FMO DATABASE

FMODB ID: QY8MY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1545422.088045
FMO2-HF: Nuclear repulsion	1482226.215444
FMO2-HF: Total energy	-63195.872601
FMO2-MP2: Total energy	-63380.05213

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.
-21.286	-14.498	5.17	-5.02	-6.939	0.013

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 : 0.023 / q_NPA : 0.000

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	-0.007	-0.002	2.328	-6.551	-4.054	2.864	-2.293	-3.068	0.023
4	A	99	ASP	-1	-0.848	-0.934	2.290	-16.228	-12.272	2.303	-2.724	-3.536	-0.010
5	A	100	LEU	0	-0.041	-0.015	3.672	0.837	1.121	0.004	0.000	-0.288	0.000
6	A	101	LEU	0	0.007	0.000	5.682	0.542	0.542	0.000	0.000	0.000	0.000
7	A	102	GLU	-1	-0.894	-0.938	7.232	-1.540	-1.540	0.000	0.000	0.000	0.000
8	A	103	THR	0	-0.012	-0.005	7.537	0.214	0.214	0.000	0.000	0.000	0.000
9	A	104	ARG	1	0.810	0.902	9.726	0.343	0.343	0.000	0.000	0.000	0.000
10	A	105	HIS	0	-0.019	0.002	11.429	0.124	0.124	0.000	0.000	0.000	0.000
11	A	106	ALA	0	-0.016	0.002	12.779	0.087	0.087	0.000	0.000	0.000	0.000
12	A	107	LEU	0	-0.004	-0.031	12.541	0.103	0.103	0.000	0.000	0.000	0.000
13	A	108	GLU	-1	-0.774	-0.911	14.641	-0.107	-0.107	0.000	0.000	0.000	0.000
14	A	109	GLY	0	0.011	0.020	17.108	0.056	0.056	0.000	0.000	0.000	0.000
15	A	110	ILE	0	-0.063	-0.042	17.925	0.044	0.044	0.000	0.000	0.000	0.000
16	A	111	ALA	0	0.022	0.013	19.143	0.028	0.028	0.000	0.000	0.000	0.000
17	A	112	ALA	0	0.057	0.018	21.016	0.028	0.028	0.000	0.000	0.000	0.000
18	A	113	TYR	0	-0.088	-0.033	23.127	0.016	0.016	0.000	0.000	0.000	0.000
19	A	114	TYR	0	-0.009	-0.027	23.634	0.019	0.019	0.000	0.000	0.000	0.000
20	A	115	ALA	0	0.039	0.042	24.925	0.014	0.014	0.000	0.000	0.000	0.000
21	A	116	ALA	0	-0.019	-0.004	26.739	0.015	0.015	0.000	0.000	0.000	0.000
22	A	117	LEU	0	-0.079	-0.038	29.058	0.008	0.008	0.000	0.000	0.000	0.000
23	A	118	ARG	1	0.853	0.922	27.451	0.152	0.152	0.000	0.000	0.000	0.000
24	A	119	SER	0	-0.001	0.033	29.516	0.009	0.009	0.000	0.000	0.000	0.000
25	A	120	THR	0	-0.015	-0.003	31.162	0.000	0.000	0.000	0.000	0.000	0.000
26	A	121	ASP	-1	-0.884	-0.954	34.003	-0.036	-0.036	0.000	0.000	0.000	0.000
27	A	122	GLU	-1	-0.866	-0.943	34.883	-0.025	-0.025	0.000	0.000	0.000	0.000
28	A	123	ASP	-1	-0.864	-0.928	29.950	-0.047	-0.047	0.000	0.000	0.000	0.000
29	A	124	LYS	1	0.865	0.917	30.862	0.064	0.064	0.000	0.000	0.000	0.000
30	A	125	GLU	-1	-0.965	-0.978	32.250	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	126	ARG	1	0.933	0.957	26.071	0.005	0.005	0.000	0.000	0.000	0.000
32	A	127	ILE	0	-0.023	-0.025	26.748	0.008	0.008	0.000	0.000	0.000	0.000
33	A	128	ARG	1	0.966	0.975	28.701	0.019	0.019	0.000	0.000	0.000	0.000
34	A	129	GLU	-1	-0.964	-0.959	30.605	0.037	0.037	0.000	0.000	0.000	0.000
35	A	130	LEU	0	-0.024	-0.020	25.333	0.011	0.011	0.000	0.000	0.000	0.000
36	A	131	HIS	0	-0.044	-0.025	26.222	0.011	0.011	0.000	0.000	0.000	0.000
37	A	132	HIS	0	0.026	0.007	27.671	0.008	0.008	0.000	0.000	0.000	0.000
38	A	133	ALA	0	-0.005	-0.008	27.621	0.009	0.009	0.000	0.000	0.000	0.000
39	A	134	ILE	0	-0.031	-0.018	23.207	0.014	0.014	0.000	0.000	0.000	0.000
40	A	135	GLU	-1	-0.878	-0.922	26.342	0.095	0.095	0.000	0.000	0.000	0.000
41	A	136	LEU	0	-0.038	-0.024	29.055	0.007	0.007	0.000	0.000	0.000	0.000
42	A	137	ALA	0	0.005	0.011	26.008	0.006	0.006	0.000	0.000	0.000	0.000
43	A	138	GLN	0	-0.059	-0.038	24.833	0.008	0.008	0.000	0.000	0.000	0.000
44	A	139	GLN	0	-0.099	-0.058	27.096	0.009	0.009	0.000	0.000	0.000	0.000
45	A	140	SER	0	-0.103	-0.034	28.978	0.002	0.002	0.000	0.000	0.000	0.000
46	A	141	GLY	0	-0.025	-0.016	27.348	0.005	0.005	0.000	0.000	0.000	0.000
47	A	142	ASP	-1	-0.887	-0.941	25.569	0.244	0.244	0.000	0.000	0.000	0.000
48	A	143	LEU	0	0.002	-0.003	18.128	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	144	ASP	-1	-0.943	-0.987	20.633	0.287	0.287	0.000	0.000	0.000	0.000
50	A	145	ALA	0	0.037	0.033	21.688	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	146	GLU	-1	-0.777	-0.885	21.991	0.163	0.163	0.000	0.000	0.000	0.000
52	A	147	SER	0	-0.033	-0.026	16.896	-0.020	-0.020	0.000	0.000	0.000	0.000
53	A	148	ASN	0	0.013	-0.009	19.024	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	149	ALA	0	0.016	0.014	20.857	-0.026	-0.026	0.000	0.000	0.000	0.000
55	A	150	VAL	0	-0.012	-0.005	17.845	-0.031	-0.031	0.000	0.000	0.000	0.000
56	A	151	LEU	0	-0.024	-0.006	15.409	-0.033	-0.033	0.000	0.000	0.000	0.000
57	A	152	GLN	0	0.008	-0.010	18.544	-0.052	-0.052	0.000	0.000	0.000	0.000
58	A	153	TYR	0	0.020	0.025	21.243	-0.023	-0.023	0.000	0.000	0.000	0.000
59	A	154	GLN	0	-0.003	-0.010	16.744	-0.048	-0.048	0.000	0.000	0.000	0.000
60	A	155	ILE	0	-0.005	0.006	18.791	-0.036	-0.036	0.000	0.000	0.000	0.000
61	A	156	ALA	0	0.014	0.019	20.702	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	157	VAL	0	0.006	0.003	21.908	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	158	THR	0	-0.018	-0.023	19.117	-0.031	-0.031	0.000	0.000	0.000	0.000
64	A	159	GLU	-1	-0.936	-0.977	21.757	-0.038	-0.038	0.000	0.000	0.000	0.000
65	A	160	ALA	0	0.024	0.024	24.655	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	161	ALA	0	-0.029	-0.006	23.712	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	162	HIS	0	-0.054	-0.027	25.764	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	163	ASN	0	-0.017	-0.017	23.038	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	164	VAL	0	0.060	0.016	22.900	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	165	VAL	0	0.023	0.021	19.094	0.002	0.002	0.000	0.000	0.000	0.000
71	A	166	LEU	0	0.029	0.027	17.634	-0.023	-0.023	0.000	0.000	0.000	0.000
72	A	167	LEU	0	0.043	0.025	17.895	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	168	HIS	0	-0.069	-0.049	18.616	0.026	0.026	0.000	0.000	0.000	0.000
74	A	169	LEU	0	-0.008	-0.007	14.328	0.003	0.003	0.000	0.000	0.000	0.000
75	A	170	LEU	0	0.012	0.022	13.698	-0.032	-0.032	0.000	0.000	0.000	0.000
76	A	171	ARG	1	0.902	0.939	14.360	0.051	0.051	0.000	0.000	0.000	0.000
77	A	172	CYS	0	-0.089	-0.028	13.212	0.048	0.048	0.000	0.000	0.000	0.000
78	A	173	MET	0	0.030	0.019	9.326	-0.034	-0.034	0.000	0.000	0.000	0.000
79	A	174	GLU	-1	-0.869	-0.931	10.693	0.149	0.149	0.000	0.000	0.000	0.000
80	A	175	PRO	0	-0.008	-0.006	11.454	0.068	0.068	0.000	0.000	0.000	0.000
81	A	176	MET	0	0.014	0.001	4.717	0.082	0.133	-0.001	-0.003	-0.047	0.000
82	A	177	LEU	0	0.012	0.018	8.730	0.071	0.071	0.000	0.000	0.000	0.000
83	A	178	ALA	0	0.044	0.005	10.775	0.069	0.069	0.000	0.000	0.000	0.000
84	A	179	GLN	0	-0.067	-0.028	8.114	0.191	0.191	0.000	0.000	0.000	0.000
85	A	180	ASN	0	0.029	0.012	7.764	-0.110	-0.110	0.000	0.000	0.000	0.000
86	A	181	VAL	0	0.016	0.012	9.919	0.045	0.045	0.000	0.000	0.000	0.000
87	A	182	ARG	1	0.940	0.971	13.607	-0.613	-0.613	0.000	0.000	0.000	0.000
88	A	183	GLN	0	0.027	0.017	7.577	0.073	0.073	0.000	0.000	0.000	0.000
89	A	184	ASN	0	-0.003	-0.004	11.253	0.111	0.111	0.000	0.000	0.000	0.000
90	A	185	PHE	0	-0.015	-0.019	13.371	-0.041	-0.041	0.000	0.000	0.000	0.000
91	A	186	GLU	-1	-0.949	-0.954	14.346	0.747	0.747	0.000	0.000	0.000	0.000
92	A	187	LEU	0	-0.055	-0.028	12.052	-0.050	-0.050	0.000	0.000	0.000	0.000
93	A	188	LEU	0	-0.032	-0.017	16.065	-0.057	-0.057	0.000	0.000	0.000	0.000
94	A	189	TYR	0	-0.046	-0.051	18.698	-0.033	-0.033	0.000	0.000	0.000	0.000
95	A	190	SER	0	-0.097	-0.029	19.154	-0.018	-0.018	0.000	0.000	0.000	0.000
96	A	191	ARG	1	0.840	0.926	20.176	-0.299	-0.299	0.000	0.000	0.000	0.000
97	A	192	ARG	1	1.022	0.998	22.294	-0.245	-0.245	0.000	0.000	0.000	0.000
98	A	193	GLU	-1	-0.861	-0.929	24.678	0.177	0.177	0.000	0.000	0.000	0.000
99	A	194	MET	0	-0.016	-0.011	20.673	-0.027	-0.027	0.000	0.000	0.000	0.000
100	A	195	LEU	0	0.008	0.008	21.348	-0.014	-0.014	0.000	0.000	0.000	0.000
101	A	196	PRO	0	0.070	0.037	23.430	-0.016	-0.016	0.000	0.000	0.000	0.000
102	A	197	LEU	0	0.025	0.007	23.512	-0.019	-0.019	0.000	0.000	0.000	0.000
103	A	198	VAL	0	0.011	0.035	19.223	-0.023	-0.023	0.000	0.000	0.000	0.000
104	A	199	SER	0	0.051	0.017	21.857	-0.022	-0.022	0.000	0.000	0.000	0.000
105	A	200	SER	0	-0.038	0.003	24.449	-0.023	-0.023	0.000	0.000	0.000	0.000
106	A	201	HIS	0	-0.063	-0.055	21.880	-0.031	-0.031	0.000	0.000	0.000	0.000
107	A	202	ARG	1	0.973	0.986	19.514	-0.103	-0.103	0.000	0.000	0.000	0.000
108	A	203	THR	0	0.018	-0.002	23.357	-0.011	-0.011	0.000	0.000	0.000	0.000
109	A	204	ARG	1	0.929	0.971	24.930	0.022	0.022	0.000	0.000	0.000	0.000
110	A	205	ILE	0	-0.017	0.011	21.055	-0.011	-0.011	0.000	0.000	0.000	0.000
111	A	206	PHE	0	0.036	0.009	25.489	-0.007	-0.007	0.000	0.000	0.000	0.000
112	A	207	GLU	-1	-0.898	-0.961	27.558	-0.020	-0.020	0.000	0.000	0.000	0.000
113	A	208	ALA	0	-0.036	-0.005	27.898	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	209	ILE	0	-0.020	-0.012	24.741	-0.008	-0.008	0.000	0.000	0.000	0.000
115	A	210	MET	0	-0.071	-0.012	29.339	0.002	0.002	0.000	0.000	0.000	0.000
116	A	211	ALA	0	-0.051	-0.029	32.518	0.001	0.001	0.000	0.000	0.000	0.000
117	A	212	GLY	0	0.020	0.026	32.386	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	213	LYS	1	0.893	0.953	31.306	0.059	0.059	0.000	0.000	0.000	0.000
119	A	214	PRO	0	0.045	0.008	28.181	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	215	GLU	-1	-0.922	-0.971	26.789	-0.167	-0.167	0.000	0.000	0.000	0.000
121	A	216	GLU	-1	-0.952	-0.984	26.394	-0.091	-0.091	0.000	0.000	0.000	0.000
122	A	217	ALA	0	0.034	0.028	25.702	0.001	0.001	0.000	0.000	0.000	0.000
123	A	218	ARG	1	0.929	0.968	21.202	0.229	0.229	0.000	0.000	0.000	0.000
124	A	219	GLU	-1	-0.921	-0.958	21.513	-0.210	-0.210	0.000	0.000	0.000	0.000
125	A	220	ALA	0	-0.062	-0.037	22.327	0.003	0.003	0.000	0.000	0.000	0.000
126	A	221	SER	0	-0.010	-0.013	18.669	0.015	0.015	0.000	0.000	0.000	0.000
127	A	222	HIS	0	0.046	0.024	17.507	-0.009	-0.009	0.000	0.000	0.000	0.000
128	A	223	ARG	1	0.966	0.964	17.672	0.121	0.121	0.000	0.000	0.000	0.000
129	A	224	HIS	0	-0.045	-0.012	17.982	0.037	0.037	0.000	0.000	0.000	0.000
130	A	225	LEU	0	-0.005	-0.001	13.753	0.050	0.050	0.000	0.000	0.000	0.000
131	A	226	ALA	0	0.044	0.030	14.166	0.039	0.039	0.000	0.000	0.000	0.000
132	A	227	PHE	0	0.008	0.003	15.432	0.047	0.047	0.000	0.000	0.000	0.000
133	A	228	ILE	0	-0.008	-0.005	12.741	0.053	0.053	0.000	0.000	0.000	0.000
134	A	229	GLU	-1	-0.919	-0.972	10.332	-0.214	-0.214	0.000	0.000	0.000	0.000
135	A	230	GLU	-1	-0.971	-0.987	12.273	0.053	0.053	0.000	0.000	0.000	0.000
136	A	231	ILE	0	0.010	0.008	15.153	0.042	0.042	0.000	0.000	0.000	0.000
137	A	232	LEU	0	-0.053	-0.022	9.346	0.070	0.070	0.000	0.000	0.000	0.000
138	A	233	LEU	0	0.012	-0.002	9.683	0.081	0.081	0.000	0.000	0.000	0.000
139	A	234	ASP	-1	-0.849	-0.928	12.859	0.141	0.141	0.000	0.000	0.000	0.000
140	A	235	ARG	1	0.916	0.970	14.133	-0.525	-0.525	0.000	0.000	0.000	0.000
141	A	236	SER	0	0.053	0.031	11.542	0.042	0.042	0.000	0.000	0.000	0.000
142	A	237	ARG	1	0.858	0.929	13.850	-0.133	-0.133	0.000	0.000	0.000	0.000
143	A	238	GLU	-1	-0.926	-0.964	16.533	0.206	0.206	0.000	0.000	0.000	0.000
144	A	239	GLU	-1	-0.906	-0.948	13.781	0.675	0.675	0.000	0.000	0.000	0.000
145	A	240	SER	0	-0.015	-0.021	15.522	-0.022	-0.022	0.000	0.000	0.000	0.000
146	A	241	ARG	1	0.882	0.935	18.103	-0.147	-0.147	0.000	0.000	0.000	0.000
147	A	242	ARG	1	0.978	1.026	21.257	-0.270	-0.270	0.000	0.000	0.000	0.000
148	A	243	GLU	-1	-0.841	-0.919	20.577	0.231	0.231	0.000	0.000	0.000	0.000
149	A	244	ARG	1	0.926	0.952	18.714	-0.188	-0.188	0.000	0.000	0.000	0.000
150	A	245	SER	0	-0.120	-0.093	23.364	-0.022	-0.022	0.000	0.000	0.000	0.000
151	A	246	LEU	0	-0.015	-0.010	25.347	-0.015	-0.015	0.000	0.000	0.000	0.000
152	A	247	ARG	1	0.968	0.999	24.614	-0.168	-0.168	0.000	0.000	0.000	0.000
153	A	248	ARG	1	0.891	0.938	24.952	-0.093	-0.093	0.000	0.000	0.000	0.000
154	A	249	LEU	0	-0.048	-0.015	29.186	-0.012	-0.012	0.000	0.000	0.000	0.000
155	A	250	GLU	-1	-0.959	-0.955	32.215	0.103	0.103	0.000	0.000	0.000	0.000

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