FMO DATABASE

FMODB ID: VR1Q1

Calculation Name: 4R1K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R1K

Chain ID: A

ChEMBL ID:

UniProt ID: B0MNI9

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	135
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1284134.48957
FMO2-HF: Nuclear repulsion	1227258.575916
FMO2-HF: Total energy	-56875.913654
FMO2-MP2: Total energy	-57037.655973

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:0:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

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.
-5.723	-2.607	3.374	-3.785	-2.703	-0.024

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : 0.000

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	31	GLU	-1	-0.833	-0.897	3.791	0.070	2.317	-0.013	-1.240	-0.993	0.001
4	A	32	GLY	0	0.016	0.012	5.410	-0.632	-0.632	0.000	0.000	0.000	0.000
5	A	33	ASN	0	-0.005	-0.019	5.091	0.531	0.531	0.000	0.000	0.000	0.000
6	A	34	ILE	0	-0.038	-0.013	7.561	0.372	0.372	0.000	0.000	0.000	0.000
7	A	35	LYS	1	0.842	0.906	8.547	0.909	0.909	0.000	0.000	0.000	0.000
8	A	36	GLU	-1	-0.800	-0.896	2.354	-7.367	-6.498	3.387	-2.545	-1.710	-0.025
9	A	37	ASN	0	-0.041	-0.043	6.532	0.762	0.762	0.000	0.000	0.000	0.000
10	A	38	ALA	0	0.039	0.023	9.363	0.134	0.134	0.000	0.000	0.000	0.000
11	A	39	VAL	0	0.017	0.006	8.819	0.071	0.071	0.000	0.000	0.000	0.000
12	A	40	ARG	1	0.890	0.942	7.108	-0.664	-0.664	0.000	0.000	0.000	0.000
13	A	41	MET	0	-0.026	0.016	11.278	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	42	MET	0	0.028	0.025	14.190	0.005	0.005	0.000	0.000	0.000	0.000
15	A	43	GLU	-1	-0.828	-0.894	12.527	0.312	0.312	0.000	0.000	0.000	0.000
16	A	44	CYS	0	-0.080	-0.030	15.110	0.023	0.023	0.000	0.000	0.000	0.000
17	A	45	ILE	0	-0.008	0.008	17.568	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	46	VAL	0	-0.030	-0.011	17.627	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	47	ASN	0	-0.080	-0.057	17.332	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	48	LYS	1	0.857	0.955	20.752	-0.101	-0.101	0.000	0.000	0.000	0.000
21	A	49	ASP	-1	-0.819	-0.892	19.683	0.332	0.332	0.000	0.000	0.000	0.000
22	A	50	SER	0	0.024	-0.024	20.774	0.004	0.004	0.000	0.000	0.000	0.000
23	A	51	GLU	-1	-0.912	-0.950	22.206	0.184	0.184	0.000	0.000	0.000	0.000
24	A	52	LYS	1	0.851	0.911	16.234	-0.422	-0.422	0.000	0.000	0.000	0.000
25	A	53	LEU	0	0.016	0.009	17.723	0.007	0.007	0.000	0.000	0.000	0.000
26	A	54	PHE	0	-0.014	-0.012	18.994	-0.024	-0.024	0.000	0.000	0.000	0.000
27	A	55	ASP	-1	-0.879	-0.918	17.930	0.312	0.312	0.000	0.000	0.000	0.000
28	A	56	PHE	0	-0.006	-0.003	11.944	0.019	0.019	0.000	0.000	0.000	0.000
29	A	57	TYR	0	-0.026	-0.018	17.306	-0.052	-0.052	0.000	0.000	0.000	0.000
30	A	58	ASN	0	-0.006	0.025	20.126	0.032	0.032	0.000	0.000	0.000	0.000
31	A	59	LYS	1	0.832	0.889	21.461	-0.106	-0.106	0.000	0.000	0.000	0.000
32	A	60	ASP	-1	-0.775	-0.872	23.257	0.033	0.033	0.000	0.000	0.000	0.000
33	A	61	MET	0	-0.034	-0.004	24.838	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	62	LYS	1	0.756	0.881	18.938	-0.221	-0.221	0.000	0.000	0.000	0.000
35	A	63	ASP	-1	-0.860	-0.910	25.808	0.110	0.110	0.000	0.000	0.000	0.000
36	A	64	ASN	0	-0.074	-0.032	28.512	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	65	TYR	0	-0.031	-0.015	29.259	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	66	LYS	1	0.909	0.958	27.729	-0.111	-0.111	0.000	0.000	0.000	0.000
39	A	67	ASP	-1	-0.852	-0.926	29.362	0.097	0.097	0.000	0.000	0.000	0.000
40	A	68	SER	0	0.009	0.000	31.559	0.001	0.001	0.000	0.000	0.000	0.000
41	A	69	SER	0	0.035	0.008	26.474	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	70	LEU	0	-0.015	-0.010	25.361	0.001	0.001	0.000	0.000	0.000	0.000
43	A	71	ASP	-1	-0.906	-0.939	28.082	0.070	0.070	0.000	0.000	0.000	0.000
44	A	72	GLU	-1	-0.845	-0.930	29.058	0.029	0.029	0.000	0.000	0.000	0.000
45	A	73	ILE	0	-0.024	-0.018	23.300	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	74	ARG	1	0.869	0.934	26.749	-0.094	-0.094	0.000	0.000	0.000	0.000
47	A	75	GLN	0	0.000	0.004	29.197	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	76	LEU	0	-0.018	-0.007	23.235	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	77	PHE	0	-0.035	-0.039	22.487	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	78	GLU	-1	-0.908	-0.952	27.482	0.063	0.063	0.000	0.000	0.000	0.000
51	A	79	TYR	0	-0.041	-0.020	28.596	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	80	ILE	0	-0.025	0.001	24.172	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	81	ASP	-1	-0.824	-0.858	28.459	0.033	0.033	0.000	0.000	0.000	0.000
54	A	82	GLY	0	0.025	0.007	29.718	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	83	ALA	0	-0.052	-0.039	25.564	0.003	0.003	0.000	0.000	0.000	0.000
56	A	84	ILE	0	0.001	-0.009	20.790	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	85	THR	0	-0.019	0.002	22.500	0.014	0.014	0.000	0.000	0.000	0.000
58	A	86	SER	0	-0.058	-0.024	20.439	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	87	TYR	0	-0.046	-0.058	13.555	-0.027	-0.027	0.000	0.000	0.000	0.000
60	A	88	ASN	0	-0.032	-0.017	16.730	0.016	0.016	0.000	0.000	0.000	0.000
61	A	89	TYR	0	-0.081	-0.051	13.127	-0.069	-0.069	0.000	0.000	0.000	0.000
62	A	90	GLU	-1	-0.814	-0.889	15.703	-0.261	-0.261	0.000	0.000	0.000	0.000
63	A	91	GLY	0	0.006	-0.018	16.259	-0.041	-0.041	0.000	0.000	0.000	0.000
64	A	92	LYS	1	0.899	0.941	15.067	0.506	0.506	0.000	0.000	0.000	0.000
65	A	93	GLY	0	0.131	0.078	16.628	0.036	0.036	0.000	0.000	0.000	0.000
66	A	94	GLY	0	-0.020	-0.022	20.276	-0.031	-0.031	0.000	0.000	0.000	0.000
67	A	95	GLY	0	-0.022	-0.008	21.603	0.011	0.011	0.000	0.000	0.000	0.000
68	A	96	GLN	0	-0.031	-0.012	22.207	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	97	GLU	-1	-0.856	-0.916	18.397	-0.473	-0.473	0.000	0.000	0.000	0.000
70	A	98	ALA	0	-0.020	-0.003	21.743	0.021	0.021	0.000	0.000	0.000	0.000
71	A	99	LYS	1	0.939	0.956	19.288	0.383	0.383	0.000	0.000	0.000	0.000
72	A	100	ASN	0	-0.023	-0.019	23.127	0.023	0.023	0.000	0.000	0.000	0.000
73	A	101	ASP	-1	-0.862	-0.931	24.366	-0.159	-0.159	0.000	0.000	0.000	0.000
74	A	102	GLY	0	-0.042	-0.017	22.919	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	103	ILE	0	-0.029	-0.012	19.822	-0.044	-0.044	0.000	0.000	0.000	0.000
76	A	104	ILE	0	-0.003	-0.001	15.744	0.022	0.022	0.000	0.000	0.000	0.000
77	A	105	CYS	0	-0.032	-0.011	19.298	0.009	0.009	0.000	0.000	0.000	0.000
78	A	106	TYR	0	0.008	-0.001	20.869	0.018	0.018	0.000	0.000	0.000	0.000
79	A	107	TYR	0	0.006	0.000	16.201	-0.058	-0.058	0.000	0.000	0.000	0.000
80	A	108	SER	0	0.008	0.002	18.236	0.005	0.005	0.000	0.000	0.000	0.000
81	A	109	CYS	0	-0.111	-0.038	16.304	-0.047	-0.047	0.000	0.000	0.000	0.000
82	A	110	HIS	1	0.854	0.916	18.911	0.202	0.202	0.000	0.000	0.000	0.000
83	A	111	PRO	0	0.019	0.001	14.532	-0.009	-0.009	0.000	0.000	0.000	0.000
84	A	112	GLU	-1	-0.914	-0.951	16.610	-0.118	-0.118	0.000	0.000	0.000	0.000
85	A	113	PHE	0	-0.019	-0.009	12.842	-0.038	-0.038	0.000	0.000	0.000	0.000
86	A	114	ASP	-1	-0.760	-0.833	18.698	-0.100	-0.100	0.000	0.000	0.000	0.000
87	A	115	PHE	0	-0.055	-0.057	20.290	0.007	0.007	0.000	0.000	0.000	0.000
88	A	116	THR	0	0.066	0.043	22.250	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	117	THR	0	-0.028	-0.014	24.490	0.012	0.012	0.000	0.000	0.000	0.000
90	A	118	GLU	-1	-0.912	-0.959	27.013	0.067	0.067	0.000	0.000	0.000	0.000
91	A	119	THR	0	-0.097	-0.068	29.339	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	120	GLY	0	-0.035	-0.013	30.372	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	121	GLN	0	-0.065	-0.013	29.808	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	122	GLU	-1	-0.889	-0.936	25.708	-0.058	-0.058	0.000	0.000	0.000	0.000
95	A	123	TYR	0	-0.077	-0.092	24.993	0.002	0.002	0.000	0.000	0.000	0.000
96	A	124	THR	0	0.023	0.001	23.181	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	125	ILE	0	-0.068	-0.040	19.647	0.014	0.014	0.000	0.000	0.000	0.000
98	A	126	SER	0	0.040	0.020	20.484	-0.022	-0.022	0.000	0.000	0.000	0.000
99	A	127	PHE	0	-0.003	-0.010	17.233	0.027	0.027	0.000	0.000	0.000	0.000
100	A	128	SER	0	-0.066	-0.058	19.338	-0.042	-0.042	0.000	0.000	0.000	0.000
101	A	129	TYR	0	0.018	-0.002	12.309	0.000	0.000	0.000	0.000	0.000	0.000
102	A	130	HIS	0	-0.013	-0.007	18.471	-0.057	-0.057	0.000	0.000	0.000	0.000
103	A	131	TYR	0	-0.021	-0.001	9.787	0.034	0.034	0.000	0.000	0.000	0.000
104	A	132	ILE	0	0.027	0.017	13.842	0.003	0.003	0.000	0.000	0.000	0.000
105	A	133	TRP	0	-0.052	-0.049	17.190	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	134	ASN	0	0.038	0.012	19.642	0.017	0.017	0.000	0.000	0.000	0.000
107	A	135	GLU	-1	-0.967	-0.973	21.897	-0.053	-0.053	0.000	0.000	0.000	0.000
108	A	136	HIS	1	0.779	0.879	23.961	0.049	0.049	0.000	0.000	0.000	0.000
109	A	137	PRO	0	0.097	0.054	20.941	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	138	GLU	-1	-0.829	-0.912	20.837	0.013	0.013	0.000	0.000	0.000	0.000
111	A	139	TYR	0	-0.046	-0.044	23.083	0.008	0.008	0.000	0.000	0.000	0.000
112	A	140	GLU	-1	-0.861	-0.916	17.357	-0.085	-0.085	0.000	0.000	0.000	0.000
113	A	141	GLY	0	0.001	-0.001	16.673	0.039	0.039	0.000	0.000	0.000	0.000
114	A	142	ILE	0	-0.035	-0.032	16.702	-0.035	-0.035	0.000	0.000	0.000	0.000
115	A	143	ASN	0	-0.011	-0.012	19.674	0.004	0.004	0.000	0.000	0.000	0.000
116	A	144	MET	0	-0.041	-0.008	22.797	0.002	0.002	0.000	0.000	0.000	0.000
117	A	145	ILE	0	0.034	0.016	21.094	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	146	GLN	0	0.002	0.006	23.758	0.006	0.006	0.000	0.000	0.000	0.000
119	A	147	ILE	0	0.016	0.006	24.493	-0.006	-0.006	0.000	0.000	0.000	0.000
120	A	148	CYS	0	-0.026	0.014	26.617	0.002	0.002	0.000	0.000	0.000	0.000
121	A	149	LYS	1	0.933	0.972	28.024	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	150	ASP	-1	-0.837	-0.920	29.457	-0.035	-0.035	0.000	0.000	0.000	0.000
123	A	151	GLY	0	0.052	0.035	28.210	-0.007	-0.007	0.000	0.000	0.000	0.000
124	A	152	ASN	0	-0.070	-0.040	29.096	-0.010	-0.010	0.000	0.000	0.000	0.000
125	A	153	TRP	0	-0.007	-0.028	25.018	0.014	0.014	0.000	0.000	0.000	0.000
126	A	154	GLY	0	-0.056	-0.021	31.649	0.001	0.001	0.000	0.000	0.000	0.000
127	A	155	GLU	-1	-0.979	-0.981	34.199	-0.019	-0.019	0.000	0.000	0.000	0.000
128	A	156	LYS	1	0.878	0.943	29.821	0.057	0.057	0.000	0.000	0.000	0.000
129	A	157	LEU	0	-0.019	-0.004	29.459	0.004	0.004	0.000	0.000	0.000	0.000
130	A	158	ILE	0	-0.055	-0.045	28.469	-0.005	-0.005	0.000	0.000	0.000	0.000
131	A	159	ILE	0	-0.002	0.014	25.067	0.004	0.004	0.000	0.000	0.000	0.000
132	A	160	GLY	0	0.012	0.003	26.599	-0.009	-0.009	0.000	0.000	0.000	0.000
133	A	161	ARG	1	0.905	0.952	27.225	-0.017	-0.017	0.000	0.000	0.000	0.000
134	A	162	ASN	0	-0.010	-0.012	27.335	-0.012	-0.012	0.000	0.000	0.000	0.000
135	A	163	TYR	0	-0.046	-0.043	25.807	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)