FMO DATABASE

FMODB ID: YYKV2

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	OptH
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	-1283292.520224
FMO2-HF: Nuclear repulsion	1226417.421177
FMO2-HF: Total energy	-56875.099047
FMO2-MP2: Total energy	-57036.770335

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.
-6.805	-4.697	4.455	-3.805	-2.758	-0.027

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 : -0.036 / q_NPA : -0.016

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	-0.909	-0.970	3.792	0.071	2.243	-0.013	-1.192	-0.967	0.001
4	A	32	GLY	0	-0.006	0.005	5.418	-0.614	-0.614	0.000	0.000	0.000	0.000
5	A	33	ASN	0	0.031	0.001	5.600	0.222	0.222	0.000	0.000	0.000	0.000
6	A	34	ILE	0	-0.038	-0.019	7.564	0.370	0.370	0.000	0.000	0.000	0.000
7	A	35	LYS	1	0.927	0.977	8.489	0.952	0.952	0.000	0.000	0.000	0.000
8	A	36	GLU	-1	-0.844	-0.923	2.309	-7.938	-8.002	4.468	-2.613	-1.791	-0.028
9	A	37	ASN	0	-0.032	-0.026	6.536	0.726	0.726	0.000	0.000	0.000	0.000
10	A	38	ALA	0	0.028	0.013	9.365	0.136	0.136	0.000	0.000	0.000	0.000
11	A	39	VAL	0	0.024	0.013	8.820	0.072	0.072	0.000	0.000	0.000	0.000
12	A	40	ARG	1	0.901	0.946	7.005	-0.724	-0.724	0.000	0.000	0.000	0.000
13	A	41	MET	0	-0.037	0.011	11.278	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	42	MET	0	0.029	0.025	14.160	0.004	0.004	0.000	0.000	0.000	0.000
15	A	43	GLU	-1	-0.839	-0.893	12.459	0.299	0.299	0.000	0.000	0.000	0.000
16	A	44	CYS	0	-0.092	-0.038	15.200	0.021	0.021	0.000	0.000	0.000	0.000
17	A	45	ILE	0	-0.011	0.009	17.566	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	46	VAL	0	-0.032	-0.013	17.592	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	47	ASN	0	-0.033	-0.025	16.930	-0.026	-0.026	0.000	0.000	0.000	0.000
20	A	48	LYS	1	0.892	0.965	20.750	-0.110	-0.110	0.000	0.000	0.000	0.000
21	A	49	ASP	-1	-0.857	-0.934	19.648	0.325	0.325	0.000	0.000	0.000	0.000
22	A	50	SER	0	0.044	-0.014	20.772	0.002	0.002	0.000	0.000	0.000	0.000
23	A	51	GLU	-1	-0.932	-0.947	21.981	0.194	0.194	0.000	0.000	0.000	0.000
24	A	52	LYS	1	0.890	0.941	16.038	-0.527	-0.527	0.000	0.000	0.000	0.000
25	A	53	LEU	0	0.026	0.013	17.720	0.007	0.007	0.000	0.000	0.000	0.000
26	A	54	PHE	0	-0.014	-0.014	18.992	-0.024	-0.024	0.000	0.000	0.000	0.000
27	A	55	ASP	-1	-0.949	-0.970	17.670	0.335	0.335	0.000	0.000	0.000	0.000
28	A	56	PHE	0	0.012	0.003	11.894	0.021	0.021	0.000	0.000	0.000	0.000
29	A	57	TYR	0	-0.031	-0.014	17.305	-0.056	-0.056	0.000	0.000	0.000	0.000
30	A	58	ASN	0	-0.009	0.020	20.130	0.032	0.032	0.000	0.000	0.000	0.000
31	A	59	LYS	1	0.910	0.947	21.464	-0.113	-0.113	0.000	0.000	0.000	0.000
32	A	60	ASP	-1	-0.816	-0.892	23.260	0.035	0.035	0.000	0.000	0.000	0.000
33	A	61	MET	0	-0.028	-0.004	24.869	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	62	LYS	1	0.792	0.918	19.097	-0.223	-0.223	0.000	0.000	0.000	0.000
35	A	63	ASP	-1	-0.924	-0.959	25.811	0.111	0.111	0.000	0.000	0.000	0.000
36	A	64	ASN	0	-0.076	-0.031	28.515	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	65	TYR	0	-0.013	-0.010	29.197	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	66	LYS	1	1.006	1.013	27.553	-0.128	-0.128	0.000	0.000	0.000	0.000
39	A	67	ASP	-1	-0.904	-0.966	29.361	0.094	0.094	0.000	0.000	0.000	0.000
40	A	68	SER	0	-0.018	-0.016	31.721	0.000	0.000	0.000	0.000	0.000	0.000
41	A	69	SER	0	0.026	0.009	26.522	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	70	LEU	0	-0.019	-0.013	25.441	0.000	0.000	0.000	0.000	0.000	0.000
43	A	71	ASP	-1	-0.978	-0.990	28.081	0.066	0.066	0.000	0.000	0.000	0.000
44	A	72	GLU	-1	-0.853	-0.934	29.235	0.027	0.027	0.000	0.000	0.000	0.000
45	A	73	ILE	0	-0.044	-0.023	23.299	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	74	ARG	1	0.923	0.969	26.748	-0.095	-0.095	0.000	0.000	0.000	0.000
47	A	75	GLN	0	0.077	0.045	29.196	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	76	LEU	0	-0.038	-0.016	23.272	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	77	PHE	0	-0.048	-0.050	22.328	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	78	GLU	-1	-0.951	-0.968	27.482	0.061	0.061	0.000	0.000	0.000	0.000
51	A	79	TYR	0	-0.060	-0.031	28.498	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	80	ILE	0	-0.039	-0.007	24.172	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	81	ASP	-1	-0.830	-0.893	28.460	0.032	0.032	0.000	0.000	0.000	0.000
54	A	82	GLY	0	0.035	0.016	29.718	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	83	ALA	0	-0.063	-0.046	25.470	0.003	0.003	0.000	0.000	0.000	0.000
56	A	84	ILE	0	-0.005	-0.010	20.776	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	85	THR	0	-0.027	-0.003	22.500	0.014	0.014	0.000	0.000	0.000	0.000
58	A	86	SER	0	-0.056	-0.017	20.449	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	87	TYR	0	-0.023	-0.064	13.435	-0.026	-0.026	0.000	0.000	0.000	0.000
60	A	88	ASN	0	-0.035	-0.015	16.708	0.014	0.014	0.000	0.000	0.000	0.000
61	A	89	TYR	0	-0.039	-0.023	13.055	-0.074	-0.074	0.000	0.000	0.000	0.000
62	A	90	GLU	-1	-0.834	-0.904	15.708	-0.259	-0.259	0.000	0.000	0.000	0.000
63	A	91	GLY	0	-0.025	-0.033	16.266	-0.043	-0.043	0.000	0.000	0.000	0.000
64	A	92	LYS	1	0.938	0.964	15.549	0.506	0.506	0.000	0.000	0.000	0.000
65	A	93	GLY	0	0.136	0.076	16.635	0.038	0.038	0.000	0.000	0.000	0.000
66	A	94	GLY	0	-0.018	-0.021	20.283	-0.032	-0.032	0.000	0.000	0.000	0.000
67	A	95	GLY	0	-0.039	-0.008	21.609	0.012	0.012	0.000	0.000	0.000	0.000
68	A	96	GLN	0	-0.025	-0.010	22.152	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	97	GLU	-1	-0.885	-0.950	18.404	-0.464	-0.464	0.000	0.000	0.000	0.000
70	A	98	ALA	0	-0.046	-0.009	21.744	0.022	0.022	0.000	0.000	0.000	0.000
71	A	99	LYS	1	0.948	0.967	19.657	0.375	0.375	0.000	0.000	0.000	0.000
72	A	100	ASN	0	-0.029	-0.024	23.127	0.023	0.023	0.000	0.000	0.000	0.000
73	A	101	ASP	-1	-0.855	-0.919	24.366	-0.159	-0.159	0.000	0.000	0.000	0.000
74	A	102	GLY	0	-0.054	-0.026	22.919	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	103	ILE	0	-0.027	-0.008	19.882	-0.047	-0.047	0.000	0.000	0.000	0.000
76	A	104	ILE	0	0.009	-0.004	15.650	0.024	0.024	0.000	0.000	0.000	0.000
77	A	105	CYS	0	-0.040	-0.016	19.298	0.009	0.009	0.000	0.000	0.000	0.000
78	A	106	TYR	0	0.006	-0.002	20.898	0.019	0.019	0.000	0.000	0.000	0.000
79	A	107	TYR	0	0.022	0.010	15.721	-0.038	-0.038	0.000	0.000	0.000	0.000
80	A	108	SER	0	0.002	0.014	18.238	0.005	0.005	0.000	0.000	0.000	0.000
81	A	109	CYS	0	-0.086	-0.028	16.311	-0.046	-0.046	0.000	0.000	0.000	0.000
82	A	110	HIS	1	0.859	0.901	18.890	0.214	0.214	0.000	0.000	0.000	0.000
83	A	111	PRO	0	0.003	-0.004	14.558	-0.013	-0.013	0.000	0.000	0.000	0.000
84	A	112	GLU	-1	-0.918	-0.950	16.615	-0.124	-0.124	0.000	0.000	0.000	0.000
85	A	113	PHE	0	-0.029	-0.020	13.035	-0.040	-0.040	0.000	0.000	0.000	0.000
86	A	114	ASP	-1	-0.724	-0.825	18.702	-0.112	-0.112	0.000	0.000	0.000	0.000
87	A	115	PHE	0	-0.073	-0.070	20.294	0.007	0.007	0.000	0.000	0.000	0.000
88	A	116	THR	0	0.048	0.037	22.253	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	117	THR	0	-0.038	-0.020	24.492	0.011	0.011	0.000	0.000	0.000	0.000
90	A	118	GLU	-1	-0.908	-0.960	27.014	0.066	0.066	0.000	0.000	0.000	0.000
91	A	119	THR	0	-0.102	-0.064	29.340	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	120	GLY	0	-0.035	-0.013	30.375	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	121	GLN	0	-0.090	-0.023	30.078	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	122	GLU	-1	-0.873	-0.933	25.649	-0.068	-0.068	0.000	0.000	0.000	0.000
95	A	123	TYR	0	-0.082	-0.065	24.978	0.003	0.003	0.000	0.000	0.000	0.000
96	A	124	THR	0	0.031	0.019	23.033	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	125	ILE	0	-0.070	-0.037	19.589	0.014	0.014	0.000	0.000	0.000	0.000
98	A	126	SER	0	0.031	0.016	20.491	-0.021	-0.021	0.000	0.000	0.000	0.000
99	A	127	PHE	0	0.002	-0.011	17.471	0.028	0.028	0.000	0.000	0.000	0.000
100	A	128	SER	0	-0.081	-0.054	19.342	-0.043	-0.043	0.000	0.000	0.000	0.000
101	A	129	TYR	0	0.021	-0.008	12.256	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	130	HIS	0	-0.027	-0.016	18.474	-0.057	-0.057	0.000	0.000	0.000	0.000
103	A	131	TYR	0	-0.012	0.002	9.775	0.030	0.030	0.000	0.000	0.000	0.000
104	A	132	ILE	0	0.032	0.020	13.941	0.003	0.003	0.000	0.000	0.000	0.000
105	A	133	TRP	0	-0.086	-0.068	17.192	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	134	ASN	0	0.066	0.022	19.549	0.025	0.025	0.000	0.000	0.000	0.000
107	A	135	GLU	-1	-1.010	-1.000	21.898	-0.063	-0.063	0.000	0.000	0.000	0.000
108	A	136	HIS	1	0.802	0.886	23.947	0.045	0.045	0.000	0.000	0.000	0.000
109	A	137	PRO	0	0.109	0.057	20.839	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	138	GLU	-1	-0.828	-0.897	20.839	0.017	0.017	0.000	0.000	0.000	0.000
111	A	139	TYR	0	-0.044	-0.043	23.080	0.008	0.008	0.000	0.000	0.000	0.000
112	A	140	GLU	-1	-0.845	-0.904	17.354	-0.087	-0.087	0.000	0.000	0.000	0.000
113	A	141	GLY	0	-0.002	0.002	16.676	0.040	0.040	0.000	0.000	0.000	0.000
114	A	142	ILE	0	-0.040	-0.036	16.462	-0.035	-0.035	0.000	0.000	0.000	0.000
115	A	143	ASN	0	-0.007	-0.010	19.676	0.005	0.005	0.000	0.000	0.000	0.000
116	A	144	MET	0	-0.037	-0.013	22.834	0.002	0.002	0.000	0.000	0.000	0.000
117	A	145	ILE	0	0.046	0.021	20.787	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	146	GLN	0	0.000	0.011	23.761	0.008	0.008	0.000	0.000	0.000	0.000
119	A	147	ILE	0	0.020	0.013	24.496	-0.007	-0.007	0.000	0.000	0.000	0.000
120	A	148	CYS	0	-0.009	0.025	26.620	0.004	0.004	0.000	0.000	0.000	0.000
121	A	149	LYS	1	1.000	1.009	28.027	0.005	0.005	0.000	0.000	0.000	0.000
122	A	150	ASP	-1	-0.867	-0.929	29.472	-0.040	-0.040	0.000	0.000	0.000	0.000
123	A	151	GLY	0	0.051	0.028	28.212	-0.007	-0.007	0.000	0.000	0.000	0.000
124	A	152	ASN	0	-0.033	-0.028	29.101	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	153	TRP	0	0.004	-0.026	25.102	0.013	0.013	0.000	0.000	0.000	0.000
126	A	154	GLY	0	-0.046	-0.021	31.653	0.001	0.001	0.000	0.000	0.000	0.000
127	A	155	GLU	-1	-1.001	-0.995	34.180	-0.019	-0.019	0.000	0.000	0.000	0.000
128	A	156	LYS	1	0.841	0.931	29.845	0.058	0.058	0.000	0.000	0.000	0.000
129	A	157	LEU	0	-0.017	-0.007	29.294	0.004	0.004	0.000	0.000	0.000	0.000
130	A	158	ILE	0	-0.062	-0.050	28.575	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	159	ILE	0	0.019	0.029	24.847	0.004	0.004	0.000	0.000	0.000	0.000
132	A	160	GLY	0	0.027	0.013	26.600	-0.009	-0.009	0.000	0.000	0.000	0.000
133	A	161	ARG	1	0.931	0.970	27.224	-0.016	-0.016	0.000	0.000	0.000	0.000
134	A	162	ASN	0	-0.003	-0.008	27.338	-0.010	-0.010	0.000	0.000	0.000	0.000
135	A	163	TYR	0	-0.073	-0.056	25.790	0.002	0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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