FMO DATABASE

FMODB ID: 3J7LL

Calculation Name: 5GKK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GKK

Chain ID: A

ChEMBL ID:

UniProt ID: Q70PR2

Base Structure: X-ray

Registration Date: 2023-09-22

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	146
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1531147.26726
FMO2-HF: Nuclear repulsion	1468715.74748
FMO2-HF: Total energy	-62431.51978
FMO2-MP2: Total energy	-62610.986793

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:1:MET)

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

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.
-15.701	-9.415	8.613	-3.856	-11.042	0.004

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.017

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	3	LEU	0	-0.015	0.000	2.318	-1.413	0.762	0.636	-0.949	-1.863	-0.001
4	A	4	LYS	1	0.995	0.990	5.854	0.786	0.786	0.000	0.000	0.000	0.000
5	A	5	PRO	0	0.076	0.027	9.585	-0.082	-0.082	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.803	-0.915	11.667	-0.345	-0.345	0.000	0.000	0.000	0.000
7	A	7	TRP	0	-0.020	0.007	4.515	-0.337	-0.141	-0.001	-0.016	-0.179	0.000
8	A	8	VAL	0	0.001	0.000	7.243	-0.082	-0.082	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.048	-0.017	9.186	0.045	0.045	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.035	0.022	12.112	0.030	0.030	0.000	0.000	0.000	0.000
11	A	11	PHE	0	0.001	-0.006	6.784	-0.031	-0.031	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.030	-0.013	10.031	0.039	0.039	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.710	-0.844	12.671	-0.238	-0.238	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.002	0.024	13.563	0.046	0.046	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.835	-0.907	10.174	-0.420	-0.420	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.080	-0.030	13.097	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	17	CYS	0	-0.052	-0.025	14.302	0.059	0.059	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.034	0.016	17.547	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	19	TYR	0	0.056	0.014	20.421	0.016	0.016	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.054	0.014	23.116	0.001	0.001	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.011	0.012	26.151	0.005	0.005	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.060	0.028	27.631	0.003	0.003	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.033	-0.008	30.369	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.871	0.919	33.097	0.051	0.051	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.042	-0.023	33.809	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	ARG	1	1.020	1.005	36.859	0.030	0.030	0.000	0.000	0.000	0.000
27	A	27	THR	0	-0.032	-0.022	37.165	0.002	0.002	0.000	0.000	0.000	0.000
28	A	28	MET	0	-0.011	0.015	35.434	0.002	0.002	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.987	0.973	39.031	0.033	0.033	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.005	0.013	38.007	0.002	0.002	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.045	0.037	40.619	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.043	-0.050	35.770	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	33	GLN	0	0.014	0.007	29.396	0.006	0.006	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.064	0.031	29.039	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.101	-0.062	25.902	0.003	0.003	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.040	0.030	24.482	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.845	-0.912	20.284	-0.160	-0.160	0.000	0.000	0.000	0.000
38	A	38	PHE	0	0.023	0.019	13.141	0.004	0.004	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.796	0.887	15.171	0.208	0.208	0.000	0.000	0.000	0.000
40	A	40	ILE	0	0.062	0.041	9.531	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.021	-0.004	11.852	-0.011	-0.011	0.000	0.000	0.000	0.000
42	A	42	GLN	0	-0.006	-0.018	7.729	-0.129	-0.129	0.000	0.000	0.000	0.000
43	A	43	HIS	0	0.026	-0.003	10.593	0.058	0.058	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.898	0.925	10.149	0.064	0.064	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.882	0.944	8.898	0.276	0.276	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.792	-0.886	6.219	-0.454	-0.454	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.009	-0.007	5.695	-0.353	-0.353	0.000	0.000	0.000	0.000
48	A	48	GLN	0	0.028	0.006	2.375	-3.832	-1.945	1.915	-0.830	-2.971	-0.003
49	A	49	VAL	0	0.033	0.016	2.200	-3.145	-2.141	3.060	-1.598	-2.466	-0.004
50	A	50	LEU	0	-0.017	0.001	3.060	1.215	0.121	0.020	1.277	-0.203	-0.001
51	A	51	TYR	0	0.030	-0.006	5.773	0.192	0.192	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.007	0.020	2.367	-0.023	0.299	2.095	-0.684	-1.732	0.001
53	A	53	LEU	0	0.015	0.005	4.409	0.469	0.701	0.000	-0.042	-0.191	0.000
54	A	54	ARG	1	0.841	0.923	7.016	0.363	0.363	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.808	0.882	2.777	-10.539	-8.975	0.888	-1.014	-1.437	0.012
56	A	56	PHE	0	0.000	0.011	7.070	0.152	0.152	0.000	0.000	0.000	0.000
57	A	57	PHE	0	0.041	0.016	8.812	0.125	0.125	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.078	0.052	10.866	0.092	0.092	0.000	0.000	0.000	0.000
59	A	59	CYS	0	-0.167	-0.087	12.251	0.030	0.030	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.080	0.040	12.984	-0.069	-0.069	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.073	-0.033	14.694	0.058	0.058	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.067	0.041	9.453	-0.039	-0.039	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.866	0.937	12.602	0.229	0.229	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.883	0.930	14.357	0.128	0.128	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.082	-0.053	15.805	0.012	0.012	0.000	0.000	0.000	0.000
66	A	66	HIS	0	0.033	0.010	17.528	0.027	0.027	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.817	-0.909	18.650	-0.143	-0.143	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.792	-0.855	16.922	-0.175	-0.175	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.978	0.993	14.458	0.168	0.168	0.000	0.000	0.000	0.000
70	A	70	TYR	0	-0.019	-0.019	11.479	0.046	0.046	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.758	-0.852	12.724	-0.266	-0.266	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.018	0.027	9.362	0.038	0.038	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.833	0.881	11.949	0.210	0.210	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.010	0.003	13.653	0.032	0.032	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.923	0.927	17.304	0.132	0.132	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.927	0.974	20.403	0.072	0.072	0.000	0.000	0.000	0.000
77	A	77	ARG	1	1.075	1.028	21.637	0.041	0.041	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.064	0.033	21.821	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.006	-0.003	18.402	-0.028	-0.028	0.000	0.000	0.000	0.000
80	A	81	LYS	1	0.867	0.917	20.527	0.073	0.073	0.000	0.000	0.000	0.000
81	A	82	LYS	1	0.902	0.946	15.111	0.072	0.072	0.000	0.000	0.000	0.000
82	A	83	VAL	0	-0.018	-0.002	15.081	-0.019	-0.019	0.000	0.000	0.000	0.000
83	A	84	VAL	0	-0.011	-0.014	17.318	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.823	-0.903	19.775	-0.115	-0.115	0.000	0.000	0.000	0.000
85	A	86	PHE	0	-0.024	0.009	12.747	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	87	PHE	0	0.032	-0.008	13.389	-0.015	-0.015	0.000	0.000	0.000	0.000
87	A	88	GLU	-1	-0.898	-0.934	18.489	-0.113	-0.113	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.809	0.892	19.291	0.146	0.146	0.000	0.000	0.000	0.000
89	A	90	HIS	0	-0.037	-0.017	16.170	0.008	0.008	0.000	0.000	0.000	0.000
90	A	91	PRO	0	0.022	0.011	17.417	-0.030	-0.030	0.000	0.000	0.000	0.000
91	A	92	LEU	0	-0.031	-0.019	15.518	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.895	0.945	16.473	0.298	0.298	0.000	0.000	0.000	0.000
93	A	94	THR	0	-0.016	-0.024	18.475	0.025	0.025	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.988	0.968	20.941	0.129	0.129	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.852	0.933	16.534	0.337	0.337	0.000	0.000	0.000	0.000
96	A	97	ASN	0	-0.010	-0.009	20.726	0.016	0.016	0.000	0.000	0.000	0.000
97	A	98	VAL	0	-0.021	-0.018	22.218	0.012	0.012	0.000	0.000	0.000	0.000
98	A	99	ASP	-1	-0.774	-0.874	22.406	-0.158	-0.158	0.000	0.000	0.000	0.000
99	A	100	PHE	0	-0.009	0.003	20.480	0.006	0.006	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.897	0.944	22.419	0.147	0.147	0.000	0.000	0.000	0.000
101	A	102	LYS	1	0.855	0.938	25.939	0.122	0.122	0.000	0.000	0.000	0.000
102	A	103	PHE	0	0.013	0.000	20.654	0.006	0.006	0.000	0.000	0.000	0.000
103	A	104	ARG	1	0.868	0.917	24.120	0.128	0.128	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.897	0.961	25.613	0.097	0.097	0.000	0.000	0.000	0.000
105	A	106	ILE	0	0.045	0.015	27.935	0.007	0.007	0.000	0.000	0.000	0.000
106	A	107	LEU	0	-0.009	-0.013	23.122	0.007	0.007	0.000	0.000	0.000	0.000
107	A	108	ILE	0	-0.007	-0.003	27.664	0.009	0.009	0.000	0.000	0.000	0.000
108	A	109	MET	0	-0.032	0.016	30.067	0.006	0.006	0.000	0.000	0.000	0.000
109	A	110	MET	0	-0.053	-0.021	29.529	0.003	0.003	0.000	0.000	0.000	0.000
110	A	111	GLU	-1	-0.885	-0.922	27.143	-0.079	-0.079	0.000	0.000	0.000	0.000
111	A	112	ARG	1	0.901	0.956	31.593	0.068	0.068	0.000	0.000	0.000	0.000
112	A	113	GLY	0	0.007	0.014	34.378	0.004	0.004	0.000	0.000	0.000	0.000
113	A	114	GLU	-1	-0.725	-0.859	35.744	-0.059	-0.059	0.000	0.000	0.000	0.000
114	A	115	HIS	0	0.007	0.009	33.326	0.000	0.000	0.000	0.000	0.000	0.000
115	A	116	LEU	0	-0.035	-0.024	36.235	0.001	0.001	0.000	0.000	0.000	0.000
116	A	117	THR	0	-0.060	-0.028	39.168	0.003	0.003	0.000	0.000	0.000	0.000
117	A	118	LYN	0	0.063	0.033	40.241	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.811	-0.932	40.889	-0.048	-0.048	0.000	0.000	0.000	0.000
119	A	120	GLY	0	0.006	0.011	38.524	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	121	LEU	0	-0.056	-0.031	35.369	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	122	ILE	0	0.027	0.010	36.276	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	123	LYS	1	0.862	0.912	36.087	0.058	0.058	0.000	0.000	0.000	0.000
123	A	124	ILE	0	-0.041	-0.033	31.235	-0.006	-0.006	0.000	0.000	0.000	0.000
124	A	125	LEU	0	-0.014	-0.013	32.520	-0.008	-0.008	0.000	0.000	0.000	0.000
125	A	126	GLU	-1	-0.775	-0.880	33.806	-0.064	-0.064	0.000	0.000	0.000	0.000
126	A	127	ILE	0	-0.046	-0.022	30.461	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	128	ALA	0	-0.022	-0.026	29.481	-0.008	-0.008	0.000	0.000	0.000	0.000
128	A	129	MET	0	-0.039	-0.013	29.900	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.816	-0.893	31.125	-0.094	-0.094	0.000	0.000	0.000	0.000
130	A	131	MET	0	-0.101	-0.039	24.341	-0.003	-0.003	0.000	0.000	0.000	0.000
131	A	132	ASN	0	-0.050	-0.041	24.575	0.014	0.014	0.000	0.000	0.000	0.000
132	A	133	THR	0	-0.065	-0.050	24.206	-0.018	-0.018	0.000	0.000	0.000	0.000
133	A	134	GLY	0	0.057	0.033	25.222	0.010	0.010	0.000	0.000	0.000	0.000
134	A	135	ASN	0	-0.055	-0.039	27.137	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	136	HIS	0	0.072	0.046	29.349	0.008	0.008	0.000	0.000	0.000	0.000
136	A	137	GLU	-1	-0.781	-0.870	32.658	-0.064	-0.064	0.000	0.000	0.000	0.000
137	A	138	ARG	1	0.835	0.908	30.435	0.088	0.088	0.000	0.000	0.000	0.000
138	A	139	LEU	0	-0.031	-0.003	30.409	0.004	0.004	0.000	0.000	0.000	0.000
139	A	140	LYS	1	0.919	0.939	34.402	0.068	0.068	0.000	0.000	0.000	0.000
140	A	141	ARG	1	0.937	0.959	35.768	0.064	0.064	0.000	0.000	0.000	0.000
141	A	142	THR	0	-0.084	-0.059	35.739	0.003	0.003	0.000	0.000	0.000	0.000
142	A	143	LEU	0	-0.019	-0.016	37.227	0.003	0.003	0.000	0.000	0.000	0.000
143	A	144	GLU	-1	-0.894	-0.934	40.104	-0.049	-0.049	0.000	0.000	0.000	0.000
144	A	145	GLU	-1	-0.747	-0.809	40.059	-0.050	-0.050	0.000	0.000	0.000	0.000
145	A	146	ILE	0	-0.077	-0.031	38.685	0.002	0.002	0.000	0.000	0.000	0.000
146	A	147	ARG	1	0.807	0.892	41.627	0.056	0.056	0.000	0.000	0.000	0.000

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