FMO DATABASE

FMODB ID: 8557Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-470748.522935
FMO2-HF: Nuclear repulsion	441265.333323
FMO2-HF: Total energy	-29483.189612
FMO2-MP2: Total energy	-29569.587969

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.
0.467	1.868	-0.017	-0.719	-0.665	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 : -0.014 / q_NPA : -0.016

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	0.035	0.021	3.881	0.511	1.912	-0.017	-0.719	-0.665	0.001
4	A	132	PRO	0	0.047	0.031	6.806	0.030	0.030	0.000	0.000	0.000	0.000
5	A	133	TRP	0	0.075	0.032	8.540	-0.070	-0.070	0.000	0.000	0.000	0.000
6	A	134	SER	0	-0.024	-0.013	7.930	-0.065	-0.065	0.000	0.000	0.000	0.000
7	A	135	THR	0	-0.052	-0.029	7.085	-0.045	-0.045	0.000	0.000	0.000	0.000
8	A	136	ILE	0	-0.034	-0.004	9.671	-0.054	-0.054	0.000	0.000	0.000	0.000
9	A	137	VAL	0	0.017	0.017	12.539	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	138	GLN	0	0.000	-0.005	15.139	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	139	GLY	0	0.005	-0.001	18.934	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	140	PRO	0	-0.012	-0.031	20.587	0.001	0.001	0.000	0.000	0.000	0.000
13	A	141	ALA	0	-0.016	-0.011	23.356	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	142	GLU	-1	-0.772	-0.845	20.460	0.070	0.070	0.000	0.000	0.000	0.000
15	A	143	SER	0	-0.011	-0.040	24.488	0.002	0.002	0.000	0.000	0.000	0.000
16	A	144	TYR	0	0.033	-0.042	23.418	0.003	0.003	0.000	0.000	0.000	0.000
17	A	145	VAL	0	0.011	0.000	24.023	0.005	0.005	0.000	0.000	0.000	0.000
18	A	146	GLU	-1	-0.845	-0.877	23.495	0.049	0.049	0.000	0.000	0.000	0.000
19	A	147	PHE	0	-0.026	0.001	17.136	0.006	0.006	0.000	0.000	0.000	0.000
20	A	148	VAL	0	0.041	0.015	19.559	0.011	0.011	0.000	0.000	0.000	0.000
21	A	149	ASN	0	-0.013	0.005	21.100	0.007	0.007	0.000	0.000	0.000	0.000
22	A	150	ARG	1	0.822	0.883	15.236	-0.091	-0.091	0.000	0.000	0.000	0.000
23	A	151	LEU	0	-0.011	0.009	15.566	0.020	0.020	0.000	0.000	0.000	0.000
24	A	152	GLN	0	-0.024	-0.028	17.185	0.009	0.009	0.000	0.000	0.000	0.000
25	A	153	ILE	0	0.018	0.021	18.228	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	154	SER	0	0.044	0.038	13.047	0.019	0.019	0.000	0.000	0.000	0.000
27	A	155	LEU	0	0.020	-0.004	14.385	0.022	0.022	0.000	0.000	0.000	0.000
28	A	156	ALA	0	-0.104	-0.049	16.266	-0.023	-0.023	0.000	0.000	0.000	0.000
29	A	157	ASP	-1	-0.880	-0.938	15.732	0.143	0.143	0.000	0.000	0.000	0.000
30	A	158	ASN	0	-0.128	-0.070	11.368	0.089	0.089	0.000	0.000	0.000	0.000
31	A	159	LEU	0	-0.009	-0.009	13.122	-0.025	-0.025	0.000	0.000	0.000	0.000
32	A	160	PRO	0	-0.012	0.002	10.929	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	161	ASP	-1	-0.913	-0.965	12.681	-0.061	-0.061	0.000	0.000	0.000	0.000
34	A	162	GLY	0	-0.010	-0.008	15.404	0.003	0.003	0.000	0.000	0.000	0.000
35	A	163	VAL	0	-0.031	-0.016	15.149	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	164	PRO	0	0.018	0.006	17.102	0.006	0.006	0.000	0.000	0.000	0.000
37	A	165	LYS	1	0.883	0.941	18.478	-0.086	-0.086	0.000	0.000	0.000	0.000
38	A	166	GLU	-1	-0.872	-0.934	19.565	0.055	0.055	0.000	0.000	0.000	0.000
39	A	167	PRO	0	0.022	-0.002	19.743	0.003	0.003	0.000	0.000	0.000	0.000
40	A	168	ILE	0	-0.010	0.012	14.508	0.003	0.003	0.000	0.000	0.000	0.000
41	A	169	ILE	0	0.029	0.008	17.810	0.010	0.010	0.000	0.000	0.000	0.000
42	A	170	ASP	-1	-0.812	-0.883	19.948	0.050	0.050	0.000	0.000	0.000	0.000
43	A	171	SER	0	-0.022	0.008	17.845	0.002	0.002	0.000	0.000	0.000	0.000
44	A	172	LEU	0	0.029	0.002	13.084	0.003	0.003	0.000	0.000	0.000	0.000
45	A	173	SER	0	-0.029	-0.027	17.340	0.000	0.000	0.000	0.000	0.000	0.000
46	A	174	TYR	0	-0.027	-0.012	20.301	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	175	ALA	0	-0.008	-0.008	16.314	0.000	0.000	0.000	0.000	0.000	0.000
48	A	176	ASN	0	-0.036	-0.031	12.320	0.006	0.006	0.000	0.000	0.000	0.000
49	A	177	ALA	0	-0.006	0.011	16.596	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	178	ASN	0	-0.001	0.000	19.954	0.000	0.000	0.000	0.000	0.000	0.000
51	A	179	LYS	1	0.894	0.909	21.649	-0.036	-0.036	0.000	0.000	0.000	0.000
52	A	180	GLU	-1	-0.831	-0.900	23.538	0.033	0.033	0.000	0.000	0.000	0.000
53	A	181	CYS	0	0.000	0.018	24.192	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	182	GLN	0	-0.044	-0.024	19.268	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	183	GLN	0	0.018	0.014	24.834	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	184	ILE	0	-0.019	0.003	28.103	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	185	LEU	0	0.012	-0.004	24.606	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	186	GLN	0	-0.010	-0.002	25.349	0.002	0.002	0.000	0.000	0.000	0.000
59	A	187	GLY	0	-0.012	0.001	29.056	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	188	ARG	1	0.844	0.916	31.970	-0.032	-0.032	0.000	0.000	0.000	0.000
61	A	189	GLY	0	0.022	0.021	31.610	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	190	LEU	0	-0.036	-0.021	29.919	0.000	0.000	0.000	0.000	0.000	0.000
63	A	191	VAL	0	0.014	0.010	24.296	0.002	0.002	0.000	0.000	0.000	0.000
64	A	192	ALA	0	0.003	0.000	25.127	0.004	0.004	0.000	0.000	0.000	0.000
65	A	193	ALA	0	-0.006	0.018	26.965	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	194	PRO	0	0.054	0.028	26.950	0.004	0.004	0.000	0.000	0.000	0.000
67	A	195	VAL	0	0.051	0.012	23.308	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	196	GLY	0	-0.004	0.005	26.044	0.000	0.000	0.000	0.000	0.000	0.000
69	A	197	GLN	0	0.030	0.001	29.422	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	198	LYS	1	0.770	0.876	23.853	-0.056	-0.056	0.000	0.000	0.000	0.000
71	A	199	LEU	0	0.026	0.005	26.015	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	200	GLN	0	-0.031	-0.018	28.766	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	201	ALA	0	-0.055	-0.018	30.311	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	202	CYS	0	0.002	-0.001	28.050	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	203	ALA	0	-0.018	-0.001	30.009	0.000	0.000	0.000	0.000	0.000	0.000
76	A	204	HIS	0	-0.028	-0.010	31.899	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	205	TRP	0	-0.036	-0.010	26.426	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	206	ALA	0	0.000	0.007	30.511	0.001	0.001	0.000	0.000	0.000	0.000

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