FMO DATABASE

FMODB ID: K9R83

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	OptHSide
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	-1547436.809071
FMO2-HF: Nuclear repulsion	1484240.098213
FMO2-HF: Total energy	-63196.710857
FMO2-MP2: Total energy	-63380.938359

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.
-35.918	-35.339	20.028	-10.138	-10.47	-0.028

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 : -0.028 / q_NPA : -0.030

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	0.009	0.007	2.263	-6.090	-4.438	3.815	-2.270	-3.197	0.022
4	A	99	ASP	-1	-0.828	-0.914	1.810	-30.849	-32.475	16.209	-7.723	-6.861	-0.050
5	A	100	LEU	0	-0.019	-0.001	3.851	0.991	1.479	0.005	-0.140	-0.353	0.000
6	A	101	LEU	0	0.003	0.002	5.719	0.459	0.459	0.000	0.000	0.000	0.000
7	A	102	GLU	-1	-0.902	-0.941	7.049	-1.878	-1.878	0.000	0.000	0.000	0.000
8	A	103	THR	0	-0.027	-0.018	7.334	0.229	0.229	0.000	0.000	0.000	0.000
9	A	104	ARG	1	0.786	0.851	9.827	0.300	0.300	0.000	0.000	0.000	0.000
10	A	105	HIS	0	-0.053	-0.022	11.557	0.136	0.136	0.000	0.000	0.000	0.000
11	A	106	ALA	0	-0.016	0.000	12.934	0.101	0.101	0.000	0.000	0.000	0.000
12	A	107	LEU	0	-0.001	-0.026	12.421	0.112	0.112	0.000	0.000	0.000	0.000
13	A	108	GLU	-1	-0.729	-0.851	14.299	-0.058	-0.058	0.000	0.000	0.000	0.000
14	A	109	GLY	0	0.028	0.027	17.151	0.058	0.058	0.000	0.000	0.000	0.000
15	A	110	ILE	0	-0.045	-0.034	18.071	0.046	0.046	0.000	0.000	0.000	0.000
16	A	111	ALA	0	0.011	0.006	19.168	0.029	0.029	0.000	0.000	0.000	0.000
17	A	112	ALA	0	0.053	0.017	21.057	0.029	0.029	0.000	0.000	0.000	0.000
18	A	113	TYR	0	-0.140	-0.072	23.157	0.015	0.015	0.000	0.000	0.000	0.000
19	A	114	TYR	0	0.009	-0.018	23.557	0.020	0.020	0.000	0.000	0.000	0.000
20	A	115	ALA	0	0.044	0.046	24.952	0.015	0.015	0.000	0.000	0.000	0.000
21	A	116	ALA	0	-0.016	0.008	26.792	0.015	0.015	0.000	0.000	0.000	0.000
22	A	117	LEU	0	-0.081	-0.038	29.094	0.008	0.008	0.000	0.000	0.000	0.000
23	A	118	ARG	1	0.854	0.914	27.726	0.152	0.152	0.000	0.000	0.000	0.000
24	A	119	SER	0	-0.003	0.026	29.546	0.009	0.009	0.000	0.000	0.000	0.000
25	A	120	THR	0	-0.052	-0.053	31.224	0.000	0.000	0.000	0.000	0.000	0.000
26	A	121	ASP	-1	-0.880	-0.956	34.076	-0.032	-0.032	0.000	0.000	0.000	0.000
27	A	122	GLU	-1	-0.844	-0.908	34.885	-0.021	-0.021	0.000	0.000	0.000	0.000
28	A	123	ASP	-1	-0.839	-0.903	30.121	-0.040	-0.040	0.000	0.000	0.000	0.000
29	A	124	LYS	1	0.863	0.915	30.952	0.061	0.061	0.000	0.000	0.000	0.000
30	A	125	GLU	-1	-0.965	-0.976	32.333	0.005	0.005	0.000	0.000	0.000	0.000
31	A	126	ARG	1	0.885	0.928	25.867	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	127	ILE	0	-0.029	-0.028	26.798	0.009	0.009	0.000	0.000	0.000	0.000
33	A	128	ARG	1	0.973	0.980	28.802	0.015	0.015	0.000	0.000	0.000	0.000
34	A	129	GLU	-1	-0.948	-0.956	30.784	0.050	0.050	0.000	0.000	0.000	0.000
35	A	130	LEU	0	-0.025	-0.021	25.623	0.012	0.012	0.000	0.000	0.000	0.000
36	A	131	HIS	0	-0.038	-0.026	26.550	0.013	0.013	0.000	0.000	0.000	0.000
37	A	132	HIS	0	0.021	0.006	27.777	0.009	0.009	0.000	0.000	0.000	0.000
38	A	133	ALA	0	-0.005	-0.008	27.796	0.009	0.009	0.000	0.000	0.000	0.000
39	A	134	ILE	0	-0.019	-0.011	23.414	0.016	0.016	0.000	0.000	0.000	0.000
40	A	135	GLU	-1	-0.868	-0.908	26.342	0.112	0.112	0.000	0.000	0.000	0.000
41	A	136	LEU	0	-0.039	-0.021	29.055	0.007	0.007	0.000	0.000	0.000	0.000
42	A	137	ALA	0	0.012	0.012	26.002	0.006	0.006	0.000	0.000	0.000	0.000
43	A	138	GLN	0	-0.065	-0.039	24.231	0.004	0.004	0.000	0.000	0.000	0.000
44	A	139	GLN	0	-0.108	-0.074	27.105	0.007	0.007	0.000	0.000	0.000	0.000
45	A	140	SER	0	-0.098	-0.034	28.946	0.001	0.001	0.000	0.000	0.000	0.000
46	A	141	GLY	0	-0.029	-0.019	27.373	0.004	0.004	0.000	0.000	0.000	0.000
47	A	142	ASP	-1	-0.886	-0.942	25.271	0.269	0.269	0.000	0.000	0.000	0.000
48	A	143	LEU	0	0.000	-0.007	18.133	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	144	ASP	-1	-0.963	-0.988	20.662	0.318	0.318	0.000	0.000	0.000	0.000
50	A	145	ALA	0	0.050	0.035	21.711	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	146	GLU	-1	-0.760	-0.885	22.430	0.189	0.189	0.000	0.000	0.000	0.000
52	A	147	SER	0	-0.044	-0.021	17.041	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	148	ASN	0	0.005	-0.015	19.157	-0.017	-0.017	0.000	0.000	0.000	0.000
54	A	149	ALA	0	0.027	0.021	20.995	-0.026	-0.026	0.000	0.000	0.000	0.000
55	A	150	VAL	0	-0.006	-0.006	18.024	-0.030	-0.030	0.000	0.000	0.000	0.000
56	A	151	LEU	0	-0.038	-0.007	15.600	-0.031	-0.031	0.000	0.000	0.000	0.000
57	A	152	GLN	0	0.009	-0.010	18.667	-0.055	-0.055	0.000	0.000	0.000	0.000
58	A	153	TYR	0	0.012	0.020	21.412	-0.026	-0.026	0.000	0.000	0.000	0.000
59	A	154	GLN	0	-0.011	-0.023	16.909	-0.023	-0.023	0.000	0.000	0.000	0.000
60	A	155	ILE	0	-0.021	0.008	18.626	-0.039	-0.039	0.000	0.000	0.000	0.000
61	A	156	ALA	0	0.015	0.017	20.802	-0.022	-0.022	0.000	0.000	0.000	0.000
62	A	157	VAL	0	0.012	0.007	22.048	-0.014	-0.014	0.000	0.000	0.000	0.000
63	A	158	THR	0	-0.029	-0.032	19.076	-0.034	-0.034	0.000	0.000	0.000	0.000
64	A	159	GLU	-1	-0.874	-0.939	21.828	-0.018	-0.018	0.000	0.000	0.000	0.000
65	A	160	ALA	0	0.029	0.026	24.732	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	161	ALA	0	-0.025	-0.003	23.763	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	162	HIS	0	-0.072	-0.042	25.817	-0.019	-0.019	0.000	0.000	0.000	0.000
68	A	163	ASN	0	-0.029	-0.019	23.100	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	164	VAL	0	0.053	0.013	22.941	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	165	VAL	0	0.024	0.016	19.129	0.004	0.004	0.000	0.000	0.000	0.000
71	A	166	LEU	0	0.017	0.024	17.233	-0.020	-0.020	0.000	0.000	0.000	0.000
72	A	167	LEU	0	0.054	0.030	17.944	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	168	HIS	0	-0.061	-0.042	18.683	0.032	0.032	0.000	0.000	0.000	0.000
74	A	169	LEU	0	-0.010	-0.006	14.034	0.008	0.008	0.000	0.000	0.000	0.000
75	A	170	LEU	0	0.007	0.017	13.756	-0.020	-0.020	0.000	0.000	0.000	0.000
76	A	171	ARG	1	0.844	0.888	14.447	0.024	0.024	0.000	0.000	0.000	0.000
77	A	172	CYS	0	-0.071	-0.025	12.532	0.038	0.038	0.000	0.000	0.000	0.000
78	A	173	MET	0	0.001	0.012	9.452	-0.018	-0.018	0.000	0.000	0.000	0.000
79	A	174	GLU	-1	-0.826	-0.896	10.792	0.218	0.218	0.000	0.000	0.000	0.000
80	A	175	PRO	0	0.000	-0.002	11.593	0.076	0.076	0.000	0.000	0.000	0.000
81	A	176	MET	0	0.019	0.003	4.408	0.003	0.068	-0.001	-0.005	-0.059	0.000
82	A	177	LEU	0	0.007	0.015	8.874	0.094	0.094	0.000	0.000	0.000	0.000
83	A	178	ALA	0	0.034	0.003	10.898	0.059	0.059	0.000	0.000	0.000	0.000
84	A	179	GLN	0	-0.051	-0.020	8.225	0.182	0.182	0.000	0.000	0.000	0.000
85	A	180	ASN	0	0.038	0.023	7.665	-0.152	-0.152	0.000	0.000	0.000	0.000
86	A	181	VAL	0	0.017	0.007	9.919	0.023	0.023	0.000	0.000	0.000	0.000
87	A	182	ARG	1	0.946	0.980	13.607	-0.704	-0.704	0.000	0.000	0.000	0.000
88	A	183	GLN	0	0.032	0.013	7.449	0.081	0.081	0.000	0.000	0.000	0.000
89	A	184	ASN	0	-0.025	-0.019	11.160	0.076	0.076	0.000	0.000	0.000	0.000
90	A	185	PHE	0	0.013	-0.008	13.393	-0.048	-0.048	0.000	0.000	0.000	0.000
91	A	186	GLU	-1	-0.945	-0.958	14.101	0.808	0.808	0.000	0.000	0.000	0.000
92	A	187	LEU	0	-0.053	-0.030	11.844	-0.048	-0.048	0.000	0.000	0.000	0.000
93	A	188	LEU	0	-0.022	-0.011	16.085	-0.062	-0.062	0.000	0.000	0.000	0.000
94	A	189	TYR	0	-0.043	-0.044	18.747	-0.038	-0.038	0.000	0.000	0.000	0.000
95	A	190	SER	0	-0.094	-0.028	19.219	-0.023	-0.023	0.000	0.000	0.000	0.000
96	A	191	ARG	1	0.791	0.898	20.509	-0.318	-0.318	0.000	0.000	0.000	0.000
97	A	192	ARG	1	1.002	0.990	22.391	-0.275	-0.275	0.000	0.000	0.000	0.000
98	A	193	GLU	-1	-0.834	-0.923	24.351	0.200	0.200	0.000	0.000	0.000	0.000
99	A	194	MET	0	-0.017	-0.009	20.634	-0.029	-0.029	0.000	0.000	0.000	0.000
100	A	195	LEU	0	-0.001	0.006	21.300	-0.015	-0.015	0.000	0.000	0.000	0.000
101	A	196	PRO	0	0.067	0.035	23.393	-0.016	-0.016	0.000	0.000	0.000	0.000
102	A	197	LEU	0	0.015	0.005	23.403	-0.020	-0.020	0.000	0.000	0.000	0.000
103	A	198	VAL	0	0.012	0.022	19.126	-0.026	-0.026	0.000	0.000	0.000	0.000
104	A	199	SER	0	0.079	0.031	21.737	-0.020	-0.020	0.000	0.000	0.000	0.000
105	A	200	SER	0	-0.034	0.008	24.308	-0.025	-0.025	0.000	0.000	0.000	0.000
106	A	201	HIS	0	-0.033	-0.038	21.760	-0.035	-0.035	0.000	0.000	0.000	0.000
107	A	202	ARG	1	0.938	0.979	19.914	-0.146	-0.146	0.000	0.000	0.000	0.000
108	A	203	THR	0	0.008	-0.010	23.140	-0.012	-0.012	0.000	0.000	0.000	0.000
109	A	204	ARG	1	0.861	0.942	24.789	0.007	0.007	0.000	0.000	0.000	0.000
110	A	205	ILE	0	-0.023	0.003	20.935	-0.012	-0.012	0.000	0.000	0.000	0.000
111	A	206	PHE	0	0.016	0.003	25.463	-0.008	-0.008	0.000	0.000	0.000	0.000
112	A	207	GLU	-1	-0.878	-0.953	27.631	-0.014	-0.014	0.000	0.000	0.000	0.000
113	A	208	ALA	0	-0.041	-0.008	27.893	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	209	ILE	0	-0.021	-0.014	24.739	-0.009	-0.009	0.000	0.000	0.000	0.000
115	A	210	MET	0	-0.065	-0.010	29.396	0.001	0.001	0.000	0.000	0.000	0.000
116	A	211	ALA	0	-0.055	-0.027	32.577	0.001	0.001	0.000	0.000	0.000	0.000
117	A	212	GLY	0	0.017	0.026	32.433	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	213	LYS	1	0.778	0.881	31.272	0.065	0.065	0.000	0.000	0.000	0.000
119	A	214	PRO	0	0.035	0.006	28.343	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	215	GLU	-1	-0.782	-0.888	26.856	-0.194	-0.194	0.000	0.000	0.000	0.000
121	A	216	GLU	-1	-0.832	-0.909	26.236	-0.092	-0.092	0.000	0.000	0.000	0.000
122	A	217	ALA	0	0.046	0.036	25.893	0.001	0.001	0.000	0.000	0.000	0.000
123	A	218	ARG	1	0.826	0.909	21.570	0.232	0.232	0.000	0.000	0.000	0.000
124	A	219	GLU	-1	-0.806	-0.882	21.367	-0.218	-0.218	0.000	0.000	0.000	0.000
125	A	220	ALA	0	-0.025	-0.015	21.919	0.002	0.002	0.000	0.000	0.000	0.000
126	A	221	SER	0	-0.020	-0.016	19.102	0.022	0.022	0.000	0.000	0.000	0.000
127	A	222	HIS	0	0.019	0.016	17.174	-0.021	-0.021	0.000	0.000	0.000	0.000
128	A	223	ARG	1	0.841	0.884	17.165	0.138	0.138	0.000	0.000	0.000	0.000
129	A	224	HIS	0	-0.036	-0.006	18.679	0.042	0.042	0.000	0.000	0.000	0.000
130	A	225	LEU	0	-0.004	-0.002	13.522	0.059	0.059	0.000	0.000	0.000	0.000
131	A	226	ALA	0	0.057	0.035	13.914	0.042	0.042	0.000	0.000	0.000	0.000
132	A	227	PHE	0	-0.013	-0.006	15.158	0.052	0.052	0.000	0.000	0.000	0.000
133	A	228	ILE	0	-0.012	-0.006	12.605	0.058	0.058	0.000	0.000	0.000	0.000
134	A	229	GLU	-1	-0.863	-0.941	9.975	-0.252	-0.252	0.000	0.000	0.000	0.000
135	A	230	GLU	-1	-0.957	-0.984	12.153	0.062	0.062	0.000	0.000	0.000	0.000
136	A	231	ILE	0	-0.006	-0.003	15.086	0.045	0.045	0.000	0.000	0.000	0.000
137	A	232	LEU	0	-0.050	-0.018	9.346	0.064	0.064	0.000	0.000	0.000	0.000
138	A	233	LEU	0	0.016	0.003	10.019	0.077	0.077	0.000	0.000	0.000	0.000
139	A	234	ASP	-1	-0.832	-0.909	13.000	0.159	0.159	0.000	0.000	0.000	0.000
140	A	235	ARG	1	0.812	0.912	14.363	-0.598	-0.598	0.000	0.000	0.000	0.000
141	A	236	SER	0	0.060	0.030	11.732	0.009	0.009	0.000	0.000	0.000	0.000
142	A	237	ARG	1	0.853	0.916	14.068	-0.157	-0.157	0.000	0.000	0.000	0.000
143	A	238	GLU	-1	-0.890	-0.938	16.870	0.242	0.242	0.000	0.000	0.000	0.000
144	A	239	GLU	-1	-0.805	-0.890	14.351	0.676	0.676	0.000	0.000	0.000	0.000
145	A	240	SER	0	-0.040	-0.028	15.929	-0.020	-0.020	0.000	0.000	0.000	0.000
146	A	241	ARG	1	0.899	0.944	18.502	-0.169	-0.169	0.000	0.000	0.000	0.000
147	A	242	ARG	1	0.973	1.024	21.545	-0.287	-0.287	0.000	0.000	0.000	0.000
148	A	243	GLU	-1	-0.779	-0.877	20.911	0.235	0.235	0.000	0.000	0.000	0.000
149	A	244	ARG	1	0.937	0.954	18.950	-0.214	-0.214	0.000	0.000	0.000	0.000
150	A	245	SER	0	-0.098	-0.075	23.862	-0.023	-0.023	0.000	0.000	0.000	0.000
151	A	246	LEU	0	-0.013	-0.013	25.282	-0.015	-0.015	0.000	0.000	0.000	0.000
152	A	247	ARG	1	0.882	0.940	24.317	-0.211	-0.211	0.000	0.000	0.000	0.000
153	A	248	ARG	1	0.899	0.941	26.055	-0.103	-0.103	0.000	0.000	0.000	0.000
154	A	249	LEU	0	-0.046	-0.011	29.725	-0.012	-0.012	0.000	0.000	0.000	0.000
155	A	250	GLU	-1	-0.956	-0.953	32.730	0.110	0.110	0.000	0.000	0.000	0.000

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