FMO DATABASE

FMODB ID: ZYJ6N

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	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	-1527683.549414
FMO2-HF: Nuclear repulsion	1468556.545107
FMO2-HF: Total energy	-59127.004307
FMO2-MP2: Total energy	-59302.582947

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.
-64.676	-57.232	23.946	-13.979	-17.412	-0.097

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 : 0.932 / q_NPA : 0.957

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	0.024	0.013	3.693	0.201	3.833	-0.043	-1.917	-1.672	0.004
4	A	18	LEU	0	0.054	0.015	4.888	-3.917	-3.855	-0.001	-0.002	-0.058	0.000
5	A	19	GLU	-1	-0.772	-0.869	7.184	-31.805	-31.805	0.000	0.000	0.000	0.000
6	A	20	GLN	0	0.036	0.023	1.993	-6.680	-5.810	8.066	-4.766	-4.170	-0.018
7	A	21	ARG	1	0.929	0.965	3.255	18.171	20.261	0.137	-0.933	-1.294	-0.006
8	A	22	ARG	1	0.779	0.852	4.476	26.227	26.349	-0.001	-0.006	-0.115	0.000
9	A	23	GLY	0	0.009	0.011	3.591	2.064	2.231	0.003	-0.038	-0.132	0.000
10	A	24	GLU	-1	-0.864	-0.916	1.887	-103.505	-103.020	15.590	-6.817	-9.259	-0.078
11	A	25	TYR	0	-0.009	-0.011	3.142	6.587	6.248	0.198	0.518	-0.378	0.001
12	A	26	ALA	0	0.006	-0.006	6.544	3.671	3.671	0.000	0.000	0.000	0.000
13	A	27	TYR	0	-0.035	-0.018	4.264	2.981	3.140	-0.001	-0.013	-0.145	0.000
14	A	28	TYR	0	0.043	0.000	4.789	4.916	5.031	-0.001	-0.002	-0.112	0.000
15	A	29	VAL	0	0.007	0.008	8.197	2.993	2.993	0.000	0.000	0.000	0.000
16	A	30	ILE	0	-0.032	-0.016	9.871	2.366	2.366	0.000	0.000	0.000	0.000
17	A	31	LYS	1	0.825	0.891	9.014	25.655	25.655	0.000	0.000	0.000	0.000
18	A	32	GLU	-1	-0.799	-0.891	11.513	-17.432	-17.432	0.000	0.000	0.000	0.000
19	A	33	VAL	0	-0.008	-0.016	14.015	1.454	1.454	0.000	0.000	0.000	0.000
20	A	34	ALA	0	-0.019	-0.008	14.308	1.120	1.120	0.000	0.000	0.000	0.000
21	A	35	ASP	-1	-0.848	-0.910	13.680	-20.682	-20.682	0.000	0.000	0.000	0.000
22	A	36	LEU	0	-0.055	-0.015	16.722	0.825	0.825	0.000	0.000	0.000	0.000
23	A	37	ASN	0	-0.056	-0.026	19.692	0.726	0.726	0.000	0.000	0.000	0.000
24	A	38	ASP	-1	-0.839	-0.905	21.659	-11.599	-11.599	0.000	0.000	0.000	0.000
25	A	39	LYS	1	1.001	0.969	22.727	11.065	11.065	0.000	0.000	0.000	0.000
26	A	40	GLN	0	0.024	0.018	24.120	0.120	0.120	0.000	0.000	0.000	0.000
27	A	41	LEU	0	-0.033	-0.006	20.289	-0.206	-0.206	0.000	0.000	0.000	0.000
28	A	42	GLU	-1	-0.781	-0.890	18.400	-15.997	-15.997	0.000	0.000	0.000	0.000
29	A	43	GLU	-1	-0.856	-0.899	20.187	-12.002	-12.002	0.000	0.000	0.000	0.000
30	A	44	LYS	1	0.841	0.897	22.590	11.372	11.372	0.000	0.000	0.000	0.000
31	A	45	TYR	0	-0.009	-0.017	14.984	-0.377	-0.377	0.000	0.000	0.000	0.000
32	A	46	ALA	0	0.015	0.010	17.839	-0.537	-0.537	0.000	0.000	0.000	0.000
33	A	47	SER	0	0.005	-0.020	18.878	-0.087	-0.087	0.000	0.000	0.000	0.000
34	A	48	LEU	0	-0.068	-0.027	21.221	0.090	0.090	0.000	0.000	0.000	0.000
35	A	49	VAL	0	0.031	0.009	14.861	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	50	LYS	1	0.803	0.886	17.615	15.110	15.110	0.000	0.000	0.000	0.000
37	A	51	LYS	1	0.871	0.945	18.937	12.542	12.542	0.000	0.000	0.000	0.000
38	A	52	ALA	0	0.034	0.025	18.401	0.281	0.281	0.000	0.000	0.000	0.000
39	A	53	PRO	0	-0.002	-0.006	17.010	0.323	0.323	0.000	0.000	0.000	0.000
40	A	54	VAL	0	0.029	0.008	19.383	0.321	0.321	0.000	0.000	0.000	0.000
41	A	55	MET	0	-0.026	0.011	22.818	0.448	0.448	0.000	0.000	0.000	0.000
42	A	56	ILE	0	0.015	0.007	19.643	0.390	0.390	0.000	0.000	0.000	0.000
43	A	57	LEU	0	-0.070	-0.023	20.707	0.309	0.309	0.000	0.000	0.000	0.000
44	A	58	SER	0	-0.044	-0.029	24.081	0.447	0.447	0.000	0.000	0.000	0.000
45	A	59	ASN	0	-0.030	-0.012	26.880	0.709	0.709	0.000	0.000	0.000	0.000
46	A	60	GLY	0	0.035	0.026	25.919	0.271	0.271	0.000	0.000	0.000	0.000
47	A	61	LEU	0	-0.006	-0.013	21.043	-0.112	-0.112	0.000	0.000	0.000	0.000
48	A	62	LEU	0	0.033	0.016	24.398	-0.108	-0.108	0.000	0.000	0.000	0.000
49	A	63	GLN	0	0.036	0.016	27.396	0.158	0.158	0.000	0.000	0.000	0.000
50	A	64	THR	0	0.018	0.008	22.888	0.108	0.108	0.000	0.000	0.000	0.000
51	A	65	LEU	0	-0.010	-0.015	21.175	-0.075	-0.075	0.000	0.000	0.000	0.000
52	A	66	ALA	0	0.003	-0.003	25.042	0.091	0.091	0.000	0.000	0.000	0.000
53	A	67	PHE	0	0.004	0.000	26.476	0.233	0.233	0.000	0.000	0.000	0.000
54	A	68	LEU	0	-0.041	-0.014	21.846	0.105	0.105	0.000	0.000	0.000	0.000
55	A	69	LEU	0	-0.021	-0.013	25.905	0.094	0.094	0.000	0.000	0.000	0.000
56	A	70	ALA	0	-0.009	0.002	28.136	0.263	0.263	0.000	0.000	0.000	0.000
57	A	71	LYS	1	0.906	0.960	28.166	10.352	10.352	0.000	0.000	0.000	0.000
58	A	72	ALA	0	0.009	0.016	27.087	0.100	0.100	0.000	0.000	0.000	0.000
59	A	73	GLU	-1	-0.948	-0.949	29.198	-9.007	-9.007	0.000	0.000	0.000	0.000
60	A	74	THR	0	-0.079	-0.045	27.911	0.051	0.051	0.000	0.000	0.000	0.000
61	A	75	SER	0	0.009	-0.004	30.817	-0.030	-0.030	0.000	0.000	0.000	0.000
62	A	76	PRO	0	0.044	0.003	27.971	-0.266	-0.266	0.000	0.000	0.000	0.000
63	A	77	GLU	-1	-0.790	-0.891	28.112	-10.261	-10.261	0.000	0.000	0.000	0.000
64	A	78	LYS	1	0.929	0.970	29.042	9.762	9.762	0.000	0.000	0.000	0.000
65	A	79	ALA	0	0.042	0.018	24.635	-0.294	-0.294	0.000	0.000	0.000	0.000
66	A	80	ASN	0	-0.016	-0.027	24.571	-1.008	-1.008	0.000	0.000	0.000	0.000
67	A	81	GLN	0	0.015	0.023	25.190	-0.622	-0.622	0.000	0.000	0.000	0.000
68	A	82	ILE	0	0.010	0.012	22.310	-0.144	-0.144	0.000	0.000	0.000	0.000
69	A	83	LEU	0	0.007	-0.003	19.342	-0.512	-0.512	0.000	0.000	0.000	0.000
70	A	84	SER	0	-0.092	-0.038	20.914	-0.418	-0.418	0.000	0.000	0.000	0.000
71	A	85	ARG	1	0.900	0.944	22.900	12.515	12.515	0.000	0.000	0.000	0.000
72	A	86	VAL	0	-0.098	-0.041	16.575	-0.229	-0.229	0.000	0.000	0.000	0.000
73	A	87	ASN	0	-0.037	-0.026	17.749	-0.458	-0.458	0.000	0.000	0.000	0.000
74	A	88	GLU	-1	-0.855	-0.888	15.202	-17.511	-17.511	0.000	0.000	0.000	0.000
75	A	89	TYR	0	-0.047	-0.046	5.482	1.052	1.052	0.000	0.000	0.000	0.000
76	A	90	PRO	0	0.007	-0.026	8.066	-0.059	-0.059	0.000	0.000	0.000	0.000
77	A	91	PRO	0	-0.028	0.016	10.437	1.586	1.586	0.000	0.000	0.000	0.000
78	A	92	ARG	1	0.793	0.888	13.285	17.722	17.722	0.000	0.000	0.000	0.000
79	A	93	PHE	0	0.019	-0.006	13.559	1.324	1.324	0.000	0.000	0.000	0.000
80	A	94	ILE	0	0.055	0.020	17.524	1.240	1.240	0.000	0.000	0.000	0.000
81	A	95	GLU	-1	-0.811	-0.889	19.602	-15.105	-15.105	0.000	0.000	0.000	0.000
82	A	96	LYS	1	0.747	0.861	18.753	16.887	16.887	0.000	0.000	0.000	0.000
83	A	97	LEU	0	-0.029	0.002	21.954	0.608	0.608	0.000	0.000	0.000	0.000
84	A	98	GLY	0	0.041	0.023	24.955	0.133	0.133	0.000	0.000	0.000	0.000
85	A	99	ASN	0	-0.002	-0.020	27.110	-0.425	-0.425	0.000	0.000	0.000	0.000
86	A	100	ASP	-1	-0.919	-0.947	28.555	-10.718	-10.718	0.000	0.000	0.000	0.000
87	A	101	LYS	1	0.835	0.917	23.076	12.529	12.529	0.000	0.000	0.000	0.000
88	A	102	ASP	-1	-0.672	-0.835	25.239	-11.948	-11.948	0.000	0.000	0.000	0.000
89	A	103	GLU	-1	-0.792	-0.894	21.817	-12.504	-12.504	0.000	0.000	0.000	0.000
90	A	104	HIS	0	-0.085	-0.063	21.573	-0.645	-0.645	0.000	0.000	0.000	0.000
91	A	105	LEU	0	0.017	0.004	22.914	-0.443	-0.443	0.000	0.000	0.000	0.000
92	A	106	LEU	0	-0.007	-0.001	17.679	-0.546	-0.546	0.000	0.000	0.000	0.000
93	A	107	LEU	0	0.025	0.018	16.891	-0.929	-0.929	0.000	0.000	0.000	0.000
94	A	108	TYR	0	0.030	0.008	18.379	-0.523	-0.523	0.000	0.000	0.000	0.000
95	A	109	LEU	0	-0.027	-0.020	19.321	-0.317	-0.317	0.000	0.000	0.000	0.000
96	A	110	HIS	0	0.041	0.038	14.334	-0.724	-0.724	0.000	0.000	0.000	0.000
97	A	111	ILE	0	0.010	0.011	14.998	-1.228	-1.228	0.000	0.000	0.000	0.000
98	A	112	VAL	0	0.013	-0.003	16.968	-0.418	-0.418	0.000	0.000	0.000	0.000
99	A	113	TYR	0	-0.018	-0.015	12.292	-0.405	-0.405	0.000	0.000	0.000	0.000
100	A	114	TRP	0	-0.012	-0.027	7.685	-1.218	-1.218	0.000	0.000	0.000	0.000
101	A	115	LEU	0	-0.009	-0.014	14.305	-0.176	-0.176	0.000	0.000	0.000	0.000
102	A	116	ARG	1	0.849	0.916	16.966	13.989	13.989	0.000	0.000	0.000	0.000
103	A	117	GLU	-1	-0.887	-0.915	12.220	-20.086	-20.086	0.000	0.000	0.000	0.000
104	A	118	ASN	0	-0.105	-0.055	10.728	-1.594	-1.594	0.000	0.000	0.000	0.000
105	A	119	VAL	0	-0.062	-0.026	14.143	0.351	0.351	0.000	0.000	0.000	0.000
106	A	120	ASP	-1	-0.770	-0.891	17.666	-12.201	-12.201	0.000	0.000	0.000	0.000
107	A	121	ARG	1	0.999	1.014	19.044	14.097	14.097	0.000	0.000	0.000	0.000
108	A	122	ASN	0	-0.080	-0.044	20.919	0.361	0.361	0.000	0.000	0.000	0.000
109	A	123	ILE	0	-0.002	0.022	20.835	0.505	0.505	0.000	0.000	0.000	0.000
110	A	124	ASP	-1	-0.803	-0.903	23.369	-11.920	-11.920	0.000	0.000	0.000	0.000
111	A	125	VAL	0	0.012	0.004	25.436	0.251	0.251	0.000	0.000	0.000	0.000
112	A	126	LYS	1	0.878	0.928	28.098	9.982	9.982	0.000	0.000	0.000	0.000
113	A	127	THR	0	0.016	0.001	26.527	0.207	0.207	0.000	0.000	0.000	0.000
114	A	128	LEU	0	-0.038	-0.028	24.340	0.145	0.145	0.000	0.000	0.000	0.000
115	A	129	LEU	0	-0.040	-0.006	28.397	0.130	0.130	0.000	0.000	0.000	0.000
116	A	130	SER	0	-0.048	-0.027	31.407	0.378	0.378	0.000	0.000	0.000	0.000
117	A	131	GLN	0	-0.048	-0.020	24.865	-0.053	-0.053	0.000	0.000	0.000	0.000
118	A	132	ASP	-1	-0.809	-0.893	27.978	-11.057	-11.057	0.000	0.000	0.000	0.000
119	A	133	TYR	0	0.078	0.014	28.504	-0.395	-0.395	0.000	0.000	0.000	0.000
120	A	134	SER	0	0.012	0.002	25.661	-0.303	-0.303	0.000	0.000	0.000	0.000
121	A	135	LYS	1	0.839	0.918	22.345	12.121	12.121	0.000	0.000	0.000	0.000
122	A	136	VAL	0	0.067	0.037	23.385	-0.695	-0.695	0.000	0.000	0.000	0.000
123	A	137	LEU	0	0.004	0.023	23.322	-0.610	-0.610	0.000	0.000	0.000	0.000
124	A	138	TRP	0	-0.017	-0.004	16.666	-0.180	-0.180	0.000	0.000	0.000	0.000
125	A	139	ALA	0	0.036	0.014	19.415	-0.952	-0.952	0.000	0.000	0.000	0.000
126	A	140	THR	0	-0.015	-0.032	19.377	-0.601	-0.601	0.000	0.000	0.000	0.000
127	A	141	LYS	1	0.931	0.961	18.343	14.355	14.355	0.000	0.000	0.000	0.000
128	A	142	GLU	-1	-0.774	-0.827	12.758	-24.051	-24.051	0.000	0.000	0.000	0.000
129	A	143	ALA	0	0.033	0.017	14.621	-1.265	-1.265	0.000	0.000	0.000	0.000
130	A	144	ILE	0	0.018	0.009	15.535	-0.838	-0.838	0.000	0.000	0.000	0.000
131	A	145	ALA	0	-0.016	0.003	12.236	-0.548	-0.548	0.000	0.000	0.000	0.000
132	A	146	LEU	0	-0.020	-0.008	10.325	-1.730	-1.730	0.000	0.000	0.000	0.000
133	A	147	LEU	0	0.094	0.016	11.432	-1.245	-1.245	0.000	0.000	0.000	0.000
134	A	148	ASN	0	-0.063	-0.023	12.845	0.655	0.655	0.000	0.000	0.000	0.000
135	A	149	TRP	0	-0.067	-0.035	5.854	-2.215	-2.215	0.000	0.000	0.000	0.000
136	A	150	MET	0	0.012	0.017	9.729	-0.626	-0.626	0.000	0.000	0.000	0.000
137	A	151	ARG	1	0.903	0.964	11.168	18.522	18.522	0.000	0.000	0.000	0.000
138	A	152	ARG	1	0.897	0.939	10.320	23.342	23.342	0.000	0.000	0.000	0.000
139	A	153	PHE	0	0.046	0.008	4.367	-0.709	-0.628	-0.001	-0.003	-0.077	0.000
140	A	154	ALA	0	0.035	0.025	10.154	0.804	0.804	0.000	0.000	0.000	0.000
141	A	155	VAL	0	-0.064	-0.031	13.644	1.077	1.077	0.000	0.000	0.000	0.000
142	A	156	ALA	0	-0.038	-0.015	10.939	0.629	0.629	0.000	0.000	0.000	0.000
143	A	157	MET	0	-0.077	-0.026	9.548	-1.172	-1.172	0.000	0.000	0.000	0.000
144	A	158	LEU	0	-0.037	0.001	13.437	0.656	0.656	0.000	0.000	0.000	0.000
145	A	159	LYS	1	0.820	0.891	16.399	15.051	15.051	0.000	0.000	0.000	0.000
146	A	160	GLU	-1	-0.863	-0.918	20.040	-13.682	-13.682	0.000	0.000	0.000	0.000

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