FMO DATABASE

FMODB ID: ZV55N

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
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
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-508303.308481
FMO2-HF: Nuclear repulsion	476034.73723
FMO2-HF: Total energy	-32268.57125
FMO2-MP2: Total energy	-32359.969684

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.
-7.949	-2.994	9.987	-5.189	-9.753	-0.023

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 : -0.006 / 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	-0.883	-0.943	3.342	-3.109	-1.110	-0.001	-0.795	-1.203	0.000
4	A	6	ARG	1	0.908	0.949	2.589	-1.103	0.335	0.669	-0.602	-1.505	0.001
5	A	7	ILE	0	0.036	0.019	2.096	-0.290	-0.679	3.924	-1.296	-2.239	-0.011
6	A	8	GLU	-1	-0.838	-0.918	4.882	-0.281	-0.136	-0.001	-0.012	-0.132	0.000
7	A	9	LYS	1	0.911	0.956	7.731	1.426	1.426	0.000	0.000	0.000	0.000
8	A	10	ASP	-1	-0.855	-0.922	7.639	-0.520	-0.520	0.000	0.000	0.000	0.000
9	A	11	LEU	0	-0.021	-0.012	8.578	0.240	0.240	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.944	-0.972	10.864	-0.494	-0.494	0.000	0.000	0.000	0.000
11	A	13	LEU	0	-0.044	-0.018	12.723	0.112	0.112	0.000	0.000	0.000	0.000
12	A	14	LEU	0	0.008	0.002	13.268	0.084	0.084	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.836	-0.909	15.057	-0.257	-0.257	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.936	0.973	17.205	0.334	0.334	0.000	0.000	0.000	0.000
15	A	17	ASN	0	0.016	-0.007	17.171	0.043	0.043	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.021	0.013	17.919	0.034	0.034	0.000	0.000	0.000	0.000
17	A	19	MET	0	-0.070	-0.039	21.043	0.031	0.031	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.948	-0.972	22.875	-0.163	-0.163	0.000	0.000	0.000	0.000
19	A	21	MET	0	-0.001	-0.006	21.632	0.022	0.022	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.952	0.985	24.415	0.178	0.178	0.000	0.000	0.000	0.000
21	A	23	SER	0	-0.075	-0.025	27.617	0.007	0.007	0.000	0.000	0.000	0.000
22	A	24	ILE	0	-0.019	-0.005	27.421	0.010	0.010	0.000	0.000	0.000	0.000
23	A	25	LYS	1	0.903	0.949	30.273	0.077	0.077	0.000	0.000	0.000	0.000
24	A	26	LEU	0	0.000	0.007	26.473	0.002	0.002	0.000	0.000	0.000	0.000
25	A	27	SER	0	-0.013	-0.006	30.870	0.004	0.004	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.794	-0.910	30.448	-0.064	-0.064	0.000	0.000	0.000	0.000
27	A	29	ASP	-1	-0.928	-0.962	29.413	-0.052	-0.052	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.862	-0.915	26.879	-0.081	-0.081	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.925	-0.966	25.639	-0.098	-0.098	0.000	0.000	0.000	0.000
30	A	32	ALA	0	0.035	0.028	25.317	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	33	VAL	0	-0.071	-0.030	21.773	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	34	VAL	0	0.006	-0.009	21.134	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	35	GLU	-1	-0.939	-0.962	20.592	-0.125	-0.125	0.000	0.000	0.000	0.000
34	A	36	ARG	1	0.894	0.942	18.916	0.050	0.050	0.000	0.000	0.000	0.000
35	A	37	ALA	0	0.004	-0.013	16.768	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.019	-0.012	15.873	-0.051	-0.051	0.000	0.000	0.000	0.000
37	A	39	ASN	0	0.044	0.026	16.709	-0.036	-0.036	0.000	0.000	0.000	0.000
38	A	40	TYR	0	-0.012	-0.010	13.359	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	41	ARG	1	0.829	0.904	12.088	0.299	0.299	0.000	0.000	0.000	0.000
40	A	42	ASP	-1	-0.864	-0.932	12.176	-0.387	-0.387	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.919	-0.960	13.014	-0.204	-0.204	0.000	0.000	0.000	0.000
42	A	44	SER	0	-0.090	-0.050	7.219	-0.074	-0.074	0.000	0.000	0.000	0.000
43	A	45	VAL	0	0.046	0.030	8.506	-0.216	-0.216	0.000	0.000	0.000	0.000
44	A	46	TYR	0	0.047	0.028	10.683	0.052	0.052	0.000	0.000	0.000	0.000
45	A	47	TYR	0	-0.027	-0.034	8.570	0.095	0.095	0.000	0.000	0.000	0.000
46	A	48	LEU	0	-0.037	-0.010	5.127	0.047	0.047	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-1.007	-0.997	7.476	-0.166	-0.166	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.859	0.935	10.862	0.105	0.105	0.000	0.000	0.000	0.000
49	A	51	GLY	0	-0.028	-0.001	7.442	0.113	0.113	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.884	-0.913	7.224	0.809	0.809	0.000	0.000	0.000	0.000
51	A	53	HIS	0	0.048	-0.014	2.438	-2.375	-2.503	4.830	-1.777	-2.925	-0.006
52	A	54	ILE	0	0.015	0.010	3.631	-1.151	-0.368	0.272	-0.384	-0.671	-0.004
53	A	55	THR	0	-0.018	-0.028	5.372	-0.490	-0.465	-0.001	0.000	-0.023	0.000
54	A	56	SER	0	-0.016	-0.016	4.814	-0.476	-0.476	0.000	0.000	0.000	0.000
55	A	57	PHE	0	-0.017	-0.013	2.898	-0.567	0.476	0.296	-0.310	-1.030	-0.003
56	A	58	GLY	0	0.015	0.012	4.866	0.183	0.222	-0.001	-0.013	-0.025	0.000
57	A	59	CYS	0	-0.056	-0.017	8.378	0.007	0.007	0.000	0.000	0.000	0.000
58	A	60	ILE	0	0.041	0.018	6.708	0.062	0.062	0.000	0.000	0.000	0.000
59	A	61	THR	0	-0.013	-0.013	7.647	0.145	0.145	0.000	0.000	0.000	0.000
60	A	62	TYR	0	-0.013	0.015	10.235	0.056	0.056	0.000	0.000	0.000	0.000
61	A	63	ALA	0	0.002	-0.005	12.549	0.025	0.025	0.000	0.000	0.000	0.000
62	A	64	HIS	0	-0.010	-0.029	11.111	0.093	0.093	0.000	0.000	0.000	0.000
63	A	65	GLY	0	0.000	0.022	14.457	0.031	0.031	0.000	0.000	0.000	0.000
64	A	66	LEU	0	-0.074	-0.033	16.505	0.018	0.018	0.000	0.000	0.000	0.000
65	A	67	LEU	0	0.026	0.006	17.761	0.014	0.014	0.000	0.000	0.000	0.000
66	A	68	ASP	-1	-0.814	-0.915	17.068	-0.182	-0.182	0.000	0.000	0.000	0.000
67	A	69	SER	0	-0.027	-0.004	19.830	0.015	0.015	0.000	0.000	0.000	0.000
68	A	70	LEU	0	0.031	0.014	22.479	0.008	0.008	0.000	0.000	0.000	0.000
69	A	71	ARG	1	0.869	0.924	19.249	0.196	0.196	0.000	0.000	0.000	0.000
70	A	72	MET	0	-0.026	-0.007	22.954	0.008	0.008	0.000	0.000	0.000	0.000
71	A	73	LEU	0	-0.048	-0.016	25.530	0.008	0.008	0.000	0.000	0.000	0.000
72	A	74	HIS	1	0.763	0.853	27.500	0.088	0.088	0.000	0.000	0.000	0.000
73	A	75	ARG	1	0.894	0.951	28.553	0.054	0.054	0.000	0.000	0.000	0.000
74	A	76	ILE	0	0.000	0.018	24.620	0.001	0.001	0.000	0.000	0.000	0.000
75	A	77	ILE	0	-0.043	-0.018	21.143	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	78	GLU	-1	-0.982	-0.989	24.742	-0.063	-0.063	0.000	0.000	0.000	0.000

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