FMO DATABASE

FMODB ID: 98VV2

Calculation Name: 2PRX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PRX

Chain ID: A

ChEMBL ID:

UniProt ID: A3QJH3

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	OptHSide
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	123
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-980217.216238
FMO2-HF: Nuclear repulsion	932852.529505
FMO2-HF: Total energy	-47364.686733
FMO2-MP2: Total energy	-47500.199587

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:6:PHE)

Summations of interaction energy for fragment #1(A:6:PHE)

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.
-20.97	-7.482	14.051	-9.169	-18.37	-0.008

Interaction energy analysis for fragmet #1(A:6:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.015

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	8	ASP	-1	-0.885	-0.916	2.698	-7.614	-2.576	3.320	-2.958	-5.400	0.010
4	A	9	ALA	0	-0.057	-0.017	2.282	-2.328	-0.652	2.985	-1.445	-3.217	0.007
5	A	10	TYR	0	-0.036	-0.041	2.110	-4.803	-4.164	5.410	-2.314	-3.735	-0.012
6	A	11	PRO	0	-0.002	0.003	5.944	0.243	0.243	0.000	0.000	0.000	0.000
7	A	12	ASP	-1	-0.765	-0.868	6.703	0.585	0.585	0.000	0.000	0.000	0.000
8	A	13	ASP	-1	-0.924	-0.957	8.349	0.279	0.279	0.000	0.000	0.000	0.000
9	A	14	LEU	0	-0.086	-0.076	11.457	-0.039	-0.039	0.000	0.000	0.000	0.000
10	A	15	SER	0	-0.008	0.019	9.842	-0.050	-0.050	0.000	0.000	0.000	0.000
11	A	16	HIS	0	-0.033	-0.020	10.897	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	17	CYS	0	-0.010	0.024	10.649	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	18	TYR	0	-0.041	-0.027	12.365	-0.079	-0.079	0.000	0.000	0.000	0.000
14	A	19	GLY	0	0.029	0.016	7.722	-0.105	-0.105	0.000	0.000	0.000	0.000
15	A	30	LEU	0	-0.052	-0.048	7.628	-0.053	-0.053	0.000	0.000	0.000	0.000
16	A	31	LYS	1	0.838	0.927	3.876	0.687	0.923	0.000	-0.022	-0.214	0.000
17	A	32	SER	0	-0.038	-0.035	3.324	0.063	0.598	0.018	-0.126	-0.427	0.000
18	A	33	TYR	0	-0.004	-0.005	2.547	-5.574	-1.877	2.198	-1.775	-4.119	-0.013
19	A	34	TRP	0	0.010	0.005	5.006	-0.487	-0.243	-0.001	-0.007	-0.237	0.000
20	A	35	ARG	1	0.897	0.941	6.801	-0.073	-0.073	0.000	0.000	0.000	0.000
21	A	36	GLY	0	0.020	0.017	10.499	-0.023	-0.023	0.000	0.000	0.000	0.000
22	A	37	GLU	-1	-0.905	-0.957	10.856	0.037	0.037	0.000	0.000	0.000	0.000
23	A	38	GLN	0	-0.044	-0.015	11.304	0.002	0.002	0.000	0.000	0.000	0.000
24	A	39	THR	0	-0.018	-0.015	5.971	-0.058	-0.058	0.000	0.000	0.000	0.000
25	A	40	ILE	0	-0.044	-0.047	7.826	-0.019	-0.019	0.000	0.000	0.000	0.000
26	A	41	ALA	0	0.011	-0.001	7.506	0.011	0.011	0.000	0.000	0.000	0.000
27	A	42	HIS	1	0.888	0.936	9.130	-0.044	-0.044	0.000	0.000	0.000	0.000
28	A	43	PHE	0	0.019	0.009	10.954	-0.029	-0.029	0.000	0.000	0.000	0.000
29	A	44	MET	0	0.036	0.046	13.583	0.010	0.010	0.000	0.000	0.000	0.000
30	A	45	PRO	0	-0.025	-0.011	16.730	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	46	LYS	1	0.978	0.997	17.632	-0.038	-0.038	0.000	0.000	0.000	0.000
32	A	47	PRO	0	0.056	0.010	21.125	0.009	0.009	0.000	0.000	0.000	0.000
33	A	48	PHE	0	0.044	0.022	21.959	0.000	0.000	0.000	0.000	0.000	0.000
34	A	49	HIS	0	-0.007	0.018	18.936	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	50	THR	0	-0.014	-0.018	23.586	0.006	0.006	0.000	0.000	0.000	0.000
36	A	51	ALA	0	-0.023	0.004	26.405	0.006	0.006	0.000	0.000	0.000	0.000
37	A	52	ILE	0	-0.002	-0.004	27.824	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	53	PRO	0	0.040	-0.011	29.747	0.003	0.003	0.000	0.000	0.000	0.000
39	A	54	GLY	0	0.040	0.030	29.625	0.000	0.000	0.000	0.000	0.000	0.000
40	A	55	PHE	0	0.002	0.001	26.608	0.001	0.001	0.000	0.000	0.000	0.000
41	A	56	VAL	0	-0.007	-0.010	20.442	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	57	TYR	0	-0.011	0.005	22.008	0.011	0.011	0.000	0.000	0.000	0.000
43	A	58	GLY	0	0.088	0.028	21.718	0.013	0.013	0.000	0.000	0.000	0.000
44	A	59	GLY	0	0.026	0.006	21.040	0.019	0.019	0.000	0.000	0.000	0.000
45	A	60	LEU	0	0.021	0.037	16.455	0.025	0.025	0.000	0.000	0.000	0.000
46	A	61	ILE	0	0.022	0.010	16.801	0.037	0.037	0.000	0.000	0.000	0.000
47	A	62	ALA	0	-0.001	-0.012	16.558	0.040	0.040	0.000	0.000	0.000	0.000
48	A	63	SER	0	-0.034	-0.034	15.408	0.038	0.038	0.000	0.000	0.000	0.000
49	A	64	LEU	0	-0.016	-0.006	12.301	0.085	0.085	0.000	0.000	0.000	0.000
50	A	65	ILE	0	0.015	-0.008	11.530	0.132	0.132	0.000	0.000	0.000	0.000
51	A	66	ASP	-1	-0.817	-0.878	11.681	0.648	0.648	0.000	0.000	0.000	0.000
52	A	67	CYS	0	0.027	0.014	8.840	0.097	0.097	0.000	0.000	0.000	0.000
53	A	68	HIS	0	0.028	0.036	7.313	0.891	0.891	0.000	0.000	0.000	0.000
54	A	69	GLY	0	0.015	0.019	7.066	0.338	0.338	0.000	0.000	0.000	0.000
55	A	70	THR	0	0.003	-0.006	7.369	-0.148	-0.148	0.000	0.000	0.000	0.000
56	A	71	GLY	0	-0.017	-0.001	4.066	-0.132	0.103	0.008	-0.108	-0.135	0.001
57	A	72	SER	0	-0.038	-0.048	3.707	-1.262	-0.816	0.013	-0.159	-0.300	-0.001
58	A	73	ALA	0	-0.001	0.008	5.668	-0.528	-0.528	0.000	0.000	0.000	0.000
59	A	74	SER	0	-0.066	-0.059	4.012	-0.272	-0.174	-0.001	-0.028	-0.069	0.000
60	A	75	ALA	0	-0.006	0.011	2.700	-1.196	-0.581	0.102	-0.217	-0.499	0.000
61	A	76	ALA	0	0.025	-0.003	4.612	0.122	0.151	-0.001	-0.010	-0.018	0.000
62	A	77	ALA	0	-0.070	-0.028	8.104	0.003	0.003	0.000	0.000	0.000	0.000
63	A	78	GLN	0	-0.084	-0.025	5.865	-0.286	-0.286	0.000	0.000	0.000	0.000
64	A	92	PRO	0	-0.038	-0.006	6.021	0.016	0.016	0.000	0.000	0.000	0.000
65	A	93	ARG	1	0.996	0.999	6.829	-0.068	-0.068	0.000	0.000	0.000	0.000
66	A	94	PHE	0	-0.026	-0.007	8.186	-0.133	-0.133	0.000	0.000	0.000	0.000
67	A	95	VAL	0	0.037	0.008	9.901	0.098	0.098	0.000	0.000	0.000	0.000
68	A	96	THR	0	0.036	-0.008	12.584	-0.017	-0.017	0.000	0.000	0.000	0.000
69	A	97	ALA	0	-0.087	-0.040	14.517	-0.044	-0.044	0.000	0.000	0.000	0.000
70	A	98	ALA	0	-0.002	-0.008	17.469	-0.029	-0.029	0.000	0.000	0.000	0.000
71	A	99	LEU	0	0.004	-0.006	15.115	0.034	0.034	0.000	0.000	0.000	0.000
72	A	100	ASN	0	-0.064	-0.013	18.217	-0.026	-0.026	0.000	0.000	0.000	0.000
73	A	101	ILE	0	0.025	0.004	17.742	0.020	0.020	0.000	0.000	0.000	0.000
74	A	102	ASP	-1	-0.909	-0.924	21.203	0.118	0.118	0.000	0.000	0.000	0.000
75	A	103	TYR	0	-0.037	-0.049	21.562	0.011	0.011	0.000	0.000	0.000	0.000
76	A	104	LEU	0	-0.021	-0.016	23.280	-0.011	-0.011	0.000	0.000	0.000	0.000
77	A	105	ALA	0	0.026	0.016	25.585	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	106	PRO	0	-0.027	-0.011	25.621	0.009	0.009	0.000	0.000	0.000	0.000
79	A	107	THR	0	0.033	0.015	20.900	0.003	0.003	0.000	0.000	0.000	0.000
80	A	108	PRO	0	0.018	0.008	24.280	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	109	MET	0	-0.048	-0.019	23.418	0.004	0.004	0.000	0.000	0.000	0.000
82	A	110	GLY	0	-0.023	-0.008	23.130	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	111	VAL	0	-0.017	-0.010	20.985	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	112	GLU	-1	-0.941	-0.974	14.376	0.008	0.008	0.000	0.000	0.000	0.000
85	A	113	LEU	0	-0.028	-0.029	15.886	0.009	0.009	0.000	0.000	0.000	0.000
86	A	114	GLU	-1	-0.873	-0.928	13.817	0.110	0.110	0.000	0.000	0.000	0.000
87	A	115	LEU	0	-0.044	-0.033	11.145	0.010	0.010	0.000	0.000	0.000	0.000
88	A	116	VAL	0	0.038	0.026	11.190	0.029	0.029	0.000	0.000	0.000	0.000
89	A	117	GLY	0	-0.016	-0.003	10.327	0.012	0.012	0.000	0.000	0.000	0.000
90	A	118	GLU	-1	-0.870	-0.946	11.318	0.091	0.091	0.000	0.000	0.000	0.000
91	A	119	ILE	0	0.029	0.005	8.627	0.038	0.038	0.000	0.000	0.000	0.000
92	A	120	LYS	1	0.862	0.919	12.773	-0.177	-0.177	0.000	0.000	0.000	0.000
93	A	121	GLU	-1	-0.758	-0.863	14.835	0.080	0.080	0.000	0.000	0.000	0.000
94	A	122	VAL	0	0.061	0.039	12.009	0.033	0.033	0.000	0.000	0.000	0.000
95	A	123	LYS	1	0.846	0.900	14.461	-0.083	-0.083	0.000	0.000	0.000	0.000
96	A	124	PRO	0	0.052	0.032	13.459	0.020	0.020	0.000	0.000	0.000	0.000
97	A	125	ARG	1	0.843	0.919	13.267	-0.079	-0.079	0.000	0.000	0.000	0.000
98	A	126	LYS	1	0.844	0.896	14.335	-0.098	-0.098	0.000	0.000	0.000	0.000
99	A	127	VAL	0	-0.006	0.020	9.998	-0.039	-0.039	0.000	0.000	0.000	0.000
100	A	128	VAL	0	-0.058	-0.008	13.027	0.037	0.037	0.000	0.000	0.000	0.000
101	A	129	VAL	0	-0.005	-0.010	10.010	-0.018	-0.018	0.000	0.000	0.000	0.000
102	A	130	GLU	-1	-0.792	-0.864	13.257	0.150	0.150	0.000	0.000	0.000	0.000
103	A	131	ILE	0	-0.006	0.005	11.568	0.022	0.022	0.000	0.000	0.000	0.000
104	A	132	ALA	0	0.009	0.008	14.199	-0.040	-0.040	0.000	0.000	0.000	0.000
105	A	133	LEU	0	0.026	0.020	15.441	0.014	0.014	0.000	0.000	0.000	0.000
106	A	134	SER	0	0.004	-0.006	17.053	-0.028	-0.028	0.000	0.000	0.000	0.000
107	A	135	ALA	0	0.060	0.011	18.512	0.005	0.005	0.000	0.000	0.000	0.000
108	A	136	ASP	-1	-0.826	-0.914	21.432	0.065	0.065	0.000	0.000	0.000	0.000
109	A	137	GLY	0	-0.001	0.010	24.074	0.000	0.000	0.000	0.000	0.000	0.000
110	A	138	LYS	1	0.753	0.863	20.659	-0.082	-0.082	0.000	0.000	0.000	0.000
111	A	139	LEU	0	0.015	0.034	19.890	0.003	0.003	0.000	0.000	0.000	0.000
112	A	140	CYS	0	-0.029	-0.011	21.173	-0.011	-0.011	0.000	0.000	0.000	0.000
113	A	141	ALA	0	0.011	0.002	19.864	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	142	ARG	1	0.844	0.922	18.658	-0.135	-0.135	0.000	0.000	0.000	0.000
115	A	143	GLY	0	0.043	0.021	17.042	-0.010	-0.010	0.000	0.000	0.000	0.000
116	A	144	HIS	0	-0.027	-0.020	16.842	0.012	0.012	0.000	0.000	0.000	0.000
117	A	145	MET	0	0.013	0.035	11.834	0.024	0.024	0.000	0.000	0.000	0.000
118	A	146	VAL	0	-0.027	-0.009	15.477	-0.031	-0.031	0.000	0.000	0.000	0.000
119	A	147	ALA	0	0.068	0.045	11.418	0.006	0.006	0.000	0.000	0.000	0.000
120	A	148	VAL	0	0.022	-0.007	13.472	-0.065	-0.065	0.000	0.000	0.000	0.000
121	A	149	LYS	1	0.935	0.982	11.881	0.093	0.093	0.000	0.000	0.000	0.000
122	A	150	MET	0	0.005	-0.013	11.439	-0.038	-0.038	0.000	0.000	0.000	0.000
123	A	151	PRO	0	-0.041	-0.007	13.778	-0.044	-0.044	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:PHE)