FMO DATABASE

FMODB ID: VQLV1

Calculation Name: 3LFJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LFJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8RD54

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	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1758358.293774
FMO2-HF: Nuclear repulsion	1691541.388589
FMO2-HF: Total energy	-66816.905185
FMO2-MP2: Total energy	-67010.07641

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:SER)

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

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.
-19.359	-13.433	4.308	-4.645	-5.591	-0.036

Interaction energy analysis for fragmet #1(A:-1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.013

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	1	MET	0	0.027	0.025	3.309	-4.125	-2.218	0.049	-0.887	-1.070	0.000
4	A	2	TRP	0	-0.006	0.003	5.981	0.228	0.228	0.000	0.000	0.000	0.000
5	A	3	LYS	1	0.928	0.970	5.482	1.967	1.967	0.000	0.000	0.000	0.000
6	A	4	ILE	0	0.013	-0.001	6.660	0.206	0.206	0.000	0.000	0.000	0.000
7	A	5	VAL	0	-0.086	-0.039	10.179	0.091	0.091	0.000	0.000	0.000	0.000
8	A	6	PHE	0	-0.009	-0.006	12.501	0.138	0.138	0.000	0.000	0.000	0.000
9	A	7	ALA	0	0.028	0.027	15.217	-0.066	-0.066	0.000	0.000	0.000	0.000
10	A	8	ARG	1	0.810	0.918	17.537	0.328	0.328	0.000	0.000	0.000	0.000
11	A	9	ILE	0	0.006	0.013	21.193	-0.011	-0.011	0.000	0.000	0.000	0.000
12	A	10	ASP	-1	-0.779	-0.892	23.999	-0.218	-0.218	0.000	0.000	0.000	0.000
13	A	11	ASP	-1	-0.833	-0.907	26.722	-0.178	-0.178	0.000	0.000	0.000	0.000
14	A	12	ARG	1	0.869	0.933	29.117	0.190	0.190	0.000	0.000	0.000	0.000
15	A	13	LEU	0	-0.030	-0.015	23.846	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	14	ILE	0	-0.022	0.005	22.821	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	15	HIS	0	-0.030	-0.035	26.724	0.027	0.027	0.000	0.000	0.000	0.000
18	A	16	GLY	0	0.021	0.001	30.037	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	17	GLN	0	0.019	-0.009	30.106	-0.022	-0.022	0.000	0.000	0.000	0.000
20	A	18	VAL	0	0.001	0.013	26.637	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	19	MET	0	0.081	0.029	20.787	0.001	0.001	0.000	0.000	0.000	0.000
22	A	20	THR	0	0.014	0.013	23.809	-0.038	-0.038	0.000	0.000	0.000	0.000
23	A	21	ARG	1	0.881	0.935	25.268	0.216	0.216	0.000	0.000	0.000	0.000
24	A	22	TRP	0	0.012	-0.006	21.889	-0.016	-0.016	0.000	0.000	0.000	0.000
25	A	23	MET	0	0.011	0.011	17.010	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	24	LYS	1	0.931	0.976	20.465	0.279	0.279	0.000	0.000	0.000	0.000
27	A	25	GLY	0	-0.006	0.015	20.881	0.004	0.004	0.000	0.000	0.000	0.000
28	A	26	PHE	0	-0.067	-0.048	15.554	-0.029	-0.029	0.000	0.000	0.000	0.000
29	A	27	PRO	0	0.013	0.003	17.188	-0.046	-0.046	0.000	0.000	0.000	0.000
30	A	28	GLU	-1	-0.923	-0.960	13.420	-0.878	-0.878	0.000	0.000	0.000	0.000
31	A	29	ALA	0	-0.089	-0.029	13.362	-0.149	-0.149	0.000	0.000	0.000	0.000
32	A	30	SER	0	-0.048	-0.022	13.511	0.136	0.136	0.000	0.000	0.000	0.000
33	A	31	ILE	0	0.027	0.001	15.269	-0.022	-0.022	0.000	0.000	0.000	0.000
34	A	32	VAL	0	-0.023	-0.007	13.421	0.006	0.006	0.000	0.000	0.000	0.000
35	A	33	ILE	0	-0.002	-0.002	16.642	0.031	0.031	0.000	0.000	0.000	0.000
36	A	34	ILE	0	-0.019	-0.007	15.159	-0.012	-0.012	0.000	0.000	0.000	0.000
37	A	35	ASP	-1	-0.850	-0.951	19.635	-0.190	-0.190	0.000	0.000	0.000	0.000
38	A	36	ASP	-1	-0.791	-0.890	23.236	-0.191	-0.191	0.000	0.000	0.000	0.000
39	A	37	GLU	-1	-0.948	-0.961	25.133	-0.143	-0.143	0.000	0.000	0.000	0.000
40	A	38	LEU	0	-0.023	-0.026	23.913	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	39	ALA	0	-0.033	-0.017	23.206	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	40	VAL	0	-0.018	-0.017	24.831	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	41	ASP	-1	-0.862	-0.912	28.229	-0.176	-0.176	0.000	0.000	0.000	0.000
44	A	42	GLU	-1	-0.890	-0.978	28.623	-0.257	-0.257	0.000	0.000	0.000	0.000
45	A	43	PHE	0	-0.026	0.003	30.331	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	44	MET	0	0.015	-0.006	29.721	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	45	LYS	1	0.889	0.964	24.717	0.264	0.264	0.000	0.000	0.000	0.000
48	A	46	ASN	0	0.012	0.012	26.988	-0.034	-0.034	0.000	0.000	0.000	0.000
49	A	47	ILE	0	-0.022	-0.007	29.422	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	48	TYR	0	0.008	-0.022	25.672	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	49	THR	0	-0.033	-0.020	24.644	-0.032	-0.032	0.000	0.000	0.000	0.000
52	A	50	MET	0	-0.065	-0.031	26.006	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	51	ALA	0	-0.051	-0.006	28.510	0.006	0.006	0.000	0.000	0.000	0.000
54	A	52	ALA	0	-0.026	-0.002	23.534	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	53	PRO	0	-0.025	-0.008	23.015	0.020	0.020	0.000	0.000	0.000	0.000
56	A	54	PRO	0	0.025	-0.005	24.489	-0.022	-0.022	0.000	0.000	0.000	0.000
57	A	55	GLY	0	-0.014	-0.003	23.290	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	56	VAL	0	-0.004	0.014	18.952	-0.055	-0.055	0.000	0.000	0.000	0.000
59	A	57	LYS	1	0.845	0.922	13.720	1.095	1.095	0.000	0.000	0.000	0.000
60	A	58	VAL	0	0.064	0.019	18.685	-0.038	-0.038	0.000	0.000	0.000	0.000
61	A	59	LYS	1	0.839	0.922	12.648	1.136	1.136	0.000	0.000	0.000	0.000
62	A	60	VAL	0	0.021	0.012	18.787	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	61	PHE	0	-0.018	-0.008	14.902	-0.026	-0.026	0.000	0.000	0.000	0.000
64	A	62	GLY	0	0.093	0.043	19.278	0.019	0.019	0.000	0.000	0.000	0.000
65	A	63	VAL	0	0.008	-0.012	19.024	-0.046	-0.046	0.000	0.000	0.000	0.000
66	A	64	ASP	-1	-0.875	-0.931	17.995	-0.131	-0.131	0.000	0.000	0.000	0.000
67	A	65	ALA	0	-0.044	-0.027	17.316	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	66	ALA	0	0.011	0.005	14.864	-0.075	-0.075	0.000	0.000	0.000	0.000
69	A	67	LEU	0	0.010	0.018	13.218	-0.118	-0.118	0.000	0.000	0.000	0.000
70	A	68	LYS	1	0.838	0.930	12.068	0.092	0.092	0.000	0.000	0.000	0.000
71	A	69	GLU	-1	-0.891	-0.945	11.017	-0.954	-0.954	0.000	0.000	0.000	0.000
72	A	70	TRP	0	0.030	0.011	7.205	-0.179	-0.179	0.000	0.000	0.000	0.000
73	A	71	SER	0	-0.069	-0.041	7.583	-0.182	-0.182	0.000	0.000	0.000	0.000
74	A	72	GLN	0	0.044	0.038	7.974	0.787	0.787	0.000	0.000	0.000	0.000
75	A	73	LYS	1	0.850	0.913	3.694	-3.406	-2.837	0.014	-0.236	-0.348	0.001
76	A	74	THR	0	0.018	0.001	2.535	0.668	1.772	0.128	-0.395	-0.837	0.000
77	A	75	SER	0	-0.003	-0.005	2.091	-8.226	-7.566	3.932	-2.385	-2.207	-0.032
78	A	76	VAL	0	-0.034	-0.016	4.497	-0.133	0.036	-0.001	-0.011	-0.157	0.000
79	A	77	GLU	-1	-0.899	-0.938	3.032	-8.766	-7.301	0.187	-0.724	-0.928	-0.005
80	A	78	GLU	-1	-0.750	-0.859	4.632	-0.399	-0.347	-0.001	-0.007	-0.044	0.000
81	A	79	LYS	1	0.935	0.961	8.047	1.865	1.865	0.000	0.000	0.000	0.000
82	A	80	VAL	0	0.013	0.016	9.828	0.209	0.209	0.000	0.000	0.000	0.000
83	A	81	PHE	0	0.017	0.011	12.035	0.053	0.053	0.000	0.000	0.000	0.000
84	A	82	LEU	0	0.000	-0.008	13.124	0.027	0.027	0.000	0.000	0.000	0.000
85	A	83	LEU	0	-0.032	-0.012	16.263	0.053	0.053	0.000	0.000	0.000	0.000
86	A	84	PHE	0	0.060	0.019	16.993	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	85	LYS	1	1.004	1.008	22.081	0.193	0.193	0.000	0.000	0.000	0.000
88	A	86	ASN	0	0.026	0.004	25.008	0.017	0.017	0.000	0.000	0.000	0.000
89	A	87	ILE	0	0.062	0.017	24.545	-0.015	-0.015	0.000	0.000	0.000	0.000
90	A	88	ASP	-1	-0.892	-0.938	24.410	-0.097	-0.097	0.000	0.000	0.000	0.000
91	A	89	THR	0	-0.017	-0.022	21.306	0.008	0.008	0.000	0.000	0.000	0.000
92	A	90	CYS	0	-0.047	-0.009	20.069	-0.015	-0.015	0.000	0.000	0.000	0.000
93	A	91	LYS	1	0.921	0.942	19.941	0.026	0.026	0.000	0.000	0.000	0.000
94	A	92	ARG	1	0.877	0.945	21.264	0.144	0.144	0.000	0.000	0.000	0.000
95	A	93	VAL	0	-0.017	-0.008	16.273	0.013	0.013	0.000	0.000	0.000	0.000
96	A	94	MET	0	-0.035	-0.008	16.588	0.004	0.004	0.000	0.000	0.000	0.000
97	A	95	ASP	-1	-0.810	-0.882	17.396	0.041	0.041	0.000	0.000	0.000	0.000
98	A	96	GLY	0	-0.061	-0.014	17.351	0.044	0.044	0.000	0.000	0.000	0.000
99	A	97	GLY	0	-0.028	-0.014	13.968	0.032	0.032	0.000	0.000	0.000	0.000
100	A	98	LEU	0	-0.031	-0.014	11.324	0.005	0.005	0.000	0.000	0.000	0.000
101	A	99	PRO	0	-0.042	-0.007	9.391	0.032	0.032	0.000	0.000	0.000	0.000
102	A	100	ILE	0	0.048	-0.007	11.824	-0.160	-0.160	0.000	0.000	0.000	0.000
103	A	101	THR	0	0.003	-0.003	13.014	0.047	0.047	0.000	0.000	0.000	0.000
104	A	102	THR	0	0.016	0.012	15.595	0.040	0.040	0.000	0.000	0.000	0.000
105	A	103	LEU	0	-0.029	-0.014	17.826	-0.046	-0.046	0.000	0.000	0.000	0.000
106	A	104	ASN	0	-0.003	0.006	20.447	0.008	0.008	0.000	0.000	0.000	0.000
107	A	105	ILE	0	0.011	-0.017	23.014	-0.013	-0.013	0.000	0.000	0.000	0.000
108	A	106	GLY	0	-0.003	-0.022	26.089	0.009	0.009	0.000	0.000	0.000	0.000
109	A	107	GLY	0	-0.020	-0.014	27.369	0.009	0.009	0.000	0.000	0.000	0.000
110	A	108	VAL	0	-0.004	0.005	29.355	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	109	ALA	0	0.030	0.017	31.767	0.010	0.010	0.000	0.000	0.000	0.000
112	A	110	LYS	1	0.896	0.954	35.252	0.082	0.082	0.000	0.000	0.000	0.000
113	A	111	THR	0	0.046	0.017	37.278	0.000	0.000	0.000	0.000	0.000	0.000
114	A	112	PRO	0	-0.024	-0.028	39.915	0.001	0.001	0.000	0.000	0.000	0.000
115	A	113	GLN	0	0.048	0.024	39.096	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	114	ARG	1	0.755	0.879	32.574	0.112	0.112	0.000	0.000	0.000	0.000
117	A	115	LYS	1	0.892	0.957	38.025	0.058	0.058	0.000	0.000	0.000	0.000
118	A	116	GLY	0	-0.013	-0.012	37.716	-0.006	-0.006	0.000	0.000	0.000	0.000
119	A	117	ILE	0	-0.039	-0.008	34.092	0.005	0.005	0.000	0.000	0.000	0.000
120	A	118	SER	0	0.019	0.005	33.564	0.002	0.002	0.000	0.000	0.000	0.000
121	A	119	GLN	0	0.000	-0.013	35.410	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	120	SER	0	-0.025	-0.010	32.192	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	121	VAL	0	0.049	0.038	30.313	-0.006	-0.006	0.000	0.000	0.000	0.000
124	A	122	SER	0	0.008	-0.003	33.430	0.013	0.013	0.000	0.000	0.000	0.000
125	A	123	LEU	0	0.039	0.013	30.402	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	124	SER	0	0.049	0.028	34.435	0.008	0.008	0.000	0.000	0.000	0.000
127	A	125	GLU	-1	-0.868	-0.950	34.715	-0.033	-0.033	0.000	0.000	0.000	0.000
128	A	126	ASP	-1	-0.856	-0.924	34.062	-0.035	-0.035	0.000	0.000	0.000	0.000
129	A	127	GLU	-1	-0.838	-0.911	30.851	-0.099	-0.099	0.000	0.000	0.000	0.000
130	A	128	VAL	0	0.012	-0.002	29.983	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	129	LYS	1	0.851	0.926	30.533	0.024	0.024	0.000	0.000	0.000	0.000
132	A	130	THR	0	0.004	0.001	26.438	0.008	0.008	0.000	0.000	0.000	0.000
133	A	131	LEU	0	-0.023	-0.018	25.290	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	132	LEU	0	0.002	0.001	25.820	0.002	0.002	0.000	0.000	0.000	0.000
135	A	133	GLU	-1	-0.904	-0.951	25.713	0.018	0.018	0.000	0.000	0.000	0.000
136	A	134	LEU	0	0.009	-0.001	21.413	0.016	0.016	0.000	0.000	0.000	0.000
137	A	135	LYS	1	0.943	0.988	22.012	0.007	0.007	0.000	0.000	0.000	0.000
138	A	136	THR	0	-0.102	-0.075	23.250	0.017	0.017	0.000	0.000	0.000	0.000
139	A	137	LYS	1	0.885	0.956	21.837	-0.026	-0.026	0.000	0.000	0.000	0.000
140	A	138	TYR	0	-0.030	-0.044	17.838	0.037	0.037	0.000	0.000	0.000	0.000
141	A	139	ASN	0	-0.062	-0.015	18.201	-0.008	-0.008	0.000	0.000	0.000	0.000
142	A	140	VAL	0	-0.024	0.007	18.833	-0.019	-0.019	0.000	0.000	0.000	0.000
143	A	141	ASP	-1	-0.923	-0.966	19.715	-0.136	-0.136	0.000	0.000	0.000	0.000
144	A	142	VAL	0	0.017	0.007	21.474	-0.034	-0.034	0.000	0.000	0.000	0.000
145	A	143	TYR	0	-0.010	-0.019	22.321	0.013	0.013	0.000	0.000	0.000	0.000
146	A	144	LEU	0	0.007	0.027	25.798	-0.021	-0.021	0.000	0.000	0.000	0.000
147	A	145	GLN	0	-0.011	-0.021	26.094	-0.009	-0.009	0.000	0.000	0.000	0.000
148	A	146	MET	0	0.027	0.040	27.345	-0.016	-0.016	0.000	0.000	0.000	0.000
149	A	147	ILE	0	-0.034	-0.039	27.522	-0.020	-0.020	0.000	0.000	0.000	0.000
150	A	148	PRO	0	0.032	0.007	24.739	0.017	0.017	0.000	0.000	0.000	0.000
151	A	149	ASP	-1	-0.863	-0.915	26.925	-0.216	-0.216	0.000	0.000	0.000	0.000
152	A	150	SER	0	-0.113	-0.047	30.205	0.016	0.016	0.000	0.000	0.000	0.000
153	A	151	GLU	-1	-0.898	-0.963	30.962	-0.116	-0.116	0.000	0.000	0.000	0.000
154	A	152	LYS	1	0.912	0.970	24.823	0.195	0.195	0.000	0.000	0.000	0.000
155	A	153	ILE	0	0.010	0.011	30.185	0.011	0.011	0.000	0.000	0.000	0.000
156	A	154	HIS	0	0.045	0.012	26.660	-0.003	-0.003	0.000	0.000	0.000	0.000
157	A	155	LEU	0	0.065	0.026	26.935	0.008	0.008	0.000	0.000	0.000	0.000
158	A	156	THR	0	0.021	-0.003	29.518	0.003	0.003	0.000	0.000	0.000	0.000
159	A	157	THR	0	0.034	0.023	31.796	0.003	0.003	0.000	0.000	0.000	0.000
160	A	158	VAL	0	-0.019	-0.009	31.720	0.003	0.003	0.000	0.000	0.000	0.000
161	A	159	VAL	0	0.014	-0.002	32.836	0.003	0.003	0.000	0.000	0.000	0.000
162	A	160	GLU	-1	-0.951	-0.971	35.399	-0.035	-0.035	0.000	0.000	0.000	0.000
163	A	161	LYS	1	0.918	0.961	37.610	0.069	0.069	0.000	0.000	0.000	0.000
164	A	162	TYR	0	-0.048	-0.028	36.855	0.000	0.000	0.000	0.000	0.000	0.000
165	A	163	PHE	0	-0.077	-0.050	35.770	-0.001	-0.001	0.000	0.000	0.000	0.000
166	A	164	PRO	0	0.045	0.032	38.716	0.003	0.003	0.000	0.000	0.000	0.000
167	A	165	GLU	-1	-0.879	-0.911	37.779	-0.015	-0.015	0.000	0.000	0.000	0.000

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