.558	-10.954	-9.142	-0.126
6	A	9	GLN	0	-0.084	-0.048	2.578	-3.263	-1.277	1.070	-0.937	-2.119	-0.005
7	A	10	ILE	0	0.022	0.020	4.453	1.750	1.861	0.000	-0.019	-0.091	0.000
8	A	11	GLY	0	0.065	0.039	7.294	2.292	2.292	0.000	0.000	0.000	0.000
9	A	12	SER	0	-0.048	-0.027	3.702	0.484	0.871	0.001	-0.148	-0.240	-0.001
10	A	13	SER	0	-0.049	-0.041	5.630	5.109	5.109	0.000	0.000	0.000	0.000
11	A	14	PHE	0	0.002	0.004	8.221	3.104	3.104	0.000	0.000	0.000	0.000
12	A	15	ILE	0	0.025	0.015	8.240	2.290	2.290	0.000	0.000	0.000	0.000
13	A	16	ASN	0	-0.028	-0.017	8.442	3.087	3.087	0.000	0.000	0.000	0.000
14	A	17	HIS	0	0.002	0.001	10.223	1.712	1.712	0.000	0.000	0.000	0.000
15	A	18	TYR	0	0.012	0.011	13.181	1.837	1.837	0.000	0.000	0.000	0.000
16	A	19	TYR	0	0.006	-0.046	12.057	0.988	0.988	0.000	0.000	0.000	0.000
17	A	20	GLN	0	-0.018	0.018	13.328	2.227	2.227	0.000	0.000	0.000	0.000
18	A	21	LEU	0	0.041	0.014	16.272	1.155	1.155	0.000	0.000	0.000	0.000
19	A	22	PHE	0	-0.040	-0.023	18.175	1.093	1.093	0.000	0.000	0.000	0.000
20	A	23	ASP	-1	-0.782	-0.867	17.820	-16.305	-16.305	0.000	0.000	0.000	0.000
21	A	24	ASN	0	-0.112	-0.057	18.804	1.056	1.056	0.000	0.000	0.000	0.000
22	A	25	ASP	-1	-0.823	-0.888	21.899	-11.538	-11.538	0.000	0.000	0.000	0.000
23	A	26	ARG	1	0.933	0.969	22.798	11.427	11.427	0.000	0.000	0.000	0.000
24	A	27	THR	0	-0.095	-0.046	23.812	0.093	0.093	0.000	0.000	0.000	0.000
25	A	28	GLN	0	-0.056	-0.050	22.937	-0.047	-0.047	0.000	0.000	0.000	0.000
26	A	29	LEU	0	0.003	0.008	19.394	-0.448	-0.448	0.000	0.000	0.000	0.000
27	A	30	GLY	0	0.010	0.002	21.832	-0.307	-0.307	0.000	0.000	0.000	0.000
28	A	31	ALA	0	-0.048	-0.026	22.052	0.110	0.110	0.000	0.000	0.000	0.000
29	A	32	ILE	0	0.004	0.014	17.338	-0.287	-0.287	0.000	0.000	0.000	0.000
30	A	33	TYR	0	-0.042	-0.027	19.810	-0.369	-0.369	0.000	0.000	0.000	0.000
31	A	34	ILE	0	0.025	0.009	22.493	0.470	0.470	0.000	0.000	0.000	0.000
32	A	35	ASP	-1	-0.870	-0.953	25.275	-10.751	-10.751	0.000	0.000	0.000	0.000
33	A	36	ALA	0	-0.027	-0.022	26.606	0.223	0.223	0.000	0.000	0.000	0.000
34	A	37	SER	0	-0.011	-0.022	22.310	-0.014	-0.014	0.000	0.000	0.000	0.000
35	A	38	CYS	0	-0.112	-0.046	23.794	0.793	0.793	0.000	0.000	0.000	0.000
36	A	39	LEU	0	0.026	0.019	22.136	-0.648	-0.648	0.000	0.000	0.000	0.000
37	A	40	THR	0	-0.051	-0.020	23.420	0.771	0.771	0.000	0.000	0.000	0.000
38	A	41	TRP	0	-0.008	-0.022	21.550	-0.655	-0.655	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.859	-0.946	24.488	-11.498	-11.498	0.000	0.000	0.000	0.000
40	A	43	GLY	0	-0.072	-0.041	26.050	0.435	0.435	0.000	0.000	0.000	0.000
41	A	44	GLN	0	0.000	0.013	27.922	0.319	0.319	0.000	0.000	0.000	0.000
42	A	45	GLN	0	-0.032	-0.016	28.134	-0.371	-0.371	0.000	0.000	0.000	0.000
43	A	46	PHE	0	0.028	0.000	27.778	0.426	0.426	0.000	0.000	0.000	0.000
44	A	47	GLN	0	0.021	0.003	27.705	-0.425	-0.425	0.000	0.000	0.000	0.000
45	A	48	GLY	0	0.059	0.033	28.283	0.434	0.434	0.000	0.000	0.000	0.000
46	A	49	LYS	1	0.871	0.933	25.385	12.272	12.272	0.000	0.000	0.000	0.000
47	A	50	ALA	0	-0.002	-0.004	28.111	-0.091	-0.091	0.000	0.000	0.000	0.000
48	A	51	ALA	0	0.061	0.035	30.686	0.075	0.075	0.000	0.000	0.000	0.000
49	A	52	ILE	0	-0.032	-0.001	24.200	-0.049	-0.049	0.000	0.000	0.000	0.000
50	A	53	VAL	0	0.018	-0.009	26.790	-0.159	-0.159	0.000	0.000	0.000	0.000
51	A	54	GLU	-1	-0.952	-0.953	28.195	-9.155	-9.155	0.000	0.000	0.000	0.000
52	A	55	LYS	1	0.912	0.981	27.509	11.203	11.203	0.000	0.000	0.000	0.000
53	A	56	LEU	0	-0.006	-0.004	23.221	0.004	0.004	0.000	0.000	0.000	0.000
54	A	57	SER	0	-0.049	-0.042	26.918	-0.027	-0.027	0.000	0.000	0.000	0.000
55	A	58	SER	0	-0.097	-0.047	29.741	0.254	0.254	0.000	0.000	0.000	0.000
56	A	59	LEU	0	-0.059	-0.021	25.190	0.190	0.190	0.000	0.000	0.000	0.000
57	A	60	PRO	0	0.038	0.005	29.346	0.046	0.046	0.000	0.000	0.000	0.000
58	A	61	PHE	0	-0.002	0.019	24.259	0.144	0.144	0.000	0.000	0.000	0.000
59	A	62	GLN	0	-0.051	-0.041	29.180	0.166	0.166	0.000	0.000	0.000	0.000
60	A	63	LYS	1	0.859	0.932	25.787	10.788	10.788	0.000	0.000	0.000	0.000
61	A	64	ILE	0	-0.053	-0.019	21.522	0.128	0.128	0.000	0.000	0.000	0.000
62	A	65	GLN	0	-0.016	0.008	18.728	-0.494	-0.494	0.000	0.000	0.000	0.000
63	A	66	HIS	1	0.803	0.871	15.727	17.278	17.278	0.000	0.000	0.000	0.000
64	A	67	SER	0	-0.014	-0.008	14.115	-0.165	-0.165	0.000	0.000	0.000	0.000
65	A	68	ILE	0	-0.037	-0.018	8.820	0.516	0.516	0.000	0.000	0.000	0.000
66	A	69	THR	0	-0.029	-0.030	10.694	-0.771	-0.771	0.000	0.000	0.000	0.000
67	A	70	ALA	0	-0.007	-0.002	8.200	-1.400	-1.400	0.000	0.000	0.000	0.000
68	A	71	GLN	0	0.025	0.016	4.900	-4.958	-4.887	-0.001	-0.001	-0.069	0.000
69	A	72	ASP	-1	-0.885	-0.912	6.396	-38.927	-38.927	0.000	0.000	0.000	0.000
70	A	73	HIS	0	0.005	-0.012	4.482	6.471	6.558	-0.001	-0.001	-0.085	0.000
71	A	74	GLN	0	-0.033	-0.010	7.956	0.503	0.503	0.000	0.000	0.000	0.000
72	A	75	PRO	0	0.018	0.023	9.619	0.571	0.571	0.000	0.000	0.000	0.000
73	A	76	THR	0	0.012	-0.005	11.691	0.754	0.754	0.000	0.000	0.000	0.000
74	A	77	PRO	0	0.034	-0.002	15.528	-0.106	-0.106	0.000	0.000	0.000	0.000
75	A	78	ASP	-1	-0.967	-0.971	18.322	-14.107	-14.107	0.000	0.000	0.000	0.000
76	A	79	SER	0	-0.056	-0.032	15.213	0.180	0.180	0.000	0.000	0.000	0.000
77	A	80	CYS	0	-0.069	-0.017	15.105	0.056	0.056	0.000	0.000	0.000	0.000
78	A	81	ILE	0	-0.004	-0.009	9.202	-0.972	-0.972	0.000	0.000	0.000	0.000
79	A	82	ILE	0	-0.015	0.006	12.500	1.241	1.241	0.000	0.000	0.000	0.000
80	A	83	SER	0	-0.030	-0.046	9.222	-1.492	-1.492	0.000	0.000	0.000	0.000
81	A	84	GLU	-1	-0.872	-0.917	9.869	-19.549	-19.549	0.000	0.000	0.000	0.000
82	A	85	VAL	0	-0.030	-0.014	9.745	-3.668	-3.668	0.000	0.000	0.000	0.000
83	A	86	VAL	0	0.034	0.021	11.391	2.585	2.585	0.000	0.000	0.000	0.000
84	A	87	GLY	0	0.048	0.020	12.210	-2.061	-2.061	0.000	0.000	0.000	0.000
85	A	88	GLN	0	-0.060	-0.025	14.593	1.942	1.942	0.000	0.000	0.000	0.000
86	A	89	LEU	0	0.006	0.000	17.456	-0.772	-0.772	0.000	0.000	0.000	0.000
87	A	90	LYS	1	0.855	0.923	20.139	12.098	12.098	0.000	0.000	0.000	0.000
88	A	91	ALA	0	0.039	0.019	23.371	-0.260	-0.260	0.000	0.000	0.000	0.000
89	A	92	ASP	-1	-0.768	-0.890	26.012	-10.258	-10.258	0.000	0.000	0.000	0.000
90	A	93	GLU	-1	-0.874	-0.948	28.618	-10.564	-10.564	0.000	0.000	0.000	0.000
91	A	94	ASP	-1	-0.921	-0.933	27.956	-10.437	-10.437	0.000	0.000	0.000	0.000
92	A	95	PRO	0	-0.043	-0.027	27.840	-0.276	-0.276	0.000	0.000	0.000	0.000
93	A	96	ILE	0	-0.012	-0.012	21.591	-0.208	-0.208	0.000	0.000	0.000	0.000
94	A	97	MET	0	-0.004	0.007	22.652	0.424	0.424	0.000	0.000	0.000	0.000
95	A	98	GLY	0	0.058	0.032	19.489	-0.756	-0.756	0.000	0.000	0.000	0.000
96	A	99	PHE	0	-0.064	-0.023	14.596	0.800	0.800	0.000	0.000	0.000	0.000
97	A	100	HIS	0	-0.042	-0.037	15.401	-0.418	-0.418	0.000	0.000	0.000	0.000
98	A	101	GLN	0	0.000	-0.020	15.325	0.761	0.761	0.000	0.000	0.000	0.000
99	A	102	MET	0	-0.017	0.008	14.338	-1.370	-1.370	0.000	0.000	0.000	0.000
100	A	103	PHE	0	0.034	-0.004	13.280	0.966	0.966	0.000	0.000	0.000	0.000
101	A	104	LEU	0	-0.031	0.005	14.382	-1.126	-1.126	0.000	0.000	0.000	0.000
102	A	105	LEU	0	0.003	-0.008	11.526	0.888	0.888	0.000	0.000	0.000	0.000
103	A	106	LYS	1	0.990	0.981	15.594	14.364	14.364	0.000	0.000	0.000	0.000
104	A	107	ASN	0	-0.039	-0.018	15.813	0.829	0.829	0.000	0.000	0.000	0.000
105	A	108	ILE	0	-0.001	-0.022	17.596	0.785	0.785	0.000	0.000	0.000	0.000
106	A	109	ASN	0	-0.070	-0.042	21.353	0.065	0.065	0.000	0.000	0.000	0.000
107	A	110	ASP	-1	-0.884	-0.927	18.422	-15.484	-15.484	0.000	0.000	0.000	0.000
108	A	111	ALA	0	0.047	0.045	18.147	-0.339	-0.339	0.000	0.000	0.000	0.000
109	A	112	TRP	0	-0.037	-0.020	12.838	-0.127	-0.127	0.000	0.000	0.000	0.000
110	A	113	VAL	0	0.006	0.013	16.357	0.112	0.112	0.000	0.000	0.000	0.000
111	A	114	CYS	0	-0.042	-0.009	16.959	-0.592	-0.592	0.000	0.000	0.000	0.000
112	A	115	THR	0	0.000	0.001	18.341	0.807	0.807	0.000	0.000	0.000	0.000
113	A	116	ASN	0	-0.004	0.003	19.499	0.674	0.674	0.000	0.000	0.000	0.000
114	A	117	ASP	-1	-0.696	-0.813	18.520	-17.717	-17.717	0.000	0.000	0.000	0.000
115	A	118	MET	0	-0.042	-0.025	18.764	1.062	1.062	0.000	0.000	0.000	0.000
116	A	119	PHE	0	0.046	0.038	18.942	-0.930	-0.930	0.000	0.000	0.000	0.000
117	A	120	ARG	1	0.952	0.968	20.360	13.732	13.732	0.000	0.000	0.000	0.000
118	A	121	LEU	0	0.055	0.043	20.896	-0.677	-0.677	0.000	0.000	0.000	0.000
119	A	122	ALA	0	-0.053	-0.041	20.297	0.189	0.189	0.000	0.000	0.000	0.000
120	A	123	LEU	0	-0.007	-0.010	22.353	0.062	0.062	0.000	0.000	0.000	0.000
121	A	124	HIS	0	-0.034	-0.010	22.410	0.030	0.030	0.000	0.000	0.000	0.000
122	A	125	ASN	0	-0.011	-0.006	17.072	-0.932	-0.932	0.000	0.000	0.000	0.000
123	A	126	PHE	0	0.052	0.027	13.865	0.377	0.377	0.000	0.000	0.000	0.000

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