FMO DATABASE

FMODB ID: 6Y37Z

Calculation Name: 3LLB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LLB

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HX36

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	OptAll
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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-537795.531226
FMO2-HF: Nuclear repulsion	506391.781633
FMO2-HF: Total energy	-31403.749593
FMO2-MP2: Total energy	-31497.332457

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.
-0.546	2.81	0.048	-1.636	-1.768	-0.002

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 : 0.052 / q_NPA : 0.012

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	ILE	0	0.003	0.017	2.924	-1.811	0.177	0.022	-0.937	-1.073	0.001
4	A	4	LYS	1	0.905	0.954	3.269	-1.909	-1.093	0.024	-0.471	-0.369	-0.004
5	A	5	PRO	0	0.072	0.054	6.018	0.227	0.227	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.055	-0.044	9.279	-0.027	-0.027	0.000	0.000	0.000	0.000
7	A	7	PRO	0	-0.002	-0.008	12.650	0.026	0.026	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.052	-0.054	15.862	0.017	0.017	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.024	0.021	15.313	0.022	0.022	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.802	-0.819	14.426	-0.243	-0.243	0.000	0.000	0.000	0.000
11	A	11	PHE	0	0.038	0.007	7.925	-0.047	-0.047	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.086	-0.041	8.688	0.085	0.085	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.059	0.026	7.639	-0.252	-0.252	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.885	0.936	3.500	2.749	3.245	0.003	-0.227	-0.272	0.001
15	A	15	ALA	0	0.016	0.017	8.773	0.077	0.077	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.018	-0.016	6.159	0.025	0.025	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.024	-0.028	7.360	-0.121	-0.121	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.028	0.024	7.690	0.044	0.044	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.020	0.022	10.661	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.782	-0.884	11.491	-0.049	-0.049	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.007	-0.008	7.805	0.014	0.014	0.000	0.000	0.000	0.000
22	A	22	PHE	0	-0.066	-0.043	9.962	0.028	0.028	0.000	0.000	0.000	0.000
23	A	23	ASN	0	0.038	0.015	11.389	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.887	-0.932	11.645	0.023	0.023	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.147	-0.085	5.221	0.199	0.255	-0.001	-0.001	-0.054	0.000
26	A	26	PHE	0	-0.076	-0.055	8.759	-0.061	-0.061	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.026	0.025	13.453	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.087	-0.051	16.115	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.917	-0.964	17.997	-0.049	-0.049	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.101	-0.049	16.779	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	31	SER	0	0.077	0.034	18.762	0.003	0.003	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.896	-0.960	16.499	-0.058	-0.058	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.982	-0.981	18.268	-0.032	-0.032	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.988	-0.985	21.210	-0.054	-0.054	0.000	0.000	0.000	0.000
35	A	35	PHE	0	-0.071	-0.051	18.294	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.862	-0.916	15.338	-0.094	-0.094	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.051	-0.041	11.859	-0.022	-0.022	0.000	0.000	0.000	0.000
38	A	38	VAL	0	0.033	0.017	11.706	0.017	0.017	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.036	-0.027	13.631	0.017	0.017	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.001	0.011	15.447	0.027	0.027	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.059	0.047	17.050	0.013	0.013	0.000	0.000	0.000	0.000
42	A	42	VAL	0	0.007	0.002	16.775	0.015	0.015	0.000	0.000	0.000	0.000
43	A	43	MET	0	-0.066	-0.042	19.067	0.006	0.006	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.039	-0.014	21.211	0.018	0.018	0.000	0.000	0.000	0.000
45	A	45	ALA	0	0.026	0.019	22.396	0.010	0.010	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.030	-0.026	20.341	0.005	0.005	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.026	0.042	25.015	0.008	0.008	0.000	0.000	0.000	0.000
48	A	48	HIS	1	0.719	0.830	25.463	0.119	0.119	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.005	0.019	20.959	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	50	PRO	0	-0.029	0.010	20.592	0.008	0.008	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.948	0.952	22.388	0.098	0.098	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.903	0.932	17.815	0.203	0.203	0.000	0.000	0.000	0.000
53	A	53	ASN	0	-0.053	-0.033	20.820	0.003	0.003	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.753	-0.831	22.409	-0.117	-0.117	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.021	-0.037	21.375	-0.024	-0.024	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.025	0.024	20.704	0.014	0.014	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.825	-0.901	21.169	-0.142	-0.142	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.006	0.004	19.847	0.011	0.011	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.065	0.030	20.762	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.825	-0.899	21.004	-0.098	-0.098	0.000	0.000	0.000	0.000
61	A	61	PHE	0	-0.007	-0.006	15.648	-0.016	-0.016	0.000	0.000	0.000	0.000
62	A	62	ARG	1	0.842	0.909	18.989	0.150	0.150	0.000	0.000	0.000	0.000
63	A	63	PHE	0	0.025	0.011	14.554	-0.038	-0.038	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.901	0.941	16.916	0.226	0.226	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.000	0.015	16.722	-0.047	-0.047	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.019	-0.016	13.146	0.032	0.032	0.000	0.000	0.000	0.000
67	A	67	ASN	0	-0.050	-0.038	13.965	0.057	0.057	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.080	0.047	16.061	-0.034	-0.034	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.731	-0.834	17.761	-0.133	-0.133	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.031	-0.030	19.916	0.006	0.006	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.877	0.937	20.018	0.091	0.091	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.943	0.966	14.173	0.168	0.168	0.000	0.000	0.000	0.000
73	A	73	VAL	0	0.052	0.013	14.858	0.002	0.002	0.000	0.000	0.000	0.000
74	A	74	HIS	0	-0.091	-0.058	12.872	-0.049	-0.049	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.050	-0.032	9.369	-0.132	-0.132	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.052	0.036	11.996	0.104	0.104	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.831	0.901	12.073	0.193	0.193	0.000	0.000	0.000	0.000
78	A	78	LEU	0	-0.001	0.020	11.975	0.025	0.025	0.000	0.000	0.000	0.000
79	A	79	SER	0	-0.009	-0.046	14.291	-0.017	-0.017	0.000	0.000	0.000	0.000
80	A	80	PRO	0	0.034	0.027	17.022	0.005	0.005	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.124	-0.062	19.144	0.003	0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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