FMO DATABASE

FMODB ID: G63K1

Calculation Name: 3RKV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RKV

Chain ID: A

ChEMBL ID:

UniProt ID: Q18888

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	147
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1386025.655399
FMO2-HF: Nuclear repulsion	1326780.966094
FMO2-HF: Total energy	-59244.689305
FMO2-MP2: Total energy	-59419.423714

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:188:LEU)

Summations of interaction energy for fragment #1(A:188:LEU)

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.
-10.739	-4.04	2.653	-2.981	-6.369	-0.003

Interaction energy analysis for fragmet #1(A:188:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.088 / q_NPA : 0.037

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	190	SER	0	0.007	0.004	2.992	-4.221	-1.697	0.046	-1.202	-1.368	0.004
4	A	191	VAL	0	0.020	0.018	2.843	-1.459	-0.085	0.242	-0.455	-1.161	-0.001
5	A	192	GLU	-1	-0.784	-0.862	4.650	-0.264	0.035	-0.001	-0.032	-0.265	0.000
6	A	193	ALA	0	-0.016	-0.009	6.363	0.135	0.135	0.000	0.000	0.000	0.000
7	A	194	LEU	0	0.005	0.010	7.495	0.006	0.006	0.000	0.000	0.000	0.000
8	A	195	ARG	1	0.849	0.903	8.291	0.459	0.459	0.000	0.000	0.000	0.000
9	A	196	GLN	0	-0.050	-0.031	9.951	-0.015	-0.015	0.000	0.000	0.000	0.000
10	A	197	LYS	1	0.896	0.939	12.412	-0.101	-0.101	0.000	0.000	0.000	0.000
11	A	198	GLY	0	0.065	0.024	13.394	0.009	0.009	0.000	0.000	0.000	0.000
12	A	199	ASN	0	-0.007	-0.001	13.940	-0.027	-0.027	0.000	0.000	0.000	0.000
13	A	200	GLU	-1	-0.851	-0.918	15.854	0.106	0.106	0.000	0.000	0.000	0.000
14	A	201	LEU	0	0.007	0.021	17.409	0.009	0.009	0.000	0.000	0.000	0.000
15	A	202	PHE	0	-0.017	-0.013	18.599	0.000	0.000	0.000	0.000	0.000	0.000
16	A	203	VAL	0	-0.078	-0.049	20.231	0.004	0.004	0.000	0.000	0.000	0.000
17	A	204	GLN	0	-0.059	-0.035	21.646	0.015	0.015	0.000	0.000	0.000	0.000
18	A	205	LYS	1	0.919	0.963	23.759	0.059	0.059	0.000	0.000	0.000	0.000
19	A	206	ASP	-1	-0.847	-0.889	22.824	-0.026	-0.026	0.000	0.000	0.000	0.000
20	A	207	TYR	0	-0.039	-0.055	21.643	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	208	LYS	1	0.875	0.933	21.334	0.076	0.076	0.000	0.000	0.000	0.000
22	A	209	GLU	-1	-0.823	-0.926	19.993	-0.069	-0.069	0.000	0.000	0.000	0.000
23	A	210	ALA	0	-0.030	-0.014	17.538	-0.012	-0.012	0.000	0.000	0.000	0.000
24	A	211	ILE	0	-0.030	-0.003	16.367	-0.042	-0.042	0.000	0.000	0.000	0.000
25	A	212	ASP	-1	-0.813	-0.890	16.423	-0.158	-0.158	0.000	0.000	0.000	0.000
26	A	213	ALA	0	0.001	-0.001	13.920	-0.025	-0.025	0.000	0.000	0.000	0.000
27	A	214	TYR	0	-0.020	-0.037	11.857	-0.058	-0.058	0.000	0.000	0.000	0.000
28	A	215	ARG	1	0.867	0.907	11.778	0.186	0.186	0.000	0.000	0.000	0.000
29	A	216	ASP	-1	-0.797	-0.853	11.581	-0.196	-0.196	0.000	0.000	0.000	0.000
30	A	217	ALA	0	-0.033	-0.031	8.036	-0.087	-0.087	0.000	0.000	0.000	0.000
31	A	218	LEU	0	0.011	0.000	7.408	-0.309	-0.309	0.000	0.000	0.000	0.000
32	A	219	THR	0	-0.005	0.001	9.243	-0.095	-0.095	0.000	0.000	0.000	0.000
33	A	220	ARG	1	0.741	0.846	4.481	0.172	0.249	-0.001	-0.003	-0.073	0.000
34	A	221	LEU	0	-0.018	-0.009	3.675	-0.762	-0.440	0.006	-0.042	-0.286	0.000
35	A	222	ASP	-1	-0.836	-0.919	5.948	-0.857	-0.857	0.000	0.000	0.000	0.000
36	A	223	THR	0	-0.041	-0.024	7.309	0.101	0.101	0.000	0.000	0.000	0.000
37	A	224	LEU	0	-0.092	-0.051	2.127	-1.780	-0.559	2.227	-1.065	-2.382	-0.004
38	A	225	ILE	0	0.048	0.026	6.625	0.132	0.132	0.000	0.000	0.000	0.000
39	A	226	LEU	0	-0.029	-0.015	8.335	0.144	0.144	0.000	0.000	0.000	0.000
40	A	227	ARG	1	0.821	0.919	6.504	0.746	0.746	0.000	0.000	0.000	0.000
41	A	228	GLU	-1	-0.929	-0.950	7.310	-1.049	-1.049	0.000	0.000	0.000	0.000
42	A	229	LYS	1	0.951	0.967	10.672	0.380	0.380	0.000	0.000	0.000	0.000
43	A	230	PRO	0	-0.003	-0.017	13.859	-0.029	-0.029	0.000	0.000	0.000	0.000
44	A	231	GLY	0	0.005	0.009	14.005	0.058	0.058	0.000	0.000	0.000	0.000
45	A	232	GLU	-1	-0.903	-0.938	13.557	-0.339	-0.339	0.000	0.000	0.000	0.000
46	A	233	PRO	0	-0.012	-0.018	12.870	-0.087	-0.087	0.000	0.000	0.000	0.000
47	A	234	GLU	-1	-0.882	-0.942	8.581	-0.650	-0.650	0.000	0.000	0.000	0.000
48	A	235	TRP	0	0.012	0.009	8.226	-0.280	-0.280	0.000	0.000	0.000	0.000
49	A	236	VAL	0	-0.003	0.002	9.350	-0.114	-0.114	0.000	0.000	0.000	0.000
50	A	237	GLU	-1	-0.845	-0.934	7.499	-1.082	-1.082	0.000	0.000	0.000	0.000
51	A	238	LEU	0	-0.044	-0.010	2.964	-1.238	-0.599	0.132	-0.149	-0.622	-0.002
52	A	239	ASP	-1	-0.755	-0.847	5.956	-0.812	-0.812	0.000	0.000	0.000	0.000
53	A	240	ARG	1	0.879	0.921	8.685	0.659	0.659	0.000	0.000	0.000	0.000
54	A	241	LYS	1	0.756	0.867	3.808	1.678	1.921	0.002	-0.033	-0.212	0.000
55	A	242	ASN	0	0.004	-0.020	7.022	0.018	0.018	0.000	0.000	0.000	0.000
56	A	243	ILE	0	-0.019	0.016	9.736	0.123	0.123	0.000	0.000	0.000	0.000
57	A	244	PRO	0	-0.018	-0.022	9.602	0.086	0.086	0.000	0.000	0.000	0.000
58	A	245	LEU	0	-0.025	0.005	7.679	0.085	0.085	0.000	0.000	0.000	0.000
59	A	246	TYR	0	0.026	-0.005	11.852	0.076	0.076	0.000	0.000	0.000	0.000
60	A	247	ALA	0	0.021	0.011	14.850	0.059	0.059	0.000	0.000	0.000	0.000
61	A	248	ASN	0	-0.056	-0.026	14.611	0.050	0.050	0.000	0.000	0.000	0.000
62	A	249	MET	0	0.007	0.010	14.755	0.026	0.026	0.000	0.000	0.000	0.000
63	A	250	SER	0	-0.007	0.010	17.568	0.034	0.034	0.000	0.000	0.000	0.000
64	A	251	GLN	0	-0.021	-0.016	20.112	0.019	0.019	0.000	0.000	0.000	0.000
65	A	252	CYS	0	-0.059	-0.030	19.135	0.024	0.024	0.000	0.000	0.000	0.000
66	A	253	TYR	0	0.070	0.024	19.412	0.011	0.011	0.000	0.000	0.000	0.000
67	A	254	LEU	0	-0.022	-0.007	23.586	0.016	0.016	0.000	0.000	0.000	0.000
68	A	255	ASN	0	-0.089	-0.037	24.883	0.008	0.008	0.000	0.000	0.000	0.000
69	A	256	ILE	0	-0.036	-0.008	24.063	0.011	0.011	0.000	0.000	0.000	0.000
70	A	257	GLY	0	0.014	0.009	27.731	0.009	0.009	0.000	0.000	0.000	0.000
71	A	258	ASP	-1	-0.881	-0.928	25.376	-0.146	-0.146	0.000	0.000	0.000	0.000
72	A	259	LEU	0	-0.012	-0.033	26.061	-0.014	-0.014	0.000	0.000	0.000	0.000
73	A	260	HIS	0	-0.003	0.017	25.493	0.004	0.004	0.000	0.000	0.000	0.000
74	A	261	GLU	-1	-0.757	-0.863	20.727	-0.260	-0.260	0.000	0.000	0.000	0.000
75	A	262	ALA	0	-0.026	0.021	22.020	-0.026	-0.026	0.000	0.000	0.000	0.000
76	A	263	GLU	-1	-0.789	-0.873	23.125	-0.170	-0.170	0.000	0.000	0.000	0.000
77	A	264	GLU	-1	-0.855	-0.914	21.872	-0.234	-0.234	0.000	0.000	0.000	0.000
78	A	265	THR	0	-0.044	-0.061	17.941	-0.028	-0.028	0.000	0.000	0.000	0.000
79	A	266	SER	0	-0.011	-0.028	18.463	-0.029	-0.029	0.000	0.000	0.000	0.000
80	A	267	SER	0	-0.004	-0.022	20.550	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	268	GLU	-1	-0.810	-0.862	16.280	-0.438	-0.438	0.000	0.000	0.000	0.000
82	A	269	VAL	0	-0.032	0.006	15.803	-0.041	-0.041	0.000	0.000	0.000	0.000
83	A	270	LEU	0	-0.015	-0.014	17.455	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	271	LYS	1	0.855	0.913	18.678	0.323	0.323	0.000	0.000	0.000	0.000
85	A	272	ARG	1	0.742	0.828	12.994	0.588	0.588	0.000	0.000	0.000	0.000
86	A	273	GLU	-1	-0.841	-0.903	15.183	-0.428	-0.428	0.000	0.000	0.000	0.000
87	A	274	GLU	-1	-0.906	-0.941	19.005	-0.212	-0.212	0.000	0.000	0.000	0.000
88	A	275	THR	0	-0.019	-0.013	22.490	0.013	0.013	0.000	0.000	0.000	0.000
89	A	276	ASN	0	-0.006	-0.006	17.845	0.041	0.041	0.000	0.000	0.000	0.000
90	A	277	GLU	-1	-0.790	-0.872	21.666	-0.156	-0.156	0.000	0.000	0.000	0.000
91	A	278	LYS	1	0.852	0.889	21.155	0.175	0.175	0.000	0.000	0.000	0.000
92	A	279	ALA	0	0.027	0.022	20.008	0.007	0.007	0.000	0.000	0.000	0.000
93	A	280	LEU	0	0.029	0.018	22.021	0.012	0.012	0.000	0.000	0.000	0.000
94	A	281	PHE	0	-0.042	-0.026	25.569	0.015	0.015	0.000	0.000	0.000	0.000
95	A	282	ARG	1	0.848	0.927	19.128	0.226	0.226	0.000	0.000	0.000	0.000
96	A	283	ARG	1	0.884	0.914	24.741	0.200	0.200	0.000	0.000	0.000	0.000
97	A	284	ALA	0	0.016	0.011	26.350	0.011	0.011	0.000	0.000	0.000	0.000
98	A	285	LYS	1	0.814	0.888	28.794	0.112	0.112	0.000	0.000	0.000	0.000
99	A	286	ALA	0	0.021	0.018	26.978	0.009	0.009	0.000	0.000	0.000	0.000
100	A	287	ARG	1	0.759	0.858	29.131	0.158	0.158	0.000	0.000	0.000	0.000
101	A	288	ILE	0	-0.019	-0.017	31.602	0.008	0.008	0.000	0.000	0.000	0.000
102	A	289	ALA	0	-0.054	-0.022	32.052	0.008	0.008	0.000	0.000	0.000	0.000
103	A	290	ALA	0	-0.002	-0.002	32.052	0.006	0.006	0.000	0.000	0.000	0.000
104	A	291	TRP	0	-0.057	-0.043	34.125	0.003	0.003	0.000	0.000	0.000	0.000
105	A	292	LYS	1	0.827	0.908	30.344	0.144	0.144	0.000	0.000	0.000	0.000
106	A	293	LEU	0	-0.023	-0.020	34.886	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	294	ASP	-1	-0.827	-0.912	36.912	-0.090	-0.090	0.000	0.000	0.000	0.000
108	A	295	GLU	-1	-0.778	-0.869	31.839	-0.136	-0.136	0.000	0.000	0.000	0.000
109	A	296	ALA	0	0.011	0.001	32.250	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	297	GLU	-1	-0.786	-0.866	33.109	-0.091	-0.091	0.000	0.000	0.000	0.000
111	A	298	GLU	-1	-0.860	-0.921	32.057	-0.139	-0.139	0.000	0.000	0.000	0.000
112	A	299	ASP	-1	-0.755	-0.838	28.251	-0.173	-0.173	0.000	0.000	0.000	0.000
113	A	300	LEU	0	-0.023	-0.017	30.123	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	301	LYS	1	0.852	0.896	32.456	0.097	0.097	0.000	0.000	0.000	0.000
115	A	302	LEU	0	-0.040	-0.015	27.109	0.005	0.005	0.000	0.000	0.000	0.000
116	A	303	LEU	0	-0.004	0.013	27.527	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	304	LEU	0	0.007	-0.006	29.378	0.000	0.000	0.000	0.000	0.000	0.000
118	A	305	ARG	1	0.877	0.949	32.214	0.134	0.134	0.000	0.000	0.000	0.000
119	A	306	ASN	0	-0.028	-0.019	27.425	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	307	HIS	0	-0.030	-0.011	24.553	0.007	0.007	0.000	0.000	0.000	0.000
121	A	308	PRO	0	0.050	0.018	29.804	0.005	0.005	0.000	0.000	0.000	0.000
122	A	309	ALA	0	0.005	-0.001	30.979	0.006	0.006	0.000	0.000	0.000	0.000
123	A	310	ALA	0	0.001	0.009	30.151	0.004	0.004	0.000	0.000	0.000	0.000
124	A	311	ALA	0	0.017	0.006	32.171	0.002	0.002	0.000	0.000	0.000	0.000
125	A	312	SER	0	0.003	0.002	35.897	0.000	0.000	0.000	0.000	0.000	0.000
126	A	313	VAL	0	-0.003	0.001	30.801	0.003	0.003	0.000	0.000	0.000	0.000
127	A	314	VAL	0	0.041	0.008	32.617	0.000	0.000	0.000	0.000	0.000	0.000
128	A	315	ALA	0	0.011	0.008	34.836	0.002	0.002	0.000	0.000	0.000	0.000
129	A	316	ARG	1	0.841	0.918	32.179	0.093	0.093	0.000	0.000	0.000	0.000
130	A	317	GLU	-1	-0.731	-0.855	32.685	-0.095	-0.095	0.000	0.000	0.000	0.000
131	A	318	MET	0	0.009	0.006	36.159	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	319	LYS	1	0.793	0.891	38.559	0.062	0.062	0.000	0.000	0.000	0.000
133	A	320	ILE	0	0.033	0.018	36.894	0.002	0.002	0.000	0.000	0.000	0.000
134	A	321	VAL	0	0.012	0.003	36.745	0.002	0.002	0.000	0.000	0.000	0.000
135	A	322	THR	0	-0.008	-0.015	39.563	0.002	0.002	0.000	0.000	0.000	0.000
136	A	323	GLU	-1	-0.841	-0.896	42.987	-0.058	-0.058	0.000	0.000	0.000	0.000
137	A	324	ARG	1	0.960	0.997	37.543	0.079	0.079	0.000	0.000	0.000	0.000
138	A	325	ARG	1	0.763	0.851	40.076	0.085	0.085	0.000	0.000	0.000	0.000
139	A	326	ALA	0	-0.042	-0.013	44.492	0.002	0.002	0.000	0.000	0.000	0.000
140	A	327	GLU	-1	-0.869	-0.946	44.153	-0.059	-0.059	0.000	0.000	0.000	0.000
141	A	328	LYS	1	0.905	0.951	43.113	0.063	0.063	0.000	0.000	0.000	0.000
142	A	329	LYS	1	0.860	0.910	46.427	0.061	0.061	0.000	0.000	0.000	0.000
143	A	330	ALA	0	0.006	0.018	49.308	0.002	0.002	0.000	0.000	0.000	0.000
144	A	331	ASP	-1	-0.804	-0.903	47.823	-0.052	-0.052	0.000	0.000	0.000	0.000
145	A	332	SER	0	-0.077	-0.042	49.487	0.000	0.000	0.000	0.000	0.000	0.000
146	A	333	ARG	1	0.900	0.966	51.456	0.047	0.047	0.000	0.000	0.000	0.000
147	A	334	VAL	0	-0.031	0.006	54.000	0.003	0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:188:LEU)