FMO DATABASE

FMODB ID: 859JY

Calculation Name: 5U50-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5U50

Chain ID: D

ChEMBL ID:

UniProt ID: G9I821

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	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1779409.554354
FMO2-HF: Nuclear repulsion	1710163.871718
FMO2-HF: Total energy	-69245.682636
FMO2-MP2: Total energy	-69447.915156

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(D:8:PRO)

Summations of interaction energy for fragment #1(D:8:PRO)

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.
-16.975	-9.08	3.98	-5.061	-6.815	-0.039

Interaction energy analysis for fragmet #1(D:8:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : -0.011

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	D	10	ASP	-1	-0.878	-0.932	2.173	-12.828	-7.383	3.779	-4.397	-4.827	-0.040
4	D	11	ARG	1	0.966	0.986	2.917	-3.917	-2.468	0.184	-0.410	-1.223	0.001
5	D	12	ILE	0	-0.015	-0.006	4.346	-0.543	-0.071	-0.001	-0.155	-0.317	0.000
6	D	13	ASN	0	0.004	-0.010	6.308	0.318	0.318	0.000	0.000	0.000	0.000
7	D	14	ASP	-1	-0.939	-0.961	7.416	0.763	0.763	0.000	0.000	0.000	0.000
8	D	15	PHE	0	0.004	0.004	8.412	0.006	0.006	0.000	0.000	0.000	0.000
9	D	16	LEU	0	-0.074	-0.046	10.066	-0.027	-0.027	0.000	0.000	0.000	0.000
10	D	17	ASP	-1	-0.831	-0.898	12.256	-0.117	-0.117	0.000	0.000	0.000	0.000
11	D	18	HIS	0	-0.094	-0.067	13.714	0.037	0.037	0.000	0.000	0.000	0.000
12	D	19	LEU	0	0.053	0.054	13.521	0.027	0.027	0.000	0.000	0.000	0.000
13	D	20	ASN	0	0.013	-0.009	16.711	-0.034	-0.034	0.000	0.000	0.000	0.000
14	D	21	LEU	0	-0.020	-0.009	18.896	0.019	0.019	0.000	0.000	0.000	0.000
15	D	22	GLY	0	-0.029	-0.002	22.038	-0.004	-0.004	0.000	0.000	0.000	0.000
16	D	23	GLU	-1	-0.938	-0.974	25.227	0.031	0.031	0.000	0.000	0.000	0.000
17	D	24	ARG	1	0.792	0.874	22.767	-0.022	-0.022	0.000	0.000	0.000	0.000
18	D	25	THR	0	-0.007	0.005	19.861	0.018	0.018	0.000	0.000	0.000	0.000
19	D	26	ILE	0	-0.019	-0.019	15.917	-0.022	-0.022	0.000	0.000	0.000	0.000
20	D	27	LYS	1	0.849	0.927	16.386	0.123	0.123	0.000	0.000	0.000	0.000
21	D	28	GLY	0	0.025	0.009	13.190	-0.002	-0.002	0.000	0.000	0.000	0.000
22	D	29	CYS	0	-0.067	-0.032	11.797	-0.025	-0.025	0.000	0.000	0.000	0.000
23	D	30	LEU	0	-0.001	0.007	6.815	0.031	0.031	0.000	0.000	0.000	0.000
24	D	31	GLU	-1	-0.776	-0.872	9.978	-0.573	-0.573	0.000	0.000	0.000	0.000
25	D	32	ALA	0	0.000	-0.002	9.047	0.051	0.051	0.000	0.000	0.000	0.000
26	D	33	TYR	0	-0.021	-0.033	11.110	0.062	0.062	0.000	0.000	0.000	0.000
27	D	34	SER	0	-0.006	-0.015	13.822	0.009	0.009	0.000	0.000	0.000	0.000
28	D	35	CYS	0	-0.052	-0.021	16.085	0.034	0.034	0.000	0.000	0.000	0.000
29	D	36	LYS	1	0.981	0.991	19.051	0.301	0.301	0.000	0.000	0.000	0.000
30	D	37	HIS	0	0.048	0.019	22.257	0.003	0.003	0.000	0.000	0.000	0.000
31	D	38	THR	0	-0.030	-0.035	25.500	0.013	0.013	0.000	0.000	0.000	0.000
32	D	39	GLY	0	0.018	0.014	26.146	-0.010	-0.010	0.000	0.000	0.000	0.000
33	D	40	THR	0	0.054	0.015	25.476	0.008	0.008	0.000	0.000	0.000	0.000
34	D	41	ASP	-1	-0.783	-0.875	22.560	-0.239	-0.239	0.000	0.000	0.000	0.000
35	D	42	LYS	1	0.926	0.986	26.179	0.138	0.138	0.000	0.000	0.000	0.000
36	D	43	ARG	1	0.969	0.982	28.835	0.117	0.117	0.000	0.000	0.000	0.000
37	D	44	LEU	0	0.047	0.025	26.654	0.007	0.007	0.000	0.000	0.000	0.000
38	D	45	SER	0	0.000	-0.004	27.572	0.006	0.006	0.000	0.000	0.000	0.000
39	D	46	ILE	0	-0.034	-0.023	29.470	0.006	0.006	0.000	0.000	0.000	0.000
40	D	47	SER	0	0.015	0.008	32.951	0.007	0.007	0.000	0.000	0.000	0.000
41	D	48	LEU	0	0.010	0.005	28.465	0.004	0.004	0.000	0.000	0.000	0.000
42	D	49	GLU	-1	-0.833	-0.903	32.348	-0.122	-0.122	0.000	0.000	0.000	0.000
43	D	50	HIS	0	0.005	-0.010	33.820	0.005	0.005	0.000	0.000	0.000	0.000
44	D	51	GLU	-1	-0.767	-0.844	33.933	-0.110	-0.110	0.000	0.000	0.000	0.000
45	D	52	ILE	0	-0.026	-0.013	31.764	0.004	0.004	0.000	0.000	0.000	0.000
46	D	53	LEU	0	-0.037	-0.033	36.427	0.004	0.004	0.000	0.000	0.000	0.000
47	D	54	ASP	-1	-0.834	-0.896	39.307	-0.070	-0.070	0.000	0.000	0.000	0.000
48	D	55	TYR	0	-0.024	-0.005	38.065	0.003	0.003	0.000	0.000	0.000	0.000
49	D	56	LEU	0	-0.010	-0.027	37.717	0.003	0.003	0.000	0.000	0.000	0.000
50	D	57	GLY	0	-0.024	-0.005	41.523	0.003	0.003	0.000	0.000	0.000	0.000
51	D	58	LYS	1	0.879	0.917	44.236	0.073	0.073	0.000	0.000	0.000	0.000
52	D	59	SER	0	-0.042	-0.014	42.847	0.002	0.002	0.000	0.000	0.000	0.000
53	D	60	LEU	0	-0.033	-0.016	44.965	0.001	0.001	0.000	0.000	0.000	0.000
54	D	61	ASP	-1	-0.961	-0.953	47.598	-0.054	-0.054	0.000	0.000	0.000	0.000
55	D	62	THR	0	-0.106	-0.050	47.459	0.002	0.002	0.000	0.000	0.000	0.000
56	D	78	LYS	1	0.896	0.910	29.789	0.116	0.116	0.000	0.000	0.000	0.000
57	D	79	ALA	0	0.018	0.018	24.399	-0.006	-0.006	0.000	0.000	0.000	0.000
58	D	80	LEU	0	0.046	0.027	24.786	-0.016	-0.016	0.000	0.000	0.000	0.000
59	D	81	ILE	0	0.021	0.016	25.809	-0.008	-0.008	0.000	0.000	0.000	0.000
60	D	82	TYR	0	0.028	0.004	21.478	-0.008	-0.008	0.000	0.000	0.000	0.000
61	D	83	LEU	0	0.030	0.041	20.722	-0.019	-0.019	0.000	0.000	0.000	0.000
62	D	84	VAL	0	0.068	0.038	22.452	-0.010	-0.010	0.000	0.000	0.000	0.000
63	D	85	LEU	0	-0.052	-0.023	22.764	-0.001	-0.001	0.000	0.000	0.000	0.000
64	D	86	THR	0	-0.079	-0.065	17.957	-0.015	-0.015	0.000	0.000	0.000	0.000
65	D	87	LEU	0	0.043	0.026	20.200	-0.013	-0.013	0.000	0.000	0.000	0.000
66	D	88	TYR	0	0.002	0.002	22.428	0.004	0.004	0.000	0.000	0.000	0.000
67	D	89	HIS	1	0.737	0.856	18.916	0.288	0.288	0.000	0.000	0.000	0.000
68	D	90	MET	0	-0.040	0.016	16.177	-0.001	-0.001	0.000	0.000	0.000	0.000
69	D	91	TYR	0	-0.041	-0.032	20.200	0.014	0.014	0.000	0.000	0.000	0.000
70	D	92	PRO	0	-0.005	-0.003	22.848	0.010	0.010	0.000	0.000	0.000	0.000
71	D	93	ASP	-1	-0.924	-0.960	25.743	-0.127	-0.127	0.000	0.000	0.000	0.000
72	D	94	TYR	0	-0.039	-0.015	27.859	0.012	0.012	0.000	0.000	0.000	0.000
73	D	95	ASP	-1	-0.872	-0.920	29.529	-0.111	-0.111	0.000	0.000	0.000	0.000
74	D	96	PHE	0	-0.047	-0.029	25.484	0.004	0.004	0.000	0.000	0.000	0.000
75	D	97	SER	0	-0.056	-0.057	30.351	0.005	0.005	0.000	0.000	0.000	0.000
76	D	98	ALA	0	0.009	-0.019	30.630	-0.006	-0.006	0.000	0.000	0.000	0.000
77	D	99	VAL	0	0.004	0.006	31.711	-0.003	-0.003	0.000	0.000	0.000	0.000
78	D	100	LYS	1	0.896	0.946	31.302	0.114	0.114	0.000	0.000	0.000	0.000
79	D	101	ALA	0	0.006	0.011	27.766	-0.003	-0.003	0.000	0.000	0.000	0.000
80	D	102	HIS	0	-0.033	-0.030	28.778	-0.012	-0.012	0.000	0.000	0.000	0.000
81	D	103	GLN	0	-0.061	-0.019	30.714	0.004	0.004	0.000	0.000	0.000	0.000
82	D	104	PHE	0	0.020	0.010	28.183	0.000	0.000	0.000	0.000	0.000	0.000
83	D	105	PHE	0	-0.052	-0.033	22.010	-0.009	-0.009	0.000	0.000	0.000	0.000
84	D	106	THR	0	-0.012	0.004	25.222	0.015	0.015	0.000	0.000	0.000	0.000
85	D	107	GLU	-1	-0.968	-0.977	24.165	-0.169	-0.169	0.000	0.000	0.000	0.000
86	D	108	GLU	-1	-0.857	-0.904	21.177	-0.141	-0.141	0.000	0.000	0.000	0.000
87	D	109	SER	0	-0.001	-0.014	21.546	-0.009	-0.009	0.000	0.000	0.000	0.000
88	D	110	TRP	0	0.065	0.018	12.197	-0.007	-0.007	0.000	0.000	0.000	0.000
89	D	111	ASN	0	-0.011	-0.023	18.349	0.009	0.009	0.000	0.000	0.000	0.000
90	D	112	THR	0	0.068	0.040	20.821	0.010	0.010	0.000	0.000	0.000	0.000
91	D	113	PHE	0	0.012	0.018	13.404	0.001	0.001	0.000	0.000	0.000	0.000
92	D	114	LYS	1	0.904	0.968	17.196	0.099	0.099	0.000	0.000	0.000	0.000
93	D	115	GLN	0	0.026	0.016	18.156	0.011	0.011	0.000	0.000	0.000	0.000
94	D	116	ILE	0	0.010	0.015	18.881	0.013	0.013	0.000	0.000	0.000	0.000
95	D	117	PHE	0	-0.004	-0.006	12.820	0.003	0.003	0.000	0.000	0.000	0.000
96	D	118	GLU	-1	-0.918	-0.981	17.903	-0.049	-0.049	0.000	0.000	0.000	0.000
97	D	119	THR	0	-0.069	-0.033	19.806	0.019	0.019	0.000	0.000	0.000	0.000
98	D	120	TYR	0	-0.035	-0.024	20.545	0.010	0.010	0.000	0.000	0.000	0.000
99	D	121	MET	0	-0.044	-0.008	14.522	0.017	0.017	0.000	0.000	0.000	0.000
100	D	122	PHE	0	0.028	0.016	17.183	0.018	0.018	0.000	0.000	0.000	0.000
101	D	123	GLU	-1	-0.777	-0.893	18.736	0.060	0.060	0.000	0.000	0.000	0.000
102	D	124	ALA	0	0.037	0.024	14.323	0.025	0.025	0.000	0.000	0.000	0.000
103	D	125	SER	0	-0.003	-0.020	13.959	0.031	0.031	0.000	0.000	0.000	0.000
104	D	126	LYS	1	0.810	0.914	15.039	-0.111	-0.111	0.000	0.000	0.000	0.000
105	D	127	GLU	-1	-0.854	-0.922	14.295	0.287	0.287	0.000	0.000	0.000	0.000
106	D	128	TRP	0	-0.024	-0.014	5.161	0.081	0.081	0.000	0.000	0.000	0.000
107	D	129	SER	0	-0.121	-0.061	12.132	0.073	0.073	0.000	0.000	0.000	0.000
108	D	130	GLU	-1	-0.868	-0.917	14.440	0.227	0.227	0.000	0.000	0.000	0.000
109	D	131	THR	0	-0.036	-0.014	9.482	0.082	0.082	0.000	0.000	0.000	0.000
110	D	132	TYR	0	-0.097	-0.066	5.637	0.033	0.033	0.000	0.000	0.000	0.000
111	D	133	GLY	0	0.061	0.043	9.439	0.043	0.043	0.000	0.000	0.000	0.000
112	D	134	GLY	0	-0.024	-0.007	12.011	-0.054	-0.054	0.000	0.000	0.000	0.000
113	D	135	SER	0	-0.008	-0.033	10.568	0.017	0.017	0.000	0.000	0.000	0.000
114	D	136	SER	0	-0.014	0.002	12.407	-0.027	-0.027	0.000	0.000	0.000	0.000
115	D	137	LEU	0	0.097	0.066	8.987	0.000	0.000	0.000	0.000	0.000	0.000
116	D	138	LEU	0	0.034	0.013	9.645	-0.098	-0.098	0.000	0.000	0.000	0.000
117	D	139	GLU	-1	-0.858	-0.918	10.645	-0.035	-0.035	0.000	0.000	0.000	0.000
118	D	140	THR	0	0.000	-0.001	5.699	-0.024	-0.024	0.000	0.000	0.000	0.000
119	D	141	LEU	0	0.011	0.012	5.665	-0.259	-0.259	0.000	0.000	0.000	0.000
120	D	142	TYR	0	-0.065	-0.051	7.654	-0.112	-0.112	0.000	0.000	0.000	0.000
121	D	143	LYS	1	0.875	0.913	7.337	-0.014	-0.014	0.000	0.000	0.000	0.000
122	D	144	ALA	0	0.031	0.037	3.348	-0.388	-0.111	0.020	-0.079	-0.218	0.000
123	D	145	LEU	0	-0.023	-0.023	4.862	-0.118	-0.075	-0.001	-0.002	-0.040	0.000
124	D	146	ASP	-1	-0.810	-0.900	8.126	-0.333	-0.333	0.000	0.000	0.000	0.000
125	D	147	GLU	-1	-1.014	-0.989	4.323	-1.412	-1.203	-0.001	-0.018	-0.190	0.000
126	D	148	VAL	0	-0.093	-0.032	5.991	0.029	0.029	0.000	0.000	0.000	0.000
127	D	149	VAL	0	-0.099	-0.078	8.581	0.129	0.129	0.000	0.000	0.000	0.000
128	D	150	LYS	1	0.926	0.960	11.911	0.280	0.280	0.000	0.000	0.000	0.000
129	D	151	LEU	0	0.078	0.039	11.663	0.039	0.039	0.000	0.000	0.000	0.000
130	D	152	PRO	0	-0.033	-0.021	14.567	0.029	0.029	0.000	0.000	0.000	0.000
131	D	153	GLU	-1	-0.874	-0.916	17.389	-0.203	-0.203	0.000	0.000	0.000	0.000
132	D	154	CYS	0	-0.117	-0.042	15.268	-0.020	-0.020	0.000	0.000	0.000	0.000
133	D	155	GLU	-1	-0.789	-0.854	17.880	-0.188	-0.188	0.000	0.000	0.000	0.000
134	D	156	ILE	0	-0.012	-0.016	17.302	-0.033	-0.033	0.000	0.000	0.000	0.000
135	D	157	TYR	0	-0.032	-0.031	19.242	0.028	0.028	0.000	0.000	0.000	0.000
136	D	158	SER	0	-0.006	-0.020	19.832	-0.025	-0.025	0.000	0.000	0.000	0.000
137	D	159	TYR	0	-0.001	-0.010	21.939	0.011	0.011	0.000	0.000	0.000	0.000
138	D	160	ASN	0	-0.033	-0.020	23.723	-0.002	-0.002	0.000	0.000	0.000	0.000
139	D	161	PRO	0	-0.009	0.007	25.834	0.007	0.007	0.000	0.000	0.000	0.000
140	D	162	ASP	-1	-0.946	-0.973	28.916	-0.084	-0.084	0.000	0.000	0.000	0.000
141	D	173	ALA	0	-0.028	-0.033	25.626	0.002	0.002	0.000	0.000	0.000	0.000
142	D	174	ILE	0	-0.023	-0.015	25.866	0.001	0.001	0.000	0.000	0.000	0.000
143	D	175	TRP	0	0.035	0.010	19.376	-0.003	-0.003	0.000	0.000	0.000	0.000
144	D	176	SER	0	-0.031	-0.020	21.745	0.000	0.000	0.000	0.000	0.000	0.000
145	D	177	PHE	0	0.022	0.024	19.274	0.007	0.007	0.000	0.000	0.000	0.000
146	D	178	ASN	0	-0.022	-0.015	18.341	-0.036	-0.036	0.000	0.000	0.000	0.000
147	D	179	PHE	0	0.065	0.026	16.122	0.023	0.023	0.000	0.000	0.000	0.000
148	D	180	PHE	0	-0.018	-0.014	16.247	-0.048	-0.048	0.000	0.000	0.000	0.000
149	D	181	PHE	0	0.023	0.019	13.128	0.038	0.038	0.000	0.000	0.000	0.000
150	D	182	TYR	0	-0.025	-0.014	15.179	-0.040	-0.040	0.000	0.000	0.000	0.000
151	D	183	ASN	0	0.086	0.038	16.470	0.036	0.036	0.000	0.000	0.000	0.000
152	D	184	ARG	1	0.892	0.929	18.217	0.185	0.185	0.000	0.000	0.000	0.000
153	D	185	LYS	1	0.863	0.901	20.283	0.204	0.204	0.000	0.000	0.000	0.000
154	D	186	LEU	0	-0.016	0.001	14.044	0.004	0.004	0.000	0.000	0.000	0.000
155	D	187	LYS	1	0.847	0.930	17.184	0.227	0.227	0.000	0.000	0.000	0.000
156	D	188	ARG	1	0.944	0.982	11.284	0.595	0.595	0.000	0.000	0.000	0.000
157	D	189	VAL	0	-0.001	0.000	15.200	0.031	0.031	0.000	0.000	0.000	0.000
158	D	190	VAL	0	-0.008	0.003	9.601	-0.045	-0.045	0.000	0.000	0.000	0.000
159	D	191	SER	0	-0.006	-0.003	12.794	0.072	0.072	0.000	0.000	0.000	0.000
160	D	192	PHE	0	0.031	0.007	11.753	-0.098	-0.098	0.000	0.000	0.000	0.000
161	D	193	ARG	1	0.925	0.964	13.540	0.328	0.328	0.000	0.000	0.000	0.000
162	D	194	PHE	0	0.042	0.011	15.127	-0.020	-0.020	0.000	0.000	0.000	0.000
163	D	195	SER	0	-0.054	-0.036	17.047	0.014	0.014	0.000	0.000	0.000	0.000
164	D	196	CYS	0	-0.030	0.016	19.606	0.012	0.012	0.000	0.000	0.000	0.000
165	D	197	LEU	0	-0.004	0.003	21.945	-0.006	-0.006	0.000	0.000	0.000	0.000
166	D	198	SER	0	0.047	0.017	24.791	0.012	0.012	0.000	0.000	0.000	0.000
167	D	199	ASN	0	0.013	0.020	25.348	-0.014	-0.014	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(D:8:PRO)