FMO DATABASE

FMODB ID: JL3G9

Calculation Name: 3P8D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P8D

Chain ID: A

ChEMBL ID:

UniProt ID: Q9BVI0

Base Structure: X-ray

Registration Date: 2023-06-21

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

DOI:

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	53
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-278810.769712
FMO2-HF: Nuclear repulsion	257502.254848
FMO2-HF: Total energy	-21308.514865
FMO2-MP2: Total energy	-21370.517829

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:85:SER)

Summations of interaction energy for fragment #1(A:85: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.
-2.412	-0.525	-0.012	-0.868	-1.006	0.001

Interaction energy analysis for fragmet #1(A:85:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.034

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	87	PHE	0	-0.047	-0.027	3.388	-2.990	-1.315	-0.010	-0.853	-0.812	0.001
4	A	88	GLN	0	0.021	0.001	4.268	1.140	1.218	-0.001	-0.003	-0.074	0.000
5	A	89	ILE	0	0.038	0.002	7.825	0.188	0.188	0.000	0.000	0.000	0.000
6	A	90	ASN	0	-0.112	-0.073	11.615	0.042	0.042	0.000	0.000	0.000	0.000
7	A	91	GLU	-1	-0.845	-0.898	7.131	-2.431	-2.431	0.000	0.000	0.000	0.000
8	A	92	GLN	0	-0.028	-0.026	11.314	0.053	0.053	0.000	0.000	0.000	0.000
9	A	93	VAL	0	-0.012	0.000	10.036	-0.130	-0.130	0.000	0.000	0.000	0.000
10	A	94	LEU	0	-0.028	-0.005	12.676	0.190	0.190	0.000	0.000	0.000	0.000
11	A	95	ALA	0	0.028	0.000	14.230	-0.079	-0.079	0.000	0.000	0.000	0.000
12	A	96	CYS	0	-0.013	-0.003	16.430	0.059	0.059	0.000	0.000	0.000	0.000
13	A	97	TRP	0	0.066	0.044	18.997	0.009	0.009	0.000	0.000	0.000	0.000
14	A	98	SER	0	0.043	0.002	22.494	0.008	0.008	0.000	0.000	0.000	0.000
15	A	99	ASP	-1	-0.841	-0.883	25.257	-0.240	-0.240	0.000	0.000	0.000	0.000
16	A	100	CYS	0	-0.061	-0.046	23.170	0.004	0.004	0.000	0.000	0.000	0.000
17	A	101	ARG	1	0.936	0.991	22.575	0.214	0.214	0.000	0.000	0.000	0.000
18	A	102	PHE	0	-0.018	-0.025	15.400	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	103	TYR	0	-0.067	-0.063	19.315	0.028	0.028	0.000	0.000	0.000	0.000
20	A	104	PRO	0	-0.002	0.000	17.114	-0.053	-0.053	0.000	0.000	0.000	0.000
21	A	105	ALA	0	-0.002	0.011	16.298	0.066	0.066	0.000	0.000	0.000	0.000
22	A	106	LYS	1	0.927	0.971	14.989	0.331	0.331	0.000	0.000	0.000	0.000
23	A	107	VAL	0	0.048	0.029	10.281	0.129	0.129	0.000	0.000	0.000	0.000
24	A	108	THR	0	-0.116	-0.066	13.452	0.067	0.067	0.000	0.000	0.000	0.000
25	A	109	ALA	0	0.017	0.001	14.482	0.064	0.064	0.000	0.000	0.000	0.000
26	A	110	VAL	0	0.060	0.040	8.420	-0.058	-0.058	0.000	0.000	0.000	0.000
27	A	111	ASN	0	-0.050	-0.016	11.711	0.139	0.139	0.000	0.000	0.000	0.000
28	A	112	LYS	1	0.977	0.962	11.630	0.014	0.014	0.000	0.000	0.000	0.000
29	A	113	ASP	-1	-0.879	-0.907	12.751	-0.097	-0.097	0.000	0.000	0.000	0.000
30	A	114	GLY	0	0.015	0.012	10.277	0.044	0.044	0.000	0.000	0.000	0.000
31	A	115	THR	0	-0.082	-0.055	11.107	-0.123	-0.123	0.000	0.000	0.000	0.000
32	A	116	TYR	0	0.016	-0.018	6.643	-0.252	-0.252	0.000	0.000	0.000	0.000
33	A	117	THR	0	0.022	0.016	13.150	0.098	0.098	0.000	0.000	0.000	0.000
34	A	118	VAL	0	-0.011	-0.003	14.170	-0.073	-0.073	0.000	0.000	0.000	0.000
35	A	119	LYS	1	0.937	0.969	16.777	0.378	0.378	0.000	0.000	0.000	0.000
36	A	120	PHE	0	0.013	0.014	19.362	-0.043	-0.043	0.000	0.000	0.000	0.000
37	A	121	TYR	0	0.025	-0.010	20.554	0.007	0.007	0.000	0.000	0.000	0.000
38	A	122	ASP	-1	-0.863	-0.926	23.407	-0.250	-0.250	0.000	0.000	0.000	0.000
39	A	123	GLY	0	-0.044	-0.023	24.416	0.020	0.020	0.000	0.000	0.000	0.000
40	A	124	VAL	0	0.001	0.008	24.068	0.004	0.004	0.000	0.000	0.000	0.000
41	A	125	VAL	0	-0.036	-0.021	20.604	-0.041	-0.041	0.000	0.000	0.000	0.000
42	A	126	GLN	0	-0.025	-0.019	18.466	0.065	0.065	0.000	0.000	0.000	0.000
43	A	127	THR	0	0.004	0.000	16.961	-0.048	-0.048	0.000	0.000	0.000	0.000
44	A	128	VAL	0	-0.024	-0.007	13.659	0.042	0.042	0.000	0.000	0.000	0.000
45	A	129	LYS	1	1.011	0.999	12.766	0.114	0.114	0.000	0.000	0.000	0.000
46	A	130	HIS	0	0.125	0.085	4.400	0.249	0.383	-0.001	-0.012	-0.120	0.000
47	A	131	ILE	0	-0.016	-0.018	8.920	-0.174	-0.174	0.000	0.000	0.000	0.000
48	A	132	HIS	0	-0.067	-0.031	10.190	0.023	0.023	0.000	0.000	0.000	0.000
49	A	133	VAL	0	-0.017	0.010	9.582	0.079	0.079	0.000	0.000	0.000	0.000
50	A	134	LYS	1	0.916	0.972	9.784	0.488	0.488	0.000	0.000	0.000	0.000
51	A	135	ALA	0	0.070	0.025	8.436	0.021	0.021	0.000	0.000	0.000	0.000
52	A	136	PHE	0	-0.005	-0.004	10.010	0.210	0.210	0.000	0.000	0.000	0.000
53	A	137	SER	0	-0.015	0.007	13.266	0.096	0.096	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:85:SER)