FMO DATABASE

FMODB ID: KG3L3

Calculation Name: 1WVT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WVT

Chain ID: A

ChEMBL ID:

UniProt ID: Q96YJ2

Base Structure: X-ray

Registration Date: 2023-09-21

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	148
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1383879.638769
FMO2-HF: Nuclear repulsion	1326622.677044
FMO2-HF: Total energy	-57256.961725
FMO2-MP2: Total energy	-57427.342929

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:22:LYS)

Summations of interaction energy for fragment #1(A:22:LYS)

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.
-22.394	-20.531	4.406	-2.61	-3.658	-0.005

Interaction energy analysis for fragmet #1(A:22:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.965 / q_NPA : 0.973

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	24	SER	0	-0.048	-0.054	3.770	1.465	3.009	0.003	-0.577	-0.969	0.005
4	A	25	GLU	-1	-0.842	-0.917	5.330	-20.633	-20.509	-0.001	-0.004	-0.118	0.000
5	A	26	ILE	0	0.036	0.006	4.171	1.115	1.310	-0.001	-0.024	-0.171	0.000
6	A	27	VAL	0	-0.030	-0.011	2.127	-0.508	-0.562	4.406	-1.988	-2.364	-0.010
7	A	28	LYS	1	0.897	0.955	4.793	21.367	21.421	-0.001	-0.017	-0.036	0.000
8	A	29	ALA	0	0.015	0.001	8.162	1.589	1.589	0.000	0.000	0.000	0.000
9	A	30	LEU	0	-0.013	-0.009	5.669	1.073	1.073	0.000	0.000	0.000	0.000
10	A	31	GLY	0	0.013	0.021	8.885	0.440	0.440	0.000	0.000	0.000	0.000
11	A	32	ASP	-1	-0.808	-0.882	10.264	-18.440	-18.440	0.000	0.000	0.000	0.000
12	A	33	LEU	0	-0.020	-0.013	11.846	1.567	1.567	0.000	0.000	0.000	0.000
13	A	34	ASP	-1	-0.899	-0.934	11.227	-22.099	-22.099	0.000	0.000	0.000	0.000
14	A	35	GLU	-1	-0.790	-0.861	13.342	-17.511	-17.511	0.000	0.000	0.000	0.000
15	A	36	LEU	0	-0.036	-0.017	15.828	1.308	1.308	0.000	0.000	0.000	0.000
16	A	37	ASN	0	0.050	0.003	16.320	1.686	1.686	0.000	0.000	0.000	0.000
17	A	38	SER	0	0.003	0.008	16.005	0.829	0.829	0.000	0.000	0.000	0.000
18	A	39	VAL	0	-0.037	-0.020	18.727	0.879	0.879	0.000	0.000	0.000	0.000
19	A	40	LEU	0	-0.013	-0.006	21.011	0.802	0.802	0.000	0.000	0.000	0.000
20	A	41	GLY	0	0.050	0.030	21.743	0.605	0.605	0.000	0.000	0.000	0.000
21	A	42	VAL	0	-0.026	-0.004	22.721	0.575	0.575	0.000	0.000	0.000	0.000
22	A	43	VAL	0	-0.010	-0.013	25.053	0.566	0.566	0.000	0.000	0.000	0.000
23	A	44	SER	0	0.016	0.015	26.171	0.563	0.563	0.000	0.000	0.000	0.000
24	A	45	SER	0	-0.064	-0.037	26.172	0.288	0.288	0.000	0.000	0.000	0.000
25	A	46	LEU	0	-0.059	-0.025	28.800	0.400	0.400	0.000	0.000	0.000	0.000
26	A	47	TYR	0	-0.082	-0.074	30.930	0.368	0.368	0.000	0.000	0.000	0.000
27	A	48	PRO	0	0.075	0.034	31.771	-0.074	-0.074	0.000	0.000	0.000	0.000
28	A	49	GLU	-1	-0.909	-0.914	32.823	-8.249	-8.249	0.000	0.000	0.000	0.000
29	A	50	LEU	0	-0.024	-0.018	31.395	0.081	0.081	0.000	0.000	0.000	0.000
30	A	51	SER	0	0.011	-0.003	28.989	-0.203	-0.203	0.000	0.000	0.000	0.000
31	A	52	GLU	-1	-0.872	-0.909	28.438	-9.659	-9.659	0.000	0.000	0.000	0.000
32	A	53	VAL	0	-0.017	-0.017	29.196	-0.223	-0.223	0.000	0.000	0.000	0.000
33	A	54	ILE	0	0.000	-0.010	25.115	-0.342	-0.342	0.000	0.000	0.000	0.000
34	A	55	GLN	0	0.037	0.009	24.353	-0.244	-0.244	0.000	0.000	0.000	0.000
35	A	56	LYS	1	0.872	0.939	23.889	9.413	9.413	0.000	0.000	0.000	0.000
36	A	57	LEU	0	-0.002	0.006	24.096	-0.327	-0.327	0.000	0.000	0.000	0.000
37	A	58	GLN	0	-0.010	-0.012	20.394	-0.166	-0.166	0.000	0.000	0.000	0.000
38	A	59	ASN	0	-0.042	-0.021	19.435	-0.410	-0.410	0.000	0.000	0.000	0.000
39	A	60	ASP	-1	-0.739	-0.831	19.919	-13.094	-13.094	0.000	0.000	0.000	0.000
40	A	61	ILE	0	-0.047	-0.019	16.386	-0.536	-0.536	0.000	0.000	0.000	0.000
41	A	62	PHE	0	-0.008	-0.002	13.702	-1.141	-1.141	0.000	0.000	0.000	0.000
42	A	63	SER	0	-0.002	-0.015	15.126	-0.804	-0.804	0.000	0.000	0.000	0.000
43	A	64	ILE	0	-0.024	-0.006	14.420	-0.543	-0.543	0.000	0.000	0.000	0.000
44	A	65	SER	0	-0.017	-0.015	11.590	-1.258	-1.258	0.000	0.000	0.000	0.000
45	A	66	SER	0	0.037	0.012	10.573	-1.767	-1.767	0.000	0.000	0.000	0.000
46	A	67	GLU	-1	-0.800	-0.880	10.970	-16.254	-16.254	0.000	0.000	0.000	0.000
47	A	68	ILE	0	-0.041	-0.014	8.064	-0.520	-0.520	0.000	0.000	0.000	0.000
48	A	69	ALA	0	-0.076	-0.028	6.591	-1.717	-1.717	0.000	0.000	0.000	0.000
49	A	70	GLY	0	-0.022	-0.015	7.548	-1.407	-1.407	0.000	0.000	0.000	0.000
50	A	71	PHE	0	-0.068	-0.026	9.369	1.286	1.286	0.000	0.000	0.000	0.000
51	A	72	ASP	-1	-0.802	-0.896	12.599	-16.081	-16.081	0.000	0.000	0.000	0.000
52	A	73	MET	0	-0.064	-0.047	15.108	0.020	0.020	0.000	0.000	0.000	0.000
53	A	74	ASN	0	-0.056	-0.014	18.332	0.320	0.320	0.000	0.000	0.000	0.000
54	A	75	PHE	0	-0.001	0.015	18.605	0.510	0.510	0.000	0.000	0.000	0.000
55	A	76	SER	0	0.062	0.026	20.499	-0.075	-0.075	0.000	0.000	0.000	0.000
56	A	77	ASP	-1	-0.883	-0.955	23.703	-11.402	-11.402	0.000	0.000	0.000	0.000
57	A	78	GLU	-1	-0.954	-0.986	25.321	-9.761	-9.761	0.000	0.000	0.000	0.000
58	A	79	LYS	1	0.859	0.911	22.810	12.344	12.344	0.000	0.000	0.000	0.000
59	A	80	VAL	0	0.003	-0.002	24.027	0.065	0.065	0.000	0.000	0.000	0.000
60	A	81	LYS	1	0.862	0.919	26.306	9.381	9.381	0.000	0.000	0.000	0.000
61	A	82	GLY	0	0.062	0.038	28.826	0.265	0.265	0.000	0.000	0.000	0.000
62	A	83	ILE	0	-0.021	-0.009	25.660	0.212	0.212	0.000	0.000	0.000	0.000
63	A	84	GLU	-1	-0.811	-0.892	29.051	-9.226	-9.226	0.000	0.000	0.000	0.000
64	A	85	GLU	-1	-0.934	-0.951	31.571	-8.217	-8.217	0.000	0.000	0.000	0.000
65	A	86	LEU	0	-0.003	-0.004	29.825	0.254	0.254	0.000	0.000	0.000	0.000
66	A	87	ILE	0	-0.032	-0.021	29.565	0.204	0.204	0.000	0.000	0.000	0.000
67	A	88	THR	0	-0.039	-0.017	33.619	0.293	0.293	0.000	0.000	0.000	0.000
68	A	89	ASN	0	0.001	-0.013	36.895	0.450	0.450	0.000	0.000	0.000	0.000
69	A	90	TYR	0	0.042	0.023	34.105	0.155	0.155	0.000	0.000	0.000	0.000
70	A	91	SER	0	-0.013	-0.027	36.588	0.099	0.099	0.000	0.000	0.000	0.000
71	A	92	LYS	1	0.848	0.940	38.835	7.597	7.597	0.000	0.000	0.000	0.000
72	A	93	GLU	-1	-0.784	-0.852	39.750	-7.727	-7.727	0.000	0.000	0.000	0.000
73	A	94	LEU	0	-0.099	-0.049	37.577	0.102	0.102	0.000	0.000	0.000	0.000
74	A	95	GLU	-1	-0.865	-0.916	42.212	-6.568	-6.568	0.000	0.000	0.000	0.000
75	A	96	PRO	0	-0.004	-0.006	42.854	-0.170	-0.170	0.000	0.000	0.000	0.000
76	A	97	LEU	0	-0.009	0.006	38.338	0.075	0.075	0.000	0.000	0.000	0.000
77	A	98	ARG	1	0.932	0.950	42.358	6.541	6.541	0.000	0.000	0.000	0.000
78	A	99	ASN	0	0.011	0.001	41.817	0.127	0.127	0.000	0.000	0.000	0.000
79	A	100	PHE	0	0.032	0.025	36.344	-0.135	-0.135	0.000	0.000	0.000	0.000
80	A	101	VAL	0	-0.004	-0.009	35.667	0.113	0.113	0.000	0.000	0.000	0.000
81	A	102	LEU	0	-0.047	-0.027	34.691	-0.226	-0.226	0.000	0.000	0.000	0.000
82	A	103	PRO	0	-0.015	-0.018	30.986	0.105	0.105	0.000	0.000	0.000	0.000
83	A	104	GLY	0	0.041	0.015	33.534	0.094	0.094	0.000	0.000	0.000	0.000
84	A	105	GLY	0	-0.009	0.016	35.974	-0.020	-0.020	0.000	0.000	0.000	0.000
85	A	106	HIS	0	0.090	0.046	35.075	-0.235	-0.235	0.000	0.000	0.000	0.000
86	A	107	ILE	0	0.020	-0.002	31.593	-0.205	-0.205	0.000	0.000	0.000	0.000
87	A	108	ALA	0	0.054	0.018	31.025	-0.342	-0.342	0.000	0.000	0.000	0.000
88	A	109	SER	0	-0.015	-0.005	30.895	-0.349	-0.349	0.000	0.000	0.000	0.000
89	A	110	SER	0	-0.026	-0.022	31.608	-0.167	-0.167	0.000	0.000	0.000	0.000
90	A	111	PHE	0	0.041	0.004	25.384	-0.316	-0.316	0.000	0.000	0.000	0.000
91	A	112	LEU	0	0.009	0.024	26.693	-0.509	-0.509	0.000	0.000	0.000	0.000
92	A	113	HIS	0	-0.009	-0.014	27.427	-0.496	-0.496	0.000	0.000	0.000	0.000
93	A	114	LEU	0	-0.024	0.001	22.956	-0.213	-0.213	0.000	0.000	0.000	0.000
94	A	115	ALA	0	0.073	0.034	23.071	-0.563	-0.563	0.000	0.000	0.000	0.000
95	A	116	ARG	1	0.911	0.948	22.659	9.959	9.959	0.000	0.000	0.000	0.000
96	A	117	ALA	0	-0.032	-0.016	23.476	-0.205	-0.205	0.000	0.000	0.000	0.000
97	A	118	VAL	0	0.001	0.001	18.073	-0.328	-0.328	0.000	0.000	0.000	0.000
98	A	119	CYS	0	0.002	0.013	18.653	-0.669	-0.669	0.000	0.000	0.000	0.000
99	A	120	ARG	1	0.914	0.952	19.468	11.407	11.407	0.000	0.000	0.000	0.000
100	A	121	ARG	1	0.673	0.791	15.099	17.995	17.995	0.000	0.000	0.000	0.000
101	A	122	ALA	0	0.069	0.023	14.940	-0.557	-0.557	0.000	0.000	0.000	0.000
102	A	123	GLU	-1	-0.876	-0.943	15.351	-12.844	-12.844	0.000	0.000	0.000	0.000
103	A	124	ARG	1	0.911	0.958	17.207	14.174	14.174	0.000	0.000	0.000	0.000
104	A	125	SER	0	-0.024	-0.022	11.544	0.138	0.138	0.000	0.000	0.000	0.000
105	A	126	VAL	0	0.056	0.033	12.572	-0.676	-0.676	0.000	0.000	0.000	0.000
106	A	127	VAL	0	-0.008	-0.008	14.049	0.200	0.200	0.000	0.000	0.000	0.000
107	A	128	THR	0	-0.077	-0.042	13.059	0.509	0.509	0.000	0.000	0.000	0.000
108	A	129	LEU	0	-0.002	-0.001	8.533	-0.169	-0.169	0.000	0.000	0.000	0.000
109	A	130	LEU	0	-0.007	0.027	12.279	0.118	0.118	0.000	0.000	0.000	0.000
110	A	131	LYS	1	0.955	0.980	15.330	13.509	13.509	0.000	0.000	0.000	0.000
111	A	132	GLU	-1	-0.954	-0.987	12.269	-17.073	-17.073	0.000	0.000	0.000	0.000
112	A	133	SER	0	-0.076	-0.030	12.944	-0.118	-0.118	0.000	0.000	0.000	0.000
113	A	134	LYS	1	0.818	0.887	8.030	22.979	22.979	0.000	0.000	0.000	0.000
114	A	135	ALA	0	-0.012	-0.013	9.995	-1.188	-1.188	0.000	0.000	0.000	0.000
115	A	136	LYS	1	0.845	0.912	12.763	16.720	16.720	0.000	0.000	0.000	0.000
116	A	137	GLU	-1	-0.915	-0.964	16.311	-11.896	-11.896	0.000	0.000	0.000	0.000
117	A	138	VAL	0	0.017	0.006	19.077	0.199	0.199	0.000	0.000	0.000	0.000
118	A	139	HIS	0	-0.025	-0.029	13.579	-0.113	-0.113	0.000	0.000	0.000	0.000
119	A	140	ALA	0	0.034	0.011	17.843	0.090	0.090	0.000	0.000	0.000	0.000
120	A	141	LYN	0	0.029	0.035	19.117	0.366	0.366	0.000	0.000	0.000	0.000
121	A	142	TYR	0	-0.002	-0.041	20.578	0.331	0.331	0.000	0.000	0.000	0.000
122	A	143	LEU	0	0.024	0.009	16.345	0.346	0.346	0.000	0.000	0.000	0.000
123	A	144	ASN	0	-0.037	-0.009	21.030	0.672	0.672	0.000	0.000	0.000	0.000
124	A	145	ARG	1	0.859	0.901	23.776	10.491	10.491	0.000	0.000	0.000	0.000
125	A	146	LEU	0	0.042	0.031	21.399	0.368	0.368	0.000	0.000	0.000	0.000
126	A	147	SER	0	-0.022	-0.013	23.731	0.388	0.388	0.000	0.000	0.000	0.000
127	A	148	SER	0	-0.046	-0.020	25.425	0.394	0.394	0.000	0.000	0.000	0.000
128	A	149	LEU	0	0.043	0.026	28.001	0.349	0.349	0.000	0.000	0.000	0.000
129	A	150	LEU	0	-0.003	-0.004	24.084	0.263	0.263	0.000	0.000	0.000	0.000
130	A	151	PHE	0	-0.024	-0.009	28.625	0.192	0.192	0.000	0.000	0.000	0.000
131	A	152	VAL	0	0.013	0.007	31.123	0.253	0.253	0.000	0.000	0.000	0.000
132	A	153	LEU	0	0.050	0.020	29.710	0.234	0.234	0.000	0.000	0.000	0.000
133	A	154	ALA	0	-0.004	0.008	31.579	0.168	0.168	0.000	0.000	0.000	0.000
134	A	155	LEU	0	-0.045	-0.010	33.424	0.254	0.254	0.000	0.000	0.000	0.000
135	A	156	VAL	0	0.002	0.008	36.116	0.244	0.244	0.000	0.000	0.000	0.000
136	A	157	VAL	0	0.006	0.014	33.599	0.211	0.211	0.000	0.000	0.000	0.000
137	A	158	ASN	0	-0.003	-0.014	36.893	0.154	0.154	0.000	0.000	0.000	0.000
138	A	159	LYS	1	0.841	0.925	39.141	7.224	7.224	0.000	0.000	0.000	0.000
139	A	160	ARG	1	0.844	0.887	37.913	8.273	8.273	0.000	0.000	0.000	0.000
140	A	161	THR	0	-0.056	-0.028	38.696	0.129	0.129	0.000	0.000	0.000	0.000
141	A	162	ASN	0	-0.060	-0.022	41.849	0.158	0.158	0.000	0.000	0.000	0.000
142	A	163	ASN	0	-0.021	-0.014	40.407	0.084	0.084	0.000	0.000	0.000	0.000
143	A	164	PRO	0	-0.002	-0.006	41.718	-0.093	-0.093	0.000	0.000	0.000	0.000
144	A	165	ASN	0	0.034	0.022	38.680	-0.349	-0.349	0.000	0.000	0.000	0.000
145	A	166	VAL	0	0.045	0.035	38.107	0.197	0.197	0.000	0.000	0.000	0.000
146	A	167	ILE	0	-0.011	-0.001	38.833	-0.177	-0.177	0.000	0.000	0.000	0.000
147	A	168	TRP	0	-0.001	-0.012	38.034	0.132	0.132	0.000	0.000	0.000	0.000
148	A	169	ARG	1	0.946	0.990	40.379	7.730	7.730	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:22:LYS)