FMO DATABASE

FMODB ID: 7G8QK

Calculation Name: 2FDQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FDQ

Chain ID: A

ChEMBL ID:

UniProt ID: P82934

Base Structure: X-ray

Registration Date: 2023-06-21

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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-596376.639165
FMO2-HF: Nuclear repulsion	561578.828123
FMO2-HF: Total energy	-34797.811043
FMO2-MP2: Total energy	-34899.308971

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:SER)

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

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.
-37.219	-30.345	11.897	-9.731	-9.04	-0.093

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.006

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	3	ALA	0	0.044	0.037	3.819	-4.387	-2.956	-0.001	-0.609	-0.821	0.003
4	A	4	GLU	-1	-0.865	-0.941	2.336	-10.939	-7.040	3.803	-4.112	-3.590	-0.039
5	A	5	PHE	0	0.007	0.007	4.343	-0.384	-0.102	-0.001	-0.108	-0.173	0.000
6	A	6	ASP	-1	-0.897	-0.971	5.735	2.014	2.014	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.800	0.897	7.468	0.022	0.022	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.066	0.034	8.040	0.004	0.004	0.000	0.000	0.000	0.000
9	A	9	ALA	0	-0.030	-0.007	9.645	0.045	0.045	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.785	-0.882	11.615	0.199	0.199	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.840	-0.886	11.525	-0.386	-0.386	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.017	-0.008	13.388	0.025	0.025	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.743	0.868	15.197	-0.145	-0.145	0.000	0.000	0.000	0.000
14	A	14	ASN	0	-0.093	-0.039	17.261	0.037	0.037	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.046	-0.031	17.069	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.912	0.966	20.125	0.148	0.148	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.013	0.006	23.270	0.018	0.018	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.920	0.963	23.321	0.139	0.139	0.000	0.000	0.000	0.000
19	A	19	PRO	0	-0.002	0.015	20.479	0.003	0.003	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.004	-0.005	23.006	0.028	0.028	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.909	-0.977	22.822	-0.219	-0.219	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.874	-0.946	22.204	-0.339	-0.339	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.686	-0.807	19.154	-0.387	-0.387	0.000	0.000	0.000	0.000
24	A	24	MET	0	-0.039	0.006	18.167	-0.024	-0.024	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.004	-0.010	18.418	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	26	PHE	0	0.030	0.020	12.605	0.007	0.007	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.034	0.022	13.582	-0.063	-0.063	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.002	-0.013	13.978	0.003	0.003	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.025	-0.020	15.140	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	30	HIS	1	0.926	0.955	10.896	0.862	0.862	0.000	0.000	0.000	0.000
31	A	31	TYR	0	0.073	0.047	10.991	-0.024	-0.024	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.896	0.958	11.891	0.107	0.107	0.000	0.000	0.000	0.000
33	A	33	GLN	0	-0.018	-0.017	11.720	0.145	0.145	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.034	-0.028	7.855	-0.046	-0.046	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.030	-0.013	8.777	0.249	0.249	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.064	-0.027	11.361	0.115	0.115	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.005	-0.007	12.997	0.059	0.059	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.792	-0.871	13.946	-0.388	-0.388	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.078	-0.044	16.650	0.056	0.056	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.004	0.001	19.382	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.010	-0.009	22.011	0.023	0.023	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.875	-0.934	24.562	-0.065	-0.065	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.753	0.851	27.505	0.137	0.137	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.002	0.001	27.225	0.008	0.008	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.058	0.025	30.324	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	46	MET	0	-0.005	-0.012	33.995	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.021	0.014	36.052	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.832	-0.918	29.905	-0.071	-0.071	0.000	0.000	0.000	0.000
49	A	49	PHE	0	0.048	0.004	30.579	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.992	1.015	26.924	0.053	0.053	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.033	0.021	26.406	-0.014	-0.014	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.841	0.902	25.894	0.073	0.073	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.015	0.018	25.988	-0.014	-0.014	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.923	0.942	21.779	0.129	0.129	0.000	0.000	0.000	0.000
55	A	55	TRP	0	0.006	-0.002	21.623	-0.034	-0.034	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.739	-0.834	22.521	-0.188	-0.188	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.025	0.013	20.106	-0.026	-0.026	0.000	0.000	0.000	0.000
58	A	58	TRP	0	0.017	0.004	15.992	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	ASN	0	0.016	0.012	18.603	-0.018	-0.018	0.000	0.000	0.000	0.000
60	A	60	GLN	0	-0.125	-0.070	20.672	0.011	0.011	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.045	-0.022	14.292	-0.059	-0.059	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.904	0.965	15.746	0.204	0.204	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.003	0.004	16.271	-0.027	-0.027	0.000	0.000	0.000	0.000
64	A	64	THR	0	-0.073	-0.046	10.776	-0.069	-0.069	0.000	0.000	0.000	0.000
65	A	65	SER	0	0.047	0.018	8.426	-0.027	-0.027	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.913	0.941	7.263	-0.405	-0.405	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.807	-0.894	1.836	-24.105	-24.312	7.887	-4.357	-3.324	-0.060
68	A	68	ASP	-1	-0.834	-0.894	4.873	-2.975	-2.908	-0.001	0.000	-0.065	0.000
69	A	69	ALA	0	-0.050	-0.018	7.611	-0.019	-0.019	0.000	0.000	0.000	0.000
70	A	70	MET	0	-0.023	-0.012	2.824	-0.302	0.782	0.202	-0.487	-0.798	0.003
71	A	71	LYS	1	0.904	0.966	4.710	2.772	2.883	-0.001	-0.008	-0.102	0.000
72	A	72	SER	0	-0.036	-0.029	5.442	0.728	0.728	0.000	0.000	0.000	0.000
73	A	73	TYR	0	-0.040	-0.036	7.776	0.362	0.362	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.055	0.017	3.565	0.219	0.426	0.009	-0.050	-0.167	0.000
75	A	75	ASP	-1	-0.871	-0.920	7.801	-1.913	-1.913	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.830	0.896	9.872	0.922	0.922	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.017	0.010	10.573	0.170	0.170	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.823	-0.911	10.400	-0.570	-0.570	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.965	-0.963	12.980	-0.519	-0.519	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.018	-0.029	15.431	0.096	0.096	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.775	0.860	12.218	0.603	0.603	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.857	0.940	14.457	0.756	0.756	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.832	0.914	19.471	0.381	0.381	0.000	0.000	0.000	0.000
84	A	84	TYR	0	-0.051	-0.054	20.373	0.032	0.032	0.000	0.000	0.000	0.000
85	A	85	GLY	0	0.024	0.026	20.822	0.034	0.034	0.000	0.000	0.000	0.000
86	A	86	ILE	0	-0.018	-0.014	17.261	0.019	0.019	0.000	0.000	0.000	0.000

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