FMO DATABASE

FMODB ID: 171GZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1382374.180945
FMO2-HF: Nuclear repulsion	1323130.194287
FMO2-HF: Total energy	-59243.986658
FMO2-MP2: Total energy	-59418.715625

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.
-13.531	-6.123	3.28	-3.48	-7.209	0.007

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 : 0.079 / q_NPA : 0.027

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	-0.010	-0.001	2.741	-6.256	-2.730	0.305	-1.906	-1.926	0.012
4	A	191	VAL	0	0.036	0.015	2.711	-2.180	-0.828	0.245	-0.368	-1.230	-0.001
5	A	192	GLU	-1	-0.794	-0.861	4.520	-0.544	-0.243	-0.001	-0.036	-0.263	0.000
6	A	193	ALA	0	-0.022	-0.011	6.496	0.076	0.076	0.000	0.000	0.000	0.000
7	A	194	LEU	0	0.022	0.010	6.980	-0.049	-0.049	0.000	0.000	0.000	0.000
8	A	195	ARG	1	0.863	0.929	8.150	0.472	0.472	0.000	0.000	0.000	0.000
9	A	196	GLN	0	-0.038	-0.043	10.275	-0.058	-0.058	0.000	0.000	0.000	0.000
10	A	197	LYS	1	1.001	1.023	12.147	-0.212	-0.212	0.000	0.000	0.000	0.000
11	A	198	GLY	0	0.053	0.012	13.364	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	199	ASN	0	-0.027	-0.009	14.223	-0.032	-0.032	0.000	0.000	0.000	0.000
13	A	200	GLU	-1	-0.909	-0.959	16.147	0.171	0.171	0.000	0.000	0.000	0.000
14	A	201	LEU	0	-0.010	0.008	16.827	0.005	0.005	0.000	0.000	0.000	0.000
15	A	202	PHE	0	-0.015	-0.012	19.021	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	203	VAL	0	-0.062	-0.033	20.450	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	204	GLN	0	-0.083	-0.047	21.620	0.012	0.012	0.000	0.000	0.000	0.000
18	A	205	LYS	1	0.892	0.937	24.570	0.035	0.035	0.000	0.000	0.000	0.000
19	A	206	ASP	-1	-0.854	-0.894	23.112	0.018	0.018	0.000	0.000	0.000	0.000
20	A	207	TYR	0	-0.018	-0.031	21.960	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	208	LYS	1	0.978	0.984	21.267	0.016	0.016	0.000	0.000	0.000	0.000
22	A	209	GLU	-1	-0.796	-0.903	19.281	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	210	ALA	0	-0.035	-0.012	17.442	0.000	0.000	0.000	0.000	0.000	0.000
24	A	211	ILE	0	-0.008	-0.003	16.236	-0.030	-0.030	0.000	0.000	0.000	0.000
25	A	212	ASP	-1	-0.870	-0.922	16.047	-0.081	-0.081	0.000	0.000	0.000	0.000
26	A	213	ALA	0	-0.029	-0.011	13.244	0.004	0.004	0.000	0.000	0.000	0.000
27	A	214	TYR	0	-0.072	-0.075	11.735	-0.039	-0.039	0.000	0.000	0.000	0.000
28	A	215	ARG	1	0.875	0.912	11.871	0.124	0.124	0.000	0.000	0.000	0.000
29	A	216	ASP	-1	-0.793	-0.869	10.481	0.003	0.003	0.000	0.000	0.000	0.000
30	A	217	ALA	0	-0.077	-0.048	7.549	-0.053	-0.053	0.000	0.000	0.000	0.000
31	A	218	LEU	0	0.026	-0.002	7.447	-0.275	-0.275	0.000	0.000	0.000	0.000
32	A	219	THR	0	-0.002	0.011	9.742	-0.073	-0.073	0.000	0.000	0.000	0.000
33	A	220	ARG	1	0.764	0.858	4.642	-0.148	-0.085	-0.001	-0.001	-0.061	0.000
34	A	221	LEU	0	-0.032	-0.020	3.912	-0.604	-0.351	0.002	-0.030	-0.225	0.000
35	A	222	ASP	-1	-0.854	-0.917	6.159	-0.770	-0.770	0.000	0.000	0.000	0.000
36	A	223	THR	0	-0.036	-0.010	7.738	0.055	0.055	0.000	0.000	0.000	0.000
37	A	224	LEU	0	-0.106	-0.073	2.183	-1.582	-0.470	2.218	-0.928	-2.402	-0.001
38	A	225	ILE	0	0.036	0.033	6.379	-0.037	-0.037	0.000	0.000	0.000	0.000
39	A	226	LEU	0	-0.041	-0.024	8.210	0.127	0.127	0.000	0.000	0.000	0.000
40	A	227	ARG	1	0.883	0.948	6.176	0.638	0.638	0.000	0.000	0.000	0.000
41	A	228	GLU	-1	-0.937	-0.946	7.023	-1.104	-1.104	0.000	0.000	0.000	0.000
42	A	229	LYS	1	0.941	0.968	10.697	0.401	0.401	0.000	0.000	0.000	0.000
43	A	230	PRO	0	0.013	-0.016	13.472	-0.048	-0.048	0.000	0.000	0.000	0.000
44	A	231	GLY	0	-0.018	0.000	14.013	0.054	0.054	0.000	0.000	0.000	0.000
45	A	232	GLU	-1	-0.902	-0.938	13.371	-0.376	-0.376	0.000	0.000	0.000	0.000
46	A	233	PRO	0	-0.004	-0.014	12.752	-0.078	-0.078	0.000	0.000	0.000	0.000
47	A	234	GLU	-1	-0.871	-0.953	8.339	-0.729	-0.729	0.000	0.000	0.000	0.000
48	A	235	TRP	0	-0.007	0.008	8.224	-0.285	-0.285	0.000	0.000	0.000	0.000
49	A	236	VAL	0	0.037	0.017	9.312	-0.125	-0.125	0.000	0.000	0.000	0.000
50	A	237	GLU	-1	-0.871	-0.939	7.077	-1.161	-1.161	0.000	0.000	0.000	0.000
51	A	238	LEU	0	-0.028	-0.015	2.578	-1.200	-0.586	0.512	-0.191	-0.935	-0.003
52	A	239	ASP	-1	-0.750	-0.844	5.804	-0.738	-0.738	0.000	0.000	0.000	0.000
53	A	240	ARG	1	0.876	0.915	8.797	0.724	0.724	0.000	0.000	0.000	0.000
54	A	241	LYS	1	0.793	0.896	3.903	1.863	2.050	0.000	-0.020	-0.167	0.000
55	A	242	ASN	0	-0.004	-0.017	7.479	0.071	0.071	0.000	0.000	0.000	0.000
56	A	243	ILE	0	-0.029	0.012	10.046	0.118	0.118	0.000	0.000	0.000	0.000
57	A	244	PRO	0	-0.018	-0.020	10.021	0.094	0.094	0.000	0.000	0.000	0.000
58	A	245	LEU	0	-0.012	0.002	7.845	0.089	0.089	0.000	0.000	0.000	0.000
59	A	246	TYR	0	0.086	0.025	12.080	0.091	0.091	0.000	0.000	0.000	0.000
60	A	247	ALA	0	-0.013	0.000	14.984	0.061	0.061	0.000	0.000	0.000	0.000
61	A	248	ASN	0	-0.054	-0.022	14.046	0.047	0.047	0.000	0.000	0.000	0.000
62	A	249	MET	0	0.058	0.038	15.162	0.031	0.031	0.000	0.000	0.000	0.000
63	A	250	SER	0	-0.050	-0.002	17.835	0.034	0.034	0.000	0.000	0.000	0.000
64	A	251	GLN	0	-0.009	-0.011	20.359	0.013	0.013	0.000	0.000	0.000	0.000
65	A	252	CYS	0	-0.070	-0.020	19.505	0.024	0.024	0.000	0.000	0.000	0.000
66	A	253	TYR	0	0.068	0.024	19.632	0.010	0.010	0.000	0.000	0.000	0.000
67	A	254	LEU	0	-0.007	-0.004	23.814	0.014	0.014	0.000	0.000	0.000	0.000
68	A	255	ASN	0	-0.093	-0.050	24.945	0.005	0.005	0.000	0.000	0.000	0.000
69	A	256	ILE	0	-0.032	-0.001	24.260	0.012	0.012	0.000	0.000	0.000	0.000
70	A	257	GLY	0	-0.005	0.007	28.047	0.008	0.008	0.000	0.000	0.000	0.000
71	A	258	ASP	-1	-0.903	-0.946	25.671	-0.110	-0.110	0.000	0.000	0.000	0.000
72	A	259	LEU	0	-0.004	-0.011	26.260	-0.014	-0.014	0.000	0.000	0.000	0.000
73	A	260	HIS	0	0.050	0.035	26.040	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	261	GLU	-1	-0.759	-0.879	21.458	-0.200	-0.200	0.000	0.000	0.000	0.000
75	A	262	ALA	0	-0.051	0.003	22.470	-0.024	-0.024	0.000	0.000	0.000	0.000
76	A	263	GLU	-1	-0.809	-0.899	22.956	-0.156	-0.156	0.000	0.000	0.000	0.000
77	A	264	GLU	-1	-0.896	-0.941	22.273	-0.206	-0.206	0.000	0.000	0.000	0.000
78	A	265	THR	0	-0.051	-0.058	18.260	-0.027	-0.027	0.000	0.000	0.000	0.000
79	A	266	SER	0	-0.014	-0.026	18.824	-0.028	-0.028	0.000	0.000	0.000	0.000
80	A	267	SER	0	0.004	-0.020	20.856	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	268	GLU	-1	-0.827	-0.867	16.441	-0.398	-0.398	0.000	0.000	0.000	0.000
82	A	269	VAL	0	-0.039	-0.013	16.225	-0.034	-0.034	0.000	0.000	0.000	0.000
83	A	270	LEU	0	-0.034	-0.011	17.780	-0.012	-0.012	0.000	0.000	0.000	0.000
84	A	271	LYS	1	0.840	0.914	18.611	0.305	0.305	0.000	0.000	0.000	0.000
85	A	272	ARG	1	0.762	0.843	13.062	0.573	0.573	0.000	0.000	0.000	0.000
86	A	273	GLU	-1	-0.860	-0.912	15.493	-0.436	-0.436	0.000	0.000	0.000	0.000
87	A	274	GLU	-1	-0.885	-0.936	19.152	-0.214	-0.214	0.000	0.000	0.000	0.000
88	A	275	THR	0	-0.039	-0.021	22.848	0.013	0.013	0.000	0.000	0.000	0.000
89	A	276	ASN	0	-0.009	-0.010	18.275	0.038	0.038	0.000	0.000	0.000	0.000
90	A	277	GLU	-1	-0.812	-0.877	22.002	-0.154	-0.154	0.000	0.000	0.000	0.000
91	A	278	LYS	1	0.858	0.891	21.278	0.181	0.181	0.000	0.000	0.000	0.000
92	A	279	ALA	0	0.034	0.026	20.363	0.013	0.013	0.000	0.000	0.000	0.000
93	A	280	LEU	0	0.055	0.025	22.342	0.014	0.014	0.000	0.000	0.000	0.000
94	A	281	PHE	0	-0.057	-0.025	25.845	0.018	0.018	0.000	0.000	0.000	0.000
95	A	282	ARG	1	0.881	0.935	19.320	0.209	0.209	0.000	0.000	0.000	0.000
96	A	283	ARG	1	0.896	0.909	24.908	0.193	0.193	0.000	0.000	0.000	0.000
97	A	284	ALA	0	0.045	0.025	26.600	0.011	0.011	0.000	0.000	0.000	0.000
98	A	285	LYS	1	0.780	0.881	28.766	0.102	0.102	0.000	0.000	0.000	0.000
99	A	286	ALA	0	0.011	0.004	27.255	0.009	0.009	0.000	0.000	0.000	0.000
100	A	287	ARG	1	0.865	0.916	29.413	0.149	0.149	0.000	0.000	0.000	0.000
101	A	288	ILE	0	-0.019	-0.002	31.783	0.008	0.008	0.000	0.000	0.000	0.000
102	A	289	ALA	0	-0.071	-0.029	32.381	0.007	0.007	0.000	0.000	0.000	0.000
103	A	290	ALA	0	-0.020	-0.009	32.243	0.006	0.006	0.000	0.000	0.000	0.000
104	A	291	TRP	0	-0.077	-0.054	34.364	0.003	0.003	0.000	0.000	0.000	0.000
105	A	292	LYS	1	0.876	0.938	30.312	0.128	0.128	0.000	0.000	0.000	0.000
106	A	293	LEU	0	-0.022	-0.013	35.007	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	294	ASP	-1	-0.832	-0.912	37.286	-0.085	-0.085	0.000	0.000	0.000	0.000
108	A	295	GLU	-1	-0.851	-0.922	32.387	-0.122	-0.122	0.000	0.000	0.000	0.000
109	A	296	ALA	0	0.005	-0.002	32.432	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	297	GLU	-1	-0.807	-0.873	33.448	-0.087	-0.087	0.000	0.000	0.000	0.000
111	A	298	GLU	-1	-0.935	-0.968	32.890	-0.128	-0.128	0.000	0.000	0.000	0.000
112	A	299	ASP	-1	-0.771	-0.839	28.815	-0.164	-0.164	0.000	0.000	0.000	0.000
113	A	300	LEU	0	0.002	-0.003	30.771	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	301	LYS	1	0.866	0.909	32.830	0.094	0.094	0.000	0.000	0.000	0.000
115	A	302	LEU	0	-0.034	-0.009	27.567	0.003	0.003	0.000	0.000	0.000	0.000
116	A	303	LEU	0	-0.007	-0.005	28.132	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	304	LEU	0	-0.006	-0.004	29.974	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	305	ARG	1	0.905	0.953	32.355	0.133	0.133	0.000	0.000	0.000	0.000
119	A	306	ASN	0	-0.046	-0.029	27.823	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	307	HIS	0	-0.011	-0.004	24.842	0.004	0.004	0.000	0.000	0.000	0.000
121	A	308	PRO	0	0.043	0.016	30.022	0.007	0.007	0.000	0.000	0.000	0.000
122	A	309	ALA	0	-0.002	0.001	31.393	0.007	0.007	0.000	0.000	0.000	0.000
123	A	310	ALA	0	-0.003	0.006	30.346	0.004	0.004	0.000	0.000	0.000	0.000
124	A	311	ALA	0	0.022	0.010	32.298	0.004	0.004	0.000	0.000	0.000	0.000
125	A	312	SER	0	0.003	0.004	36.117	0.000	0.000	0.000	0.000	0.000	0.000
126	A	313	VAL	0	0.020	0.003	31.162	0.004	0.004	0.000	0.000	0.000	0.000
127	A	314	VAL	0	0.034	0.010	33.054	0.001	0.001	0.000	0.000	0.000	0.000
128	A	315	ALA	0	-0.012	-0.009	35.262	0.003	0.003	0.000	0.000	0.000	0.000
129	A	316	ARG	1	0.859	0.924	32.480	0.085	0.085	0.000	0.000	0.000	0.000
130	A	317	GLU	-1	-0.748	-0.859	33.188	-0.085	-0.085	0.000	0.000	0.000	0.000
131	A	318	MET	0	0.017	0.006	36.672	0.000	0.000	0.000	0.000	0.000	0.000
132	A	319	LYS	1	0.816	0.906	38.838	0.057	0.057	0.000	0.000	0.000	0.000
133	A	320	ILE	0	0.024	0.019	37.062	0.003	0.003	0.000	0.000	0.000	0.000
134	A	321	VAL	0	0.000	-0.008	37.041	0.003	0.003	0.000	0.000	0.000	0.000
135	A	322	THR	0	-0.015	-0.011	39.910	0.002	0.002	0.000	0.000	0.000	0.000
136	A	323	GLU	-1	-0.855	-0.899	43.263	-0.052	-0.052	0.000	0.000	0.000	0.000
137	A	324	ARG	1	1.013	1.025	37.688	0.068	0.068	0.000	0.000	0.000	0.000
138	A	325	ARG	1	0.762	0.838	40.381	0.080	0.080	0.000	0.000	0.000	0.000
139	A	326	ALA	0	-0.042	-0.017	44.676	0.001	0.001	0.000	0.000	0.000	0.000
140	A	327	GLU	-1	-0.889	-0.951	44.806	-0.051	-0.051	0.000	0.000	0.000	0.000
141	A	328	LYS	1	0.943	0.961	43.553	0.054	0.054	0.000	0.000	0.000	0.000
142	A	329	LYS	1	0.874	0.917	46.691	0.054	0.054	0.000	0.000	0.000	0.000
143	A	330	ALA	0	-0.014	0.003	49.360	0.001	0.001	0.000	0.000	0.000	0.000
144	A	331	ASP	-1	-0.837	-0.909	48.082	-0.043	-0.043	0.000	0.000	0.000	0.000
145	A	332	SER	0	-0.051	-0.028	50.046	0.000	0.000	0.000	0.000	0.000	0.000
146	A	333	ARG	1	0.880	0.959	52.010	0.043	0.043	0.000	0.000	0.000	0.000
147	A	334	VAL	0	-0.004	0.014	54.079	0.003	0.003	0.000	0.000	0.000	0.000

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