FMO DATABASE

FMODB ID: N187Q

Calculation Name: 2D1H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D1H

Chain ID: A

ChEMBL ID:

UniProt ID: F9VNN8

Base Structure: X-ray

Registration Date: 2023-03-13

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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-790280.621577
FMO2-HF: Nuclear repulsion	748107.552121
FMO2-HF: Total energy	-42173.069456
FMO2-MP2: Total energy	-42292.485586

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.
-26.763	-24.593	24.988	-10.15	-17.005	0.027

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 : 0.042 / q_NPA : 0.038

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	LYS	1	0.822	0.917	3.898	0.500	3.223	-0.015	-1.528	-1.180	0.004
4	A	4	GLU	-1	-0.753	-0.872	6.733	-0.975	-0.975	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.841	0.898	3.799	0.275	0.577	0.002	-0.050	-0.255	0.000
6	A	6	LEU	0	0.011	0.010	2.342	0.373	1.078	0.806	-0.236	-1.275	-0.003
7	A	7	GLU	-1	-0.770	-0.851	5.591	0.665	0.665	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.075	-0.051	7.224	-0.062	-0.062	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.884	0.936	2.142	-18.321	-26.071	17.025	-5.455	-3.820	0.054
10	A	10	LYS	1	0.842	0.907	7.142	-0.617	-0.617	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.794	-0.878	9.294	0.769	0.769	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.840	-0.939	7.109	3.961	3.961	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.031	-0.016	4.366	-0.450	-0.378	-0.001	-0.005	-0.066	0.000
14	A	14	ARG	1	0.783	0.870	7.742	-0.870	-0.870	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.012	-0.005	11.527	-0.143	-0.143	0.000	0.000	0.000	0.000
16	A	16	CYS	0	-0.168	-0.083	8.935	-0.228	-0.228	0.000	0.000	0.000	0.000
17	A	17	TYR	0	-0.058	-0.064	6.666	-0.167	-0.167	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.891	0.958	11.888	-0.547	-0.547	0.000	0.000	0.000	0.000
19	A	19	ILE	0	-0.034	0.000	11.003	-0.087	-0.087	0.000	0.000	0.000	0.000
20	A	20	THR	0	0.004	-0.031	15.295	0.061	0.061	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.783	-0.909	15.187	0.382	0.382	0.000	0.000	0.000	0.000
22	A	22	THR	0	0.003	0.009	15.892	-0.029	-0.029	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.769	-0.845	14.731	-0.038	-0.038	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.000	0.003	10.203	-0.108	-0.108	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.014	0.015	12.144	-0.081	-0.081	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.007	-0.012	14.778	-0.087	-0.087	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.015	0.002	7.794	-0.094	-0.094	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.001	-0.006	7.871	-0.210	-0.210	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.807	0.901	11.160	0.272	0.272	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.050	-0.035	13.375	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.014	-0.004	7.824	-0.126	-0.126	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.854	-0.916	10.972	-0.562	-0.562	0.000	0.000	0.000	0.000
33	A	33	ILE	0	0.012	0.014	12.961	-0.025	-0.025	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.884	-0.937	12.083	-1.458	-1.458	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.846	0.915	15.088	0.487	0.487	0.000	0.000	0.000	0.000
36	A	36	PRO	0	-0.007	0.004	17.923	0.014	0.014	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.012	-0.003	18.133	0.051	0.051	0.000	0.000	0.000	0.000
38	A	38	THR	0	-0.035	-0.044	20.867	0.010	0.010	0.000	0.000	0.000	0.000
39	A	39	SER	0	0.006	-0.019	22.811	0.007	0.007	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.783	-0.886	24.010	-0.218	-0.218	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.737	-0.833	23.380	-0.346	-0.346	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.020	0.005	18.134	0.014	0.014	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.017	-0.006	22.165	0.024	0.024	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.822	-0.894	25.210	-0.121	-0.121	0.000	0.000	0.000	0.000
45	A	45	ILE	0	-0.042	-0.020	20.285	0.014	0.014	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.034	-0.022	17.242	0.014	0.014	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.813	0.899	23.273	0.142	0.142	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.004	0.019	22.231	0.018	0.018	0.000	0.000	0.000	0.000
49	A	49	SER	0	0.033	0.016	26.340	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.877	0.903	26.176	0.175	0.175	0.000	0.000	0.000	0.000
51	A	51	THR	0	0.019	0.005	25.418	-0.014	-0.014	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.019	-0.004	22.794	0.007	0.007	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.055	0.032	20.924	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.785	-0.890	20.686	-0.212	-0.212	0.000	0.000	0.000	0.000
55	A	55	ASN	0	-0.044	-0.005	21.997	-0.018	-0.018	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.040	0.009	17.306	0.000	0.000	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.025	-0.020	16.880	-0.030	-0.030	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.837	0.907	17.424	0.088	0.088	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.866	0.934	15.350	-0.044	-0.044	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.035	0.006	11.489	-0.015	-0.015	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.048	-0.015	13.571	-0.089	-0.089	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.871	-0.917	15.951	-0.059	-0.059	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.009	0.003	11.304	0.025	0.025	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.007	0.001	11.612	-0.059	-0.059	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.047	-0.004	7.457	-0.231	-0.231	0.000	0.000	0.000	0.000
66	A	66	VAL	0	-0.006	-0.005	10.850	-0.138	-0.138	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.027	0.018	14.183	0.077	0.077	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.907	0.944	17.407	0.266	0.266	0.000	0.000	0.000	0.000
69	A	69	THR	0	0.033	0.020	20.966	0.020	0.020	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.944	0.970	23.385	0.245	0.245	0.000	0.000	0.000	0.000
71	A	71	THR	0	0.023	0.017	26.157	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	79	PRO	0	-0.009	-0.022	32.671	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	80	LYS	1	0.897	0.954	27.797	0.261	0.261	0.000	0.000	0.000	0.000
74	A	81	TYR	0	-0.006	-0.009	24.759	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	82	TYR	0	0.003	0.012	22.309	0.019	0.019	0.000	0.000	0.000	0.000
76	A	83	TYR	0	-0.031	-0.023	18.525	0.002	0.002	0.000	0.000	0.000	0.000
77	A	84	SER	0	0.030	0.003	16.280	0.022	0.022	0.000	0.000	0.000	0.000
78	A	85	ILE	0	0.028	0.019	9.703	0.049	0.049	0.000	0.000	0.000	0.000
79	A	86	SER	0	-0.020	-0.023	10.480	0.059	0.059	0.000	0.000	0.000	0.000
80	A	87	SER	0	0.006	-0.008	10.435	-0.250	-0.250	0.000	0.000	0.000	0.000
81	A	88	ASN	0	0.007	0.007	9.170	-0.188	-0.188	0.000	0.000	0.000	0.000
82	A	89	ILE	0	0.043	0.019	5.713	-0.308	-0.308	0.000	0.000	0.000	0.000
83	A	90	LEU	0	-0.004	0.010	2.628	-1.649	-0.082	0.426	-0.450	-1.542	-0.001
84	A	91	GLU	-1	-0.719	-0.828	2.479	-5.118	-3.593	1.273	-1.042	-1.755	-0.016
85	A	92	LYS	1	0.775	0.906	5.088	1.490	1.609	-0.001	-0.006	-0.111	0.000
86	A	93	ILE	0	0.086	0.032	2.252	-0.224	-0.013	1.834	-0.373	-1.672	-0.004
87	A	94	ARG	1	0.818	0.879	2.313	-2.818	-0.239	3.469	-1.581	-4.467	-0.005
88	A	95	ASN	0	-0.019	-0.036	3.119	2.152	1.728	0.121	0.712	-0.408	-0.001
89	A	96	ASP	-1	-0.770	-0.828	6.384	-0.126	-0.126	0.000	0.000	0.000	0.000
90	A	97	LEU	0	-0.017	-0.019	3.279	-0.136	0.405	0.049	-0.136	-0.454	-0.001
91	A	98	LEU	0	-0.002	0.007	6.789	-0.049	-0.049	0.000	0.000	0.000	0.000
92	A	99	ASN	0	-0.031	-0.031	8.940	-0.397	-0.397	0.000	0.000	0.000	0.000
93	A	101	ALA	0	0.044	0.021	10.314	-0.173	-0.173	0.000	0.000	0.000	0.000
94	A	102	LYS	1	0.818	0.893	12.161	-1.048	-1.048	0.000	0.000	0.000	0.000
95	A	103	ARG	1	0.947	0.964	11.697	-0.877	-0.877	0.000	0.000	0.000	0.000
96	A	104	MET	0	-0.019	-0.008	13.961	-0.068	-0.068	0.000	0.000	0.000	0.000
97	A	105	GLU	-1	-0.803	-0.881	16.242	0.831	0.831	0.000	0.000	0.000	0.000
98	A	106	LEU	0	0.006	-0.002	18.017	-0.088	-0.088	0.000	0.000	0.000	0.000
99	A	107	ALA	0	-0.040	-0.004	19.676	-0.073	-0.073	0.000	0.000	0.000	0.000
100	A	108	ALA	0	-0.024	0.003	20.954	-0.036	-0.036	0.000	0.000	0.000	0.000
101	A	109	THR	0	-0.089	-0.048	22.678	-0.051	-0.051	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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