FMO DATABASE

FMODB ID: V5K81

Calculation Name: 3BJV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BJV

Chain ID: A

ChEMBL ID:

UniProt ID: Q93DA9

Base Structure: X-ray

Registration Date: 2023-06-22

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	156
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1517564.975445
FMO2-HF: Nuclear repulsion	1457228.893029
FMO2-HF: Total energy	-60336.082416
FMO2-MP2: Total energy	-60511.219136

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:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-20.516	-9.859	7.637	-6.075	-12.222	-0.047

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.014

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	3	LEU	0	0.045	0.011	3.674	-0.209	2.439	0.304	-1.130	-1.822	-0.003
4	A	4	ALA	0	0.045	0.023	5.562	0.037	0.037	0.000	0.000	0.000	0.000
5	A	5	GLN	0	-0.077	-0.044	2.319	-0.173	0.123	2.568	-0.676	-2.188	0.001
6	A	6	ALA	0	0.049	0.024	2.875	-2.551	-1.275	0.717	-0.470	-1.524	-0.001
7	A	7	PHE	0	-0.008	0.000	4.415	-1.513	-1.545	0.033	0.148	-0.150	0.000
8	A	8	LYS	1	0.973	0.986	7.126	-0.866	-0.866	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.882	-0.923	2.576	-12.931	-10.443	2.609	-2.256	-2.841	-0.034
10	A	10	ASN	0	-0.070	-0.046	4.670	-0.333	-0.252	-0.001	-0.001	-0.079	0.000
11	A	11	HIS	0	0.032	0.026	8.229	0.173	0.173	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.024	-0.026	8.635	0.077	0.077	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.020	0.023	11.466	0.022	0.022	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.750	0.850	13.636	0.386	0.386	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.018	0.004	16.776	0.004	0.004	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.007	0.013	19.675	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.047	-0.015	19.506	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	18	THR	0	0.024	0.005	23.353	0.009	0.009	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.030	-0.012	23.830	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.946	0.975	25.975	0.119	0.119	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.823	-0.913	27.244	-0.136	-0.136	0.000	0.000	0.000	0.000
22	A	22	TRP	0	0.087	0.023	23.143	-0.015	-0.015	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.810	0.905	22.984	0.133	0.133	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.856	-0.918	22.980	-0.188	-0.188	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.049	0.017	21.411	-0.019	-0.019	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.012	0.006	18.391	-0.023	-0.023	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.873	0.924	18.111	0.174	0.174	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.032	-0.010	18.350	-0.047	-0.047	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.021	0.004	14.676	-0.024	-0.024	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.028	0.027	13.571	-0.066	-0.066	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.037	-0.027	13.864	-0.075	-0.075	0.000	0.000	0.000	0.000
32	A	32	PRO	0	-0.016	0.000	12.317	-0.048	-0.048	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.019	0.009	7.985	-0.097	-0.097	0.000	0.000	0.000	0.000
34	A	34	ILE	0	-0.033	-0.003	11.024	-0.111	-0.111	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.866	-0.918	13.979	-0.484	-0.484	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.036	-0.026	8.489	0.015	0.015	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.025	0.012	10.493	-0.156	-0.156	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.044	-0.017	7.218	-0.117	-0.117	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.004	-0.010	8.680	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.868	0.935	11.719	0.598	0.598	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.028	-0.016	15.391	0.005	0.005	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.882	-0.933	18.068	-0.418	-0.418	0.000	0.000	0.000	0.000
43	A	43	TYR	0	-0.017	-0.019	11.341	0.043	0.043	0.000	0.000	0.000	0.000
44	A	44	TYR	0	0.029	0.016	16.671	0.032	0.032	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.044	-0.026	18.620	0.028	0.028	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.053	0.027	18.232	0.028	0.028	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.004	0.028	14.897	0.029	0.029	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.016	0.009	19.252	0.034	0.034	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.833	-0.922	22.797	-0.179	-0.179	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.071	-0.036	20.744	0.022	0.022	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.023	-0.018	21.510	0.018	0.018	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.838	-0.903	23.673	-0.122	-0.122	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.089	-0.047	26.218	0.016	0.016	0.000	0.000	0.000	0.000
54	A	54	TYR	0	-0.090	-0.044	24.159	0.015	0.015	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.012	0.027	26.170	0.014	0.014	0.000	0.000	0.000	0.000
56	A	56	PRO	0	-0.038	-0.028	22.403	-0.017	-0.017	0.000	0.000	0.000	0.000
57	A	57	TYR	0	-0.035	-0.028	17.131	0.024	0.024	0.000	0.000	0.000	0.000
58	A	58	TYR	0	-0.036	-0.051	16.475	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.024	-0.002	17.651	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.007	-0.017	14.953	0.015	0.015	0.000	0.000	0.000	0.000
61	A	61	MET	0	0.030	0.023	19.270	0.024	0.024	0.000	0.000	0.000	0.000
62	A	62	PRO	0	0.000	-0.016	21.430	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.072	0.053	22.853	0.012	0.012	0.000	0.000	0.000	0.000
64	A	64	MET	0	-0.025	0.015	15.057	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.019	-0.002	17.645	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	66	MET	0	0.001	0.003	12.093	0.016	0.016	0.000	0.000	0.000	0.000
67	A	67	PRO	0	0.013	0.016	14.233	-0.029	-0.029	0.000	0.000	0.000	0.000
68	A	68	HIS	0	-0.012	-0.013	12.287	-0.061	-0.061	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.043	0.038	13.622	0.084	0.084	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.848	0.891	13.553	0.226	0.226	0.000	0.000	0.000	0.000
71	A	71	PRO	0	0.047	0.026	11.404	-0.017	-0.017	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.823	-0.905	12.891	-0.408	-0.408	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.029	0.000	15.972	0.021	0.021	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.045	0.012	15.242	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.005	0.020	8.561	-0.059	-0.059	0.000	0.000	0.000	0.000
76	A	76	GLN	0	-0.099	-0.033	10.088	0.169	0.169	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.850	0.908	5.201	2.612	2.612	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.819	-0.905	2.523	-3.352	-2.575	0.735	-0.385	-1.126	-0.002
79	A	79	ALA	0	-0.036	-0.012	3.010	-3.125	-1.620	0.181	-0.749	-0.937	-0.007
80	A	80	PHE	0	0.054	0.012	2.457	-0.328	0.405	0.400	-0.214	-0.920	-0.001
81	A	81	SER	0	-0.054	-0.032	6.676	0.057	0.057	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.017	0.004	10.091	0.043	0.043	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.025	0.015	12.806	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.019	0.001	16.452	0.007	0.007	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.009	-0.007	19.557	-0.015	-0.015	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.023	-0.037	22.992	0.013	0.013	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.907	-0.927	26.414	-0.050	-0.050	0.000	0.000	0.000	0.000
88	A	88	PRO	0	-0.032	-0.014	25.560	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.002	0.014	24.060	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	90	THR	0	0.003	-0.009	26.208	0.003	0.003	0.000	0.000	0.000	0.000
91	A	91	PHE	0	-0.007	-0.021	20.959	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	92	THR	0	0.014	-0.014	26.503	0.009	0.009	0.000	0.000	0.000	0.000
93	A	93	ASP	-1	-0.856	-0.936	25.947	-0.073	-0.073	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.024	-0.004	29.238	0.009	0.009	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.888	0.962	23.543	0.050	0.050	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.924	-0.953	26.559	-0.048	-0.048	0.000	0.000	0.000	0.000
97	A	97	VAL	0	-0.107	-0.056	20.356	0.005	0.005	0.000	0.000	0.000	0.000
98	A	98	GLN	0	-0.009	-0.011	22.164	0.002	0.002	0.000	0.000	0.000	0.000
99	A	99	VAL	0	0.007	0.010	16.201	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.035	-0.026	16.209	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.007	0.004	8.728	0.003	0.003	0.000	0.000	0.000	0.000
102	A	102	ALA	0	-0.016	0.018	11.630	-0.012	-0.012	0.000	0.000	0.000	0.000
103	A	103	LEU	0	0.022	0.013	6.918	-0.079	-0.079	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.011	0.001	7.278	0.156	0.156	0.000	0.000	0.000	0.000
105	A	105	ALA	0	0.030	0.020	5.822	-0.528	-0.528	0.000	0.000	0.000	0.000
106	A	106	THR	0	0.012	-0.018	6.442	0.491	0.491	0.000	0.000	0.000	0.000
107	A	107	SER	0	-0.026	-0.024	8.665	0.308	0.308	0.000	0.000	0.000	0.000
108	A	108	SER	0	0.046	0.012	9.419	-0.045	-0.045	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.986	0.992	10.349	0.021	0.021	0.000	0.000	0.000	0.000
110	A	110	ILE	0	0.035	0.047	3.681	0.116	0.280	0.001	-0.026	-0.139	0.000
111	A	111	HIS	0	-0.007	-0.009	6.500	-0.026	-0.026	0.000	0.000	0.000	0.000
112	A	112	THR	0	-0.006	-0.008	8.669	0.066	0.066	0.000	0.000	0.000	0.000
113	A	113	SER	0	-0.043	-0.053	8.859	0.119	0.119	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.004	0.015	2.895	-0.304	0.181	0.091	-0.191	-0.386	0.000
115	A	115	ALA	0	-0.016	-0.008	5.877	-0.015	-0.015	0.000	0.000	0.000	0.000
116	A	116	ILE	0	0.027	0.010	6.567	0.130	0.130	0.000	0.000	0.000	0.000
117	A	117	PRO	0	0.054	0.029	8.778	0.004	0.004	0.000	0.000	0.000	0.000
118	A	118	GLN	0	-0.018	-0.016	4.173	0.477	0.713	-0.001	-0.125	-0.110	0.000
119	A	119	ILE	0	-0.023	-0.009	8.927	0.006	0.006	0.000	0.000	0.000	0.000
120	A	120	ILE	0	-0.028	-0.017	11.159	0.005	0.005	0.000	0.000	0.000	0.000
121	A	121	ALA	0	0.011	0.017	12.712	-0.008	-0.008	0.000	0.000	0.000	0.000
122	A	122	LEU	0	-0.015	-0.004	11.755	-0.007	-0.007	0.000	0.000	0.000	0.000
123	A	123	PHE	0	-0.028	-0.042	13.649	-0.026	-0.026	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.900	-0.923	16.974	0.215	0.215	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.059	-0.002	16.802	0.004	0.004	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.875	-0.954	20.088	0.110	0.110	0.000	0.000	0.000	0.000
127	A	127	HIS	0	0.003	-0.005	23.089	-0.007	-0.007	0.000	0.000	0.000	0.000
128	A	128	SER	0	-0.023	-0.024	18.531	-0.017	-0.017	0.000	0.000	0.000	0.000
129	A	129	ILE	0	0.025	-0.002	19.507	-0.008	-0.008	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.925	-0.966	21.431	0.051	0.051	0.000	0.000	0.000	0.000
131	A	131	ARG	1	0.804	0.886	20.987	-0.203	-0.203	0.000	0.000	0.000	0.000
132	A	132	LEU	0	0.005	-0.021	15.746	-0.006	-0.006	0.000	0.000	0.000	0.000
133	A	133	VAL	0	0.000	0.005	19.544	-0.014	-0.014	0.000	0.000	0.000	0.000
134	A	134	ASN	0	-0.087	-0.035	22.338	-0.018	-0.018	0.000	0.000	0.000	0.000
135	A	135	CYS	0	-0.038	0.015	19.425	0.016	0.016	0.000	0.000	0.000	0.000
136	A	136	LYS	1	0.834	0.895	21.422	-0.053	-0.053	0.000	0.000	0.000	0.000
137	A	137	THR	0	-0.058	-0.053	19.738	-0.017	-0.017	0.000	0.000	0.000	0.000
138	A	138	PRO	0	0.052	0.007	14.362	0.025	0.025	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.902	-0.970	15.172	0.145	0.145	0.000	0.000	0.000	0.000
140	A	140	GLU	-1	-0.798	-0.862	16.748	0.114	0.114	0.000	0.000	0.000	0.000
141	A	141	VAL	0	0.036	0.021	13.214	0.027	0.027	0.000	0.000	0.000	0.000
142	A	142	LEU	0	-0.027	-0.016	10.283	0.095	0.095	0.000	0.000	0.000	0.000
143	A	143	ALA	0	-0.009	0.006	13.656	0.079	0.079	0.000	0.000	0.000	0.000
144	A	144	MET	0	-0.004	-0.001	16.190	0.020	0.020	0.000	0.000	0.000	0.000
145	A	145	VAL	0	-0.010	-0.001	9.607	0.040	0.040	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.852	-0.905	12.019	1.052	1.052	0.000	0.000	0.000	0.000
147	A	147	GLU	-1	-0.808	-0.869	14.570	0.293	0.293	0.000	0.000	0.000	0.000
148	A	148	SER	0	-0.052	-0.028	12.994	-0.005	-0.005	0.000	0.000	0.000	0.000
149	A	149	LYS	1	0.786	0.857	10.770	-1.095	-1.095	0.000	0.000	0.000	0.000
150	A	150	SER	0	-0.010	0.006	14.154	0.042	0.042	0.000	0.000	0.000	0.000
151	A	151	SER	0	-0.013	-0.002	14.857	-0.049	-0.049	0.000	0.000	0.000	0.000
152	A	152	PRO	0	0.072	0.021	15.925	0.062	0.062	0.000	0.000	0.000	0.000
153	A	153	TYR	0	-0.094	-0.043	13.098	0.042	0.042	0.000	0.000	0.000	0.000
154	A	154	LEU	0	-0.060	-0.042	9.596	0.096	0.096	0.000	0.000	0.000	0.000
155	A	155	GLU	-1	-0.945	-0.946	12.223	0.653	0.653	0.000	0.000	0.000	0.000
156	A	156	GLY	0	-0.064	-0.022	10.162	0.108	0.108	0.000	0.000	0.000	0.000

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