FMO DATABASE

FMODB ID: RYYG8

Calculation Name: 5TP1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5TP1

Chain ID: A

ChEMBL ID:

UniProt ID: P0DJI4

Base Structure: X-ray

Registration Date: 2023-09-27

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	-1403718.550031
FMO2-HF: Nuclear repulsion	1343401.392446
FMO2-HF: Total energy	-60317.157585
FMO2-MP2: Total energy	-60495.025668

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:29:PRO)

Summations of interaction energy for fragment #1(A:29: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.
-3.895	-0.526	0.234	-1.417	-2.186	0

Interaction energy analysis for fragmet #1(A:29:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / q_NPA : 0.018

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	31	LEU	0	-0.022	0.002	3.499	-2.932	-0.932	-0.001	-0.921	-1.079	0.002
4	A	32	GLN	0	-0.051	-0.031	2.981	-0.868	0.478	0.236	-0.495	-1.087	-0.002
5	A	33	ILE	0	-0.008	0.001	5.398	0.084	0.107	-0.001	-0.001	-0.020	0.000
6	A	34	ASP	-1	-0.795	-0.870	9.079	-0.345	-0.345	0.000	0.000	0.000	0.000
7	A	35	ILE	0	-0.017	-0.014	11.645	0.038	0.038	0.000	0.000	0.000	0.000
8	A	36	PRO	0	-0.036	0.005	14.734	0.002	0.002	0.000	0.000	0.000	0.000
9	A	37	ASP	-1	-0.853	-0.903	16.992	-0.076	-0.076	0.000	0.000	0.000	0.000
10	A	38	ALA	0	0.017	-0.008	20.197	0.004	0.004	0.000	0.000	0.000	0.000
11	A	39	LEU	0	0.006	0.009	22.822	0.000	0.000	0.000	0.000	0.000	0.000
12	A	40	SER	0	0.015	0.011	26.594	0.003	0.003	0.000	0.000	0.000	0.000
13	A	41	GLU	-1	-0.813	-0.897	29.570	-0.017	-0.017	0.000	0.000	0.000	0.000
14	A	42	ARG	1	0.851	0.898	32.140	0.017	0.017	0.000	0.000	0.000	0.000
15	A	43	ASP	-1	-0.801	-0.883	34.484	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	44	LYS	1	0.806	0.903	29.946	0.008	0.008	0.000	0.000	0.000	0.000
17	A	45	VAL	0	-0.011	-0.008	25.074	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	46	LYS	1	0.833	0.912	24.520	0.023	0.023	0.000	0.000	0.000	0.000
19	A	47	PHE	0	0.002	-0.010	19.381	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	48	THR	0	-0.018	-0.030	17.738	0.015	0.015	0.000	0.000	0.000	0.000
21	A	49	VAL	0	-0.018	-0.011	14.382	-0.019	-0.019	0.000	0.000	0.000	0.000
22	A	50	HIS	1	0.762	0.851	12.312	0.236	0.236	0.000	0.000	0.000	0.000
23	A	51	THR	0	0.006	-0.010	9.604	-0.025	-0.025	0.000	0.000	0.000	0.000
24	A	52	LYS	1	0.881	0.946	7.149	0.500	0.500	0.000	0.000	0.000	0.000
25	A	53	THR	0	-0.040	-0.049	6.663	-0.049	-0.049	0.000	0.000	0.000	0.000
26	A	54	THR	0	0.018	0.002	5.632	-0.017	-0.017	0.000	0.000	0.000	0.000
27	A	55	LEU	0	-0.050	-0.015	7.509	0.126	0.126	0.000	0.000	0.000	0.000
28	A	56	SER	0	0.038	0.012	10.245	-0.063	-0.063	0.000	0.000	0.000	0.000
29	A	57	THR	0	-0.026	-0.009	12.411	0.002	0.002	0.000	0.000	0.000	0.000
30	A	58	PHE	0	-0.049	-0.035	10.530	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	59	GLN	0	-0.038	-0.019	14.580	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	60	SER	0	-0.023	-0.021	15.301	-0.024	-0.024	0.000	0.000	0.000	0.000
33	A	61	PRO	0	0.006	0.014	11.428	0.024	0.024	0.000	0.000	0.000	0.000
34	A	62	GLU	-1	-0.848	-0.913	10.703	-0.303	-0.303	0.000	0.000	0.000	0.000
35	A	63	PHE	0	-0.026	-0.009	12.563	0.029	0.029	0.000	0.000	0.000	0.000
36	A	64	SER	0	0.025	-0.005	14.155	-0.032	-0.032	0.000	0.000	0.000	0.000
37	A	65	VAL	0	0.009	0.041	16.683	0.010	0.010	0.000	0.000	0.000	0.000
38	A	66	THR	0	0.001	0.006	18.982	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	67	ARG	1	0.758	0.864	19.302	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	68	GLN	0	0.013	-0.016	22.164	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	69	HIS	0	0.038	0.025	23.608	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	70	GLU	-1	-0.801	-0.912	24.161	0.001	0.001	0.000	0.000	0.000	0.000
43	A	71	ASP	-1	-0.797	-0.872	22.283	0.016	0.016	0.000	0.000	0.000	0.000
44	A	72	PHE	0	0.000	-0.009	17.205	0.009	0.009	0.000	0.000	0.000	0.000
45	A	73	VAL	0	-0.017	-0.003	20.991	0.007	0.007	0.000	0.000	0.000	0.000
46	A	74	TRP	0	0.039	0.017	21.353	0.007	0.007	0.000	0.000	0.000	0.000
47	A	75	LEU	0	-0.017	0.015	16.198	0.008	0.008	0.000	0.000	0.000	0.000
48	A	76	HIS	0	-0.018	-0.025	19.613	0.010	0.010	0.000	0.000	0.000	0.000
49	A	77	ASP	-1	-0.898	-0.942	20.890	0.049	0.049	0.000	0.000	0.000	0.000
50	A	78	THR	0	-0.003	-0.012	22.348	0.004	0.004	0.000	0.000	0.000	0.000
51	A	79	LEU	0	-0.083	-0.033	16.793	0.012	0.012	0.000	0.000	0.000	0.000
52	A	80	THR	0	-0.034	-0.031	20.978	0.006	0.006	0.000	0.000	0.000	0.000
53	A	81	GLU	-1	-0.917	-0.952	23.600	0.054	0.054	0.000	0.000	0.000	0.000
54	A	82	THR	0	-0.100	-0.049	22.150	0.003	0.003	0.000	0.000	0.000	0.000
55	A	83	THR	0	0.028	-0.005	24.057	0.004	0.004	0.000	0.000	0.000	0.000
56	A	84	ASP	-1	-0.928	-0.948	23.260	0.115	0.115	0.000	0.000	0.000	0.000
57	A	85	TYR	0	-0.123	-0.093	18.950	0.029	0.029	0.000	0.000	0.000	0.000
58	A	86	ALA	0	0.031	0.023	21.431	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	87	GLY	0	0.011	0.003	22.796	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	88	LEU	0	-0.073	-0.020	16.930	0.007	0.007	0.000	0.000	0.000	0.000
61	A	89	ILE	0	-0.017	-0.010	16.607	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	90	ILE	0	0.003	-0.001	16.261	0.006	0.006	0.000	0.000	0.000	0.000
63	A	91	PRO	0	-0.069	-0.020	14.055	-0.017	-0.017	0.000	0.000	0.000	0.000
64	A	92	PRO	0	0.021	-0.003	16.936	0.004	0.004	0.000	0.000	0.000	0.000
65	A	93	ALA	0	0.051	0.030	19.341	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	94	PRO	0	-0.033	0.002	19.386	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	95	THR	0	0.042	0.004	21.634	0.003	0.003	0.000	0.000	0.000	0.000
68	A	96	LYS	1	0.828	0.900	25.145	0.013	0.013	0.000	0.000	0.000	0.000
69	A	97	PRO	0	-0.023	0.003	25.786	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	98	ASP	-1	-0.853	-0.927	27.900	-0.019	-0.019	0.000	0.000	0.000	0.000
71	A	99	PHE	0	0.036	-0.002	26.723	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	100	ASP	-1	-0.821	-0.891	32.375	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	101	GLY	0	0.059	0.033	35.900	0.001	0.001	0.000	0.000	0.000	0.000
74	A	102	PRO	0	0.027	0.007	32.976	0.001	0.001	0.000	0.000	0.000	0.000
75	A	103	ARG	1	0.837	0.916	35.465	0.017	0.017	0.000	0.000	0.000	0.000
76	A	104	GLU	-1	-0.881	-0.929	37.102	-0.015	-0.015	0.000	0.000	0.000	0.000
77	A	105	LYS	1	0.784	0.868	37.804	0.027	0.027	0.000	0.000	0.000	0.000
78	A	106	MET	0	-0.001	-0.009	35.196	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	107	GLN	0	-0.041	-0.010	39.445	0.000	0.000	0.000	0.000	0.000	0.000
80	A	108	LYS	1	0.925	0.950	42.406	0.017	0.017	0.000	0.000	0.000	0.000
81	A	109	LEU	0	-0.048	-0.007	40.910	0.000	0.000	0.000	0.000	0.000	0.000
82	A	110	GLY	0	0.018	0.007	43.471	0.000	0.000	0.000	0.000	0.000	0.000
83	A	111	GLU	-1	-0.952	-0.993	44.712	-0.015	-0.015	0.000	0.000	0.000	0.000
84	A	112	GLY	0	0.014	0.016	47.517	0.001	0.001	0.000	0.000	0.000	0.000
85	A	113	GLU	-1	-0.946	-0.975	45.424	-0.022	-0.022	0.000	0.000	0.000	0.000
86	A	114	GLY	0	-0.029	-0.007	48.327	0.000	0.000	0.000	0.000	0.000	0.000
87	A	115	SER	0	-0.113	-0.072	51.626	0.001	0.001	0.000	0.000	0.000	0.000
88	A	116	MET	0	-0.043	0.012	46.833	0.000	0.000	0.000	0.000	0.000	0.000
89	A	117	THR	0	0.008	0.006	51.205	0.000	0.000	0.000	0.000	0.000	0.000
90	A	118	LYS	1	1.006	0.988	48.438	0.020	0.020	0.000	0.000	0.000	0.000
91	A	119	GLU	-1	-0.871	-0.946	46.899	-0.024	-0.024	0.000	0.000	0.000	0.000
92	A	120	GLU	-1	-0.848	-0.907	46.418	-0.026	-0.026	0.000	0.000	0.000	0.000
93	A	121	PHE	0	0.002	-0.016	43.418	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	122	ALA	0	-0.003	-0.005	42.382	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	123	LYS	1	0.805	0.907	41.232	0.024	0.024	0.000	0.000	0.000	0.000
96	A	124	MET	0	0.082	0.037	40.909	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	125	LYS	1	0.816	0.901	36.394	0.037	0.037	0.000	0.000	0.000	0.000
98	A	126	GLN	0	0.001	0.005	36.129	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	127	GLU	-1	-0.919	-0.969	35.975	-0.034	-0.034	0.000	0.000	0.000	0.000
100	A	128	LEU	0	-0.010	0.007	36.255	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	129	GLU	-1	-0.823	-0.908	33.146	-0.044	-0.044	0.000	0.000	0.000	0.000
102	A	130	ALA	0	-0.019	-0.006	31.746	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	131	GLU	-1	-0.838	-0.897	31.433	-0.033	-0.033	0.000	0.000	0.000	0.000
104	A	132	TYR	0	0.029	-0.007	30.263	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	133	LEU	0	-0.010	0.001	25.785	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	134	ALA	0	-0.009	-0.001	26.565	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	135	VAL	0	-0.027	-0.004	26.670	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	136	PHE	0	0.020	-0.001	24.331	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	137	LYS	1	0.947	0.974	22.212	0.093	0.093	0.000	0.000	0.000	0.000
110	A	138	LYS	1	0.968	0.989	21.508	0.037	0.037	0.000	0.000	0.000	0.000
111	A	139	THR	0	-0.010	-0.008	22.151	0.000	0.000	0.000	0.000	0.000	0.000
112	A	140	VAL	0	0.064	0.037	17.834	0.004	0.004	0.000	0.000	0.000	0.000
113	A	141	SER	0	-0.004	0.017	17.223	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	142	THR	0	-0.008	-0.019	16.960	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	143	HIS	1	0.818	0.894	17.856	0.046	0.046	0.000	0.000	0.000	0.000
116	A	144	GLU	-1	-0.789	-0.886	12.360	-0.207	-0.207	0.000	0.000	0.000	0.000
117	A	145	VAL	0	0.023	0.007	12.755	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	146	PHE	0	-0.025	-0.012	12.786	0.010	0.010	0.000	0.000	0.000	0.000
119	A	147	LEU	0	0.037	0.020	12.429	0.030	0.030	0.000	0.000	0.000	0.000
120	A	148	GLN	0	-0.035	-0.021	8.502	0.054	0.054	0.000	0.000	0.000	0.000
121	A	149	ARG	1	0.949	0.983	8.256	0.016	0.016	0.000	0.000	0.000	0.000
122	A	150	LEU	0	-0.006	0.012	10.591	0.058	0.058	0.000	0.000	0.000	0.000
123	A	151	SER	0	-0.066	-0.048	6.618	0.023	0.023	0.000	0.000	0.000	0.000
124	A	152	SER	0	-0.025	-0.026	5.668	0.328	0.328	0.000	0.000	0.000	0.000
125	A	153	HIS	0	0.071	0.064	6.729	0.115	0.115	0.000	0.000	0.000	0.000
126	A	154	PRO	0	0.018	0.016	10.003	0.104	0.104	0.000	0.000	0.000	0.000
127	A	155	VAL	0	-0.006	0.006	10.923	0.040	0.040	0.000	0.000	0.000	0.000
128	A	156	LEU	0	0.057	0.012	13.147	0.005	0.005	0.000	0.000	0.000	0.000
129	A	157	SER	0	-0.048	-0.025	8.884	0.006	0.006	0.000	0.000	0.000	0.000
130	A	158	LYS	1	0.822	0.889	9.842	-0.786	-0.786	0.000	0.000	0.000	0.000
131	A	159	ASP	-1	-0.732	-0.833	13.512	0.117	0.117	0.000	0.000	0.000	0.000
132	A	160	ARG	1	0.947	0.967	16.514	-0.139	-0.139	0.000	0.000	0.000	0.000
133	A	161	ASN	0	0.031	0.016	19.212	-0.023	-0.023	0.000	0.000	0.000	0.000
134	A	162	PHE	0	0.054	0.029	10.531	-0.022	-0.022	0.000	0.000	0.000	0.000
135	A	163	HIS	1	0.812	0.896	14.996	-0.201	-0.201	0.000	0.000	0.000	0.000
136	A	164	VAL	0	-0.023	-0.021	16.160	-0.020	-0.020	0.000	0.000	0.000	0.000
137	A	165	PHE	0	0.024	-0.004	16.085	-0.016	-0.016	0.000	0.000	0.000	0.000
138	A	166	LEU	0	0.008	0.010	11.673	-0.018	-0.018	0.000	0.000	0.000	0.000
139	A	167	GLU	-1	-0.748	-0.853	15.689	0.101	0.101	0.000	0.000	0.000	0.000
140	A	168	TYR	0	-0.114	-0.054	17.507	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	169	ASP	-1	-0.882	-0.942	21.305	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	170	GLN	0	0.019	0.037	22.683	-0.003	-0.003	0.000	0.000	0.000	0.000
143	A	171	ASP	-1	-0.803	-0.878	24.498	0.011	0.011	0.000	0.000	0.000	0.000
144	A	172	LEU	0	-0.010	-0.001	21.658	0.006	0.006	0.000	0.000	0.000	0.000
145	A	173	SER	0	-0.059	-0.062	26.280	0.005	0.005	0.000	0.000	0.000	0.000
146	A	174	VAL	0	0.010	-0.006	29.775	0.002	0.002	0.000	0.000	0.000	0.000
147	A	175	ARG	1	0.884	0.940	24.000	-0.071	-0.071	0.000	0.000	0.000	0.000
148	A	176	ARG	1	0.813	0.900	25.935	-0.013	-0.013	0.000	0.000	0.000	0.000
149	A	177	LYS	1	0.897	0.957	29.207	-0.027	-0.027	0.000	0.000	0.000	0.000
150	A	178	ASN	0	0.015	0.022	30.401	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:29:PRO)