FMO DATABASE

FMODB ID: K9GJ3

Calculation Name: 1WDV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WDV

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y8U3

Base Structure: X-ray

Registration Date: 2023-06-22

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	150
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1346411.922596
FMO2-HF: Nuclear repulsion	1291107.677755
FMO2-HF: Total energy	-55304.24484
FMO2-MP2: Total energy	-55468.86674

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:3:GLU)

Summations of interaction energy for fragment #1(A:3:GLU)

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.
-96.894	-114.862	62.594	-25.518	-19.109	0.045

Interaction energy analysis for fragmet #1(A:3:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.817 / q_NPA : -0.876

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	5	VAL	0	-0.005	0.011	3.004	-7.834	-5.654	0.045	-0.866	-1.360	0.004
4	A	6	GLU	-1	-0.790	-0.904	1.801	18.241	13.049	20.159	-9.066	-5.901	-0.092
5	A	7	GLU	-1	-0.958	-0.983	3.297	40.320	42.204	0.081	-0.972	-0.993	-0.005
6	A	8	TRP	0	0.010	0.002	5.861	-2.369	-2.369	0.000	0.000	0.000	0.000
7	A	9	ILE	0	-0.005	-0.008	7.164	-1.811	-1.811	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.938	0.972	8.461	-22.796	-22.796	0.000	0.000	0.000	0.000
9	A	11	ALA	0	-0.044	-0.024	9.862	-1.280	-1.280	0.000	0.000	0.000	0.000
10	A	12	ARG	1	0.832	0.917	11.823	-18.098	-18.098	0.000	0.000	0.000	0.000
11	A	13	GLY	0	-0.007	0.010	13.436	-0.854	-0.854	0.000	0.000	0.000	0.000
12	A	14	LEU	0	-0.024	0.001	12.697	-0.695	-0.695	0.000	0.000	0.000	0.000
13	A	15	THR	0	-0.018	-0.022	13.320	0.574	0.574	0.000	0.000	0.000	0.000
14	A	16	TRP	0	-0.037	-0.032	10.947	0.259	0.259	0.000	0.000	0.000	0.000
15	A	17	ARG	1	0.860	0.900	10.088	-14.808	-14.808	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.014	0.026	3.958	-0.228	-0.149	-0.001	-0.021	-0.057	0.000
17	A	19	LEU	0	-0.039	-0.008	8.581	-0.891	-0.891	0.000	0.000	0.000	0.000
18	A	20	ILE	0	-0.006	-0.008	7.333	1.259	1.259	0.000	0.000	0.000	0.000
19	A	21	MET	0	0.033	0.032	11.351	-1.409	-1.409	0.000	0.000	0.000	0.000
20	A	22	GLN	0	0.001	-0.013	13.695	0.260	0.260	0.000	0.000	0.000	0.000
21	A	23	LYS	1	0.917	0.953	16.086	-13.562	-13.562	0.000	0.000	0.000	0.000
22	A	24	PRO	0	0.020	0.013	14.456	-0.129	-0.129	0.000	0.000	0.000	0.000
23	A	25	THR	0	0.004	0.008	15.798	-0.767	-0.767	0.000	0.000	0.000	0.000
24	A	26	ARG	1	0.932	0.960	17.997	-13.706	-13.706	0.000	0.000	0.000	0.000
25	A	27	THR	0	-0.048	-0.024	20.651	-0.412	-0.412	0.000	0.000	0.000	0.000
26	A	28	VAL	0	0.029	0.017	20.395	0.359	0.359	0.000	0.000	0.000	0.000
27	A	29	ALA	0	0.064	0.034	21.564	0.078	0.078	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.852	-0.919	21.008	13.965	13.965	0.000	0.000	0.000	0.000
29	A	31	ALA	0	0.022	0.001	17.712	0.004	0.004	0.000	0.000	0.000	0.000
30	A	32	ALA	0	-0.013	-0.009	19.482	0.038	0.038	0.000	0.000	0.000	0.000
31	A	33	ALA	0	-0.002	0.000	21.931	-0.183	-0.183	0.000	0.000	0.000	0.000
32	A	34	LEU	0	-0.058	-0.037	19.681	-0.174	-0.174	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.038	-0.013	15.880	0.342	0.342	0.000	0.000	0.000	0.000
34	A	36	GLY	0	-0.025	0.006	20.146	-0.179	-0.179	0.000	0.000	0.000	0.000
35	A	37	VAL	0	-0.054	-0.016	20.486	-0.314	-0.314	0.000	0.000	0.000	0.000
36	A	38	SER	0	-0.011	-0.022	23.738	-0.186	-0.186	0.000	0.000	0.000	0.000
37	A	39	GLU	-1	-0.822	-0.952	22.990	11.919	11.919	0.000	0.000	0.000	0.000
38	A	40	SER	0	-0.111	-0.050	22.904	0.314	0.314	0.000	0.000	0.000	0.000
39	A	41	GLU	-1	-0.765	-0.857	20.875	11.171	11.171	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.037	-0.003	17.609	0.625	0.625	0.000	0.000	0.000	0.000
41	A	43	VAL	0	-0.031	-0.012	16.238	-0.206	-0.206	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.795	0.888	16.670	-12.163	-12.163	0.000	0.000	0.000	0.000
43	A	45	THR	0	-0.021	-0.022	13.374	-1.419	-1.419	0.000	0.000	0.000	0.000
44	A	46	LEU	0	-0.017	-0.003	16.477	0.656	0.656	0.000	0.000	0.000	0.000
45	A	47	ILE	0	0.043	0.029	14.572	-0.464	-0.464	0.000	0.000	0.000	0.000
46	A	48	VAL	0	-0.030	-0.015	18.580	-0.696	-0.696	0.000	0.000	0.000	0.000
47	A	49	LEU	0	0.003	0.006	20.152	0.497	0.497	0.000	0.000	0.000	0.000
48	A	50	ASP	-1	-0.704	-0.829	23.675	11.519	11.519	0.000	0.000	0.000	0.000
49	A	51	ASN	0	-0.029	-0.031	26.955	0.350	0.350	0.000	0.000	0.000	0.000
50	A	52	ALA	0	-0.033	-0.015	28.405	-0.300	-0.300	0.000	0.000	0.000	0.000
51	A	53	GLY	0	-0.004	0.008	24.684	0.030	0.030	0.000	0.000	0.000	0.000
52	A	54	GLY	0	-0.004	0.014	23.121	0.600	0.600	0.000	0.000	0.000	0.000
53	A	55	VAL	0	-0.018	-0.025	17.802	0.008	0.008	0.000	0.000	0.000	0.000
54	A	56	TYR	0	-0.030	-0.033	20.120	-0.078	-0.078	0.000	0.000	0.000	0.000
55	A	57	ALA	0	0.015	0.004	16.194	0.610	0.610	0.000	0.000	0.000	0.000
56	A	58	VAL	0	0.007	-0.007	18.171	-0.383	-0.383	0.000	0.000	0.000	0.000
57	A	59	VAL	0	0.004	0.006	16.637	0.149	0.149	0.000	0.000	0.000	0.000
58	A	60	ILE	0	-0.016	-0.003	19.315	-0.811	-0.811	0.000	0.000	0.000	0.000
59	A	61	PRO	0	0.052	0.014	20.896	0.564	0.564	0.000	0.000	0.000	0.000
60	A	62	GLY	0	0.084	0.043	21.999	0.038	0.038	0.000	0.000	0.000	0.000
61	A	63	ASP	-1	-0.852	-0.933	22.571	10.547	10.547	0.000	0.000	0.000	0.000
62	A	64	LYS	1	0.833	0.927	25.451	-10.797	-10.797	0.000	0.000	0.000	0.000
63	A	65	ARG	1	0.958	0.974	25.731	-10.146	-10.146	0.000	0.000	0.000	0.000
64	A	66	LEU	0	0.068	0.028	24.112	-0.128	-0.128	0.000	0.000	0.000	0.000
65	A	67	ASN	0	-0.009	-0.005	26.865	-0.203	-0.203	0.000	0.000	0.000	0.000
66	A	68	ILE	0	0.011	-0.012	27.757	0.128	0.128	0.000	0.000	0.000	0.000
67	A	69	ASN	0	-0.040	-0.031	30.096	0.044	0.044	0.000	0.000	0.000	0.000
68	A	70	SER	0	0.045	0.012	30.288	-0.108	-0.108	0.000	0.000	0.000	0.000
69	A	71	MET	0	-0.014	0.002	24.316	0.101	0.101	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.926	0.969	28.593	-8.856	-8.856	0.000	0.000	0.000	0.000
71	A	73	GLU	-1	-0.929	-0.956	31.216	8.667	8.667	0.000	0.000	0.000	0.000
72	A	74	LEU	0	-0.034	-0.015	26.256	-0.063	-0.063	0.000	0.000	0.000	0.000
73	A	75	ALA	0	-0.016	-0.010	27.734	0.077	0.077	0.000	0.000	0.000	0.000
74	A	76	GLY	0	-0.009	0.011	29.275	-0.054	-0.054	0.000	0.000	0.000	0.000
75	A	77	LYS	1	0.813	0.907	27.742	-11.616	-11.616	0.000	0.000	0.000	0.000
76	A	78	PRO	0	-0.036	-0.025	31.931	0.037	0.037	0.000	0.000	0.000	0.000
77	A	79	VAL	0	0.015	0.007	27.080	0.278	0.278	0.000	0.000	0.000	0.000
78	A	80	ARG	1	0.772	0.853	24.121	-13.537	-13.537	0.000	0.000	0.000	0.000
79	A	81	LEU	0	0.052	0.026	22.418	0.365	0.365	0.000	0.000	0.000	0.000
80	A	82	ALA	0	-0.019	0.001	19.618	-0.369	-0.369	0.000	0.000	0.000	0.000
81	A	83	ARG	1	0.868	0.895	21.544	-13.326	-13.326	0.000	0.000	0.000	0.000
82	A	84	ALA	0	0.035	0.002	19.106	0.690	0.690	0.000	0.000	0.000	0.000
83	A	85	ASN	0	-0.011	-0.007	17.653	0.554	0.554	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.674	-0.774	16.782	15.292	15.292	0.000	0.000	0.000	0.000
85	A	87	VAL	0	-0.005	0.003	14.558	0.693	0.693	0.000	0.000	0.000	0.000
86	A	88	VAL	0	0.005	0.024	11.545	1.232	1.232	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.934	-0.965	12.203	19.829	19.829	0.000	0.000	0.000	0.000
88	A	90	LEU	0	-0.014	-0.004	13.931	0.408	0.408	0.000	0.000	0.000	0.000
89	A	91	THR	0	-0.057	-0.054	11.051	0.829	0.829	0.000	0.000	0.000	0.000
90	A	92	GLY	0	0.002	0.008	8.018	2.207	2.207	0.000	0.000	0.000	0.000
91	A	93	TYR	0	-0.056	-0.047	4.154	9.222	9.387	-0.001	-0.012	-0.152	0.000
92	A	94	PRO	0	-0.042	-0.011	8.393	-3.278	-3.278	0.000	0.000	0.000	0.000
93	A	95	VAL	0	0.013	-0.015	11.336	-0.463	-0.463	0.000	0.000	0.000	0.000
94	A	96	GLY	0	0.010	0.008	14.194	-1.185	-1.185	0.000	0.000	0.000	0.000
95	A	97	GLY	0	-0.005	0.000	10.155	-0.531	-0.531	0.000	0.000	0.000	0.000
96	A	98	VAL	0	-0.035	-0.010	9.526	1.825	1.825	0.000	0.000	0.000	0.000
97	A	99	PRO	0	0.011	0.032	7.360	-2.218	-2.218	0.000	0.000	0.000	0.000
98	A	100	PRO	0	-0.002	-0.006	10.022	-0.362	-0.362	0.000	0.000	0.000	0.000
99	A	101	VAL	0	0.007	-0.007	8.692	-1.208	-1.208	0.000	0.000	0.000	0.000
100	A	102	ALA	0	-0.011	-0.012	6.786	1.926	1.926	0.000	0.000	0.000	0.000
101	A	103	LEU	0	0.012	0.034	8.032	3.882	3.882	0.000	0.000	0.000	0.000
102	A	104	PRO	0	0.013	0.008	10.348	-0.633	-0.633	0.000	0.000	0.000	0.000
103	A	105	PRO	0	0.015	0.002	12.206	-1.211	-1.211	0.000	0.000	0.000	0.000
104	A	106	ASN	0	-0.021	-0.006	14.985	-0.273	-0.273	0.000	0.000	0.000	0.000
105	A	107	ILE	0	-0.057	-0.013	14.001	-0.941	-0.941	0.000	0.000	0.000	0.000
106	A	108	VAL	0	0.020	0.007	17.434	0.128	0.128	0.000	0.000	0.000	0.000
107	A	109	LEU	0	-0.011	0.004	15.730	-0.112	-0.112	0.000	0.000	0.000	0.000
108	A	110	VAL	0	-0.020	-0.015	19.010	-0.825	-0.825	0.000	0.000	0.000	0.000
109	A	111	VAL	0	0.002	-0.003	19.404	0.598	0.598	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.788	-0.877	22.049	10.327	10.327	0.000	0.000	0.000	0.000
111	A	113	ARG	1	0.855	0.883	24.619	-9.662	-9.662	0.000	0.000	0.000	0.000
112	A	114	ILE	0	-0.012	0.007	26.157	-0.113	-0.113	0.000	0.000	0.000	0.000
113	A	115	LEU	0	0.016	0.006	20.573	-0.125	-0.125	0.000	0.000	0.000	0.000
114	A	116	LEU	0	0.015	0.014	22.941	0.092	0.092	0.000	0.000	0.000	0.000
115	A	117	SER	0	-0.063	-0.023	25.009	-0.200	-0.200	0.000	0.000	0.000	0.000
116	A	118	ARG	1	0.843	0.925	22.868	-11.027	-11.027	0.000	0.000	0.000	0.000
117	A	119	LYS	1	0.969	0.961	22.474	-9.558	-9.558	0.000	0.000	0.000	0.000
118	A	120	LYS	1	0.843	0.922	17.380	-13.230	-13.230	0.000	0.000	0.000	0.000
119	A	121	VAL	0	-0.017	0.000	16.671	-0.570	-0.570	0.000	0.000	0.000	0.000
120	A	122	TYR	0	-0.019	-0.036	14.462	0.294	0.294	0.000	0.000	0.000	0.000
121	A	123	GLY	0	0.049	0.029	13.332	-0.693	-0.693	0.000	0.000	0.000	0.000
122	A	124	GLY	0	0.015	0.018	11.166	0.474	0.474	0.000	0.000	0.000	0.000
123	A	125	GLY	0	0.028	-0.007	7.453	-0.611	-0.611	0.000	0.000	0.000	0.000
124	A	126	GLY	0	-0.007	-0.003	5.259	3.043	3.043	0.000	0.000	0.000	0.000
125	A	127	ARG	1	0.816	0.839	1.688	-126.074	-143.158	42.311	-14.581	-10.646	0.138
126	A	128	GLU	-1	-0.803	-0.906	8.126	21.399	21.399	0.000	0.000	0.000	0.000
127	A	129	ASN	0	-0.054	-0.026	10.148	0.009	0.009	0.000	0.000	0.000	0.000
128	A	130	ALA	0	-0.014	0.008	7.019	-0.927	-0.927	0.000	0.000	0.000	0.000
129	A	131	LEU	0	0.017	0.004	9.044	0.339	0.339	0.000	0.000	0.000	0.000
130	A	132	LEU	0	0.003	0.005	8.298	-0.280	-0.280	0.000	0.000	0.000	0.000
131	A	133	GLU	-1	-0.734	-0.810	10.221	13.511	13.511	0.000	0.000	0.000	0.000
132	A	134	PHE	0	0.004	-0.014	12.701	0.289	0.289	0.000	0.000	0.000	0.000
133	A	135	SER	0	0.018	-0.004	14.578	-0.767	-0.767	0.000	0.000	0.000	0.000
134	A	136	PRO	0	0.014	-0.003	17.821	0.365	0.365	0.000	0.000	0.000	0.000
135	A	137	ARG	1	0.870	0.922	19.578	-10.394	-10.394	0.000	0.000	0.000	0.000
136	A	138	GLU	-1	-0.749	-0.851	17.533	13.399	13.399	0.000	0.000	0.000	0.000
137	A	139	LEU	0	-0.021	0.002	14.306	0.388	0.388	0.000	0.000	0.000	0.000
138	A	140	VAL	0	-0.018	0.013	17.162	0.301	0.301	0.000	0.000	0.000	0.000
139	A	141	GLU	-1	-0.952	-0.971	20.522	11.771	11.771	0.000	0.000	0.000	0.000
140	A	142	ALA	0	-0.040	-0.009	16.201	0.021	0.021	0.000	0.000	0.000	0.000
141	A	143	THR	0	-0.040	-0.067	15.849	0.606	0.606	0.000	0.000	0.000	0.000
142	A	144	GLY	0	0.027	0.027	18.679	-0.032	-0.032	0.000	0.000	0.000	0.000
143	A	145	ALA	0	-0.046	-0.008	19.374	-0.308	-0.308	0.000	0.000	0.000	0.000
144	A	146	VAL	0	0.010	0.001	21.458	-0.551	-0.551	0.000	0.000	0.000	0.000
145	A	147	VAL	0	0.017	0.007	24.271	0.188	0.188	0.000	0.000	0.000	0.000
146	A	148	ALA	0	0.000	-0.002	25.992	-0.475	-0.475	0.000	0.000	0.000	0.000
147	A	149	ASP	-1	-0.801	-0.866	27.817	9.673	9.673	0.000	0.000	0.000	0.000
148	A	150	VAL	0	0.013	-0.001	25.029	-0.185	-0.185	0.000	0.000	0.000	0.000
149	A	151	SER	0	-0.062	-0.044	26.046	0.297	0.297	0.000	0.000	0.000	0.000
150	A	152	GLU	-1	-0.900	-0.936	28.107	9.442	9.442	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:GLU)