FMO DATABASE

FMODB ID: 85YMY

Calculation Name: 3ITW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ITW

Chain ID: A

ChEMBL ID:

UniProt ID: Q333U2

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	123
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1022438.74834
FMO2-HF: Nuclear repulsion	973598.662899
FMO2-HF: Total energy	-48840.085442
FMO2-MP2: Total energy	-48981.995291

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:-2:GLY)

Summations of interaction energy for fragment #1(A:-2: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.
-0.42	0.52	-0.011	-0.456	-0.474	0

Interaction energy analysis for fragmet #1(A:-2:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : -0.004

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].
3	A	0	HIS	0	0.023	0.007	3.819	-0.450	0.490	-0.011	-0.456	-0.474
4	A	1	MET	0	0.008	0.011	6.807	0.224	0.224	0.000	0.000	0.000
5	A	2	VAL	0	0.016	0.013	10.209	-0.087	-0.087	0.000	0.000	0.000
6	A	3	VAL	0	-0.010	-0.004	13.009	0.077	0.077	0.000	0.000	0.000
7	A	4	GLU	-1	-0.849	-0.922	16.406	-0.167	-0.167	0.000	0.000	0.000
8	A	5	LEU	0	-0.033	-0.024	19.312	0.027	0.027	0.000	0.000	0.000
9	A	6	ALA	0	-0.008	0.005	22.410	-0.010	-0.010	0.000	0.000	0.000
10	A	7	TYR	0	-0.002	-0.045	22.918	0.000	0.000	0.000	0.000	0.000
11	A	8	THR	0	0.005	-0.035	27.630	0.000	0.000	0.000	0.000	0.000
12	A	9	ASP	-1	-0.901	-0.964	30.102	-0.104	-0.104	0.000	0.000	0.000
13	A	10	PRO	0	0.000	-0.010	25.001	-0.004	-0.004	0.000	0.000	0.000
14	A	11	ASP	-1	-0.817	-0.896	25.681	-0.143	-0.143	0.000	0.000	0.000
15	A	12	ARG	1	0.856	0.914	27.238	0.109	0.109	0.000	0.000	0.000
16	A	13	ALA	0	0.043	0.032	25.340	-0.001	-0.001	0.000	0.000	0.000
17	A	14	VAL	0	0.005	0.003	21.580	-0.009	-0.009	0.000	0.000	0.000
18	A	15	ASP	-1	-0.856	-0.912	23.342	-0.137	-0.137	0.000	0.000	0.000
19	A	16	TRP	0	0.047	0.012	25.078	-0.003	-0.003	0.000	0.000	0.000
20	A	17	LEU	0	-0.017	-0.007	20.982	-0.001	-0.001	0.000	0.000	0.000
21	A	18	VAL	0	-0.039	-0.015	20.164	-0.007	-0.007	0.000	0.000	0.000
22	A	19	ARG	1	0.832	0.910	22.155	0.117	0.117	0.000	0.000	0.000
23	A	20	VAL	0	-0.038	-0.015	25.201	0.005	0.005	0.000	0.000	0.000
24	A	21	PHE	0	-0.017	-0.021	20.480	0.010	0.010	0.000	0.000	0.000
25	A	22	GLY	0	-0.106	-0.026	20.110	-0.006	-0.006	0.000	0.000	0.000
26	A	23	PHE	0	0.018	0.015	16.926	-0.024	-0.024	0.000	0.000	0.000
27	A	24	ARG	1	0.934	0.958	13.418	0.464	0.464	0.000	0.000	0.000
28	A	25	LEU	0	-0.025	-0.015	15.686	-0.041	-0.041	0.000	0.000	0.000
29	A	26	LEU	0	-0.034	-0.007	10.604	-0.010	-0.010	0.000	0.000	0.000
30	A	27	LEU	0	-0.009	0.001	14.845	0.015	0.015	0.000	0.000	0.000
31	A	28	ARG	1	0.869	0.924	17.023	0.179	0.179	0.000	0.000	0.000
32	A	29	GLN	0	-0.036	0.012	20.611	0.018	0.018	0.000	0.000	0.000
33	A	30	PRO	0	0.024	0.002	22.828	0.005	0.005	0.000	0.000	0.000
34	A	31	ALA	0	0.053	0.012	24.787	-0.006	-0.006	0.000	0.000	0.000
35	A	32	ILE	0	0.016	0.007	25.695	0.000	0.000	0.000	0.000	0.000
36	A	33	GLY	0	0.022	0.019	29.251	0.003	0.003	0.000	0.000	0.000
37	A	34	THR	0	-0.017	-0.005	29.103	-0.006	-0.006	0.000	0.000	0.000
38	A	35	ILE	0	-0.006	0.004	23.388	-0.001	-0.001	0.000	0.000	0.000
39	A	36	ARG	1	0.899	0.944	25.482	0.131	0.131	0.000	0.000	0.000
40	A	37	HIS	0	-0.053	-0.033	17.291	0.037	0.037	0.000	0.000	0.000
41	A	38	ALA	0	0.008	0.001	19.425	0.001	0.001	0.000	0.000	0.000
42	A	39	ASP	-1	-0.819	-0.887	14.000	-0.391	-0.391	0.000	0.000	0.000
43	A	40	LEU	0	0.010	-0.015	15.666	0.003	0.003	0.000	0.000	0.000
44	A	41	ASP	-1	-0.820	-0.902	10.805	-0.728	-0.728	0.000	0.000	0.000
45	A	42	THR	0	-0.016	-0.031	12.223	0.088	0.088	0.000	0.000	0.000
46	A	43	GLY	0	-0.021	-0.005	10.653	0.078	0.078	0.000	0.000	0.000
47	A	44	GLY	0	-0.041	-0.028	8.508	-0.061	-0.061	0.000	0.000	0.000
48	A	45	GLY	0	0.004	0.020	9.016	0.135	0.135	0.000	0.000	0.000
49	A	46	ILE	0	-0.021	-0.009	8.837	-0.015	-0.015	0.000	0.000	0.000
50	A	47	VAL	0	0.026	0.021	12.359	0.073	0.073	0.000	0.000	0.000
51	A	48	MET	0	-0.003	0.009	15.713	-0.004	-0.004	0.000	0.000	0.000
52	A	49	VAL	0	-0.020	-0.006	17.563	0.037	0.037	0.000	0.000	0.000
53	A	50	ARG	1	0.898	0.931	20.440	0.168	0.168	0.000	0.000	0.000
54	A	51	ARG	1	0.921	0.973	23.598	0.118	0.118	0.000	0.000	0.000
55	A	52	THR	0	-0.005	-0.018	27.325	-0.001	-0.001	0.000	0.000	0.000
56	A	53	GLY	0	-0.010	-0.001	29.524	0.003	0.003	0.000	0.000	0.000
57	A	54	GLU	-1	-0.923	-0.957	27.157	-0.109	-0.109	0.000	0.000	0.000
58	A	55	PRO	0	0.016	0.014	24.768	-0.015	-0.015	0.000	0.000	0.000
59	A	56	TYR	0	-0.038	-0.028	16.021	-0.010	-0.010	0.000	0.000	0.000
60	A	57	THR	0	-0.025	-0.010	21.413	0.002	0.002	0.000	0.000	0.000
61	A	58	VAL	0	-0.010	0.000	23.416	0.005	0.005	0.000	0.000	0.000
62	A	59	SER	0	0.011	-0.001	25.936	0.001	0.001	0.000	0.000	0.000
63	A	60	CYS	0	-0.015	-0.002	28.323	0.005	0.005	0.000	0.000	0.000
64	A	61	ALA	0	0.001	0.000	31.398	-0.004	-0.004	0.000	0.000	0.000
65	A	62	GLY	0	0.023	-0.002	33.715	0.005	0.005	0.000	0.000	0.000
66	A	63	GLY	0	-0.026	-0.005	33.388	-0.004	-0.004	0.000	0.000	0.000
67	A	64	HIS	0	-0.051	-0.032	28.708	0.001	0.001	0.000	0.000	0.000
68	A	65	THR	0	0.002	-0.004	30.176	0.003	0.003	0.000	0.000	0.000
69	A	66	CYS	0	0.005	-0.002	29.251	-0.005	-0.005	0.000	0.000	0.000
70	A	67	LYS	1	0.913	0.963	24.361	0.083	0.083	0.000	0.000	0.000
71	A	68	GLN	0	0.014	0.003	23.891	-0.005	-0.005	0.000	0.000	0.000
72	A	69	VAL	0	-0.003	0.001	19.312	0.000	0.000	0.000	0.000	0.000
73	A	70	ILE	0	-0.012	-0.005	19.305	0.006	0.006	0.000	0.000	0.000
74	A	71	VAL	0	0.010	0.003	16.228	-0.015	-0.015	0.000	0.000	0.000
75	A	72	TRP	0	0.003	0.002	15.765	0.011	0.011	0.000	0.000	0.000
76	A	73	VAL	0	0.008	-0.011	16.275	-0.028	-0.028	0.000	0.000	0.000
77	A	74	SER	0	0.035	0.008	17.075	0.019	0.019	0.000	0.000	0.000
78	A	75	ASP	-1	-0.844	-0.919	18.865	-0.044	-0.044	0.000	0.000	0.000
79	A	76	VAL	0	-0.015	-0.024	22.110	-0.010	-0.010	0.000	0.000	0.000
80	A	77	ASP	-1	-0.825	-0.918	23.780	-0.040	-0.040	0.000	0.000	0.000
81	A	78	GLU	-1	-0.924	-0.953	23.397	-0.112	-0.112	0.000	0.000	0.000
82	A	79	HIS	1	0.875	0.931	20.126	0.125	0.125	0.000	0.000	0.000
83	A	80	PHE	0	0.021	0.008	24.134	-0.003	-0.003	0.000	0.000	0.000
84	A	81	MET	0	0.026	0.016	27.433	0.002	0.002	0.000	0.000	0.000
85	A	82	ARG	1	0.956	0.979	21.076	0.152	0.152	0.000	0.000	0.000
86	A	83	SER	0	-0.007	-0.010	25.830	-0.003	-0.003	0.000	0.000	0.000
87	A	84	THR	0	-0.008	-0.021	27.910	0.002	0.002	0.000	0.000	0.000
88	A	85	ALA	0	-0.034	0.002	30.786	0.002	0.002	0.000	0.000	0.000
89	A	86	ALA	0	-0.053	-0.026	29.039	0.000	0.000	0.000	0.000	0.000
90	A	87	GLY	0	-0.023	-0.008	31.076	-0.001	-0.001	0.000	0.000	0.000
91	A	88	ALA	0	-0.047	-0.015	29.151	0.001	0.001	0.000	0.000	0.000
92	A	89	ASP	-1	-0.873	-0.930	31.144	-0.057	-0.057	0.000	0.000	0.000
93	A	90	ILE	0	-0.046	-0.031	30.094	-0.002	-0.002	0.000	0.000	0.000
94	A	91	VAL	0	-0.052	-0.026	31.455	0.004	0.004	0.000	0.000	0.000
95	A	92	GLN	0	0.001	-0.004	30.940	0.005	0.005	0.000	0.000	0.000
96	A	93	PRO	0	0.021	0.012	31.046	-0.004	-0.004	0.000	0.000	0.000
97	A	94	LEU	0	-0.031	-0.004	27.615	0.003	0.003	0.000	0.000	0.000
98	A	95	GLN	0	-0.040	-0.015	30.343	0.007	0.007	0.000	0.000	0.000
99	A	96	ASP	-1	-0.802	-0.885	30.184	-0.012	-0.012	0.000	0.000	0.000
100	A	97	LYS	1	0.863	0.930	29.494	0.011	0.011	0.000	0.000	0.000
101	A	98	PRO	0	0.008	-0.008	30.610	0.002	0.002	0.000	0.000	0.000
102	A	99	TRP	0	-0.007	0.006	28.306	0.002	0.002	0.000	0.000	0.000
103	A	100	GLY	0	0.020	0.008	27.393	-0.003	-0.003	0.000	0.000	0.000
104	A	101	LEU	0	-0.024	0.003	25.335	-0.004	-0.004	0.000	0.000	0.000
105	A	102	ARG	1	0.825	0.894	25.698	0.020	0.020	0.000	0.000	0.000
106	A	103	GLN	0	-0.049	-0.035	25.178	-0.003	-0.003	0.000	0.000	0.000
107	A	104	TYR	0	-0.002	0.002	24.757	0.000	0.000	0.000	0.000	0.000
108	A	105	LEU	0	-0.010	0.002	26.310	-0.003	-0.003	0.000	0.000	0.000
109	A	106	VAL	0	-0.009	-0.004	25.887	0.002	0.002	0.000	0.000	0.000
110	A	107	ARG	1	0.946	0.998	27.461	0.052	0.052	0.000	0.000	0.000
111	A	108	ASP	-1	-0.755	-0.857	25.534	-0.112	-0.112	0.000	0.000	0.000
112	A	109	LEU	0	-0.023	-0.024	27.917	0.006	0.006	0.000	0.000	0.000
113	A	110	GLU	-1	-0.790	-0.844	28.473	-0.088	-0.088	0.000	0.000	0.000
114	A	111	GLY	0	-0.003	-0.009	29.820	0.007	0.007	0.000	0.000	0.000
115	A	112	HIS	0	-0.036	-0.013	25.500	0.014	0.014	0.000	0.000	0.000
116	A	113	LEU	0	-0.059	-0.022	26.969	0.000	0.000	0.000	0.000	0.000
117	A	114	TRP	0	0.015	-0.010	18.756	-0.010	-0.010	0.000	0.000	0.000
118	A	115	GLU	-1	-0.819	-0.913	23.197	-0.017	-0.017	0.000	0.000	0.000
119	A	116	PHE	0	-0.016	0.001	19.513	-0.008	-0.008	0.000	0.000	0.000
120	A	117	THR	0	0.012	-0.011	21.110	0.009	0.009	0.000	0.000	0.000
121	A	118	ARG	1	0.865	0.922	20.480	0.025	0.025	0.000	0.000	0.000
122	A	119	HIS	0	-0.061	-0.027	14.509	-0.008	-0.008	0.000	0.000	0.000
123	A	120	LEU	0	0.026	0.037	19.258	0.017	0.017	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:GLY)