FMO DATABASE

FMODB ID: RY5R8

Calculation Name: 3WTP-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WTP

Chain ID: C

ChEMBL ID:

UniProt ID: P49450

Base Structure: X-ray

Registration Date: 2023-09-26

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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-665505.145524
FMO2-HF: Nuclear repulsion	625751.796806
FMO2-HF: Total energy	-39753.348718
FMO2-MP2: Total energy	-39873.021826

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(C:12:ALA)

Summations of interaction energy for fragment #1(C:12:ALA)

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.
1.675	3.68	-0.011	-1.074	-0.92	0.006

Interaction energy analysis for fragmet #1(C:12:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.094 / q_NPA : 0.051

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

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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	C	14	ALA	0	0.043	0.029	3.877	-0.638	1.367	-0.011	-1.074	-0.920	0.006
4	C	15	LYS	1	0.971	0.979	6.390	0.672	0.672	0.000	0.000	0.000	0.000
5	C	16	THR	0	0.062	0.041	8.738	0.082	0.082	0.000	0.000	0.000	0.000
6	C	17	ARG	1	0.955	0.954	11.749	0.298	0.298	0.000	0.000	0.000	0.000
7	C	18	SER	0	0.004	-0.005	13.731	0.023	0.023	0.000	0.000	0.000	0.000
8	C	19	SER	0	0.027	0.007	12.529	0.027	0.027	0.000	0.000	0.000	0.000
9	C	20	ARG	1	0.771	0.866	6.639	0.456	0.456	0.000	0.000	0.000	0.000
10	C	21	ALA	0	0.013	0.014	14.041	0.032	0.032	0.000	0.000	0.000	0.000
11	C	22	GLY	0	0.011	0.028	17.373	0.020	0.020	0.000	0.000	0.000	0.000
12	C	23	LEU	0	-0.034	-0.008	18.828	0.009	0.009	0.000	0.000	0.000	0.000
13	C	24	GLN	0	0.017	-0.009	19.461	-0.038	-0.038	0.000	0.000	0.000	0.000
14	C	25	PHE	0	0.011	0.013	21.428	-0.023	-0.023	0.000	0.000	0.000	0.000
15	C	26	PRO	0	-0.006	0.013	19.252	-0.021	-0.021	0.000	0.000	0.000	0.000
16	C	27	VAL	0	0.057	0.019	17.203	0.005	0.005	0.000	0.000	0.000	0.000
17	C	28	GLY	0	-0.032	-0.017	16.562	0.011	0.011	0.000	0.000	0.000	0.000
18	C	29	ARG	1	0.952	0.971	17.321	0.254	0.254	0.000	0.000	0.000	0.000
19	C	30	VAL	0	0.078	0.041	20.721	0.015	0.015	0.000	0.000	0.000	0.000
20	C	31	HIS	0	0.022	0.022	17.945	-0.015	-0.015	0.000	0.000	0.000	0.000
21	C	32	ARG	1	0.915	0.959	19.985	0.218	0.218	0.000	0.000	0.000	0.000
22	C	33	LEU	0	-0.025	-0.016	21.509	0.011	0.011	0.000	0.000	0.000	0.000
23	C	34	LEU	0	0.037	0.015	23.492	0.010	0.010	0.000	0.000	0.000	0.000
24	C	35	ARG	1	0.942	0.966	18.391	0.193	0.193	0.000	0.000	0.000	0.000
25	C	36	LYS	1	0.928	0.964	24.842	0.124	0.124	0.000	0.000	0.000	0.000
26	C	37	GLY	0	0.012	-0.001	26.835	0.006	0.006	0.000	0.000	0.000	0.000
27	C	38	ASN	0	-0.064	-0.027	28.772	0.009	0.009	0.000	0.000	0.000	0.000
28	C	39	TYR	0	0.013	0.016	28.434	0.002	0.002	0.000	0.000	0.000	0.000
29	C	40	SER	0	-0.009	-0.021	27.195	0.004	0.004	0.000	0.000	0.000	0.000
30	C	41	GLU	-1	-0.887	-0.925	27.735	-0.055	-0.055	0.000	0.000	0.000	0.000
31	C	42	ARG	1	0.937	0.966	22.642	0.025	0.025	0.000	0.000	0.000	0.000
32	C	43	VAL	0	0.021	0.025	22.362	0.000	0.000	0.000	0.000	0.000	0.000
33	C	44	GLY	0	0.053	0.026	21.074	-0.009	-0.009	0.000	0.000	0.000	0.000
34	C	45	ALA	0	0.005	-0.019	16.522	-0.012	-0.012	0.000	0.000	0.000	0.000
35	C	46	GLY	0	0.052	0.018	18.459	-0.021	-0.021	0.000	0.000	0.000	0.000
36	C	47	ALA	0	0.038	0.033	20.523	-0.003	-0.003	0.000	0.000	0.000	0.000
37	C	48	PRO	0	-0.041	-0.024	19.417	-0.003	-0.003	0.000	0.000	0.000	0.000
38	C	49	VAL	0	-0.013	-0.011	18.058	-0.014	-0.014	0.000	0.000	0.000	0.000
39	C	50	TYR	0	0.053	0.032	20.895	-0.002	-0.002	0.000	0.000	0.000	0.000
40	C	51	LEU	0	0.036	0.018	24.493	0.000	0.000	0.000	0.000	0.000	0.000
41	C	52	ALA	0	-0.046	-0.030	22.154	-0.001	-0.001	0.000	0.000	0.000	0.000
42	C	53	ALA	0	0.052	0.023	23.839	0.000	0.000	0.000	0.000	0.000	0.000
43	C	54	VAL	0	0.022	0.017	25.271	0.004	0.004	0.000	0.000	0.000	0.000
44	C	55	LEU	0	-0.014	-0.009	26.916	0.002	0.002	0.000	0.000	0.000	0.000
45	C	56	GLU	-1	-0.787	-0.875	23.733	-0.165	-0.165	0.000	0.000	0.000	0.000
46	C	57	TYR	0	-0.037	-0.036	27.746	0.001	0.001	0.000	0.000	0.000	0.000
47	C	58	LEU	0	0.035	0.013	30.306	0.003	0.003	0.000	0.000	0.000	0.000
48	C	59	THR	0	-0.069	-0.050	30.377	0.002	0.002	0.000	0.000	0.000	0.000
49	C	60	ALA	0	-0.019	-0.014	30.483	0.002	0.002	0.000	0.000	0.000	0.000
50	C	61	GLU	-1	-0.810	-0.880	32.492	-0.062	-0.062	0.000	0.000	0.000	0.000
51	C	62	ILE	0	-0.028	-0.014	35.753	0.004	0.004	0.000	0.000	0.000	0.000
52	C	63	LEU	0	-0.051	-0.038	32.552	0.002	0.002	0.000	0.000	0.000	0.000
53	C	64	GLU	-1	-0.826	-0.885	36.039	-0.068	-0.068	0.000	0.000	0.000	0.000
54	C	65	LEU	0	0.007	0.008	37.564	0.003	0.003	0.000	0.000	0.000	0.000
55	C	66	ALA	0	-0.012	-0.015	39.602	0.003	0.003	0.000	0.000	0.000	0.000
56	C	67	GLY	0	0.003	-0.010	39.422	0.001	0.001	0.000	0.000	0.000	0.000
57	C	68	ASN	0	-0.026	-0.010	40.371	0.003	0.003	0.000	0.000	0.000	0.000
58	C	69	ALA	0	0.067	0.043	43.091	0.002	0.002	0.000	0.000	0.000	0.000
59	C	70	ALA	0	-0.056	-0.033	42.622	0.002	0.002	0.000	0.000	0.000	0.000
60	C	71	ARG	1	0.924	0.950	40.755	0.062	0.062	0.000	0.000	0.000	0.000
61	C	72	ASP	-1	-0.866	-0.924	45.373	-0.048	-0.048	0.000	0.000	0.000	0.000
62	C	73	ASN	0	-0.085	-0.035	48.003	0.000	0.000	0.000	0.000	0.000	0.000
63	C	74	LYS	1	0.910	0.946	48.158	0.045	0.045	0.000	0.000	0.000	0.000
64	C	75	LYS	1	0.842	0.919	45.372	0.055	0.055	0.000	0.000	0.000	0.000
65	C	76	THR	0	0.025	0.016	41.538	0.000	0.000	0.000	0.000	0.000	0.000
66	C	77	ARG	1	0.940	0.964	39.985	0.079	0.079	0.000	0.000	0.000	0.000
67	C	78	ILE	0	0.049	0.040	37.574	0.004	0.004	0.000	0.000	0.000	0.000
68	C	79	ILE	0	-0.016	-0.011	41.049	-0.003	-0.003	0.000	0.000	0.000	0.000
69	C	80	PRO	0	0.047	0.005	42.514	0.001	0.001	0.000	0.000	0.000	0.000
70	C	81	ARG	1	0.846	0.921	43.932	0.050	0.050	0.000	0.000	0.000	0.000
71	C	82	HIS	0	0.027	0.006	43.297	0.000	0.000	0.000	0.000	0.000	0.000
72	C	83	LEU	0	0.023	0.022	39.067	0.001	0.001	0.000	0.000	0.000	0.000
73	C	84	GLN	0	0.011	0.017	42.765	0.000	0.000	0.000	0.000	0.000	0.000
74	C	85	LEU	0	-0.034	-0.014	46.023	0.002	0.002	0.000	0.000	0.000	0.000
75	C	86	ALA	0	0.034	0.026	42.083	0.002	0.002	0.000	0.000	0.000	0.000
76	C	87	ILE	0	-0.010	-0.020	40.601	0.002	0.002	0.000	0.000	0.000	0.000
77	C	88	ARG	1	0.748	0.850	43.906	0.053	0.053	0.000	0.000	0.000	0.000
78	C	89	ASN	0	-0.054	-0.034	47.215	0.004	0.004	0.000	0.000	0.000	0.000
79	C	90	ASP	-1	-0.808	-0.884	42.783	-0.048	-0.048	0.000	0.000	0.000	0.000
80	C	91	GLU	-1	-0.941	-0.971	45.669	-0.035	-0.035	0.000	0.000	0.000	0.000
81	C	92	GLU	-1	-0.901	-0.951	41.788	-0.043	-0.043	0.000	0.000	0.000	0.000
82	C	93	LEU	0	-0.014	-0.019	38.399	-0.002	-0.002	0.000	0.000	0.000	0.000
83	C	94	ASN	0	0.014	0.018	42.145	-0.002	-0.002	0.000	0.000	0.000	0.000
84	C	95	LYS	1	0.918	0.960	44.415	0.039	0.039	0.000	0.000	0.000	0.000
85	C	96	LEU	0	-0.046	-0.021	37.444	0.000	0.000	0.000	0.000	0.000	0.000
86	C	97	LEU	0	0.014	0.004	39.131	-0.002	-0.002	0.000	0.000	0.000	0.000
87	C	98	GLY	0	0.030	0.034	43.158	0.000	0.000	0.000	0.000	0.000	0.000
88	C	99	ARG	1	0.841	0.902	45.533	0.043	0.043	0.000	0.000	0.000	0.000
89	C	100	VAL	0	0.029	0.029	41.465	-0.001	-0.001	0.000	0.000	0.000	0.000
90	C	101	THR	0	0.007	0.004	44.694	0.001	0.001	0.000	0.000	0.000	0.000
91	C	102	ILE	0	0.003	0.012	42.086	-0.003	-0.003	0.000	0.000	0.000	0.000
92	C	103	ALA	0	0.045	0.014	44.646	0.003	0.003	0.000	0.000	0.000	0.000
93	C	104	GLN	0	0.012	-0.010	45.586	-0.001	-0.001	0.000	0.000	0.000	0.000
94	C	105	GLY	0	0.031	0.024	47.131	0.000	0.000	0.000	0.000	0.000	0.000
95	C	106	GLY	0	0.002	0.004	47.748	0.002	0.002	0.000	0.000	0.000	0.000
96	C	107	VAL	0	0.046	0.022	50.569	-0.001	-0.001	0.000	0.000	0.000	0.000
97	C	108	LEU	0	0.038	0.025	50.053	-0.001	-0.001	0.000	0.000	0.000	0.000
98	C	109	PRO	0	-0.018	-0.015	53.668	0.001	0.001	0.000	0.000	0.000	0.000
99	C	110	ASN	0	0.008	0.008	57.055	0.002	0.002	0.000	0.000	0.000	0.000
100	C	111	ILE	0	0.028	0.019	59.444	0.000	0.000	0.000	0.000	0.000	0.000
101	C	112	GLN	0	0.009	0.004	61.709	0.001	0.001	0.000	0.000	0.000	0.000
102	C	113	ALA	0	0.072	0.024	65.093	0.000	0.000	0.000	0.000	0.000	0.000
103	C	114	VAL	0	0.028	0.017	67.625	0.000	0.000	0.000	0.000	0.000	0.000
104	C	115	LEU	0	-0.015	-0.006	66.403	0.001	0.001	0.000	0.000	0.000	0.000
105	C	116	LEU	0	-0.012	0.020	66.842	0.000	0.000	0.000	0.000	0.000	0.000
106	C	117	PRO	0	0.006	0.008	70.757	0.001	0.001	0.000	0.000	0.000	0.000
107	C	118	LYS	1	0.883	0.932	73.573	0.021	0.021	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:12:ALA)