FMO DATABASE

FMODB ID: N9YQQ

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:

Apendix: None

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1027005.794657
FMO2-HF: Nuclear repulsion	978165.386073
FMO2-HF: Total energy	-48840.408584
FMO2-MP2: Total energy	-48982.400479

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.
-0.734	0.248	-0.002	-0.511	-0.468	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 : 0.021 / 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	0.017	0.006	3.745	-0.874	0.108	-0.002	-0.511	-0.468
4	A	1	MET	0	0.007	0.012	6.476	0.370	0.370	0.000	0.000	0.000
5	A	2	VAL	0	0.000	-0.004	9.850	-0.109	-0.109	0.000	0.000	0.000
6	A	3	VAL	0	-0.009	-0.003	12.802	0.086	0.086	0.000	0.000	0.000
7	A	4	GLU	-1	-0.846	-0.917	16.286	-0.192	-0.192	0.000	0.000	0.000
8	A	5	LEU	0	-0.031	-0.015	19.270	0.022	0.022	0.000	0.000	0.000
9	A	6	ALA	0	0.016	0.015	22.106	-0.007	-0.007	0.000	0.000	0.000
10	A	7	TYR	0	-0.007	-0.043	22.765	-0.002	-0.002	0.000	0.000	0.000
11	A	8	THR	0	-0.005	-0.039	27.458	0.002	0.002	0.000	0.000	0.000
12	A	9	ASP	-1	-0.834	-0.939	29.782	-0.124	-0.124	0.000	0.000	0.000
13	A	10	PRO	0	0.003	0.008	24.396	-0.005	-0.005	0.000	0.000	0.000
14	A	11	ASP	-1	-0.804	-0.873	25.208	-0.160	-0.160	0.000	0.000	0.000
15	A	12	ARG	1	0.856	0.897	26.727	0.126	0.126	0.000	0.000	0.000
16	A	13	ALA	0	0.030	0.032	25.063	-0.002	-0.002	0.000	0.000	0.000
17	A	14	VAL	0	-0.002	-0.004	21.162	-0.011	-0.011	0.000	0.000	0.000
18	A	15	ASP	-1	-0.818	-0.877	22.819	-0.156	-0.156	0.000	0.000	0.000
19	A	16	TRP	0	0.031	0.014	25.064	-0.005	-0.005	0.000	0.000	0.000
20	A	17	LEU	0	-0.001	-0.003	20.662	-0.002	-0.002	0.000	0.000	0.000
21	A	18	VAL	0	-0.052	-0.022	19.511	-0.010	-0.010	0.000	0.000	0.000
22	A	19	ARG	1	0.796	0.867	21.524	0.139	0.139	0.000	0.000	0.000
23	A	20	VAL	0	-0.016	0.006	24.885	0.008	0.008	0.000	0.000	0.000
24	A	21	PHE	0	0.003	-0.005	20.290	0.008	0.008	0.000	0.000	0.000
25	A	22	GLY	0	-0.017	0.002	20.025	-0.004	-0.004	0.000	0.000	0.000
26	A	23	PHE	0	-0.019	-0.005	16.652	-0.032	-0.032	0.000	0.000	0.000
27	A	24	ARG	1	0.900	0.930	12.743	0.536	0.536	0.000	0.000	0.000
28	A	25	LEU	0	-0.012	-0.012	14.897	-0.054	-0.054	0.000	0.000	0.000
29	A	26	LEU	0	-0.034	-0.006	10.227	-0.005	-0.005	0.000	0.000	0.000
30	A	27	LEU	0	-0.012	0.003	14.508	0.028	0.028	0.000	0.000	0.000
31	A	28	ARG	1	0.847	0.904	16.887	0.183	0.183	0.000	0.000	0.000
32	A	29	GLN	0	-0.029	0.006	20.559	0.025	0.025	0.000	0.000	0.000
33	A	30	PRO	0	0.042	0.010	22.835	0.003	0.003	0.000	0.000	0.000
34	A	31	ALA	0	0.052	0.018	24.271	-0.006	-0.006	0.000	0.000	0.000
35	A	32	ILE	0	0.000	0.003	25.233	0.001	0.001	0.000	0.000	0.000
36	A	33	GLY	0	0.025	0.019	28.846	0.002	0.002	0.000	0.000	0.000
37	A	34	THR	0	-0.019	-0.005	28.866	-0.006	-0.006	0.000	0.000	0.000
38	A	35	ILE	0	-0.018	-0.009	22.782	0.001	0.001	0.000	0.000	0.000
39	A	36	ARG	1	0.806	0.877	25.182	0.140	0.140	0.000	0.000	0.000
40	A	37	HIS	0	-0.043	-0.022	17.252	0.040	0.040	0.000	0.000	0.000
41	A	38	ALA	0	0.002	-0.003	19.180	0.007	0.007	0.000	0.000	0.000
42	A	39	ASP	-1	-0.810	-0.886	13.902	-0.418	-0.418	0.000	0.000	0.000
43	A	40	LEU	0	-0.002	-0.009	15.452	-0.007	-0.007	0.000	0.000	0.000
44	A	41	ASP	-1	-0.782	-0.880	10.615	-0.819	-0.819	0.000	0.000	0.000
45	A	42	THR	0	-0.031	-0.029	11.947	0.110	0.110	0.000	0.000	0.000
46	A	43	GLY	0	-0.024	-0.010	10.795	0.086	0.086	0.000	0.000	0.000
47	A	44	GLY	0	-0.037	-0.021	8.765	-0.057	-0.057	0.000	0.000	0.000
48	A	45	GLY	0	0.006	0.014	9.123	0.075	0.075	0.000	0.000	0.000
49	A	46	ILE	0	-0.024	-0.004	8.586	0.028	0.028	0.000	0.000	0.000
50	A	47	VAL	0	0.031	0.015	12.258	0.065	0.065	0.000	0.000	0.000
51	A	48	MET	0	0.004	0.025	15.482	0.012	0.012	0.000	0.000	0.000
52	A	49	VAL	0	0.001	0.012	17.393	0.041	0.041	0.000	0.000	0.000
53	A	50	ARG	1	0.870	0.909	20.041	0.201	0.201	0.000	0.000	0.000
54	A	51	ARG	1	0.867	0.926	23.467	0.134	0.134	0.000	0.000	0.000
55	A	52	THR	0	-0.029	-0.025	27.262	-0.001	-0.001	0.000	0.000	0.000
56	A	53	GLY	0	0.012	0.012	29.104	0.007	0.007	0.000	0.000	0.000
57	A	54	GLU	-1	-0.867	-0.909	26.668	-0.122	-0.122	0.000	0.000	0.000
58	A	55	PRO	0	0.034	0.023	24.582	-0.017	-0.017	0.000	0.000	0.000
59	A	56	TYR	0	-0.046	-0.038	15.633	-0.005	-0.005	0.000	0.000	0.000
60	A	57	THR	0	-0.021	-0.009	21.544	0.005	0.005	0.000	0.000	0.000
61	A	58	VAL	0	0.001	0.007	23.556	0.004	0.004	0.000	0.000	0.000
62	A	59	SER	0	-0.001	-0.009	25.998	0.001	0.001	0.000	0.000	0.000
63	A	60	CYS	0	-0.048	-0.024	28.233	0.007	0.007	0.000	0.000	0.000
64	A	61	ALA	0	0.018	0.014	31.384	-0.005	-0.005	0.000	0.000	0.000
65	A	62	GLY	0	0.034	0.008	33.377	0.005	0.005	0.000	0.000	0.000
66	A	63	GLY	0	-0.011	0.006	33.952	-0.003	-0.003	0.000	0.000	0.000
67	A	64	HIS	0	-0.024	-0.033	28.750	0.000	0.000	0.000	0.000	0.000
68	A	65	THR	0	0.013	0.008	30.224	0.004	0.004	0.000	0.000	0.000
69	A	66	CYS	0	-0.010	0.012	28.943	-0.006	-0.006	0.000	0.000	0.000
70	A	67	LYS	1	0.857	0.917	24.132	0.107	0.107	0.000	0.000	0.000
71	A	68	GLN	0	0.023	-0.006	23.732	-0.002	-0.002	0.000	0.000	0.000
72	A	69	VAL	0	-0.017	0.011	18.991	-0.001	-0.001	0.000	0.000	0.000
73	A	70	ILE	0	-0.003	0.001	19.222	0.013	0.013	0.000	0.000	0.000
74	A	71	VAL	0	0.002	0.006	16.077	-0.022	-0.022	0.000	0.000	0.000
75	A	72	TRP	0	0.004	-0.003	15.216	0.018	0.018	0.000	0.000	0.000
76	A	73	VAL	0	0.014	0.004	16.169	-0.037	-0.037	0.000	0.000	0.000
77	A	74	SER	0	0.021	0.003	16.615	0.024	0.024	0.000	0.000	0.000
78	A	75	ASP	-1	-0.817	-0.910	18.467	-0.074	-0.074	0.000	0.000	0.000
79	A	76	VAL	0	-0.003	-0.006	21.857	-0.012	-0.012	0.000	0.000	0.000
80	A	77	ASP	-1	-0.802	-0.910	23.468	-0.071	-0.071	0.000	0.000	0.000
81	A	78	GLU	-1	-0.823	-0.889	22.880	-0.159	-0.159	0.000	0.000	0.000
82	A	79	HIS	1	0.868	0.936	20.228	0.183	0.183	0.000	0.000	0.000
83	A	80	PHE	0	0.032	0.026	23.922	-0.001	-0.001	0.000	0.000	0.000
84	A	81	MET	0	0.008	0.004	27.246	0.004	0.004	0.000	0.000	0.000
85	A	82	ARG	1	0.822	0.891	21.024	0.182	0.182	0.000	0.000	0.000
86	A	83	SER	0	0.000	-0.012	25.517	-0.004	-0.004	0.000	0.000	0.000
87	A	84	THR	0	-0.029	-0.026	27.697	0.004	0.004	0.000	0.000	0.000
88	A	85	ALA	0	-0.035	-0.009	30.595	0.003	0.003	0.000	0.000	0.000
89	A	86	ALA	0	-0.050	-0.024	28.607	0.002	0.002	0.000	0.000	0.000
90	A	87	GLY	0	-0.030	-0.007	30.599	-0.001	-0.001	0.000	0.000	0.000
91	A	88	ALA	0	-0.030	-0.008	28.865	0.001	0.001	0.000	0.000	0.000
92	A	89	ASP	-1	-0.888	-0.947	30.850	-0.079	-0.079	0.000	0.000	0.000
93	A	90	ILE	0	-0.043	-0.028	29.812	-0.003	-0.003	0.000	0.000	0.000
94	A	91	VAL	0	-0.045	-0.022	31.182	0.006	0.006	0.000	0.000	0.000
95	A	92	GLN	0	-0.007	-0.003	30.684	0.007	0.007	0.000	0.000	0.000
96	A	93	PRO	0	0.025	0.013	30.823	-0.007	-0.007	0.000	0.000	0.000
97	A	94	LEU	0	-0.050	-0.008	27.413	0.002	0.002	0.000	0.000	0.000
98	A	95	GLN	0	-0.046	-0.020	30.221	0.009	0.009	0.000	0.000	0.000
99	A	96	ASP	-1	-0.785	-0.868	29.981	-0.043	-0.043	0.000	0.000	0.000
100	A	97	LYS	1	0.866	0.936	29.445	0.042	0.042	0.000	0.000	0.000
101	A	98	PRO	0	0.019	-0.003	30.765	0.001	0.001	0.000	0.000	0.000
102	A	99	TRP	0	0.002	0.001	28.221	-0.002	-0.002	0.000	0.000	0.000
103	A	100	GLY	0	0.019	0.004	27.623	0.003	0.003	0.000	0.000	0.000
104	A	101	LEU	0	-0.028	0.010	25.028	-0.005	-0.005	0.000	0.000	0.000
105	A	102	ARG	1	0.776	0.867	25.992	0.051	0.051	0.000	0.000	0.000
106	A	103	GLN	0	-0.062	-0.053	25.144	-0.002	-0.002	0.000	0.000	0.000
107	A	104	TYR	0	0.002	0.002	24.508	0.003	0.003	0.000	0.000	0.000
108	A	105	LEU	0	-0.004	0.011	26.120	-0.006	-0.006	0.000	0.000	0.000
109	A	106	VAL	0	-0.022	-0.004	25.620	0.005	0.005	0.000	0.000	0.000
110	A	107	ARG	1	0.921	0.965	27.429	0.078	0.078	0.000	0.000	0.000
111	A	108	ASP	-1	-0.741	-0.847	25.399	-0.148	-0.148	0.000	0.000	0.000
112	A	109	LEU	0	-0.011	-0.018	27.802	0.008	0.008	0.000	0.000	0.000
113	A	110	GLU	-1	-0.787	-0.830	28.473	-0.108	-0.108	0.000	0.000	0.000
114	A	111	GLY	0	-0.013	-0.013	30.369	0.007	0.007	0.000	0.000	0.000
115	A	112	HIS	0	-0.027	-0.010	25.597	0.015	0.015	0.000	0.000	0.000
116	A	113	LEU	0	-0.049	-0.022	26.858	0.002	0.002	0.000	0.000	0.000
117	A	114	TRP	0	0.022	-0.016	18.620	-0.019	-0.019	0.000	0.000	0.000
118	A	115	GLU	-1	-0.796	-0.883	22.987	-0.066	-0.066	0.000	0.000	0.000
119	A	116	PHE	0	-0.017	-0.003	19.343	-0.019	-0.019	0.000	0.000	0.000
120	A	117	THR	0	0.014	-0.031	21.043	0.016	0.016	0.000	0.000	0.000
121	A	118	ARG	1	0.846	0.922	20.358	0.062	0.062	0.000	0.000	0.000
122	A	119	HIS	0	-0.058	-0.030	14.310	-0.006	-0.006	0.000	0.000	0.000
123	A	120	LEU	0	0.025	0.030	19.141	0.019	0.019	0.000	0.000	0.000

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