FMO DATABASE

FMODB ID: YZQ92

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	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	-1621102.937875
FMO2-HF: Nuclear repulsion	1558909.852925
FMO2-HF: Total energy	-62193.084951
FMO2-MP2: Total energy	-62376.619005

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.
-25.107	-19.438	11.521	-7.966	-9.225	-0.074

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 : -0.042 / q_NPA : -0.029

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	-0.818	-0.887	1.795	-20.338	-20.897	8.927	-4.625	-3.743	-0.046
4	A	5	PHE	0	-0.021	-0.022	5.157	1.212	1.308	-0.001	-0.004	-0.091	0.000
5	A	6	VAL	0	0.015	0.010	8.861	-0.082	-0.082	0.000	0.000	0.000	0.000
6	A	7	ARG	1	0.753	0.863	11.180	0.456	0.456	0.000	0.000	0.000	0.000
7	A	8	ILE	0	0.002	0.013	14.774	0.004	0.004	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.807	-0.920	18.054	-0.305	-0.305	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.744	-0.848	20.181	-0.167	-0.167	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.824	0.915	22.528	0.207	0.207	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.012	-0.002	18.341	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	13	VAL	0	0.003	0.000	16.817	-0.030	-0.030	0.000	0.000	0.000	0.000
13	A	14	HIS	0	-0.040	-0.023	19.001	0.033	0.033	0.000	0.000	0.000	0.000
14	A	15	GLY	0	0.019	0.008	22.670	0.005	0.005	0.000	0.000	0.000	0.000
15	A	16	GLN	0	0.049	0.002	21.875	-0.046	-0.046	0.000	0.000	0.000	0.000
16	A	17	VAL	0	0.009	0.017	19.965	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	18	VAL	0	0.078	0.045	15.573	-0.031	-0.031	0.000	0.000	0.000	0.000
18	A	19	THR	0	0.031	0.010	15.910	-0.072	-0.072	0.000	0.000	0.000	0.000
19	A	20	THR	0	-0.037	-0.021	16.335	-0.029	-0.029	0.000	0.000	0.000	0.000
20	A	21	TRP	0	0.010	-0.005	13.356	-0.046	-0.046	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.022	-0.021	11.737	-0.118	-0.118	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.920	0.965	11.866	0.302	0.302	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.934	0.994	12.600	0.449	0.449	0.000	0.000	0.000	0.000
24	A	25	TYR	0	0.006	-0.006	7.845	0.092	0.092	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.895	-0.933	7.614	-0.945	-0.945	0.000	0.000	0.000	0.000
26	A	27	ILE	0	-0.083	-0.037	7.093	-0.091	-0.091	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.827	-0.915	6.481	-0.279	-0.279	0.000	0.000	0.000	0.000
28	A	29	GLN	0	-0.030	-0.036	6.323	0.739	0.739	0.000	0.000	0.000	0.000
29	A	30	VAL	0	0.025	0.027	8.360	-0.327	-0.327	0.000	0.000	0.000	0.000
30	A	31	ILE	0	-0.017	-0.008	7.718	0.113	0.113	0.000	0.000	0.000	0.000
31	A	32	ILE	0	-0.013	-0.005	11.679	0.018	0.018	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.004	0.003	12.070	0.027	0.027	0.000	0.000	0.000	0.000
33	A	34	ASN	0	0.047	0.001	15.167	0.021	0.021	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.779	-0.881	18.952	-0.076	-0.076	0.000	0.000	0.000	0.000
35	A	36	ARG	1	0.899	0.941	21.532	0.118	0.118	0.000	0.000	0.000	0.000
36	A	37	ILE	0	-0.032	-0.029	20.513	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	38	SER	0	0.011	0.021	19.034	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.914	-0.957	20.740	-0.089	-0.089	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.838	-0.900	24.255	-0.133	-0.133	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.949	0.958	23.596	0.124	0.124	0.000	0.000	0.000	0.000
41	A	42	THR	0	0.039	0.038	25.913	-0.012	-0.012	0.000	0.000	0.000	0.000
42	A	43	ARG	1	0.967	0.976	23.864	0.171	0.171	0.000	0.000	0.000	0.000
43	A	44	GLN	0	-0.058	-0.020	20.841	-0.025	-0.025	0.000	0.000	0.000	0.000
44	A	45	SER	0	-0.060	-0.053	22.200	-0.025	-0.025	0.000	0.000	0.000	0.000
45	A	46	ILE	0	0.025	0.020	24.602	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.028	-0.014	20.107	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.934	0.961	19.307	0.212	0.212	0.000	0.000	0.000	0.000
48	A	49	ILE	0	-0.030	-0.003	20.986	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	50	SER	0	-0.054	-0.025	22.392	0.011	0.011	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.039	0.000	17.538	-0.015	-0.015	0.000	0.000	0.000	0.000
51	A	52	PRO	0	-0.011	-0.021	17.182	0.022	0.022	0.000	0.000	0.000	0.000
52	A	53	VAL	0	0.037	0.018	18.387	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	54	GLY	0	-0.001	0.002	16.057	0.007	0.007	0.000	0.000	0.000	0.000
54	A	55	LEU	0	-0.040	-0.003	11.776	-0.057	-0.057	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.918	0.968	10.790	0.823	0.823	0.000	0.000	0.000	0.000
56	A	57	ILE	0	0.005	-0.005	12.028	-0.130	-0.130	0.000	0.000	0.000	0.000
57	A	58	VAL	0	-0.052	-0.027	11.241	0.065	0.065	0.000	0.000	0.000	0.000
58	A	59	PHE	0	0.025	-0.002	14.264	-0.031	-0.031	0.000	0.000	0.000	0.000
59	A	60	PHE	0	-0.010	-0.004	10.346	0.015	0.015	0.000	0.000	0.000	0.000
60	A	61	SER	0	0.069	0.037	15.717	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	62	VAL	0	0.080	0.027	15.963	0.001	0.001	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.975	0.992	15.692	0.019	0.019	0.000	0.000	0.000	0.000
63	A	64	ARG	1	0.857	0.919	15.359	0.079	0.079	0.000	0.000	0.000	0.000
64	A	65	PHE	0	0.027	0.007	8.139	-0.021	-0.021	0.000	0.000	0.000	0.000
65	A	66	VAL	0	0.051	0.037	11.319	0.078	0.078	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.856	-0.907	12.530	0.087	0.087	0.000	0.000	0.000	0.000
67	A	68	VAL	0	-0.015	-0.008	8.843	0.013	0.013	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.050	-0.012	6.676	0.069	0.069	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.055	-0.041	8.603	0.213	0.213	0.000	0.000	0.000	0.000
70	A	71	SER	0	-0.047	-0.023	10.995	-0.032	-0.032	0.000	0.000	0.000	0.000
71	A	72	VAL	0	-0.068	-0.038	8.564	-0.077	-0.077	0.000	0.000	0.000	0.000
72	A	73	PRO	0	-0.018	0.013	5.744	0.130	0.130	0.000	0.000	0.000	0.000
73	A	74	ILE	0	0.016	-0.005	2.444	-1.109	-0.225	0.372	-0.375	-0.882	0.002
74	A	75	LYS	1	0.927	0.955	2.451	-6.133	-4.009	1.684	-1.607	-2.201	-0.020
75	A	76	LYS	1	0.883	0.948	3.134	0.520	1.576	0.162	-0.454	-0.763	-0.003
76	A	77	ARG	1	0.865	0.925	2.840	-2.474	-0.763	0.377	-0.835	-1.253	-0.007
77	A	78	THR	0	-0.018	-0.013	3.659	2.096	2.453	0.000	-0.066	-0.292	0.000
78	A	79	MET	0	-0.018	0.013	5.500	-0.320	-0.320	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.001	0.004	7.831	0.159	0.159	0.000	0.000	0.000	0.000
80	A	81	ILE	0	-0.040	-0.025	10.772	0.045	0.045	0.000	0.000	0.000	0.000
81	A	82	TYR	0	0.032	0.004	12.273	0.027	0.027	0.000	0.000	0.000	0.000
82	A	83	THR	0	0.005	-0.011	17.015	-0.017	-0.017	0.000	0.000	0.000	0.000
83	A	84	ASN	0	-0.021	-0.012	20.063	0.027	0.027	0.000	0.000	0.000	0.000
84	A	85	PRO	0	0.058	0.029	19.750	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.899	0.950	19.933	0.021	0.021	0.000	0.000	0.000	0.000
86	A	87	ASP	-1	-0.821	-0.914	17.815	-0.066	-0.066	0.000	0.000	0.000	0.000
87	A	88	VAL	0	-0.030	-0.004	14.585	0.026	0.026	0.000	0.000	0.000	0.000
88	A	89	TYR	0	-0.027	-0.045	15.842	0.060	0.060	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.834	-0.912	17.833	0.075	0.075	0.000	0.000	0.000	0.000
90	A	91	SER	0	-0.025	-0.026	12.781	0.016	0.016	0.000	0.000	0.000	0.000
91	A	92	ILE	0	-0.050	-0.013	13.598	0.090	0.090	0.000	0.000	0.000	0.000
92	A	93	GLU	-1	-0.832	-0.877	14.875	0.207	0.207	0.000	0.000	0.000	0.000
93	A	94	GLY	0	-0.051	-0.016	14.984	0.003	0.003	0.000	0.000	0.000	0.000
94	A	95	ASN	0	-0.033	-0.022	12.401	0.030	0.030	0.000	0.000	0.000	0.000
95	A	96	LEU	0	-0.025	-0.005	8.073	0.248	0.248	0.000	0.000	0.000	0.000
96	A	97	LYS	1	0.840	0.905	8.766	-0.865	-0.865	0.000	0.000	0.000	0.000
97	A	98	LEU	0	0.013	-0.002	9.224	0.068	0.068	0.000	0.000	0.000	0.000
98	A	99	GLU	-1	-0.780	-0.867	10.135	0.350	0.350	0.000	0.000	0.000	0.000
99	A	100	TYR	0	-0.061	-0.040	11.774	-0.061	-0.061	0.000	0.000	0.000	0.000
100	A	101	LEU	0	0.009	0.012	12.248	-0.042	-0.042	0.000	0.000	0.000	0.000
101	A	102	ASN	0	-0.005	0.015	14.442	0.018	0.018	0.000	0.000	0.000	0.000
102	A	103	VAL	0	0.034	0.006	16.287	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	104	GLY	0	0.003	-0.014	19.454	0.002	0.002	0.000	0.000	0.000	0.000
104	A	105	GLN	0	-0.013	-0.012	20.749	0.044	0.044	0.000	0.000	0.000	0.000
105	A	106	MET	0	0.002	0.004	23.344	-0.012	-0.012	0.000	0.000	0.000	0.000
106	A	107	SER	0	-0.033	-0.059	25.679	0.008	0.008	0.000	0.000	0.000	0.000
107	A	108	LYS	1	0.970	0.963	29.051	0.137	0.137	0.000	0.000	0.000	0.000
108	A	109	THR	0	-0.085	-0.065	30.783	0.002	0.002	0.000	0.000	0.000	0.000
109	A	110	GLU	-1	-0.847	-0.905	34.354	-0.077	-0.077	0.000	0.000	0.000	0.000
110	A	111	GLU	-1	-0.854	-0.933	36.660	-0.061	-0.061	0.000	0.000	0.000	0.000
111	A	112	ASN	0	-0.107	-0.062	37.029	0.006	0.006	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.832	-0.898	33.620	-0.052	-0.052	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.785	0.889	32.274	0.062	0.062	0.000	0.000	0.000	0.000
114	A	115	VAL	0	-0.012	0.004	28.552	0.006	0.006	0.000	0.000	0.000	0.000
115	A	116	THR	0	-0.008	-0.012	27.175	0.004	0.004	0.000	0.000	0.000	0.000
116	A	117	GLY	0	0.018	0.010	30.191	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	118	GLY	0	-0.067	-0.039	26.921	-0.012	-0.012	0.000	0.000	0.000	0.000
118	A	119	VAL	0	0.003	0.012	24.336	-0.011	-0.011	0.000	0.000	0.000	0.000
119	A	120	ALA	0	-0.003	0.027	27.204	0.009	0.009	0.000	0.000	0.000	0.000
120	A	121	LEU	0	-0.067	-0.026	25.762	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	122	GLY	0	0.101	0.041	29.288	0.005	0.005	0.000	0.000	0.000	0.000
122	A	123	GLU	-1	-0.855	-0.933	30.594	-0.028	-0.028	0.000	0.000	0.000	0.000
123	A	124	GLU	-1	-0.909	-0.961	26.764	-0.027	-0.027	0.000	0.000	0.000	0.000
124	A	125	ASP	-1	-0.828	-0.922	25.821	-0.071	-0.071	0.000	0.000	0.000	0.000
125	A	126	LYS	1	0.868	0.923	25.883	0.044	0.044	0.000	0.000	0.000	0.000
126	A	127	TYR	0	-0.008	0.011	26.908	0.009	0.009	0.000	0.000	0.000	0.000
127	A	128	TYR	0	0.052	0.015	22.572	0.007	0.007	0.000	0.000	0.000	0.000
128	A	129	PHE	0	0.023	-0.010	20.211	0.007	0.007	0.000	0.000	0.000	0.000
129	A	130	LYS	1	0.829	0.921	22.975	-0.003	-0.003	0.000	0.000	0.000	0.000
130	A	131	LYS	1	0.849	0.908	22.895	-0.064	-0.064	0.000	0.000	0.000	0.000
131	A	132	ILE	0	-0.039	-0.021	17.683	0.017	0.017	0.000	0.000	0.000	0.000
132	A	133	VAL	0	-0.038	-0.027	19.729	0.014	0.014	0.000	0.000	0.000	0.000
133	A	134	ASP	-1	-0.887	-0.917	21.711	0.088	0.088	0.000	0.000	0.000	0.000
134	A	135	LYS	1	0.848	0.917	18.279	-0.170	-0.170	0.000	0.000	0.000	0.000
135	A	136	GLY	0	-0.010	0.003	18.517	0.034	0.034	0.000	0.000	0.000	0.000
136	A	137	THR	0	-0.075	-0.037	14.889	-0.009	-0.009	0.000	0.000	0.000	0.000
137	A	138	ARG	1	0.858	0.916	16.255	0.084	0.084	0.000	0.000	0.000	0.000
138	A	139	VAL	0	0.020	0.002	16.634	-0.036	-0.036	0.000	0.000	0.000	0.000
139	A	140	GLU	-1	-0.818	-0.903	18.034	-0.193	-0.193	0.000	0.000	0.000	0.000
140	A	141	ILE	0	0.007	0.013	19.455	-0.031	-0.031	0.000	0.000	0.000	0.000
141	A	142	GLN	0	-0.020	-0.030	18.684	-0.016	-0.016	0.000	0.000	0.000	0.000
142	A	143	MET	0	0.017	0.041	19.803	-0.049	-0.049	0.000	0.000	0.000	0.000
143	A	144	VAL	0	0.003	-0.013	19.825	-0.039	-0.039	0.000	0.000	0.000	0.000
144	A	145	PRO	0	0.043	0.027	16.455	0.025	0.025	0.000	0.000	0.000	0.000
145	A	146	ASN	0	-0.033	-0.030	18.837	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	147	ASP	-1	-0.857	-0.914	22.091	-0.160	-0.160	0.000	0.000	0.000	0.000
147	A	148	LYS	1	0.917	0.962	23.110	0.097	0.097	0.000	0.000	0.000	0.000
148	A	149	VAL	0	0.042	0.036	20.639	-0.002	-0.002	0.000	0.000	0.000	0.000
149	A	150	THR	0	-0.075	-0.047	23.391	0.026	0.026	0.000	0.000	0.000	0.000
150	A	151	MET	0	0.010	0.013	20.828	-0.010	-0.010	0.000	0.000	0.000	0.000
151	A	152	LEU	0	0.047	0.019	22.646	0.007	0.007	0.000	0.000	0.000	0.000
152	A	153	GLU	-1	-0.766	-0.886	24.364	0.002	0.002	0.000	0.000	0.000	0.000
153	A	154	LYS	1	0.858	0.957	26.135	0.061	0.061	0.000	0.000	0.000	0.000
154	A	155	PHE	0	-0.015	-0.026	27.706	0.002	0.002	0.000	0.000	0.000	0.000
155	A	156	LEU	0	-0.033	0.013	24.831	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)