FMO DATABASE

FMODB ID: JQ2N9

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	OptHSide
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	-1529761.412909
FMO2-HF: Nuclear repulsion	1467330.200578
FMO2-HF: Total energy	-62431.212331
FMO2-MP2: Total energy	-62610.677453

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.
-14.1	-7.676	7.814	-3.412	-10.826	0.005

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 : 0.021 / q_NPA : 0.011

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	-0.024	-0.010	2.284	-1.861	0.493	0.856	-0.944	-2.266	-0.001
4	A	4	LYS	1	0.999	0.991	5.350	0.448	0.511	-0.001	-0.005	-0.056	0.000
5	A	5	PRO	0	0.081	0.025	9.058	-0.074	-0.074	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.858	-0.935	11.625	-0.269	-0.269	0.000	0.000	0.000	0.000
7	A	7	TRP	0	-0.027	-0.009	4.650	-0.296	-0.077	-0.001	-0.016	-0.202	0.000
8	A	8	VAL	0	-0.004	-0.003	7.338	-0.079	-0.079	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.022	-0.003	9.165	0.025	0.025	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.025	0.026	12.001	0.022	0.022	0.000	0.000	0.000	0.000
11	A	11	PHE	0	0.022	0.006	7.056	-0.040	-0.040	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.020	-0.001	9.915	0.034	0.034	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.701	-0.834	12.182	-0.213	-0.213	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.006	0.020	13.359	0.043	0.043	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.860	-0.942	10.236	-0.441	-0.441	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.103	-0.045	13.158	0.001	0.001	0.000	0.000	0.000	0.000
17	A	17	CYS	0	-0.044	-0.021	14.304	0.055	0.055	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.019	0.007	16.912	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	19	TYR	0	0.064	0.015	20.050	0.018	0.018	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.071	0.024	22.514	0.001	0.001	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.010	0.024	25.841	0.004	0.004	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.055	0.026	27.649	0.003	0.003	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.040	-0.012	30.145	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.887	0.920	32.806	0.052	0.052	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.038	-0.019	33.597	0.003	0.003	0.000	0.000	0.000	0.000
26	A	26	ARG	1	1.010	0.996	36.699	0.032	0.032	0.000	0.000	0.000	0.000
27	A	27	THR	0	-0.039	-0.025	37.124	0.002	0.002	0.000	0.000	0.000	0.000
28	A	28	MET	0	-0.010	0.018	35.107	0.002	0.002	0.000	0.000	0.000	0.000
29	A	29	LYS	1	1.006	0.986	39.125	0.033	0.033	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.001	0.000	37.669	0.002	0.002	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.045	0.042	40.108	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.045	-0.055	35.314	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	33	GLN	0	-0.001	0.005	29.378	0.005	0.005	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.075	0.034	28.610	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.088	-0.058	25.734	0.002	0.002	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.026	0.021	23.816	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.824	-0.905	19.780	-0.163	-0.163	0.000	0.000	0.000	0.000
38	A	38	PHE	0	0.034	0.036	12.637	0.001	0.001	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.798	0.891	15.108	0.204	0.204	0.000	0.000	0.000	0.000
40	A	40	ILE	0	0.057	0.034	9.433	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.012	-0.009	12.084	-0.017	-0.017	0.000	0.000	0.000	0.000
42	A	42	GLN	0	0.001	-0.001	7.720	-0.160	-0.160	0.000	0.000	0.000	0.000
43	A	43	HIS	0	0.033	0.007	10.902	0.036	0.036	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.918	0.944	10.071	0.103	0.103	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.902	0.959	9.289	0.315	0.315	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.854	-0.923	6.212	-0.668	-0.668	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.001	-0.009	5.910	-0.286	-0.286	0.000	0.000	0.000	0.000
48	A	48	GLN	0	0.015	0.001	2.372	-3.788	-1.456	0.716	-0.788	-2.261	-0.005
49	A	49	VAL	0	0.045	0.019	2.206	-2.247	-1.866	4.023	-1.632	-2.772	0.001
50	A	50	LEU	0	-0.016	0.001	3.031	1.560	0.065	0.042	1.700	-0.247	-0.001
51	A	51	TYR	0	0.016	-0.013	5.746	0.231	0.231	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.020	0.022	2.429	-0.152	0.392	1.704	-0.626	-1.621	0.001
53	A	53	LEU	0	0.011	0.010	4.308	0.468	0.693	0.000	-0.041	-0.184	0.000
54	A	54	ARG	1	0.874	0.940	6.888	0.338	0.338	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.802	0.879	2.931	-9.139	-7.338	0.475	-1.060	-1.217	0.010
56	A	56	PHE	0	-0.010	0.009	6.889	0.146	0.146	0.000	0.000	0.000	0.000
57	A	57	PHE	0	0.026	0.010	8.609	0.126	0.126	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.045	0.022	10.791	0.084	0.084	0.000	0.000	0.000	0.000
59	A	59	CYS	0	-0.185	-0.097	12.295	0.041	0.041	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.069	0.034	12.964	-0.066	-0.066	0.000	0.000	0.000	0.000
61	A	61	VAL	0	-0.066	-0.030	14.051	0.046	0.046	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.068	0.041	9.633	-0.036	-0.036	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.890	0.954	12.864	0.229	0.229	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.930	0.965	14.712	0.127	0.127	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.119	-0.087	16.182	0.011	0.011	0.000	0.000	0.000	0.000
66	A	66	HIS	0	0.040	0.013	17.824	0.029	0.029	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.858	-0.916	18.763	-0.165	-0.165	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.808	-0.892	16.916	-0.213	-0.213	0.000	0.000	0.000	0.000
69	A	69	ARG	1	0.974	0.991	14.282	0.181	0.181	0.000	0.000	0.000	0.000
70	A	70	TYR	0	0.003	-0.007	11.502	0.052	0.052	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.751	-0.848	12.588	-0.275	-0.275	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.019	0.016	9.356	0.047	0.047	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.840	0.890	12.208	0.209	0.209	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.006	0.005	13.077	0.038	0.038	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.889	0.903	16.940	0.136	0.136	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.937	0.979	20.352	0.070	0.070	0.000	0.000	0.000	0.000
77	A	77	ARG	1	1.088	1.033	21.432	0.040	0.040	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.044	0.024	21.783	-0.010	-0.010	0.000	0.000	0.000	0.000
79	A	80	LEU	0	0.022	0.001	18.297	-0.024	-0.024	0.000	0.000	0.000	0.000
80	A	81	LYS	1	0.858	0.927	20.053	0.069	0.069	0.000	0.000	0.000	0.000
81	A	82	LYS	1	0.961	0.980	15.152	0.064	0.064	0.000	0.000	0.000	0.000
82	A	83	VAL	0	-0.034	-0.014	14.779	-0.019	-0.019	0.000	0.000	0.000	0.000
83	A	84	VAL	0	-0.015	-0.013	17.021	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.837	-0.923	19.385	-0.104	-0.104	0.000	0.000	0.000	0.000
85	A	86	PHE	0	-0.055	-0.013	12.758	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	87	PHE	0	0.039	-0.005	12.904	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	88	GLU	-1	-0.888	-0.918	18.248	-0.104	-0.104	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.851	0.927	18.931	0.135	0.135	0.000	0.000	0.000	0.000
89	A	90	HIS	0	-0.030	-0.009	16.087	0.013	0.013	0.000	0.000	0.000	0.000
90	A	91	PRO	0	0.015	0.013	17.467	-0.027	-0.027	0.000	0.000	0.000	0.000
91	A	92	LEU	0	-0.025	-0.012	15.398	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.916	0.942	17.221	0.237	0.237	0.000	0.000	0.000	0.000
93	A	94	THR	0	-0.001	-0.014	18.362	0.022	0.022	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.963	0.962	20.831	0.122	0.122	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.877	0.943	16.220	0.323	0.323	0.000	0.000	0.000	0.000
96	A	97	ASN	0	-0.029	-0.020	20.508	0.012	0.012	0.000	0.000	0.000	0.000
97	A	98	VAL	0	0.004	-0.002	22.041	0.009	0.009	0.000	0.000	0.000	0.000
98	A	99	ASP	-1	-0.755	-0.860	22.084	-0.153	-0.153	0.000	0.000	0.000	0.000
99	A	100	PHE	0	-0.029	-0.004	20.026	0.005	0.005	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.902	0.943	22.051	0.137	0.137	0.000	0.000	0.000	0.000
101	A	102	LYS	1	0.823	0.916	25.369	0.115	0.115	0.000	0.000	0.000	0.000
102	A	103	PHE	0	0.010	-0.002	20.251	0.005	0.005	0.000	0.000	0.000	0.000
103	A	104	ARG	1	0.863	0.915	23.786	0.119	0.119	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.954	0.985	25.221	0.090	0.090	0.000	0.000	0.000	0.000
105	A	106	ILE	0	0.051	0.024	27.517	0.007	0.007	0.000	0.000	0.000	0.000
106	A	107	LEU	0	0.005	-0.004	22.754	0.007	0.007	0.000	0.000	0.000	0.000
107	A	108	ILE	0	0.000	0.003	27.268	0.008	0.008	0.000	0.000	0.000	0.000
108	A	109	MET	0	-0.039	-0.008	29.602	0.005	0.005	0.000	0.000	0.000	0.000
109	A	110	MET	0	-0.073	-0.033	28.812	0.002	0.002	0.000	0.000	0.000	0.000
110	A	111	GLU	-1	-0.894	-0.924	26.735	-0.075	-0.075	0.000	0.000	0.000	0.000
111	A	112	ARG	1	0.922	0.971	31.156	0.062	0.062	0.000	0.000	0.000	0.000
112	A	113	GLY	0	0.022	0.022	34.000	0.004	0.004	0.000	0.000	0.000	0.000
113	A	114	GLU	-1	-0.742	-0.880	35.316	-0.056	-0.056	0.000	0.000	0.000	0.000
114	A	115	HIS	0	-0.003	0.001	32.924	0.000	0.000	0.000	0.000	0.000	0.000
115	A	116	LEU	0	-0.055	-0.034	35.675	0.001	0.001	0.000	0.000	0.000	0.000
116	A	117	THR	0	-0.047	-0.011	38.586	0.003	0.003	0.000	0.000	0.000	0.000
117	A	118	LYN	0	0.051	0.030	39.793	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.824	-0.938	40.691	-0.046	-0.046	0.000	0.000	0.000	0.000
119	A	120	GLY	0	-0.013	0.005	38.361	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	121	LEU	0	-0.045	-0.040	34.880	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	122	ILE	0	0.036	0.018	36.058	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	123	LYS	1	0.895	0.944	35.681	0.056	0.056	0.000	0.000	0.000	0.000
123	A	124	ILE	0	-0.045	-0.027	31.029	-0.005	-0.005	0.000	0.000	0.000	0.000
124	A	125	LEU	0	-0.032	-0.020	32.252	-0.008	-0.008	0.000	0.000	0.000	0.000
125	A	126	GLU	-1	-0.789	-0.890	33.516	-0.063	-0.063	0.000	0.000	0.000	0.000
126	A	127	ILE	0	-0.031	-0.014	29.862	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	128	ALA	0	-0.018	-0.026	29.037	-0.007	-0.007	0.000	0.000	0.000	0.000
128	A	129	MET	0	-0.015	-0.002	29.466	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.875	-0.907	31.261	-0.088	-0.088	0.000	0.000	0.000	0.000
130	A	131	MET	0	-0.114	-0.053	23.939	-0.004	-0.004	0.000	0.000	0.000	0.000
131	A	132	ASN	0	-0.053	-0.038	24.523	0.013	0.013	0.000	0.000	0.000	0.000
132	A	133	THR	0	-0.063	-0.032	23.700	-0.018	-0.018	0.000	0.000	0.000	0.000
133	A	134	GLY	0	0.062	0.030	24.777	0.010	0.010	0.000	0.000	0.000	0.000
134	A	135	ASN	0	-0.095	-0.080	26.761	0.001	0.001	0.000	0.000	0.000	0.000
135	A	136	HIS	0	0.081	0.041	29.070	0.006	0.006	0.000	0.000	0.000	0.000
136	A	137	GLU	-1	-0.778	-0.866	32.178	-0.065	-0.065	0.000	0.000	0.000	0.000
137	A	138	ARG	1	0.840	0.919	30.430	0.092	0.092	0.000	0.000	0.000	0.000
138	A	139	LEU	0	-0.026	-0.006	29.995	0.005	0.005	0.000	0.000	0.000	0.000
139	A	140	LYS	1	0.915	0.933	34.144	0.070	0.070	0.000	0.000	0.000	0.000
140	A	141	ARG	1	0.942	0.962	35.817	0.065	0.065	0.000	0.000	0.000	0.000
141	A	142	THR	0	-0.063	-0.048	35.650	0.003	0.003	0.000	0.000	0.000	0.000
142	A	143	LEU	0	-0.011	-0.004	37.308	0.003	0.003	0.000	0.000	0.000	0.000
143	A	144	GLU	-1	-0.908	-0.943	39.894	-0.048	-0.048	0.000	0.000	0.000	0.000
144	A	145	GLU	-1	-0.760	-0.805	39.841	-0.051	-0.051	0.000	0.000	0.000	0.000
145	A	146	ILE	0	-0.073	-0.030	38.439	0.002	0.002	0.000	0.000	0.000	0.000
146	A	147	ARG	1	0.806	0.895	41.264	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)