FMO DATABASE

FMODB ID: VRYM1

Calculation Name: 3WTS-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WTS

Chain ID: B

ChEMBL ID:

UniProt ID: P14921

Base Structure: X-ray

Registration Date: 2023-03-14

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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1188276.89737
FMO2-HF: Nuclear repulsion	1134210.918008
FMO2-HF: Total energy	-54065.979361
FMO2-MP2: Total energy	-54222.034642

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(B:2:PRO)

Summations of interaction energy for fragment #1(B:2:PRO)

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.
-3.76	-0.245	0.018	-1.623	-1.908	0.005

Interaction energy analysis for fragmet #1(B:2:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.001

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	B	4	VAL	0	0.000	-0.005	3.115	-2.679	0.201	0.010	-1.427	-1.463	0.006
4	B	5	VAL	0	-0.023	0.005	3.732	-1.471	-0.903	0.009	-0.187	-0.389	-0.001
5	B	6	PRO	0	0.050	0.009	5.231	0.268	0.268	0.000	0.000	0.000	0.000
6	B	7	ASP	-1	-0.854	-0.902	8.153	-0.505	-0.505	0.000	0.000	0.000	0.000
7	B	8	GLN	0	0.098	0.026	8.472	0.147	0.147	0.000	0.000	0.000	0.000
8	B	9	ARG	1	0.871	0.940	10.966	0.208	0.208	0.000	0.000	0.000	0.000
9	B	10	SER	0	0.002	-0.003	14.216	0.025	0.025	0.000	0.000	0.000	0.000
10	B	11	LYS	1	0.905	0.953	9.569	0.587	0.587	0.000	0.000	0.000	0.000
11	B	12	PHE	0	-0.027	-0.014	13.543	0.029	0.029	0.000	0.000	0.000	0.000
12	B	13	GLU	-1	-0.954	-0.966	15.947	-0.129	-0.129	0.000	0.000	0.000	0.000
13	B	14	ASN	0	-0.034	-0.013	16.585	0.019	0.019	0.000	0.000	0.000	0.000
14	B	15	GLU	-1	-0.872	-0.939	13.435	-0.333	-0.333	0.000	0.000	0.000	0.000
15	B	16	GLU	-1	-0.881	-0.958	17.229	-0.110	-0.110	0.000	0.000	0.000	0.000
16	B	17	PHE	0	-0.042	-0.017	14.731	0.021	0.021	0.000	0.000	0.000	0.000
17	B	18	PHE	0	0.062	0.019	12.413	0.016	0.016	0.000	0.000	0.000	0.000
18	B	19	ARG	1	0.948	0.990	18.351	0.169	0.169	0.000	0.000	0.000	0.000
19	B	20	LYS	1	0.917	0.967	21.514	0.095	0.095	0.000	0.000	0.000	0.000
20	B	21	LEU	0	-0.061	-0.038	19.019	0.017	0.017	0.000	0.000	0.000	0.000
21	B	22	SER	0	0.025	0.013	21.619	0.002	0.002	0.000	0.000	0.000	0.000
22	B	23	ARG	1	0.940	0.968	23.586	0.065	0.065	0.000	0.000	0.000	0.000
23	B	24	GLU	-1	-0.834	-0.922	26.825	-0.031	-0.031	0.000	0.000	0.000	0.000
24	B	25	CYS	0	-0.105	-0.037	26.205	0.000	0.000	0.000	0.000	0.000	0.000
25	B	26	GLU	-1	-0.875	-0.946	28.618	-0.019	-0.019	0.000	0.000	0.000	0.000
26	B	27	ILE	0	-0.091	-0.028	26.667	-0.003	-0.003	0.000	0.000	0.000	0.000
27	B	28	LYS	1	0.948	0.960	28.591	0.013	0.013	0.000	0.000	0.000	0.000
28	B	29	TYR	0	0.050	0.060	28.753	0.001	0.001	0.000	0.000	0.000	0.000
29	B	30	THR	0	-0.050	-0.039	26.218	0.000	0.000	0.000	0.000	0.000	0.000
30	B	31	GLY	0	0.087	0.039	29.058	0.001	0.001	0.000	0.000	0.000	0.000
31	B	32	PHE	0	0.037	0.011	30.314	-0.004	-0.004	0.000	0.000	0.000	0.000
32	B	33	ARG	1	0.973	0.983	30.726	-0.004	-0.004	0.000	0.000	0.000	0.000
33	B	34	ASP	-1	-0.941	-0.951	34.318	0.023	0.023	0.000	0.000	0.000	0.000
34	B	35	ARG	1	0.861	0.928	36.380	-0.025	-0.025	0.000	0.000	0.000	0.000
35	B	36	PRO	0	0.018	0.001	38.462	-0.002	-0.002	0.000	0.000	0.000	0.000
36	B	37	HIS	0	0.018	-0.009	38.877	0.002	0.002	0.000	0.000	0.000	0.000
37	B	38	GLU	-1	-0.939	-0.973	40.099	0.022	0.022	0.000	0.000	0.000	0.000
38	B	39	GLU	-1	-0.736	-0.851	37.753	0.031	0.031	0.000	0.000	0.000	0.000
39	B	40	ARG	1	0.749	0.858	32.579	-0.012	-0.012	0.000	0.000	0.000	0.000
40	B	41	GLN	0	0.063	0.021	35.755	-0.001	-0.001	0.000	0.000	0.000	0.000
41	B	42	THR	0	0.000	0.007	37.103	0.002	0.002	0.000	0.000	0.000	0.000
42	B	43	ARG	1	0.847	0.917	33.694	-0.038	-0.038	0.000	0.000	0.000	0.000
43	B	44	PHE	0	0.043	0.020	30.202	0.004	0.004	0.000	0.000	0.000	0.000
44	B	45	GLN	0	0.059	0.029	32.554	0.000	0.000	0.000	0.000	0.000	0.000
45	B	46	ASN	0	-0.039	-0.044	33.984	0.001	0.001	0.000	0.000	0.000	0.000
46	B	47	ALA	0	0.011	0.022	29.630	0.004	0.004	0.000	0.000	0.000	0.000
47	B	48	CYS	0	0.016	0.002	29.662	0.004	0.004	0.000	0.000	0.000	0.000
48	B	49	ARG	1	0.856	0.941	30.322	-0.031	-0.031	0.000	0.000	0.000	0.000
49	B	50	ASP	-1	-0.917	-0.955	29.486	0.065	0.065	0.000	0.000	0.000	0.000
50	B	51	GLY	0	-0.015	-0.010	26.807	0.008	0.008	0.000	0.000	0.000	0.000
51	B	52	ARG	1	0.926	0.967	24.900	-0.068	-0.068	0.000	0.000	0.000	0.000
52	B	53	SER	0	0.005	-0.010	25.001	-0.008	-0.008	0.000	0.000	0.000	0.000
53	B	54	GLU	-1	-0.926	-0.951	24.285	0.057	0.057	0.000	0.000	0.000	0.000
54	B	55	ILE	0	0.010	0.017	24.590	-0.004	-0.004	0.000	0.000	0.000	0.000
55	B	56	ALA	0	-0.005	0.004	24.075	-0.001	-0.001	0.000	0.000	0.000	0.000
56	B	57	PHE	0	0.029	0.012	21.195	0.002	0.002	0.000	0.000	0.000	0.000
57	B	58	VAL	0	0.010	-0.003	25.977	-0.004	-0.004	0.000	0.000	0.000	0.000
58	B	59	ALA	0	-0.021	-0.007	27.912	-0.002	-0.002	0.000	0.000	0.000	0.000
59	B	60	THR	0	-0.047	-0.020	23.021	-0.005	-0.005	0.000	0.000	0.000	0.000
60	B	61	GLY	0	0.012	0.016	24.891	-0.003	-0.003	0.000	0.000	0.000	0.000
61	B	62	THR	0	0.000	-0.002	19.363	-0.002	-0.002	0.000	0.000	0.000	0.000
62	B	63	ASN	0	-0.046	-0.048	21.633	0.012	0.012	0.000	0.000	0.000	0.000
63	B	64	LEU	0	0.032	0.012	17.490	-0.008	-0.008	0.000	0.000	0.000	0.000
64	B	65	SER	0	-0.013	0.009	19.402	0.007	0.007	0.000	0.000	0.000	0.000
65	B	66	LEU	0	-0.037	-0.020	19.693	0.006	0.006	0.000	0.000	0.000	0.000
66	B	67	GLN	0	0.046	0.001	19.450	0.018	0.018	0.000	0.000	0.000	0.000
67	B	68	PHE	0	-0.073	-0.024	21.295	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	69	PHE	0	-0.007	-0.004	21.763	0.000	0.000	0.000	0.000	0.000	0.000
69	B	70	PRO	0	0.018	0.018	20.824	-0.003	-0.003	0.000	0.000	0.000	0.000
70	B	71	ALA	0	-0.005	0.002	16.161	0.020	0.020	0.000	0.000	0.000	0.000
71	B	81	PRO	0	0.037	0.017	28.918	0.001	0.001	0.000	0.000	0.000	0.000
72	B	82	SER	0	-0.040	-0.020	26.541	0.004	0.004	0.000	0.000	0.000	0.000
73	B	83	ARG	1	0.913	0.934	29.442	-0.044	-0.044	0.000	0.000	0.000	0.000
74	B	84	GLU	-1	-0.880	-0.936	26.597	0.026	0.026	0.000	0.000	0.000	0.000
75	B	85	TYR	0	-0.009	-0.007	22.260	0.000	0.000	0.000	0.000	0.000	0.000
76	B	86	VAL	0	-0.028	-0.018	27.186	-0.002	-0.002	0.000	0.000	0.000	0.000
77	B	87	ASP	-1	-0.826	-0.915	29.977	0.015	0.015	0.000	0.000	0.000	0.000
78	B	88	LEU	0	-0.059	-0.056	33.160	0.000	0.000	0.000	0.000	0.000	0.000
79	B	89	GLU	-1	-0.918	-0.946	36.508	0.017	0.017	0.000	0.000	0.000	0.000
80	B	90	ARG	1	0.844	0.937	31.897	0.002	0.002	0.000	0.000	0.000	0.000
81	B	91	GLU	-1	-0.885	-0.971	37.905	-0.006	-0.006	0.000	0.000	0.000	0.000
82	B	92	ALA	0	0.013	0.023	39.664	0.002	0.002	0.000	0.000	0.000	0.000
83	B	93	GLY	0	-0.021	-0.003	40.874	-0.002	-0.002	0.000	0.000	0.000	0.000
84	B	94	LYS	1	0.859	0.944	35.696	0.005	0.005	0.000	0.000	0.000	0.000
85	B	95	VAL	0	0.035	0.015	32.414	0.002	0.002	0.000	0.000	0.000	0.000
86	B	96	TYR	0	-0.031	-0.014	31.307	-0.004	-0.004	0.000	0.000	0.000	0.000
87	B	97	LEU	0	-0.004	0.006	27.093	0.005	0.005	0.000	0.000	0.000	0.000
88	B	98	LYS	1	0.958	0.970	23.496	-0.011	-0.011	0.000	0.000	0.000	0.000
89	B	99	ALA	0	-0.003	-0.012	20.831	0.011	0.011	0.000	0.000	0.000	0.000
90	B	100	PRO	0	0.013	0.041	16.869	-0.021	-0.021	0.000	0.000	0.000	0.000
91	B	101	MET	0	-0.014	-0.006	14.619	0.027	0.027	0.000	0.000	0.000	0.000
92	B	102	ILE	0	0.005	0.007	8.065	-0.031	-0.031	0.000	0.000	0.000	0.000
93	B	103	LEU	0	0.001	0.005	11.277	0.024	0.024	0.000	0.000	0.000	0.000
94	B	104	ASN	0	-0.029	-0.014	9.280	-0.051	-0.051	0.000	0.000	0.000	0.000
95	B	105	GLY	0	0.025	0.015	6.474	-0.160	-0.160	0.000	0.000	0.000	0.000
96	B	106	VAL	0	0.026	-0.012	7.214	-0.064	-0.064	0.000	0.000	0.000	0.000
97	B	107	CYS	0	-0.093	-0.012	10.389	0.102	0.102	0.000	0.000	0.000	0.000
98	B	108	VAL	0	-0.028	-0.010	12.549	-0.015	-0.015	0.000	0.000	0.000	0.000
99	B	109	ILE	0	-0.011	-0.004	16.136	0.035	0.035	0.000	0.000	0.000	0.000
100	B	110	TRP	0	-0.003	-0.010	19.429	-0.008	-0.008	0.000	0.000	0.000	0.000
101	B	111	LYS	1	0.838	0.888	21.639	0.039	0.039	0.000	0.000	0.000	0.000
102	B	112	GLY	0	0.080	0.048	25.290	-0.008	-0.008	0.000	0.000	0.000	0.000
103	B	113	TRP	0	-0.041	-0.008	28.457	0.008	0.008	0.000	0.000	0.000	0.000
104	B	114	ILE	0	-0.015	-0.012	29.355	-0.002	-0.002	0.000	0.000	0.000	0.000
105	B	115	ASP	-1	-0.793	-0.909	33.506	0.005	0.005	0.000	0.000	0.000	0.000
106	B	116	LEU	0	-0.042	-0.018	36.183	0.001	0.001	0.000	0.000	0.000	0.000
107	B	117	HIS	1	0.837	0.928	38.229	-0.008	-0.008	0.000	0.000	0.000	0.000
108	B	118	ARG	1	0.917	0.971	38.287	0.006	0.006	0.000	0.000	0.000	0.000
109	B	119	LEU	0	-0.063	-0.017	34.688	0.000	0.000	0.000	0.000	0.000	0.000
110	B	120	ASP	-1	-0.871	-0.962	32.870	-0.007	-0.007	0.000	0.000	0.000	0.000
111	B	121	GLY	0	0.054	0.036	32.754	0.002	0.002	0.000	0.000	0.000	0.000
112	B	122	MET	0	-0.029	-0.009	30.604	-0.003	-0.003	0.000	0.000	0.000	0.000
113	B	123	GLY	0	0.028	0.001	26.968	0.006	0.006	0.000	0.000	0.000	0.000
114	B	124	CYS	0	-0.111	-0.037	24.227	-0.005	-0.005	0.000	0.000	0.000	0.000
115	B	125	LEU	0	0.009	0.002	17.667	0.009	0.009	0.000	0.000	0.000	0.000
116	B	126	GLU	-1	-0.825	-0.911	20.246	-0.047	-0.047	0.000	0.000	0.000	0.000
117	B	127	PHE	0	0.025	0.008	13.789	0.004	0.004	0.000	0.000	0.000	0.000
118	B	128	ASP	-1	-0.807	-0.914	15.541	0.001	0.001	0.000	0.000	0.000	0.000
119	B	129	GLU	-1	-0.888	-0.959	15.606	-0.123	-0.123	0.000	0.000	0.000	0.000
120	B	130	GLU	-1	-0.953	-0.971	16.252	0.000	0.000	0.000	0.000	0.000	0.000
121	B	131	ARG	1	0.848	0.927	11.516	-0.149	-0.149	0.000	0.000	0.000	0.000
122	B	132	ALA	0	0.027	0.002	11.457	0.013	0.013	0.000	0.000	0.000	0.000
123	B	133	GLN	0	-0.020	0.002	11.094	-0.020	-0.020	0.000	0.000	0.000	0.000
124	B	134	GLN	0	0.002	-0.015	12.103	0.033	0.033	0.000	0.000	0.000	0.000
125	B	135	GLU	-1	-0.836	-0.907	6.915	0.505	0.505	0.000	0.000	0.000	0.000
126	B	136	ASP	-1	-0.944	-0.975	7.740	-0.343	-0.343	0.000	0.000	0.000	0.000
127	B	137	ALA	0	0.012	0.013	8.766	-0.005	-0.005	0.000	0.000	0.000	0.000
128	B	138	LEU	0	-0.079	-0.036	6.669	0.040	0.040	0.000	0.000	0.000	0.000
129	B	139	ALA	0	-0.054	-0.021	4.456	0.019	0.086	-0.001	-0.009	-0.056	0.000
130	B	140	GLN	0	-0.065	-0.017	6.015	-0.055	-0.055	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:PRO)