FMO DATABASE

FMODB ID: V5311

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1380941.799935
FMO2-HF: Nuclear repulsion	1321699.216807
FMO2-HF: Total energy	-59242.583128
FMO2-MP2: Total energy	-59417.3913

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.
-15.573	-7.409	2.723	-3.569	-7.318	0.014

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 : 0.078 / q_NPA : 0.032

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	-0.016	-0.003	2.925	-7.107	-3.401	0.309	-2.068	-1.947	0.016
4	A	191	VAL	0	0.031	0.017	2.988	-2.425	-1.325	0.127	-0.259	-0.968	0.000
5	A	192	GLU	-1	-0.871	-0.937	4.508	-0.296	0.010	-0.001	-0.037	-0.268	0.000
6	A	193	ALA	0	-0.011	-0.001	6.137	-0.034	-0.034	0.000	0.000	0.000	0.000
7	A	194	LEU	0	0.013	0.004	6.881	-0.127	-0.127	0.000	0.000	0.000	0.000
8	A	195	ARG	1	0.956	0.999	7.323	0.213	0.213	0.000	0.000	0.000	0.000
9	A	196	GLN	0	-0.059	-0.047	10.119	-0.115	-0.115	0.000	0.000	0.000	0.000
10	A	197	LYS	1	1.008	1.021	12.205	-0.398	-0.398	0.000	0.000	0.000	0.000
11	A	198	GLY	0	0.058	0.015	13.406	-0.027	-0.027	0.000	0.000	0.000	0.000
12	A	199	ASN	0	0.002	0.023	13.535	-0.038	-0.038	0.000	0.000	0.000	0.000
13	A	200	GLU	-1	-0.963	-0.972	15.981	0.259	0.259	0.000	0.000	0.000	0.000
14	A	201	LEU	0	0.000	0.000	16.956	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	202	PHE	0	-0.025	-0.015	18.742	-0.018	-0.018	0.000	0.000	0.000	0.000
16	A	203	VAL	0	-0.070	-0.040	19.912	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	204	GLN	0	-0.066	-0.026	21.959	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	205	LYS	1	0.889	0.942	24.266	-0.018	-0.018	0.000	0.000	0.000	0.000
19	A	206	ASP	-1	-0.845	-0.889	23.432	0.066	0.066	0.000	0.000	0.000	0.000
20	A	207	TYR	0	0.004	-0.023	21.916	0.003	0.003	0.000	0.000	0.000	0.000
21	A	208	LYS	1	0.972	0.976	21.258	-0.027	-0.027	0.000	0.000	0.000	0.000
22	A	209	GLU	-1	-0.797	-0.905	19.439	0.072	0.072	0.000	0.000	0.000	0.000
23	A	210	ALA	0	-0.022	-0.006	17.538	0.013	0.013	0.000	0.000	0.000	0.000
24	A	211	ILE	0	-0.014	-0.005	16.236	-0.014	-0.014	0.000	0.000	0.000	0.000
25	A	212	ASP	-1	-0.876	-0.934	16.117	0.005	0.005	0.000	0.000	0.000	0.000
26	A	213	ALA	0	-0.008	0.002	13.385	0.018	0.018	0.000	0.000	0.000	0.000
27	A	214	TYR	0	-0.087	-0.107	11.844	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	215	ARG	1	0.957	0.969	11.857	0.069	0.069	0.000	0.000	0.000	0.000
29	A	216	ASP	-1	-0.862	-0.927	10.734	0.061	0.061	0.000	0.000	0.000	0.000
30	A	217	ALA	0	-0.059	-0.041	7.612	-0.028	-0.028	0.000	0.000	0.000	0.000
31	A	218	LEU	0	0.032	-0.005	7.439	-0.266	-0.266	0.000	0.000	0.000	0.000
32	A	219	THR	0	0.027	0.037	9.742	-0.102	-0.102	0.000	0.000	0.000	0.000
33	A	220	ARG	1	0.802	0.894	4.564	-0.404	-0.337	-0.001	-0.001	-0.064	0.000
34	A	221	LEU	0	-0.048	-0.029	3.932	-0.684	-0.424	0.002	-0.033	-0.230	0.000
35	A	222	ASP	-1	-0.832	-0.904	6.037	-0.766	-0.766	0.000	0.000	0.000	0.000
36	A	223	THR	0	-0.063	-0.024	7.595	0.031	0.031	0.000	0.000	0.000	0.000
37	A	224	LEU	0	-0.118	-0.078	2.459	-1.698	-0.308	1.594	-0.799	-2.185	0.000
38	A	225	ILE	0	0.042	0.039	6.456	-0.070	-0.070	0.000	0.000	0.000	0.000
39	A	226	LEU	0	-0.041	-0.028	8.279	0.120	0.120	0.000	0.000	0.000	0.000
40	A	227	ARG	1	0.887	0.947	6.108	0.868	0.868	0.000	0.000	0.000	0.000
41	A	228	GLU	-1	-0.933	-0.943	6.304	-1.432	-1.432	0.000	0.000	0.000	0.000
42	A	229	LYS	1	0.947	0.970	10.273	0.458	0.458	0.000	0.000	0.000	0.000
43	A	230	PRO	0	0.001	-0.017	13.118	-0.044	-0.044	0.000	0.000	0.000	0.000
44	A	231	GLY	0	-0.012	0.000	14.131	0.054	0.054	0.000	0.000	0.000	0.000
45	A	232	GLU	-1	-0.908	-0.941	13.021	-0.394	-0.394	0.000	0.000	0.000	0.000
46	A	233	PRO	0	0.017	-0.008	12.432	-0.070	-0.070	0.000	0.000	0.000	0.000
47	A	234	GLU	-1	-0.883	-0.958	7.993	-0.747	-0.747	0.000	0.000	0.000	0.000
48	A	235	TRP	0	-0.003	0.012	7.925	-0.258	-0.258	0.000	0.000	0.000	0.000
49	A	236	VAL	0	0.025	0.016	9.316	-0.093	-0.093	0.000	0.000	0.000	0.000
50	A	237	GLU	-1	-0.904	-0.954	7.355	-0.754	-0.754	0.000	0.000	0.000	0.000
51	A	238	LEU	0	-0.049	-0.040	3.083	-1.235	-0.417	0.225	-0.197	-0.846	-0.002
52	A	239	ASP	-1	-0.750	-0.863	5.753	-0.591	-0.591	0.000	0.000	0.000	0.000
53	A	240	ARG	1	0.902	0.940	8.659	0.626	0.626	0.000	0.000	0.000	0.000
54	A	241	LYS	1	0.878	0.942	2.435	1.362	1.879	0.468	-0.175	-0.810	0.000
55	A	242	ASN	0	0.000	-0.005	7.237	0.056	0.056	0.000	0.000	0.000	0.000
56	A	243	ILE	0	-0.020	0.015	10.075	0.100	0.100	0.000	0.000	0.000	0.000
57	A	244	PRO	0	-0.045	-0.028	9.474	0.078	0.078	0.000	0.000	0.000	0.000
58	A	245	LEU	0	-0.029	-0.005	7.545	0.074	0.074	0.000	0.000	0.000	0.000
59	A	246	TYR	0	0.088	0.024	11.959	0.076	0.076	0.000	0.000	0.000	0.000
60	A	247	ALA	0	-0.017	0.007	14.888	0.046	0.046	0.000	0.000	0.000	0.000
61	A	248	ASN	0	-0.042	-0.020	13.760	0.020	0.020	0.000	0.000	0.000	0.000
62	A	249	MET	0	0.046	0.021	15.504	0.025	0.025	0.000	0.000	0.000	0.000
63	A	250	SER	0	-0.047	-0.002	17.702	0.024	0.024	0.000	0.000	0.000	0.000
64	A	251	GLN	0	-0.006	-0.004	20.215	0.006	0.006	0.000	0.000	0.000	0.000
65	A	252	CYS	0	-0.081	-0.014	19.222	0.020	0.020	0.000	0.000	0.000	0.000
66	A	253	TYR	0	0.060	0.030	19.832	0.005	0.005	0.000	0.000	0.000	0.000
67	A	254	LEU	0	-0.005	-0.006	23.698	0.008	0.008	0.000	0.000	0.000	0.000
68	A	255	ASN	0	-0.100	-0.050	24.698	0.000	0.000	0.000	0.000	0.000	0.000
69	A	256	ILE	0	-0.007	0.014	24.572	0.009	0.009	0.000	0.000	0.000	0.000
70	A	257	GLY	0	-0.022	-0.006	27.897	0.005	0.005	0.000	0.000	0.000	0.000
71	A	258	ASP	-1	-0.895	-0.941	25.599	-0.067	-0.067	0.000	0.000	0.000	0.000
72	A	259	LEU	0	-0.007	-0.016	26.194	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	260	HIS	0	0.049	0.034	26.249	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	261	GLU	-1	-0.824	-0.916	22.481	-0.130	-0.130	0.000	0.000	0.000	0.000
75	A	262	ALA	0	-0.054	-0.003	22.447	-0.018	-0.018	0.000	0.000	0.000	0.000
76	A	263	GLU	-1	-0.837	-0.915	22.912	-0.120	-0.120	0.000	0.000	0.000	0.000
77	A	264	GLU	-1	-0.901	-0.948	22.203	-0.159	-0.159	0.000	0.000	0.000	0.000
78	A	265	THR	0	-0.056	-0.066	18.191	-0.022	-0.022	0.000	0.000	0.000	0.000
79	A	266	SER	0	-0.002	-0.022	18.819	-0.024	-0.024	0.000	0.000	0.000	0.000
80	A	267	SER	0	0.008	-0.004	20.801	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	268	GLU	-1	-0.877	-0.915	16.450	-0.324	-0.324	0.000	0.000	0.000	0.000
82	A	269	VAL	0	-0.031	-0.009	16.419	-0.032	-0.032	0.000	0.000	0.000	0.000
83	A	270	LEU	0	-0.036	-0.013	17.564	-0.013	-0.013	0.000	0.000	0.000	0.000
84	A	271	LYS	1	0.875	0.947	18.460	0.258	0.258	0.000	0.000	0.000	0.000
85	A	272	ARG	1	0.748	0.854	12.990	0.471	0.471	0.000	0.000	0.000	0.000
86	A	273	GLU	-1	-0.887	-0.936	15.671	-0.319	-0.319	0.000	0.000	0.000	0.000
87	A	274	GLU	-1	-0.875	-0.934	18.973	-0.173	-0.173	0.000	0.000	0.000	0.000
88	A	275	THR	0	-0.042	-0.016	22.666	0.011	0.011	0.000	0.000	0.000	0.000
89	A	276	ASN	0	0.008	0.008	18.498	0.031	0.031	0.000	0.000	0.000	0.000
90	A	277	GLU	-1	-0.916	-0.950	21.790	-0.102	-0.102	0.000	0.000	0.000	0.000
91	A	278	LYS	1	0.933	0.951	20.913	0.119	0.119	0.000	0.000	0.000	0.000
92	A	279	ALA	0	0.029	0.021	20.229	0.011	0.011	0.000	0.000	0.000	0.000
93	A	280	LEU	0	0.058	0.028	22.229	0.010	0.010	0.000	0.000	0.000	0.000
94	A	281	PHE	0	-0.059	-0.023	25.648	0.014	0.014	0.000	0.000	0.000	0.000
95	A	282	ARG	1	0.879	0.916	19.457	0.129	0.129	0.000	0.000	0.000	0.000
96	A	283	ARG	1	0.892	0.910	24.896	0.151	0.151	0.000	0.000	0.000	0.000
97	A	284	ALA	0	0.047	0.023	26.542	0.007	0.007	0.000	0.000	0.000	0.000
98	A	285	LYS	1	0.858	0.935	28.520	0.062	0.062	0.000	0.000	0.000	0.000
99	A	286	ALA	0	0.019	0.007	27.213	0.008	0.008	0.000	0.000	0.000	0.000
100	A	287	ARG	1	0.898	0.950	28.989	0.117	0.117	0.000	0.000	0.000	0.000
101	A	288	ILE	0	-0.014	0.002	31.742	0.006	0.006	0.000	0.000	0.000	0.000
102	A	289	ALA	0	-0.073	-0.027	32.286	0.005	0.005	0.000	0.000	0.000	0.000
103	A	290	ALA	0	-0.026	-0.009	32.199	0.005	0.005	0.000	0.000	0.000	0.000
104	A	291	TRP	0	-0.054	-0.046	34.321	0.001	0.001	0.000	0.000	0.000	0.000
105	A	292	LYS	1	0.913	0.963	30.716	0.090	0.090	0.000	0.000	0.000	0.000
106	A	293	LEU	0	0.000	-0.007	34.990	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	294	ASP	-1	-0.899	-0.945	37.250	-0.066	-0.066	0.000	0.000	0.000	0.000
108	A	295	GLU	-1	-0.900	-0.959	32.425	-0.091	-0.091	0.000	0.000	0.000	0.000
109	A	296	ALA	0	-0.026	-0.018	32.392	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	297	GLU	-1	-0.828	-0.901	33.333	-0.066	-0.066	0.000	0.000	0.000	0.000
111	A	298	GLU	-1	-0.954	-0.978	32.739	-0.099	-0.099	0.000	0.000	0.000	0.000
112	A	299	ASP	-1	-0.774	-0.865	28.542	-0.125	-0.125	0.000	0.000	0.000	0.000
113	A	300	LEU	0	-0.005	-0.010	30.541	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	301	LYS	1	0.864	0.920	32.591	0.072	0.072	0.000	0.000	0.000	0.000
115	A	302	LEU	0	-0.032	-0.004	27.411	0.001	0.001	0.000	0.000	0.000	0.000
116	A	303	LEU	0	-0.001	-0.007	28.059	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	304	LEU	0	-0.014	-0.005	29.754	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	305	ARG	1	0.903	0.955	31.930	0.107	0.107	0.000	0.000	0.000	0.000
119	A	306	ASN	0	-0.047	-0.034	27.642	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	307	HIS	0	-0.005	-0.007	24.664	0.004	0.004	0.000	0.000	0.000	0.000
121	A	308	PRO	0	0.049	0.023	29.827	0.006	0.006	0.000	0.000	0.000	0.000
122	A	309	ALA	0	-0.008	-0.003	31.197	0.006	0.006	0.000	0.000	0.000	0.000
123	A	310	ALA	0	0.011	0.013	30.175	0.004	0.004	0.000	0.000	0.000	0.000
124	A	311	ALA	0	0.011	0.000	32.073	0.003	0.003	0.000	0.000	0.000	0.000
125	A	312	SER	0	-0.015	-0.007	35.893	0.000	0.000	0.000	0.000	0.000	0.000
126	A	313	VAL	0	0.041	0.017	31.107	0.003	0.003	0.000	0.000	0.000	0.000
127	A	314	VAL	0	0.035	0.008	32.739	0.001	0.001	0.000	0.000	0.000	0.000
128	A	315	ALA	0	-0.023	-0.009	35.075	0.002	0.002	0.000	0.000	0.000	0.000
129	A	316	ARG	1	0.879	0.939	32.148	0.051	0.051	0.000	0.000	0.000	0.000
130	A	317	GLU	-1	-0.817	-0.923	33.106	-0.051	-0.051	0.000	0.000	0.000	0.000
131	A	318	MET	0	0.009	0.003	36.544	0.000	0.000	0.000	0.000	0.000	0.000
132	A	319	LYS	1	0.927	0.966	38.737	0.036	0.036	0.000	0.000	0.000	0.000
133	A	320	ILE	0	0.042	0.032	37.205	0.002	0.002	0.000	0.000	0.000	0.000
134	A	321	VAL	0	-0.005	-0.009	37.060	0.002	0.002	0.000	0.000	0.000	0.000
135	A	322	THR	0	-0.062	-0.028	39.828	0.002	0.002	0.000	0.000	0.000	0.000
136	A	323	GLU	-1	-0.940	-0.952	43.184	-0.033	-0.033	0.000	0.000	0.000	0.000
137	A	324	ARG	1	1.021	1.024	37.520	0.042	0.042	0.000	0.000	0.000	0.000
138	A	325	ARG	1	0.856	0.909	39.750	0.058	0.058	0.000	0.000	0.000	0.000
139	A	326	ALA	0	-0.045	-0.015	44.624	0.001	0.001	0.000	0.000	0.000	0.000
140	A	327	GLU	-1	-0.889	-0.950	44.867	-0.032	-0.032	0.000	0.000	0.000	0.000
141	A	328	LYS	1	1.035	1.017	42.920	0.039	0.039	0.000	0.000	0.000	0.000
142	A	329	LYS	1	0.885	0.930	46.647	0.040	0.040	0.000	0.000	0.000	0.000
143	A	330	ALA	0	-0.017	-0.002	49.329	0.000	0.000	0.000	0.000	0.000	0.000
144	A	331	ASP	-1	-0.894	-0.944	48.477	-0.027	-0.027	0.000	0.000	0.000	0.000
145	A	332	SER	0	-0.068	-0.047	49.963	0.000	0.000	0.000	0.000	0.000	0.000
146	A	333	ARG	1	0.825	0.925	51.993	0.030	0.030	0.000	0.000	0.000	0.000
147	A	334	VAL	0	0.024	0.038	53.968	0.001	0.001	0.000	0.000	0.000	0.000

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