FMO DATABASE

FMODB ID: R5Z98

Calculation Name: 4GKF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GKF

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U1T0

Base Structure: X-ray

Registration Date: 2023-06-20

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1531659.495339
FMO2-HF: Nuclear repulsion	1472532.276815
FMO2-HF: Total energy	-59127.218524
FMO2-MP2: Total energy	-59302.770299

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:15:ARG)

Summations of interaction energy for fragment #1(A:15:ARG)

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.
-88.937	-80.973	27.566	-15.366	-20.162	-0.159

Interaction energy analysis for fragmet #1(A:15:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.919 / q_NPA : 0.970

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	17	THR	0	0.049	0.029	3.881	-1.440	2.116	-0.024	-2.031	-1.502	0.004
4	A	18	LEU	0	0.053	0.019	5.304	-4.513	-4.513	0.000	0.000	0.000	0.000
5	A	19	GLU	-1	-0.773	-0.856	6.746	-32.472	-32.472	0.000	0.000	0.000	0.000
6	A	20	GLN	0	0.029	0.019	2.089	-7.858	-5.697	3.651	-2.683	-3.129	-0.012
7	A	21	ARG	1	0.929	0.961	2.068	-2.415	-0.685	6.939	-4.147	-4.522	-0.064
8	A	22	ARG	1	0.778	0.846	4.566	25.847	25.992	-0.001	-0.010	-0.134	0.000
9	A	23	GLY	0	0.025	0.015	3.281	2.761	3.028	0.023	-0.076	-0.214	0.000
10	A	24	GLU	-1	-0.860	-0.914	1.871	-107.347	-106.825	16.688	-7.188	-10.022	-0.088
11	A	25	TYR	0	-0.013	-0.029	3.147	8.302	7.661	0.292	0.780	-0.430	0.001
12	A	26	ALA	0	0.010	-0.001	6.423	3.817	3.817	0.000	0.000	0.000	0.000
13	A	27	TYR	0	-0.021	-0.003	4.524	3.580	3.720	-0.001	-0.008	-0.130	0.000
14	A	28	TYR	0	0.049	0.004	5.092	5.591	5.591	0.000	0.000	0.000	0.000
15	A	29	VAL	0	0.006	0.000	8.473	3.095	3.095	0.000	0.000	0.000	0.000
16	A	30	ILE	0	-0.040	-0.017	9.945	2.431	2.431	0.000	0.000	0.000	0.000
17	A	31	LYS	1	0.796	0.872	9.225	25.598	25.598	0.000	0.000	0.000	0.000
18	A	32	GLU	-1	-0.755	-0.873	11.623	-17.363	-17.363	0.000	0.000	0.000	0.000
19	A	33	VAL	0	-0.003	-0.012	14.338	1.476	1.476	0.000	0.000	0.000	0.000
20	A	34	ALA	0	-0.018	-0.005	14.233	1.100	1.100	0.000	0.000	0.000	0.000
21	A	35	ASP	-1	-0.839	-0.908	13.976	-20.505	-20.505	0.000	0.000	0.000	0.000
22	A	36	LEU	0	-0.024	0.000	16.809	0.869	0.869	0.000	0.000	0.000	0.000
23	A	37	ASN	0	-0.061	-0.032	19.774	0.751	0.751	0.000	0.000	0.000	0.000
24	A	38	ASP	-1	-0.852	-0.917	21.740	-11.563	-11.563	0.000	0.000	0.000	0.000
25	A	39	LYS	1	0.988	0.982	23.002	11.083	11.083	0.000	0.000	0.000	0.000
26	A	40	GLN	0	0.029	0.015	24.021	0.044	0.044	0.000	0.000	0.000	0.000
27	A	41	LEU	0	-0.025	0.002	20.252	-0.179	-0.179	0.000	0.000	0.000	0.000
28	A	42	GLU	-1	-0.767	-0.882	18.608	-15.748	-15.748	0.000	0.000	0.000	0.000
29	A	43	GLU	-1	-0.840	-0.884	20.184	-12.142	-12.142	0.000	0.000	0.000	0.000
30	A	44	LYS	1	0.836	0.898	22.544	11.445	11.445	0.000	0.000	0.000	0.000
31	A	45	TYR	0	-0.011	-0.026	14.747	-0.348	-0.348	0.000	0.000	0.000	0.000
32	A	46	ALA	0	0.009	0.003	17.863	-0.557	-0.557	0.000	0.000	0.000	0.000
33	A	47	SER	0	-0.002	-0.025	18.910	-0.137	-0.137	0.000	0.000	0.000	0.000
34	A	48	LEU	0	-0.063	-0.011	21.021	0.111	0.111	0.000	0.000	0.000	0.000
35	A	49	VAL	0	0.023	0.004	14.632	0.011	0.011	0.000	0.000	0.000	0.000
36	A	50	LYS	1	0.797	0.876	17.299	15.158	15.158	0.000	0.000	0.000	0.000
37	A	51	LYS	1	0.867	0.929	18.679	12.660	12.660	0.000	0.000	0.000	0.000
38	A	52	ALA	0	0.046	0.026	18.482	0.253	0.253	0.000	0.000	0.000	0.000
39	A	53	PRO	0	-0.008	-0.006	16.696	0.255	0.255	0.000	0.000	0.000	0.000
40	A	54	VAL	0	0.024	0.007	18.969	0.353	0.353	0.000	0.000	0.000	0.000
41	A	55	MET	0	-0.015	0.020	22.343	0.416	0.416	0.000	0.000	0.000	0.000
42	A	56	ILE	0	0.027	0.013	18.918	0.423	0.423	0.000	0.000	0.000	0.000
43	A	57	LEU	0	-0.062	-0.041	20.059	0.352	0.352	0.000	0.000	0.000	0.000
44	A	58	SER	0	-0.040	-0.022	23.486	0.458	0.458	0.000	0.000	0.000	0.000
45	A	59	ASN	0	-0.052	-0.012	26.290	0.757	0.757	0.000	0.000	0.000	0.000
46	A	60	GLY	0	0.058	0.038	25.366	0.293	0.293	0.000	0.000	0.000	0.000
47	A	61	LEU	0	0.002	-0.004	20.143	-0.066	-0.066	0.000	0.000	0.000	0.000
48	A	62	LEU	0	0.022	0.014	23.510	-0.113	-0.113	0.000	0.000	0.000	0.000
49	A	63	GLN	0	0.011	0.004	26.566	0.269	0.269	0.000	0.000	0.000	0.000
50	A	64	THR	0	0.002	-0.004	22.439	0.113	0.113	0.000	0.000	0.000	0.000
51	A	65	LEU	0	-0.019	-0.017	20.599	-0.086	-0.086	0.000	0.000	0.000	0.000
52	A	66	ALA	0	0.006	-0.005	24.562	0.095	0.095	0.000	0.000	0.000	0.000
53	A	67	PHE	0	0.006	0.006	26.134	0.218	0.218	0.000	0.000	0.000	0.000
54	A	68	LEU	0	-0.039	-0.021	21.486	0.122	0.122	0.000	0.000	0.000	0.000
55	A	69	LEU	0	-0.033	-0.014	25.602	0.051	0.051	0.000	0.000	0.000	0.000
56	A	70	ALA	0	0.013	0.005	27.738	0.233	0.233	0.000	0.000	0.000	0.000
57	A	71	LYS	1	0.887	0.953	28.071	10.567	10.567	0.000	0.000	0.000	0.000
58	A	72	ALA	0	0.008	0.016	26.919	0.080	0.080	0.000	0.000	0.000	0.000
59	A	73	GLU	-1	-0.939	-0.943	29.047	-9.022	-9.022	0.000	0.000	0.000	0.000
60	A	74	THR	0	-0.068	-0.043	27.701	0.074	0.074	0.000	0.000	0.000	0.000
61	A	75	SER	0	-0.043	-0.052	30.591	0.052	0.052	0.000	0.000	0.000	0.000
62	A	76	PRO	0	0.035	0.009	27.490	-0.256	-0.256	0.000	0.000	0.000	0.000
63	A	77	GLU	-1	-0.748	-0.834	27.539	-10.392	-10.392	0.000	0.000	0.000	0.000
64	A	78	LYS	1	0.932	0.969	29.081	9.847	9.847	0.000	0.000	0.000	0.000
65	A	79	ALA	0	0.049	0.022	24.293	-0.263	-0.263	0.000	0.000	0.000	0.000
66	A	80	ASN	0	-0.028	-0.038	24.349	-0.983	-0.983	0.000	0.000	0.000	0.000
67	A	81	GLN	0	0.027	0.029	25.038	-0.668	-0.668	0.000	0.000	0.000	0.000
68	A	82	ILE	0	0.012	0.017	22.163	-0.183	-0.183	0.000	0.000	0.000	0.000
69	A	83	LEU	0	-0.002	-0.007	19.268	-0.540	-0.540	0.000	0.000	0.000	0.000
70	A	84	SER	0	-0.095	-0.051	20.905	-0.392	-0.392	0.000	0.000	0.000	0.000
71	A	85	ARG	1	0.866	0.930	22.902	12.692	12.692	0.000	0.000	0.000	0.000
72	A	86	VAL	0	-0.067	-0.023	16.401	-0.201	-0.201	0.000	0.000	0.000	0.000
73	A	87	ASN	0	-0.047	-0.022	17.539	-0.625	-0.625	0.000	0.000	0.000	0.000
74	A	88	GLU	-1	-0.818	-0.886	15.352	-17.177	-17.177	0.000	0.000	0.000	0.000
75	A	89	TYR	0	-0.042	-0.045	5.188	0.595	0.595	0.000	0.000	0.000	0.000
76	A	90	PRO	0	-0.004	-0.019	8.108	0.241	0.241	0.000	0.000	0.000	0.000
77	A	91	PRO	0	-0.036	0.009	10.429	1.708	1.708	0.000	0.000	0.000	0.000
78	A	92	ARG	1	0.792	0.872	13.271	18.073	18.073	0.000	0.000	0.000	0.000
79	A	93	PHE	0	0.000	-0.029	13.576	1.075	1.075	0.000	0.000	0.000	0.000
80	A	94	ILE	0	0.017	0.002	17.376	1.172	1.172	0.000	0.000	0.000	0.000
81	A	95	GLU	-1	-0.799	-0.878	19.628	-15.464	-15.464	0.000	0.000	0.000	0.000
82	A	96	LYS	1	0.757	0.884	18.681	17.282	17.282	0.000	0.000	0.000	0.000
83	A	97	LEU	0	-0.018	0.000	22.116	0.662	0.662	0.000	0.000	0.000	0.000
84	A	98	GLY	0	0.037	0.020	24.966	0.089	0.089	0.000	0.000	0.000	0.000
85	A	99	ASN	0	0.016	-0.006	27.405	-0.367	-0.367	0.000	0.000	0.000	0.000
86	A	100	ASP	-1	-0.884	-0.923	28.718	-10.883	-10.883	0.000	0.000	0.000	0.000
87	A	101	LYS	1	0.780	0.876	23.321	12.483	12.483	0.000	0.000	0.000	0.000
88	A	102	ASP	-1	-0.714	-0.836	24.654	-12.183	-12.183	0.000	0.000	0.000	0.000
89	A	103	GLU	-1	-0.762	-0.880	21.859	-12.554	-12.554	0.000	0.000	0.000	0.000
90	A	104	HIS	0	-0.085	-0.067	21.343	-0.709	-0.709	0.000	0.000	0.000	0.000
91	A	105	LEU	0	0.032	0.007	22.496	-0.502	-0.502	0.000	0.000	0.000	0.000
92	A	106	LEU	0	-0.010	0.008	17.626	-0.555	-0.555	0.000	0.000	0.000	0.000
93	A	107	LEU	0	0.013	0.004	16.543	-1.012	-1.012	0.000	0.000	0.000	0.000
94	A	108	TYR	0	0.024	-0.007	18.026	-0.604	-0.604	0.000	0.000	0.000	0.000
95	A	109	LEU	0	-0.039	-0.018	19.196	-0.405	-0.405	0.000	0.000	0.000	0.000
96	A	110	HIS	0	0.048	0.050	14.072	-0.847	-0.847	0.000	0.000	0.000	0.000
97	A	111	ILE	0	0.011	0.018	14.463	-1.449	-1.449	0.000	0.000	0.000	0.000
98	A	112	VAL	0	-0.002	-0.016	16.150	-0.547	-0.547	0.000	0.000	0.000	0.000
99	A	113	TYR	0	-0.009	-0.018	12.376	0.090	0.090	0.000	0.000	0.000	0.000
100	A	114	TRP	0	-0.026	-0.025	7.672	-1.427	-1.427	0.000	0.000	0.000	0.000
101	A	115	LEU	0	-0.006	-0.012	13.884	-0.170	-0.170	0.000	0.000	0.000	0.000
102	A	116	ARG	1	0.828	0.907	16.730	14.216	14.216	0.000	0.000	0.000	0.000
103	A	117	GLU	-1	-0.870	-0.909	11.704	-20.874	-20.874	0.000	0.000	0.000	0.000
104	A	118	ASN	0	-0.099	-0.047	10.523	-1.962	-1.962	0.000	0.000	0.000	0.000
105	A	119	VAL	0	-0.054	-0.019	13.873	0.323	0.323	0.000	0.000	0.000	0.000
106	A	120	ASP	-1	-0.754	-0.880	17.576	-12.255	-12.255	0.000	0.000	0.000	0.000
107	A	121	ARG	1	0.997	1.006	18.468	14.486	14.486	0.000	0.000	0.000	0.000
108	A	122	ASN	0	-0.055	-0.031	20.662	0.430	0.430	0.000	0.000	0.000	0.000
109	A	123	ILE	0	-0.019	0.020	20.301	0.498	0.498	0.000	0.000	0.000	0.000
110	A	124	ASP	-1	-0.780	-0.888	22.944	-12.104	-12.104	0.000	0.000	0.000	0.000
111	A	125	VAL	0	0.014	0.005	25.092	0.189	0.189	0.000	0.000	0.000	0.000
112	A	126	LYS	1	0.857	0.908	27.699	10.117	10.117	0.000	0.000	0.000	0.000
113	A	127	THR	0	0.006	-0.007	26.326	0.198	0.198	0.000	0.000	0.000	0.000
114	A	128	LEU	0	0.010	-0.010	23.340	0.106	0.106	0.000	0.000	0.000	0.000
115	A	129	LEU	0	-0.024	0.001	27.614	0.133	0.133	0.000	0.000	0.000	0.000
116	A	130	SER	0	-0.067	-0.040	30.613	0.429	0.429	0.000	0.000	0.000	0.000
117	A	131	GLN	0	-0.039	-0.009	24.277	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	132	ASP	-1	-0.815	-0.898	27.645	-11.300	-11.300	0.000	0.000	0.000	0.000
119	A	133	TYR	0	0.059	0.013	27.741	-0.444	-0.444	0.000	0.000	0.000	0.000
120	A	134	SER	0	0.015	0.006	25.807	-0.298	-0.298	0.000	0.000	0.000	0.000
121	A	135	LYS	1	0.837	0.917	21.939	12.327	12.327	0.000	0.000	0.000	0.000
122	A	136	VAL	0	0.063	0.033	22.792	-0.722	-0.722	0.000	0.000	0.000	0.000
123	A	137	LEU	0	-0.004	0.019	22.574	-0.596	-0.596	0.000	0.000	0.000	0.000
124	A	138	TRP	0	-0.022	-0.012	16.691	-0.168	-0.168	0.000	0.000	0.000	0.000
125	A	139	ALA	0	0.041	0.014	18.592	-0.990	-0.990	0.000	0.000	0.000	0.000
126	A	140	THR	0	-0.019	-0.029	18.466	-0.620	-0.620	0.000	0.000	0.000	0.000
127	A	141	LYS	1	0.947	0.963	17.645	14.576	14.576	0.000	0.000	0.000	0.000
128	A	142	GLU	-1	-0.778	-0.829	12.012	-24.668	-24.668	0.000	0.000	0.000	0.000
129	A	143	ALA	0	0.034	0.013	13.774	-1.453	-1.453	0.000	0.000	0.000	0.000
130	A	144	ILE	0	0.021	0.013	15.112	-0.674	-0.674	0.000	0.000	0.000	0.000
131	A	145	ALA	0	-0.018	0.001	11.627	-0.511	-0.511	0.000	0.000	0.000	0.000
132	A	146	LEU	0	-0.018	-0.002	9.840	-1.707	-1.707	0.000	0.000	0.000	0.000
133	A	147	LEU	0	0.085	0.017	10.953	-1.240	-1.240	0.000	0.000	0.000	0.000
134	A	148	ASN	0	-0.066	-0.031	12.763	0.972	0.972	0.000	0.000	0.000	0.000
135	A	149	TRP	0	-0.064	-0.038	6.424	-2.192	-2.192	0.000	0.000	0.000	0.000
136	A	150	MET	0	0.005	0.009	9.311	-0.809	-0.809	0.000	0.000	0.000	0.000
137	A	151	ARG	1	0.902	0.964	10.974	18.602	18.602	0.000	0.000	0.000	0.000
138	A	152	ARG	1	0.910	0.953	9.778	24.192	24.192	0.000	0.000	0.000	0.000
139	A	153	PHE	0	0.036	0.004	4.428	-0.504	-0.420	-0.001	-0.003	-0.079	0.000
140	A	154	ALA	0	0.033	0.012	9.994	0.997	0.997	0.000	0.000	0.000	0.000
141	A	155	VAL	0	-0.066	-0.042	13.594	1.230	1.230	0.000	0.000	0.000	0.000
142	A	156	ALA	0	-0.040	-0.009	10.992	0.724	0.724	0.000	0.000	0.000	0.000
143	A	157	MET	0	-0.068	-0.018	9.748	-1.493	-1.493	0.000	0.000	0.000	0.000
144	A	158	LEU	0	-0.026	0.009	13.670	0.551	0.551	0.000	0.000	0.000	0.000
145	A	159	LYS	1	0.795	0.881	16.755	14.997	14.997	0.000	0.000	0.000	0.000
146	A	160	GLU	-1	-0.841	-0.911	20.423	-13.576	-13.576	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:ARG)