FMO DATABASE

FMODB ID: YZN62

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1515516.015066
FMO2-HF: Nuclear repulsion	1455180.993365
FMO2-HF: Total energy	-60335.021701
FMO2-MP2: Total energy	-60510.140406

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.
-8.273	-0.467	7.074	-4.613	-10.269	-0.018

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 : 0.007 / q_NPA : -0.007

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	0.062	0.014	3.614	0.839	3.289	0.357	-0.965	-1.842	0.000
4	A	4	ALA	0	0.016	0.011	5.536	0.275	0.275	0.000	0.000	0.000	0.000
5	A	5	GLN	0	-0.002	-0.002	2.281	-1.042	-1.876	4.886	-1.191	-2.862	-0.003
6	A	6	ALA	0	0.048	0.035	2.854	-1.656	-0.210	0.460	-0.520	-1.386	-0.002
7	A	7	PHE	0	-0.014	-0.003	4.394	-0.916	-0.878	0.020	0.045	-0.103	0.000
8	A	8	LYS	1	0.951	0.971	7.646	-1.144	-1.144	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.952	-0.967	4.534	1.614	2.142	0.029	-0.178	-0.379	-0.001
10	A	10	ASN	0	-0.085	-0.041	4.737	-0.514	-0.462	-0.001	-0.001	-0.050	0.000
11	A	11	HIS	0	0.029	0.025	8.657	-0.098	-0.098	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.035	-0.023	8.683	0.002	0.002	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.035	0.028	11.541	-0.062	-0.062	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.786	0.881	13.601	0.119	0.119	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.010	-0.001	16.959	-0.022	-0.022	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.001	0.008	19.650	0.004	0.004	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.044	-0.015	19.667	0.000	0.000	0.000	0.000	0.000	0.000
18	A	18	THR	0	0.020	0.006	23.341	0.001	0.001	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.003	-0.001	23.854	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.948	0.976	25.985	0.085	0.085	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.838	-0.915	27.188	-0.136	-0.136	0.000	0.000	0.000	0.000
22	A	22	TRP	0	0.093	0.022	23.078	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.902	0.975	23.019	0.134	0.134	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.893	-0.954	23.008	-0.145	-0.145	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.023	0.005	21.426	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.008	0.002	18.310	-0.021	-0.021	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.906	0.951	18.137	0.127	0.127	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.033	-0.023	18.289	-0.022	-0.022	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.014	0.010	14.655	-0.014	-0.014	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.041	0.037	13.522	-0.061	-0.061	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.017	-0.003	13.796	-0.036	-0.036	0.000	0.000	0.000	0.000
32	A	32	PRO	0	-0.027	-0.006	12.286	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.028	0.017	8.011	0.002	0.002	0.000	0.000	0.000	0.000
34	A	34	ILE	0	-0.029	0.000	10.964	-0.060	-0.060	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.921	-0.964	13.910	-0.161	-0.161	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.048	-0.040	8.571	0.011	0.011	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.001	-0.002	10.875	0.002	0.002	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.040	-0.017	7.141	-0.094	-0.094	0.000	0.000	0.000	0.000
39	A	39	VAL	0	0.001	-0.005	8.598	-0.136	-0.136	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.928	0.962	11.622	0.542	0.542	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.028	-0.014	15.295	-0.017	-0.017	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.939	-0.966	17.834	-0.378	-0.378	0.000	0.000	0.000	0.000
43	A	43	TYR	0	-0.010	-0.012	11.395	0.019	0.019	0.000	0.000	0.000	0.000
44	A	44	TYR	0	0.022	0.008	16.567	0.012	0.012	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.009	-0.006	18.527	0.013	0.013	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.056	0.026	18.225	0.018	0.018	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.002	0.020	14.865	0.016	0.016	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.013	0.007	19.218	0.024	0.024	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.867	-0.943	22.761	-0.185	-0.185	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.061	-0.021	20.691	0.016	0.016	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.032	-0.017	21.451	0.008	0.008	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.924	-0.971	23.633	-0.144	-0.144	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.078	-0.043	26.351	0.017	0.017	0.000	0.000	0.000	0.000
54	A	54	TYR	0	-0.095	-0.046	24.145	0.012	0.012	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.009	0.025	26.125	0.010	0.010	0.000	0.000	0.000	0.000
56	A	56	PRO	0	-0.037	-0.026	22.453	-0.024	-0.024	0.000	0.000	0.000	0.000
57	A	57	TYR	0	-0.039	-0.030	17.188	0.025	0.025	0.000	0.000	0.000	0.000
58	A	58	TYR	0	-0.050	-0.061	16.504	-0.021	-0.021	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.012	0.001	17.711	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.001	-0.011	15.315	0.020	0.020	0.000	0.000	0.000	0.000
61	A	61	MET	0	0.017	0.020	19.236	0.021	0.021	0.000	0.000	0.000	0.000
62	A	62	PRO	0	-0.030	-0.030	21.477	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.083	0.058	22.886	0.008	0.008	0.000	0.000	0.000	0.000
64	A	64	MET	0	-0.023	0.013	14.846	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.037	0.007	17.678	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	66	MET	0	-0.003	0.001	12.389	0.001	0.001	0.000	0.000	0.000	0.000
67	A	67	PRO	0	0.013	0.013	14.158	-0.040	-0.040	0.000	0.000	0.000	0.000
68	A	68	HIS	0	-0.037	-0.030	12.271	-0.088	-0.088	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.046	0.038	13.591	0.105	0.105	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.955	0.971	13.536	0.282	0.282	0.000	0.000	0.000	0.000
71	A	71	PRO	0	0.045	0.018	11.336	0.006	0.006	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.923	-0.970	12.902	-0.510	-0.510	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.046	-0.009	15.939	0.044	0.044	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.063	0.026	15.165	0.005	0.005	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.007	0.010	8.477	-0.010	-0.010	0.000	0.000	0.000	0.000
76	A	76	GLN	0	-0.088	-0.025	9.847	0.084	0.084	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.901	0.937	5.043	1.119	1.119	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.809	-0.898	2.492	-4.291	-3.529	0.817	-0.409	-1.170	-0.002
79	A	79	ALA	0	-0.049	-0.024	2.903	-3.594	-1.862	0.242	-0.888	-1.086	-0.009
80	A	80	PHE	0	0.046	0.018	2.778	-0.284	0.401	0.123	-0.153	-0.655	-0.001
81	A	81	SER	0	-0.072	-0.060	6.691	0.218	0.218	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.027	0.014	10.089	-0.032	-0.032	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.024	0.018	12.802	0.050	0.050	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.014	0.006	16.449	-0.015	-0.015	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.002	0.002	19.554	0.002	0.002	0.000	0.000	0.000	0.000
86	A	86	THR	0	0.000	-0.015	22.994	0.007	0.007	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.978	-0.979	26.410	-0.049	-0.049	0.000	0.000	0.000	0.000
88	A	88	PRO	0	-0.024	-0.019	25.580	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.005	0.026	24.012	0.001	0.001	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.007	-0.017	26.241	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	91	PHE	0	-0.005	-0.019	20.936	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	92	THR	0	0.012	-0.014	26.551	0.008	0.008	0.000	0.000	0.000	0.000
93	A	93	ASP	-1	-0.847	-0.929	26.088	-0.150	-0.150	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.027	-0.009	29.298	0.008	0.008	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.899	0.962	24.552	0.145	0.145	0.000	0.000	0.000	0.000
96	A	96	GLU	-1	-0.911	-0.949	26.603	-0.087	-0.087	0.000	0.000	0.000	0.000
97	A	97	VAL	0	-0.093	-0.040	20.303	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	98	GLN	0	-0.003	-0.005	22.182	0.006	0.006	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.002	0.003	16.213	0.008	0.008	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.028	-0.024	16.233	-0.023	-0.023	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.010	0.006	8.738	0.015	0.015	0.000	0.000	0.000	0.000
102	A	102	ALA	0	-0.021	0.018	11.590	-0.048	-0.048	0.000	0.000	0.000	0.000
103	A	103	LEU	0	0.013	0.015	7.332	-0.142	-0.142	0.000	0.000	0.000	0.000
104	A	104	ALA	0	0.001	-0.002	7.232	0.245	0.245	0.000	0.000	0.000	0.000
105	A	105	ALA	0	0.033	0.020	5.803	-0.680	-0.680	0.000	0.000	0.000	0.000
106	A	106	THR	0	-0.008	-0.025	6.386	0.602	0.602	0.000	0.000	0.000	0.000
107	A	107	SER	0	-0.030	-0.024	8.696	0.372	0.372	0.000	0.000	0.000	0.000
108	A	108	SER	0	0.030	0.004	9.480	-0.115	-0.115	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.993	0.991	10.582	0.320	0.320	0.000	0.000	0.000	0.000
110	A	110	ILE	0	0.045	0.034	3.308	-0.017	0.235	0.012	-0.056	-0.208	0.000
111	A	111	HIS	0	0.016	0.008	6.502	-0.191	-0.191	0.000	0.000	0.000	0.000
112	A	112	THR	0	-0.003	0.001	8.696	0.076	0.076	0.000	0.000	0.000	0.000
113	A	113	SER	0	-0.040	-0.036	8.955	0.109	0.109	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.010	0.020	2.761	-0.386	0.107	0.130	-0.201	-0.423	0.000
115	A	115	ALA	0	-0.016	-0.013	5.879	-0.110	-0.110	0.000	0.000	0.000	0.000
116	A	116	ILE	0	0.031	0.014	6.546	0.191	0.191	0.000	0.000	0.000	0.000
117	A	117	PRO	0	0.049	0.026	8.625	0.064	0.064	0.000	0.000	0.000	0.000
118	A	118	GLN	0	-0.003	-0.010	4.216	0.696	0.898	-0.001	-0.096	-0.105	0.000
119	A	119	ILE	0	-0.020	-0.006	8.898	0.091	0.091	0.000	0.000	0.000	0.000
120	A	120	ILE	0	-0.020	-0.018	11.200	0.067	0.067	0.000	0.000	0.000	0.000
121	A	121	ALA	0	0.016	0.021	12.701	0.039	0.039	0.000	0.000	0.000	0.000
122	A	122	LEU	0	-0.022	-0.010	11.660	0.036	0.036	0.000	0.000	0.000	0.000
123	A	123	PHE	0	-0.023	-0.045	13.489	0.022	0.022	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.919	-0.928	16.998	-0.037	-0.037	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.053	0.005	16.694	0.018	0.018	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.911	-0.969	20.096	0.007	0.007	0.000	0.000	0.000	0.000
127	A	127	HIS	0	0.026	0.004	23.090	0.000	0.000	0.000	0.000	0.000	0.000
128	A	128	SER	0	-0.022	-0.032	18.474	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	129	ILE	0	0.021	0.002	19.707	0.000	0.000	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.933	-0.971	21.442	0.001	0.001	0.000	0.000	0.000	0.000
131	A	131	ARG	1	0.775	0.881	20.895	-0.066	-0.066	0.000	0.000	0.000	0.000
132	A	132	LEU	0	0.005	-0.020	15.665	0.008	0.008	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.013	-0.001	19.534	0.004	0.004	0.000	0.000	0.000	0.000
134	A	134	ASN	0	-0.062	-0.020	22.329	-0.002	-0.002	0.000	0.000	0.000	0.000
135	A	135	CYS	0	-0.046	0.006	19.385	0.019	0.019	0.000	0.000	0.000	0.000
136	A	136	LYS	1	0.928	0.964	21.392	-0.047	-0.047	0.000	0.000	0.000	0.000
137	A	137	THR	0	-0.024	-0.011	19.758	0.002	0.002	0.000	0.000	0.000	0.000
138	A	138	PRO	0	0.057	0.010	14.408	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.920	-0.975	15.240	0.302	0.302	0.000	0.000	0.000	0.000
140	A	140	GLU	-1	-0.861	-0.934	16.813	0.109	0.109	0.000	0.000	0.000	0.000
141	A	141	VAL	0	0.045	0.026	13.062	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	142	LEU	0	-0.033	-0.025	10.451	0.039	0.039	0.000	0.000	0.000	0.000
143	A	143	ALA	0	0.000	0.010	13.748	0.029	0.029	0.000	0.000	0.000	0.000
144	A	144	MET	0	-0.001	0.000	16.059	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	145	VAL	0	-0.015	-0.004	9.638	0.005	0.005	0.000	0.000	0.000	0.000
146	A	146	GLU	-1	-0.934	-0.953	11.618	0.613	0.613	0.000	0.000	0.000	0.000
147	A	147	GLU	-1	-0.815	-0.893	13.885	0.119	0.119	0.000	0.000	0.000	0.000
148	A	148	SER	0	-0.064	-0.045	12.956	-0.025	-0.025	0.000	0.000	0.000	0.000
149	A	149	LYS	1	0.869	0.913	8.543	-0.751	-0.751	0.000	0.000	0.000	0.000
150	A	150	SER	0	-0.046	-0.008	13.886	0.019	0.019	0.000	0.000	0.000	0.000
151	A	151	SER	0	0.030	0.021	14.728	-0.029	-0.029	0.000	0.000	0.000	0.000
152	A	152	PRO	0	0.072	0.023	15.814	0.029	0.029	0.000	0.000	0.000	0.000
153	A	153	TYR	0	-0.082	-0.035	13.028	0.013	0.013	0.000	0.000	0.000	0.000
154	A	154	LEU	0	-0.063	-0.036	9.713	-0.001	-0.001	0.000	0.000	0.000	0.000
155	A	155	GLU	-1	-0.931	-0.947	12.103	0.293	0.293	0.000	0.000	0.000	0.000
156	A	156	GLY	0	-0.075	-0.024	9.943	0.082	0.082	0.000	0.000	0.000	0.000

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