FMO DATABASE

FMODB ID: 529YZ

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	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	-1619632.527501
FMO2-HF: Nuclear repulsion	1557440.279333
FMO2-HF: Total energy	-62192.248168
FMO2-MP2: Total energy	-62375.765286

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.
-9.292	0.306	3.458	-5.063	-7.991	-0.027

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 : -0.005 / q_NPA : -0.003

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	-0.848	-0.910	2.609	-2.790	-0.275	0.131	-1.000	-1.645	0.000
4	A	5	PHE	0	-0.044	-0.036	5.020	1.086	1.183	-0.001	-0.004	-0.091	0.000
5	A	6	VAL	0	0.018	0.013	8.587	-0.164	-0.164	0.000	0.000	0.000	0.000
6	A	7	ARG	1	0.804	0.890	11.180	0.363	0.363	0.000	0.000	0.000	0.000
7	A	8	ILE	0	-0.004	0.009	14.643	-0.012	-0.012	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.837	-0.920	18.054	-0.230	-0.230	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.756	-0.874	19.889	-0.143	-0.143	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.831	0.912	21.804	0.166	0.166	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.021	-0.012	18.465	-0.006	-0.006	0.000	0.000	0.000	0.000
12	A	13	VAL	0	-0.003	-0.002	16.645	-0.020	-0.020	0.000	0.000	0.000	0.000
13	A	14	HIS	0	-0.031	-0.017	18.646	0.032	0.032	0.000	0.000	0.000	0.000
14	A	15	GLY	0	0.018	0.005	22.178	0.008	0.008	0.000	0.000	0.000	0.000
15	A	16	GLN	0	0.044	0.001	21.145	-0.035	-0.035	0.000	0.000	0.000	0.000
16	A	17	VAL	0	0.014	0.017	19.442	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	18	VAL	0	0.076	0.050	14.806	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	19	THR	0	0.014	-0.002	15.295	-0.053	-0.053	0.000	0.000	0.000	0.000
19	A	20	THR	0	-0.052	-0.033	15.791	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	21	TRP	0	-0.003	-0.009	12.931	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.013	-0.021	11.131	-0.076	-0.076	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.959	0.989	11.344	0.192	0.192	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.937	0.998	12.256	0.203	0.203	0.000	0.000	0.000	0.000
24	A	25	TYR	0	0.019	0.001	7.576	0.124	0.124	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.892	-0.933	7.337	-0.385	-0.385	0.000	0.000	0.000	0.000
26	A	27	ILE	0	-0.082	-0.034	6.585	-0.053	-0.053	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.850	-0.932	6.691	0.135	0.135	0.000	0.000	0.000	0.000
28	A	29	GLN	0	-0.029	-0.040	6.225	0.760	0.760	0.000	0.000	0.000	0.000
29	A	30	VAL	0	0.037	0.030	8.398	-0.343	-0.343	0.000	0.000	0.000	0.000
30	A	31	ILE	0	-0.025	-0.012	7.808	0.096	0.096	0.000	0.000	0.000	0.000
31	A	32	ILE	0	-0.015	-0.003	11.637	0.033	0.033	0.000	0.000	0.000	0.000
32	A	33	VAL	0	0.008	0.010	12.246	0.013	0.013	0.000	0.000	0.000	0.000
33	A	34	ASN	0	0.059	0.009	15.258	0.034	0.034	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.766	-0.886	19.043	-0.105	-0.105	0.000	0.000	0.000	0.000
35	A	36	ARG	1	0.980	0.995	21.617	0.111	0.111	0.000	0.000	0.000	0.000
36	A	37	ILE	0	-0.042	-0.031	20.471	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	38	SER	0	0.008	0.021	18.977	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.915	-0.960	20.820	-0.108	-0.108	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.904	-0.957	24.388	-0.133	-0.133	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.914	0.949	23.626	0.151	0.151	0.000	0.000	0.000	0.000
41	A	42	THR	0	0.031	0.032	25.809	-0.011	-0.011	0.000	0.000	0.000	0.000
42	A	43	ARG	1	0.985	0.986	24.102	0.160	0.160	0.000	0.000	0.000	0.000
43	A	44	GLN	0	-0.066	-0.026	20.860	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	45	SER	0	-0.061	-0.045	22.159	-0.022	-0.022	0.000	0.000	0.000	0.000
45	A	46	ILE	0	0.021	0.016	24.604	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.029	-0.019	20.122	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.948	0.961	19.256	0.226	0.226	0.000	0.000	0.000	0.000
48	A	49	ILE	0	-0.035	-0.002	21.008	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	50	SER	0	-0.047	-0.023	22.417	0.014	0.014	0.000	0.000	0.000	0.000
50	A	51	ALA	0	-0.039	0.001	17.472	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	52	PRO	0	-0.010	-0.020	16.838	0.022	0.022	0.000	0.000	0.000	0.000
52	A	53	VAL	0	0.033	0.016	18.322	-0.021	-0.021	0.000	0.000	0.000	0.000
53	A	54	GLY	0	0.002	0.004	15.990	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	55	LEU	0	-0.040	-0.003	11.463	-0.051	-0.051	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.900	0.961	10.004	0.951	0.951	0.000	0.000	0.000	0.000
56	A	57	ILE	0	0.004	-0.004	12.062	-0.130	-0.130	0.000	0.000	0.000	0.000
57	A	58	VAL	0	-0.041	-0.021	11.225	0.059	0.059	0.000	0.000	0.000	0.000
58	A	59	PHE	0	0.031	-0.002	14.118	-0.023	-0.023	0.000	0.000	0.000	0.000
59	A	60	PHE	0	-0.014	-0.002	10.673	0.007	0.007	0.000	0.000	0.000	0.000
60	A	61	SER	0	0.056	0.030	15.794	0.005	0.005	0.000	0.000	0.000	0.000
61	A	62	VAL	0	0.092	0.040	16.042	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.976	0.993	15.766	0.060	0.060	0.000	0.000	0.000	0.000
63	A	64	ARG	1	0.858	0.915	15.570	0.144	0.144	0.000	0.000	0.000	0.000
64	A	65	PHE	0	0.024	0.006	8.412	-0.031	-0.031	0.000	0.000	0.000	0.000
65	A	66	VAL	0	0.054	0.038	11.383	0.053	0.053	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.842	-0.911	12.578	-0.013	-0.013	0.000	0.000	0.000	0.000
67	A	68	VAL	0	-0.027	-0.010	8.875	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.062	-0.017	6.800	0.024	0.024	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.046	-0.030	8.626	0.170	0.170	0.000	0.000	0.000	0.000
70	A	71	SER	0	-0.053	-0.025	11.025	-0.023	-0.023	0.000	0.000	0.000	0.000
71	A	72	VAL	0	-0.063	-0.036	8.100	-0.065	-0.065	0.000	0.000	0.000	0.000
72	A	73	PRO	0	-0.022	0.012	5.717	0.078	0.078	0.000	0.000	0.000	0.000
73	A	74	ILE	0	0.030	-0.002	2.575	-1.157	-0.047	0.363	-0.436	-1.036	0.002
74	A	75	LYS	1	0.924	0.955	2.401	-6.565	-4.481	2.273	-1.872	-2.485	-0.024
75	A	76	LYS	1	0.901	0.952	3.085	0.932	1.987	0.193	-0.477	-0.772	-0.004
76	A	77	ARG	1	0.862	0.930	2.578	-5.079	-2.814	0.496	-1.170	-1.591	-0.001
77	A	78	THR	0	-0.015	-0.006	3.332	2.416	2.888	0.003	-0.104	-0.371	0.000
78	A	79	MET	0	-0.018	0.020	5.456	-0.221	-0.221	0.000	0.000	0.000	0.000
79	A	80	LEU	0	0.001	0.000	8.096	0.125	0.125	0.000	0.000	0.000	0.000
80	A	81	ILE	0	-0.042	-0.014	10.772	0.076	0.076	0.000	0.000	0.000	0.000
81	A	82	TYR	0	0.030	-0.008	12.361	0.014	0.014	0.000	0.000	0.000	0.000
82	A	83	THR	0	0.004	-0.015	17.015	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	84	ASN	0	-0.022	-0.012	20.063	0.026	0.026	0.000	0.000	0.000	0.000
84	A	85	PRO	0	0.061	0.017	19.751	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.964	1.007	19.933	0.035	0.035	0.000	0.000	0.000	0.000
86	A	87	ASP	-1	-0.806	-0.905	17.927	-0.071	-0.071	0.000	0.000	0.000	0.000
87	A	88	VAL	0	-0.038	-0.007	14.773	0.018	0.018	0.000	0.000	0.000	0.000
88	A	89	TYR	0	0.033	0.002	15.842	0.057	0.057	0.000	0.000	0.000	0.000
89	A	90	ASP	-1	-0.863	-0.938	17.833	0.047	0.047	0.000	0.000	0.000	0.000
90	A	91	SER	0	-0.032	-0.022	12.790	0.003	0.003	0.000	0.000	0.000	0.000
91	A	92	ILE	0	-0.049	-0.012	13.598	0.075	0.075	0.000	0.000	0.000	0.000
92	A	93	GLU	-1	-0.903	-0.948	14.875	0.161	0.161	0.000	0.000	0.000	0.000
93	A	94	GLY	0	-0.043	-0.006	14.988	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	95	ASN	0	-0.025	-0.018	12.356	0.018	0.018	0.000	0.000	0.000	0.000
95	A	96	LEU	0	-0.031	-0.008	7.922	0.206	0.206	0.000	0.000	0.000	0.000
96	A	97	LYS	1	0.881	0.926	8.780	-0.850	-0.850	0.000	0.000	0.000	0.000
97	A	98	LEU	0	0.008	-0.002	9.302	0.100	0.100	0.000	0.000	0.000	0.000
98	A	99	GLU	-1	-0.830	-0.896	10.313	0.418	0.418	0.000	0.000	0.000	0.000
99	A	100	TYR	0	-0.016	-0.009	11.607	-0.067	-0.067	0.000	0.000	0.000	0.000
100	A	101	LEU	0	0.016	0.012	12.295	-0.029	-0.029	0.000	0.000	0.000	0.000
101	A	102	ASN	0	-0.006	0.011	14.478	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	103	VAL	0	0.023	0.003	16.316	-0.020	-0.020	0.000	0.000	0.000	0.000
103	A	104	GLY	0	-0.002	-0.023	19.187	0.006	0.006	0.000	0.000	0.000	0.000
104	A	105	GLN	0	-0.022	-0.019	20.331	0.036	0.036	0.000	0.000	0.000	0.000
105	A	106	MET	0	0.010	0.011	23.109	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	107	SER	0	-0.062	-0.066	25.576	0.010	0.010	0.000	0.000	0.000	0.000
107	A	108	LYS	1	1.003	0.985	28.894	0.094	0.094	0.000	0.000	0.000	0.000
108	A	109	THR	0	-0.076	-0.051	30.671	0.003	0.003	0.000	0.000	0.000	0.000
109	A	110	GLU	-1	-0.847	-0.902	34.424	-0.058	-0.058	0.000	0.000	0.000	0.000
110	A	111	GLU	-1	-0.840	-0.929	36.590	-0.040	-0.040	0.000	0.000	0.000	0.000
111	A	112	ASN	0	-0.120	-0.073	36.993	0.005	0.005	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.835	-0.885	33.635	-0.037	-0.037	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.762	0.873	32.289	0.042	0.042	0.000	0.000	0.000	0.000
114	A	115	VAL	0	-0.018	0.004	28.410	0.005	0.005	0.000	0.000	0.000	0.000
115	A	116	THR	0	-0.013	-0.014	27.063	0.005	0.005	0.000	0.000	0.000	0.000
116	A	117	GLY	0	0.018	0.011	29.938	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	118	GLY	0	-0.064	-0.036	26.540	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	119	VAL	0	-0.006	0.004	24.384	-0.011	-0.011	0.000	0.000	0.000	0.000
119	A	120	ALA	0	0.013	0.035	27.060	0.008	0.008	0.000	0.000	0.000	0.000
120	A	121	LEU	0	-0.074	-0.034	26.027	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	122	GLY	0	0.083	0.033	29.286	0.003	0.003	0.000	0.000	0.000	0.000
122	A	123	GLU	-1	-0.926	-0.965	30.600	-0.010	-0.010	0.000	0.000	0.000	0.000
123	A	124	GLU	-1	-0.929	-0.978	27.315	-0.029	-0.029	0.000	0.000	0.000	0.000
124	A	125	ASP	-1	-0.825	-0.914	25.819	-0.051	-0.051	0.000	0.000	0.000	0.000
125	A	126	LYS	1	0.964	0.976	25.890	0.026	0.026	0.000	0.000	0.000	0.000
126	A	127	TYR	0	0.002	0.018	26.549	0.009	0.009	0.000	0.000	0.000	0.000
127	A	128	TYR	0	0.034	0.004	22.619	0.008	0.008	0.000	0.000	0.000	0.000
128	A	129	PHE	0	0.020	-0.007	20.452	0.009	0.009	0.000	0.000	0.000	0.000
129	A	130	LYS	1	0.903	0.977	23.041	-0.024	-0.024	0.000	0.000	0.000	0.000
130	A	131	LYS	1	0.844	0.913	22.671	-0.064	-0.064	0.000	0.000	0.000	0.000
131	A	132	ILE	0	-0.036	-0.019	17.819	0.016	0.016	0.000	0.000	0.000	0.000
132	A	133	VAL	0	-0.034	-0.027	19.799	0.016	0.016	0.000	0.000	0.000	0.000
133	A	134	ASP	-1	-0.870	-0.918	21.776	0.094	0.094	0.000	0.000	0.000	0.000
134	A	135	LYS	1	0.842	0.929	18.380	-0.144	-0.144	0.000	0.000	0.000	0.000
135	A	136	GLY	0	-0.009	0.001	18.592	0.031	0.031	0.000	0.000	0.000	0.000
136	A	137	THR	0	-0.076	-0.036	15.008	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	138	ARG	1	0.872	0.916	16.311	-0.051	-0.051	0.000	0.000	0.000	0.000
138	A	139	VAL	0	0.018	0.001	16.680	-0.021	-0.021	0.000	0.000	0.000	0.000
139	A	140	GLU	-1	-0.848	-0.927	18.203	-0.043	-0.043	0.000	0.000	0.000	0.000
140	A	141	ILE	0	0.013	0.021	19.484	-0.027	-0.027	0.000	0.000	0.000	0.000
141	A	142	GLN	0	0.008	-0.019	18.446	-0.006	-0.006	0.000	0.000	0.000	0.000
142	A	143	MET	0	0.022	0.038	19.534	-0.040	-0.040	0.000	0.000	0.000	0.000
143	A	144	VAL	0	0.030	0.006	19.497	-0.033	-0.033	0.000	0.000	0.000	0.000
144	A	145	PRO	0	0.020	0.014	16.223	0.024	0.024	0.000	0.000	0.000	0.000
145	A	146	ASN	0	-0.035	-0.025	18.699	0.005	0.005	0.000	0.000	0.000	0.000
146	A	147	ASP	-1	-0.898	-0.942	21.942	-0.087	-0.087	0.000	0.000	0.000	0.000
147	A	148	LYS	1	0.912	0.963	23.072	0.037	0.037	0.000	0.000	0.000	0.000
148	A	149	VAL	0	0.040	0.033	20.750	-0.006	-0.006	0.000	0.000	0.000	0.000
149	A	150	THR	0	-0.075	-0.048	23.419	0.015	0.015	0.000	0.000	0.000	0.000
150	A	151	MET	0	0.012	0.015	21.001	-0.006	-0.006	0.000	0.000	0.000	0.000
151	A	152	LEU	0	0.053	0.024	22.736	0.002	0.002	0.000	0.000	0.000	0.000
152	A	153	GLU	-1	-0.912	-0.963	24.425	0.037	0.037	0.000	0.000	0.000	0.000
153	A	154	LYS	1	0.887	0.961	26.185	0.019	0.019	0.000	0.000	0.000	0.000
154	A	155	PHE	0	0.001	-0.016	27.765	0.000	0.000	0.000	0.000	0.000	0.000
155	A	156	LEU	0	-0.033	0.004	24.936	0.001	0.001	0.000	0.000	0.000	0.000

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