FMO DATABASE

FMODB ID: LNRY9

Calculation Name: 5BMU-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5BMU

Chain ID: B

ChEMBL ID:

UniProt ID: O43324

Base Structure: X-ray

Registration Date: 2023-09-23

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	166
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1639266.949664
FMO2-HF: Nuclear repulsion	1576016.618223
FMO2-HF: Total energy	-63250.33144
FMO2-MP2: Total energy	-63439.130277

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(B:3:THR)

Summations of interaction energy for fragment #1(B:3:THR)

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.
-10.066	-5.085	0.684	-2.428	-3.236	0.002

Interaction energy analysis for fragmet #1(B:3:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.063 / q_NPA : -0.051

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	B	5	SER	0	-0.006	-0.031	3.288	0.611	2.068	0.004	-0.422	-1.039	0.002
4	B	6	LEU	0	0.006	0.007	4.824	0.181	0.216	-0.001	-0.004	-0.030	0.000
5	B	7	THR	0	-0.011	0.012	8.481	0.040	0.040	0.000	0.000	0.000	0.000
6	B	8	VAL	0	0.001	-0.020	10.912	0.084	0.084	0.000	0.000	0.000	0.000
7	B	9	ASN	0	-0.004	-0.004	14.237	-0.022	-0.022	0.000	0.000	0.000	0.000
8	B	10	SER	0	0.018	-0.006	17.732	0.033	0.033	0.000	0.000	0.000	0.000
9	B	11	GLY	0	-0.028	-0.003	18.947	0.028	0.028	0.000	0.000	0.000	0.000
10	B	12	ASP	-1	-0.962	-0.981	21.356	-0.130	-0.130	0.000	0.000	0.000	0.000
11	B	13	PRO	0	0.016	0.010	18.053	-0.012	-0.012	0.000	0.000	0.000	0.000
12	B	14	PRO	0	0.011	0.040	16.439	0.025	0.025	0.000	0.000	0.000	0.000
13	B	15	LEU	0	0.061	0.001	18.069	0.017	0.017	0.000	0.000	0.000	0.000
14	B	16	GLY	0	0.016	-0.018	19.402	-0.006	-0.006	0.000	0.000	0.000	0.000
15	B	17	ALA	0	-0.030	-0.023	15.118	0.037	0.037	0.000	0.000	0.000	0.000
16	B	18	LEU	0	0.046	0.025	13.024	0.047	0.047	0.000	0.000	0.000	0.000
17	B	19	LEU	0	-0.034	0.011	14.829	0.070	0.070	0.000	0.000	0.000	0.000
18	B	20	ALA	0	0.039	0.013	14.831	0.062	0.062	0.000	0.000	0.000	0.000
19	B	21	VAL	0	0.006	0.005	9.557	0.097	0.097	0.000	0.000	0.000	0.000
20	B	22	GLU	-1	-0.863	-0.935	11.412	0.385	0.385	0.000	0.000	0.000	0.000
21	B	23	HIS	0	-0.062	-0.049	13.859	0.025	0.025	0.000	0.000	0.000	0.000
22	B	24	VAL	0	-0.020	-0.005	9.719	0.024	0.024	0.000	0.000	0.000	0.000
23	B	25	LYS	1	0.832	0.903	9.213	-0.577	-0.577	0.000	0.000	0.000	0.000
24	B	26	ASP	-1	-0.897	-0.917	9.265	1.258	1.258	0.000	0.000	0.000	0.000
25	B	27	ASP	-1	-0.858	-0.933	10.349	1.003	1.003	0.000	0.000	0.000	0.000
26	B	28	VAL	0	-0.016	-0.021	6.179	0.283	0.283	0.000	0.000	0.000	0.000
27	B	29	SER	0	-0.039	-0.003	2.627	-6.114	-3.603	0.613	-1.463	-1.661	0.004
28	B	30	ILE	0	-0.003	-0.018	3.345	-0.935	-0.152	0.068	-0.503	-0.348	-0.004
29	B	31	SER	0	-0.077	-0.026	3.965	0.243	0.443	0.001	-0.036	-0.165	0.000
30	B	32	VAL	0	0.015	-0.014	5.342	-0.142	-0.147	-0.001	0.000	0.007	0.000
31	B	33	GLU	-1	-0.863	-0.891	6.174	-2.054	-2.054	0.000	0.000	0.000	0.000
32	B	34	GLU	-1	-0.926	-0.960	10.276	-0.253	-0.253	0.000	0.000	0.000	0.000
33	B	35	GLY	0	0.010	0.009	13.864	-0.044	-0.044	0.000	0.000	0.000	0.000
34	B	36	LYS	1	0.863	0.914	14.672	0.688	0.688	0.000	0.000	0.000	0.000
35	B	37	GLU	-1	-0.902	-0.936	15.908	-0.414	-0.414	0.000	0.000	0.000	0.000
36	B	38	ASN	0	-0.017	-0.031	14.701	-0.035	-0.035	0.000	0.000	0.000	0.000
37	B	39	ILE	0	-0.039	-0.001	11.864	0.053	0.053	0.000	0.000	0.000	0.000
38	B	40	LEU	0	0.019	0.002	8.322	-0.056	-0.056	0.000	0.000	0.000	0.000
39	B	41	HIS	0	-0.010	-0.006	6.596	0.258	0.258	0.000	0.000	0.000	0.000
40	B	42	VAL	0	-0.031	-0.032	6.261	-0.743	-0.743	0.000	0.000	0.000	0.000
41	B	43	SER	0	0.021	0.019	5.976	0.154	0.154	0.000	0.000	0.000	0.000
42	B	44	GLU	-1	-0.941	-0.965	6.037	-4.032	-4.032	0.000	0.000	0.000	0.000
43	B	45	ASN	0	-0.033	-0.010	10.019	0.105	0.105	0.000	0.000	0.000	0.000
44	B	46	VAL	0	-0.014	-0.003	10.971	0.143	0.143	0.000	0.000	0.000	0.000
45	B	47	ILE	0	-0.021	-0.021	11.069	-0.198	-0.198	0.000	0.000	0.000	0.000
46	B	48	PHE	0	-0.004	-0.005	12.589	0.184	0.184	0.000	0.000	0.000	0.000
47	B	49	THR	0	0.026	0.001	13.707	-0.088	-0.088	0.000	0.000	0.000	0.000
48	B	50	ASP	-1	-0.753	-0.862	16.342	-0.127	-0.127	0.000	0.000	0.000	0.000
49	B	51	VAL	0	0.016	0.016	17.557	-0.008	-0.008	0.000	0.000	0.000	0.000
50	B	52	ASN	0	0.019	-0.023	18.145	0.026	0.026	0.000	0.000	0.000	0.000
51	B	53	SER	0	-0.070	-0.046	17.393	0.043	0.043	0.000	0.000	0.000	0.000
52	B	54	ILE	0	-0.007	0.006	12.684	0.047	0.047	0.000	0.000	0.000	0.000
53	B	55	LEU	0	0.027	0.011	13.910	0.081	0.081	0.000	0.000	0.000	0.000
54	B	56	ARG	1	0.817	0.891	15.902	0.061	0.061	0.000	0.000	0.000	0.000
55	B	57	TYR	0	0.012	0.003	9.218	0.050	0.050	0.000	0.000	0.000	0.000
56	B	58	LEU	0	0.034	0.013	9.099	0.133	0.133	0.000	0.000	0.000	0.000
57	B	59	ALA	0	-0.007	-0.001	12.093	0.168	0.168	0.000	0.000	0.000	0.000
58	B	60	ARG	1	0.819	0.905	15.109	-0.130	-0.130	0.000	0.000	0.000	0.000
59	B	61	VAL	0	-0.019	-0.003	8.430	0.038	0.038	0.000	0.000	0.000	0.000
60	B	62	ALA	0	0.015	0.017	10.837	0.189	0.189	0.000	0.000	0.000	0.000
61	B	63	THR	0	-0.052	-0.030	12.389	-0.095	-0.095	0.000	0.000	0.000	0.000
62	B	64	THR	0	-0.035	-0.005	13.963	-0.118	-0.118	0.000	0.000	0.000	0.000
63	B	65	ALA	0	0.040	0.047	14.797	-0.089	-0.089	0.000	0.000	0.000	0.000
64	B	66	GLY	0	0.018	0.000	16.588	-0.030	-0.030	0.000	0.000	0.000	0.000
65	B	67	LEU	0	-0.015	-0.018	15.468	-0.067	-0.067	0.000	0.000	0.000	0.000
66	B	68	TYR	0	-0.004	-0.014	18.182	-0.052	-0.052	0.000	0.000	0.000	0.000
67	B	69	GLY	0	-0.011	0.008	20.730	-0.037	-0.037	0.000	0.000	0.000	0.000
68	B	70	SER	0	-0.006	-0.020	23.271	0.026	0.026	0.000	0.000	0.000	0.000
69	B	71	ASN	0	-0.042	-0.003	25.757	0.007	0.007	0.000	0.000	0.000	0.000
70	B	72	LEU	0	0.056	0.007	26.748	0.008	0.008	0.000	0.000	0.000	0.000
71	B	73	MET	0	-0.010	-0.009	28.408	-0.008	-0.008	0.000	0.000	0.000	0.000
72	B	74	GLU	-1	-0.798	-0.898	26.972	0.196	0.196	0.000	0.000	0.000	0.000
73	B	75	HIS	1	0.852	0.919	23.304	-0.247	-0.247	0.000	0.000	0.000	0.000
74	B	76	THR	0	0.025	0.009	25.668	-0.012	-0.012	0.000	0.000	0.000	0.000
75	B	77	GLU	-1	-0.799	-0.871	28.400	0.096	0.096	0.000	0.000	0.000	0.000
76	B	78	ILE	0	-0.025	0.007	22.243	-0.012	-0.012	0.000	0.000	0.000	0.000
77	B	79	ASP	-1	-0.831	-0.885	23.393	0.087	0.087	0.000	0.000	0.000	0.000
78	B	80	HIS	0	0.006	0.000	25.606	-0.020	-0.020	0.000	0.000	0.000	0.000
79	B	81	TRP	0	-0.018	-0.026	26.803	-0.017	-0.017	0.000	0.000	0.000	0.000
80	B	82	LEU	0	-0.005	0.010	21.102	-0.010	-0.010	0.000	0.000	0.000	0.000
81	B	83	GLU	-1	-0.852	-0.910	25.448	-0.017	-0.017	0.000	0.000	0.000	0.000
82	B	84	PHE	0	-0.009	0.008	28.241	-0.012	-0.012	0.000	0.000	0.000	0.000
83	B	85	SER	0	-0.017	-0.028	25.656	-0.010	-0.010	0.000	0.000	0.000	0.000
84	B	86	ALA	0	0.047	0.017	25.769	-0.010	-0.010	0.000	0.000	0.000	0.000
85	B	87	THR	0	-0.059	-0.037	27.753	-0.009	-0.009	0.000	0.000	0.000	0.000
86	B	88	LYS	1	0.836	0.911	31.448	-0.013	-0.013	0.000	0.000	0.000	0.000
87	B	89	LEU	0	-0.064	-0.025	30.295	0.003	0.003	0.000	0.000	0.000	0.000
88	B	90	SER	0	-0.013	0.006	29.233	-0.005	-0.005	0.000	0.000	0.000	0.000
89	B	91	SER	0	0.017	0.005	30.397	-0.005	-0.005	0.000	0.000	0.000	0.000
90	B	92	SER	0	-0.094	-0.042	33.699	0.005	0.005	0.000	0.000	0.000	0.000
91	B	93	ASP	-1	-0.843	-0.941	36.752	-0.033	-0.033	0.000	0.000	0.000	0.000
92	B	94	SER	0	0.003	0.011	39.595	0.004	0.004	0.000	0.000	0.000	0.000
93	B	95	PHE	0	0.060	0.031	35.533	0.004	0.004	0.000	0.000	0.000	0.000
94	B	96	THR	0	0.007	0.000	39.496	0.004	0.004	0.000	0.000	0.000	0.000
95	B	97	SER	0	0.033	0.004	41.795	0.005	0.005	0.000	0.000	0.000	0.000
96	B	98	THR	0	-0.027	-0.002	35.325	0.003	0.003	0.000	0.000	0.000	0.000
97	B	99	ILE	0	-0.036	-0.027	35.640	0.006	0.006	0.000	0.000	0.000	0.000
98	B	100	ASN	0	-0.019	-0.003	37.766	0.008	0.008	0.000	0.000	0.000	0.000
99	B	101	GLU	-1	-0.796	-0.895	37.343	0.024	0.024	0.000	0.000	0.000	0.000
100	B	102	LEU	0	0.018	0.024	31.807	0.006	0.006	0.000	0.000	0.000	0.000
101	B	103	ASN	0	0.031	-0.015	35.705	0.009	0.009	0.000	0.000	0.000	0.000
102	B	104	HIS	0	-0.059	-0.014	38.305	0.005	0.005	0.000	0.000	0.000	0.000
103	B	105	SER	0	0.022	0.005	35.540	0.005	0.005	0.000	0.000	0.000	0.000
104	B	106	LEU	0	0.035	0.018	31.834	0.007	0.007	0.000	0.000	0.000	0.000
105	B	107	SER	0	-0.067	-0.032	35.827	0.003	0.003	0.000	0.000	0.000	0.000
106	B	108	LEU	0	-0.033	-0.032	38.681	0.001	0.001	0.000	0.000	0.000	0.000
107	B	109	ARG	1	0.787	0.881	31.917	-0.107	-0.107	0.000	0.000	0.000	0.000
108	B	110	THR	0	-0.011	0.003	31.271	-0.010	-0.010	0.000	0.000	0.000	0.000
109	B	111	TYR	0	0.024	0.005	26.280	0.002	0.002	0.000	0.000	0.000	0.000
110	B	112	LEU	0	-0.053	-0.034	27.752	-0.005	-0.005	0.000	0.000	0.000	0.000
111	B	113	VAL	0	0.019	0.018	25.334	-0.006	-0.006	0.000	0.000	0.000	0.000
112	B	114	GLY	0	-0.009	0.013	28.469	0.000	0.000	0.000	0.000	0.000	0.000
113	B	115	ASN	0	-0.027	-0.012	28.662	-0.011	-0.011	0.000	0.000	0.000	0.000
114	B	116	SER	0	-0.052	-0.040	24.835	0.008	0.008	0.000	0.000	0.000	0.000
115	B	117	LEU	0	0.021	0.019	20.858	-0.013	-0.013	0.000	0.000	0.000	0.000
116	B	118	SER	0	0.005	0.002	21.458	0.027	0.027	0.000	0.000	0.000	0.000
117	B	119	LEU	0	0.040	0.012	17.295	-0.022	-0.022	0.000	0.000	0.000	0.000
118	B	120	ALA	0	-0.008	0.010	21.121	-0.028	-0.028	0.000	0.000	0.000	0.000
119	B	121	ASP	-1	-0.755	-0.905	24.160	0.137	0.137	0.000	0.000	0.000	0.000
120	B	122	LEU	0	0.014	0.017	18.090	-0.022	-0.022	0.000	0.000	0.000	0.000
121	B	123	SER	0	0.023	0.015	22.084	-0.028	-0.028	0.000	0.000	0.000	0.000
122	B	124	VAL	0	-0.001	-0.009	22.979	-0.023	-0.023	0.000	0.000	0.000	0.000
123	B	125	TRP	0	-0.019	-0.011	23.830	-0.016	-0.016	0.000	0.000	0.000	0.000
124	B	126	ALA	0	0.009	0.006	22.483	-0.010	-0.010	0.000	0.000	0.000	0.000
125	B	127	THR	0	-0.018	0.000	24.568	-0.020	-0.020	0.000	0.000	0.000	0.000
126	B	128	LEU	0	-0.045	-0.040	26.955	-0.006	-0.006	0.000	0.000	0.000	0.000
127	B	129	LYS	1	0.818	0.899	25.013	0.003	0.003	0.000	0.000	0.000	0.000
128	B	130	GLY	0	-0.002	0.007	27.564	-0.004	-0.004	0.000	0.000	0.000	0.000
129	B	131	ASN	0	-0.017	0.014	28.497	-0.007	-0.007	0.000	0.000	0.000	0.000
130	B	132	ALA	0	0.072	0.015	31.856	0.007	0.007	0.000	0.000	0.000	0.000
131	B	133	ALA	0	0.008	0.004	34.582	0.004	0.004	0.000	0.000	0.000	0.000
132	B	134	TRP	0	-0.008	-0.007	31.776	0.006	0.006	0.000	0.000	0.000	0.000
133	B	135	GLN	0	0.074	0.035	33.237	0.006	0.006	0.000	0.000	0.000	0.000
134	B	136	GLU	-1	-0.812	-0.901	35.844	-0.015	-0.015	0.000	0.000	0.000	0.000
135	B	137	GLN	0	-0.026	-0.027	38.883	0.003	0.003	0.000	0.000	0.000	0.000
136	B	138	LEU	0	-0.008	0.020	34.730	0.005	0.005	0.000	0.000	0.000	0.000
137	B	139	LYS	1	0.842	0.900	37.940	0.023	0.023	0.000	0.000	0.000	0.000
138	B	140	GLN	0	-0.012	-0.001	40.885	0.003	0.003	0.000	0.000	0.000	0.000
139	B	141	LYS	1	0.823	0.923	41.462	-0.011	-0.011	0.000	0.000	0.000	0.000
140	B	142	LYS	1	0.915	0.962	42.889	0.004	0.004	0.000	0.000	0.000	0.000
141	B	143	ALA	0	-0.012	-0.006	39.004	-0.001	-0.001	0.000	0.000	0.000	0.000
142	B	144	PRO	0	0.028	0.018	38.415	0.002	0.002	0.000	0.000	0.000	0.000
143	B	145	VAL	0	0.019	-0.002	38.875	0.003	0.003	0.000	0.000	0.000	0.000
144	B	146	HIS	0	0.048	0.027	37.687	0.008	0.008	0.000	0.000	0.000	0.000
145	B	147	VAL	0	0.032	0.022	33.648	0.006	0.006	0.000	0.000	0.000	0.000
146	B	148	LYS	1	0.935	0.988	34.046	-0.050	-0.050	0.000	0.000	0.000	0.000
147	B	149	ARG	1	0.839	0.917	34.588	-0.080	-0.080	0.000	0.000	0.000	0.000
148	B	150	TRP	0	-0.008	0.020	27.918	0.000	0.000	0.000	0.000	0.000	0.000
149	B	151	PHE	0	0.035	0.002	29.092	0.010	0.010	0.000	0.000	0.000	0.000
150	B	152	GLY	0	-0.021	-0.011	30.094	0.001	0.001	0.000	0.000	0.000	0.000
151	B	153	PHE	0	-0.038	-0.027	29.212	0.006	0.006	0.000	0.000	0.000	0.000
152	B	154	LEU	0	-0.006	-0.001	25.370	0.012	0.012	0.000	0.000	0.000	0.000
153	B	155	GLU	-1	-0.939	-0.974	26.076	0.061	0.061	0.000	0.000	0.000	0.000
154	B	156	ALA	0	-0.023	-0.019	26.772	0.003	0.003	0.000	0.000	0.000	0.000
155	B	157	GLN	0	-0.042	-0.012	24.332	0.027	0.027	0.000	0.000	0.000	0.000
156	B	158	GLN	0	0.024	0.002	21.030	-0.032	-0.032	0.000	0.000	0.000	0.000
157	B	159	ALA	0	0.054	0.028	18.021	-0.016	-0.016	0.000	0.000	0.000	0.000
158	B	160	PHE	0	0.012	-0.016	19.716	-0.020	-0.020	0.000	0.000	0.000	0.000
159	B	161	GLN	0	0.007	0.020	22.264	-0.038	-0.038	0.000	0.000	0.000	0.000
160	B	162	SER	0	-0.046	-0.009	18.523	-0.030	-0.030	0.000	0.000	0.000	0.000
161	B	163	VAL	0	-0.029	-0.023	16.962	-0.032	-0.032	0.000	0.000	0.000	0.000
162	B	164	GLY	0	0.014	0.012	19.316	-0.031	-0.031	0.000	0.000	0.000	0.000
163	B	165	THR	0	-0.049	-0.038	21.630	-0.020	-0.020	0.000	0.000	0.000	0.000
164	B	166	LYS	1	0.806	0.898	14.768	-0.129	-0.129	0.000	0.000	0.000	0.000
165	B	167	TRP	0	-0.020	-0.002	14.185	-0.036	-0.036	0.000	0.000	0.000	0.000
166	B	168	ASP	-1	-0.832	-0.883	20.939	-0.012	-0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:3:THR)