FMO DATABASE

FMODB ID: R8GG8

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	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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-509098.411444
FMO2-HF: Nuclear repulsion	476829.495513
FMO2-HF: Total energy	-32268.915931
FMO2-MP2: Total energy	-32360.332464

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.
-8.333	-2.083	6.869	-4.307	-8.807	-0.016

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 : 0.002 / q_NPA : -0.012

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	-0.880	-0.936	3.281	-3.160	-1.115	0.000	-0.800	-1.245	0.000
4	A	6	ARG	1	0.906	0.947	2.747	-1.379	0.091	0.548	-0.551	-1.466	0.002
5	A	7	ILE	0	0.036	0.020	2.079	-0.277	-0.466	3.771	-1.314	-2.267	-0.010
6	A	8	GLU	-1	-0.809	-0.905	4.824	-0.451	-0.310	-0.001	-0.014	-0.126	0.000
7	A	9	LYS	1	0.783	0.872	7.738	1.472	1.472	0.000	0.000	0.000	0.000
8	A	10	ASP	-1	-0.870	-0.927	7.490	-0.512	-0.512	0.000	0.000	0.000	0.000
9	A	11	LEU	0	-0.004	-0.009	8.599	0.252	0.252	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.841	-0.901	10.834	-0.617	-0.617	0.000	0.000	0.000	0.000
11	A	13	LEU	0	-0.040	-0.017	12.608	0.114	0.114	0.000	0.000	0.000	0.000
12	A	14	LEU	0	0.012	0.006	13.190	0.087	0.087	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.841	-0.914	14.970	-0.258	-0.258	0.000	0.000	0.000	0.000
14	A	16	LYS	1	0.925	0.969	17.118	0.324	0.324	0.000	0.000	0.000	0.000
15	A	17	ASN	0	0.006	-0.011	16.772	0.038	0.038	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.035	0.019	17.885	0.035	0.035	0.000	0.000	0.000	0.000
17	A	19	MET	0	-0.020	0.004	20.971	0.032	0.032	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.897	-0.928	22.771	-0.157	-0.157	0.000	0.000	0.000	0.000
19	A	21	MET	0	0.019	0.010	21.805	0.022	0.022	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.892	0.940	23.700	0.198	0.198	0.000	0.000	0.000	0.000
21	A	23	SER	0	-0.069	-0.022	27.552	0.007	0.007	0.000	0.000	0.000	0.000
22	A	24	ILE	0	-0.031	-0.018	27.354	0.011	0.011	0.000	0.000	0.000	0.000
23	A	25	LYS	1	0.907	0.952	30.201	0.078	0.078	0.000	0.000	0.000	0.000
24	A	26	LEU	0	-0.010	0.002	26.359	0.003	0.003	0.000	0.000	0.000	0.000
25	A	27	SER	0	-0.014	-0.036	30.807	0.003	0.003	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.835	-0.927	30.412	-0.059	-0.059	0.000	0.000	0.000	0.000
27	A	29	ASP	-1	-0.916	-0.959	29.415	-0.046	-0.046	0.000	0.000	0.000	0.000
28	A	30	GLU	-1	-0.822	-0.875	26.818	-0.072	-0.072	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.934	-0.969	25.598	-0.099	-0.099	0.000	0.000	0.000	0.000
30	A	32	ALA	0	0.027	0.025	25.317	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	33	VAL	0	-0.063	-0.028	21.734	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	34	VAL	0	0.004	-0.008	21.113	-0.017	-0.017	0.000	0.000	0.000	0.000
33	A	35	GLU	-1	-0.927	-0.964	20.596	-0.125	-0.125	0.000	0.000	0.000	0.000
34	A	36	ARG	1	0.892	0.947	18.959	0.035	0.035	0.000	0.000	0.000	0.000
35	A	37	ALA	0	0.007	-0.008	16.763	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.007	-0.006	15.897	-0.050	-0.050	0.000	0.000	0.000	0.000
37	A	39	ASN	0	0.011	0.009	16.790	-0.035	-0.035	0.000	0.000	0.000	0.000
38	A	40	TYR	0	0.005	-0.003	13.347	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	41	ARG	1	0.783	0.873	12.143	0.318	0.318	0.000	0.000	0.000	0.000
40	A	42	ASP	-1	-0.819	-0.904	12.289	-0.413	-0.413	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.908	-0.950	12.824	-0.203	-0.203	0.000	0.000	0.000	0.000
42	A	44	SER	0	-0.105	-0.062	7.350	-0.102	-0.102	0.000	0.000	0.000	0.000
43	A	45	VAL	0	0.040	0.032	8.708	-0.226	-0.226	0.000	0.000	0.000	0.000
44	A	46	TYR	0	0.059	0.036	10.875	0.034	0.034	0.000	0.000	0.000	0.000
45	A	47	TYR	0	-0.017	-0.031	8.816	0.087	0.087	0.000	0.000	0.000	0.000
46	A	48	LEU	0	-0.032	-0.010	5.272	0.019	0.019	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.998	-0.999	7.751	-0.297	-0.297	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.834	0.926	10.891	0.169	0.169	0.000	0.000	0.000	0.000
49	A	51	GLY	0	-0.022	0.000	7.427	0.122	0.122	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.883	-0.914	7.213	0.658	0.658	0.000	0.000	0.000	0.000
51	A	53	HIS	0	0.049	-0.009	2.324	-2.630	-1.700	2.123	-1.004	-2.048	-0.003
52	A	54	ILE	0	0.004	0.005	3.816	-0.473	0.245	0.126	-0.282	-0.561	-0.002
53	A	55	THR	0	-0.010	-0.024	5.582	-0.384	-0.352	-0.001	-0.001	-0.029	0.000
54	A	56	SER	0	-0.013	-0.013	4.988	-0.407	-0.407	0.000	0.000	0.000	0.000
55	A	57	PHE	0	-0.011	-0.004	2.832	-0.649	0.422	0.304	-0.331	-1.044	-0.003
56	A	58	GLY	0	0.014	0.018	4.861	0.132	0.164	-0.001	-0.010	-0.021	0.000
57	A	59	CYS	0	-0.065	-0.025	8.362	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	60	ILE	0	0.044	0.017	6.655	0.057	0.057	0.000	0.000	0.000	0.000
59	A	61	THR	0	-0.015	-0.021	7.583	0.144	0.144	0.000	0.000	0.000	0.000
60	A	62	TYR	0	-0.031	0.008	10.111	0.050	0.050	0.000	0.000	0.000	0.000
61	A	63	ALA	0	0.006	-0.001	12.508	0.021	0.021	0.000	0.000	0.000	0.000
62	A	64	HIS	0	0.004	-0.018	10.831	0.097	0.097	0.000	0.000	0.000	0.000
63	A	65	GLY	0	-0.006	0.018	14.332	0.030	0.030	0.000	0.000	0.000	0.000
64	A	66	LEU	0	-0.073	-0.035	16.367	0.015	0.015	0.000	0.000	0.000	0.000
65	A	67	LEU	0	0.024	0.005	17.661	0.013	0.013	0.000	0.000	0.000	0.000
66	A	68	ASP	-1	-0.799	-0.908	17.119	-0.156	-0.156	0.000	0.000	0.000	0.000
67	A	69	SER	0	-0.043	-0.007	19.669	0.015	0.015	0.000	0.000	0.000	0.000
68	A	70	LEU	0	0.021	0.010	22.329	0.007	0.007	0.000	0.000	0.000	0.000
69	A	71	ARG	1	0.833	0.873	19.106	0.183	0.183	0.000	0.000	0.000	0.000
70	A	72	MET	0	-0.033	-0.003	22.877	0.008	0.008	0.000	0.000	0.000	0.000
71	A	73	LEU	0	-0.047	-0.017	25.345	0.006	0.006	0.000	0.000	0.000	0.000
72	A	74	HIS	1	0.772	0.866	27.342	0.080	0.080	0.000	0.000	0.000	0.000
73	A	75	ARG	1	0.886	0.948	28.365	0.043	0.043	0.000	0.000	0.000	0.000
74	A	76	ILE	0	-0.003	0.012	24.944	0.001	0.001	0.000	0.000	0.000	0.000
75	A	77	ILE	0	-0.042	-0.016	21.017	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	78	GLU	-1	-0.975	-0.983	24.657	-0.048	-0.048	0.000	0.000	0.000	0.000

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