FMO DATABASE

FMODB ID: LNVR9

Calculation Name: 3BOQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BOQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q5LLB8

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	136
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1052181.949258
FMO2-HF: Nuclear repulsion	1000107.368005
FMO2-HF: Total energy	-52074.581253
FMO2-MP2: Total energy	-52225.428026

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:7:LYS)

Summations of interaction energy for fragment #1(A:7:LYS)

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.
45.687	52.105	0.96	-3.202	-4.175	-0.009

Interaction energy analysis for fragmet #1(A:7:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.979 / q_NPA : 0.987

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	9	ASP	-1	-0.820	-0.923	3.765	-36.779	-34.716	0.000	-0.912	-1.151	0.004
4	A	10	ARG	1	0.989	1.006	6.024	25.661	25.661	0.000	0.000	0.000	0.000
5	A	11	GLN	0	0.014	-0.006	2.612	-8.286	-5.094	0.934	-1.963	-2.163	-0.014
6	A	12	GLN	0	-0.004	0.002	3.537	8.863	9.980	0.027	-0.326	-0.818	0.001
7	A	13	ASN	0	0.032	0.007	5.681	2.115	2.161	-0.001	-0.001	-0.043	0.000
8	A	14	GLN	0	-0.020	-0.004	7.673	2.773	2.773	0.000	0.000	0.000	0.000
9	A	15	THR	0	0.015	0.009	6.231	1.850	1.850	0.000	0.000	0.000	0.000
10	A	16	ARG	1	0.958	0.979	8.374	30.189	30.189	0.000	0.000	0.000	0.000
11	A	17	LEU	0	0.002	0.016	11.014	1.225	1.225	0.000	0.000	0.000	0.000
12	A	18	TRP	0	0.038	0.004	12.117	1.274	1.274	0.000	0.000	0.000	0.000
13	A	19	LEU	0	0.015	-0.001	10.748	0.906	0.906	0.000	0.000	0.000	0.000
14	A	20	ASN	0	0.003	0.002	14.246	1.101	1.101	0.000	0.000	0.000	0.000
15	A	21	ILE	0	-0.009	0.011	16.744	0.816	0.816	0.000	0.000	0.000	0.000
16	A	22	LEU	0	-0.013	-0.008	15.504	0.781	0.781	0.000	0.000	0.000	0.000
17	A	23	ARG	1	0.951	0.985	18.358	13.959	13.959	0.000	0.000	0.000	0.000
18	A	24	LEU	0	0.033	0.017	20.071	0.501	0.501	0.000	0.000	0.000	0.000
19	A	25	HIS	0	0.022	0.008	22.110	0.523	0.523	0.000	0.000	0.000	0.000
20	A	26	GLY	0	-0.032	-0.025	22.685	0.484	0.484	0.000	0.000	0.000	0.000
21	A	27	LEU	0	-0.042	-0.030	24.174	0.313	0.313	0.000	0.000	0.000	0.000
22	A	28	VAL	0	0.019	0.029	26.169	0.367	0.367	0.000	0.000	0.000	0.000
23	A	29	PHE	0	-0.026	-0.015	27.344	0.454	0.454	0.000	0.000	0.000	0.000
24	A	30	GLY	0	-0.008	-0.014	28.701	0.328	0.328	0.000	0.000	0.000	0.000
25	A	31	ASP	-1	-0.850	-0.925	30.597	-8.756	-8.756	0.000	0.000	0.000	0.000
26	A	32	LEU	0	0.026	0.013	32.003	0.278	0.278	0.000	0.000	0.000	0.000
27	A	33	ASN	0	-0.058	-0.027	32.926	0.350	0.350	0.000	0.000	0.000	0.000
28	A	34	ARG	1	0.931	0.960	33.442	8.543	8.543	0.000	0.000	0.000	0.000
29	A	35	GLN	0	0.053	0.023	36.167	0.331	0.331	0.000	0.000	0.000	0.000
30	A	36	LEU	0	0.007	0.020	37.235	0.154	0.154	0.000	0.000	0.000	0.000
31	A	37	LEU	0	-0.070	-0.035	37.816	0.179	0.179	0.000	0.000	0.000	0.000
32	A	38	ASP	-1	-0.954	-0.965	40.692	-6.602	-6.602	0.000	0.000	0.000	0.000
33	A	39	GLU	-1	-0.824	-0.868	42.479	-6.869	-6.869	0.000	0.000	0.000	0.000
34	A	40	THR	0	-0.061	-0.059	42.357	0.111	0.111	0.000	0.000	0.000	0.000
35	A	41	GLY	0	0.009	0.019	44.026	0.111	0.111	0.000	0.000	0.000	0.000
36	A	42	LEU	0	-0.086	-0.053	40.764	-0.056	-0.056	0.000	0.000	0.000	0.000
37	A	43	SER	0	0.025	0.024	36.379	-0.082	-0.082	0.000	0.000	0.000	0.000
38	A	44	LEU	0	0.118	0.023	31.707	0.099	0.099	0.000	0.000	0.000	0.000
39	A	45	ALA	0	-0.055	-0.014	33.671	0.000	0.000	0.000	0.000	0.000	0.000
40	A	46	LYS	1	0.847	0.892	34.921	6.948	6.948	0.000	0.000	0.000	0.000
41	A	47	PHE	0	0.044	0.024	36.534	0.032	0.032	0.000	0.000	0.000	0.000
42	A	48	ASP	-1	-0.757	-0.872	32.878	-8.591	-8.591	0.000	0.000	0.000	0.000
43	A	49	ALA	0	0.003	-0.009	35.893	0.025	0.025	0.000	0.000	0.000	0.000
44	A	50	MET	0	-0.029	-0.017	37.827	0.084	0.084	0.000	0.000	0.000	0.000
45	A	51	ALA	0	0.038	0.030	37.287	0.128	0.128	0.000	0.000	0.000	0.000
46	A	52	GLN	0	-0.041	-0.019	34.682	0.074	0.074	0.000	0.000	0.000	0.000
47	A	53	LEU	0	-0.013	-0.019	38.594	0.095	0.095	0.000	0.000	0.000	0.000
48	A	54	ALA	0	-0.022	0.004	42.048	0.143	0.143	0.000	0.000	0.000	0.000
49	A	55	ARG	1	0.866	0.924	36.335	7.852	7.852	0.000	0.000	0.000	0.000
50	A	56	ASN	0	-0.069	-0.024	40.552	-0.073	-0.073	0.000	0.000	0.000	0.000
51	A	57	PRO	0	0.108	0.061	43.816	0.013	0.013	0.000	0.000	0.000	0.000
52	A	58	ASP	-1	-0.918	-0.963	47.347	-5.939	-5.939	0.000	0.000	0.000	0.000
53	A	59	GLY	0	-0.059	-0.034	45.183	0.070	0.070	0.000	0.000	0.000	0.000
54	A	60	LEU	0	-0.030	-0.006	38.709	-0.087	-0.087	0.000	0.000	0.000	0.000
55	A	61	SER	0	-0.003	-0.013	40.355	0.027	0.027	0.000	0.000	0.000	0.000
56	A	62	MET	0	0.054	0.030	38.965	-0.162	-0.162	0.000	0.000	0.000	0.000
57	A	63	GLY	0	-0.003	0.005	36.143	-0.180	-0.180	0.000	0.000	0.000	0.000
58	A	64	LYS	1	0.994	0.981	35.251	6.958	6.958	0.000	0.000	0.000	0.000
59	A	65	LEU	0	0.023	0.023	36.002	-0.134	-0.134	0.000	0.000	0.000	0.000
60	A	66	SER	0	-0.038	-0.032	33.066	-0.213	-0.213	0.000	0.000	0.000	0.000
61	A	67	GLY	0	0.000	0.008	31.329	-0.219	-0.219	0.000	0.000	0.000	0.000
62	A	68	ALA	0	-0.020	0.000	31.529	-0.152	-0.152	0.000	0.000	0.000	0.000
63	A	69	LEU	0	-0.091	-0.047	31.952	0.012	0.012	0.000	0.000	0.000	0.000
64	A	70	LYS	1	0.912	0.963	29.279	8.640	8.640	0.000	0.000	0.000	0.000
65	A	71	VAL	0	-0.064	-0.026	28.204	-0.343	-0.343	0.000	0.000	0.000	0.000
66	A	72	THR	0	0.023	0.005	24.628	0.237	0.237	0.000	0.000	0.000	0.000
67	A	73	ASN	0	-0.021	-0.024	27.781	0.345	0.345	0.000	0.000	0.000	0.000
68	A	74	GLY	0	0.060	0.041	29.805	-0.145	-0.145	0.000	0.000	0.000	0.000
69	A	75	ASN	0	-0.045	-0.037	30.904	0.253	0.253	0.000	0.000	0.000	0.000
70	A	76	VAL	0	0.092	0.048	34.679	0.160	0.160	0.000	0.000	0.000	0.000
71	A	77	SER	0	0.031	0.011	36.471	0.224	0.224	0.000	0.000	0.000	0.000
72	A	78	GLY	0	0.025	0.018	38.768	0.178	0.178	0.000	0.000	0.000	0.000
73	A	79	LEU	0	-0.047	-0.020	35.741	0.138	0.138	0.000	0.000	0.000	0.000
74	A	80	VAL	0	0.046	0.016	39.132	0.133	0.133	0.000	0.000	0.000	0.000
75	A	81	ASN	0	-0.036	-0.033	41.803	0.219	0.219	0.000	0.000	0.000	0.000
76	A	82	ARG	1	0.945	0.969	36.997	7.573	7.573	0.000	0.000	0.000	0.000
77	A	83	LEU	0	0.034	0.022	40.468	0.077	0.077	0.000	0.000	0.000	0.000
78	A	84	ILE	0	-0.050	-0.022	44.529	0.114	0.114	0.000	0.000	0.000	0.000
79	A	85	LYS	1	0.892	0.950	46.600	6.353	6.353	0.000	0.000	0.000	0.000
80	A	86	ASP	-1	-0.826	-0.878	44.874	-6.483	-6.483	0.000	0.000	0.000	0.000
81	A	87	GLY	0	0.031	0.037	48.384	0.086	0.086	0.000	0.000	0.000	0.000
82	A	88	MET	0	-0.006	0.023	45.582	0.043	0.043	0.000	0.000	0.000	0.000
83	A	89	VAL	0	-0.008	-0.018	43.706	-0.054	-0.054	0.000	0.000	0.000	0.000
84	A	90	VAL	0	0.026	0.016	47.204	0.082	0.082	0.000	0.000	0.000	0.000
85	A	91	LYS	1	0.956	0.965	48.043	5.671	5.671	0.000	0.000	0.000	0.000
86	A	92	ALA	0	-0.015	-0.011	48.313	0.115	0.115	0.000	0.000	0.000	0.000
87	A	101	PHE	0	0.055	0.023	42.549	0.062	0.062	0.000	0.000	0.000	0.000
88	A	102	SER	0	-0.073	-0.054	43.830	-0.179	-0.179	0.000	0.000	0.000	0.000
89	A	103	ALA	0	0.023	0.023	43.242	0.135	0.135	0.000	0.000	0.000	0.000
90	A	104	LYS	1	0.966	0.998	44.973	5.838	5.838	0.000	0.000	0.000	0.000
91	A	105	LEU	0	0.025	0.020	44.266	0.010	0.010	0.000	0.000	0.000	0.000
92	A	106	THR	0	-0.022	-0.024	47.260	0.083	0.083	0.000	0.000	0.000	0.000
93	A	107	ASP	-1	-0.821	-0.917	50.243	-5.592	-5.592	0.000	0.000	0.000	0.000
94	A	108	ALA	0	-0.012	-0.009	51.842	-0.037	-0.037	0.000	0.000	0.000	0.000
95	A	109	GLY	0	0.024	0.002	47.808	-0.087	-0.087	0.000	0.000	0.000	0.000
96	A	110	LEU	0	-0.032	-0.013	46.859	-0.151	-0.151	0.000	0.000	0.000	0.000
97	A	111	THR	0	-0.023	-0.008	48.292	-0.041	-0.041	0.000	0.000	0.000	0.000
98	A	112	THR	0	0.044	0.014	45.597	-0.049	-0.049	0.000	0.000	0.000	0.000
99	A	113	PHE	0	-0.009	-0.012	39.998	-0.105	-0.105	0.000	0.000	0.000	0.000
100	A	114	LYS	1	0.945	0.975	43.972	5.937	5.937	0.000	0.000	0.000	0.000
101	A	115	GLN	0	0.074	0.043	45.830	-0.120	-0.120	0.000	0.000	0.000	0.000
102	A	116	ALA	0	0.021	0.000	42.359	-0.094	-0.094	0.000	0.000	0.000	0.000
103	A	117	SER	0	-0.060	-0.044	40.839	-0.236	-0.236	0.000	0.000	0.000	0.000
104	A	118	GLU	-1	-0.929	-0.956	41.044	-6.544	-6.544	0.000	0.000	0.000	0.000
105	A	119	ALA	0	0.024	0.021	42.362	-0.103	-0.103	0.000	0.000	0.000	0.000
106	A	120	HIS	1	0.897	0.956	34.365	7.994	7.994	0.000	0.000	0.000	0.000
107	A	121	ASN	0	-0.017	-0.023	37.359	-0.368	-0.368	0.000	0.000	0.000	0.000
108	A	122	ARG	1	0.890	0.934	38.190	6.875	6.875	0.000	0.000	0.000	0.000
109	A	123	ILE	0	0.038	0.026	35.794	-0.119	-0.119	0.000	0.000	0.000	0.000
110	A	124	LEU	0	-0.037	-0.025	31.186	-0.206	-0.206	0.000	0.000	0.000	0.000
111	A	125	ALA	0	-0.015	-0.010	34.097	-0.233	-0.233	0.000	0.000	0.000	0.000
112	A	126	GLU	-1	-0.896	-0.952	35.975	-8.029	-8.029	0.000	0.000	0.000	0.000
113	A	127	LEU	0	-0.055	-0.030	31.481	-0.172	-0.172	0.000	0.000	0.000	0.000
114	A	128	LEU	0	-0.044	-0.026	28.975	-0.304	-0.304	0.000	0.000	0.000	0.000
115	A	129	ARG	1	0.946	0.979	32.240	8.478	8.478	0.000	0.000	0.000	0.000
116	A	130	ALA	0	-0.059	-0.026	31.771	0.128	0.128	0.000	0.000	0.000	0.000
117	A	131	VAL	0	-0.042	-0.011	28.329	-0.248	-0.248	0.000	0.000	0.000	0.000
118	A	132	SER	0	0.032	0.022	29.250	0.288	0.288	0.000	0.000	0.000	0.000
119	A	133	ASP	-1	-0.833	-0.938	30.367	-8.979	-8.979	0.000	0.000	0.000	0.000
120	A	134	GLN	0	-0.081	-0.041	27.288	0.140	0.140	0.000	0.000	0.000	0.000
121	A	135	ASP	-1	-0.830	-0.912	26.092	-12.001	-12.001	0.000	0.000	0.000	0.000
122	A	136	MET	0	-0.087	-0.040	25.933	-0.361	-0.361	0.000	0.000	0.000	0.000
123	A	137	VAL	0	-0.021	-0.017	27.902	-0.086	-0.086	0.000	0.000	0.000	0.000
124	A	138	GLU	-1	-0.881	-0.945	24.566	-11.793	-11.793	0.000	0.000	0.000	0.000
125	A	139	ALA	0	-0.006	0.003	22.814	-0.421	-0.421	0.000	0.000	0.000	0.000
126	A	140	SER	0	-0.012	-0.003	23.505	-0.176	-0.176	0.000	0.000	0.000	0.000
127	A	141	ALA	0	-0.025	-0.014	25.798	0.049	0.049	0.000	0.000	0.000	0.000
128	A	142	ALA	0	0.015	0.010	20.439	-0.114	-0.114	0.000	0.000	0.000	0.000
129	A	143	LEU	0	-0.045	-0.040	19.999	-0.329	-0.329	0.000	0.000	0.000	0.000
130	A	144	ARG	1	0.946	0.972	22.299	10.221	10.221	0.000	0.000	0.000	0.000
131	A	145	GLY	0	0.057	0.048	22.706	0.096	0.096	0.000	0.000	0.000	0.000
132	A	146	ILE	0	-0.057	-0.033	17.260	-0.218	-0.218	0.000	0.000	0.000	0.000
133	A	147	LEU	0	-0.034	-0.039	20.170	-0.035	-0.035	0.000	0.000	0.000	0.000
134	A	148	GLU	-1	-0.969	-0.962	22.664	-10.490	-10.490	0.000	0.000	0.000	0.000
135	A	149	SER	0	-0.071	-0.030	19.783	-0.103	-0.103	0.000	0.000	0.000	0.000
136	A	150	MET	0	-0.085	-0.025	18.538	-0.060	-0.060	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:LYS)