FMO DATABASE

FMODB ID: 6NM6Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1300581.555721
FMO2-HF: Nuclear repulsion	1241012.106102
FMO2-HF: Total energy	-59569.449619
FMO2-MP2: Total energy	-59746.580494

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.
-10.879	-5.332	1.593	-3.225	-3.915	0.033

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 : 0.075 / q_NPA : 0.031

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	0.063	0.036	2.593	-7.032	-1.890	1.590	-3.121	-3.610	0.033
4	A	87	ARG	1	0.965	0.972	3.828	-2.209	-1.804	0.003	-0.104	-0.305	0.000
5	A	88	LEU	0	0.041	0.017	7.937	-0.245	-0.245	0.000	0.000	0.000	0.000
6	A	89	ARG	1	0.874	0.957	7.097	-1.041	-1.041	0.000	0.000	0.000	0.000
7	A	90	LYS	1	0.986	0.998	7.208	-0.513	-0.513	0.000	0.000	0.000	0.000
8	A	91	LEU	0	-0.022	-0.038	9.221	-0.137	-0.137	0.000	0.000	0.000	0.000
9	A	92	PHE	0	0.025	0.023	11.964	-0.070	-0.070	0.000	0.000	0.000	0.000
10	A	93	SER	0	0.049	0.043	13.182	-0.054	-0.054	0.000	0.000	0.000	0.000
11	A	94	SER	0	0.021	-0.001	15.601	-0.026	-0.026	0.000	0.000	0.000	0.000
12	A	95	HIS	1	0.799	0.897	17.207	-0.347	-0.347	0.000	0.000	0.000	0.000
13	A	96	ARG	1	1.043	1.005	20.648	-0.164	-0.164	0.000	0.000	0.000	0.000
14	A	97	PHE	0	0.037	0.017	16.175	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	98	GLN	0	0.063	0.039	21.399	0.013	0.013	0.000	0.000	0.000	0.000
16	A	99	VAL	0	0.042	0.024	23.480	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	100	ILE	0	-0.005	0.005	22.821	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	101	ILE	0	0.063	0.031	21.497	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	102	ILE	0	0.001	0.006	25.040	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	103	CYS	0	-0.068	-0.044	28.218	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	104	LEU	0	0.013	0.009	24.326	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	105	VAL	0	-0.011	0.002	27.420	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	106	VAL	0	-0.002	-0.004	29.795	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	107	LEU	0	-0.001	0.011	30.626	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	108	ASP	-1	-0.680	-0.814	29.789	0.163	0.163	0.000	0.000	0.000	0.000
26	A	109	ALA	0	-0.042	-0.001	32.335	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	110	LEU	0	-0.011	-0.019	34.939	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	111	LEU	0	-0.001	0.010	32.831	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	112	VAL	0	0.046	0.020	34.736	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	113	LEU	0	-0.019	0.008	37.555	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	114	ALA	0	0.002	-0.010	40.167	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	115	GLU	-1	-0.814	-0.907	37.213	0.098	0.098	0.000	0.000	0.000	0.000
33	A	116	LEU	0	0.036	0.023	41.115	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	117	LEU	0	-0.035	-0.020	43.147	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	118	LEU	0	-0.071	-0.026	42.906	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	119	ASP	-1	-0.768	-0.881	43.291	0.071	0.071	0.000	0.000	0.000	0.000
37	A	120	LEU	0	-0.096	-0.039	46.266	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	121	LYS	1	0.797	0.902	48.522	-0.066	-0.066	0.000	0.000	0.000	0.000
39	A	132	VAL	0	0.038	0.012	46.275	0.000	0.000	0.000	0.000	0.000	0.000
40	A	133	THR	0	0.025	0.001	44.611	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	134	ALA	0	0.029	0.014	42.437	0.003	0.003	0.000	0.000	0.000	0.000
42	A	135	PHE	0	0.006	-0.007	40.909	0.003	0.003	0.000	0.000	0.000	0.000
43	A	136	HIS	0	-0.024	0.014	39.568	0.006	0.006	0.000	0.000	0.000	0.000
44	A	137	TYR	0	0.026	0.013	35.331	0.004	0.004	0.000	0.000	0.000	0.000
45	A	138	MET	0	0.001	-0.012	36.132	0.005	0.005	0.000	0.000	0.000	0.000
46	A	139	SER	0	-0.038	-0.019	35.374	0.006	0.006	0.000	0.000	0.000	0.000
47	A	140	PHE	0	0.053	0.024	32.994	0.010	0.010	0.000	0.000	0.000	0.000
48	A	141	ALA	0	-0.014	-0.004	32.166	0.009	0.009	0.000	0.000	0.000	0.000
49	A	142	ILE	0	-0.035	-0.019	30.519	0.010	0.010	0.000	0.000	0.000	0.000
50	A	143	LEU	0	0.021	0.007	29.916	0.015	0.015	0.000	0.000	0.000	0.000
51	A	144	VAL	0	0.003	0.000	27.117	0.017	0.017	0.000	0.000	0.000	0.000
52	A	145	PHE	0	-0.056	-0.027	26.028	0.015	0.015	0.000	0.000	0.000	0.000
53	A	146	PHE	0	0.064	0.028	24.913	0.023	0.023	0.000	0.000	0.000	0.000
54	A	147	MET	0	-0.046	-0.014	24.684	0.022	0.022	0.000	0.000	0.000	0.000
55	A	148	LEU	0	-0.019	-0.002	21.381	0.031	0.031	0.000	0.000	0.000	0.000
56	A	149	ASP	-1	-0.924	-0.974	20.290	0.290	0.290	0.000	0.000	0.000	0.000
57	A	150	LEU	0	0.016	0.010	20.095	0.053	0.053	0.000	0.000	0.000	0.000
58	A	151	GLY	0	0.042	0.022	19.132	0.042	0.042	0.000	0.000	0.000	0.000
59	A	152	LEU	0	-0.029	-0.027	15.650	0.089	0.089	0.000	0.000	0.000	0.000
60	A	153	ARG	1	0.853	0.926	14.474	-0.415	-0.415	0.000	0.000	0.000	0.000
61	A	154	ILE	0	-0.013	-0.002	16.066	0.036	0.036	0.000	0.000	0.000	0.000
62	A	155	PHE	0	0.039	0.033	10.741	0.087	0.087	0.000	0.000	0.000	0.000
63	A	156	ALA	0	-0.043	-0.004	10.936	0.222	0.222	0.000	0.000	0.000	0.000
64	A	157	TYR	0	-0.002	-0.025	11.171	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	158	GLY	0	0.060	0.030	7.874	-0.051	-0.051	0.000	0.000	0.000	0.000
66	A	158	PRO	0	-0.118	-0.085	4.995	0.427	0.427	0.000	0.000	0.000	0.000
67	A	159	LYS	1	0.978	1.004	6.919	-0.070	-0.070	0.000	0.000	0.000	0.000
68	A	160	ASN	0	0.005	0.002	10.226	-0.096	-0.096	0.000	0.000	0.000	0.000
69	A	161	PHE	0	0.042	0.027	13.777	-0.019	-0.019	0.000	0.000	0.000	0.000
70	A	162	PHE	0	0.007	-0.008	16.832	0.026	0.026	0.000	0.000	0.000	0.000
71	A	163	THR	0	-0.001	-0.011	18.812	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	164	ASN	0	-0.033	-0.027	14.913	0.067	0.067	0.000	0.000	0.000	0.000
73	A	165	PRO	0	0.006	0.004	18.142	0.027	0.027	0.000	0.000	0.000	0.000
74	A	166	TRP	0	0.032	0.009	20.872	0.014	0.014	0.000	0.000	0.000	0.000
75	A	167	GLU	-1	-0.780	-0.848	17.414	0.320	0.320	0.000	0.000	0.000	0.000
76	A	168	VAL	0	-0.026	-0.021	16.062	0.030	0.030	0.000	0.000	0.000	0.000
77	A	169	ALA	0	0.010	0.012	18.635	0.005	0.005	0.000	0.000	0.000	0.000
78	A	170	ASP	-1	-0.800	-0.868	21.689	0.246	0.246	0.000	0.000	0.000	0.000
79	A	171	GLY	0	0.016	0.004	18.730	0.001	0.001	0.000	0.000	0.000	0.000
80	A	172	LEU	0	-0.026	-0.018	19.755	0.004	0.004	0.000	0.000	0.000	0.000
81	A	173	ILE	0	0.037	0.019	21.151	-0.019	-0.019	0.000	0.000	0.000	0.000
82	A	174	VAL	0	-0.014	0.005	21.718	-0.017	-0.017	0.000	0.000	0.000	0.000
83	A	175	VAL	0	-0.023	-0.013	18.769	-0.010	-0.010	0.000	0.000	0.000	0.000
84	A	176	VAL	0	-0.007	-0.022	22.155	-0.017	-0.017	0.000	0.000	0.000	0.000
85	A	177	SER	0	-0.022	-0.012	25.267	-0.024	-0.024	0.000	0.000	0.000	0.000
86	A	178	PHE	0	0.032	0.006	24.366	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	179	VAL	0	-0.021	-0.009	23.413	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	180	LEU	0	0.001	0.004	26.171	-0.017	-0.017	0.000	0.000	0.000	0.000
89	A	181	ASP	-1	-0.808	-0.928	28.750	0.157	0.157	0.000	0.000	0.000	0.000
90	A	182	LEU	0	-0.026	-0.013	25.168	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	183	VAL	0	0.002	-0.002	29.252	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	184	LEU	0	-0.017	-0.012	31.584	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	185	LEU	0	-0.041	0.010	29.984	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	186	PHE	0	0.012	0.000	30.486	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	187	LYS	1	0.793	0.901	35.588	-0.099	-0.099	0.000	0.000	0.000	0.000
96	A	188	SER	0	-0.004	-0.019	39.048	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	189	HIS	0	-0.005	-0.003	35.157	0.003	0.003	0.000	0.000	0.000	0.000
98	A	190	HIS	0	0.026	0.016	39.028	0.004	0.004	0.000	0.000	0.000	0.000
99	A	191	PHE	0	0.004	-0.010	42.048	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	192	GLU	-1	-0.873	-0.938	42.513	0.071	0.071	0.000	0.000	0.000	0.000
101	A	193	ALA	0	-0.028	-0.009	38.723	0.003	0.003	0.000	0.000	0.000	0.000
102	A	194	LEU	0	0.045	0.022	38.325	0.008	0.008	0.000	0.000	0.000	0.000
103	A	195	GLY	0	0.013	0.003	38.428	0.005	0.005	0.000	0.000	0.000	0.000
104	A	196	LEU	0	-0.021	-0.013	36.662	0.004	0.004	0.000	0.000	0.000	0.000
105	A	197	LEU	0	0.066	0.031	32.495	0.008	0.008	0.000	0.000	0.000	0.000
106	A	198	ILE	0	-0.036	-0.006	33.999	0.009	0.009	0.000	0.000	0.000	0.000
107	A	199	LEU	0	-0.004	-0.004	34.981	0.007	0.007	0.000	0.000	0.000	0.000
108	A	200	LEU	0	0.006	0.020	30.946	0.005	0.005	0.000	0.000	0.000	0.000
109	A	201	ARG	1	0.849	0.890	30.195	-0.126	-0.126	0.000	0.000	0.000	0.000
110	A	202	LEU	0	-0.028	-0.008	31.078	0.007	0.007	0.000	0.000	0.000	0.000
111	A	203	TRP	0	0.004	0.003	27.935	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	204	ARG	1	0.823	0.881	26.093	-0.182	-0.182	0.000	0.000	0.000	0.000
113	A	205	VAL	0	-0.024	-0.003	27.851	0.011	0.011	0.000	0.000	0.000	0.000
114	A	206	ALA	0	0.007	0.000	29.902	0.004	0.004	0.000	0.000	0.000	0.000
115	A	207	ARG	1	0.823	0.909	25.079	-0.212	-0.212	0.000	0.000	0.000	0.000
116	A	208	ILE	0	0.006	-0.006	23.940	0.011	0.011	0.000	0.000	0.000	0.000
117	A	209	ILE	0	-0.013	-0.005	25.945	0.003	0.003	0.000	0.000	0.000	0.000
118	A	210	ASN	0	-0.006	-0.016	27.800	-0.010	-0.010	0.000	0.000	0.000	0.000
119	A	211	GLY	0	0.055	0.028	23.774	0.000	0.000	0.000	0.000	0.000	0.000
120	A	212	ILE	0	-0.058	-0.030	24.151	0.002	0.002	0.000	0.000	0.000	0.000
121	A	213	ILE	0	-0.012	0.002	25.915	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	214	ILE	0	0.056	0.031	22.747	-0.007	-0.007	0.000	0.000	0.000	0.000
123	A	215	SER	0	-0.079	-0.038	22.017	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	216	ARG	1	0.908	0.943	23.662	-0.152	-0.152	0.000	0.000	0.000	0.000
125	A	217	MET	0	0.002	0.017	26.697	-0.012	-0.012	0.000	0.000	0.000	0.000
126	A	218	LYS	1	0.918	0.950	20.783	-0.147	-0.147	0.000	0.000	0.000	0.000
127	A	219	GLN	0	-0.017	-0.011	23.706	-0.021	-0.021	0.000	0.000	0.000	0.000
128	A	220	LEU	0	-0.039	-0.028	24.675	-0.010	-0.010	0.000	0.000	0.000	0.000
129	A	221	GLU	-1	-0.887	-0.965	26.420	0.115	0.115	0.000	0.000	0.000	0.000
130	A	222	ASP	-1	-0.834	-0.898	22.311	0.117	0.117	0.000	0.000	0.000	0.000
131	A	223	LYS	1	0.903	0.942	25.663	-0.112	-0.112	0.000	0.000	0.000	0.000
132	A	224	ILE	0	-0.021	-0.002	28.498	-0.006	-0.006	0.000	0.000	0.000	0.000
133	A	225	GLU	-1	-0.818	-0.882	27.076	0.040	0.040	0.000	0.000	0.000	0.000
134	A	226	GLU	-1	-1.001	-1.002	26.610	0.062	0.062	0.000	0.000	0.000	0.000
135	A	227	LEU	0	-0.061	-0.027	29.836	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	228	LEU	0	-0.006	-0.005	32.222	-0.005	-0.005	0.000	0.000	0.000	0.000
137	A	229	SER	0	-0.002	-0.019	30.233	-0.005	-0.005	0.000	0.000	0.000	0.000
138	A	230	LYS	1	0.877	0.936	31.429	-0.033	-0.033	0.000	0.000	0.000	0.000
139	A	231	ILE	0	0.026	0.012	34.712	-0.003	-0.003	0.000	0.000	0.000	0.000
140	A	232	TYR	0	0.043	0.033	35.388	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	233	HIS	0	-0.083	-0.038	34.854	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	234	LEU	0	-0.002	-0.011	37.279	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	235	GLU	-1	-0.900	-0.954	40.472	0.023	0.023	0.000	0.000	0.000	0.000
144	A	236	ASN	0	-0.056	-0.032	39.028	-0.004	-0.004	0.000	0.000	0.000	0.000
145	A	237	GLU	-1	-0.872	-0.927	39.079	0.010	0.010	0.000	0.000	0.000	0.000
146	A	238	ILE	0	-0.038	-0.008	42.762	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	239	ALA	0	-0.007	0.002	45.191	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	240	ARG	1	0.799	0.892	42.674	-0.009	-0.009	0.000	0.000	0.000	0.000
149	A	241	LEU	0	-0.024	-0.004	46.878	-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)