FMO DATABASE

FMODB ID: R81K8

Calculation Name: 3PH0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PH0

Chain ID: A

ChEMBL ID:

UniProt ID: Q1EHA4

Base Structure: X-ray

Registration Date: 2023-09-20

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	65
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-345457.867441
FMO2-HF: Nuclear repulsion	319581.53191
FMO2-HF: Total energy	-25876.33553
FMO2-MP2: Total energy	-25951.887767

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:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-1.109	0.489	-0.011	-0.802	-0.784	0.001

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.011

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	3	THR	0	0.013	0.010	3.703	-0.277	1.321	-0.011	-0.802	-0.784	0.001
4	A	4	ASN	0	0.044	0.002	6.116	0.301	0.301	0.000	0.000	0.000	0.000
5	A	5	LEU	0	0.052	0.020	9.083	0.093	0.093	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.817	-0.918	6.114	-1.681	-1.681	0.000	0.000	0.000	0.000
7	A	7	THR	0	-0.032	0.004	8.999	0.168	0.168	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.841	0.931	11.678	0.284	0.284	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.005	-0.007	12.587	0.040	0.040	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.026	-0.038	11.849	0.000	0.000	0.000	0.000	0.000	0.000
11	A	11	GLY	0	-0.012	-0.004	14.517	0.040	0.040	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.034	-0.011	15.945	0.027	0.027	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.823	-0.926	17.659	-0.112	-0.112	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.006	-0.002	19.341	-0.027	-0.027	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.023	-0.015	21.816	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	16	PHE	0	0.041	0.029	16.089	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.040	0.016	18.486	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.925	0.958	19.614	0.118	0.118	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.936	-0.959	21.893	-0.164	-0.164	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.009	0.010	16.380	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	21	HIS	0	-0.005	-0.007	20.689	0.002	0.002	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.037	0.017	21.527	0.006	0.006	0.000	0.000	0.000	0.000
23	A	23	GLN	0	-0.003	-0.013	22.562	0.006	0.006	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.009	0.013	17.709	0.005	0.005	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.015	0.007	22.398	0.005	0.005	0.000	0.000	0.000	0.000
26	A	26	GLN	0	-0.050	-0.010	25.190	0.010	0.010	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.020	0.009	24.179	0.009	0.009	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.003	0.007	23.683	0.012	0.012	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.002	-0.008	26.092	0.010	0.010	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.957	-0.985	28.950	-0.125	-0.125	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.003	-0.003	25.980	0.012	0.012	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.971	0.974	26.866	0.193	0.193	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.896	0.960	30.609	0.127	0.127	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.907	0.975	28.564	0.147	0.147	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.024	-0.006	28.853	0.007	0.007	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.010	0.005	33.386	0.005	0.005	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.864	0.911	35.825	0.104	0.104	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.019	0.030	33.073	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.012	0.019	33.945	0.003	0.003	0.000	0.000	0.000	0.000
40	A	40	THR	0	0.005	-0.027	31.763	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	41	GLN	0	0.003	-0.019	30.790	0.000	0.000	0.000	0.000	0.000	0.000
42	A	42	GLN	0	0.049	0.028	33.801	0.006	0.006	0.000	0.000	0.000	0.000
43	A	43	GLN	0	0.045	0.038	32.843	0.000	0.000	0.000	0.000	0.000	0.000
44	A	44	TYR	0	-0.042	-0.014	31.862	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	45	GLN	0	0.036	0.005	26.973	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	46	GLN	0	0.028	0.029	27.291	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	47	TRP	0	0.048	0.011	26.395	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	48	GLN	0	-0.004	-0.004	26.027	0.005	0.005	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.004	0.002	22.307	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.931	-0.968	22.231	-0.200	-0.200	0.000	0.000	0.000	0.000
51	A	51	ALA	0	-0.043	-0.035	22.548	-0.016	-0.016	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.880	-0.933	20.835	-0.245	-0.245	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.042	-0.016	18.175	-0.034	-0.034	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.019	-0.013	17.871	-0.040	-0.040	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.940	-0.968	19.242	-0.264	-0.264	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.017	0.005	15.645	-0.026	-0.026	0.000	0.000	0.000	0.000
57	A	57	GLY	0	-0.012	-0.012	14.629	-0.063	-0.063	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.001	-0.017	15.499	-0.035	-0.035	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.007	-0.004	16.278	0.008	0.008	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.028	-0.016	10.207	-0.027	-0.027	0.000	0.000	0.000	0.000
61	A	61	ILE	0	0.008	0.011	12.967	-0.038	-0.038	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.985	-0.998	14.644	-0.296	-0.296	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.882	0.932	12.690	0.585	0.585	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.038	-0.008	9.006	-0.059	-0.059	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.916	1.000	11.981	0.367	0.367	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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