FMO DATABASE

FMODB ID: G63G1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1021269.54124
FMO2-HF: Nuclear repulsion	972429.955064
FMO2-HF: Total energy	-48839.586176
FMO2-MP2: Total energy	-48981.450039

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.
-0.765	0.161	-0.011	-0.453	-0.461	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 : 0.012 / q_NPA : -0.007

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	0.035	0.014	3.819	-0.635	0.291	-0.011	-0.453	-0.461
4	A	1	MET	0	0.005	0.008	6.818	0.236	0.236	0.000	0.000	0.000
5	A	2	VAL	0	0.016	0.015	10.223	-0.086	-0.086	0.000	0.000	0.000
6	A	3	VAL	0	-0.011	-0.004	13.009	0.078	0.078	0.000	0.000	0.000
7	A	4	GLU	-1	-0.867	-0.933	16.417	-0.166	-0.166	0.000	0.000	0.000
8	A	5	LEU	0	-0.025	-0.017	19.312	0.027	0.027	0.000	0.000	0.000
9	A	6	ALA	0	-0.014	0.001	22.420	-0.010	-0.010	0.000	0.000	0.000
10	A	7	TYR	0	-0.012	-0.041	23.009	0.001	0.001	0.000	0.000	0.000
11	A	8	THR	0	-0.005	-0.041	27.628	0.000	0.000	0.000	0.000	0.000
12	A	9	ASP	-1	-0.896	-0.959	30.119	-0.103	-0.103	0.000	0.000	0.000
13	A	10	PRO	0	-0.004	-0.012	25.058	-0.004	-0.004	0.000	0.000	0.000
14	A	11	ASP	-1	-0.836	-0.913	25.679	-0.144	-0.144	0.000	0.000	0.000
15	A	12	ARG	1	0.894	0.943	27.237	0.108	0.108	0.000	0.000	0.000
16	A	13	ALA	0	0.045	0.028	25.317	-0.001	-0.001	0.000	0.000	0.000
17	A	14	VAL	0	0.004	0.003	21.633	-0.009	-0.009	0.000	0.000	0.000
18	A	15	ASP	-1	-0.929	-0.962	23.339	-0.143	-0.143	0.000	0.000	0.000
19	A	16	TRP	0	0.007	-0.003	25.007	-0.002	-0.002	0.000	0.000	0.000
20	A	17	LEU	0	-0.013	-0.007	21.046	0.000	0.000	0.000	0.000	0.000
21	A	18	VAL	0	-0.029	-0.007	20.156	-0.007	-0.007	0.000	0.000	0.000
22	A	19	ARG	1	0.918	0.963	22.155	0.114	0.114	0.000	0.000	0.000
23	A	20	VAL	0	-0.047	-0.021	25.207	0.006	0.006	0.000	0.000	0.000
24	A	21	PHE	0	-0.024	-0.025	20.412	0.010	0.010	0.000	0.000	0.000
25	A	22	GLY	0	-0.060	-0.023	20.111	-0.006	-0.006	0.000	0.000	0.000
26	A	23	PHE	0	-0.003	0.003	16.919	-0.025	-0.025	0.000	0.000	0.000
27	A	24	ARG	1	0.973	0.981	14.175	0.417	0.417	0.000	0.000	0.000
28	A	25	LEU	0	-0.004	-0.010	15.684	-0.040	-0.040	0.000	0.000	0.000
29	A	26	LEU	0	-0.047	-0.008	10.634	-0.003	-0.003	0.000	0.000	0.000
30	A	27	LEU	0	-0.002	0.006	14.844	0.017	0.017	0.000	0.000	0.000
31	A	28	ARG	1	0.884	0.938	17.022	0.184	0.184	0.000	0.000	0.000
32	A	29	GLN	0	-0.034	0.010	20.610	0.016	0.016	0.000	0.000	0.000
33	A	30	PRO	0	0.028	0.005	22.828	0.005	0.005	0.000	0.000	0.000
34	A	31	ALA	0	0.056	0.020	24.785	-0.006	-0.006	0.000	0.000	0.000
35	A	32	ILE	0	0.010	0.005	25.694	0.000	0.000	0.000	0.000	0.000
36	A	33	GLY	0	0.004	0.008	29.251	0.003	0.003	0.000	0.000	0.000
37	A	34	THR	0	0.000	-0.008	29.102	-0.010	-0.010	0.000	0.000	0.000
38	A	35	ILE	0	-0.003	0.011	23.482	-0.002	-0.002	0.000	0.000	0.000
39	A	36	ARG	1	0.901	0.948	25.471	0.135	0.135	0.000	0.000	0.000
40	A	37	HIS	0	-0.043	-0.025	17.406	0.032	0.032	0.000	0.000	0.000
41	A	38	ALA	0	0.018	0.005	19.434	0.001	0.001	0.000	0.000	0.000
42	A	39	ASP	-1	-0.842	-0.904	13.962	-0.408	-0.408	0.000	0.000	0.000
43	A	40	LEU	0	-0.007	-0.022	15.664	0.002	0.002	0.000	0.000	0.000
44	A	41	ASP	-1	-0.852	-0.938	10.368	-0.860	-0.860	0.000	0.000	0.000
45	A	42	THR	0	-0.033	-0.031	12.193	0.095	0.095	0.000	0.000	0.000
46	A	43	GLY	0	-0.032	-0.008	10.648	0.080	0.080	0.000	0.000	0.000
47	A	44	GLY	0	-0.030	-0.022	8.512	-0.056	-0.056	0.000	0.000	0.000
48	A	45	GLY	0	-0.001	0.017	9.054	0.137	0.137	0.000	0.000	0.000
49	A	46	ILE	0	-0.004	-0.004	8.893	-0.018	-0.018	0.000	0.000	0.000
50	A	47	VAL	0	0.019	0.019	12.365	0.075	0.075	0.000	0.000	0.000
51	A	48	MET	0	-0.020	-0.005	15.658	-0.007	-0.007	0.000	0.000	0.000
52	A	49	VAL	0	-0.008	-0.001	17.562	0.037	0.037	0.000	0.000	0.000
53	A	50	ARG	1	0.898	0.938	20.602	0.171	0.171	0.000	0.000	0.000
54	A	51	ARG	1	0.946	0.976	23.597	0.119	0.119	0.000	0.000	0.000
55	A	52	THR	0	0.004	-0.014	27.324	-0.001	-0.001	0.000	0.000	0.000
56	A	53	GLY	0	-0.014	-0.003	29.523	0.003	0.003	0.000	0.000	0.000
57	A	54	GLU	-1	-0.956	-0.972	27.260	-0.105	-0.105	0.000	0.000	0.000
58	A	55	PRO	0	0.023	0.014	24.772	-0.015	-0.015	0.000	0.000	0.000
59	A	56	TYR	0	-0.036	-0.024	16.335	0.000	0.000	0.000	0.000	0.000
60	A	57	THR	0	-0.022	-0.005	21.441	0.002	0.002	0.000	0.000	0.000
61	A	58	VAL	0	-0.015	-0.001	23.416	0.005	0.005	0.000	0.000	0.000
62	A	59	SER	0	0.003	-0.004	25.936	0.001	0.001	0.000	0.000	0.000
63	A	60	CYS	0	-0.018	-0.007	28.323	0.005	0.005	0.000	0.000	0.000
64	A	61	ALA	0	0.022	0.008	31.398	-0.004	-0.004	0.000	0.000	0.000
65	A	62	GLY	0	0.019	-0.002	33.694	0.005	0.005	0.000	0.000	0.000
66	A	63	GLY	0	-0.035	-0.009	33.388	-0.004	-0.004	0.000	0.000	0.000
67	A	64	HIS	0	-0.033	-0.016	28.543	0.002	0.002	0.000	0.000	0.000
68	A	65	THR	0	-0.016	-0.011	29.996	0.002	0.002	0.000	0.000	0.000
69	A	66	CYS	0	0.001	-0.004	29.262	-0.007	-0.007	0.000	0.000	0.000
70	A	67	LYS	1	0.927	0.968	24.292	0.081	0.081	0.000	0.000	0.000
71	A	68	GLN	0	0.031	0.010	23.961	-0.002	-0.002	0.000	0.000	0.000
72	A	69	VAL	0	-0.012	-0.004	19.325	0.001	0.001	0.000	0.000	0.000
73	A	70	ILE	0	-0.010	-0.004	19.390	0.005	0.005	0.000	0.000	0.000
74	A	71	VAL	0	0.016	0.006	16.232	-0.014	-0.014	0.000	0.000	0.000
75	A	72	TRP	0	0.002	-0.001	15.762	0.010	0.010	0.000	0.000	0.000
76	A	73	VAL	0	0.013	-0.006	16.281	-0.028	-0.028	0.000	0.000	0.000
77	A	74	SER	0	0.032	0.005	17.073	0.018	0.018	0.000	0.000	0.000
78	A	75	ASP	-1	-0.877	-0.943	18.868	-0.048	-0.048	0.000	0.000	0.000
79	A	76	VAL	0	-0.017	-0.031	22.111	-0.009	-0.009	0.000	0.000	0.000
80	A	77	ASP	-1	-0.859	-0.941	23.783	-0.038	-0.038	0.000	0.000	0.000
81	A	78	GLU	-1	-0.920	-0.950	23.414	-0.106	-0.106	0.000	0.000	0.000
82	A	79	HIS	1	0.852	0.922	20.115	0.118	0.118	0.000	0.000	0.000
83	A	80	PHE	0	0.012	-0.005	24.136	-0.003	-0.003	0.000	0.000	0.000
84	A	81	MET	0	0.026	0.007	27.436	0.002	0.002	0.000	0.000	0.000
85	A	82	ARG	1	0.966	1.009	21.021	0.154	0.154	0.000	0.000	0.000
86	A	83	SER	0	-0.021	-0.015	25.611	-0.003	-0.003	0.000	0.000	0.000
87	A	84	THR	0	-0.007	-0.009	27.912	0.002	0.002	0.000	0.000	0.000
88	A	85	ALA	0	-0.018	0.007	30.843	0.002	0.002	0.000	0.000	0.000
89	A	86	ALA	0	-0.061	-0.028	29.021	0.000	0.000	0.000	0.000	0.000
90	A	87	GLY	0	-0.026	-0.012	31.076	-0.001	-0.001	0.000	0.000	0.000
91	A	88	ALA	0	-0.047	-0.013	29.153	0.001	0.001	0.000	0.000	0.000
92	A	89	ASP	-1	-0.867	-0.928	31.148	-0.057	-0.057	0.000	0.000	0.000
93	A	90	ILE	0	-0.045	-0.031	30.163	-0.002	-0.002	0.000	0.000	0.000
94	A	91	VAL	0	-0.047	-0.021	31.459	0.004	0.004	0.000	0.000	0.000
95	A	92	GLN	0	-0.007	-0.016	30.974	0.005	0.005	0.000	0.000	0.000
96	A	93	PRO	0	0.017	0.010	31.053	-0.004	-0.004	0.000	0.000	0.000
97	A	94	LEU	0	-0.022	-0.011	27.499	0.003	0.003	0.000	0.000	0.000
98	A	95	GLN	0	-0.021	0.000	30.359	0.006	0.006	0.000	0.000	0.000
99	A	96	ASP	-1	-0.842	-0.918	30.191	-0.009	-0.009	0.000	0.000	0.000
100	A	97	LYS	1	0.837	0.914	29.438	0.010	0.010	0.000	0.000	0.000
101	A	98	PRO	0	0.011	-0.007	30.619	0.002	0.002	0.000	0.000	0.000
102	A	99	TRP	0	-0.002	0.011	28.231	0.003	0.003	0.000	0.000	0.000
103	A	100	GLY	0	0.017	0.006	27.400	-0.003	-0.003	0.000	0.000	0.000
104	A	101	LEU	0	-0.027	0.001	25.302	-0.004	-0.004	0.000	0.000	0.000
105	A	102	ARG	1	0.917	0.966	25.706	0.020	0.020	0.000	0.000	0.000
106	A	103	GLN	0	-0.013	-0.016	25.131	-0.004	-0.004	0.000	0.000	0.000
107	A	104	TYR	0	-0.001	0.011	24.971	0.000	0.000	0.000	0.000	0.000
108	A	105	LEU	0	-0.008	0.008	26.318	-0.003	-0.003	0.000	0.000	0.000
109	A	106	VAL	0	-0.005	0.000	25.963	0.002	0.002	0.000	0.000	0.000
110	A	107	ARG	1	0.944	0.995	27.469	0.050	0.050	0.000	0.000	0.000
111	A	108	ASP	-1	-0.767	-0.863	25.558	-0.112	-0.112	0.000	0.000	0.000
112	A	109	LEU	0	-0.014	-0.025	27.395	0.005	0.005	0.000	0.000	0.000
113	A	110	GLU	-1	-0.807	-0.855	28.477	-0.086	-0.086	0.000	0.000	0.000
114	A	111	GLY	0	-0.002	-0.009	29.836	0.007	0.007	0.000	0.000	0.000
115	A	112	HIS	0	-0.032	-0.006	25.475	0.014	0.014	0.000	0.000	0.000
116	A	113	LEU	0	-0.034	-0.018	26.970	0.000	0.000	0.000	0.000	0.000
117	A	114	TRP	0	-0.004	-0.016	18.770	-0.009	-0.009	0.000	0.000	0.000
118	A	115	GLU	-1	-0.904	-0.957	23.194	-0.015	-0.015	0.000	0.000	0.000
119	A	116	PHE	0	-0.019	-0.004	19.779	-0.007	-0.007	0.000	0.000	0.000
120	A	117	THR	0	0.034	0.004	21.109	0.010	0.010	0.000	0.000	0.000
121	A	118	ARG	1	0.931	0.966	20.487	0.018	0.018	0.000	0.000	0.000
122	A	119	HIS	0	-0.063	-0.034	14.446	-0.012	-0.012	0.000	0.000	0.000
123	A	120	LEU	0	0.017	0.035	19.265	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)