FMO DATABASE

FMODB ID: 49N6N

Calculation Name: 5TPM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5TPM

Chain ID: A

ChEMBL ID:

UniProt ID: P0ACL9

Base Structure: X-ray

Registration Date: 2023-06-21

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	155
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1556798.161693
FMO2-HF: Nuclear repulsion	1493601.173571
FMO2-HF: Total energy	-63196.988122
FMO2-MP2: Total energy	-63381.302047

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:-2:SER)

Summations of interaction energy for fragment #1(A:-2:SER)

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.
-36.063	-37.284	22.476	-11.983	-9.273	-0.048

Interaction energy analysis for fragmet #1(A:-2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.049

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	0	ALA	0	0.030	0.026	2.605	-6.375	-2.644	0.932	-2.134	-2.530	0.016
4	A	99	ASP	-1	-0.796	-0.880	1.646	-31.514	-36.985	21.544	-9.703	-6.371	-0.064
5	A	100	LEU	0	-0.037	0.000	3.805	1.506	1.966	0.001	-0.142	-0.319	0.000
6	A	101	LEU	0	-0.013	-0.003	5.802	0.575	0.575	0.000	0.000	0.000	0.000
7	A	102	GLU	-1	-0.891	-0.938	6.958	-1.901	-1.901	0.000	0.000	0.000	0.000
8	A	103	THR	0	-0.051	-0.046	7.046	0.334	0.334	0.000	0.000	0.000	0.000
9	A	104	ARG	1	0.762	0.835	9.505	0.324	0.324	0.000	0.000	0.000	0.000
10	A	105	HIS	0	-0.069	-0.045	11.392	0.147	0.147	0.000	0.000	0.000	0.000
11	A	106	ALA	0	-0.002	0.009	12.703	0.102	0.102	0.000	0.000	0.000	0.000
12	A	107	LEU	0	-0.017	-0.022	12.476	0.127	0.127	0.000	0.000	0.000	0.000
13	A	108	GLU	-1	-0.709	-0.838	14.348	-0.055	-0.055	0.000	0.000	0.000	0.000
14	A	109	GLY	0	0.044	0.048	16.975	0.062	0.062	0.000	0.000	0.000	0.000
15	A	110	ILE	0	-0.034	-0.035	18.204	0.050	0.050	0.000	0.000	0.000	0.000
16	A	111	ALA	0	0.001	0.006	19.371	0.033	0.033	0.000	0.000	0.000	0.000
17	A	112	ALA	0	0.052	0.023	21.207	0.030	0.030	0.000	0.000	0.000	0.000
18	A	113	TYR	0	-0.116	-0.063	22.979	0.016	0.016	0.000	0.000	0.000	0.000
19	A	114	TYR	0	-0.006	-0.023	23.429	0.022	0.022	0.000	0.000	0.000	0.000
20	A	115	ALA	0	0.044	0.034	25.107	0.016	0.016	0.000	0.000	0.000	0.000
21	A	116	ALA	0	-0.010	0.013	26.927	0.016	0.016	0.000	0.000	0.000	0.000
22	A	117	LEU	0	-0.090	-0.035	28.973	0.008	0.008	0.000	0.000	0.000	0.000
23	A	118	ARG	1	0.849	0.918	28.277	0.161	0.161	0.000	0.000	0.000	0.000
24	A	119	SER	0	-0.006	0.016	29.561	0.010	0.010	0.000	0.000	0.000	0.000
25	A	120	THR	0	-0.046	-0.058	31.209	0.000	0.000	0.000	0.000	0.000	0.000
26	A	121	ASP	-1	-0.880	-0.950	34.077	-0.036	-0.036	0.000	0.000	0.000	0.000
27	A	122	GLU	-1	-0.829	-0.896	35.077	-0.023	-0.023	0.000	0.000	0.000	0.000
28	A	123	ASP	-1	-0.817	-0.898	30.303	-0.044	-0.044	0.000	0.000	0.000	0.000
29	A	124	LYS	1	0.835	0.916	30.913	0.065	0.065	0.000	0.000	0.000	0.000
30	A	125	GLU	-1	-0.955	-0.978	32.703	0.007	0.007	0.000	0.000	0.000	0.000
31	A	126	ARG	1	0.863	0.916	25.752	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	127	ILE	0	-0.024	-0.029	26.890	0.010	0.010	0.000	0.000	0.000	0.000
33	A	128	ARG	1	0.900	0.942	29.057	0.019	0.019	0.000	0.000	0.000	0.000
34	A	129	GLU	-1	-0.937	-0.958	30.764	0.053	0.053	0.000	0.000	0.000	0.000
35	A	130	LEU	0	-0.025	-0.018	25.721	0.014	0.014	0.000	0.000	0.000	0.000
36	A	131	HIS	0	-0.033	-0.028	26.888	0.015	0.015	0.000	0.000	0.000	0.000
37	A	132	HIS	0	0.024	0.007	28.088	0.012	0.012	0.000	0.000	0.000	0.000
38	A	133	ALA	0	-0.003	-0.004	27.882	0.010	0.010	0.000	0.000	0.000	0.000
39	A	134	ILE	0	-0.009	-0.005	23.405	0.018	0.018	0.000	0.000	0.000	0.000
40	A	135	GLU	-1	-0.876	-0.908	26.227	0.112	0.112	0.000	0.000	0.000	0.000
41	A	136	LEU	0	-0.038	-0.023	29.002	0.008	0.008	0.000	0.000	0.000	0.000
42	A	137	ALA	0	0.009	0.017	25.900	0.007	0.007	0.000	0.000	0.000	0.000
43	A	138	GLN	0	-0.006	0.000	23.923	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	139	GLN	0	-0.120	-0.082	27.006	0.006	0.006	0.000	0.000	0.000	0.000
45	A	140	SER	0	-0.102	-0.056	28.698	0.002	0.002	0.000	0.000	0.000	0.000
46	A	141	GLY	0	-0.025	-0.010	27.351	0.004	0.004	0.000	0.000	0.000	0.000
47	A	142	ASP	-1	-0.899	-0.946	25.019	0.291	0.291	0.000	0.000	0.000	0.000
48	A	143	LEU	0	0.001	-0.001	18.118	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	144	ASP	-1	-0.959	-0.985	20.345	0.363	0.363	0.000	0.000	0.000	0.000
50	A	145	ALA	0	0.057	0.032	21.364	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	146	GLU	-1	-0.742	-0.857	22.135	0.192	0.192	0.000	0.000	0.000	0.000
52	A	147	SER	0	-0.047	-0.027	16.865	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	148	ASN	0	0.029	0.002	19.116	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	149	ALA	0	0.018	0.018	21.037	-0.030	-0.030	0.000	0.000	0.000	0.000
55	A	150	VAL	0	-0.005	-0.012	18.143	-0.032	-0.032	0.000	0.000	0.000	0.000
56	A	151	LEU	0	-0.030	-0.004	15.792	-0.034	-0.034	0.000	0.000	0.000	0.000
57	A	152	GLN	0	0.006	-0.014	18.925	-0.063	-0.063	0.000	0.000	0.000	0.000
58	A	153	TYR	0	0.012	0.018	21.604	-0.028	-0.028	0.000	0.000	0.000	0.000
59	A	154	GLN	0	-0.003	-0.020	17.334	-0.023	-0.023	0.000	0.000	0.000	0.000
60	A	155	ILE	0	-0.032	0.000	18.794	-0.044	-0.044	0.000	0.000	0.000	0.000
61	A	156	ALA	0	0.001	0.006	20.957	-0.024	-0.024	0.000	0.000	0.000	0.000
62	A	157	VAL	0	0.003	0.005	22.275	-0.016	-0.016	0.000	0.000	0.000	0.000
63	A	158	THR	0	-0.033	-0.043	19.024	-0.037	-0.037	0.000	0.000	0.000	0.000
64	A	159	GLU	-1	-0.864	-0.913	22.004	-0.020	-0.020	0.000	0.000	0.000	0.000
65	A	160	ALA	0	0.032	0.027	24.786	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	161	ALA	0	-0.026	-0.004	23.829	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	162	HIS	0	-0.060	-0.042	25.850	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	163	ASN	0	-0.024	-0.012	23.127	-0.016	-0.016	0.000	0.000	0.000	0.000
69	A	164	VAL	0	0.059	0.025	23.094	-0.008	-0.008	0.000	0.000	0.000	0.000
70	A	165	VAL	0	0.024	0.017	19.616	0.005	0.005	0.000	0.000	0.000	0.000
71	A	166	LEU	0	0.018	0.018	17.478	-0.025	-0.025	0.000	0.000	0.000	0.000
72	A	167	LEU	0	0.048	0.029	18.178	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	168	HIS	0	-0.066	-0.044	18.848	0.035	0.035	0.000	0.000	0.000	0.000
74	A	169	LEU	0	-0.026	-0.013	14.220	0.007	0.007	0.000	0.000	0.000	0.000
75	A	170	LEU	0	0.016	0.017	14.009	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	171	ARG	1	0.832	0.875	14.589	0.020	0.020	0.000	0.000	0.000	0.000
77	A	172	CYS	0	-0.075	-0.035	12.746	0.046	0.046	0.000	0.000	0.000	0.000
78	A	173	MET	0	-0.005	0.008	9.665	-0.051	-0.051	0.000	0.000	0.000	0.000
79	A	174	GLU	-1	-0.812	-0.879	10.957	0.244	0.244	0.000	0.000	0.000	0.000
80	A	175	PRO	0	0.003	-0.011	11.533	0.076	0.076	0.000	0.000	0.000	0.000
81	A	176	MET	0	0.012	0.004	4.440	0.024	0.083	-0.001	-0.004	-0.053	0.000
82	A	177	LEU	0	0.019	0.021	9.056	0.111	0.111	0.000	0.000	0.000	0.000
83	A	178	ALA	0	0.036	0.014	11.297	0.055	0.055	0.000	0.000	0.000	0.000
84	A	179	GLN	0	-0.036	-0.014	7.669	0.245	0.245	0.000	0.000	0.000	0.000
85	A	180	ASN	0	0.038	0.023	7.250	-0.091	-0.091	0.000	0.000	0.000	0.000
86	A	181	VAL	0	0.012	0.001	9.883	0.001	0.001	0.000	0.000	0.000	0.000
87	A	182	ARG	1	0.865	0.929	13.390	-0.842	-0.842	0.000	0.000	0.000	0.000
88	A	183	GLN	0	0.026	0.020	7.355	0.132	0.132	0.000	0.000	0.000	0.000
89	A	184	ASN	0	-0.005	-0.010	11.368	0.031	0.031	0.000	0.000	0.000	0.000
90	A	185	PHE	0	0.010	0.013	13.465	-0.062	-0.062	0.000	0.000	0.000	0.000
91	A	186	GLU	-1	-0.867	-0.933	13.635	0.915	0.915	0.000	0.000	0.000	0.000
92	A	187	LEU	0	-0.041	-0.015	11.652	-0.047	-0.047	0.000	0.000	0.000	0.000
93	A	188	LEU	0	0.009	-0.002	15.951	-0.070	-0.070	0.000	0.000	0.000	0.000
94	A	189	TYR	0	-0.028	-0.040	18.677	-0.044	-0.044	0.000	0.000	0.000	0.000
95	A	190	SER	0	-0.078	-0.025	19.248	-0.017	-0.017	0.000	0.000	0.000	0.000
96	A	191	ARG	1	0.718	0.824	20.470	-0.304	-0.304	0.000	0.000	0.000	0.000
97	A	192	ARG	1	0.986	0.986	22.335	-0.298	-0.298	0.000	0.000	0.000	0.000
98	A	193	GLU	-1	-0.842	-0.926	24.185	0.210	0.210	0.000	0.000	0.000	0.000
99	A	194	MET	0	-0.006	-0.006	20.470	-0.033	-0.033	0.000	0.000	0.000	0.000
100	A	195	LEU	0	-0.012	0.014	21.156	-0.017	-0.017	0.000	0.000	0.000	0.000
101	A	196	PRO	0	0.076	0.032	23.561	-0.016	-0.016	0.000	0.000	0.000	0.000
102	A	197	LEU	0	-0.004	0.002	23.572	-0.022	-0.022	0.000	0.000	0.000	0.000
103	A	198	VAL	0	0.013	0.009	19.248	-0.028	-0.028	0.000	0.000	0.000	0.000
104	A	199	SER	0	0.039	0.012	21.789	-0.021	-0.021	0.000	0.000	0.000	0.000
105	A	200	SER	0	-0.001	0.027	24.603	-0.026	-0.026	0.000	0.000	0.000	0.000
106	A	201	HIS	0	-0.033	-0.026	21.692	-0.037	-0.037	0.000	0.000	0.000	0.000
107	A	202	ARG	1	0.892	0.945	20.185	-0.155	-0.155	0.000	0.000	0.000	0.000
108	A	203	THR	0	0.005	-0.014	23.142	-0.013	-0.013	0.000	0.000	0.000	0.000
109	A	204	ARG	1	0.823	0.907	25.090	0.013	0.013	0.000	0.000	0.000	0.000
110	A	205	ILE	0	-0.020	0.003	20.668	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	206	PHE	0	0.027	0.017	25.157	-0.009	-0.009	0.000	0.000	0.000	0.000
112	A	207	GLU	-1	-0.799	-0.912	27.621	-0.019	-0.019	0.000	0.000	0.000	0.000
113	A	208	ALA	0	-0.043	-0.002	27.862	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	209	ILE	0	-0.014	-0.013	24.782	-0.009	-0.009	0.000	0.000	0.000	0.000
115	A	210	MET	0	-0.074	-0.012	29.356	0.002	0.002	0.000	0.000	0.000	0.000
116	A	211	ALA	0	-0.054	-0.030	32.711	0.001	0.001	0.000	0.000	0.000	0.000
117	A	212	GLY	0	0.017	0.028	32.704	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	213	LYS	1	0.778	0.869	31.022	0.075	0.075	0.000	0.000	0.000	0.000
119	A	214	PRO	0	0.018	0.005	27.905	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	215	GLU	-1	-0.789	-0.881	26.554	-0.214	-0.214	0.000	0.000	0.000	0.000
121	A	216	GLU	-1	-0.817	-0.902	26.154	-0.104	-0.104	0.000	0.000	0.000	0.000
122	A	217	ALA	0	0.039	0.028	25.858	0.000	0.000	0.000	0.000	0.000	0.000
123	A	218	ARG	1	0.838	0.912	21.460	0.249	0.249	0.000	0.000	0.000	0.000
124	A	219	GLU	-1	-0.791	-0.863	21.244	-0.250	-0.250	0.000	0.000	0.000	0.000
125	A	220	ALA	0	-0.021	-0.016	21.956	0.002	0.002	0.000	0.000	0.000	0.000
126	A	221	SER	0	-0.048	-0.040	19.285	0.022	0.022	0.000	0.000	0.000	0.000
127	A	222	HIS	0	0.008	-0.009	17.213	-0.026	-0.026	0.000	0.000	0.000	0.000
128	A	223	ARG	1	0.826	0.887	17.105	0.157	0.157	0.000	0.000	0.000	0.000
129	A	224	HIS	0	-0.046	-0.017	18.880	0.045	0.045	0.000	0.000	0.000	0.000
130	A	225	LEU	0	-0.013	0.010	13.469	0.064	0.064	0.000	0.000	0.000	0.000
131	A	226	ALA	0	0.078	0.039	14.136	0.047	0.047	0.000	0.000	0.000	0.000
132	A	227	PHE	0	0.006	0.003	15.291	0.056	0.056	0.000	0.000	0.000	0.000
133	A	228	ILE	0	-0.020	-0.010	12.649	0.066	0.066	0.000	0.000	0.000	0.000
134	A	229	GLU	-1	-0.844	-0.923	10.109	-0.343	-0.343	0.000	0.000	0.000	0.000
135	A	230	GLU	-1	-0.958	-0.982	12.285	0.021	0.021	0.000	0.000	0.000	0.000
136	A	231	ILE	0	0.008	0.002	15.288	0.059	0.059	0.000	0.000	0.000	0.000
137	A	232	LEU	0	-0.046	-0.018	9.281	0.073	0.073	0.000	0.000	0.000	0.000
138	A	233	LEU	0	-0.001	0.003	10.477	0.083	0.083	0.000	0.000	0.000	0.000
139	A	234	ASP	-1	-0.855	-0.925	13.250	0.148	0.148	0.000	0.000	0.000	0.000
140	A	235	ARG	1	0.834	0.913	14.723	-0.625	-0.625	0.000	0.000	0.000	0.000
141	A	236	SER	0	0.049	0.004	12.499	0.039	0.039	0.000	0.000	0.000	0.000
142	A	237	ARG	1	0.817	0.896	14.580	-0.125	-0.125	0.000	0.000	0.000	0.000
143	A	238	GLU	-1	-0.844	-0.880	17.317	0.264	0.264	0.000	0.000	0.000	0.000
144	A	239	GLU	-1	-0.804	-0.871	14.502	0.697	0.697	0.000	0.000	0.000	0.000
145	A	240	SER	0	-0.037	-0.028	15.974	-0.029	-0.029	0.000	0.000	0.000	0.000
146	A	241	ARG	1	0.909	0.948	18.582	-0.170	-0.170	0.000	0.000	0.000	0.000
147	A	242	ARG	1	0.962	1.012	21.836	-0.298	-0.298	0.000	0.000	0.000	0.000
148	A	243	GLU	-1	-0.753	-0.860	21.021	0.250	0.250	0.000	0.000	0.000	0.000
149	A	244	ARG	1	0.922	0.956	18.694	-0.224	-0.224	0.000	0.000	0.000	0.000
150	A	245	SER	0	-0.063	-0.052	23.910	-0.029	-0.029	0.000	0.000	0.000	0.000
151	A	246	LEU	0	0.016	0.008	25.105	-0.014	-0.014	0.000	0.000	0.000	0.000
152	A	247	ARG	1	0.865	0.915	24.303	-0.230	-0.230	0.000	0.000	0.000	0.000
153	A	248	ARG	1	0.852	0.928	26.016	-0.115	-0.115	0.000	0.000	0.000	0.000
154	A	249	LEU	0	-0.019	0.000	30.175	-0.012	-0.012	0.000	0.000	0.000	0.000
155	A	250	GLU	-1	-0.970	-0.967	33.060	0.117	0.117	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:SER)