FMO DATABASE

FMODB ID: 5J86Z

Calculation Name: 3PH9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PH9

Chain ID: A

ChEMBL ID:

UniProt ID: Q8TD06

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1318396.101308
FMO2-HF: Nuclear repulsion	1263048.606522
FMO2-HF: Total energy	-55347.494786
FMO2-MP2: Total energy	-55506.821635

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:31:PRO)

Summations of interaction energy for fragment #1(A:31:PRO)

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.
-0.607	0.71	-0.015	-0.501	-0.801	0.002

Interaction energy analysis for fragmet #1(A:31:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : -0.018

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	33	THR	0	0.055	0.040	3.834	-0.605	0.712	-0.015	-0.501	-0.801	0.002
4	A	34	LEU	0	0.011	-0.002	6.300	0.338	0.338	0.000	0.000	0.000	0.000
5	A	35	SER	0	0.018	-0.012	9.491	0.057	0.057	0.000	0.000	0.000	0.000
6	A	36	ARG	1	0.864	0.932	8.089	0.690	0.690	0.000	0.000	0.000	0.000
7	A	37	GLY	0	0.070	0.026	9.285	0.178	0.178	0.000	0.000	0.000	0.000
8	A	38	TRP	0	-0.005	-0.016	11.368	0.142	0.142	0.000	0.000	0.000	0.000
9	A	39	GLY	0	0.075	0.017	13.312	0.091	0.091	0.000	0.000	0.000	0.000
10	A	40	ASP	-1	-0.885	-0.907	9.969	-1.242	-1.242	0.000	0.000	0.000	0.000
11	A	41	ASP	-1	-0.908	-0.938	12.404	-0.502	-0.502	0.000	0.000	0.000	0.000
12	A	42	ILE	0	-0.046	-0.014	15.352	0.074	0.074	0.000	0.000	0.000	0.000
13	A	43	THR	0	-0.047	-0.017	14.989	-0.054	-0.054	0.000	0.000	0.000	0.000
14	A	44	TRP	0	-0.057	-0.026	13.418	0.064	0.064	0.000	0.000	0.000	0.000
15	A	45	VAL	0	0.005	0.002	16.055	0.006	0.006	0.000	0.000	0.000	0.000
16	A	46	GLN	0	-0.051	-0.037	13.590	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	47	THR	0	-0.033	-0.042	15.932	0.011	0.011	0.000	0.000	0.000	0.000
18	A	48	TYR	0	0.015	-0.025	18.886	-0.019	-0.019	0.000	0.000	0.000	0.000
19	A	49	GLU	-1	-0.823	-0.902	21.490	-0.046	-0.046	0.000	0.000	0.000	0.000
20	A	50	GLU	-1	-0.841	-0.915	18.738	-0.170	-0.170	0.000	0.000	0.000	0.000
21	A	51	GLY	0	0.036	0.001	22.088	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	52	LEU	0	-0.005	-0.010	23.182	0.000	0.000	0.000	0.000	0.000	0.000
23	A	53	PHE	0	-0.048	-0.006	25.690	0.005	0.005	0.000	0.000	0.000	0.000
24	A	54	TYR	0	0.013	-0.012	22.350	0.006	0.006	0.000	0.000	0.000	0.000
25	A	55	ALA	0	0.012	0.036	26.616	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	56	GLN	0	-0.005	0.002	28.173	0.006	0.006	0.000	0.000	0.000	0.000
27	A	57	LYS	1	0.890	0.948	29.623	0.077	0.077	0.000	0.000	0.000	0.000
28	A	58	SER	0	-0.065	-0.056	28.110	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	59	LYS	1	0.924	0.963	30.417	0.072	0.072	0.000	0.000	0.000	0.000
30	A	60	LYS	1	0.927	0.990	25.766	0.167	0.167	0.000	0.000	0.000	0.000
31	A	61	PRO	0	0.011	0.005	28.448	0.004	0.004	0.000	0.000	0.000	0.000
32	A	62	LEU	0	-0.019	0.003	22.232	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	63	MET	0	-0.030	-0.004	22.365	0.009	0.009	0.000	0.000	0.000	0.000
34	A	64	VAL	0	0.010	0.004	20.745	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	65	ILE	0	-0.015	-0.009	17.610	0.020	0.020	0.000	0.000	0.000	0.000
36	A	66	HIS	0	0.002	-0.005	17.576	-0.013	-0.013	0.000	0.000	0.000	0.000
37	A	67	HIS	0	-0.036	-0.042	11.478	0.029	0.029	0.000	0.000	0.000	0.000
38	A	68	LEU	0	0.041	0.013	13.993	0.030	0.030	0.000	0.000	0.000	0.000
39	A	69	GLU	-1	-0.731	-0.856	8.163	-0.739	-0.739	0.000	0.000	0.000	0.000
40	A	70	ASP	-1	-0.912	-0.940	11.658	0.124	0.124	0.000	0.000	0.000	0.000
41	A	71	CYS	0	-0.060	0.013	14.070	0.013	0.013	0.000	0.000	0.000	0.000
42	A	72	GLN	0	0.039	0.003	16.461	-0.051	-0.051	0.000	0.000	0.000	0.000
43	A	73	TYR	0	0.034	0.009	18.338	-0.027	-0.027	0.000	0.000	0.000	0.000
44	A	74	SER	0	0.039	-0.010	15.825	-0.011	-0.011	0.000	0.000	0.000	0.000
45	A	75	GLN	0	-0.050	-0.042	10.692	-0.085	-0.085	0.000	0.000	0.000	0.000
46	A	76	ALA	0	-0.035	-0.015	15.573	-0.036	-0.036	0.000	0.000	0.000	0.000
47	A	77	LEU	0	-0.026	-0.019	18.901	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	78	LYS	1	0.808	0.895	10.486	0.644	0.644	0.000	0.000	0.000	0.000
49	A	79	LYS	1	0.977	1.003	16.240	0.293	0.293	0.000	0.000	0.000	0.000
50	A	80	VAL	0	-0.039	-0.028	17.035	0.002	0.002	0.000	0.000	0.000	0.000
51	A	81	PHE	0	-0.013	-0.009	18.495	0.017	0.017	0.000	0.000	0.000	0.000
52	A	82	ALA	0	-0.012	-0.005	15.571	0.010	0.010	0.000	0.000	0.000	0.000
53	A	83	GLN	0	-0.037	-0.014	16.584	0.020	0.020	0.000	0.000	0.000	0.000
54	A	84	ASN	0	-0.018	0.010	19.950	0.033	0.033	0.000	0.000	0.000	0.000
55	A	85	GLU	-1	-0.849	-0.937	22.788	-0.225	-0.225	0.000	0.000	0.000	0.000
56	A	86	GLU	-1	-0.852	-0.920	24.492	-0.149	-0.149	0.000	0.000	0.000	0.000
57	A	87	ILE	0	-0.023	-0.029	21.989	0.006	0.006	0.000	0.000	0.000	0.000
58	A	88	GLN	0	0.004	-0.011	17.967	-0.019	-0.019	0.000	0.000	0.000	0.000
59	A	89	GLU	-1	-0.764	-0.852	21.894	-0.177	-0.177	0.000	0.000	0.000	0.000
60	A	90	MET	0	-0.032	-0.034	24.741	0.013	0.013	0.000	0.000	0.000	0.000
61	A	91	ALA	0	-0.004	-0.011	20.654	0.009	0.009	0.000	0.000	0.000	0.000
62	A	92	GLN	0	-0.039	-0.013	19.062	0.017	0.017	0.000	0.000	0.000	0.000
63	A	93	ASN	0	-0.056	-0.037	21.998	0.004	0.004	0.000	0.000	0.000	0.000
64	A	94	LYS	1	0.753	0.857	25.588	0.175	0.175	0.000	0.000	0.000	0.000
65	A	95	PHE	0	-0.021	-0.006	24.075	0.017	0.017	0.000	0.000	0.000	0.000
66	A	96	ILE	0	-0.036	0.010	22.318	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	97	MET	0	0.016	0.015	18.752	0.022	0.022	0.000	0.000	0.000	0.000
68	A	98	LEU	0	0.031	0.025	16.859	-0.018	-0.018	0.000	0.000	0.000	0.000
69	A	99	ASN	0	-0.009	0.001	12.898	0.010	0.010	0.000	0.000	0.000	0.000
70	A	100	LEU	0	-0.015	-0.006	14.782	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	101	MET	0	-0.010	-0.005	9.368	-0.035	-0.035	0.000	0.000	0.000	0.000
72	A	102	HIS	0	-0.034	-0.021	14.783	0.075	0.075	0.000	0.000	0.000	0.000
73	A	103	GLU	-1	-0.808	-0.874	17.440	-0.066	-0.066	0.000	0.000	0.000	0.000
74	A	104	THR	0	0.032	0.027	21.094	0.019	0.019	0.000	0.000	0.000	0.000
75	A	105	THR	0	0.020	-0.004	22.789	0.008	0.008	0.000	0.000	0.000	0.000
76	A	106	ASP	-1	-0.811	-0.879	26.039	-0.034	-0.034	0.000	0.000	0.000	0.000
77	A	107	LYS	1	0.996	0.981	27.537	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	108	ASN	0	-0.049	-0.029	29.753	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	109	LEU	0	-0.022	-0.001	24.035	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	110	SER	0	-0.025	-0.026	26.039	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	111	PRO	0	-0.012	0.009	27.890	0.009	0.009	0.000	0.000	0.000	0.000
82	A	112	ASP	-1	-0.769	-0.865	30.026	-0.045	-0.045	0.000	0.000	0.000	0.000
83	A	113	GLY	0	0.007	0.010	28.817	0.001	0.001	0.000	0.000	0.000	0.000
84	A	114	GLN	0	-0.023	-0.027	23.755	0.001	0.001	0.000	0.000	0.000	0.000
85	A	115	TYR	0	-0.091	-0.051	23.110	0.001	0.001	0.000	0.000	0.000	0.000
86	A	116	VAL	0	0.011	0.024	18.518	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	117	PRO	0	0.001	-0.016	19.106	0.010	0.010	0.000	0.000	0.000	0.000
88	A	118	ARG	1	0.744	0.855	20.622	0.073	0.073	0.000	0.000	0.000	0.000
89	A	119	ILE	0	-0.032	-0.005	21.453	-0.012	-0.012	0.000	0.000	0.000	0.000
90	A	120	MET	0	-0.020	0.018	23.627	0.014	0.014	0.000	0.000	0.000	0.000
91	A	121	PHE	0	0.058	0.009	25.146	-0.014	-0.014	0.000	0.000	0.000	0.000
92	A	122	VAL	0	-0.013	-0.005	26.639	0.012	0.012	0.000	0.000	0.000	0.000
93	A	123	ASP	-1	-0.717	-0.836	29.172	-0.084	-0.084	0.000	0.000	0.000	0.000
94	A	124	PRO	0	0.022	0.017	31.250	0.003	0.003	0.000	0.000	0.000	0.000
95	A	125	SER	0	-0.094	-0.082	32.266	0.005	0.005	0.000	0.000	0.000	0.000
96	A	126	LEU	0	-0.018	-0.016	30.274	0.006	0.006	0.000	0.000	0.000	0.000
97	A	127	THR	0	-0.018	0.012	32.135	0.005	0.005	0.000	0.000	0.000	0.000
98	A	128	VAL	0	0.029	0.003	29.312	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	129	ARG	1	0.809	0.880	31.044	0.082	0.082	0.000	0.000	0.000	0.000
100	A	130	ALA	0	0.040	0.025	32.010	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	131	ASP	-1	-0.778	-0.860	33.436	-0.069	-0.069	0.000	0.000	0.000	0.000
102	A	132	ILE	0	-0.105	-0.034	30.709	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	133	ALA	0	0.051	0.030	30.935	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	134	GLY	0	0.003	0.002	30.203	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	135	ARG	1	0.842	0.890	31.144	0.095	0.095	0.000	0.000	0.000	0.000
106	A	136	TYR	0	-0.070	-0.040	28.744	0.010	0.010	0.000	0.000	0.000	0.000
107	A	137	SER	0	0.033	0.012	32.951	0.000	0.000	0.000	0.000	0.000	0.000
108	A	138	ASN	0	-0.019	-0.015	33.494	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	139	ARG	1	0.938	0.967	25.475	0.049	0.049	0.000	0.000	0.000	0.000
110	A	140	LEU	0	0.047	0.031	29.680	-0.009	-0.009	0.000	0.000	0.000	0.000
111	A	141	TYR	0	0.006	-0.015	27.007	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	142	THR	0	-0.084	-0.034	24.058	-0.014	-0.014	0.000	0.000	0.000	0.000
113	A	143	TYR	0	0.002	-0.007	24.344	0.004	0.004	0.000	0.000	0.000	0.000
114	A	144	GLU	-1	-0.816	-0.884	23.851	-0.102	-0.102	0.000	0.000	0.000	0.000
115	A	145	PRO	0	0.045	0.004	22.320	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	146	ARG	1	0.824	0.895	24.804	0.088	0.088	0.000	0.000	0.000	0.000
117	A	147	ASP	-1	-0.778	-0.862	27.445	-0.098	-0.098	0.000	0.000	0.000	0.000
118	A	148	LEU	0	0.032	0.012	23.488	0.002	0.002	0.000	0.000	0.000	0.000
119	A	149	PRO	0	0.029	0.011	27.604	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	150	LEU	0	0.025	0.025	30.840	0.003	0.003	0.000	0.000	0.000	0.000
121	A	151	LEU	0	0.001	0.006	23.556	0.003	0.003	0.000	0.000	0.000	0.000
122	A	152	ILE	0	-0.002	0.004	27.657	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	153	GLU	-1	-0.871	-0.943	29.394	-0.105	-0.105	0.000	0.000	0.000	0.000
124	A	154	ASN	0	-0.029	-0.043	30.044	0.010	0.010	0.000	0.000	0.000	0.000
125	A	155	MET	0	-0.033	0.000	24.441	0.002	0.002	0.000	0.000	0.000	0.000
126	A	156	LYS	1	0.858	0.913	29.401	0.132	0.132	0.000	0.000	0.000	0.000
127	A	157	LYS	1	0.787	0.899	32.607	0.080	0.080	0.000	0.000	0.000	0.000
128	A	158	ALA	0	-0.007	-0.007	30.189	0.007	0.007	0.000	0.000	0.000	0.000
129	A	159	LEU	0	-0.013	-0.008	29.392	0.004	0.004	0.000	0.000	0.000	0.000
130	A	160	ARG	1	0.863	0.959	32.943	0.094	0.094	0.000	0.000	0.000	0.000
131	A	161	LEU	0	-0.001	-0.008	33.274	0.004	0.004	0.000	0.000	0.000	0.000
132	A	162	ILE	0	0.000	-0.002	35.945	0.004	0.004	0.000	0.000	0.000	0.000
133	A	163	GLN	0	-0.080	-0.026	38.626	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:31:PRO)