FMO DATABASE

FMODB ID: KGGR3

Calculation Name: 3PH0-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PH0

Chain ID: C

ChEMBL ID:

UniProt ID: Q1EHA4

Base Structure: X-ray

Registration Date: 2023-09-21

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

DOI:

Apendix: None

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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-260111.860337
FMO2-HF: Nuclear repulsion	238339.894313
FMO2-HF: Total energy	-21771.966025
FMO2-MP2: Total energy	-21830.813969

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(C:1:MET)

Summations of interaction energy for fragment #1(C: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.
-6.788	-1.894	4.922	-3.187	-6.625	0.012

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / 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

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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	C	3	VAL	0	0.099	0.032	3.578	-0.088	1.173	0.005	-0.679	-0.586	0.002
4	C	4	GLN	0	0.028	0.015	6.217	0.214	0.214	0.000	0.000	0.000	0.000
5	C	5	LEU	0	0.028	0.013	2.137	-1.223	-0.817	3.488	-1.069	-2.824	0.000
6	C	6	LYS	1	0.798	0.895	3.110	-2.910	-1.267	0.277	-0.620	-1.299	0.005
7	C	7	LYS	1	0.924	0.962	4.585	-1.213	-1.114	0.000	-0.021	-0.077	0.000
8	C	8	GLN	0	-0.028	-0.017	6.761	-0.118	-0.118	0.000	0.000	0.000	0.000
9	C	9	LEU	0	-0.010	-0.002	3.617	-0.571	-0.220	0.015	-0.093	-0.274	0.000
10	C	10	ALA	0	0.019	0.004	7.483	-0.152	-0.152	0.000	0.000	0.000	0.000
11	C	11	GLU	-1	-0.907	-0.942	9.980	0.082	0.082	0.000	0.000	0.000	0.000
12	C	12	LEU	0	-0.009	-0.006	10.104	-0.054	-0.054	0.000	0.000	0.000	0.000
13	C	13	ALA	0	-0.007	-0.003	11.332	-0.050	-0.050	0.000	0.000	0.000	0.000
14	C	14	LEU	0	-0.016	-0.017	13.079	-0.030	-0.030	0.000	0.000	0.000	0.000
15	C	15	ALA	0	0.005	0.011	15.270	-0.017	-0.017	0.000	0.000	0.000	0.000
16	C	16	GLY	0	0.023	0.014	15.784	-0.017	-0.017	0.000	0.000	0.000	0.000
17	C	17	THR	0	-0.042	-0.033	17.088	-0.013	-0.013	0.000	0.000	0.000	0.000
18	C	18	GLY	0	-0.009	0.010	19.379	-0.004	-0.004	0.000	0.000	0.000	0.000
19	C	19	HIS	0	-0.099	-0.063	19.914	-0.003	-0.003	0.000	0.000	0.000	0.000
20	C	20	HIS	0	0.029	0.019	21.656	-0.020	-0.020	0.000	0.000	0.000	0.000
21	C	21	CYS	0	-0.041	0.001	17.049	-0.017	-0.017	0.000	0.000	0.000	0.000
22	C	22	HIS	0	0.025	-0.012	17.193	-0.004	-0.004	0.000	0.000	0.000	0.000
23	C	23	GLN	0	-0.038	-0.018	17.253	0.020	0.020	0.000	0.000	0.000	0.000
24	C	24	GLU	-1	-0.838	-0.909	13.902	-0.213	-0.213	0.000	0.000	0.000	0.000
25	C	25	ALA	0	0.029	0.007	12.766	-0.001	-0.001	0.000	0.000	0.000	0.000
26	C	26	ALA	0	-0.007	-0.003	13.378	0.055	0.055	0.000	0.000	0.000	0.000
27	C	27	SER	0	-0.020	-0.021	12.172	0.014	0.014	0.000	0.000	0.000	0.000
28	C	28	ILE	0	-0.044	-0.019	7.858	-0.003	-0.003	0.000	0.000	0.000	0.000
29	C	29	ALA	0	-0.002	-0.005	9.596	0.196	0.196	0.000	0.000	0.000	0.000
30	C	30	ASP	-1	-0.813	-0.904	12.299	0.055	0.055	0.000	0.000	0.000	0.000
31	C	31	TRP	0	-0.045	-0.013	2.779	-1.506	-0.372	1.137	-0.705	-1.565	0.005
32	C	32	LEU	0	-0.034	-0.030	6.860	0.169	0.169	0.000	0.000	0.000	0.000
33	C	33	ALA	0	-0.020	-0.009	9.463	-0.030	-0.030	0.000	0.000	0.000	0.000
34	C	34	GLN	0	-0.070	-0.025	9.139	-0.101	-0.101	0.000	0.000	0.000	0.000
35	C	35	GLU	-1	-0.838	-0.912	6.955	0.656	0.656	0.000	0.000	0.000	0.000
36	C	36	GLU	-1	-0.879	-0.937	10.676	0.163	0.163	0.000	0.000	0.000	0.000
37	C	37	CYS	0	-0.076	-0.036	11.118	0.021	0.021	0.000	0.000	0.000	0.000
38	C	38	MET	0	-0.021	-0.014	8.890	0.119	0.119	0.000	0.000	0.000	0.000
39	C	39	ALA	0	0.030	0.030	12.270	-0.018	-0.018	0.000	0.000	0.000	0.000
40	C	40	GLU	-1	-0.835	-0.923	15.628	0.115	0.115	0.000	0.000	0.000	0.000
41	C	41	CYS	0	-0.038	-0.018	12.551	0.001	0.001	0.000	0.000	0.000	0.000
42	C	42	VAL	0	0.007	0.006	13.284	-0.022	-0.022	0.000	0.000	0.000	0.000
43	C	43	THR	0	-0.028	-0.022	14.825	-0.042	-0.042	0.000	0.000	0.000	0.000
44	C	44	LEU	0	-0.001	-0.001	17.167	-0.024	-0.024	0.000	0.000	0.000	0.000
45	C	45	ILE	0	-0.011	0.007	12.300	-0.020	-0.020	0.000	0.000	0.000	0.000
46	C	46	ARG	1	0.867	0.912	16.187	-0.094	-0.094	0.000	0.000	0.000	0.000
47	C	47	LEU	0	0.007	0.010	18.843	-0.020	-0.020	0.000	0.000	0.000	0.000
48	C	48	SER	0	0.052	0.031	19.334	-0.019	-0.019	0.000	0.000	0.000	0.000
49	C	49	SER	0	-0.006	-0.004	18.849	-0.018	-0.018	0.000	0.000	0.000	0.000
50	C	50	LEU	0	-0.028	-0.025	20.890	-0.012	-0.012	0.000	0.000	0.000	0.000
51	C	51	MET	0	-0.066	-0.035	24.196	-0.004	-0.004	0.000	0.000	0.000	0.000
52	C	52	ASN	0	-0.038	-0.015	22.892	-0.005	-0.005	0.000	0.000	0.000	0.000
53	C	53	GLN	0	-0.084	-0.015	23.290	-0.012	-0.012	0.000	0.000	0.000	0.000

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