FMO DATABASE

FMODB ID: LZJ49

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

Total energy (hartree)

FMO2-HF: Electronic energy	-278822.723585
FMO2-HF: Nuclear repulsion	257513.991969
FMO2-HF: Total energy	-21308.731616
FMO2-MP2: Total energy	-21370.766003

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.
2.518	4.655	-0.02	-1	-1.118	0.006

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 : 0.013 / q_NPA : 0.007

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	-0.012	0.000	3.833	0.095	2.019	-0.019	-0.971	-0.935	0.006
4	A	88	GLN	0	-0.016	-0.030	5.156	1.135	1.135	0.000	0.000	0.000	0.000
5	A	89	ILE	0	-0.008	-0.011	8.385	0.154	0.154	0.000	0.000	0.000	0.000
6	A	90	ASN	0	-0.043	-0.028	12.226	0.203	0.203	0.000	0.000	0.000	0.000
7	A	91	GLU	-1	-0.815	-0.883	6.958	-2.133	-2.133	0.000	0.000	0.000	0.000
8	A	92	GLN	0	-0.040	-0.035	11.239	0.055	0.055	0.000	0.000	0.000	0.000
9	A	93	VAL	0	0.005	0.009	9.511	-0.072	-0.072	0.000	0.000	0.000	0.000
10	A	94	LEU	0	-0.040	-0.011	12.209	0.189	0.189	0.000	0.000	0.000	0.000
11	A	95	ALA	0	0.031	0.002	14.257	-0.156	-0.156	0.000	0.000	0.000	0.000
12	A	96	CYS	0	-0.028	-0.006	16.312	0.124	0.124	0.000	0.000	0.000	0.000
13	A	97	TRP	0	0.050	0.027	19.047	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	98	SER	0	0.031	-0.003	22.479	0.002	0.002	0.000	0.000	0.000	0.000
15	A	99	ASP	-1	-0.778	-0.855	25.414	-0.353	-0.353	0.000	0.000	0.000	0.000
16	A	100	CYS	0	-0.065	-0.030	23.520	0.019	0.019	0.000	0.000	0.000	0.000
17	A	101	ARG	1	0.881	0.944	22.914	0.301	0.301	0.000	0.000	0.000	0.000
18	A	102	PHE	0	0.028	-0.016	15.436	-0.031	-0.031	0.000	0.000	0.000	0.000
19	A	103	TYR	0	-0.025	-0.028	19.349	0.062	0.062	0.000	0.000	0.000	0.000
20	A	104	PRO	0	-0.017	-0.010	16.657	-0.086	-0.086	0.000	0.000	0.000	0.000
21	A	105	ALA	0	0.003	0.011	15.908	0.073	0.073	0.000	0.000	0.000	0.000
22	A	106	LYS	1	0.861	0.936	14.658	0.472	0.472	0.000	0.000	0.000	0.000
23	A	107	VAL	0	0.029	0.017	10.071	0.075	0.075	0.000	0.000	0.000	0.000
24	A	108	THR	0	-0.042	-0.047	13.474	0.127	0.127	0.000	0.000	0.000	0.000
25	A	109	ALA	0	-0.027	-0.011	14.732	0.117	0.117	0.000	0.000	0.000	0.000
26	A	110	VAL	0	0.051	0.025	8.265	-0.114	-0.114	0.000	0.000	0.000	0.000
27	A	111	ASN	0	-0.079	-0.033	11.384	0.259	0.259	0.000	0.000	0.000	0.000
28	A	112	LYS	1	0.976	0.961	10.846	0.545	0.545	0.000	0.000	0.000	0.000
29	A	113	ASP	-1	-0.837	-0.892	12.172	-1.146	-1.146	0.000	0.000	0.000	0.000
30	A	114	GLY	0	0.005	0.015	9.009	0.038	0.038	0.000	0.000	0.000	0.000
31	A	115	THR	0	-0.096	-0.065	10.011	-0.135	-0.135	0.000	0.000	0.000	0.000
32	A	116	TYR	0	0.038	0.005	6.199	-0.264	-0.264	0.000	0.000	0.000	0.000
33	A	117	THR	0	-0.035	-0.012	12.749	0.153	0.153	0.000	0.000	0.000	0.000
34	A	118	VAL	0	-0.002	-0.003	13.885	-0.073	-0.073	0.000	0.000	0.000	0.000
35	A	119	LYS	1	0.871	0.929	16.609	0.562	0.562	0.000	0.000	0.000	0.000
36	A	120	PHE	0	0.004	0.016	18.891	-0.033	-0.033	0.000	0.000	0.000	0.000
37	A	121	TYR	0	0.015	-0.008	19.551	0.017	0.017	0.000	0.000	0.000	0.000
38	A	122	ASP	-1	-0.837	-0.908	23.144	-0.377	-0.377	0.000	0.000	0.000	0.000
39	A	123	GLY	0	-0.010	0.005	24.334	0.024	0.024	0.000	0.000	0.000	0.000
40	A	124	VAL	0	0.008	0.009	23.899	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	125	VAL	0	-0.047	-0.036	20.488	-0.042	-0.042	0.000	0.000	0.000	0.000
42	A	126	GLN	0	-0.002	0.000	18.147	0.103	0.103	0.000	0.000	0.000	0.000
43	A	127	THR	0	0.023	0.006	16.004	-0.064	-0.064	0.000	0.000	0.000	0.000
44	A	128	VAL	0	-0.002	0.011	13.972	0.092	0.092	0.000	0.000	0.000	0.000
45	A	129	LYS	1	1.016	0.997	12.047	0.719	0.719	0.000	0.000	0.000	0.000
46	A	130	HIS	0	0.100	0.067	4.328	0.590	0.803	-0.001	-0.029	-0.183	0.000
47	A	131	ILE	0	-0.022	-0.016	8.911	-0.028	-0.028	0.000	0.000	0.000	0.000
48	A	132	HIS	0	-0.056	-0.030	10.386	0.211	0.211	0.000	0.000	0.000	0.000
49	A	133	VAL	0	-0.031	-0.002	9.627	0.214	0.214	0.000	0.000	0.000	0.000
50	A	134	LYS	1	0.884	0.965	9.797	0.583	0.583	0.000	0.000	0.000	0.000
51	A	135	ALA	0	0.083	0.037	8.648	0.030	0.030	0.000	0.000	0.000	0.000
52	A	136	PHE	0	-0.017	-0.012	10.139	0.182	0.182	0.000	0.000	0.000	0.000
53	A	137	SER	0	0.005	0.014	13.275	0.128	0.128	0.000	0.000	0.000	0.000

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