FMO DATABASE

FMODB ID: V52V1

Calculation Name: 5T5D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5T5D

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

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	-1624023.677445
FMO2-HF: Nuclear repulsion	1561829.807166
FMO2-HF: Total energy	-62193.870279
FMO2-MP2: Total energy	-62377.279972

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.
-27.375	-28.939	23.604	-11.209	-10.829	-0.096

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 : -0.038

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	4	GLU	-1	-0.822	-0.880	1.686	-22.232	-26.155	14.491	-6.166	-4.402	-0.052
4	A	5	PHE	0	-0.011	-0.015	5.072	1.300	1.399	-0.001	-0.004	-0.094	0.000
5	A	6	VAL	0	0.010	0.005	8.502	-0.087	-0.087	0.000	0.000	0.000	0.000
6	A	7	ARG	1	0.735	0.855	11.050	0.527	0.527	0.000	0.000	0.000	0.000
7	A	8	ILE	0	0.027	0.027	14.751	0.007	0.007	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.779	-0.909	18.139	-0.365	-0.365	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.751	-0.857	20.203	-0.205	-0.205	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.796	0.901	21.800	0.262	0.262	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.029	-0.007	17.872	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	13	VAL	0	0.026	0.005	16.285	-0.066	-0.066	0.000	0.000	0.000	0.000
13	A	14	HIS	0	-0.052	-0.033	18.592	0.029	0.029	0.000	0.000	0.000	0.000
14	A	15	GLY	0	0.042	0.024	22.013	0.016	0.016	0.000	0.000	0.000	0.000
15	A	16	GLN	0	0.030	-0.005	20.826	-0.065	-0.065	0.000	0.000	0.000	0.000
16	A	17	VAL	0	0.022	0.025	19.906	-0.027	-0.027	0.000	0.000	0.000	0.000
17	A	18	VAL	0	0.067	0.048	15.000	-0.041	-0.041	0.000	0.000	0.000	0.000
18	A	19	THR	0	0.028	0.002	15.643	-0.089	-0.089	0.000	0.000	0.000	0.000
19	A	20	THR	0	-0.056	-0.033	16.083	-0.045	-0.045	0.000	0.000	0.000	0.000
20	A	21	TRP	0	0.006	-0.009	13.610	-0.060	-0.060	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.018	-0.017	11.402	-0.140	-0.140	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.901	0.946	11.417	0.357	0.357	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.910	0.976	12.843	0.591	0.591	0.000	0.000	0.000	0.000
24	A	25	TYR	0	0.026	0.010	7.895	0.113	0.113	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.889	-0.925	7.601	-1.517	-1.517	0.000	0.000	0.000	0.000
26	A	27	ILE	0	-0.069	-0.030	6.733	-0.208	-0.208	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.804	-0.897	5.941	-0.889	-0.889	0.000	0.000	0.000	0.000
28	A	29	GLN	0	-0.038	-0.039	6.371	0.881	0.881	0.000	0.000	0.000	0.000
29	A	30	VAL	0	0.015	0.014	8.073	-0.332	-0.332	0.000	0.000	0.000	0.000
30	A	31	ILE	0	-0.020	-0.006	7.675	0.129	0.129	0.000	0.000	0.000	0.000
31	A	32	ILE	0	-0.006	-0.004	11.625	0.033	0.033	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.013	-0.003	12.437	0.041	0.041	0.000	0.000	0.000	0.000
33	A	34	ASN	0	0.033	-0.011	15.532	0.014	0.014	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.793	-0.890	19.316	-0.075	-0.075	0.000	0.000	0.000	0.000
35	A	36	ARG	1	0.875	0.933	21.681	0.134	0.134	0.000	0.000	0.000	0.000
36	A	37	ILE	0	-0.022	-0.020	20.270	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	38	SER	0	0.007	0.018	19.625	-0.017	-0.017	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.861	-0.929	20.864	-0.099	-0.099	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.787	-0.881	24.631	-0.157	-0.157	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.893	0.931	23.665	0.120	0.120	0.000	0.000	0.000	0.000
41	A	42	THR	0	0.013	0.029	25.573	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	43	ARG	1	0.954	0.968	23.558	0.194	0.194	0.000	0.000	0.000	0.000
43	A	44	GLN	0	-0.043	-0.017	20.796	-0.029	-0.029	0.000	0.000	0.000	0.000
44	A	45	SER	0	-0.043	-0.048	21.774	-0.034	-0.034	0.000	0.000	0.000	0.000
45	A	46	ILE	0	0.028	0.021	24.291	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.021	-0.009	19.613	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.907	0.955	19.261	0.238	0.238	0.000	0.000	0.000	0.000
48	A	49	ILE	0	-0.016	0.000	20.678	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	50	SER	0	-0.052	-0.026	21.590	0.012	0.012	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.026	0.002	17.035	-0.026	-0.026	0.000	0.000	0.000	0.000
51	A	52	PRO	0	-0.023	-0.023	16.329	0.027	0.027	0.000	0.000	0.000	0.000
52	A	53	VAL	0	0.030	0.005	17.084	-0.044	-0.044	0.000	0.000	0.000	0.000
53	A	54	GLY	0	0.019	0.024	15.374	0.028	0.028	0.000	0.000	0.000	0.000
54	A	55	LEU	0	-0.046	-0.013	11.189	-0.085	-0.085	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.886	0.949	10.600	0.944	0.944	0.000	0.000	0.000	0.000
56	A	57	ILE	0	0.020	0.012	11.535	-0.165	-0.165	0.000	0.000	0.000	0.000
57	A	58	VAL	0	-0.043	-0.025	11.663	0.079	0.079	0.000	0.000	0.000	0.000
58	A	59	PHE	0	0.029	-0.001	14.634	-0.042	-0.042	0.000	0.000	0.000	0.000
59	A	60	PHE	0	-0.009	0.002	10.762	0.024	0.024	0.000	0.000	0.000	0.000
60	A	61	SER	0	0.065	0.030	16.240	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	62	VAL	0	0.051	0.020	16.274	0.001	0.001	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.974	0.994	15.981	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	64	ARG	1	0.860	0.925	15.539	0.051	0.051	0.000	0.000	0.000	0.000
64	A	65	PHE	0	0.035	0.008	8.368	-0.020	-0.020	0.000	0.000	0.000	0.000
65	A	66	VAL	0	0.039	0.041	11.544	0.093	0.093	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.869	-0.920	12.925	0.153	0.153	0.000	0.000	0.000	0.000
67	A	68	VAL	0	-0.028	-0.008	9.125	0.022	0.022	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.027	-0.015	6.983	0.092	0.092	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.063	-0.041	8.937	0.311	0.311	0.000	0.000	0.000	0.000
70	A	71	SER	0	-0.034	-0.018	11.009	-0.028	-0.028	0.000	0.000	0.000	0.000
71	A	72	VAL	0	-0.039	-0.020	8.266	-0.101	-0.101	0.000	0.000	0.000	0.000
72	A	73	PRO	0	-0.020	0.004	5.844	0.216	0.216	0.000	0.000	0.000	0.000
73	A	74	ILE	0	0.029	0.000	2.823	-1.362	-0.469	0.098	-0.362	-0.629	0.001
74	A	75	LYS	1	0.940	0.964	1.959	-8.247	-9.565	7.336	-3.124	-2.893	-0.037
75	A	76	LYS	1	0.864	0.948	3.086	0.899	1.979	0.160	-0.499	-0.741	-0.004
76	A	77	ARG	1	0.840	0.922	2.331	-1.158	0.283	1.505	-1.304	-1.641	-0.004
77	A	78	THR	0	-0.037	-0.033	3.033	3.053	3.261	0.016	0.257	-0.481	0.000
78	A	79	MET	0	-0.022	0.005	5.004	-0.275	-0.319	-0.001	-0.007	0.052	0.000
79	A	80	LEU	0	-0.005	0.002	8.216	0.209	0.209	0.000	0.000	0.000	0.000
80	A	81	ILE	0	-0.046	-0.032	10.546	0.025	0.025	0.000	0.000	0.000	0.000
81	A	82	TYR	0	0.031	0.017	12.603	0.031	0.031	0.000	0.000	0.000	0.000
82	A	83	THR	0	0.003	-0.014	17.232	-0.018	-0.018	0.000	0.000	0.000	0.000
83	A	84	ASN	0	-0.010	-0.008	20.270	0.029	0.029	0.000	0.000	0.000	0.000
84	A	85	PRO	0	0.057	0.029	19.890	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.883	0.946	20.418	0.019	0.019	0.000	0.000	0.000	0.000
86	A	87	ASP	-1	-0.809	-0.906	18.330	-0.077	-0.077	0.000	0.000	0.000	0.000
87	A	88	VAL	0	-0.015	0.007	14.929	0.025	0.025	0.000	0.000	0.000	0.000
88	A	89	TYR	0	-0.015	-0.040	16.231	0.062	0.062	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.778	-0.882	18.248	0.092	0.092	0.000	0.000	0.000	0.000
90	A	91	SER	0	-0.023	-0.035	13.353	0.019	0.019	0.000	0.000	0.000	0.000
91	A	92	ILE	0	-0.070	-0.023	14.112	0.096	0.096	0.000	0.000	0.000	0.000
92	A	93	GLU	-1	-0.835	-0.877	15.361	0.241	0.241	0.000	0.000	0.000	0.000
93	A	94	GLY	0	-0.038	-0.015	15.376	0.008	0.008	0.000	0.000	0.000	0.000
94	A	95	ASN	0	-0.026	-0.021	12.840	0.047	0.047	0.000	0.000	0.000	0.000
95	A	96	LEU	0	-0.009	-0.003	8.722	0.246	0.246	0.000	0.000	0.000	0.000
96	A	97	LYS	1	0.833	0.889	9.066	-1.064	-1.064	0.000	0.000	0.000	0.000
97	A	98	LEU	0	0.002	-0.004	9.660	0.073	0.073	0.000	0.000	0.000	0.000
98	A	99	GLU	-1	-0.746	-0.839	11.023	0.442	0.442	0.000	0.000	0.000	0.000
99	A	100	TYR	0	-0.095	-0.074	11.890	-0.085	-0.085	0.000	0.000	0.000	0.000
100	A	101	LEU	0	0.037	0.028	12.343	-0.031	-0.031	0.000	0.000	0.000	0.000
101	A	102	ASN	0	-0.009	0.011	14.620	0.004	0.004	0.000	0.000	0.000	0.000
102	A	103	VAL	0	0.036	0.011	16.297	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	104	GLY	0	0.010	-0.005	19.421	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	105	GLN	0	-0.019	-0.013	21.204	0.051	0.051	0.000	0.000	0.000	0.000
105	A	106	MET	0	0.027	0.020	23.209	-0.014	-0.014	0.000	0.000	0.000	0.000
106	A	107	SER	0	-0.028	-0.061	25.694	0.008	0.008	0.000	0.000	0.000	0.000
107	A	108	LYS	1	0.844	0.941	29.037	0.170	0.170	0.000	0.000	0.000	0.000
108	A	109	THR	0	0.000	-0.018	30.976	0.002	0.002	0.000	0.000	0.000	0.000
109	A	110	GLU	-1	-0.852	-0.901	34.006	-0.094	-0.094	0.000	0.000	0.000	0.000
110	A	111	GLU	-1	-0.851	-0.927	36.372	-0.075	-0.075	0.000	0.000	0.000	0.000
111	A	112	ASN	0	-0.069	-0.042	37.094	0.006	0.006	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.847	-0.901	32.786	-0.062	-0.062	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.764	0.861	32.137	0.076	0.076	0.000	0.000	0.000	0.000
114	A	115	VAL	0	-0.004	0.009	28.233	0.006	0.006	0.000	0.000	0.000	0.000
115	A	116	THR	0	-0.013	-0.016	27.193	0.002	0.002	0.000	0.000	0.000	0.000
116	A	117	GLY	0	0.029	0.013	30.054	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	118	GLY	0	-0.078	-0.047	26.275	-0.008	-0.008	0.000	0.000	0.000	0.000
118	A	119	VAL	0	0.012	0.003	24.296	-0.010	-0.010	0.000	0.000	0.000	0.000
119	A	120	ALA	0	0.010	0.020	27.332	0.010	0.010	0.000	0.000	0.000	0.000
120	A	121	LEU	0	-0.026	-0.017	25.655	-0.008	-0.008	0.000	0.000	0.000	0.000
121	A	122	GLY	0	0.108	0.056	29.312	0.007	0.007	0.000	0.000	0.000	0.000
122	A	123	GLU	-1	-0.818	-0.919	30.250	-0.036	-0.036	0.000	0.000	0.000	0.000
123	A	124	GLU	-1	-0.915	-0.959	27.176	-0.023	-0.023	0.000	0.000	0.000	0.000
124	A	125	ASP	-1	-0.829	-0.930	25.921	-0.082	-0.082	0.000	0.000	0.000	0.000
125	A	126	LYS	1	0.800	0.886	25.931	0.055	0.055	0.000	0.000	0.000	0.000
126	A	127	TYR	0	0.014	0.015	27.008	0.008	0.008	0.000	0.000	0.000	0.000
127	A	128	TYR	0	-0.010	-0.016	22.875	0.007	0.007	0.000	0.000	0.000	0.000
128	A	129	PHE	0	0.023	-0.011	20.092	0.007	0.007	0.000	0.000	0.000	0.000
129	A	130	LYS	1	0.817	0.916	22.995	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	131	LYS	1	0.847	0.895	23.559	-0.081	-0.081	0.000	0.000	0.000	0.000
131	A	132	ILE	0	-0.024	-0.010	17.888	0.021	0.021	0.000	0.000	0.000	0.000
132	A	133	VAL	0	-0.028	-0.019	19.941	0.020	0.020	0.000	0.000	0.000	0.000
133	A	134	ASP	-1	-0.908	-0.925	21.847	0.108	0.108	0.000	0.000	0.000	0.000
134	A	135	LYS	1	0.862	0.924	18.495	-0.206	-0.206	0.000	0.000	0.000	0.000
135	A	136	GLY	0	-0.014	0.000	18.873	0.037	0.037	0.000	0.000	0.000	0.000
136	A	137	THR	0	-0.088	-0.041	15.170	-0.008	-0.008	0.000	0.000	0.000	0.000
137	A	138	ARG	1	0.855	0.912	16.538	0.116	0.116	0.000	0.000	0.000	0.000
138	A	139	VAL	0	0.049	0.018	16.871	-0.035	-0.035	0.000	0.000	0.000	0.000
139	A	140	GLU	-1	-0.818	-0.882	18.252	-0.232	-0.232	0.000	0.000	0.000	0.000
140	A	141	ILE	0	0.009	0.002	19.537	-0.031	-0.031	0.000	0.000	0.000	0.000
141	A	142	GLN	0	-0.030	-0.032	19.142	-0.016	-0.016	0.000	0.000	0.000	0.000
142	A	143	MET	0	0.014	0.032	20.204	-0.055	-0.055	0.000	0.000	0.000	0.000
143	A	144	VAL	0	0.022	0.003	20.156	-0.040	-0.040	0.000	0.000	0.000	0.000
144	A	145	PRO	0	0.016	0.005	16.703	0.033	0.033	0.000	0.000	0.000	0.000
145	A	146	ASN	0	-0.031	-0.016	19.025	-0.012	-0.012	0.000	0.000	0.000	0.000
146	A	147	ASP	-1	-0.836	-0.889	22.534	-0.201	-0.201	0.000	0.000	0.000	0.000
147	A	148	LYS	1	0.899	0.948	23.596	0.127	0.127	0.000	0.000	0.000	0.000
148	A	149	VAL	0	0.034	0.030	20.740	0.006	0.006	0.000	0.000	0.000	0.000
149	A	150	THR	0	-0.069	-0.042	23.383	0.032	0.032	0.000	0.000	0.000	0.000
150	A	151	MET	0	0.013	0.019	20.875	-0.012	-0.012	0.000	0.000	0.000	0.000
151	A	152	LEU	0	0.033	0.008	22.521	0.009	0.009	0.000	0.000	0.000	0.000
152	A	153	GLU	-1	-0.749	-0.877	24.414	0.001	0.001	0.000	0.000	0.000	0.000
153	A	154	LYS	1	0.846	0.945	26.212	0.078	0.078	0.000	0.000	0.000	0.000
154	A	155	PHE	0	-0.026	-0.023	27.585	0.000	0.000	0.000	0.000	0.000	0.000
155	A	156	LEU	0	-0.034	0.015	25.093	0.003	0.003	0.000	0.000	0.000	0.000

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