FMO DATABASE

FMODB ID: YVY12

Calculation Name: 1H3L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1H3L

Chain ID: A

ChEMBL ID:

UniProt ID: Q7AKG9

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	75
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-498289.932017
FMO2-HF: Nuclear repulsion	467349.066645
FMO2-HF: Total energy	-30940.865372
FMO2-MP2: Total energy	-31031.55211

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:28:SER)

Summations of interaction energy for fragment #1(A:28: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.
-37.491	-39.717	21.594	-10.355	-9.014	-0.094

Interaction energy analysis for fragmet #1(A:28:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.016

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	30	ALA	0	0.067	0.032	3.285	-1.285	0.463	0.023	-0.789	-0.983	0.002
4	A	31	GLU	-1	-0.857	-0.900	1.695	-38.785	-43.415	21.566	-9.355	-7.581	-0.096
5	A	32	ARG	1	0.793	0.853	3.908	0.032	0.688	0.005	-0.211	-0.450	0.000
6	A	33	SER	0	-0.047	-0.021	5.771	0.312	0.312	0.000	0.000	0.000	0.000
7	A	34	ALA	0	0.096	0.044	7.143	0.248	0.248	0.000	0.000	0.000	0.000
8	A	35	ARG	1	0.779	0.885	7.809	0.846	0.846	0.000	0.000	0.000	0.000
9	A	36	PHE	0	0.023	0.011	9.568	0.266	0.266	0.000	0.000	0.000	0.000
10	A	37	GLU	-1	-0.863	-0.936	10.483	-0.899	-0.899	0.000	0.000	0.000	0.000
11	A	38	ARG	1	0.933	0.973	8.934	1.742	1.742	0.000	0.000	0.000	0.000
12	A	39	ASP	-1	-0.826	-0.921	12.111	-0.608	-0.608	0.000	0.000	0.000	0.000
13	A	40	ALA	0	-0.012	-0.011	15.188	0.083	0.083	0.000	0.000	0.000	0.000
14	A	41	LEU	0	-0.014	-0.001	16.471	0.055	0.055	0.000	0.000	0.000	0.000
15	A	42	GLU	-1	-0.932	-0.943	18.551	-0.307	-0.307	0.000	0.000	0.000	0.000
16	A	43	PHE	0	-0.031	-0.038	19.086	0.046	0.046	0.000	0.000	0.000	0.000
17	A	44	LEU	0	0.047	0.034	22.284	0.030	0.030	0.000	0.000	0.000	0.000
18	A	45	ASP	-1	-0.815	-0.903	23.936	-0.155	-0.155	0.000	0.000	0.000	0.000
19	A	46	GLN	0	-0.010	0.000	25.462	0.021	0.021	0.000	0.000	0.000	0.000
20	A	47	MET	0	-0.042	-0.012	23.208	0.030	0.030	0.000	0.000	0.000	0.000
21	A	48	TYR	0	0.030	0.018	27.247	0.016	0.016	0.000	0.000	0.000	0.000
22	A	49	SER	0	0.006	-0.017	29.583	0.018	0.018	0.000	0.000	0.000	0.000
23	A	50	ALA	0	-0.091	-0.035	30.133	0.012	0.012	0.000	0.000	0.000	0.000
24	A	51	ALA	0	0.038	0.007	30.431	0.012	0.012	0.000	0.000	0.000	0.000
25	A	52	LEU	0	0.020	0.018	32.448	0.010	0.010	0.000	0.000	0.000	0.000
26	A	53	ARG	1	0.902	0.951	35.440	0.088	0.088	0.000	0.000	0.000	0.000
27	A	54	MET	0	-0.075	-0.016	31.798	0.005	0.005	0.000	0.000	0.000	0.000
28	A	55	THR	0	0.020	-0.003	34.552	0.008	0.008	0.000	0.000	0.000	0.000
29	A	56	ARG	1	0.823	0.914	37.406	0.062	0.062	0.000	0.000	0.000	0.000
30	A	57	ASN	0	0.038	0.005	38.217	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	58	PRO	0	0.026	-0.001	35.856	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	59	ALA	0	0.024	0.029	34.494	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	60	ASP	-1	-0.784	-0.895	33.849	-0.078	-0.078	0.000	0.000	0.000	0.000
34	A	61	ALA	0	-0.074	-0.027	33.010	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	62	GLU	-1	-0.839	-0.913	29.068	-0.171	-0.171	0.000	0.000	0.000	0.000
36	A	63	ASP	-1	-0.865	-0.933	29.005	-0.117	-0.117	0.000	0.000	0.000	0.000
37	A	64	LEU	0	-0.043	-0.012	28.969	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	65	VAL	0	-0.022	-0.009	25.896	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	66	GLN	0	-0.028	-0.021	24.780	-0.028	-0.028	0.000	0.000	0.000	0.000
40	A	67	GLU	-1	-0.810	-0.892	24.022	-0.087	-0.087	0.000	0.000	0.000	0.000
41	A	68	THR	0	-0.046	-0.045	23.622	0.006	0.006	0.000	0.000	0.000	0.000
42	A	69	TYR	0	-0.027	-0.050	19.305	0.013	0.013	0.000	0.000	0.000	0.000
43	A	70	ALA	0	0.006	0.017	19.441	-0.025	-0.025	0.000	0.000	0.000	0.000
44	A	71	LYS	1	0.829	0.901	19.660	0.069	0.069	0.000	0.000	0.000	0.000
45	A	72	ALA	0	-0.014	-0.005	18.430	0.017	0.017	0.000	0.000	0.000	0.000
46	A	73	TYR	0	0.035	0.001	14.959	0.007	0.007	0.000	0.000	0.000	0.000
47	A	74	ALA	0	-0.020	0.003	14.936	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	75	SER	0	-0.033	-0.021	16.920	0.067	0.067	0.000	0.000	0.000	0.000
49	A	76	PHE	0	0.016	0.018	7.484	0.024	0.024	0.000	0.000	0.000	0.000
50	A	77	HIS	0	0.012	0.005	11.913	0.045	0.045	0.000	0.000	0.000	0.000
51	A	78	GLN	0	-0.041	-0.018	12.908	0.122	0.122	0.000	0.000	0.000	0.000
52	A	79	PHE	0	0.007	0.027	12.716	0.015	0.015	0.000	0.000	0.000	0.000
53	A	80	ARG	1	0.824	0.889	13.238	-0.256	-0.256	0.000	0.000	0.000	0.000
54	A	81	GLU	-1	-0.819	-0.878	9.965	0.851	0.851	0.000	0.000	0.000	0.000
55	A	82	GLY	0	0.039	0.020	13.429	-0.078	-0.078	0.000	0.000	0.000	0.000
56	A	83	THR	0	-0.046	-0.018	16.254	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	84	ASN	0	0.036	0.009	17.761	-0.047	-0.047	0.000	0.000	0.000	0.000
58	A	85	LEU	0	0.060	0.038	15.443	0.020	0.020	0.000	0.000	0.000	0.000
59	A	86	LYS	1	0.918	0.973	18.934	0.161	0.161	0.000	0.000	0.000	0.000
60	A	87	ALA	0	0.000	-0.004	22.438	0.006	0.006	0.000	0.000	0.000	0.000
61	A	88	TRP	0	-0.034	-0.018	17.013	0.002	0.002	0.000	0.000	0.000	0.000
62	A	89	LEU	0	0.055	0.025	19.289	0.008	0.008	0.000	0.000	0.000	0.000
63	A	90	TYR	0	0.021	0.001	22.454	0.004	0.004	0.000	0.000	0.000	0.000
64	A	91	ARG	1	0.936	0.987	24.422	0.000	0.000	0.000	0.000	0.000	0.000
65	A	92	ILE	0	0.004	0.016	20.503	0.010	0.010	0.000	0.000	0.000	0.000
66	A	93	LEU	0	0.037	0.032	25.082	0.004	0.004	0.000	0.000	0.000	0.000
67	A	94	THR	0	-0.037	-0.044	27.665	0.009	0.009	0.000	0.000	0.000	0.000
68	A	95	ASN	0	-0.020	-0.006	27.384	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	96	THR	0	0.055	0.030	27.186	0.007	0.007	0.000	0.000	0.000	0.000
70	A	97	PHE	0	-0.035	-0.023	29.877	0.003	0.003	0.000	0.000	0.000	0.000
71	A	98	ILE	0	-0.065	-0.040	32.822	0.003	0.003	0.000	0.000	0.000	0.000
72	A	99	ASN	0	-0.110	-0.064	31.660	0.010	0.010	0.000	0.000	0.000	0.000
73	A	100	SER	0	-0.013	-0.002	30.377	0.005	0.005	0.000	0.000	0.000	0.000
74	A	101	TYR	0	-0.031	0.004	33.544	0.001	0.001	0.000	0.000	0.000	0.000
75	A	102	ARG	1	0.943	0.977	35.759	0.037	0.037	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:28:SER)