FMO DATABASE

FMODB ID: MVKGZ

Calculation Name: 1JKG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JKG

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UBU9

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	OptH
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	-1256882.479045
FMO2-HF: Nuclear repulsion	1200827.372831
FMO2-HF: Total energy	-56055.106214
FMO2-MP2: Total energy	-56215.752732

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-2.534	1.94	0.909	-2.462	-2.921	-0.001

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / q_NPA : 0.026

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	4	VAL	0	-0.009	-0.003	2.554	-1.784	1.237	0.209	-1.634	-1.596	0.007
4	A	5	ASP	-1	-0.886	-0.941	2.806	-2.870	-1.662	0.701	-0.809	-1.100	-0.008
5	A	6	PHE	0	0.067	0.019	4.503	0.365	0.494	-0.001	-0.006	-0.121	0.000
6	A	7	LYS	1	0.902	0.925	5.602	0.498	0.498	0.000	0.000	0.000	0.000
7	A	8	THR	0	0.012	0.010	7.603	0.116	0.116	0.000	0.000	0.000	0.000
8	A	9	TYR	0	0.016	0.000	3.870	0.161	0.277	0.000	-0.013	-0.104	0.000
9	A	10	VAL	0	-0.009	-0.001	9.074	0.094	0.094	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.810	-0.885	11.680	-0.289	-0.289	0.000	0.000	0.000	0.000
11	A	12	GLN	0	-0.054	-0.030	11.649	0.040	0.040	0.000	0.000	0.000	0.000
12	A	13	ALA	0	-0.005	-0.006	13.042	0.032	0.032	0.000	0.000	0.000	0.000
13	A	14	CYS	0	0.020	-0.005	14.685	0.030	0.030	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.965	0.992	17.188	0.209	0.209	0.000	0.000	0.000	0.000
15	A	16	ALA	0	-0.014	-0.011	17.206	0.012	0.012	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.007	-0.001	18.729	0.015	0.015	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.922	-0.956	20.497	-0.090	-0.090	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.958	-0.983	22.506	-0.117	-0.117	0.000	0.000	0.000	0.000
19	A	20	PHE	0	-0.006	-0.007	22.529	0.009	0.009	0.000	0.000	0.000	0.000
20	A	21	VAL	0	0.025	0.011	24.073	0.008	0.008	0.000	0.000	0.000	0.000
21	A	22	ASN	0	0.001	0.009	26.291	0.011	0.011	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.007	0.010	27.494	0.004	0.004	0.000	0.000	0.000	0.000
23	A	24	TYR	0	-0.010	-0.020	27.544	0.004	0.004	0.000	0.000	0.000	0.000
24	A	25	TYR	0	0.058	-0.011	28.248	0.003	0.003	0.000	0.000	0.000	0.000
25	A	26	THR	0	-0.025	0.003	32.096	0.002	0.002	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.089	-0.057	32.013	0.000	0.000	0.000	0.000	0.000	0.000
27	A	28	MET	0	-0.027	0.007	33.185	0.001	0.001	0.000	0.000	0.000	0.000
28	A	29	ASP	-1	-0.754	-0.832	35.270	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	30	LYS	1	0.898	0.944	37.483	0.020	0.020	0.000	0.000	0.000	0.000
30	A	31	ARG	1	0.867	0.930	36.392	0.026	0.026	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.874	0.915	36.896	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	33	ARG	1	0.974	0.973	36.966	0.011	0.011	0.000	0.000	0.000	0.000
33	A	34	LEU	0	-0.036	-0.012	33.524	0.000	0.000	0.000	0.000	0.000	0.000
34	A	35	LEU	0	0.036	0.017	31.559	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	36	SER	0	0.069	0.044	31.241	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	37	ARG	1	0.920	0.967	30.943	0.029	0.029	0.000	0.000	0.000	0.000
37	A	38	LEU	0	-0.048	-0.013	27.353	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	39	TYR	0	-0.003	-0.010	26.179	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	40	MET	0	-0.022	-0.009	22.214	-0.011	-0.011	0.000	0.000	0.000	0.000
40	A	41	GLY	0	0.034	0.010	26.166	0.004	0.004	0.000	0.000	0.000	0.000
41	A	42	THR	0	-0.024	-0.025	25.473	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	43	ALA	0	-0.008	0.017	26.340	0.008	0.008	0.000	0.000	0.000	0.000
43	A	44	THR	0	-0.001	-0.001	27.274	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.013	-0.003	28.173	0.001	0.001	0.000	0.000	0.000	0.000
45	A	46	VAL	0	-0.014	0.004	29.790	0.000	0.000	0.000	0.000	0.000	0.000
46	A	47	TRP	0	0.074	0.022	31.798	0.002	0.002	0.000	0.000	0.000	0.000
47	A	48	ASN	0	-0.004	-0.021	34.398	0.002	0.002	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.037	-0.027	34.673	0.000	0.000	0.000	0.000	0.000	0.000
49	A	50	ASN	0	-0.042	-0.005	35.989	0.001	0.001	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.006	0.005	33.422	0.000	0.000	0.000	0.000	0.000	0.000
51	A	52	VAL	0	0.004	0.019	33.419	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	53	SER	0	0.002	-0.025	32.085	0.004	0.004	0.000	0.000	0.000	0.000
53	A	54	GLY	0	0.028	0.024	31.409	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	55	GLN	0	-0.031	-0.032	30.381	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.922	-0.964	32.610	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.065	0.031	35.746	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	58	LEU	0	-0.058	-0.028	30.338	0.000	0.000	0.000	0.000	0.000	0.000
58	A	59	SER	0	-0.021	-0.017	34.875	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.909	-0.955	36.866	0.008	0.008	0.000	0.000	0.000	0.000
60	A	61	PHE	0	-0.013	-0.008	36.163	0.001	0.001	0.000	0.000	0.000	0.000
61	A	62	PHE	0	-0.005	-0.026	32.009	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-1.018	-0.985	38.032	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	MET	0	-0.027	0.002	41.343	0.001	0.001	0.000	0.000	0.000	0.000
64	A	65	LEU	0	-0.068	-0.019	37.678	0.000	0.000	0.000	0.000	0.000	0.000
65	A	66	PRO	0	0.020	0.018	41.857	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	67	SER	0	0.031	0.009	41.956	0.000	0.000	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.039	-0.045	38.244	0.002	0.002	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.968	-0.965	39.691	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	70	PHE	0	-0.016	-0.038	34.062	0.004	0.004	0.000	0.000	0.000	0.000
70	A	71	GLN	0	-0.034	-0.009	34.976	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.016	-0.006	29.049	0.004	0.004	0.000	0.000	0.000	0.000
72	A	73	SER	0	-0.011	-0.009	31.750	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	74	VAL	0	-0.019	-0.004	26.582	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	75	VAL	0	0.013	-0.007	22.723	0.002	0.002	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.891	-0.932	20.136	0.064	0.064	0.000	0.000	0.000	0.000
76	A	77	CYS	0	-0.088	-0.038	17.747	-0.010	-0.010	0.000	0.000	0.000	0.000
77	A	78	GLN	0	0.028	0.006	14.133	0.030	0.030	0.000	0.000	0.000	0.000
78	A	79	PRO	0	-0.030	0.004	9.683	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	80	VAL	0	-0.014	-0.011	11.607	0.071	0.071	0.000	0.000	0.000	0.000
80	A	81	HIS	0	0.022	0.020	7.316	-0.208	-0.208	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.846	-0.938	5.743	0.498	0.498	0.000	0.000	0.000	0.000
82	A	83	GLU	-1	-1.027	-1.025	9.174	0.720	0.720	0.000	0.000	0.000	0.000
83	A	84	ALA	0	-0.050	-0.016	11.712	-0.078	-0.078	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.054	-0.024	12.466	-0.052	-0.052	0.000	0.000	0.000	0.000
85	A	86	PRO	0	0.054	0.031	11.799	-0.036	-0.036	0.000	0.000	0.000	0.000
86	A	87	SER	0	-0.071	-0.037	11.341	-0.062	-0.062	0.000	0.000	0.000	0.000
87	A	88	GLN	0	-0.006	-0.008	12.312	-0.030	-0.030	0.000	0.000	0.000	0.000
88	A	89	THR	0	0.017	0.018	10.408	0.019	0.019	0.000	0.000	0.000	0.000
89	A	90	THR	0	-0.011	-0.020	12.282	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	91	VAL	0	-0.001	0.004	13.029	0.008	0.008	0.000	0.000	0.000	0.000
91	A	92	LEU	0	-0.006	0.017	15.425	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	93	VAL	0	0.000	-0.002	17.903	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	94	VAL	0	-0.018	-0.011	20.827	0.009	0.009	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.002	-0.005	23.699	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	96	CYS	0	-0.056	-0.027	26.971	0.008	0.008	0.000	0.000	0.000	0.000
96	A	97	GLY	0	0.055	0.026	30.265	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	98	SER	0	0.007	0.018	33.492	0.003	0.003	0.000	0.000	0.000	0.000
98	A	99	VAL	0	0.003	-0.004	36.638	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	100	LYS	1	0.927	0.961	38.515	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	101	PHE	0	-0.001	0.001	37.507	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	102	GLU	-1	-0.905	-0.968	42.996	0.003	0.003	0.000	0.000	0.000	0.000
102	A	103	GLY	0	-0.011	-0.001	46.452	0.001	0.001	0.000	0.000	0.000	0.000
103	A	104	ASN	0	-0.058	-0.027	44.406	0.002	0.002	0.000	0.000	0.000	0.000
104	A	105	LYS	1	0.936	0.964	45.526	-0.018	-0.018	0.000	0.000	0.000	0.000
105	A	106	GLN	0	0.002	-0.004	41.320	0.002	0.002	0.000	0.000	0.000	0.000
106	A	107	ARG	1	0.821	0.921	39.506	-0.026	-0.026	0.000	0.000	0.000	0.000
107	A	108	ASP	-1	-0.806	-0.903	36.185	0.022	0.022	0.000	0.000	0.000	0.000
108	A	109	PHE	0	-0.083	-0.050	30.758	0.003	0.003	0.000	0.000	0.000	0.000
109	A	110	ASN	0	0.043	0.020	29.257	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	111	GLN	0	-0.023	-0.017	27.592	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	112	ASN	0	-0.054	-0.017	23.548	0.007	0.007	0.000	0.000	0.000	0.000
112	A	113	PHE	0	0.046	0.016	22.227	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	114	ILE	0	0.018	0.019	17.589	0.001	0.001	0.000	0.000	0.000	0.000
114	A	115	LEU	0	-0.015	-0.004	18.481	-0.009	-0.009	0.000	0.000	0.000	0.000
115	A	116	THR	0	0.021	0.000	16.902	0.016	0.016	0.000	0.000	0.000	0.000
116	A	117	ALA	0	-0.019	-0.007	15.044	-0.009	-0.009	0.000	0.000	0.000	0.000
117	A	118	GLN	0	-0.054	-0.029	17.022	0.002	0.002	0.000	0.000	0.000	0.000
118	A	119	ALA	0	0.042	0.022	17.213	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	120	SER	0	0.000	-0.020	19.123	0.020	0.020	0.000	0.000	0.000	0.000
120	A	121	PRO	0	-0.020	-0.001	22.424	-0.013	-0.013	0.000	0.000	0.000	0.000
121	A	122	SER	0	-0.014	0.005	24.328	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	123	ASN	0	0.028	0.005	21.550	-0.020	-0.020	0.000	0.000	0.000	0.000
123	A	124	THR	0	-0.005	0.000	16.612	0.009	0.009	0.000	0.000	0.000	0.000
124	A	125	VAL	0	-0.021	0.001	19.762	0.009	0.009	0.000	0.000	0.000	0.000
125	A	126	TRP	0	0.032	0.011	13.782	0.006	0.006	0.000	0.000	0.000	0.000
126	A	127	LYS	1	0.913	0.960	20.732	0.048	0.048	0.000	0.000	0.000	0.000
127	A	128	ILE	0	0.025	0.030	21.550	0.005	0.005	0.000	0.000	0.000	0.000
128	A	129	ALA	0	-0.019	-0.020	20.984	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	130	SER	0	-0.013	-0.010	22.711	0.003	0.003	0.000	0.000	0.000	0.000
130	A	131	ASP	-1	-0.719	-0.846	24.026	0.028	0.028	0.000	0.000	0.000	0.000
131	A	132	CYS	0	-0.008	0.013	26.644	0.004	0.004	0.000	0.000	0.000	0.000
132	A	133	PHE	0	0.007	0.016	28.611	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	134	ARG	1	0.927	0.968	31.442	-0.058	-0.058	0.000	0.000	0.000	0.000
134	A	135	PHE	0	-0.008	0.005	34.002	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	136	GLN	0	0.008	-0.020	33.419	0.003	0.003	0.000	0.000	0.000	0.000
136	A	137	ASP	-1	-0.821	-0.904	36.894	0.033	0.033	0.000	0.000	0.000	0.000
137	A	138	TRP	0	-0.028	-0.020	37.450	-0.003	-0.003	0.000	0.000	0.000	0.000
138	A	139	ALA	0	-0.033	-0.011	40.339	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	140	SER	0	-0.031	-0.005	42.899	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)