FMO DATABASE

FMODB ID: R5G78

Calculation Name: 1PD3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PD3

Chain ID: A

ChEMBL ID:

UniProt ID: P03508

Base Structure: X-ray

Registration Date: 2023-06-20

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	54
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-300684.75802
FMO2-HF: Nuclear repulsion	277501.018111
FMO2-HF: Total energy	-23183.739909
FMO2-MP2: Total energy	-23252.718462

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:63:GLY)

Summations of interaction energy for fragment #1(A:63:GLY)

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.
2.789	5.355	0.012	-1.038	-1.54	-0.002

Interaction energy analysis for fragmet #1(A:63:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / 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

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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	65	TRP	0	0.040	0.028	3.860	-0.527	1.176	-0.002	-0.852	-0.849	-0.002
4	A	66	ARG	1	0.999	0.987	3.188	2.000	2.528	0.015	-0.141	-0.402	0.000
5	A	67	GLU	-1	-0.935	-0.935	4.211	0.556	0.891	-0.001	-0.045	-0.289	0.000
6	A	68	GLN	0	-0.029	-0.039	5.753	0.650	0.650	0.000	0.000	0.000	0.000
7	A	69	LEU	0	0.008	0.023	8.231	0.259	0.259	0.000	0.000	0.000	0.000
8	A	70	GLY	0	0.020	0.020	8.509	0.203	0.203	0.000	0.000	0.000	0.000
9	A	71	GLN	0	-0.004	-0.017	9.259	0.072	0.072	0.000	0.000	0.000	0.000
10	A	72	LYS	1	0.944	0.979	11.939	0.643	0.643	0.000	0.000	0.000	0.000
11	A	73	PHE	0	-0.001	-0.016	12.087	0.046	0.046	0.000	0.000	0.000	0.000
12	A	74	GLU	-1	-0.771	-0.852	14.039	-0.112	-0.112	0.000	0.000	0.000	0.000
13	A	75	GLU	-1	-0.871	-0.928	15.885	-0.122	-0.122	0.000	0.000	0.000	0.000
14	A	76	ILE	0	-0.039	-0.014	17.295	0.025	0.025	0.000	0.000	0.000	0.000
15	A	77	ARG	1	0.805	0.887	16.322	0.178	0.178	0.000	0.000	0.000	0.000
16	A	78	TRP	0	0.026	0.017	19.931	0.026	0.026	0.000	0.000	0.000	0.000
17	A	79	LEU	0	0.012	0.001	21.829	0.012	0.012	0.000	0.000	0.000	0.000
18	A	80	ILE	0	-0.044	-0.034	22.748	0.012	0.012	0.000	0.000	0.000	0.000
19	A	81	GLU	-1	-0.903	-0.952	23.763	-0.076	-0.076	0.000	0.000	0.000	0.000
20	A	82	GLU	-1	-0.952	-0.959	25.715	-0.069	-0.069	0.000	0.000	0.000	0.000
21	A	83	VAL	0	-0.082	-0.050	28.080	0.009	0.009	0.000	0.000	0.000	0.000
22	A	84	ARG	1	0.902	0.945	29.090	0.066	0.066	0.000	0.000	0.000	0.000
23	A	85	HIS	0	-0.050	-0.015	30.369	0.007	0.007	0.000	0.000	0.000	0.000
24	A	86	ARG	1	0.879	0.943	31.985	0.057	0.057	0.000	0.000	0.000	0.000
25	A	87	LEU	0	0.011	0.025	33.650	0.002	0.002	0.000	0.000	0.000	0.000
26	A	88	LYS	1	0.904	0.949	36.216	0.037	0.037	0.000	0.000	0.000	0.000
27	A	89	ILE	0	-0.008	-0.001	34.528	0.001	0.001	0.000	0.000	0.000	0.000
28	A	90	THR	0	0.015	-0.002	38.681	0.000	0.000	0.000	0.000	0.000	0.000
29	A	91	GLU	-1	-0.861	-0.941	35.200	-0.051	-0.051	0.000	0.000	0.000	0.000
30	A	92	ASN	0	0.007	-0.019	37.412	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	93	SER	0	-0.047	0.003	37.877	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	94	PHE	0	0.088	0.022	35.525	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	95	GLU	-1	-0.936	-0.978	34.576	-0.073	-0.073	0.000	0.000	0.000	0.000
34	A	96	GLN	0	0.077	0.055	32.454	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	97	ILE	0	-0.031	-0.011	32.286	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	98	THR	0	-0.018	-0.014	30.777	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	99	PHE	0	0.019	0.001	28.175	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	100	MET	0	-0.008	0.001	27.408	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	101	GLN	0	0.021	0.018	26.728	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	102	ALA	0	0.003	0.005	25.120	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	103	LEU	0	0.026	0.009	22.938	-0.019	-0.019	0.000	0.000	0.000	0.000
42	A	104	GLN	0	-0.064	-0.044	21.767	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	105	LEU	0	0.026	0.024	21.479	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	106	LEU	0	-0.017	-0.002	18.060	-0.029	-0.029	0.000	0.000	0.000	0.000
45	A	107	LEU	0	0.000	-0.008	17.329	-0.028	-0.028	0.000	0.000	0.000	0.000
46	A	108	GLU	-1	-0.959	-0.966	16.600	-0.209	-0.209	0.000	0.000	0.000	0.000
47	A	109	VAL	0	0.051	0.012	15.154	-0.035	-0.035	0.000	0.000	0.000	0.000
48	A	110	GLH	0	-0.059	-0.034	12.236	-0.070	-0.070	0.000	0.000	0.000	0.000
49	A	111	GLN	0	-0.006	-0.025	11.899	-0.063	-0.063	0.000	0.000	0.000	0.000
50	A	112	GLU	-1	-0.900	-0.942	12.410	-0.349	-0.349	0.000	0.000	0.000	0.000
51	A	113	ILE	0	-0.051	-0.030	8.278	-0.113	-0.113	0.000	0.000	0.000	0.000
52	A	114	ARG	1	0.802	0.917	7.739	-0.048	-0.048	0.000	0.000	0.000	0.000
53	A	115	THR	0	-0.045	-0.039	8.221	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	116	PHE	0	-0.023	0.019	8.211	0.006	0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:63:GLY)