FMO DATABASE

FMODB ID: 2JY2R

Calculation Name: 3WKV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WKV

Chain ID: A

ChEMBL ID:

UniProt ID: Q3U2S8

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	149
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1303116.119541
FMO2-HF: Nuclear repulsion	1243549.205345
FMO2-HF: Total energy	-59566.914196
FMO2-MP2: Total energy	-59744.645094

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:84:PHE)

Summations of interaction energy for fragment #1(A:84:PHE)

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.
-7.715	-3.371	0.431	-2.001	-2.774	0.015

Interaction energy analysis for fragmet #1(A:84:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : 0.020

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	86	SER	0	0.059	0.032	2.876	-3.711	0.319	0.431	-1.955	-2.506	0.015
4	A	87	ARG	1	0.990	0.983	3.933	-1.493	-1.179	0.000	-0.046	-0.268	0.000
5	A	88	LEU	0	0.024	0.019	7.982	-0.250	-0.250	0.000	0.000	0.000	0.000
6	A	89	ARG	1	0.899	0.954	7.546	-1.225	-1.225	0.000	0.000	0.000	0.000
7	A	90	LYS	1	0.947	0.993	7.340	-0.509	-0.509	0.000	0.000	0.000	0.000
8	A	91	LEU	0	-0.014	-0.032	9.334	-0.140	-0.140	0.000	0.000	0.000	0.000
9	A	92	PHE	0	0.052	0.032	12.333	-0.065	-0.065	0.000	0.000	0.000	0.000
10	A	93	SER	0	0.076	0.034	12.479	-0.053	-0.053	0.000	0.000	0.000	0.000
11	A	94	SER	0	0.538	0.594	15.135	-0.058	-0.058	0.000	0.000	0.000	0.000
12	A	95	HIS	1	0.347	0.375	17.515	-0.364	-0.364	0.000	0.000	0.000	0.000
13	A	96	ARG	1	0.981	0.972	21.942	-0.167	-0.167	0.000	0.000	0.000	0.000
14	A	97	PHE	0	0.024	0.002	16.486	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	98	GLN	0	0.034	0.022	21.366	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	99	VAL	0	0.053	0.026	23.484	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	100	ILE	0	-0.017	-0.004	23.038	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	101	ILE	0	0.065	0.021	21.673	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	102	ILE	0	0.002	0.016	25.183	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	103	CYS	0	-0.073	-0.043	28.438	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	104	LEU	0	0.034	0.008	24.495	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	105	VAL	0	-0.002	0.013	27.697	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	106	VAL	0	-0.031	-0.023	29.905	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	107	LEU	0	0.008	0.010	30.878	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	108	ASP	-1	-0.660	-0.815	29.719	0.158	0.158	0.000	0.000	0.000	0.000
26	A	109	ALA	0	-0.034	0.001	32.617	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	110	LEU	0	0.016	-0.019	35.056	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	111	LEU	0	0.004	0.018	32.414	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	112	VAL	0	0.030	0.016	34.588	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	113	LEU	0	-0.045	-0.004	37.311	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	114	ALA	0	0.012	-0.010	40.079	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	115	GLU	-1	-0.822	-0.902	37.269	0.088	0.088	0.000	0.000	0.000	0.000
33	A	116	LEU	0	0.053	0.023	40.873	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	117	LEU	0	-0.038	-0.027	43.058	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	118	LEU	0	-0.094	-0.051	43.069	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	119	ASP	-1	-0.795	-0.901	43.546	0.065	0.065	0.000	0.000	0.000	0.000
37	A	120	LEU	0	-0.092	-0.031	46.116	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	121	LYS	1	0.808	0.926	47.869	-0.063	-0.063	0.000	0.000	0.000	0.000
39	A	132	VAL	0	-0.002	-0.012	46.608	0.000	0.000	0.000	0.000	0.000	0.000
40	A	133	THR	0	0.054	0.026	45.118	0.001	0.001	0.000	0.000	0.000	0.000
41	A	134	ALA	0	0.026	0.006	42.310	0.002	0.002	0.000	0.000	0.000	0.000
42	A	135	PHE	0	-0.001	-0.002	40.895	0.003	0.003	0.000	0.000	0.000	0.000
43	A	136	HIS	0	0.004	0.017	39.646	0.006	0.006	0.000	0.000	0.000	0.000
44	A	137	TYR	0	0.026	0.018	35.636	0.003	0.003	0.000	0.000	0.000	0.000
45	A	138	MET	0	-0.008	-0.021	36.338	0.005	0.005	0.000	0.000	0.000	0.000
46	A	139	SER	0	-0.033	-0.011	35.236	0.006	0.006	0.000	0.000	0.000	0.000
47	A	140	PHE	0	0.070	0.031	32.646	0.009	0.009	0.000	0.000	0.000	0.000
48	A	141	ALA	0	-0.020	-0.003	32.031	0.009	0.009	0.000	0.000	0.000	0.000
49	A	142	ILE	0	-0.022	-0.017	30.448	0.010	0.010	0.000	0.000	0.000	0.000
50	A	143	LEU	0	0.061	0.027	29.971	0.014	0.014	0.000	0.000	0.000	0.000
51	A	144	VAL	0	-0.017	-0.001	26.924	0.017	0.017	0.000	0.000	0.000	0.000
52	A	145	PHE	0	-0.074	-0.040	26.122	0.014	0.014	0.000	0.000	0.000	0.000
53	A	146	PHE	0	0.074	0.028	25.045	0.020	0.020	0.000	0.000	0.000	0.000
54	A	147	MET	0	-0.056	-0.014	24.661	0.023	0.023	0.000	0.000	0.000	0.000
55	A	148	LEU	0	0.006	0.000	21.583	0.033	0.033	0.000	0.000	0.000	0.000
56	A	149	ASP	-1	-0.940	-0.977	20.382	0.271	0.271	0.000	0.000	0.000	0.000
57	A	150	LEU	0	0.021	0.014	20.030	0.052	0.052	0.000	0.000	0.000	0.000
58	A	151	GLY	0	0.048	0.024	19.379	0.046	0.046	0.000	0.000	0.000	0.000
59	A	152	LEU	0	-0.034	-0.027	15.636	0.084	0.084	0.000	0.000	0.000	0.000
60	A	153	ARG	1	0.843	0.916	14.406	-0.354	-0.354	0.000	0.000	0.000	0.000
61	A	154	ILE	0	-0.006	0.003	16.534	0.017	0.017	0.000	0.000	0.000	0.000
62	A	155	PHE	0	-0.005	0.016	10.762	0.104	0.104	0.000	0.000	0.000	0.000
63	A	156	ALA	0	-0.052	-0.022	10.950	0.224	0.224	0.000	0.000	0.000	0.000
64	A	157	TYR	0	0.027	0.005	10.532	-0.077	-0.077	0.000	0.000	0.000	0.000
65	A	158	GLY	0	0.053	0.061	7.290	0.069	0.069	0.000	0.000	0.000	0.000
66	A	158	PRO	0	-0.084	-0.066	4.817	0.187	0.187	0.000	0.000	0.000	0.000
67	A	159	LYS	1	0.992	0.970	6.177	-0.564	-0.564	0.000	0.000	0.000	0.000
68	A	160	ASN	0	-0.011	-0.002	9.692	-0.112	-0.112	0.000	0.000	0.000	0.000
69	A	161	PHE	0	0.088	0.057	13.741	-0.028	-0.028	0.000	0.000	0.000	0.000
70	A	162	PHE	0	-0.070	-0.038	17.543	0.008	0.008	0.000	0.000	0.000	0.000
71	A	163	THR	0	-0.003	-0.024	18.853	-0.015	-0.015	0.000	0.000	0.000	0.000
72	A	164	ASN	0	-0.035	-0.015	14.964	0.075	0.075	0.000	0.000	0.000	0.000
73	A	165	PRO	0	0.014	0.013	18.169	0.027	0.027	0.000	0.000	0.000	0.000
74	A	166	TRP	0	0.050	0.011	20.697	0.017	0.017	0.000	0.000	0.000	0.000
75	A	167	GLU	-1	-0.768	-0.865	17.313	0.398	0.398	0.000	0.000	0.000	0.000
76	A	168	VAL	0	-0.033	-0.026	16.072	0.018	0.018	0.000	0.000	0.000	0.000
77	A	169	ALA	0	-0.009	0.002	18.644	0.000	0.000	0.000	0.000	0.000	0.000
78	A	170	ASP	-1	-0.776	-0.861	21.642	0.270	0.270	0.000	0.000	0.000	0.000
79	A	171	GLY	0	0.013	0.005	18.973	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	172	LEU	0	-0.021	-0.017	19.750	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	173	ILE	0	0.051	0.027	21.024	-0.025	-0.025	0.000	0.000	0.000	0.000
82	A	174	VAL	0	-0.015	0.013	22.044	-0.021	-0.021	0.000	0.000	0.000	0.000
83	A	175	VAL	0	-0.028	-0.013	18.819	-0.014	-0.014	0.000	0.000	0.000	0.000
84	A	176	VAL	0	-0.001	-0.012	22.188	-0.020	-0.020	0.000	0.000	0.000	0.000
85	A	177	SER	0	-0.019	-0.022	25.068	-0.025	-0.025	0.000	0.000	0.000	0.000
86	A	178	PHE	0	0.057	0.011	24.678	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	179	VAL	0	-0.051	-0.020	23.119	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	180	LEU	0	-0.011	-0.006	26.061	-0.018	-0.018	0.000	0.000	0.000	0.000
89	A	181	ASP	-1	-0.808	-0.916	28.653	0.153	0.153	0.000	0.000	0.000	0.000
90	A	182	LEU	0	-0.019	-0.011	25.187	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	183	VAL	0	-0.031	-0.014	29.098	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	184	LEU	0	-0.026	-0.029	31.396	-0.012	-0.012	0.000	0.000	0.000	0.000
93	A	185	LEU	0	-0.057	0.006	30.193	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	186	PHE	0	0.007	-0.020	30.636	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	187	LYS	1	0.807	0.936	35.771	-0.090	-0.090	0.000	0.000	0.000	0.000
96	A	188	SER	0	-0.008	-0.022	39.400	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	189	HIS	0	-0.017	-0.012	35.259	0.004	0.004	0.000	0.000	0.000	0.000
98	A	190	HIS	0	0.051	0.024	39.168	0.005	0.005	0.000	0.000	0.000	0.000
99	A	191	PHE	0	-0.003	-0.016	42.014	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	192	GLU	-1	-0.878	-0.937	42.767	0.069	0.069	0.000	0.000	0.000	0.000
101	A	193	ALA	0	-0.033	-0.023	38.929	0.003	0.003	0.000	0.000	0.000	0.000
102	A	194	LEU	0	0.045	0.035	38.149	0.008	0.008	0.000	0.000	0.000	0.000
103	A	195	GLY	0	0.044	0.022	38.188	0.006	0.006	0.000	0.000	0.000	0.000
104	A	196	LEU	0	0.009	0.003	36.679	0.005	0.005	0.000	0.000	0.000	0.000
105	A	197	LEU	0	0.082	0.036	32.376	0.007	0.007	0.000	0.000	0.000	0.000
106	A	198	ILE	0	-0.079	-0.044	34.062	0.009	0.009	0.000	0.000	0.000	0.000
107	A	199	LEU	0	-0.042	-0.030	35.010	0.007	0.007	0.000	0.000	0.000	0.000
108	A	200	LEU	0	0.011	0.013	30.918	0.006	0.006	0.000	0.000	0.000	0.000
109	A	201	ARG	1	0.851	0.933	30.486	-0.119	-0.119	0.000	0.000	0.000	0.000
110	A	202	LEU	0	-0.084	-0.051	31.048	0.009	0.009	0.000	0.000	0.000	0.000
111	A	203	TRP	0	0.012	0.017	27.511	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	204	ARG	1	0.847	0.907	26.224	-0.181	-0.181	0.000	0.000	0.000	0.000
113	A	205	VAL	0	0.088	0.054	27.935	0.012	0.012	0.000	0.000	0.000	0.000
114	A	206	ALA	0	-0.005	0.013	29.547	0.009	0.009	0.000	0.000	0.000	0.000
115	A	207	ARG	1	0.782	0.880	25.019	-0.235	-0.235	0.000	0.000	0.000	0.000
116	A	208	ILE	0	-0.027	-0.027	24.058	0.012	0.012	0.000	0.000	0.000	0.000
117	A	209	ILE	0	0.029	0.005	26.131	0.006	0.006	0.000	0.000	0.000	0.000
118	A	210	ASN	0	-0.016	-0.012	28.152	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	211	GLY	0	0.028	0.010	23.835	0.001	0.001	0.000	0.000	0.000	0.000
120	A	212	ILE	0	-0.062	-0.026	23.574	0.015	0.015	0.000	0.000	0.000	0.000
121	A	213	ILE	0	-0.038	-0.007	26.055	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	214	ILE	0	0.052	0.024	22.684	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	215	SER	0	-0.055	-0.035	22.698	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	216	ARG	1	0.933	0.972	24.250	-0.166	-0.166	0.000	0.000	0.000	0.000
125	A	217	MET	0	0.017	0.030	26.976	-0.011	-0.011	0.000	0.000	0.000	0.000
126	A	218	LYS	1	1.000	0.972	20.695	-0.197	-0.197	0.000	0.000	0.000	0.000
127	A	219	GLN	0	-0.028	-0.019	23.585	-0.024	-0.024	0.000	0.000	0.000	0.000
128	A	220	LEU	0	-0.110	-0.060	24.763	-0.012	-0.012	0.000	0.000	0.000	0.000
129	A	221	GLU	-1	-0.928	-0.993	26.827	0.139	0.139	0.000	0.000	0.000	0.000
130	A	222	ASP	-1	-0.834	-0.894	22.713	0.161	0.161	0.000	0.000	0.000	0.000
131	A	223	LYS	1	0.895	0.950	25.941	-0.133	-0.133	0.000	0.000	0.000	0.000
132	A	224	ILE	0	-0.008	0.003	28.721	-0.008	-0.008	0.000	0.000	0.000	0.000
133	A	225	GLU	-1	-0.792	-0.883	27.142	0.062	0.062	0.000	0.000	0.000	0.000
134	A	226	GLU	-1	-1.016	-0.999	26.639	0.081	0.081	0.000	0.000	0.000	0.000
135	A	227	LEU	0	-0.114	-0.062	29.888	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	228	LEU	0	0.019	0.013	32.470	-0.006	-0.006	0.000	0.000	0.000	0.000
137	A	229	SER	0	0.024	0.017	30.527	-0.006	-0.006	0.000	0.000	0.000	0.000
138	A	230	LYS	1	0.938	0.977	31.338	-0.051	-0.051	0.000	0.000	0.000	0.000
139	A	231	ILE	0	0.029	0.001	34.800	-0.004	-0.004	0.000	0.000	0.000	0.000
140	A	232	TYR	0	0.043	0.021	35.142	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	233	HIS	0	-0.150	-0.078	35.167	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	234	LEU	0	-0.019	-0.031	37.258	-0.003	-0.003	0.000	0.000	0.000	0.000
143	A	235	GLU	-1	-0.896	-0.939	40.429	0.033	0.033	0.000	0.000	0.000	0.000
144	A	236	ASN	0	-0.056	-0.032	38.527	-0.004	-0.004	0.000	0.000	0.000	0.000
145	A	237	GLU	-1	-0.889	-0.927	39.246	0.018	0.018	0.000	0.000	0.000	0.000
146	A	238	ILE	0	-0.046	-0.016	42.811	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	239	ALA	0	0.018	0.006	45.600	-0.002	-0.002	0.000	0.000	0.000	0.000
148	A	240	ARG	1	0.792	0.883	42.815	-0.017	-0.017	0.000	0.000	0.000	0.000
149	A	241	LEU	0	-0.024	0.011	47.000	-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:84:PHE)