FMO DATABASE

FMODB ID: 2J3QR

Calculation Name: 3HFN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HFN

Chain ID: A

ChEMBL ID:

UniProt ID: Q8YVD1

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	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	63
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-347429.074668
FMO2-HF: Nuclear repulsion	322854.962504
FMO2-HF: Total energy	-24574.112165
FMO2-MP2: Total energy	-24645.861026

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:8:SER)

Summations of interaction energy for fragment #1(A:8: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.
-0.948	2.114	1.091	-1.436	-2.718	-0.003

Interaction energy analysis for fragmet #1(A:8:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.071 / q_NPA : 0.021

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	A	10	PRO	0	-0.019	-0.015	3.044	-2.202	-0.622	0.079	-0.635	-1.024	0.001
4	A	11	SER	0	0.078	0.045	2.998	-1.748	-0.861	0.104	-0.332	-0.659	-0.003
5	A	12	ILE	0	0.046	0.022	2.521	0.182	0.777	0.908	-0.469	-1.035	-0.001
6	A	13	ARG	1	0.938	0.954	5.490	0.917	0.917	0.000	0.000	0.000	0.000
7	A	14	GLN	0	0.006	0.015	7.924	0.163	0.163	0.000	0.000	0.000	0.000
8	A	15	LEU	0	0.056	0.023	7.192	0.177	0.177	0.000	0.000	0.000	0.000
9	A	16	GLN	0	0.005	-0.002	8.778	0.237	0.237	0.000	0.000	0.000	0.000
10	A	17	ASN	0	-0.030	-0.024	11.349	0.116	0.116	0.000	0.000	0.000	0.000
11	A	18	LEU	0	0.011	0.012	13.018	0.078	0.078	0.000	0.000	0.000	0.000
12	A	19	ILE	0	0.013	0.005	12.981	0.056	0.056	0.000	0.000	0.000	0.000
13	A	20	LYS	1	0.829	0.927	14.530	0.494	0.494	0.000	0.000	0.000	0.000
14	A	21	GLN	0	0.023	0.015	17.605	0.030	0.030	0.000	0.000	0.000	0.000
15	A	22	ALA	0	0.003	0.013	19.237	0.028	0.028	0.000	0.000	0.000	0.000
16	A	23	ALA	0	0.006	0.004	17.675	0.030	0.030	0.000	0.000	0.000	0.000
17	A	24	PRO	0	-0.047	-0.018	18.903	-0.023	-0.023	0.000	0.000	0.000	0.000
18	A	25	VAL	0	-0.005	-0.014	15.033	0.003	0.003	0.000	0.000	0.000	0.000
19	A	26	GLU	-1	-0.813	-0.891	17.938	-0.062	-0.062	0.000	0.000	0.000	0.000
20	A	27	ILE	0	-0.010	-0.011	13.447	-0.017	-0.017	0.000	0.000	0.000	0.000
21	A	28	LYS	1	0.897	0.972	16.539	0.047	0.047	0.000	0.000	0.000	0.000
22	A	29	LEU	0	0.046	0.012	16.649	0.003	0.003	0.000	0.000	0.000	0.000
23	A	30	VAL	0	-0.025	-0.028	16.528	0.023	0.023	0.000	0.000	0.000	0.000
24	A	31	THR	0	-0.021	-0.032	19.180	0.014	0.014	0.000	0.000	0.000	0.000
25	A	32	GLY	0	-0.014	0.003	21.506	0.007	0.007	0.000	0.000	0.000	0.000
26	A	33	ASP	-1	-0.867	-0.913	21.440	-0.100	-0.100	0.000	0.000	0.000	0.000
27	A	34	ALA	0	0.007	-0.002	20.707	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	35	ILE	0	0.018	0.018	19.376	0.000	0.000	0.000	0.000	0.000	0.000
29	A	36	THR	0	-0.018	-0.017	20.053	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	37	GLY	0	0.054	0.024	21.121	0.007	0.007	0.000	0.000	0.000	0.000
31	A	38	ARG	1	0.877	0.948	19.753	0.190	0.190	0.000	0.000	0.000	0.000
32	A	39	VAL	0	0.010	0.002	13.549	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	40	LEU	0	0.002	0.005	16.970	0.012	0.012	0.000	0.000	0.000	0.000
34	A	41	TRP	0	0.010	0.001	14.804	-0.015	-0.015	0.000	0.000	0.000	0.000
35	A	42	GLN	0	-0.008	-0.002	7.702	-0.124	-0.124	0.000	0.000	0.000	0.000
36	A	43	ASP	-1	-0.754	-0.840	10.390	-0.858	-0.858	0.000	0.000	0.000	0.000
37	A	44	PRO	0	-0.012	-0.024	7.710	-0.119	-0.119	0.000	0.000	0.000	0.000
38	A	45	THR	0	-0.047	-0.016	8.796	0.086	0.086	0.000	0.000	0.000	0.000
39	A	46	CYS	0	-0.004	0.006	11.480	0.138	0.138	0.000	0.000	0.000	0.000
40	A	47	VAL	0	-0.021	-0.019	10.758	-0.199	-0.199	0.000	0.000	0.000	0.000
41	A	48	CYS	0	-0.031	0.009	13.342	0.086	0.086	0.000	0.000	0.000	0.000
42	A	49	ILE	0	-0.009	0.000	15.956	-0.025	-0.025	0.000	0.000	0.000	0.000
43	A	50	ALA	0	0.016	0.007	19.003	0.014	0.014	0.000	0.000	0.000	0.000
44	A	51	ASP	-1	-0.848	-0.956	22.575	-0.183	-0.183	0.000	0.000	0.000	0.000
45	A	52	GLU	-1	-0.804	-0.869	25.230	-0.114	-0.114	0.000	0.000	0.000	0.000
46	A	53	ASN	0	-0.074	-0.035	28.772	0.006	0.006	0.000	0.000	0.000	0.000
47	A	54	SER	0	-0.089	-0.061	29.235	0.001	0.001	0.000	0.000	0.000	0.000
48	A	55	ARG	1	0.885	0.941	26.965	0.122	0.122	0.000	0.000	0.000	0.000
49	A	56	GLN	0	0.031	0.008	22.436	-0.025	-0.025	0.000	0.000	0.000	0.000
50	A	57	THR	0	-0.004	0.007	20.190	0.007	0.007	0.000	0.000	0.000	0.000
51	A	58	THR	0	0.012	0.002	17.985	-0.024	-0.024	0.000	0.000	0.000	0.000
52	A	59	ILE	0	0.019	0.015	14.922	0.028	0.028	0.000	0.000	0.000	0.000
53	A	60	TRP	0	0.069	0.015	14.401	-0.075	-0.075	0.000	0.000	0.000	0.000
54	A	61	LYS	1	0.806	0.862	6.676	1.341	1.341	0.000	0.000	0.000	0.000
55	A	62	GLN	0	-0.027	-0.018	11.381	0.070	0.070	0.000	0.000	0.000	0.000
56	A	63	ALA	0	0.045	0.039	13.003	0.053	0.053	0.000	0.000	0.000	0.000
57	A	64	ILE	0	-0.062	-0.018	11.021	0.001	0.001	0.000	0.000	0.000	0.000
58	A	65	ALA	0	-0.004	0.004	13.332	0.049	0.049	0.000	0.000	0.000	0.000
59	A	66	TYR	0	-0.043	-0.029	13.161	0.054	0.054	0.000	0.000	0.000	0.000
60	A	67	LEU	0	-0.013	-0.005	10.837	-0.047	-0.047	0.000	0.000	0.000	0.000
61	A	68	GLN	0	-0.041	-0.027	13.774	0.037	0.037	0.000	0.000	0.000	0.000
62	A	69	PRO	0	-0.003	-0.009	14.811	-0.017	-0.017	0.000	0.000	0.000	0.000
63	A	70	LYS	1	0.831	0.918	17.704	0.147	0.147	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:SER)