FMO DATABASE

FMODB ID: 39J2L

Calculation Name: 2XI1-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2XI1

Chain ID: B

ChEMBL ID:

UniProt ID: C6KEI3

Base Structure: X-ray

Registration Date: 2023-06-22

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	100
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-826841.095876
FMO2-HF: Nuclear repulsion	785586.46349
FMO2-HF: Total energy	-41254.632385
FMO2-MP2: Total energy	-41376.053808

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(B:74:VAL)

Summations of interaction energy for fragment #1(B:74:VAL)

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.
-8.865	-3.435	1.063	-2.533	-3.961	-0.01

Interaction energy analysis for fragmet #1(B:74:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : -0.016

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	B	76	LEU	0	0.013	0.026	3.291	-3.435	-1.808	0.036	-0.920	-0.743	-0.001
4	B	77	ARG	1	0.906	0.966	2.365	-0.537	0.231	0.601	-0.404	-0.965	0.002
5	B	78	PRO	0	0.074	0.049	7.467	-0.234	-0.234	0.000	0.000	0.000	0.000
6	B	79	MET	0	0.030	-0.011	10.034	0.086	0.086	0.000	0.000	0.000	0.000
7	B	80	THR	0	-0.042	-0.016	9.908	0.118	0.118	0.000	0.000	0.000	0.000
8	B	81	TYR	0	0.001	-0.009	12.323	-0.020	-0.020	0.000	0.000	0.000	0.000
9	B	82	LYS	1	1.016	0.997	10.888	-0.181	-0.181	0.000	0.000	0.000	0.000
10	B	83	GLY	0	0.033	0.027	10.044	0.001	0.001	0.000	0.000	0.000	0.000
11	B	84	ALA	0	0.010	-0.021	10.759	-0.042	-0.042	0.000	0.000	0.000	0.000
12	B	85	VAL	0	-0.006	0.022	13.473	0.000	0.000	0.000	0.000	0.000	0.000
13	B	86	ASP	-1	-0.902	-0.955	11.276	-0.061	-0.061	0.000	0.000	0.000	0.000
14	B	87	LEU	0	-0.045	-0.023	9.712	-0.019	-0.019	0.000	0.000	0.000	0.000
15	B	88	SER	0	0.050	0.009	12.252	0.000	0.000	0.000	0.000	0.000	0.000
16	B	89	PHE	0	-0.010	-0.015	15.904	0.005	0.005	0.000	0.000	0.000	0.000
17	B	90	PHE	0	-0.017	0.011	12.148	-0.003	-0.003	0.000	0.000	0.000	0.000
18	B	91	LEU	0	0.010	-0.004	12.609	0.004	0.004	0.000	0.000	0.000	0.000
19	B	92	LYS	1	0.896	0.965	15.966	0.143	0.143	0.000	0.000	0.000	0.000
20	B	93	GLU	-1	-1.029	-1.009	18.239	-0.087	-0.087	0.000	0.000	0.000	0.000
21	B	94	LYS	1	0.929	0.962	14.756	0.136	0.136	0.000	0.000	0.000	0.000
22	B	95	GLY	0	0.012	0.005	16.682	-0.026	-0.026	0.000	0.000	0.000	0.000
23	B	96	GLY	0	0.058	0.019	17.631	0.028	0.028	0.000	0.000	0.000	0.000
24	B	97	LEU	0	-0.015	0.010	16.564	-0.014	-0.014	0.000	0.000	0.000	0.000
25	B	98	GLU	-1	-0.823	-0.941	19.743	-0.161	-0.161	0.000	0.000	0.000	0.000
26	B	99	GLY	0	-0.044	-0.012	22.867	0.004	0.004	0.000	0.000	0.000	0.000
27	B	100	LEU	0	0.000	0.005	20.890	0.011	0.011	0.000	0.000	0.000	0.000
28	B	101	VAL	0	-0.034	-0.029	24.245	0.005	0.005	0.000	0.000	0.000	0.000
29	B	102	TYR	0	0.023	0.011	21.932	-0.023	-0.023	0.000	0.000	0.000	0.000
30	B	103	SER	0	-0.021	-0.017	23.024	0.015	0.015	0.000	0.000	0.000	0.000
31	B	104	GLN	0	0.091	0.031	22.379	-0.046	-0.046	0.000	0.000	0.000	0.000
32	B	105	LYS	1	1.010	0.972	18.835	0.411	0.411	0.000	0.000	0.000	0.000
33	B	106	ARG	1	0.878	0.940	19.772	0.222	0.222	0.000	0.000	0.000	0.000
34	B	107	LYS	1	0.860	0.944	17.904	0.428	0.428	0.000	0.000	0.000	0.000
35	B	108	GLU	-1	-0.853	-0.906	16.739	-0.476	-0.476	0.000	0.000	0.000	0.000
36	B	109	ILE	0	-0.037	-0.019	15.255	-0.082	-0.082	0.000	0.000	0.000	0.000
37	B	110	LEU	0	-0.054	0.003	13.250	-0.095	-0.095	0.000	0.000	0.000	0.000
38	B	111	ASP	-1	-0.774	-0.893	12.325	-0.704	-0.704	0.000	0.000	0.000	0.000
39	B	112	LEU	0	0.021	0.002	10.979	-0.181	-0.181	0.000	0.000	0.000	0.000
40	B	113	TRP	0	0.010	0.024	9.293	-0.319	-0.319	0.000	0.000	0.000	0.000
41	B	114	VAL	0	0.015	0.011	7.878	-0.290	-0.290	0.000	0.000	0.000	0.000
42	B	115	TYR	0	-0.002	0.019	5.812	-0.141	-0.141	0.000	0.000	0.000	0.000
43	B	116	HIS	0	-0.100	-0.049	4.940	-0.804	-0.742	-0.001	-0.001	-0.060	0.000
44	B	117	THR	0	-0.038	-0.029	4.700	-0.116	0.033	-0.001	-0.015	-0.133	0.000
45	B	118	GLN	0	-0.041	-0.044	2.872	-2.506	-0.711	0.351	-0.857	-1.289	-0.009
46	B	119	GLY	0	-0.019	-0.007	3.100	-0.473	0.467	0.077	-0.333	-0.684	-0.002
47	B	120	TYR	0	-0.038	-0.004	4.005	0.475	0.564	0.000	-0.003	-0.087	0.000
48	B	121	PHE	0	0.011	-0.008	7.456	-0.115	-0.115	0.000	0.000	0.000	0.000
49	B	122	PRO	0	0.006	0.010	10.201	0.122	0.122	0.000	0.000	0.000	0.000
50	B	123	ASP	-1	-0.904	-0.950	12.698	-0.540	-0.540	0.000	0.000	0.000	0.000
51	B	124	TRP	0	0.047	0.015	11.363	0.128	0.128	0.000	0.000	0.000	0.000
52	B	125	GLN	0	-0.013	0.002	15.733	0.115	0.115	0.000	0.000	0.000	0.000
53	B	126	CYS	0	-0.015	-0.008	17.539	0.006	0.006	0.000	0.000	0.000	0.000
54	B	127	TYR	0	-0.028	-0.042	19.307	0.010	0.010	0.000	0.000	0.000	0.000
55	B	128	THR	0	0.022	0.024	23.990	0.003	0.003	0.000	0.000	0.000	0.000
56	B	129	PRO	0	0.044	0.022	27.602	-0.008	-0.008	0.000	0.000	0.000	0.000
57	B	130	GLY	0	-0.041	-0.031	30.011	0.005	0.005	0.000	0.000	0.000	0.000
58	B	131	PRO	0	0.018	0.014	32.836	0.001	0.001	0.000	0.000	0.000	0.000
59	B	132	GLY	0	0.072	0.022	34.186	0.005	0.005	0.000	0.000	0.000	0.000
60	B	133	VAL	0	-0.029	-0.030	28.979	-0.009	-0.009	0.000	0.000	0.000	0.000
61	B	134	ARG	1	0.821	0.940	26.480	0.173	0.173	0.000	0.000	0.000	0.000
62	B	135	TYR	0	0.046	0.006	26.002	-0.007	-0.007	0.000	0.000	0.000	0.000
63	B	136	PRO	0	0.032	0.037	20.688	-0.007	-0.007	0.000	0.000	0.000	0.000
64	B	137	LEU	0	0.030	-0.011	21.542	0.018	0.018	0.000	0.000	0.000	0.000
65	B	138	THR	0	0.006	-0.002	15.721	0.013	0.013	0.000	0.000	0.000	0.000
66	B	139	PHE	0	0.012	0.004	19.068	-0.003	-0.003	0.000	0.000	0.000	0.000
67	B	140	GLY	0	0.088	0.013	17.385	0.000	0.000	0.000	0.000	0.000	0.000
68	B	141	TRP	0	-0.031	0.006	14.925	-0.018	-0.018	0.000	0.000	0.000	0.000
69	B	142	CYS	0	-0.055	-0.045	17.679	0.026	0.026	0.000	0.000	0.000	0.000
70	B	143	PHE	0	0.026	0.000	17.621	0.010	0.010	0.000	0.000	0.000	0.000
71	B	144	LYS	1	0.927	0.961	21.609	0.134	0.134	0.000	0.000	0.000	0.000
72	B	145	LEU	0	-0.040	-0.004	23.187	-0.003	-0.003	0.000	0.000	0.000	0.000
73	B	146	VAL	0	-0.026	-0.011	26.469	0.013	0.013	0.000	0.000	0.000	0.000
74	B	147	PRO	0	0.057	0.024	29.929	-0.006	-0.006	0.000	0.000	0.000	0.000
75	B	148	VAL	0	-0.027	-0.002	32.130	0.005	0.005	0.000	0.000	0.000	0.000
76	B	179	GLU	-1	-0.869	-0.950	33.055	-0.138	-0.138	0.000	0.000	0.000	0.000
77	B	180	VAL	0	-0.049	-0.020	30.842	-0.012	-0.012	0.000	0.000	0.000	0.000
78	B	181	LEU	0	0.000	0.002	27.919	0.004	0.004	0.000	0.000	0.000	0.000
79	B	182	LYS	1	0.916	0.962	26.610	0.138	0.138	0.000	0.000	0.000	0.000
80	B	183	TRP	0	0.012	0.007	19.849	0.008	0.008	0.000	0.000	0.000	0.000
81	B	184	LYS	1	0.917	0.971	23.974	0.142	0.142	0.000	0.000	0.000	0.000
82	B	185	PHE	0	0.031	0.043	19.576	-0.005	-0.005	0.000	0.000	0.000	0.000
83	B	186	ASP	-1	-0.895	-0.962	23.147	-0.109	-0.109	0.000	0.000	0.000	0.000
84	B	187	SER	0	0.072	0.020	22.756	-0.011	-0.011	0.000	0.000	0.000	0.000
85	B	188	HIS	0	0.009	0.008	23.736	0.000	0.000	0.000	0.000	0.000	0.000
86	B	189	LEU	0	-0.075	-0.028	22.870	0.004	0.004	0.000	0.000	0.000	0.000
87	B	190	ALA	0	0.040	0.016	20.467	-0.014	-0.014	0.000	0.000	0.000	0.000
88	B	191	HIS	0	-0.031	0.000	22.008	0.012	0.012	0.000	0.000	0.000	0.000
89	B	192	THR	0	0.047	0.033	25.026	0.009	0.009	0.000	0.000	0.000	0.000
90	B	193	HIS	0	-0.082	-0.029	22.469	-0.001	-0.001	0.000	0.000	0.000	0.000
91	B	194	MET	0	0.053	0.017	26.017	0.001	0.001	0.000	0.000	0.000	0.000
92	B	195	ALA	0	-0.008	-0.006	24.958	0.003	0.003	0.000	0.000	0.000	0.000
93	B	196	ARG	1	0.934	0.980	25.594	0.121	0.121	0.000	0.000	0.000	0.000
94	B	197	GLU	-1	-0.929	-0.973	28.375	-0.089	-0.089	0.000	0.000	0.000	0.000
95	B	198	LEU	0	-0.039	-0.018	31.076	0.006	0.006	0.000	0.000	0.000	0.000
96	B	199	HIS	1	0.837	0.938	29.816	0.136	0.136	0.000	0.000	0.000	0.000
97	B	200	PRO	0	0.040	0.002	29.864	-0.011	-0.011	0.000	0.000	0.000	0.000
98	B	201	GLU	-1	-0.847	-0.918	30.798	-0.134	-0.134	0.000	0.000	0.000	0.000
99	B	202	PHE	0	-0.054	-0.013	26.574	-0.003	-0.003	0.000	0.000	0.000	0.000
100	B	203	TYR	0	-0.061	-0.028	23.660	-0.009	-0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:74:VAL)