FMO DATABASE

FMODB ID: LZ3K9

Calculation Name: 3L7P-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L7P

Chain ID: E

ChEMBL ID:

UniProt ID: Q8DSV2

Base Structure: X-ray

Registration Date: 2023-09-19

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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-557918.307996
FMO2-HF: Nuclear repulsion	524130.22349
FMO2-HF: Total energy	-33788.084506
FMO2-MP2: Total energy	-33886.447429

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(E:0:SER)

Summations of interaction energy for fragment #1(E:0: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.
-3.954	1.495	0.284	-2.466	-3.266	0.01

Interaction energy analysis for fragmet #1(E:0:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.027

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

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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	E	2	LYS	1	0.991	1.001	3.289	-5.265	-2.209	0.016	-1.595	-1.478	0.007
4	E	3	LYS	1	0.886	0.949	6.401	-0.611	-0.611	0.000	0.000	0.000	0.000
5	E	4	ILE	0	0.013	0.000	10.128	0.133	0.133	0.000	0.000	0.000	0.000
6	E	5	GLU	-1	-0.872	-0.957	12.493	0.045	0.045	0.000	0.000	0.000	0.000
7	E	6	ALA	0	0.025	0.021	16.027	0.022	0.022	0.000	0.000	0.000	0.000
8	E	7	ILE	0	-0.050	-0.013	19.076	-0.007	-0.007	0.000	0.000	0.000	0.000
9	E	8	ILE	0	0.032	0.002	22.394	0.005	0.005	0.000	0.000	0.000	0.000
10	E	9	ARG	1	0.815	0.864	25.009	0.040	0.040	0.000	0.000	0.000	0.000
11	E	10	SER	0	0.031	-0.015	28.406	-0.009	-0.009	0.000	0.000	0.000	0.000
12	E	11	ASP	-1	-0.856	-0.877	30.195	-0.050	-0.050	0.000	0.000	0.000	0.000
13	E	12	LYS	1	0.950	0.982	27.501	0.060	0.060	0.000	0.000	0.000	0.000
14	E	13	LEU	0	-0.011	0.013	26.171	-0.011	-0.011	0.000	0.000	0.000	0.000
15	E	14	GLU	-1	-0.833	-0.920	27.058	-0.119	-0.119	0.000	0.000	0.000	0.000
16	E	15	ASP	-1	-0.856	-0.929	28.021	-0.099	-0.099	0.000	0.000	0.000	0.000
17	E	16	LEU	0	-0.001	0.003	20.724	-0.014	-0.014	0.000	0.000	0.000	0.000
18	E	17	LYS	1	0.858	0.922	23.277	0.097	0.097	0.000	0.000	0.000	0.000
19	E	18	ALA	0	0.011	0.002	24.459	-0.019	-0.019	0.000	0.000	0.000	0.000
20	E	19	ALA	0	0.014	0.005	22.785	-0.013	-0.013	0.000	0.000	0.000	0.000
21	E	20	LEU	0	-0.004	-0.019	17.825	-0.025	-0.025	0.000	0.000	0.000	0.000
22	E	21	VAL	0	-0.057	-0.029	20.611	-0.028	-0.028	0.000	0.000	0.000	0.000
23	E	22	GLN	0	-0.029	0.000	22.463	-0.018	-0.018	0.000	0.000	0.000	0.000
24	E	23	SER	0	-0.015	-0.012	18.226	-0.006	-0.006	0.000	0.000	0.000	0.000
25	E	24	GLY	0	0.005	0.009	18.359	-0.042	-0.042	0.000	0.000	0.000	0.000
26	E	25	PHE	0	-0.027	-0.023	12.197	-0.064	-0.064	0.000	0.000	0.000	0.000
27	E	26	ILE	0	-0.007	0.006	17.197	0.002	0.002	0.000	0.000	0.000	0.000
28	E	27	LYS	1	0.950	0.966	17.894	0.287	0.287	0.000	0.000	0.000	0.000
29	E	28	GLY	0	-0.038	-0.010	15.135	0.001	0.001	0.000	0.000	0.000	0.000
30	E	29	MET	0	-0.037	-0.001	15.694	0.008	0.008	0.000	0.000	0.000	0.000
31	E	30	THR	0	0.023	0.021	18.210	0.012	0.012	0.000	0.000	0.000	0.000
32	E	31	ILE	0	-0.042	-0.028	20.081	0.010	0.010	0.000	0.000	0.000	0.000
33	E	32	SER	0	0.004	0.002	23.012	0.009	0.009	0.000	0.000	0.000	0.000
34	E	33	GLN	0	-0.004	-0.001	25.184	0.002	0.002	0.000	0.000	0.000	0.000
35	E	34	VAL	0	0.003	0.005	24.867	0.005	0.005	0.000	0.000	0.000	0.000
36	E	35	LEU	0	0.009	0.004	28.111	-0.003	-0.003	0.000	0.000	0.000	0.000
37	E	36	GLY	0	-0.005	0.000	29.368	0.006	0.006	0.000	0.000	0.000	0.000
38	E	37	PHE	0	-0.018	-0.022	30.066	-0.003	-0.003	0.000	0.000	0.000	0.000
39	E	38	GLY	0	0.027	0.018	31.527	0.002	0.002	0.000	0.000	0.000	0.000
40	E	39	ASN	0	-0.005	0.000	34.067	0.002	0.002	0.000	0.000	0.000	0.000
41	E	54	PRO	0	-0.017	-0.001	36.925	0.000	0.000	0.000	0.000	0.000	0.000
42	E	55	THR	0	0.001	-0.004	35.812	-0.003	-0.003	0.000	0.000	0.000	0.000
43	E	56	LEU	0	0.020	0.003	35.463	0.003	0.003	0.000	0.000	0.000	0.000
44	E	57	LEU	0	-0.018	-0.012	31.614	-0.004	-0.004	0.000	0.000	0.000	0.000
45	E	58	ALA	0	0.033	0.039	32.017	0.003	0.003	0.000	0.000	0.000	0.000
46	E	59	LYS	1	0.814	0.907	26.812	0.008	0.008	0.000	0.000	0.000	0.000
47	E	60	VAL	0	0.059	0.031	24.382	-0.002	-0.002	0.000	0.000	0.000	0.000
48	E	61	LYS	1	0.802	0.911	18.465	-0.012	-0.012	0.000	0.000	0.000	0.000
49	E	62	VAL	0	0.027	0.011	18.228	-0.011	-0.011	0.000	0.000	0.000	0.000
50	E	63	GLU	-1	-0.848	-0.927	16.022	-0.017	-0.017	0.000	0.000	0.000	0.000
51	E	64	ILE	0	0.032	0.010	12.588	-0.032	-0.032	0.000	0.000	0.000	0.000
52	E	65	VAL	0	-0.013	0.010	8.339	0.060	0.060	0.000	0.000	0.000	0.000
53	E	66	ALA	0	-0.016	-0.007	8.869	-0.102	-0.102	0.000	0.000	0.000	0.000
54	E	67	HIS	0	0.013	-0.012	4.469	0.580	0.647	-0.001	-0.021	-0.044	0.000
55	E	68	ASP	-1	-0.886	-0.944	2.736	-1.334	0.625	0.271	-0.807	-1.422	0.003
56	E	69	ALA	0	0.027	0.001	4.690	0.723	0.918	-0.001	-0.017	-0.177	0.000
57	E	70	ALA	0	-0.030	-0.011	6.862	0.392	0.392	0.000	0.000	0.000	0.000
58	E	71	VAL	0	-0.023	-0.009	7.246	0.287	0.287	0.000	0.000	0.000	0.000
59	E	72	GLU	-1	-0.896	-0.954	9.965	-0.037	-0.037	0.000	0.000	0.000	0.000
60	E	73	GLU	-1	-0.878	-0.939	12.524	-0.298	-0.298	0.000	0.000	0.000	0.000
61	E	74	MET	0	0.000	0.007	12.981	0.090	0.090	0.000	0.000	0.000	0.000
62	E	75	ILE	0	0.016	0.012	12.560	0.063	0.063	0.000	0.000	0.000	0.000
63	E	76	THR	0	0.002	0.004	15.905	0.051	0.051	0.000	0.000	0.000	0.000
64	E	77	THR	0	-0.034	-0.018	17.802	0.032	0.032	0.000	0.000	0.000	0.000
65	E	78	ILE	0	-0.022	-0.032	16.413	0.025	0.025	0.000	0.000	0.000	0.000
66	E	79	SER	0	-0.011	-0.011	19.592	0.030	0.030	0.000	0.000	0.000	0.000
67	E	80	GLN	0	-0.047	-0.039	21.723	0.035	0.035	0.000	0.000	0.000	0.000
68	E	81	ALA	0	-0.009	0.002	23.391	0.010	0.010	0.000	0.000	0.000	0.000
69	E	82	VAL	0	0.003	-0.002	23.234	0.009	0.009	0.000	0.000	0.000	0.000
70	E	83	LYS	1	0.880	0.978	25.672	0.089	0.089	0.000	0.000	0.000	0.000
71	E	84	THR	0	-0.082	-0.072	27.157	-0.003	-0.003	0.000	0.000	0.000	0.000
72	E	85	GLY	0	-0.003	0.008	30.639	0.004	0.004	0.000	0.000	0.000	0.000
73	E	86	GLU	-1	-0.816	-0.897	33.135	-0.025	-0.025	0.000	0.000	0.000	0.000
74	E	87	VAL	0	-0.010	-0.018	29.466	0.004	0.004	0.000	0.000	0.000	0.000
75	E	88	GLY	0	0.002	0.001	29.543	0.004	0.004	0.000	0.000	0.000	0.000
76	E	89	ASP	-1	-0.873	-0.934	27.428	-0.005	-0.005	0.000	0.000	0.000	0.000
77	E	90	GLY	0	0.049	0.015	24.352	-0.011	-0.011	0.000	0.000	0.000	0.000
78	E	91	LYS	1	0.862	0.950	20.690	-0.036	-0.036	0.000	0.000	0.000	0.000
79	E	92	ILE	0	0.067	0.021	14.954	-0.013	-0.013	0.000	0.000	0.000	0.000
80	E	93	PHE	0	-0.051	-0.025	14.851	0.016	0.016	0.000	0.000	0.000	0.000
81	E	94	VAL	0	0.028	0.012	8.588	-0.025	-0.025	0.000	0.000	0.000	0.000
82	E	95	SER	0	-0.018	-0.006	10.024	0.070	0.070	0.000	0.000	0.000	0.000
83	E	96	PRO	0	-0.046	-0.023	6.192	0.153	0.153	0.000	0.000	0.000	0.000
84	E	97	VAL	0	0.008	0.000	4.963	-0.420	-0.420	0.000	0.000	0.000	0.000
85	E	98	ASP	-1	-0.914	-0.940	4.232	0.391	0.563	-0.001	-0.026	-0.145	0.000
86	E	99	GLU	-1	-0.966	-0.991	5.699	-0.127	-0.127	0.000	0.000	0.000	0.000
87	E	100	ILE	0	-0.055	-0.031	6.460	-0.023	-0.023	0.000	0.000	0.000	0.000
88	E	101	VAL	0	0.056	0.033	8.811	-0.007	-0.007	0.000	0.000	0.000	0.000
89	E	102	ARG	1	0.888	0.943	7.875	1.097	1.097	0.000	0.000	0.000	0.000
90	E	103	ILE	0	0.032	0.024	13.801	0.022	0.022	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:0:SER)