FMO DATABASE

FMODB ID: ZVGQN

Calculation Name: 2PD2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PD2

Chain ID: A

ChEMBL ID:

UniProt ID: Q976P3

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	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	108
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-863931.958303
FMO2-HF: Nuclear repulsion	822119.228769
FMO2-HF: Total energy	-41812.729533
FMO2-MP2: Total energy	-41936.632965

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:1:MET)

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

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.
-7.474	-2.092	10.104	-5.082	-10.404	-0.032

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.002

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	3	VAL	0	-0.016	0.003	2.587	-0.736	1.462	0.342	-0.855	-1.685	0.000
4	A	4	VAL	0	-0.020	-0.003	5.002	-0.055	-0.019	-0.001	-0.006	-0.028	0.000
5	A	5	VAL	0	0.021	0.002	8.779	0.076	0.076	0.000	0.000	0.000	0.000
6	A	6	GLN	0	0.034	0.032	10.667	0.060	0.060	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.016	-0.016	14.365	-0.043	-0.043	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.913	0.953	17.367	0.041	0.041	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.804	-0.874	20.878	-0.050	-0.050	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.027	-0.012	22.353	-0.024	-0.024	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.804	-0.908	24.388	-0.115	-0.115	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.784	0.873	20.466	0.086	0.086	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.010	0.018	19.889	-0.035	-0.035	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.039	0.010	19.577	-0.041	-0.041	0.000	0.000	0.000	0.000
15	A	15	GLN	0	0.014	0.015	19.698	-0.060	-0.060	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.013	0.021	16.038	-0.055	-0.055	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.041	0.011	14.896	-0.080	-0.080	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.922	0.962	15.359	0.305	0.305	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.024	-0.024	13.367	-0.068	-0.068	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.006	0.001	10.221	-0.137	-0.137	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.007	0.004	10.801	-0.209	-0.209	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.050	-0.032	11.996	-0.086	-0.086	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.018	0.006	5.565	-0.046	-0.046	0.000	0.000	0.000	0.000
24	A	24	TYR	0	-0.004	-0.014	7.108	-0.510	-0.510	0.000	0.000	0.000	0.000
25	A	25	ASN	0	-0.053	-0.031	8.426	-0.116	-0.116	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.975	-0.962	7.510	-1.838	-1.838	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.026	-0.012	2.194	-1.262	-1.110	2.658	-0.620	-2.191	-0.006
28	A	28	LYS	1	0.921	0.960	4.916	1.232	1.301	-0.001	-0.006	-0.062	0.000
29	A	29	ASP	-1	-0.902	-0.971	4.002	-3.556	-3.062	0.003	-0.124	-0.373	0.000
30	A	30	ALA	0	0.005	0.017	2.233	-7.455	-4.693	3.596	-3.262	-3.097	-0.026
31	A	31	GLU	-1	-0.845	-0.899	2.757	5.208	5.852	0.073	0.357	-1.073	-0.001
32	A	32	ILE	0	0.001	-0.004	4.555	0.344	0.417	-0.001	-0.017	-0.055	0.000
33	A	33	GLH	0	-0.032	-0.040	7.392	0.404	0.404	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.024	-0.016	10.072	-0.044	-0.044	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.015	0.005	12.714	0.040	0.040	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.004	0.000	15.565	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	37	HIS	0	0.045	-0.004	18.383	0.035	0.035	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.021	-0.017	21.563	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	39	SER	0	0.011	0.004	24.689	-0.010	-0.010	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.014	-0.001	20.926	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.030	0.002	22.457	-0.018	-0.018	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.930	0.962	23.673	0.047	0.047	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.007	0.010	22.014	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.005	0.000	19.698	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.019	0.021	23.712	0.010	0.010	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.840	0.899	27.172	0.037	0.037	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.892	-0.945	29.164	-0.091	-0.091	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.031	-0.002	24.801	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.866	-0.936	27.419	-0.146	-0.146	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.058	-0.042	22.172	-0.019	-0.019	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.803	0.888	22.481	0.113	0.113	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.027	0.011	22.630	-0.017	-0.017	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.001	0.003	18.196	-0.027	-0.027	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.016	0.008	18.279	-0.053	-0.053	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.812	-0.900	18.293	-0.198	-0.198	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.836	-0.897	16.939	-0.576	-0.576	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.003	-0.005	12.967	-0.058	-0.058	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.000	-0.002	13.980	-0.045	-0.045	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.903	0.960	15.487	0.314	0.314	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.788	0.881	11.975	0.723	0.723	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.054	-0.024	9.884	-0.076	-0.076	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.002	0.015	9.701	0.016	0.016	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.016	-0.009	10.894	0.126	0.126	0.000	0.000	0.000	0.000
64	A	64	ILE	0	0.003	0.001	12.845	0.023	0.023	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.023	-0.016	15.337	0.054	0.054	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.046	0.018	17.660	-0.026	-0.026	0.000	0.000	0.000	0.000
67	A	67	CYM	-1	-0.911	-0.849	20.666	0.107	0.107	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.730	-0.851	22.538	0.043	0.043	0.000	0.000	0.000	0.000
69	A	69	ASN	0	-0.012	-0.036	25.239	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	70	SER	0	0.034	-0.030	24.152	-0.009	-0.009	0.000	0.000	0.000	0.000
71	A	71	ILE	0	-0.001	0.007	24.959	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.855	0.914	27.954	-0.069	-0.069	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.033	-0.029	28.935	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	74	GLN	0	-0.049	-0.026	28.253	-0.016	-0.016	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.055	-0.024	31.253	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.005	0.014	27.997	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	77	SER	0	0.009	-0.024	31.884	0.012	0.012	0.000	0.000	0.000	0.000
78	A	78	HIS	0	0.019	-0.010	28.250	-0.020	-0.020	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.859	-0.899	29.223	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	80	GLN	0	0.003	-0.004	30.912	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.015	0.009	25.116	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	82	ILE	0	-0.007	-0.002	22.727	0.003	0.003	0.000	0.000	0.000	0.000
83	A	83	PRO	0	-0.001	-0.017	24.100	0.010	0.010	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.029	0.024	21.209	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	85	ILE	0	0.002	0.013	19.610	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.872	0.947	16.593	0.086	0.086	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.019	0.010	20.217	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.010	0.009	18.526	0.028	0.028	0.000	0.000	0.000	0.000
89	A	89	THR	0	0.010	-0.009	21.853	-0.012	-0.012	0.000	0.000	0.000	0.000
90	A	90	SER	0	0.047	0.011	22.379	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.027	-0.011	19.155	0.024	0.024	0.000	0.000	0.000	0.000
92	A	92	VAL	0	0.017	0.004	17.933	0.022	0.022	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.030	0.015	18.533	0.039	0.039	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.768	-0.863	15.008	0.407	0.407	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.005	-0.009	13.577	0.071	0.071	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.008	0.009	13.883	0.088	0.088	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.874	0.938	15.506	-0.271	-0.271	0.000	0.000	0.000	0.000
98	A	98	LYS	1	0.841	0.931	10.562	-0.605	-0.605	0.000	0.000	0.000	0.000
99	A	99	GLN	0	-0.005	-0.007	11.065	0.244	0.244	0.000	0.000	0.000	0.000
100	A	100	SER	0	-0.093	-0.051	12.198	0.110	0.110	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.846	-0.915	11.184	0.923	0.923	0.000	0.000	0.000	0.000
102	A	102	GLY	0	-0.012	0.002	9.225	0.235	0.235	0.000	0.000	0.000	0.000
103	A	103	TRP	0	-0.091	-0.061	6.606	0.872	0.872	0.000	0.000	0.000	0.000
104	A	104	ILE	0	0.022	0.004	3.031	-0.188	-1.234	3.435	-0.549	-1.840	0.001
105	A	105	TYR	0	-0.017	-0.023	6.486	-0.675	-0.675	0.000	0.000	0.000	0.000
106	A	106	LEU	0	0.009	0.009	8.274	-0.017	-0.017	0.000	0.000	0.000	0.000
107	A	107	ALA	0	0.009	0.002	10.211	-0.060	-0.060	0.000	0.000	0.000	0.000
108	A	108	LEU	0	-0.031	-0.001	12.198	-0.007	-0.007	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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