FMO DATABASE

FMODB ID: 4J3VN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1387233.492835
FMO2-HF: Nuclear repulsion	1329976.201463
FMO2-HF: Total energy	-57257.291372
FMO2-MP2: Total energy	-57427.562718

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.
-23.184	-20.706	2.199	-1.523	-3.153	-0.003

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 : 0.984 / q_NPA : 0.983

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	0.021	-0.003	3.842	-1.672	-0.115	-0.003	-0.664	-0.890	0.003
4	A	25	GLU	-1	-0.897	-0.939	5.635	-20.077	-20.077	0.000	0.000	0.000	0.000
5	A	26	ILE	0	0.031	0.017	4.371	0.689	0.835	-0.001	-0.011	-0.133	0.000
6	A	27	VAL	0	-0.020	-0.019	2.436	-1.101	-0.366	2.204	-0.844	-2.096	-0.006
7	A	28	LYS	1	0.859	0.941	5.183	21.831	21.871	-0.001	-0.004	-0.034	0.000
8	A	29	ALA	0	0.014	0.000	8.657	1.634	1.634	0.000	0.000	0.000	0.000
9	A	30	LEU	0	-0.012	-0.002	5.577	1.063	1.063	0.000	0.000	0.000	0.000
10	A	31	GLY	0	0.028	0.020	9.149	0.935	0.935	0.000	0.000	0.000	0.000
11	A	32	ASP	-1	-0.790	-0.873	10.625	-18.595	-18.595	0.000	0.000	0.000	0.000
12	A	33	LEU	0	-0.024	-0.016	11.919	1.721	1.721	0.000	0.000	0.000	0.000
13	A	34	ASP	-1	-0.898	-0.934	11.591	-22.264	-22.264	0.000	0.000	0.000	0.000
14	A	35	GLU	-1	-0.797	-0.864	13.710	-17.568	-17.568	0.000	0.000	0.000	0.000
15	A	36	LEU	0	-0.041	-0.015	16.225	1.250	1.250	0.000	0.000	0.000	0.000
16	A	37	ASN	0	0.051	0.006	16.302	1.697	1.697	0.000	0.000	0.000	0.000
17	A	38	SER	0	0.003	0.006	16.223	0.834	0.834	0.000	0.000	0.000	0.000
18	A	39	VAL	0	-0.040	-0.025	18.908	0.874	0.874	0.000	0.000	0.000	0.000
19	A	40	LEU	0	-0.018	-0.007	21.125	0.810	0.810	0.000	0.000	0.000	0.000
20	A	41	GLY	0	0.048	0.029	21.924	0.606	0.606	0.000	0.000	0.000	0.000
21	A	42	VAL	0	-0.029	-0.002	23.067	0.565	0.565	0.000	0.000	0.000	0.000
22	A	43	VAL	0	-0.001	-0.009	25.478	0.535	0.535	0.000	0.000	0.000	0.000
23	A	44	SER	0	0.032	0.018	26.377	0.520	0.520	0.000	0.000	0.000	0.000
24	A	45	SER	0	-0.075	-0.040	26.405	0.283	0.283	0.000	0.000	0.000	0.000
25	A	46	LEU	0	-0.063	-0.026	29.040	0.350	0.350	0.000	0.000	0.000	0.000
26	A	47	TYR	0	-0.061	-0.076	31.434	0.334	0.334	0.000	0.000	0.000	0.000
27	A	48	PRO	0	0.079	0.042	31.863	-0.093	-0.093	0.000	0.000	0.000	0.000
28	A	49	GLU	-1	-0.895	-0.910	32.918	-8.201	-8.201	0.000	0.000	0.000	0.000
29	A	50	LEU	0	-0.005	-0.001	31.416	0.081	0.081	0.000	0.000	0.000	0.000
30	A	51	SER	0	-0.009	-0.009	29.127	-0.200	-0.200	0.000	0.000	0.000	0.000
31	A	52	GLU	-1	-0.839	-0.900	28.697	-9.662	-9.662	0.000	0.000	0.000	0.000
32	A	53	VAL	0	-0.034	-0.005	29.471	-0.039	-0.039	0.000	0.000	0.000	0.000
33	A	54	ILE	0	0.004	-0.014	25.209	-0.346	-0.346	0.000	0.000	0.000	0.000
34	A	55	GLN	0	0.046	0.014	24.402	-0.194	-0.194	0.000	0.000	0.000	0.000
35	A	56	LYS	1	0.824	0.902	23.851	9.569	9.569	0.000	0.000	0.000	0.000
36	A	57	LEU	0	-0.002	0.002	23.976	-0.359	-0.359	0.000	0.000	0.000	0.000
37	A	58	GLN	0	-0.005	-0.013	20.419	-0.135	-0.135	0.000	0.000	0.000	0.000
38	A	59	ASN	0	-0.035	-0.017	19.356	-0.405	-0.405	0.000	0.000	0.000	0.000
39	A	60	ASP	-1	-0.748	-0.820	19.788	-13.094	-13.094	0.000	0.000	0.000	0.000
40	A	61	ILE	0	-0.027	-0.013	16.621	-0.492	-0.492	0.000	0.000	0.000	0.000
41	A	62	PHE	0	-0.017	-0.007	13.565	-1.140	-1.140	0.000	0.000	0.000	0.000
42	A	63	SER	0	-0.003	-0.027	15.024	-0.818	-0.818	0.000	0.000	0.000	0.000
43	A	64	ILE	0	-0.031	-0.012	14.494	-0.412	-0.412	0.000	0.000	0.000	0.000
44	A	65	SER	0	-0.013	-0.011	11.402	-1.311	-1.311	0.000	0.000	0.000	0.000
45	A	66	SER	0	-0.007	-0.016	10.833	-1.846	-1.846	0.000	0.000	0.000	0.000
46	A	67	GLU	-1	-0.781	-0.884	11.842	-15.967	-15.967	0.000	0.000	0.000	0.000
47	A	68	ILE	0	-0.043	-0.016	8.404	-0.417	-0.417	0.000	0.000	0.000	0.000
48	A	69	ALA	0	-0.071	-0.025	7.284	-1.821	-1.821	0.000	0.000	0.000	0.000
49	A	70	GLY	0	-0.008	-0.002	8.212	-1.117	-1.117	0.000	0.000	0.000	0.000
50	A	71	PHE	0	-0.074	-0.028	9.410	1.194	1.194	0.000	0.000	0.000	0.000
51	A	72	ASP	-1	-0.771	-0.872	13.037	-16.364	-16.364	0.000	0.000	0.000	0.000
52	A	73	MET	0	-0.071	-0.041	15.690	0.054	0.054	0.000	0.000	0.000	0.000
53	A	74	ASN	0	-0.046	-0.009	19.112	0.352	0.352	0.000	0.000	0.000	0.000
54	A	75	PHE	0	-0.015	-0.012	19.148	0.534	0.534	0.000	0.000	0.000	0.000
55	A	76	SER	0	0.025	-0.002	21.136	-0.065	-0.065	0.000	0.000	0.000	0.000
56	A	77	ASP	-1	-0.873	-0.959	24.617	-11.322	-11.322	0.000	0.000	0.000	0.000
57	A	78	GLU	-1	-0.912	-0.936	26.132	-9.941	-9.941	0.000	0.000	0.000	0.000
58	A	79	LYS	1	0.866	0.927	23.349	12.387	12.387	0.000	0.000	0.000	0.000
59	A	80	VAL	0	0.015	-0.001	24.320	0.074	0.074	0.000	0.000	0.000	0.000
60	A	81	LYS	1	0.856	0.913	26.638	9.411	9.411	0.000	0.000	0.000	0.000
61	A	82	GLY	0	0.072	0.048	29.444	0.282	0.282	0.000	0.000	0.000	0.000
62	A	83	ILE	0	-0.030	-0.013	25.704	0.213	0.213	0.000	0.000	0.000	0.000
63	A	84	GLU	-1	-0.773	-0.873	29.148	-9.260	-9.260	0.000	0.000	0.000	0.000
64	A	85	GLU	-1	-0.923	-0.945	31.732	-8.161	-8.161	0.000	0.000	0.000	0.000
65	A	86	LEU	0	0.007	-0.002	29.890	0.234	0.234	0.000	0.000	0.000	0.000
66	A	87	ILE	0	-0.014	-0.005	29.732	0.190	0.190	0.000	0.000	0.000	0.000
67	A	88	THR	0	-0.034	-0.014	33.784	0.297	0.297	0.000	0.000	0.000	0.000
68	A	89	ASN	0	-0.021	-0.009	36.601	0.498	0.498	0.000	0.000	0.000	0.000
69	A	90	TYR	0	0.039	0.012	34.547	0.176	0.176	0.000	0.000	0.000	0.000
70	A	91	SER	0	-0.019	-0.039	36.701	0.096	0.096	0.000	0.000	0.000	0.000
71	A	92	LYS	1	0.826	0.920	38.902	7.666	7.666	0.000	0.000	0.000	0.000
72	A	93	GLU	-1	-0.777	-0.846	39.645	-7.761	-7.761	0.000	0.000	0.000	0.000
73	A	94	LEU	0	-0.075	-0.034	37.881	0.092	0.092	0.000	0.000	0.000	0.000
74	A	95	GLU	-1	-0.864	-0.924	42.567	-6.547	-6.547	0.000	0.000	0.000	0.000
75	A	96	PRO	0	-0.011	-0.025	43.300	-0.180	-0.180	0.000	0.000	0.000	0.000
76	A	97	LEU	0	-0.013	0.015	38.703	0.112	0.112	0.000	0.000	0.000	0.000
77	A	98	ARG	1	0.930	0.954	42.749	6.547	6.547	0.000	0.000	0.000	0.000
78	A	99	ASN	0	0.013	0.006	42.310	0.128	0.128	0.000	0.000	0.000	0.000
79	A	100	PHE	0	0.024	0.009	37.080	-0.136	-0.136	0.000	0.000	0.000	0.000
80	A	101	VAL	0	0.012	0.008	36.123	0.063	0.063	0.000	0.000	0.000	0.000
81	A	102	LEU	0	-0.058	-0.025	35.084	-0.220	-0.220	0.000	0.000	0.000	0.000
82	A	103	PRO	0	-0.021	-0.024	31.362	0.090	0.090	0.000	0.000	0.000	0.000
83	A	104	GLY	0	0.034	0.020	33.744	0.070	0.070	0.000	0.000	0.000	0.000
84	A	105	GLY	0	-0.003	0.021	36.266	0.013	0.013	0.000	0.000	0.000	0.000
85	A	106	HIS	0	0.070	0.036	35.168	-0.202	-0.202	0.000	0.000	0.000	0.000
86	A	107	ILE	0	0.029	0.012	31.910	-0.225	-0.225	0.000	0.000	0.000	0.000
87	A	108	ALA	0	0.049	0.017	31.107	-0.353	-0.353	0.000	0.000	0.000	0.000
88	A	109	SER	0	-0.009	-0.002	31.052	-0.361	-0.361	0.000	0.000	0.000	0.000
89	A	110	SER	0	-0.034	-0.029	31.862	-0.167	-0.167	0.000	0.000	0.000	0.000
90	A	111	PHE	0	0.034	-0.001	25.870	-0.318	-0.318	0.000	0.000	0.000	0.000
91	A	112	LEU	0	0.005	0.021	26.974	-0.519	-0.519	0.000	0.000	0.000	0.000
92	A	113	HIS	0	0.021	0.000	27.822	-0.467	-0.467	0.000	0.000	0.000	0.000
93	A	114	LEU	0	-0.034	-0.003	23.525	-0.240	-0.240	0.000	0.000	0.000	0.000
94	A	115	ALA	0	0.050	0.017	23.294	-0.547	-0.547	0.000	0.000	0.000	0.000
95	A	116	ARG	1	0.898	0.941	23.090	9.910	9.910	0.000	0.000	0.000	0.000
96	A	117	ALA	0	-0.032	-0.017	23.999	-0.184	-0.184	0.000	0.000	0.000	0.000
97	A	118	VAL	0	-0.003	0.000	18.408	-0.290	-0.290	0.000	0.000	0.000	0.000
98	A	119	CYS	0	0.010	0.019	19.121	-0.645	-0.645	0.000	0.000	0.000	0.000
99	A	120	ARG	1	0.897	0.939	19.921	11.477	11.477	0.000	0.000	0.000	0.000
100	A	121	ARG	1	0.669	0.802	15.397	18.294	18.294	0.000	0.000	0.000	0.000
101	A	122	ALA	0	0.073	0.028	15.325	-0.485	-0.485	0.000	0.000	0.000	0.000
102	A	123	GLU	-1	-0.815	-0.897	15.835	-12.638	-12.638	0.000	0.000	0.000	0.000
103	A	124	ARG	1	0.909	0.954	17.803	13.991	13.991	0.000	0.000	0.000	0.000
104	A	125	SER	0	-0.026	-0.021	12.321	0.181	0.181	0.000	0.000	0.000	0.000
105	A	126	VAL	0	0.042	0.018	13.131	-0.525	-0.525	0.000	0.000	0.000	0.000
106	A	127	VAL	0	-0.010	-0.010	14.504	0.270	0.270	0.000	0.000	0.000	0.000
107	A	128	THR	0	-0.074	-0.046	13.426	0.460	0.460	0.000	0.000	0.000	0.000
108	A	129	LEU	0	-0.019	-0.015	8.939	-0.072	-0.072	0.000	0.000	0.000	0.000
109	A	130	LEU	0	0.014	0.029	12.730	0.017	0.017	0.000	0.000	0.000	0.000
110	A	131	LYS	1	0.919	0.960	15.449	13.742	13.742	0.000	0.000	0.000	0.000
111	A	132	GLU	-1	-0.922	-0.979	12.357	-16.619	-16.619	0.000	0.000	0.000	0.000
112	A	133	SER	0	-0.085	-0.030	13.192	-0.098	-0.098	0.000	0.000	0.000	0.000
113	A	134	LYS	1	0.818	0.887	8.658	22.706	22.706	0.000	0.000	0.000	0.000
114	A	135	ALA	0	-0.006	0.007	10.868	-1.081	-1.081	0.000	0.000	0.000	0.000
115	A	136	LYS	1	0.832	0.896	13.575	17.142	17.142	0.000	0.000	0.000	0.000
116	A	137	GLU	-1	-0.905	-0.963	17.277	-11.794	-11.794	0.000	0.000	0.000	0.000
117	A	138	VAL	0	0.015	0.008	19.961	0.030	0.030	0.000	0.000	0.000	0.000
118	A	139	HIS	0	-0.006	-0.015	14.616	-0.214	-0.214	0.000	0.000	0.000	0.000
119	A	140	ALA	0	0.033	0.016	18.328	0.025	0.025	0.000	0.000	0.000	0.000
120	A	141	LYN	0	-0.005	0.002	19.396	0.326	0.326	0.000	0.000	0.000	0.000
121	A	142	TYR	0	-0.006	-0.038	20.813	0.358	0.358	0.000	0.000	0.000	0.000
122	A	143	LEU	0	0.014	0.007	16.521	0.289	0.289	0.000	0.000	0.000	0.000
123	A	144	ASN	0	-0.047	-0.021	21.152	0.661	0.661	0.000	0.000	0.000	0.000
124	A	145	ARG	1	0.860	0.917	23.996	10.499	10.499	0.000	0.000	0.000	0.000
125	A	146	LEU	0	0.051	0.032	21.522	0.377	0.377	0.000	0.000	0.000	0.000
126	A	147	SER	0	-0.031	-0.027	23.890	0.378	0.378	0.000	0.000	0.000	0.000
127	A	148	SER	0	-0.049	-0.012	25.573	0.406	0.406	0.000	0.000	0.000	0.000
128	A	149	LEU	0	0.037	0.011	28.140	0.324	0.324	0.000	0.000	0.000	0.000
129	A	150	LEU	0	-0.006	-0.006	24.397	0.275	0.275	0.000	0.000	0.000	0.000
130	A	151	PHE	0	-0.016	-0.009	28.969	0.184	0.184	0.000	0.000	0.000	0.000
131	A	152	VAL	0	0.001	0.008	31.604	0.247	0.247	0.000	0.000	0.000	0.000
132	A	153	LEU	0	0.044	0.016	29.900	0.230	0.230	0.000	0.000	0.000	0.000
133	A	154	ALA	0	0.007	0.011	31.991	0.174	0.174	0.000	0.000	0.000	0.000
134	A	155	LEU	0	-0.037	-0.006	33.843	0.250	0.250	0.000	0.000	0.000	0.000
135	A	156	VAL	0	0.002	0.008	36.552	0.236	0.236	0.000	0.000	0.000	0.000
136	A	157	VAL	0	0.006	0.009	33.809	0.198	0.198	0.000	0.000	0.000	0.000
137	A	158	ASN	0	-0.022	-0.010	37.150	0.126	0.126	0.000	0.000	0.000	0.000
138	A	159	LYS	1	0.853	0.928	39.379	7.190	7.190	0.000	0.000	0.000	0.000
139	A	160	ARG	1	0.822	0.880	37.828	8.322	8.322	0.000	0.000	0.000	0.000
140	A	161	THR	0	-0.062	-0.044	38.708	0.145	0.145	0.000	0.000	0.000	0.000
141	A	162	ASN	0	-0.043	-0.019	41.904	0.181	0.181	0.000	0.000	0.000	0.000
142	A	163	ASN	0	-0.016	-0.004	40.547	0.094	0.094	0.000	0.000	0.000	0.000
143	A	164	PRO	0	-0.008	-0.013	42.093	-0.079	-0.079	0.000	0.000	0.000	0.000
144	A	165	ASN	0	0.026	0.018	39.128	-0.365	-0.365	0.000	0.000	0.000	0.000
145	A	166	VAL	0	0.043	0.033	38.479	0.198	0.198	0.000	0.000	0.000	0.000
146	A	167	ILE	0	-0.003	-0.004	39.375	-0.160	-0.160	0.000	0.000	0.000	0.000
147	A	168	TRP	0	0.020	0.009	38.266	0.121	0.121	0.000	0.000	0.000	0.000
148	A	169	ARG	1	0.923	0.972	40.454	7.779	7.779	0.000	0.000	0.000	0.000

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