FMO DATABASE

FMODB ID: KGRK3

Calculation Name: 3IF0-X-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IF0

Chain ID: X

ChEMBL ID:

UniProt ID: Q74MS9

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	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	149
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1598012.756429
FMO2-HF: Nuclear repulsion	1536106.730419
FMO2-HF: Total energy	-61906.026009
FMO2-MP2: Total energy	-62089.433339

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(X:1:MET)

Summations of interaction energy for fragment #1(X: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.
-9.421	-3.409	11.135	-3.845	-13.299	-0.03

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.012

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	X	3	LEU	0	0.012	0.005	2.671	-0.245	1.720	0.151	-0.730	-1.386	0.000
4	X	4	ARG	1	0.875	0.923	5.184	-0.783	-0.724	-0.001	-0.004	-0.054	0.000
5	X	5	ILE	0	0.003	0.008	8.431	0.070	0.070	0.000	0.000	0.000	0.000
6	X	6	PRO	0	0.033	0.009	10.495	-0.138	-0.138	0.000	0.000	0.000	0.000
7	X	7	TRP	0	0.032	0.004	10.670	0.135	0.135	0.000	0.000	0.000	0.000
8	X	8	LYS	1	0.924	0.955	12.582	0.112	0.112	0.000	0.000	0.000	0.000
9	X	9	GLU	-1	-0.855	-0.920	13.155	-0.086	-0.086	0.000	0.000	0.000	0.000
10	X	10	VAL	0	0.001	0.002	8.175	0.083	0.083	0.000	0.000	0.000	0.000
11	X	11	TYR	0	0.055	0.015	10.754	-0.125	-0.125	0.000	0.000	0.000	0.000
12	X	12	TYR	0	-0.029	-0.025	12.857	0.060	0.060	0.000	0.000	0.000	0.000
13	X	13	LEU	0	0.028	0.037	8.612	-0.024	-0.024	0.000	0.000	0.000	0.000
14	X	14	GLY	0	0.005	0.007	7.253	-0.164	-0.164	0.000	0.000	0.000	0.000
15	X	15	TYR	0	-0.018	-0.025	8.027	0.499	0.499	0.000	0.000	0.000	0.000
16	X	16	ASN	0	-0.007	-0.003	9.017	-0.125	-0.125	0.000	0.000	0.000	0.000
17	X	17	MET	0	-0.006	0.000	8.858	0.003	0.003	0.000	0.000	0.000	0.000
18	X	18	GLY	0	0.019	0.027	11.840	0.141	0.141	0.000	0.000	0.000	0.000
19	X	19	ASN	0	0.000	-0.011	12.298	0.014	0.014	0.000	0.000	0.000	0.000
20	X	20	TYR	0	0.004	-0.001	6.535	0.298	0.298	0.000	0.000	0.000	0.000
21	X	21	ILE	0	-0.006	0.012	7.063	-0.044	-0.044	0.000	0.000	0.000	0.000
22	X	22	LYS	1	0.937	0.983	4.634	0.825	0.886	-0.001	-0.032	-0.027	0.000
23	X	23	ILE	0	-0.033	-0.012	2.517	0.130	1.247	0.433	-0.351	-1.200	0.000
24	X	24	SER	0	0.004	-0.021	2.394	-6.048	-4.569	2.881	-1.807	-2.553	-0.023
25	X	25	GLU	-1	-0.710	-0.847	2.179	-6.184	-4.859	3.502	-1.511	-3.316	-0.008
26	X	26	PRO	0	0.013	0.015	3.002	2.212	0.887	0.035	1.574	-0.284	-0.001
27	X	27	GLU	-1	-0.704	-0.829	5.567	-2.126	-2.126	0.000	0.000	0.000	0.000
28	X	28	LEU	0	-0.016	-0.013	2.598	-0.399	0.190	2.464	-0.613	-2.440	-0.001
29	X	29	LEU	0	0.010	0.013	4.659	0.688	0.771	-0.001	-0.004	-0.077	0.000
30	X	30	PHE	0	0.045	0.023	6.873	0.185	0.185	0.000	0.000	0.000	0.000
31	X	31	VAL	0	-0.016	-0.006	7.431	0.168	0.168	0.000	0.000	0.000	0.000
32	X	32	LEU	0	-0.040	-0.031	6.799	0.129	0.129	0.000	0.000	0.000	0.000
33	X	33	ARG	1	0.852	0.917	9.725	-0.042	-0.042	0.000	0.000	0.000	0.000
34	X	34	ASN	0	-0.049	-0.020	12.210	0.019	0.019	0.000	0.000	0.000	0.000
35	X	35	LYS	1	0.807	0.918	12.218	0.255	0.255	0.000	0.000	0.000	0.000
36	X	36	PRO	0	0.084	0.048	13.051	0.065	0.065	0.000	0.000	0.000	0.000
37	X	37	GLN	0	0.047	0.006	14.330	0.065	0.065	0.000	0.000	0.000	0.000
38	X	38	ILE	0	-0.040	-0.019	8.990	0.035	0.035	0.000	0.000	0.000	0.000
39	X	39	LYS	1	0.857	0.914	9.811	-0.411	-0.411	0.000	0.000	0.000	0.000
40	X	40	ASP	-1	-0.818	-0.897	10.593	0.574	0.574	0.000	0.000	0.000	0.000
41	X	41	ARG	1	0.854	0.927	10.761	-0.097	-0.097	0.000	0.000	0.000	0.000
42	X	42	LEU	0	-0.041	-0.028	5.273	-0.001	-0.001	0.000	0.000	0.000	0.000
43	X	43	LYS	1	0.795	0.895	7.857	-0.280	-0.280	0.000	0.000	0.000	0.000
44	X	44	LEU	0	0.009	0.025	4.451	-0.056	0.171	0.002	-0.042	-0.188	0.000
45	X	45	ASP	-1	-0.764	-0.906	8.608	0.504	0.504	0.000	0.000	0.000	0.000
46	X	46	GLU	-1	-0.820	-0.891	8.751	0.594	0.594	0.000	0.000	0.000	0.000
47	X	47	LYN	0	0.044	0.022	9.625	0.004	0.004	0.000	0.000	0.000	0.000
48	X	48	THR	0	-0.013	-0.003	7.817	-0.138	-0.138	0.000	0.000	0.000	0.000
49	X	49	ILE	0	0.033	0.016	2.216	-0.575	-0.264	1.671	-0.300	-1.681	0.003
50	X	50	ILE	0	0.014	0.010	6.476	-0.356	-0.345	-0.001	-0.002	-0.007	0.000
51	X	51	LYS	1	0.794	0.884	9.000	-1.308	-1.308	0.000	0.000	0.000	0.000
52	X	52	GLU	-1	-0.885	-0.925	5.031	1.248	1.358	0.000	-0.023	-0.086	0.000
53	X	53	GLY	0	0.029	-0.004	6.820	-0.420	-0.420	0.000	0.000	0.000	0.000
54	X	54	VAL	0	-0.004	-0.010	7.554	-0.233	-0.233	0.000	0.000	0.000	0.000
55	X	55	LYS	1	0.888	0.954	10.043	-0.232	-0.232	0.000	0.000	0.000	0.000
56	X	56	LYS	1	0.795	0.894	5.397	2.276	2.276	0.000	0.000	0.000	0.000
57	X	57	TYR	0	-0.024	-0.042	4.943	-0.077	-0.077	0.000	0.000	0.000	0.000
58	X	58	LYS	1	0.961	0.985	11.178	0.324	0.324	0.000	0.000	0.000	0.000
59	X	59	ASN	0	0.015	0.007	13.690	0.019	0.019	0.000	0.000	0.000	0.000
60	X	60	PHE	0	0.005	0.013	6.280	-0.044	-0.044	0.000	0.000	0.000	0.000
61	X	61	TRP	0	0.047	0.011	10.642	-0.075	-0.075	0.000	0.000	0.000	0.000
62	X	62	GLU	-1	-0.748	-0.862	12.858	-0.336	-0.336	0.000	0.000	0.000	0.000
63	X	63	ILE	0	-0.030	0.006	9.679	-0.020	-0.020	0.000	0.000	0.000	0.000
64	X	64	TYR	0	-0.004	-0.004	9.338	-0.019	-0.019	0.000	0.000	0.000	0.000
65	X	65	TYR	0	0.017	-0.003	10.838	0.018	0.018	0.000	0.000	0.000	0.000
66	X	66	THR	0	0.009	-0.005	14.347	0.040	0.040	0.000	0.000	0.000	0.000
67	X	67	VAL	0	-0.044	-0.029	9.873	-0.005	-0.005	0.000	0.000	0.000	0.000
68	X	68	LYS	1	0.815	0.887	12.910	0.263	0.263	0.000	0.000	0.000	0.000
69	X	69	ASP	-1	-0.834	-0.884	14.497	-0.252	-0.252	0.000	0.000	0.000	0.000
70	X	70	LEU	0	-0.001	-0.006	16.194	0.022	0.022	0.000	0.000	0.000	0.000
71	X	71	ILE	0	-0.030	-0.009	13.012	0.024	0.024	0.000	0.000	0.000	0.000
72	X	72	LEU	0	-0.020	-0.005	16.416	0.042	0.042	0.000	0.000	0.000	0.000
73	X	73	ARG	1	0.936	0.989	18.798	0.287	0.287	0.000	0.000	0.000	0.000
74	X	74	GLY	0	-0.020	-0.008	19.922	0.024	0.024	0.000	0.000	0.000	0.000
75	X	75	TYR	0	-0.044	-0.025	19.418	0.014	0.014	0.000	0.000	0.000	0.000
76	X	76	ARG	1	0.851	0.925	16.573	0.392	0.392	0.000	0.000	0.000	0.000
77	X	77	VAL	0	0.025	-0.002	12.857	0.028	0.028	0.000	0.000	0.000	0.000
78	X	78	ARG	1	0.855	0.911	10.641	0.847	0.847	0.000	0.000	0.000	0.000
79	X	79	PHE	0	-0.028	-0.004	7.592	0.147	0.147	0.000	0.000	0.000	0.000
80	X	80	ASP	-1	-0.791	-0.888	9.754	-1.096	-1.096	0.000	0.000	0.000	0.000
81	X	81	GLY	0	-0.008	0.000	9.536	-0.043	-0.043	0.000	0.000	0.000	0.000
82	X	82	PHE	0	-0.044	-0.037	10.506	0.133	0.133	0.000	0.000	0.000	0.000
83	X	83	PHE	0	-0.006	-0.019	13.660	0.091	0.091	0.000	0.000	0.000	0.000
84	X	84	ILE	0	-0.013	0.004	12.382	-0.165	-0.165	0.000	0.000	0.000	0.000
85	X	85	GLU	-1	-0.758	-0.828	14.360	-0.715	-0.715	0.000	0.000	0.000	0.000
86	X	86	LEU	0	0.001	-0.005	15.953	-0.048	-0.048	0.000	0.000	0.000	0.000
87	X	87	TYR	0	-0.048	-0.049	15.996	0.054	0.054	0.000	0.000	0.000	0.000
88	X	88	GLU	-1	-0.786	-0.888	20.526	-0.276	-0.276	0.000	0.000	0.000	0.000
89	X	89	LYS	1	0.890	0.921	22.008	0.214	0.214	0.000	0.000	0.000	0.000
90	X	90	GLY	0	-0.031	-0.004	21.586	0.020	0.020	0.000	0.000	0.000	0.000
91	X	91	ILE	0	0.008	0.013	20.195	-0.002	-0.002	0.000	0.000	0.000	0.000
92	X	92	ILE	0	-0.033	-0.006	16.824	-0.039	-0.039	0.000	0.000	0.000	0.000
93	X	93	PRO	0	0.017	0.001	14.137	0.040	0.040	0.000	0.000	0.000	0.000
94	X	94	GLY	0	0.002	-0.001	16.420	-0.039	-0.039	0.000	0.000	0.000	0.000
95	X	95	THR	0	-0.067	-0.022	18.346	0.041	0.041	0.000	0.000	0.000	0.000
96	X	96	ILE	0	-0.031	-0.016	21.166	0.046	0.046	0.000	0.000	0.000	0.000
97	X	97	GLU	-1	-0.852	-0.927	20.978	-0.463	-0.463	0.000	0.000	0.000	0.000
98	X	98	GLN	0	-0.073	-0.029	18.923	-0.036	-0.036	0.000	0.000	0.000	0.000
99	X	99	ASP	-1	-0.825	-0.915	20.934	-0.263	-0.263	0.000	0.000	0.000	0.000
100	X	100	TYR	0	-0.054	-0.051	21.809	0.034	0.034	0.000	0.000	0.000	0.000
101	X	101	LEU	0	-0.025	0.006	17.866	-0.058	-0.058	0.000	0.000	0.000	0.000
102	X	102	VAL	0	0.027	-0.005	17.432	0.047	0.047	0.000	0.000	0.000	0.000
103	X	103	TYR	0	0.000	-0.009	16.995	-0.073	-0.073	0.000	0.000	0.000	0.000
104	X	104	PRO	0	-0.015	0.010	14.124	0.045	0.045	0.000	0.000	0.000	0.000
105	X	105	VAL	0	-0.006	-0.009	16.950	-0.020	-0.020	0.000	0.000	0.000	0.000
106	X	106	SER	0	0.054	0.004	19.036	0.013	0.013	0.000	0.000	0.000	0.000
107	X	107	GLY	0	0.011	0.006	20.871	0.000	0.000	0.000	0.000	0.000	0.000
108	X	108	GLU	-1	-0.886	-0.941	24.310	-0.122	-0.122	0.000	0.000	0.000	0.000
109	X	109	ILE	0	-0.095	-0.024	19.043	0.006	0.006	0.000	0.000	0.000	0.000
110	X	110	ARG	1	0.767	0.831	23.269	0.144	0.144	0.000	0.000	0.000	0.000
111	X	111	MET	0	-0.015	0.013	23.414	-0.018	-0.018	0.000	0.000	0.000	0.000
112	X	112	THR	0	-0.006	-0.038	26.311	0.017	0.017	0.000	0.000	0.000	0.000
113	X	113	TRP	0	0.054	0.007	28.268	-0.017	-0.017	0.000	0.000	0.000	0.000
114	X	114	GLY	0	0.020	0.022	30.016	-0.006	-0.006	0.000	0.000	0.000	0.000
115	X	115	GLU	-1	-0.716	-0.804	24.657	-0.198	-0.198	0.000	0.000	0.000	0.000
116	X	116	LEU	0	0.009	0.006	24.994	-0.022	-0.022	0.000	0.000	0.000	0.000
117	X	117	LEU	0	-0.025	-0.006	26.113	-0.015	-0.015	0.000	0.000	0.000	0.000
118	X	118	ASP	-1	-0.827	-0.915	24.833	-0.234	-0.234	0.000	0.000	0.000	0.000
119	X	119	ILE	0	-0.114	-0.048	20.555	-0.031	-0.031	0.000	0.000	0.000	0.000
120	X	120	TYR	0	0.022	0.020	22.984	-0.013	-0.013	0.000	0.000	0.000	0.000
121	X	121	ASN	0	-0.022	-0.026	25.615	-0.002	-0.002	0.000	0.000	0.000	0.000
122	X	122	LYS	1	0.839	0.939	18.249	0.443	0.443	0.000	0.000	0.000	0.000
123	X	123	ALA	0	0.009	0.011	22.094	-0.025	-0.025	0.000	0.000	0.000	0.000
124	X	124	ILE	0	-0.005	-0.005	23.010	0.003	0.003	0.000	0.000	0.000	0.000
125	X	125	ALA	0	-0.030	-0.011	24.091	0.010	0.010	0.000	0.000	0.000	0.000
126	X	126	ARG	1	0.779	0.866	16.060	0.619	0.619	0.000	0.000	0.000	0.000
127	X	127	LYS	1	0.911	0.959	23.534	0.234	0.234	0.000	0.000	0.000	0.000
128	X	128	SER	0	0.023	0.018	22.940	0.001	0.001	0.000	0.000	0.000	0.000
129	X	129	LYS	1	0.802	0.898	25.263	0.288	0.288	0.000	0.000	0.000	0.000
130	X	130	PHE	0	0.027	0.005	21.074	-0.028	-0.028	0.000	0.000	0.000	0.000
131	X	131	MET	0	-0.014	-0.003	22.240	0.019	0.019	0.000	0.000	0.000	0.000
132	X	132	LEU	0	-0.014	0.008	21.727	-0.035	-0.035	0.000	0.000	0.000	0.000
133	X	133	ALA	0	0.012	-0.005	18.964	0.013	0.013	0.000	0.000	0.000	0.000
134	X	134	ILE	0	-0.016	-0.011	20.320	-0.017	-0.017	0.000	0.000	0.000	0.000
135	X	135	VAL	0	-0.038	-0.012	17.742	0.004	0.004	0.000	0.000	0.000	0.000
136	X	136	ASP	-1	-0.802	-0.912	20.567	-0.141	-0.141	0.000	0.000	0.000	0.000
137	X	137	SER	0	-0.007	-0.027	21.509	-0.008	-0.008	0.000	0.000	0.000	0.000
138	X	138	GLU	-1	-0.986	-0.983	22.868	-0.062	-0.062	0.000	0.000	0.000	0.000
139	X	139	GLY	0	-0.033	-0.002	19.112	0.003	0.003	0.000	0.000	0.000	0.000
140	X	140	ASP	-1	-0.877	-0.926	19.048	-0.201	-0.201	0.000	0.000	0.000	0.000
141	X	141	VAL	0	-0.024	-0.024	18.196	-0.008	-0.008	0.000	0.000	0.000	0.000
142	X	142	THR	0	-0.027	0.013	21.594	0.015	0.015	0.000	0.000	0.000	0.000
143	X	143	TYR	0	-0.035	-0.071	19.468	-0.035	-0.035	0.000	0.000	0.000	0.000
144	X	144	TYR	0	0.000	-0.007	24.566	0.026	0.026	0.000	0.000	0.000	0.000
145	X	145	GLU	-1	-0.809	-0.859	26.009	-0.235	-0.235	0.000	0.000	0.000	0.000
146	X	146	PHE	0	-0.030	-0.014	26.906	0.017	0.017	0.000	0.000	0.000	0.000
147	X	147	ARG	1	0.874	0.904	28.145	0.167	0.167	0.000	0.000	0.000	0.000
148	X	148	LYS	1	0.984	1.001	30.882	0.167	0.167	0.000	0.000	0.000	0.000
149	X	149	LEU	0	0.009	0.007	33.821	0.000	0.000	0.000	0.000	0.000	0.000

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