FMO DATABASE

FMODB ID: YVJG2

Calculation Name: 3PH9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	133
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1323233.523748
FMO2-HF: Nuclear repulsion	1267885.931741
FMO2-HF: Total energy	-55347.592007
FMO2-MP2: Total energy	-55506.940904

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: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.
-0.984	0.247	-0.013	-0.479	-0.74	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 : -0.004 / q_NPA : -0.026

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	0.046	0.028	3.865	-0.930	0.301	-0.013	-0.479	-0.740	0.002
4	A	34	LEU	0	0.003	-0.001	6.483	0.335	0.335	0.000	0.000	0.000	0.000
5	A	35	SER	0	0.020	-0.020	9.363	0.055	0.055	0.000	0.000	0.000	0.000
6	A	36	ARG	1	0.866	0.934	8.570	0.307	0.307	0.000	0.000	0.000	0.000
7	A	37	GLY	0	0.059	0.033	9.629	0.120	0.120	0.000	0.000	0.000	0.000
8	A	38	TRP	0	-0.015	-0.022	10.886	0.107	0.107	0.000	0.000	0.000	0.000
9	A	39	GLY	0	0.073	0.018	12.955	0.070	0.070	0.000	0.000	0.000	0.000
10	A	40	ASP	-1	-0.881	-0.905	9.419	-1.042	-1.042	0.000	0.000	0.000	0.000
11	A	41	ASP	-1	-0.899	-0.936	12.259	-0.418	-0.418	0.000	0.000	0.000	0.000
12	A	42	ILE	0	-0.041	-0.007	15.225	0.064	0.064	0.000	0.000	0.000	0.000
13	A	43	THR	0	-0.037	-0.019	15.146	-0.037	-0.037	0.000	0.000	0.000	0.000
14	A	44	TRP	0	-0.058	-0.028	13.555	0.067	0.067	0.000	0.000	0.000	0.000
15	A	45	VAL	0	-0.018	-0.002	16.159	0.003	0.003	0.000	0.000	0.000	0.000
16	A	46	GLN	0	-0.040	-0.030	13.348	0.001	0.001	0.000	0.000	0.000	0.000
17	A	47	THR	0	-0.043	-0.057	15.835	0.020	0.020	0.000	0.000	0.000	0.000
18	A	48	TYR	0	0.004	-0.026	18.892	-0.021	-0.021	0.000	0.000	0.000	0.000
19	A	49	GLU	-1	-0.811	-0.893	21.754	0.006	0.006	0.000	0.000	0.000	0.000
20	A	50	GLU	-1	-0.838	-0.916	18.666	-0.094	-0.094	0.000	0.000	0.000	0.000
21	A	51	GLY	0	0.032	0.001	22.187	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	52	LEU	0	-0.001	-0.006	23.249	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	53	PHE	0	-0.037	-0.007	25.504	0.000	0.000	0.000	0.000	0.000	0.000
24	A	54	TYR	0	0.008	-0.011	21.957	0.000	0.000	0.000	0.000	0.000	0.000
25	A	55	ALA	0	0.001	0.030	26.387	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	56	GLN	0	-0.031	-0.022	28.108	0.003	0.003	0.000	0.000	0.000	0.000
27	A	57	LYS	1	0.882	0.948	29.237	0.048	0.048	0.000	0.000	0.000	0.000
28	A	58	SER	0	-0.038	-0.042	28.169	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	59	LYS	1	0.905	0.953	30.552	0.046	0.046	0.000	0.000	0.000	0.000
30	A	60	LYS	1	0.899	0.971	24.902	0.135	0.135	0.000	0.000	0.000	0.000
31	A	61	PRO	0	0.001	-0.001	28.486	0.005	0.005	0.000	0.000	0.000	0.000
32	A	62	LEU	0	-0.030	0.002	22.379	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	63	MET	0	-0.037	-0.009	22.454	0.005	0.005	0.000	0.000	0.000	0.000
34	A	64	VAL	0	0.008	-0.004	20.799	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	65	ILE	0	-0.012	-0.002	17.935	0.016	0.016	0.000	0.000	0.000	0.000
36	A	66	HIS	0	0.036	0.014	17.886	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	67	HIS	0	-0.046	-0.041	11.804	0.010	0.010	0.000	0.000	0.000	0.000
38	A	68	LEU	0	0.044	0.009	14.270	0.038	0.038	0.000	0.000	0.000	0.000
39	A	69	GLU	-1	-0.742	-0.853	8.480	-0.453	-0.453	0.000	0.000	0.000	0.000
40	A	70	ASP	-1	-0.882	-0.929	11.942	0.239	0.239	0.000	0.000	0.000	0.000
41	A	71	CYS	0	-0.102	-0.008	14.301	-0.024	-0.024	0.000	0.000	0.000	0.000
42	A	72	GLN	0	0.050	0.009	16.838	-0.049	-0.049	0.000	0.000	0.000	0.000
43	A	73	TYR	0	-0.007	-0.021	18.320	-0.026	-0.026	0.000	0.000	0.000	0.000
44	A	74	SER	0	0.025	-0.011	16.127	-0.011	-0.011	0.000	0.000	0.000	0.000
45	A	75	GLN	0	-0.055	-0.043	10.904	-0.095	-0.095	0.000	0.000	0.000	0.000
46	A	76	ALA	0	-0.031	-0.015	15.749	-0.035	-0.035	0.000	0.000	0.000	0.000
47	A	77	LEU	0	-0.026	-0.013	19.213	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	78	LYS	1	0.817	0.892	10.614	0.431	0.431	0.000	0.000	0.000	0.000
49	A	79	LYS	1	0.965	0.991	16.178	0.247	0.247	0.000	0.000	0.000	0.000
50	A	80	VAL	0	-0.032	-0.015	17.096	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	81	PHE	0	0.004	-0.007	18.231	0.011	0.011	0.000	0.000	0.000	0.000
52	A	82	ALA	0	0.003	0.010	15.125	0.008	0.008	0.000	0.000	0.000	0.000
53	A	83	GLN	0	-0.067	-0.036	16.947	-0.012	-0.012	0.000	0.000	0.000	0.000
54	A	84	ASN	0	-0.010	0.012	19.724	0.023	0.023	0.000	0.000	0.000	0.000
55	A	85	GLU	-1	-0.854	-0.937	22.703	-0.188	-0.188	0.000	0.000	0.000	0.000
56	A	86	GLU	-1	-0.841	-0.915	24.131	-0.113	-0.113	0.000	0.000	0.000	0.000
57	A	87	ILE	0	-0.019	-0.026	21.661	0.007	0.007	0.000	0.000	0.000	0.000
58	A	88	GLN	0	0.005	-0.007	17.645	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	89	GLU	-1	-0.745	-0.837	21.601	-0.137	-0.137	0.000	0.000	0.000	0.000
60	A	90	MET	0	-0.026	-0.023	24.579	0.012	0.012	0.000	0.000	0.000	0.000
61	A	91	ALA	0	0.007	-0.014	20.331	0.009	0.009	0.000	0.000	0.000	0.000
62	A	92	GLN	0	-0.043	-0.018	18.968	0.018	0.018	0.000	0.000	0.000	0.000
63	A	93	ASN	0	-0.037	-0.046	22.106	0.007	0.007	0.000	0.000	0.000	0.000
64	A	94	LYS	1	0.720	0.845	25.838	0.136	0.136	0.000	0.000	0.000	0.000
65	A	95	PHE	0	0.001	0.004	24.092	0.014	0.014	0.000	0.000	0.000	0.000
66	A	96	ILE	0	-0.010	0.024	22.270	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	97	MET	0	0.022	0.021	18.777	0.019	0.019	0.000	0.000	0.000	0.000
68	A	98	LEU	0	0.035	0.028	16.859	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	99	ASN	0	-0.016	-0.004	13.037	0.021	0.021	0.000	0.000	0.000	0.000
70	A	100	LEU	0	-0.019	-0.008	15.118	0.005	0.005	0.000	0.000	0.000	0.000
71	A	101	MET	0	0.001	0.004	9.644	-0.043	-0.043	0.000	0.000	0.000	0.000
72	A	102	HIS	0	-0.033	-0.027	15.117	0.071	0.071	0.000	0.000	0.000	0.000
73	A	103	GLU	-1	-0.786	-0.859	18.013	0.008	0.008	0.000	0.000	0.000	0.000
74	A	104	THR	0	0.039	0.032	21.317	0.016	0.016	0.000	0.000	0.000	0.000
75	A	105	THR	0	-0.003	-0.011	23.163	0.006	0.006	0.000	0.000	0.000	0.000
76	A	106	ASP	-1	-0.814	-0.885	26.268	0.002	0.002	0.000	0.000	0.000	0.000
77	A	107	LYS	1	1.001	0.988	27.801	-0.048	-0.048	0.000	0.000	0.000	0.000
78	A	108	ASN	0	-0.041	-0.021	30.042	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	109	LEU	0	-0.012	0.004	24.027	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	110	SER	0	-0.019	-0.021	26.321	0.000	0.000	0.000	0.000	0.000	0.000
81	A	111	PRO	0	-0.016	0.013	28.175	0.006	0.006	0.000	0.000	0.000	0.000
82	A	112	ASP	-1	-0.790	-0.882	30.309	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	113	GLY	0	-0.008	-0.005	29.256	0.002	0.002	0.000	0.000	0.000	0.000
84	A	114	GLN	0	-0.025	-0.021	24.426	0.002	0.002	0.000	0.000	0.000	0.000
85	A	115	TYR	0	-0.069	-0.042	23.729	0.009	0.009	0.000	0.000	0.000	0.000
86	A	116	VAL	0	0.019	0.023	18.833	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	117	PRO	0	-0.012	-0.017	19.422	0.006	0.006	0.000	0.000	0.000	0.000
88	A	118	ARG	1	0.726	0.828	20.889	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	119	ILE	0	-0.036	-0.001	21.662	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	120	MET	0	-0.018	0.018	23.832	0.006	0.006	0.000	0.000	0.000	0.000
91	A	121	PHE	0	0.054	0.001	25.329	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	122	VAL	0	-0.010	0.000	26.865	0.010	0.010	0.000	0.000	0.000	0.000
93	A	123	ASP	-1	-0.716	-0.827	29.456	-0.052	-0.052	0.000	0.000	0.000	0.000
94	A	124	PRO	0	0.006	0.020	31.406	0.004	0.004	0.000	0.000	0.000	0.000
95	A	125	SER	0	-0.063	-0.063	32.396	0.005	0.005	0.000	0.000	0.000	0.000
96	A	126	LEU	0	-0.027	-0.017	30.203	0.005	0.005	0.000	0.000	0.000	0.000
97	A	127	THR	0	-0.020	-0.003	32.113	0.005	0.005	0.000	0.000	0.000	0.000
98	A	128	VAL	0	0.027	0.001	29.444	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	129	ARG	1	0.784	0.864	31.224	0.050	0.050	0.000	0.000	0.000	0.000
100	A	130	ALA	0	0.037	0.013	32.503	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	131	ASP	-1	-0.808	-0.868	33.783	-0.039	-0.039	0.000	0.000	0.000	0.000
102	A	132	ILE	0	-0.072	-0.018	30.946	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	133	ALA	0	0.046	0.028	31.119	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	134	GLY	0	0.048	0.031	30.359	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	135	ARG	1	0.802	0.870	31.271	0.063	0.063	0.000	0.000	0.000	0.000
106	A	136	TYR	0	-0.077	-0.053	29.025	0.007	0.007	0.000	0.000	0.000	0.000
107	A	137	SER	0	0.023	0.003	33.083	0.002	0.002	0.000	0.000	0.000	0.000
108	A	138	ASN	0	-0.012	-0.005	33.821	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	139	ARG	1	0.941	0.962	25.394	0.011	0.011	0.000	0.000	0.000	0.000
110	A	140	LEU	0	0.061	0.047	29.636	-0.007	-0.007	0.000	0.000	0.000	0.000
111	A	141	TYR	0	-0.005	-0.022	27.397	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	142	THR	0	-0.079	-0.035	24.578	-0.008	-0.008	0.000	0.000	0.000	0.000
113	A	143	TYR	0	0.003	-0.012	24.630	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	144	GLU	-1	-0.775	-0.853	24.294	-0.058	-0.058	0.000	0.000	0.000	0.000
115	A	145	PRO	0	0.040	0.000	22.477	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	146	ARG	1	0.831	0.897	25.010	0.054	0.054	0.000	0.000	0.000	0.000
117	A	147	ASP	-1	-0.757	-0.839	27.630	-0.061	-0.061	0.000	0.000	0.000	0.000
118	A	148	LEU	0	0.023	0.019	23.376	0.002	0.002	0.000	0.000	0.000	0.000
119	A	149	PRO	0	0.032	0.008	27.454	0.000	0.000	0.000	0.000	0.000	0.000
120	A	150	LEU	0	0.006	0.019	30.996	0.002	0.002	0.000	0.000	0.000	0.000
121	A	151	LEU	0	0.010	0.000	23.832	0.003	0.003	0.000	0.000	0.000	0.000
122	A	152	ILE	0	0.001	0.011	27.436	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	153	GLU	-1	-0.815	-0.915	29.276	-0.076	-0.076	0.000	0.000	0.000	0.000
124	A	154	ASN	0	-0.025	-0.040	30.188	0.007	0.007	0.000	0.000	0.000	0.000
125	A	155	MET	0	-0.022	-0.002	24.070	0.003	0.003	0.000	0.000	0.000	0.000
126	A	156	LYS	1	0.885	0.923	29.145	0.098	0.098	0.000	0.000	0.000	0.000
127	A	157	LYS	1	0.770	0.910	32.342	0.049	0.049	0.000	0.000	0.000	0.000
128	A	158	ALA	0	0.008	0.003	29.959	0.006	0.006	0.000	0.000	0.000	0.000
129	A	159	LEU	0	-0.009	-0.011	29.250	0.004	0.004	0.000	0.000	0.000	0.000
130	A	160	ARG	1	0.781	0.895	32.684	0.068	0.068	0.000	0.000	0.000	0.000
131	A	161	LEU	0	0.004	0.008	33.363	0.004	0.004	0.000	0.000	0.000	0.000
132	A	162	ILE	0	-0.009	-0.005	36.107	0.002	0.002	0.000	0.000	0.000	0.000
133	A	163	GLN	0	-0.072	-0.022	38.810	0.004	0.004	0.000	0.000	0.000	0.000

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