FMO DATABASE

FMODB ID: R9868

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	OptH
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	-1345079.896938
FMO2-HF: Nuclear repulsion	1289776.411035
FMO2-HF: Total energy	-55303.485903
FMO2-MP2: Total energy	-55468.171316

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.
-9.286	-2.551	0.324	-2.716	-4.345	0.001

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 : -0.942 / q_NPA : -0.977

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	-0.007	-0.004	3.341	-10.405	-8.223	0.042	-0.762	-1.462	0.008
4	A	6	GLU	-1	-0.935	-0.976	2.832	28.025	29.985	0.194	-0.861	-1.295	-0.004
5	A	7	GLU	-1	-0.930	-0.977	3.370	50.024	52.005	0.084	-0.931	-1.134	-0.004
6	A	8	TRP	0	-0.015	-0.009	5.724	-3.306	-3.306	0.000	0.000	0.000	0.000
7	A	9	ILE	0	-0.009	-0.010	7.529	-2.317	-2.317	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.962	0.987	8.435	-25.137	-25.137	0.000	0.000	0.000	0.000
9	A	11	ALA	0	-0.042	-0.017	9.829	-1.588	-1.588	0.000	0.000	0.000	0.000
10	A	12	ARG	1	0.835	0.916	11.833	-19.707	-19.707	0.000	0.000	0.000	0.000
11	A	13	GLY	0	0.003	0.013	13.308	-1.058	-1.058	0.000	0.000	0.000	0.000
12	A	14	LEU	0	-0.021	0.000	13.329	-0.854	-0.854	0.000	0.000	0.000	0.000
13	A	15	THR	0	-0.019	-0.023	13.534	0.630	0.630	0.000	0.000	0.000	0.000
14	A	16	TRP	0	-0.043	-0.028	11.214	0.265	0.265	0.000	0.000	0.000	0.000
15	A	17	ARG	1	0.897	0.949	10.502	-14.678	-14.678	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.016	0.022	4.222	-0.461	-0.427	-0.001	-0.005	-0.028	0.000
17	A	19	LEU	0	-0.052	-0.019	8.861	-0.686	-0.686	0.000	0.000	0.000	0.000
18	A	20	ILE	0	0.002	-0.004	7.974	0.854	0.854	0.000	0.000	0.000	0.000
19	A	21	MET	0	0.019	0.019	11.639	-1.175	-1.175	0.000	0.000	0.000	0.000
20	A	22	GLN	0	0.014	-0.007	13.878	0.208	0.208	0.000	0.000	0.000	0.000
21	A	23	LYS	1	0.897	0.948	16.003	-12.662	-12.662	0.000	0.000	0.000	0.000
22	A	24	PRO	0	0.026	0.013	14.129	-0.186	-0.186	0.000	0.000	0.000	0.000
23	A	25	THR	0	0.032	0.030	15.716	-0.704	-0.704	0.000	0.000	0.000	0.000
24	A	26	ARG	1	0.936	0.956	17.688	-12.504	-12.504	0.000	0.000	0.000	0.000
25	A	27	THR	0	-0.020	-0.009	20.405	-0.357	-0.357	0.000	0.000	0.000	0.000
26	A	28	VAL	0	0.051	0.021	20.473	0.328	0.328	0.000	0.000	0.000	0.000
27	A	29	ALA	0	0.047	0.033	21.669	0.033	0.033	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.917	-0.964	20.790	12.904	12.904	0.000	0.000	0.000	0.000
29	A	31	ALA	0	0.025	0.009	17.895	0.042	0.042	0.000	0.000	0.000	0.000
30	A	32	ALA	0	0.000	-0.007	19.529	0.043	0.043	0.000	0.000	0.000	0.000
31	A	33	ALA	0	-0.009	-0.002	22.053	-0.167	-0.167	0.000	0.000	0.000	0.000
32	A	34	LEU	0	-0.054	-0.033	19.637	-0.140	-0.140	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.028	-0.011	16.233	0.193	0.193	0.000	0.000	0.000	0.000
34	A	36	GLY	0	-0.033	0.003	20.405	-0.162	-0.162	0.000	0.000	0.000	0.000
35	A	37	VAL	0	-0.056	-0.015	20.723	-0.267	-0.267	0.000	0.000	0.000	0.000
36	A	38	SER	0	-0.054	-0.045	23.968	-0.208	-0.208	0.000	0.000	0.000	0.000
37	A	39	GLU	-1	-0.829	-0.954	23.356	11.150	11.150	0.000	0.000	0.000	0.000
38	A	40	SER	0	-0.077	-0.022	22.923	0.393	0.393	0.000	0.000	0.000	0.000
39	A	41	GLU	-1	-0.851	-0.919	21.228	11.179	11.179	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.007	0.016	17.559	0.646	0.646	0.000	0.000	0.000	0.000
41	A	43	VAL	0	-0.047	-0.026	16.303	-0.394	-0.394	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.870	0.944	16.689	-11.578	-11.578	0.000	0.000	0.000	0.000
43	A	45	THR	0	-0.008	-0.004	13.716	-1.017	-1.017	0.000	0.000	0.000	0.000
44	A	46	LEU	0	-0.041	-0.025	16.748	0.401	0.401	0.000	0.000	0.000	0.000
45	A	47	ILE	0	0.054	0.030	15.764	-0.124	-0.124	0.000	0.000	0.000	0.000
46	A	48	VAL	0	-0.041	-0.021	19.694	-0.639	-0.639	0.000	0.000	0.000	0.000
47	A	49	LEU	0	0.007	0.005	21.155	0.379	0.379	0.000	0.000	0.000	0.000
48	A	50	ASP	-1	-0.759	-0.873	24.603	11.176	11.176	0.000	0.000	0.000	0.000
49	A	51	ASN	0	-0.054	-0.048	27.532	0.286	0.286	0.000	0.000	0.000	0.000
50	A	52	ALA	0	-0.042	-0.034	28.684	-0.303	-0.303	0.000	0.000	0.000	0.000
51	A	53	GLY	0	0.006	0.009	25.222	0.060	0.060	0.000	0.000	0.000	0.000
52	A	54	GLY	0	-0.004	0.016	23.498	0.612	0.612	0.000	0.000	0.000	0.000
53	A	55	VAL	0	-0.009	-0.018	18.526	-0.028	-0.028	0.000	0.000	0.000	0.000
54	A	56	TYR	0	-0.013	-0.002	20.716	0.131	0.131	0.000	0.000	0.000	0.000
55	A	57	ALA	0	0.015	0.011	16.672	0.356	0.356	0.000	0.000	0.000	0.000
56	A	58	VAL	0	0.004	-0.012	18.643	-0.306	-0.306	0.000	0.000	0.000	0.000
57	A	59	VAL	0	0.011	0.009	16.979	0.181	0.181	0.000	0.000	0.000	0.000
58	A	60	ILE	0	-0.032	-0.007	19.628	-0.695	-0.695	0.000	0.000	0.000	0.000
59	A	61	PRO	0	0.036	0.005	21.089	0.500	0.500	0.000	0.000	0.000	0.000
60	A	62	GLY	0	0.056	0.029	22.151	-0.049	-0.049	0.000	0.000	0.000	0.000
61	A	63	ASP	-1	-0.891	-0.949	22.746	10.322	10.322	0.000	0.000	0.000	0.000
62	A	64	LYS	1	0.911	0.965	25.572	-9.957	-9.957	0.000	0.000	0.000	0.000
63	A	65	ARG	1	0.943	0.944	25.743	-9.848	-9.848	0.000	0.000	0.000	0.000
64	A	66	LEU	0	0.046	0.016	24.623	-0.115	-0.115	0.000	0.000	0.000	0.000
65	A	67	ASN	0	0.048	0.051	27.064	-0.237	-0.237	0.000	0.000	0.000	0.000
66	A	68	ILE	0	0.015	-0.022	28.416	0.118	0.118	0.000	0.000	0.000	0.000
67	A	69	ASN	0	-0.027	-0.019	30.748	0.059	0.059	0.000	0.000	0.000	0.000
68	A	70	SER	0	0.057	0.035	30.719	-0.084	-0.084	0.000	0.000	0.000	0.000
69	A	71	MET	0	-0.001	0.004	25.243	0.102	0.102	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.913	0.967	29.386	-8.684	-8.684	0.000	0.000	0.000	0.000
71	A	73	GLU	-1	-0.933	-0.963	32.305	8.529	8.529	0.000	0.000	0.000	0.000
72	A	74	LEU	0	-0.046	-0.019	26.991	-0.017	-0.017	0.000	0.000	0.000	0.000
73	A	75	ALA	0	-0.019	-0.008	28.422	0.057	0.057	0.000	0.000	0.000	0.000
74	A	76	GLY	0	0.006	0.020	29.833	-0.047	-0.047	0.000	0.000	0.000	0.000
75	A	77	LYS	1	0.896	0.944	29.647	-10.714	-10.714	0.000	0.000	0.000	0.000
76	A	78	PRO	0	-0.073	-0.042	32.044	0.066	0.066	0.000	0.000	0.000	0.000
77	A	79	VAL	0	0.057	0.031	27.917	0.251	0.251	0.000	0.000	0.000	0.000
78	A	80	ARG	1	0.733	0.839	24.967	-12.605	-12.605	0.000	0.000	0.000	0.000
79	A	81	LEU	0	0.027	0.025	23.757	0.345	0.345	0.000	0.000	0.000	0.000
80	A	82	ALA	0	0.006	0.008	20.673	-0.351	-0.351	0.000	0.000	0.000	0.000
81	A	83	ARG	1	0.940	0.953	22.485	-12.218	-12.218	0.000	0.000	0.000	0.000
82	A	84	ALA	0	0.059	0.014	19.598	0.564	0.564	0.000	0.000	0.000	0.000
83	A	85	ASN	0	0.020	-0.001	18.159	0.621	0.621	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.703	-0.810	18.113	14.015	14.015	0.000	0.000	0.000	0.000
85	A	87	VAL	0	-0.016	0.002	15.123	0.680	0.680	0.000	0.000	0.000	0.000
86	A	88	VAL	0	-0.006	0.008	12.628	1.105	1.105	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.967	-0.978	13.185	18.156	18.156	0.000	0.000	0.000	0.000
88	A	90	LEU	0	-0.012	-0.010	14.765	0.805	0.805	0.000	0.000	0.000	0.000
89	A	91	THR	0	-0.059	-0.040	11.904	1.122	1.122	0.000	0.000	0.000	0.000
90	A	92	GLY	0	0.003	0.008	9.465	2.188	2.188	0.000	0.000	0.000	0.000
91	A	93	TYR	0	-0.070	-0.053	5.474	6.204	6.204	0.000	0.000	0.000	0.000
92	A	94	PRO	0	-0.044	-0.018	9.055	-2.309	-2.309	0.000	0.000	0.000	0.000
93	A	95	VAL	0	0.040	0.006	12.007	-0.347	-0.347	0.000	0.000	0.000	0.000
94	A	96	GLY	0	-0.004	-0.011	14.558	-0.601	-0.601	0.000	0.000	0.000	0.000
95	A	97	GLY	0	-0.021	-0.016	10.319	-0.228	-0.228	0.000	0.000	0.000	0.000
96	A	98	VAL	0	-0.049	-0.017	9.536	2.260	2.260	0.000	0.000	0.000	0.000
97	A	99	PRO	0	0.013	0.025	7.852	-1.839	-1.839	0.000	0.000	0.000	0.000
98	A	100	PRO	0	0.003	-0.004	10.405	-0.392	-0.392	0.000	0.000	0.000	0.000
99	A	101	VAL	0	0.015	0.003	9.077	-1.036	-1.036	0.000	0.000	0.000	0.000
100	A	102	ALA	0	-0.015	-0.013	6.975	1.623	1.623	0.000	0.000	0.000	0.000
101	A	103	LEU	0	0.010	0.026	8.292	3.348	3.348	0.000	0.000	0.000	0.000
102	A	104	PRO	0	-0.010	-0.007	10.947	-0.168	-0.168	0.000	0.000	0.000	0.000
103	A	105	PRO	0	0.025	-0.004	12.590	-1.036	-1.036	0.000	0.000	0.000	0.000
104	A	106	ASN	0	-0.001	0.010	15.186	-0.048	-0.048	0.000	0.000	0.000	0.000
105	A	107	ILE	0	-0.069	-0.024	14.692	-0.982	-0.982	0.000	0.000	0.000	0.000
106	A	108	VAL	0	0.028	0.021	17.658	0.209	0.209	0.000	0.000	0.000	0.000
107	A	109	LEU	0	-0.026	-0.005	16.351	-0.091	-0.091	0.000	0.000	0.000	0.000
108	A	110	VAL	0	-0.014	-0.007	19.621	-0.649	-0.649	0.000	0.000	0.000	0.000
109	A	111	VAL	0	0.002	-0.006	19.620	0.462	0.462	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.763	-0.881	22.217	10.085	10.085	0.000	0.000	0.000	0.000
111	A	113	ARG	1	0.905	0.927	24.746	-9.398	-9.398	0.000	0.000	0.000	0.000
112	A	114	ILE	0	-0.059	-0.016	26.308	-0.130	-0.130	0.000	0.000	0.000	0.000
113	A	115	LEU	0	-0.012	-0.020	20.717	-0.055	-0.055	0.000	0.000	0.000	0.000
114	A	116	LEU	0	-0.006	-0.006	23.418	0.130	0.130	0.000	0.000	0.000	0.000
115	A	117	SER	0	-0.078	-0.028	25.373	0.091	0.091	0.000	0.000	0.000	0.000
116	A	118	ARG	1	0.918	0.975	22.812	-10.839	-10.839	0.000	0.000	0.000	0.000
117	A	119	LYS	1	0.961	0.962	22.978	-9.856	-9.856	0.000	0.000	0.000	0.000
118	A	120	LYS	1	0.924	0.974	17.975	-12.652	-12.652	0.000	0.000	0.000	0.000
119	A	121	VAL	0	0.000	0.013	17.009	-0.567	-0.567	0.000	0.000	0.000	0.000
120	A	122	TYR	0	-0.002	-0.013	14.939	0.439	0.439	0.000	0.000	0.000	0.000
121	A	123	GLY	0	0.030	0.020	13.621	-0.586	-0.586	0.000	0.000	0.000	0.000
122	A	124	GLY	0	0.009	0.017	11.350	0.330	0.330	0.000	0.000	0.000	0.000
123	A	125	GLY	0	0.033	-0.005	7.851	0.260	0.260	0.000	0.000	0.000	0.000
124	A	126	GLY	0	0.002	0.005	5.383	3.005	3.005	0.000	0.000	0.000	0.000
125	A	127	ARG	1	0.922	0.941	3.344	-51.253	-50.675	0.005	-0.157	-0.426	0.001
126	A	128	GLU	-1	-0.806	-0.898	7.844	18.314	18.314	0.000	0.000	0.000	0.000
127	A	129	ASN	0	-0.037	-0.008	9.399	0.015	0.015	0.000	0.000	0.000	0.000
128	A	130	ALA	0	0.005	0.018	7.317	-0.615	-0.615	0.000	0.000	0.000	0.000
129	A	131	LEU	0	0.025	0.012	9.289	0.017	0.017	0.000	0.000	0.000	0.000
130	A	132	LEU	0	-0.003	-0.002	8.583	0.479	0.479	0.000	0.000	0.000	0.000
131	A	133	GLU	-1	-0.842	-0.923	10.621	13.735	13.735	0.000	0.000	0.000	0.000
132	A	134	PHE	0	0.005	-0.020	13.246	0.394	0.394	0.000	0.000	0.000	0.000
133	A	135	SER	0	0.074	0.043	15.149	-0.784	-0.784	0.000	0.000	0.000	0.000
134	A	136	PRO	0	0.026	0.004	18.261	0.385	0.385	0.000	0.000	0.000	0.000
135	A	137	ARG	1	0.972	0.978	19.948	-10.303	-10.303	0.000	0.000	0.000	0.000
136	A	138	GLU	-1	-0.842	-0.908	17.963	13.866	13.866	0.000	0.000	0.000	0.000
137	A	139	LEU	0	-0.009	0.004	14.779	0.399	0.399	0.000	0.000	0.000	0.000
138	A	140	VAL	0	-0.042	-0.015	17.606	0.247	0.247	0.000	0.000	0.000	0.000
139	A	141	GLU	-1	-0.961	-0.974	20.906	11.906	11.906	0.000	0.000	0.000	0.000
140	A	142	ALA	0	-0.020	-0.006	16.798	0.094	0.094	0.000	0.000	0.000	0.000
141	A	143	THR	0	-0.054	-0.054	16.141	0.437	0.437	0.000	0.000	0.000	0.000
142	A	144	GLY	0	0.021	0.031	18.877	-0.013	-0.013	0.000	0.000	0.000	0.000
143	A	145	ALA	0	-0.060	-0.020	19.902	-0.360	-0.360	0.000	0.000	0.000	0.000
144	A	146	VAL	0	0.034	0.021	21.907	-0.537	-0.537	0.000	0.000	0.000	0.000
145	A	147	VAL	0	0.002	-0.001	24.380	0.228	0.228	0.000	0.000	0.000	0.000
146	A	148	ALA	0	-0.038	-0.021	26.243	-0.384	-0.384	0.000	0.000	0.000	0.000
147	A	149	ASP	-1	-0.841	-0.895	27.783	9.527	9.527	0.000	0.000	0.000	0.000
148	A	150	VAL	0	0.026	-0.013	25.183	-0.135	-0.135	0.000	0.000	0.000	0.000
149	A	151	SER	0	-0.042	-0.023	26.514	0.182	0.182	0.000	0.000	0.000	0.000
150	A	152	GLU	-1	-0.978	-0.987	28.425	8.871	8.871	0.000	0.000	0.000	0.000

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