FMO DATABASE

FMODB ID: N86YQ

Calculation Name: 4PH1-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4PH1

Chain ID: A

ChEMBL ID:

UniProt ID: A7KWZ1

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

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. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-473361.577607
FMO2-HF: Nuclear repulsion	443878.655586
FMO2-HF: Total energy	-29482.922021
FMO2-MP2: Total energy	-29569.35367

3D Structure Molmil

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.
-53.101	-50.192	0.072	-1.627	-1.354	-0.012

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 : 1 / q_Mulliken : 0.825 / q_NPA : 0.903

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	0.030	0.018	2.941	-15.173	-12.264	0.072	-1.627	-1.354	-0.012
4	A	132	PRO	0	0.055	0.044	5.664	2.027	2.027	0.000	0.000	0.000	0.000
5	A	133	TRP	0	0.121	0.060	7.568	0.469	0.469	0.000	0.000	0.000	0.000
6	A	134	SER	0	-0.051	-0.043	7.824	2.480	2.480	0.000	0.000	0.000	0.000
7	A	135	THR	0	-0.084	-0.044	7.182	1.490	1.490	0.000	0.000	0.000	0.000
8	A	136	ILE	0	-0.022	0.001	9.944	1.847	1.847	0.000	0.000	0.000	0.000
9	A	137	VAL	0	0.016	0.013	12.796	0.579	0.579	0.000	0.000	0.000	0.000
10	A	138	GLN	0	-0.001	-0.006	15.396	0.109	0.109	0.000	0.000	0.000	0.000
11	A	139	GLY	0	0.004	-0.002	19.175	-0.058	-0.058	0.000	0.000	0.000	0.000
12	A	140	PRO	0	-0.026	-0.037	20.750	0.354	0.354	0.000	0.000	0.000	0.000
13	A	141	ALA	0	0.024	0.012	23.708	0.455	0.455	0.000	0.000	0.000	0.000
14	A	142	GLU	-1	-0.776	-0.848	20.370	-15.246	-15.246	0.000	0.000	0.000	0.000
15	A	143	SER	0	0.020	-0.023	24.506	-0.069	-0.069	0.000	0.000	0.000	0.000
16	A	144	TYR	0	0.034	-0.039	23.464	-0.355	-0.355	0.000	0.000	0.000	0.000
17	A	145	VAL	0	0.009	-0.004	24.128	-0.461	-0.461	0.000	0.000	0.000	0.000
18	A	146	GLU	-1	-0.859	-0.884	23.645	-12.191	-12.191	0.000	0.000	0.000	0.000
19	A	147	PHE	0	-0.027	0.002	17.236	-0.530	-0.530	0.000	0.000	0.000	0.000
20	A	148	VAL	0	0.028	0.009	19.571	-0.891	-0.891	0.000	0.000	0.000	0.000
21	A	149	ASN	0	-0.011	0.004	20.672	-0.495	-0.495	0.000	0.000	0.000	0.000
22	A	150	ARG	1	0.828	0.886	15.339	17.048	17.048	0.000	0.000	0.000	0.000
23	A	151	LEU	0	-0.023	0.000	14.847	-1.182	-1.182	0.000	0.000	0.000	0.000
24	A	152	GLN	0	-0.030	-0.027	16.366	-0.744	-0.744	0.000	0.000	0.000	0.000
25	A	153	ILE	0	-0.020	0.002	17.287	0.134	0.134	0.000	0.000	0.000	0.000
26	A	154	SER	0	0.003	0.007	12.364	-1.219	-1.219	0.000	0.000	0.000	0.000
27	A	155	LEU	0	-0.068	-0.044	13.076	-1.699	-1.699	0.000	0.000	0.000	0.000
28	A	156	ALA	0	0.015	0.019	14.802	-0.205	-0.205	0.000	0.000	0.000	0.000
29	A	157	ASP	-1	-0.923	-0.953	13.811	-19.130	-19.130	0.000	0.000	0.000	0.000
30	A	158	ASN	0	-0.114	-0.083	9.633	-4.608	-4.608	0.000	0.000	0.000	0.000
31	A	159	LEU	0	0.036	0.021	12.901	1.040	1.040	0.000	0.000	0.000	0.000
32	A	160	PRO	0	-0.013	-0.028	11.537	1.203	1.203	0.000	0.000	0.000	0.000
33	A	161	ASP	-1	-0.705	-0.831	14.793	-16.059	-16.059	0.000	0.000	0.000	0.000
34	A	162	GLY	0	-0.030	-0.007	17.632	0.977	0.977	0.000	0.000	0.000	0.000
35	A	163	VAL	0	-0.037	-0.027	16.770	0.525	0.525	0.000	0.000	0.000	0.000
36	A	164	PRO	0	-0.056	-0.009	16.187	0.650	0.650	0.000	0.000	0.000	0.000
37	A	165	LYS	1	0.824	0.905	18.059	15.427	15.427	0.000	0.000	0.000	0.000
38	A	166	GLU	-1	-0.843	-0.944	19.045	-14.121	-14.121	0.000	0.000	0.000	0.000
39	A	167	PRO	0	0.001	-0.015	19.085	-0.075	-0.075	0.000	0.000	0.000	0.000
40	A	168	ILE	0	-0.011	0.011	13.683	-0.483	-0.483	0.000	0.000	0.000	0.000
41	A	169	ILE	0	0.028	0.022	17.145	-0.444	-0.444	0.000	0.000	0.000	0.000
42	A	170	ASP	-1	-0.818	-0.882	19.185	-13.066	-13.066	0.000	0.000	0.000	0.000
43	A	171	SER	0	-0.027	0.003	17.415	0.425	0.425	0.000	0.000	0.000	0.000
44	A	172	LEU	0	0.018	-0.002	12.794	0.035	0.035	0.000	0.000	0.000	0.000
45	A	173	SER	0	-0.019	-0.024	17.172	0.343	0.343	0.000	0.000	0.000	0.000
46	A	174	TYR	0	-0.024	-0.010	20.430	0.778	0.778	0.000	0.000	0.000	0.000
47	A	175	ALA	0	-0.010	-0.006	16.388	0.085	0.085	0.000	0.000	0.000	0.000
48	A	176	ASN	0	-0.056	-0.045	12.497	-0.299	-0.299	0.000	0.000	0.000	0.000
49	A	177	ALA	0	0.005	0.013	16.778	0.141	0.141	0.000	0.000	0.000	0.000
50	A	178	ASN	0	-0.003	0.003	20.122	0.071	0.071	0.000	0.000	0.000	0.000
51	A	179	LYS	1	0.991	0.981	21.883	11.508	11.508	0.000	0.000	0.000	0.000
52	A	180	GLU	-1	-0.914	-0.947	23.912	-10.287	-10.287	0.000	0.000	0.000	0.000
53	A	181	CYS	0	0.015	0.020	24.358	0.409	0.409	0.000	0.000	0.000	0.000
54	A	182	GLN	0	-0.065	-0.030	19.296	0.614	0.614	0.000	0.000	0.000	0.000
55	A	183	GLN	0	0.014	-0.004	24.894	0.338	0.338	0.000	0.000	0.000	0.000
56	A	184	ILE	0	-0.011	0.007	28.236	0.410	0.410	0.000	0.000	0.000	0.000
57	A	185	LEU	0	0.007	-0.007	24.807	0.291	0.291	0.000	0.000	0.000	0.000
58	A	186	GLN	0	-0.017	-0.004	25.465	-0.254	-0.254	0.000	0.000	0.000	0.000
59	A	187	GLY	0	-0.012	0.003	29.152	0.257	0.257	0.000	0.000	0.000	0.000
60	A	188	ARG	1	0.844	0.915	32.039	9.715	9.715	0.000	0.000	0.000	0.000
61	A	189	GLY	0	0.019	0.020	31.730	0.166	0.166	0.000	0.000	0.000	0.000
62	A	190	LEU	0	-0.035	-0.020	29.923	-0.075	-0.075	0.000	0.000	0.000	0.000
63	A	191	VAL	0	0.016	0.012	24.392	-0.316	-0.316	0.000	0.000	0.000	0.000
64	A	192	ALA	0	-0.003	-0.007	25.019	-0.565	-0.565	0.000	0.000	0.000	0.000
65	A	193	ALA	0	-0.006	0.020	26.751	0.087	0.087	0.000	0.000	0.000	0.000
66	A	194	PRO	0	0.062	0.031	26.300	-0.446	-0.446	0.000	0.000	0.000	0.000
67	A	195	VAL	0	0.047	0.015	22.848	0.424	0.424	0.000	0.000	0.000	0.000
68	A	196	GLY	0	0.006	0.007	25.544	0.200	0.200	0.000	0.000	0.000	0.000
69	A	197	GLN	0	0.015	-0.007	28.861	0.193	0.193	0.000	0.000	0.000	0.000
70	A	198	LYS	1	0.775	0.879	23.543	13.502	13.502	0.000	0.000	0.000	0.000
71	A	199	LEU	0	0.028	0.008	25.819	0.131	0.131	0.000	0.000	0.000	0.000
72	A	200	GLN	0	-0.036	-0.020	28.708	0.136	0.136	0.000	0.000	0.000	0.000
73	A	201	ALA	0	-0.060	-0.020	30.492	0.286	0.286	0.000	0.000	0.000	0.000
74	A	202	CYS	0	-0.002	-0.006	28.112	0.168	0.168	0.000	0.000	0.000	0.000
75	A	203	ALA	0	-0.028	-0.005	30.106	-0.035	-0.035	0.000	0.000	0.000	0.000
76	A	204	HIS	0	-0.045	-0.023	31.933	0.191	0.191	0.000	0.000	0.000	0.000
77	A	205	TRP	0	-0.053	-0.025	26.608	0.020	0.020	0.000	0.000	0.000	0.000
78	A	206	ALA	-1	-0.931	-0.952	30.940	-10.058	-10.058	0.000	0.000	0.000	0.000

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