FMO DATABASE

FMODB ID: 39QRL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-278877.005048
FMO2-HF: Nuclear repulsion	257568.358833
FMO2-HF: Total energy	-21308.646215
FMO2-MP2: Total energy	-21370.67778

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.
-0.758	2.166	0.007	-1.51	-1.421	0.002

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 : 0.018 / 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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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	-0.016	-0.011	3.156	-2.931	-0.264	0.009	-1.487	-1.189	0.002
4	A	88	GLN	0	-0.024	-0.022	4.115	1.500	1.598	-0.001	-0.006	-0.091	0.000
5	A	89	ILE	0	0.040	0.002	7.656	0.161	0.161	0.000	0.000	0.000	0.000
6	A	90	ASN	0	-0.082	-0.053	11.455	0.119	0.119	0.000	0.000	0.000	0.000
7	A	91	GLU	-1	-0.826	-0.892	6.713	-2.474	-2.474	0.000	0.000	0.000	0.000
8	A	92	GLN	0	-0.035	-0.028	10.984	0.013	0.013	0.000	0.000	0.000	0.000
9	A	93	VAL	0	-0.004	0.001	9.678	-0.107	-0.107	0.000	0.000	0.000	0.000
10	A	94	LEU	0	-0.043	-0.010	12.431	0.235	0.235	0.000	0.000	0.000	0.000
11	A	95	ALA	0	0.021	-0.003	14.155	-0.156	-0.156	0.000	0.000	0.000	0.000
12	A	96	CYS	0	-0.016	-0.003	16.345	0.114	0.114	0.000	0.000	0.000	0.000
13	A	97	TRP	0	0.062	0.042	18.911	0.000	0.000	0.000	0.000	0.000	0.000
14	A	98	SER	0	0.049	0.006	22.402	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	99	ASP	-1	-0.805	-0.873	25.193	-0.368	-0.368	0.000	0.000	0.000	0.000
16	A	100	CYS	0	-0.059	-0.035	23.087	0.012	0.012	0.000	0.000	0.000	0.000
17	A	101	ARG	1	0.889	0.952	22.507	0.327	0.327	0.000	0.000	0.000	0.000
18	A	102	PHE	0	0.013	-0.020	15.120	-0.019	-0.019	0.000	0.000	0.000	0.000
19	A	103	TYR	0	-0.043	-0.033	19.360	0.063	0.063	0.000	0.000	0.000	0.000
20	A	104	PRO	0	-0.001	-0.001	16.923	-0.088	-0.088	0.000	0.000	0.000	0.000
21	A	105	ALA	0	-0.010	0.006	15.909	0.074	0.074	0.000	0.000	0.000	0.000
22	A	106	LYS	1	0.884	0.945	14.608	0.469	0.469	0.000	0.000	0.000	0.000
23	A	107	VAL	0	0.050	0.029	9.917	0.105	0.105	0.000	0.000	0.000	0.000
24	A	108	THR	0	-0.044	-0.031	13.143	0.095	0.095	0.000	0.000	0.000	0.000
25	A	109	ALA	0	-0.019	-0.012	14.372	0.109	0.109	0.000	0.000	0.000	0.000
26	A	110	VAL	0	0.054	0.035	8.411	-0.107	-0.107	0.000	0.000	0.000	0.000
27	A	111	ASN	0	-0.067	-0.022	11.734	0.272	0.272	0.000	0.000	0.000	0.000
28	A	112	LYS	1	0.984	0.966	11.517	0.356	0.356	0.000	0.000	0.000	0.000
29	A	113	ASP	-1	-0.870	-0.903	12.278	-0.955	-0.955	0.000	0.000	0.000	0.000
30	A	114	GLY	0	0.014	0.014	9.507	0.025	0.025	0.000	0.000	0.000	0.000
31	A	115	THR	0	-0.084	-0.061	10.433	-0.186	-0.186	0.000	0.000	0.000	0.000
32	A	116	TYR	0	0.016	-0.015	6.564	-0.171	-0.171	0.000	0.000	0.000	0.000
33	A	117	THR	0	-0.029	-0.007	13.126	0.163	0.163	0.000	0.000	0.000	0.000
34	A	118	VAL	0	0.000	-0.002	13.762	-0.062	-0.062	0.000	0.000	0.000	0.000
35	A	119	LYS	1	0.920	0.967	16.438	0.554	0.554	0.000	0.000	0.000	0.000
36	A	120	PHE	0	0.008	0.011	18.975	-0.034	-0.034	0.000	0.000	0.000	0.000
37	A	121	TYR	0	0.031	-0.004	20.001	0.014	0.014	0.000	0.000	0.000	0.000
38	A	122	ASP	-1	-0.855	-0.919	22.991	-0.384	-0.384	0.000	0.000	0.000	0.000
39	A	123	GLY	0	-0.038	-0.020	24.051	0.025	0.025	0.000	0.000	0.000	0.000
40	A	124	VAL	0	0.003	0.004	23.787	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	125	VAL	0	-0.042	-0.027	20.255	-0.052	-0.052	0.000	0.000	0.000	0.000
42	A	126	GLN	0	-0.014	-0.013	18.246	0.101	0.101	0.000	0.000	0.000	0.000
43	A	127	THR	0	0.011	-0.004	16.564	-0.070	-0.070	0.000	0.000	0.000	0.000
44	A	128	VAL	0	-0.011	0.004	13.856	0.072	0.072	0.000	0.000	0.000	0.000
45	A	129	LYS	1	1.014	1.001	12.503	0.638	0.638	0.000	0.000	0.000	0.000
46	A	130	HIS	0	0.113	0.077	4.429	0.525	0.684	-0.001	-0.017	-0.141	0.000
47	A	131	ILE	0	-0.019	-0.019	8.778	-0.121	-0.121	0.000	0.000	0.000	0.000
48	A	132	HIS	0	-0.065	-0.030	10.099	0.176	0.176	0.000	0.000	0.000	0.000
49	A	133	VAL	0	-0.019	0.009	9.547	0.220	0.220	0.000	0.000	0.000	0.000
50	A	134	LYS	1	0.880	0.959	9.731	0.597	0.597	0.000	0.000	0.000	0.000
51	A	135	ALA	0	0.077	0.031	8.429	0.037	0.037	0.000	0.000	0.000	0.000
52	A	136	PHE	0	-0.003	-0.004	10.069	0.222	0.222	0.000	0.000	0.000	0.000
53	A	137	SER	0	-0.003	0.011	13.359	0.143	0.143	0.000	0.000	0.000	0.000

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