FMO DATABASE

FMODB ID: G66R1

Calculation Name: 4PH1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PH1

Chain ID: A

ChEMBL ID:

UniProt ID: A7KWZ1

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:

Apendix: None

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	78
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-469095.651324
FMO2-HF: Nuclear repulsion	439612.706065
FMO2-HF: Total energy	-29482.945259
FMO2-MP2: Total energy	-29569.371741

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:129:SER)

Summations of interaction energy for fragment #1(A:129: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.
0.456	1.727	-0.015	-0.591	-0.664	0.001

Interaction energy analysis for fragmet #1(A:129: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 : -0.014

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	131	GLN	0	0.026	0.017	3.863	0.479	1.750	-0.015	-0.591	-0.664	0.001
4	A	132	PRO	0	0.029	0.010	6.333	0.154	0.154	0.000	0.000	0.000	0.000
5	A	133	TRP	0	0.079	0.030	8.667	-0.019	-0.019	0.000	0.000	0.000	0.000
6	A	134	SER	0	-0.041	-0.019	7.858	-0.065	-0.065	0.000	0.000	0.000	0.000
7	A	135	THR	0	-0.030	-0.008	7.330	-0.031	-0.031	0.000	0.000	0.000	0.000
8	A	136	ILE	0	-0.027	-0.005	9.982	-0.051	-0.051	0.000	0.000	0.000	0.000
9	A	137	VAL	0	0.021	0.016	13.100	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	138	GLN	0	-0.030	-0.030	15.725	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	139	GLY	0	0.020	0.002	19.492	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	140	PRO	0	-0.010	-0.028	20.697	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	141	ALA	0	0.000	-0.005	23.561	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	142	GLU	-1	-0.804	-0.860	20.434	0.097	0.097	0.000	0.000	0.000	0.000
15	A	143	SER	0	0.002	-0.033	24.429	0.002	0.002	0.000	0.000	0.000	0.000
16	A	144	TYR	0	0.054	-0.024	23.509	0.003	0.003	0.000	0.000	0.000	0.000
17	A	145	VAL	0	0.018	-0.002	24.290	0.005	0.005	0.000	0.000	0.000	0.000
18	A	146	GLU	-1	-0.845	-0.878	24.002	0.060	0.060	0.000	0.000	0.000	0.000
19	A	147	PHE	0	-0.036	0.000	17.321	0.005	0.005	0.000	0.000	0.000	0.000
20	A	148	VAL	0	0.024	0.003	19.916	0.010	0.010	0.000	0.000	0.000	0.000
21	A	149	ASN	0	-0.012	0.003	21.345	0.002	0.002	0.000	0.000	0.000	0.000
22	A	150	ARG	1	0.852	0.910	15.477	-0.128	-0.128	0.000	0.000	0.000	0.000
23	A	151	LEU	0	-0.003	0.008	15.503	0.017	0.017	0.000	0.000	0.000	0.000
24	A	152	GLN	0	-0.040	-0.031	17.243	0.000	0.000	0.000	0.000	0.000	0.000
25	A	153	ILE	0	0.021	0.011	18.284	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	154	SER	0	0.026	0.023	13.178	0.011	0.011	0.000	0.000	0.000	0.000
27	A	155	LEU	0	0.006	-0.009	13.911	0.006	0.006	0.000	0.000	0.000	0.000
28	A	156	ALA	0	-0.095	-0.043	15.676	-0.014	-0.014	0.000	0.000	0.000	0.000
29	A	157	ASP	-1	-0.887	-0.932	15.574	0.111	0.111	0.000	0.000	0.000	0.000
30	A	158	ASN	0	-0.145	-0.080	11.012	0.055	0.055	0.000	0.000	0.000	0.000
31	A	159	LEU	0	0.015	-0.004	12.048	-0.023	-0.023	0.000	0.000	0.000	0.000
32	A	160	PRO	0	-0.022	0.001	10.603	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	161	ASP	-1	-0.915	-0.965	12.226	-0.141	-0.141	0.000	0.000	0.000	0.000
34	A	162	GLY	0	-0.010	-0.007	15.198	0.017	0.017	0.000	0.000	0.000	0.000
35	A	163	VAL	0	-0.038	-0.017	14.596	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	164	PRO	0	0.010	0.000	16.711	0.012	0.012	0.000	0.000	0.000	0.000
37	A	165	LYS	1	0.908	0.959	18.313	-0.062	-0.062	0.000	0.000	0.000	0.000
38	A	166	GLU	-1	-0.882	-0.946	19.419	0.039	0.039	0.000	0.000	0.000	0.000
39	A	167	PRO	0	0.017	0.001	19.236	0.006	0.006	0.000	0.000	0.000	0.000
40	A	168	ILE	0	0.003	0.009	13.979	0.007	0.007	0.000	0.000	0.000	0.000
41	A	169	ILE	0	0.016	0.010	17.386	0.016	0.016	0.000	0.000	0.000	0.000
42	A	170	ASP	-1	-0.807	-0.884	19.707	0.053	0.053	0.000	0.000	0.000	0.000
43	A	171	SER	0	-0.037	0.000	17.762	0.006	0.006	0.000	0.000	0.000	0.000
44	A	172	LEU	0	0.036	0.001	13.188	0.007	0.007	0.000	0.000	0.000	0.000
45	A	173	SER	0	-0.025	-0.021	17.568	0.005	0.005	0.000	0.000	0.000	0.000
46	A	174	TYR	0	-0.013	-0.005	20.703	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	175	ALA	0	-0.008	-0.006	16.627	0.001	0.001	0.000	0.000	0.000	0.000
48	A	176	ASN	0	-0.036	-0.041	12.647	0.003	0.003	0.000	0.000	0.000	0.000
49	A	177	ALA	0	0.004	0.019	16.964	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	178	ASN	0	0.000	0.010	20.256	0.001	0.001	0.000	0.000	0.000	0.000
51	A	179	LYS	1	0.995	0.983	21.881	-0.056	-0.056	0.000	0.000	0.000	0.000
52	A	180	GLU	-1	-0.920	-0.964	23.958	0.047	0.047	0.000	0.000	0.000	0.000
53	A	181	CYS	0	0.006	0.025	24.597	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	182	GLN	0	-0.055	-0.016	19.481	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	183	GLN	0	-0.001	-0.015	25.071	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	184	ILE	0	-0.027	0.000	28.280	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	185	LEU	0	0.010	-0.001	25.056	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	186	GLN	0	-0.001	0.014	25.442	0.002	0.002	0.000	0.000	0.000	0.000
59	A	187	GLY	0	-0.013	0.004	29.235	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	188	ARG	1	0.851	0.929	32.293	-0.040	-0.040	0.000	0.000	0.000	0.000
61	A	189	GLY	0	0.029	0.028	31.383	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	190	LEU	0	-0.057	-0.041	30.058	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	191	VAL	0	0.014	0.000	24.346	0.002	0.002	0.000	0.000	0.000	0.000
64	A	192	ALA	0	0.019	0.006	24.984	0.004	0.004	0.000	0.000	0.000	0.000
65	A	193	ALA	0	-0.007	0.023	26.673	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	194	PRO	0	0.063	0.037	26.757	0.004	0.004	0.000	0.000	0.000	0.000
67	A	195	VAL	0	0.056	0.011	23.729	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	196	GLY	0	-0.002	0.005	26.209	0.001	0.001	0.000	0.000	0.000	0.000
69	A	197	GLN	0	0.027	0.001	29.651	0.000	0.000	0.000	0.000	0.000	0.000
70	A	198	LYS	1	0.779	0.881	23.903	-0.062	-0.062	0.000	0.000	0.000	0.000
71	A	199	LEU	0	0.006	-0.001	26.371	0.000	0.000	0.000	0.000	0.000	0.000
72	A	200	GLN	0	-0.023	-0.014	29.100	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	201	ALA	0	-0.058	-0.018	30.788	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	202	CYS	0	-0.004	-0.013	28.260	0.000	0.000	0.000	0.000	0.000	0.000
75	A	203	ALA	0	-0.002	0.011	30.264	0.001	0.001	0.000	0.000	0.000	0.000
76	A	204	HIS	0	-0.029	-0.017	32.248	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	205	TRP	0	-0.040	-0.012	26.539	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	206	ALA	0	0.006	0.008	30.752	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:129:SER)