FMO DATABASE

FMODB ID: 3JGLL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1640119.888472
FMO2-HF: Nuclear repulsion	1576870.792326
FMO2-HF: Total energy	-63249.096146
FMO2-MP2: Total energy	-63437.912311

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.
-8.53	-4.742	0.782	-1.906	-2.663	0.001

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 : -0.051 / q_NPA : -0.047

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	0.009	-0.010	3.498	1.054	2.463	0.003	-0.424	-0.988	0.002
4	B	6	LEU	0	0.017	0.011	4.946	0.049	0.088	-0.001	-0.004	-0.034	0.000
5	B	7	THR	0	-0.037	0.012	8.567	0.111	0.111	0.000	0.000	0.000	0.000
6	B	8	VAL	0	0.029	-0.013	11.050	0.072	0.072	0.000	0.000	0.000	0.000
7	B	9	ASN	0	0.013	0.002	14.221	-0.021	-0.021	0.000	0.000	0.000	0.000
8	B	10	SER	0	-0.002	-0.016	17.782	0.036	0.036	0.000	0.000	0.000	0.000
9	B	11	GLY	0	-0.014	0.004	18.884	0.030	0.030	0.000	0.000	0.000	0.000
10	B	12	ASP	-1	-0.963	-0.981	21.314	-0.109	-0.109	0.000	0.000	0.000	0.000
11	B	13	PRO	0	0.022	0.013	17.955	-0.013	-0.013	0.000	0.000	0.000	0.000
12	B	14	PRO	0	0.015	0.049	16.289	0.020	0.020	0.000	0.000	0.000	0.000
13	B	15	LEU	0	0.068	-0.005	17.812	0.026	0.026	0.000	0.000	0.000	0.000
14	B	16	GLY	0	0.013	-0.031	19.240	-0.012	-0.012	0.000	0.000	0.000	0.000
15	B	17	ALA	0	-0.018	-0.027	15.170	0.037	0.037	0.000	0.000	0.000	0.000
16	B	18	LEU	0	0.034	0.020	12.621	0.056	0.056	0.000	0.000	0.000	0.000
17	B	19	LEU	0	-0.034	0.025	14.810	0.084	0.084	0.000	0.000	0.000	0.000
18	B	20	ALA	0	0.048	0.014	14.757	0.068	0.068	0.000	0.000	0.000	0.000
19	B	21	VAL	0	-0.007	0.004	9.544	0.104	0.104	0.000	0.000	0.000	0.000
20	B	22	GLU	-1	-0.874	-0.970	11.408	0.549	0.549	0.000	0.000	0.000	0.000
21	B	23	HIS	0	-0.051	-0.044	13.853	0.030	0.030	0.000	0.000	0.000	0.000
22	B	24	VAL	0	-0.026	-0.013	9.748	0.009	0.009	0.000	0.000	0.000	0.000
23	B	25	LYS	1	0.916	0.974	9.226	-0.711	-0.711	0.000	0.000	0.000	0.000
24	B	26	ASP	-1	-0.974	-0.980	9.276	1.525	1.525	0.000	0.000	0.000	0.000
25	B	27	ASP	-1	-0.854	-0.925	10.352	1.114	1.114	0.000	0.000	0.000	0.000
26	B	28	VAL	0	-0.041	-0.025	6.311	0.247	0.247	0.000	0.000	0.000	0.000
27	B	29	SER	0	-0.025	-0.006	2.419	-4.013	-2.692	0.714	-0.919	-1.117	0.003
28	B	30	ILE	0	-0.005	-0.012	3.353	-1.087	-0.272	0.068	-0.528	-0.356	-0.004
29	B	31	SER	0	-0.034	0.000	4.116	0.184	0.373	0.000	-0.028	-0.160	0.000
30	B	32	VAL	0	0.005	-0.013	5.372	-0.260	-0.258	-0.001	0.000	0.000	0.000
31	B	33	GLU	-1	-0.956	-0.967	7.046	-1.661	-1.661	0.000	0.000	0.000	0.000
32	B	34	GLU	-1	-0.926	-0.966	10.146	-0.188	-0.188	0.000	0.000	0.000	0.000
33	B	35	GLY	0	-0.008	0.001	13.826	-0.046	-0.046	0.000	0.000	0.000	0.000
34	B	36	LYS	1	0.872	0.924	14.532	0.668	0.668	0.000	0.000	0.000	0.000
35	B	37	GLU	-1	-0.895	-0.935	15.920	-0.427	-0.427	0.000	0.000	0.000	0.000
36	B	38	ASN	0	-0.029	-0.034	14.845	-0.030	-0.030	0.000	0.000	0.000	0.000
37	B	39	ILE	0	-0.038	0.013	12.147	0.039	0.039	0.000	0.000	0.000	0.000
38	B	40	LEU	0	0.016	0.005	8.044	-0.034	-0.034	0.000	0.000	0.000	0.000
39	B	41	HIS	0	-0.012	-0.010	6.271	0.148	0.148	0.000	0.000	0.000	0.000
40	B	42	VAL	0	-0.031	-0.030	6.031	-0.771	-0.771	0.000	0.000	0.000	0.000
41	B	43	SER	0	0.015	0.009	5.893	0.026	0.026	0.000	0.000	0.000	0.000
42	B	44	GLU	-1	-0.928	-0.955	4.886	-5.099	-5.086	-0.001	-0.003	-0.008	0.000
43	B	45	ASN	0	-0.019	-0.003	9.424	0.075	0.075	0.000	0.000	0.000	0.000
44	B	46	VAL	0	-0.037	-0.009	10.671	0.181	0.181	0.000	0.000	0.000	0.000
45	B	47	ILE	0	0.008	-0.011	10.479	-0.233	-0.233	0.000	0.000	0.000	0.000
46	B	48	PHE	0	-0.018	-0.012	12.478	0.199	0.199	0.000	0.000	0.000	0.000
47	B	49	THR	0	0.021	-0.051	13.603	-0.073	-0.073	0.000	0.000	0.000	0.000
48	B	50	ASP	-1	-0.835	-0.885	16.250	-0.147	-0.147	0.000	0.000	0.000	0.000
49	B	51	VAL	0	0.034	0.017	17.611	-0.008	-0.008	0.000	0.000	0.000	0.000
50	B	52	ASN	0	0.041	-0.010	18.134	0.027	0.027	0.000	0.000	0.000	0.000
51	B	53	SER	0	-0.042	-0.008	17.250	0.042	0.042	0.000	0.000	0.000	0.000
52	B	54	ILE	0	0.006	0.011	12.520	0.042	0.042	0.000	0.000	0.000	0.000
53	B	55	LEU	0	0.024	0.014	13.906	0.083	0.083	0.000	0.000	0.000	0.000
54	B	56	ARG	1	0.893	0.954	15.905	0.072	0.072	0.000	0.000	0.000	0.000
55	B	57	TYR	0	-0.009	-0.001	9.019	0.046	0.046	0.000	0.000	0.000	0.000
56	B	58	LEU	0	0.035	0.012	8.979	0.117	0.117	0.000	0.000	0.000	0.000
57	B	59	ALA	0	-0.006	0.003	12.098	0.172	0.172	0.000	0.000	0.000	0.000
58	B	60	ARG	1	0.892	0.940	15.099	-0.097	-0.097	0.000	0.000	0.000	0.000
59	B	61	VAL	0	-0.029	-0.005	8.402	0.018	0.018	0.000	0.000	0.000	0.000
60	B	62	ALA	0	0.016	0.014	10.859	0.186	0.186	0.000	0.000	0.000	0.000
61	B	63	THR	0	-0.047	-0.030	12.410	-0.078	-0.078	0.000	0.000	0.000	0.000
62	B	64	THR	0	-0.034	0.005	14.017	-0.122	-0.122	0.000	0.000	0.000	0.000
63	B	65	ALA	0	0.035	0.040	14.813	-0.083	-0.083	0.000	0.000	0.000	0.000
64	B	66	GLY	0	0.011	-0.001	16.606	-0.040	-0.040	0.000	0.000	0.000	0.000
65	B	67	LEU	0	-0.040	-0.029	15.676	-0.072	-0.072	0.000	0.000	0.000	0.000
66	B	68	TYR	0	-0.049	-0.054	18.296	-0.052	-0.052	0.000	0.000	0.000	0.000
67	B	69	GLY	0	0.010	0.015	20.744	-0.040	-0.040	0.000	0.000	0.000	0.000
68	B	70	SER	0	-0.005	-0.024	23.289	0.025	0.025	0.000	0.000	0.000	0.000
69	B	71	ASN	0	-0.045	0.002	25.777	0.008	0.008	0.000	0.000	0.000	0.000
70	B	72	LEU	0	0.050	-0.002	26.651	0.008	0.008	0.000	0.000	0.000	0.000
71	B	73	MET	0	-0.009	0.002	28.408	-0.010	-0.010	0.000	0.000	0.000	0.000
72	B	74	GLU	-1	-0.787	-0.891	27.000	0.205	0.205	0.000	0.000	0.000	0.000
73	B	75	HIS	1	0.856	0.931	23.400	-0.232	-0.232	0.000	0.000	0.000	0.000
74	B	76	THR	0	0.025	-0.008	25.681	-0.012	-0.012	0.000	0.000	0.000	0.000
75	B	77	GLU	-1	-0.878	-0.944	28.410	0.108	0.108	0.000	0.000	0.000	0.000
76	B	78	ILE	0	-0.033	0.004	22.242	-0.010	-0.010	0.000	0.000	0.000	0.000
77	B	79	ASP	-1	-0.843	-0.898	23.539	0.076	0.076	0.000	0.000	0.000	0.000
78	B	80	HIS	0	0.000	-0.006	25.610	-0.020	-0.020	0.000	0.000	0.000	0.000
79	B	81	TRP	0	0.014	-0.011	26.771	-0.016	-0.016	0.000	0.000	0.000	0.000
80	B	82	LEU	0	-0.018	-0.004	20.949	-0.010	-0.010	0.000	0.000	0.000	0.000
81	B	83	GLU	-1	-0.940	-0.956	25.445	-0.035	-0.035	0.000	0.000	0.000	0.000
82	B	84	PHE	0	-0.006	0.003	28.236	-0.011	-0.011	0.000	0.000	0.000	0.000
83	B	85	SER	0	-0.017	-0.028	25.876	-0.011	-0.011	0.000	0.000	0.000	0.000
84	B	86	ALA	0	0.044	0.014	25.754	-0.009	-0.009	0.000	0.000	0.000	0.000
85	B	87	THR	0	-0.029	-0.012	27.762	-0.010	-0.010	0.000	0.000	0.000	0.000
86	B	88	LYS	1	0.900	0.961	31.497	-0.011	-0.011	0.000	0.000	0.000	0.000
87	B	89	LEU	0	-0.081	-0.030	30.181	0.004	0.004	0.000	0.000	0.000	0.000
88	B	90	SER	0	-0.017	-0.003	29.142	-0.004	-0.004	0.000	0.000	0.000	0.000
89	B	91	SER	0	0.017	0.004	30.377	-0.004	-0.004	0.000	0.000	0.000	0.000
90	B	92	SER	0	-0.111	-0.052	33.708	0.006	0.006	0.000	0.000	0.000	0.000
91	B	93	ASP	-1	-0.835	-0.929	36.694	-0.034	-0.034	0.000	0.000	0.000	0.000
92	B	94	SER	0	-0.003	-0.007	39.561	0.004	0.004	0.000	0.000	0.000	0.000
93	B	95	PHE	0	0.052	0.039	35.189	0.004	0.004	0.000	0.000	0.000	0.000
94	B	96	THR	0	0.004	-0.003	39.433	0.005	0.005	0.000	0.000	0.000	0.000
95	B	97	SER	0	0.025	-0.003	41.787	0.007	0.007	0.000	0.000	0.000	0.000
96	B	98	THR	0	-0.012	0.007	35.334	0.003	0.003	0.000	0.000	0.000	0.000
97	B	99	ILE	0	-0.026	-0.022	35.304	0.006	0.006	0.000	0.000	0.000	0.000
98	B	100	ASN	0	-0.025	-0.008	37.759	0.010	0.010	0.000	0.000	0.000	0.000
99	B	101	GLU	-1	-0.854	-0.938	37.236	0.031	0.031	0.000	0.000	0.000	0.000
100	B	102	LEU	0	0.002	0.019	32.013	0.006	0.006	0.000	0.000	0.000	0.000
101	B	103	ASN	0	0.020	-0.023	35.701	0.012	0.012	0.000	0.000	0.000	0.000
102	B	104	HIS	0	-0.034	0.004	38.302	0.005	0.005	0.000	0.000	0.000	0.000
103	B	105	SER	0	0.015	0.028	35.616	0.005	0.005	0.000	0.000	0.000	0.000
104	B	106	LEU	0	0.023	0.011	31.913	0.008	0.008	0.000	0.000	0.000	0.000
105	B	107	SER	0	-0.082	-0.062	35.828	0.004	0.004	0.000	0.000	0.000	0.000
106	B	108	LEU	0	-0.026	-0.031	38.685	0.002	0.002	0.000	0.000	0.000	0.000
107	B	109	ARG	1	0.864	0.967	31.882	-0.112	-0.112	0.000	0.000	0.000	0.000
108	B	110	THR	0	-0.015	0.000	31.042	-0.010	-0.010	0.000	0.000	0.000	0.000
109	B	111	TYR	0	0.020	0.007	26.336	0.005	0.005	0.000	0.000	0.000	0.000
110	B	112	LEU	0	-0.048	-0.039	27.736	-0.006	-0.006	0.000	0.000	0.000	0.000
111	B	113	VAL	0	0.009	0.023	25.392	-0.009	-0.009	0.000	0.000	0.000	0.000
112	B	114	GLY	0	0.008	0.026	28.478	-0.003	-0.003	0.000	0.000	0.000	0.000
113	B	115	ASN	0	-0.015	-0.010	28.871	-0.012	-0.012	0.000	0.000	0.000	0.000
114	B	116	SER	0	-0.044	-0.034	24.962	0.008	0.008	0.000	0.000	0.000	0.000
115	B	117	LEU	0	0.022	0.017	20.941	-0.014	-0.014	0.000	0.000	0.000	0.000
116	B	118	SER	0	0.011	0.006	21.521	0.025	0.025	0.000	0.000	0.000	0.000
117	B	119	LEU	0	0.035	0.001	17.265	-0.021	-0.021	0.000	0.000	0.000	0.000
118	B	120	ALA	0	0.006	0.017	21.124	-0.027	-0.027	0.000	0.000	0.000	0.000
119	B	121	ASP	-1	-0.771	-0.909	24.041	0.156	0.156	0.000	0.000	0.000	0.000
120	B	122	LEU	0	0.010	0.013	18.020	-0.022	-0.022	0.000	0.000	0.000	0.000
121	B	123	SER	0	0.016	0.015	22.013	-0.025	-0.025	0.000	0.000	0.000	0.000
122	B	124	VAL	0	0.018	-0.003	22.972	-0.023	-0.023	0.000	0.000	0.000	0.000
123	B	125	TRP	0	-0.026	-0.015	24.230	-0.017	-0.017	0.000	0.000	0.000	0.000
124	B	126	ALA	0	0.012	0.003	22.404	-0.009	-0.009	0.000	0.000	0.000	0.000
125	B	127	THR	0	-0.012	0.006	24.425	-0.021	-0.021	0.000	0.000	0.000	0.000
126	B	128	LEU	0	-0.051	-0.043	26.723	-0.007	-0.007	0.000	0.000	0.000	0.000
127	B	129	LYS	1	0.911	0.969	25.553	-0.047	-0.047	0.000	0.000	0.000	0.000
128	B	130	GLY	0	0.032	0.021	27.319	-0.004	-0.004	0.000	0.000	0.000	0.000
129	B	131	ASN	0	0.008	0.042	28.242	-0.012	-0.012	0.000	0.000	0.000	0.000
130	B	132	ALA	0	0.099	0.022	31.635	0.008	0.008	0.000	0.000	0.000	0.000
131	B	133	ALA	0	0.002	-0.003	34.341	0.004	0.004	0.000	0.000	0.000	0.000
132	B	134	TRP	0	-0.046	-0.031	31.480	0.005	0.005	0.000	0.000	0.000	0.000
133	B	135	GLN	0	0.056	0.028	33.866	0.002	0.002	0.000	0.000	0.000	0.000
134	B	136	GLU	-1	-0.861	-0.948	35.641	-0.003	-0.003	0.000	0.000	0.000	0.000
135	B	137	GLN	0	-0.025	-0.030	38.664	0.005	0.005	0.000	0.000	0.000	0.000
136	B	138	LEU	0	0.009	0.026	34.387	0.004	0.004	0.000	0.000	0.000	0.000
137	B	139	LYS	1	0.861	0.924	38.206	0.008	0.008	0.000	0.000	0.000	0.000
138	B	140	GLN	0	0.016	0.020	40.766	0.001	0.001	0.000	0.000	0.000	0.000
139	B	141	LYS	1	0.839	0.937	41.540	-0.026	-0.026	0.000	0.000	0.000	0.000
140	B	142	LYS	1	0.899	0.954	42.755	-0.006	-0.006	0.000	0.000	0.000	0.000
141	B	143	ALA	0	-0.006	-0.008	38.985	-0.002	-0.002	0.000	0.000	0.000	0.000
142	B	144	PRO	0	0.017	0.013	38.648	0.001	0.001	0.000	0.000	0.000	0.000
143	B	145	VAL	0	0.019	0.003	38.869	0.004	0.004	0.000	0.000	0.000	0.000
144	B	146	HIS	0	0.037	0.011	37.827	0.010	0.010	0.000	0.000	0.000	0.000
145	B	147	VAL	0	0.030	0.023	33.588	0.007	0.007	0.000	0.000	0.000	0.000
146	B	148	LYS	1	0.958	0.995	34.039	-0.068	-0.068	0.000	0.000	0.000	0.000
147	B	149	ARG	1	0.857	0.922	34.582	-0.096	-0.096	0.000	0.000	0.000	0.000
148	B	150	TRP	0	-0.019	0.017	27.979	0.001	0.001	0.000	0.000	0.000	0.000
149	B	151	PHE	0	0.053	0.006	28.682	0.011	0.011	0.000	0.000	0.000	0.000
150	B	152	GLY	0	-0.013	-0.002	30.086	0.004	0.004	0.000	0.000	0.000	0.000
151	B	153	PHE	0	-0.031	-0.026	29.094	0.008	0.008	0.000	0.000	0.000	0.000
152	B	154	LEU	0	-0.009	-0.007	25.318	0.014	0.014	0.000	0.000	0.000	0.000
153	B	155	GLU	-1	-0.954	-0.976	26.071	0.098	0.098	0.000	0.000	0.000	0.000
154	B	156	ALA	0	-0.027	-0.019	26.812	0.007	0.007	0.000	0.000	0.000	0.000
155	B	157	GLN	0	-0.056	-0.016	24.369	0.033	0.033	0.000	0.000	0.000	0.000
156	B	158	GLN	0	0.028	0.004	21.030	-0.027	-0.027	0.000	0.000	0.000	0.000
157	B	159	ALA	0	0.042	0.017	18.000	-0.014	-0.014	0.000	0.000	0.000	0.000
158	B	160	PHE	0	0.004	-0.013	19.831	-0.016	-0.016	0.000	0.000	0.000	0.000
159	B	161	GLN	0	0.012	0.022	22.272	-0.039	-0.039	0.000	0.000	0.000	0.000
160	B	162	SER	0	-0.040	-0.012	18.948	-0.034	-0.034	0.000	0.000	0.000	0.000
161	B	163	VAL	0	-0.027	-0.016	17.060	-0.030	-0.030	0.000	0.000	0.000	0.000
162	B	164	GLY	0	0.020	0.017	19.379	-0.032	-0.032	0.000	0.000	0.000	0.000
163	B	165	THR	0	-0.026	-0.018	21.886	-0.021	-0.021	0.000	0.000	0.000	0.000
164	B	166	LYS	1	0.789	0.895	14.427	-0.267	-0.267	0.000	0.000	0.000	0.000
165	B	167	TRP	0	-0.043	-0.012	14.132	-0.036	-0.036	0.000	0.000	0.000	0.000
166	B	168	ASP	-1	-0.938	-0.956	20.862	0.027	0.027	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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