FMO DATABASE

FMODB ID: QVGGY

Calculation Name: 2PMR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PMR

Chain ID: A

ChEMBL ID:

UniProt ID: O27725

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	76
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-511613.01983
FMO2-HF: Nuclear repulsion	479343.984344
FMO2-HF: Total energy	-32269.035485
FMO2-MP2: Total energy	-32360.464162

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:3:CYS)

Summations of interaction energy for fragment #1(A:3:CYS)

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.
-8.643	-2.258	4.28	-3.183	-7.482	-0.008

Interaction energy analysis for fragmet #1(A:3:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.010

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

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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	5	GLU	-1	-0.889	-0.937	3.576	-3.657	-1.800	-0.004	-0.703	-1.149	0.000
4	A	6	ARG	1	0.903	0.954	3.157	-2.150	-0.720	0.472	-0.533	-1.369	0.005
5	A	7	ILE	0	0.063	0.034	2.294	-0.298	0.205	2.021	-0.746	-1.777	-0.007
6	A	8	GLU	-1	-0.815	-0.908	4.941	-0.546	-0.433	-0.001	-0.010	-0.102	0.000
7	A	9	LYS	1	0.795	0.881	7.805	1.504	1.504	0.000	0.000	0.000	0.000
8	A	10	ASP	-1	-0.887	-0.940	6.820	-0.508	-0.508	0.000	0.000	0.000	0.000
9	A	11	LEU	0	-0.005	-0.010	8.608	0.243	0.243	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.848	-0.904	10.915	-0.665	-0.665	0.000	0.000	0.000	0.000
11	A	13	LEU	0	-0.036	-0.014	12.483	0.107	0.107	0.000	0.000	0.000	0.000
12	A	14	LEU	0	0.013	0.012	13.213	0.079	0.079	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.766	-0.887	14.935	-0.184	-0.184	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.907	0.968	16.953	0.280	0.280	0.000	0.000	0.000	0.000
15	A	17	ASN	0	0.027	-0.001	16.332	0.027	0.027	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.017	0.015	17.959	0.031	0.031	0.000	0.000	0.000	0.000
17	A	19	MET	0	-0.079	-0.040	20.890	0.024	0.024	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.895	-0.915	22.403	-0.121	-0.121	0.000	0.000	0.000	0.000
19	A	21	MET	0	0.015	0.011	22.000	0.020	0.020	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.871	0.935	21.717	0.186	0.186	0.000	0.000	0.000	0.000
21	A	23	SER	0	-0.023	0.001	27.247	0.007	0.007	0.000	0.000	0.000	0.000
22	A	24	ILE	0	-0.019	-0.001	27.291	0.009	0.009	0.000	0.000	0.000	0.000
23	A	25	LYS	1	0.837	0.908	30.623	0.064	0.064	0.000	0.000	0.000	0.000
24	A	26	LEU	0	-0.016	-0.006	26.776	0.001	0.001	0.000	0.000	0.000	0.000
25	A	27	SER	0	-0.003	-0.025	31.179	0.002	0.002	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.846	-0.935	30.520	-0.032	-0.032	0.000	0.000	0.000	0.000
27	A	29	ASP	-1	-0.913	-0.955	29.413	-0.015	-0.015	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.809	-0.868	26.848	-0.039	-0.039	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.917	-0.963	25.682	-0.068	-0.068	0.000	0.000	0.000	0.000
30	A	32	ALA	0	0.024	0.022	25.477	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	33	VAL	0	-0.054	-0.025	21.832	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	34	VAL	0	-0.001	-0.007	21.278	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	35	GLU	-1	-0.899	-0.952	20.859	-0.079	-0.079	0.000	0.000	0.000	0.000
34	A	36	ARG	1	0.894	0.957	19.328	-0.022	-0.022	0.000	0.000	0.000	0.000
35	A	37	ALA	0	0.001	-0.012	17.002	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.004	-0.006	16.191	-0.038	-0.038	0.000	0.000	0.000	0.000
37	A	39	ASN	0	-0.028	-0.021	17.039	-0.024	-0.024	0.000	0.000	0.000	0.000
38	A	40	TYR	0	-0.007	-0.017	13.757	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	41	ARG	1	0.788	0.878	12.547	0.251	0.251	0.000	0.000	0.000	0.000
40	A	42	ASP	-1	-0.819	-0.898	12.620	-0.318	-0.318	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.887	-0.955	13.905	-0.068	-0.068	0.000	0.000	0.000	0.000
42	A	44	SER	0	-0.068	-0.044	7.939	-0.074	-0.074	0.000	0.000	0.000	0.000
43	A	45	VAL	0	0.040	0.035	9.239	-0.146	-0.146	0.000	0.000	0.000	0.000
44	A	46	TYR	0	0.046	0.027	11.220	0.038	0.038	0.000	0.000	0.000	0.000
45	A	47	TYR	0	-0.037	-0.035	9.404	0.082	0.082	0.000	0.000	0.000	0.000
46	A	48	LEU	0	-0.018	-0.004	5.400	0.026	0.026	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.997	-1.008	8.140	-0.231	-0.231	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.835	0.936	10.961	0.043	0.043	0.000	0.000	0.000	0.000
49	A	51	GLY	0	-0.016	0.009	7.384	0.093	0.093	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.850	-0.897	6.803	0.747	0.747	0.000	0.000	0.000	0.000
51	A	53	HIS	0	0.043	-0.020	2.260	-2.635	-1.439	1.685	-0.874	-2.008	-0.005
52	A	54	ILE	0	-0.012	0.005	4.301	0.237	0.736	0.029	-0.131	-0.397	0.000
53	A	55	THR	0	-0.015	-0.036	6.310	-0.184	-0.154	-0.001	0.000	-0.029	0.000
54	A	56	SER	0	-0.020	-0.010	5.705	-0.313	-0.313	0.000	0.000	0.000	0.000
55	A	57	PHE	0	0.001	0.006	3.293	-0.562	0.186	0.080	-0.184	-0.644	-0.001
56	A	58	GLY	0	0.016	0.027	5.335	0.005	0.014	-0.001	-0.002	-0.007	0.000
57	A	59	CYS	0	-0.065	-0.024	8.877	-0.067	-0.067	0.000	0.000	0.000	0.000
58	A	60	ILE	0	0.046	0.021	6.927	0.021	0.021	0.000	0.000	0.000	0.000
59	A	61	THR	0	-0.021	-0.031	7.671	0.088	0.088	0.000	0.000	0.000	0.000
60	A	62	TYR	0	-0.029	0.009	10.289	0.021	0.021	0.000	0.000	0.000	0.000
61	A	63	ALA	0	0.000	0.001	12.868	0.003	0.003	0.000	0.000	0.000	0.000
62	A	64	HIS	0	0.013	-0.014	10.908	0.075	0.075	0.000	0.000	0.000	0.000
63	A	65	GLY	0	-0.021	0.003	14.376	0.019	0.019	0.000	0.000	0.000	0.000
64	A	66	LEU	0	-0.069	-0.036	16.359	0.008	0.008	0.000	0.000	0.000	0.000
65	A	67	LEU	0	0.024	0.009	17.617	0.004	0.004	0.000	0.000	0.000	0.000
66	A	68	ASP	-1	-0.804	-0.911	17.179	-0.112	-0.112	0.000	0.000	0.000	0.000
67	A	69	SER	0	-0.034	0.000	19.627	0.009	0.009	0.000	0.000	0.000	0.000
68	A	70	LEU	0	0.019	0.012	22.176	0.002	0.002	0.000	0.000	0.000	0.000
69	A	71	ARG	1	0.816	0.853	18.779	0.136	0.136	0.000	0.000	0.000	0.000
70	A	72	MET	0	-0.032	-0.006	22.718	0.006	0.006	0.000	0.000	0.000	0.000
71	A	73	LEU	0	-0.037	-0.008	25.217	0.003	0.003	0.000	0.000	0.000	0.000
72	A	74	HIS	1	0.755	0.858	27.247	0.049	0.049	0.000	0.000	0.000	0.000
73	A	75	ARG	1	0.896	0.949	28.252	0.018	0.018	0.000	0.000	0.000	0.000
74	A	76	ILE	0	0.002	0.012	24.891	0.000	0.000	0.000	0.000	0.000	0.000
75	A	77	ILE	0	-0.036	-0.012	20.835	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	78	GLU	-1	-0.969	-0.982	24.291	-0.022	-0.022	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:CYS)