FMO DATABASE

FMODB ID: 2JYYR

Calculation Name: 1L4A-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1L4A

Chain ID: B

ChEMBL ID:

UniProt ID: Q95PA1

Base Structure: X-ray

Registration Date: 2023-09-20

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	82
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-361386.661517
FMO2-HF: Nuclear repulsion	327598.486678
FMO2-HF: Total energy	-33788.174839
FMO2-MP2: Total energy	-33881.705266

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(B:178:GLY)

Summations of interaction energy for fragment #1(B:178:GLY)

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.
-3.7	-1.078	1.618	-1.869	-2.368	0.003

Interaction energy analysis for fragmet #1(B:178:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.006

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	B	180	SER	0	0.086	0.028	2.920	-2.011	0.019	0.060	-1.002	-1.087	0.003
4	B	181	ALA	0	-0.057	-0.024	2.157	-1.593	-1.190	1.552	-0.795	-1.159	0.000
5	B	182	SER	0	0.083	0.035	3.924	-0.174	0.015	0.006	-0.072	-0.122	0.000
6	B	183	GLY	0	0.013	0.026	6.323	0.073	0.073	0.000	0.000	0.000	0.000
7	B	184	ILE	0	0.019	0.006	6.577	0.125	0.125	0.000	0.000	0.000	0.000
8	B	185	ILE	0	-0.007	-0.007	8.652	0.063	0.063	0.000	0.000	0.000	0.000
9	B	186	MET	0	0.032	-0.003	10.407	-0.030	-0.030	0.000	0.000	0.000	0.000
10	B	187	GLU	-1	-0.963	-0.971	10.013	-0.043	-0.043	0.000	0.000	0.000	0.000
11	B	188	THR	0	-0.010	-0.006	12.916	0.015	0.015	0.000	0.000	0.000	0.000
12	B	189	GLN	0	-0.069	-0.027	13.761	-0.038	-0.038	0.000	0.000	0.000	0.000
13	B	190	GLN	0	0.051	0.026	16.886	-0.002	-0.002	0.000	0.000	0.000	0.000
14	B	191	ALA	0	0.016	0.017	17.820	-0.004	-0.004	0.000	0.000	0.000	0.000
15	B	192	LYS	1	0.951	0.950	18.115	-0.190	-0.190	0.000	0.000	0.000	0.000
16	B	193	GLN	0	-0.044	-0.003	21.316	0.000	0.000	0.000	0.000	0.000	0.000
17	B	194	THR	0	0.062	0.035	22.569	-0.005	-0.005	0.000	0.000	0.000	0.000
18	B	195	LEU	0	-0.054	-0.029	23.572	-0.002	-0.002	0.000	0.000	0.000	0.000
19	B	196	ALA	0	0.025	0.014	25.345	-0.001	-0.001	0.000	0.000	0.000	0.000
20	B	197	ASP	-1	-0.870	-0.933	26.656	0.013	0.013	0.000	0.000	0.000	0.000
21	B	198	ILE	0	-0.089	-0.052	26.347	-0.003	-0.003	0.000	0.000	0.000	0.000
22	B	199	GLU	-1	-0.948	-0.987	28.644	0.068	0.068	0.000	0.000	0.000	0.000
23	B	200	ALA	0	-0.002	0.012	31.199	-0.002	-0.002	0.000	0.000	0.000	0.000
24	B	201	ARG	1	0.994	0.992	30.972	-0.020	-0.020	0.000	0.000	0.000	0.000
25	B	202	HIS	0	-0.083	-0.038	33.541	-0.003	-0.003	0.000	0.000	0.000	0.000
26	B	203	ALA	0	0.059	0.027	35.330	-0.001	-0.001	0.000	0.000	0.000	0.000
27	B	204	ASP	-1	-0.902	-0.936	37.546	0.017	0.017	0.000	0.000	0.000	0.000
28	B	205	ILE	0	-0.024	-0.025	36.897	-0.001	-0.001	0.000	0.000	0.000	0.000
29	B	206	MET	0	0.014	0.018	38.596	-0.001	-0.001	0.000	0.000	0.000	0.000
30	B	207	LYS	1	0.956	0.978	40.908	-0.021	-0.021	0.000	0.000	0.000	0.000
31	B	208	LEU	0	-0.041	-0.021	43.167	-0.001	-0.001	0.000	0.000	0.000	0.000
32	B	209	GLU	-1	-0.817	-0.909	43.400	0.026	0.026	0.000	0.000	0.000	0.000
33	B	210	THR	0	-0.054	-0.023	44.635	0.001	0.001	0.000	0.000	0.000	0.000
34	B	211	SER	0	0.011	0.007	47.067	0.000	0.000	0.000	0.000	0.000	0.000
35	B	212	ILE	0	-0.022	-0.013	47.356	-0.001	-0.001	0.000	0.000	0.000	0.000
36	B	213	ARG	1	0.833	0.910	44.262	-0.027	-0.027	0.000	0.000	0.000	0.000
37	B	214	GLU	-1	-0.911	-0.939	50.802	0.017	0.017	0.000	0.000	0.000	0.000
38	B	215	LEU	0	-0.019	-0.015	53.226	-0.001	-0.001	0.000	0.000	0.000	0.000
39	B	216	HIS	0	-0.081	-0.061	53.076	-0.001	-0.001	0.000	0.000	0.000	0.000
40	B	217	ASP	-1	-0.869	-0.939	54.370	0.019	0.019	0.000	0.000	0.000	0.000
41	B	218	MET	0	-0.012	-0.006	56.617	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	219	PHE	0	-0.051	-0.033	57.385	-0.001	-0.001	0.000	0.000	0.000	0.000
43	B	220	MET	0	-0.033	-0.023	56.834	-0.001	-0.001	0.000	0.000	0.000	0.000
44	B	221	ASP	-1	-0.860	-0.927	60.503	0.015	0.015	0.000	0.000	0.000	0.000
45	B	222	MET	0	-0.066	-0.032	62.881	0.000	0.000	0.000	0.000	0.000	0.000
46	B	223	ALA	0	-0.007	-0.006	63.735	0.000	0.000	0.000	0.000	0.000	0.000
47	B	224	MET	0	0.014	0.028	61.822	0.000	0.000	0.000	0.000	0.000	0.000
48	B	225	LEU	0	-0.020	0.004	66.269	0.000	0.000	0.000	0.000	0.000	0.000
49	B	226	VAL	0	-0.069	-0.041	68.634	0.000	0.000	0.000	0.000	0.000	0.000
50	B	227	GLU	-1	-0.910	-0.943	68.635	0.010	0.010	0.000	0.000	0.000	0.000
51	B	228	SER	0	-0.053	-0.032	70.082	0.000	0.000	0.000	0.000	0.000	0.000
52	B	229	GLN	0	-0.122	-0.079	71.765	0.000	0.000	0.000	0.000	0.000	0.000
53	B	230	GLY	0	0.109	0.052	74.079	0.000	0.000	0.000	0.000	0.000	0.000
54	B	231	GLU	-1	-0.726	-0.858	75.569	0.010	0.010	0.000	0.000	0.000	0.000
55	B	232	MET	0	-0.163	-0.084	75.583	0.000	0.000	0.000	0.000	0.000	0.000
56	B	233	ILE	0	-0.047	-0.040	77.287	0.000	0.000	0.000	0.000	0.000	0.000
57	B	234	ASP	-1	-0.855	-0.895	79.079	0.007	0.007	0.000	0.000	0.000	0.000
58	B	235	ARG	1	0.808	0.876	78.674	-0.010	-0.010	0.000	0.000	0.000	0.000
59	B	236	ILE	0	-0.115	-0.038	82.771	0.000	0.000	0.000	0.000	0.000	0.000
60	B	237	GLU	-1	-0.875	-0.933	84.348	0.006	0.006	0.000	0.000	0.000	0.000
61	B	238	TYR	0	0.052	0.022	85.938	0.000	0.000	0.000	0.000	0.000	0.000
62	B	239	ASN	0	-0.014	-0.021	87.213	0.000	0.000	0.000	0.000	0.000	0.000
63	B	240	VAL	0	-0.039	-0.037	88.603	0.000	0.000	0.000	0.000	0.000	0.000
64	B	241	GLU	-1	-1.021	-0.977	88.880	0.005	0.005	0.000	0.000	0.000	0.000
65	B	242	ALA	0	0.007	-0.025	91.569	0.000	0.000	0.000	0.000	0.000	0.000
66	B	243	ALA	0	-0.015	0.018	92.977	0.000	0.000	0.000	0.000	0.000	0.000
67	B	244	VAL	0	-0.018	-0.030	94.132	0.000	0.000	0.000	0.000	0.000	0.000
68	B	245	ASP	-1	-0.799	-0.910	95.998	0.005	0.005	0.000	0.000	0.000	0.000
69	B	246	TYR	0	0.006	0.031	96.312	0.000	0.000	0.000	0.000	0.000	0.000
70	B	247	ILE	0	-0.129	-0.033	99.016	0.000	0.000	0.000	0.000	0.000	0.000
71	B	248	GLU	-1	-0.814	-0.913	100.249	0.004	0.004	0.000	0.000	0.000	0.000
72	B	249	THR	0	-0.001	-0.011	101.325	0.000	0.000	0.000	0.000	0.000	0.000
73	B	250	ALA	0	-0.017	-0.006	103.746	0.000	0.000	0.000	0.000	0.000	0.000
74	B	251	LYS	1	0.773	0.880	101.354	-0.004	-0.004	0.000	0.000	0.000	0.000
75	B	252	VAL	0	-0.009	-0.017	105.887	0.000	0.000	0.000	0.000	0.000	0.000
76	B	253	ASP	-1	-0.844	-0.911	108.481	0.004	0.004	0.000	0.000	0.000	0.000
77	B	254	THR	0	-0.079	-0.039	108.618	0.000	0.000	0.000	0.000	0.000	0.000
78	B	255	LYS	1	0.967	0.984	111.310	-0.003	-0.003	0.000	0.000	0.000	0.000
79	B	256	LYS	1	0.848	0.945	113.591	-0.004	-0.004	0.000	0.000	0.000	0.000
80	B	257	ALA	0	0.006	-0.012	114.967	0.000	0.000	0.000	0.000	0.000	0.000
81	B	258	VAL	0	-0.041	-0.015	116.960	0.000	0.000	0.000	0.000	0.000	0.000
82	B	259	LYS	1	0.988	0.993	118.112	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:178:GLY)