FMO DATABASE

FMODB ID: ZY41N

Calculation Name: 3UT4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3UT4

Chain ID: A

ChEMBL ID:

UniProt ID: A3DJ21

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	128
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1237821.042968
FMO2-HF: Nuclear repulsion	1184780.048774
FMO2-HF: Total energy	-53040.994193
FMO2-MP2: Total energy	-53197.667825

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:THR)

Summations of interaction energy for fragment #1(A:2:THR)

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.
-6.132	-1.33	0.989	-2.093	-3.698	0.01

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.003

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

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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	4	LEU	0	0.084	0.034	3.876	-2.343	-0.502	0.000	-0.785	-1.057	0.002
4	A	5	ARG	1	0.854	0.905	2.649	-4.576	-2.436	0.988	-1.084	-2.044	0.008
5	A	6	ASP	-1	-0.883	-0.928	3.696	-2.949	-2.240	0.002	-0.217	-0.494	0.000
6	A	7	LEU	0	0.021	0.005	4.947	0.765	0.877	-0.001	-0.007	-0.103	0.000
7	A	8	ILE	0	-0.033	0.003	6.498	0.386	0.386	0.000	0.000	0.000	0.000
8	A	9	PRO	0	-0.006	0.008	8.887	-0.217	-0.217	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.824	0.902	6.585	1.508	1.508	0.000	0.000	0.000	0.000
10	A	11	HIS	0	0.014	-0.004	11.403	0.114	0.114	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.924	0.966	15.171	0.011	0.011	0.000	0.000	0.000	0.000
12	A	13	PHE	0	-0.028	-0.027	17.876	0.025	0.025	0.000	0.000	0.000	0.000
13	A	14	ASP	-1	-0.811	-0.860	12.444	-0.493	-0.493	0.000	0.000	0.000	0.000
14	A	15	ASN	0	-0.016	-0.022	14.739	-0.044	-0.044	0.000	0.000	0.000	0.000
15	A	16	SER	0	-0.047	-0.047	13.353	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	17	THR	0	-0.012	-0.005	9.910	0.018	0.018	0.000	0.000	0.000	0.000
17	A	18	ILE	0	0.009	0.007	13.024	0.061	0.061	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.810	-0.895	16.040	-0.076	-0.076	0.000	0.000	0.000	0.000
19	A	20	GLN	0	0.007	-0.005	11.187	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.003	-0.002	10.573	0.094	0.094	0.000	0.000	0.000	0.000
21	A	22	CYS	0	-0.072	-0.041	13.769	0.068	0.068	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.762	0.872	15.842	0.077	0.077	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.019	0.021	10.550	0.028	0.028	0.000	0.000	0.000	0.000
24	A	25	ILE	0	-0.010	-0.020	14.760	-0.043	-0.043	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.798	-0.907	14.707	0.310	0.310	0.000	0.000	0.000	0.000
26	A	27	ASN	0	-0.008	-0.027	14.459	0.036	0.036	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.886	-0.926	11.291	0.527	0.527	0.000	0.000	0.000	0.000
28	A	29	ILE	0	-0.009	-0.008	9.800	0.160	0.160	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.861	-0.921	11.134	0.604	0.604	0.000	0.000	0.000	0.000
30	A	31	PRO	0	0.023	0.006	7.278	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	32	ILE	0	-0.055	-0.032	6.435	0.211	0.211	0.000	0.000	0.000	0.000
32	A	33	ILE	0	0.003	0.019	9.128	-0.143	-0.143	0.000	0.000	0.000	0.000
33	A	34	PHE	0	0.054	0.022	12.654	-0.078	-0.078	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.821	-0.896	9.377	0.771	0.771	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.008	-0.002	11.273	-0.098	-0.098	0.000	0.000	0.000	0.000
36	A	37	LEU	0	0.036	0.005	13.834	-0.046	-0.046	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.886	0.945	11.929	-0.462	-0.462	0.000	0.000	0.000	0.000
38	A	39	TRP	0	-0.038	-0.008	12.112	-0.029	-0.029	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.027	-0.015	17.274	-0.025	-0.025	0.000	0.000	0.000	0.000
40	A	41	GLN	0	-0.061	-0.048	18.745	0.005	0.005	0.000	0.000	0.000	0.000
41	A	42	ASP	-1	-0.750	-0.889	21.762	0.017	0.017	0.000	0.000	0.000	0.000
42	A	43	TYR	0	0.024	0.012	23.396	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	44	ASN	0	-0.026	-0.029	24.994	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	45	TRP	0	-0.044	-0.034	18.527	-0.019	-0.019	0.000	0.000	0.000	0.000
45	A	46	PRO	0	-0.041	-0.031	21.856	0.005	0.005	0.000	0.000	0.000	0.000
46	A	47	ILE	0	0.033	0.032	15.930	0.008	0.008	0.000	0.000	0.000	0.000
47	A	48	ALA	0	0.037	0.026	19.333	0.009	0.009	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.829	0.925	20.932	0.033	0.033	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.817	-0.911	19.567	-0.069	-0.069	0.000	0.000	0.000	0.000
50	A	51	ILE	0	-0.017	-0.012	14.838	0.008	0.008	0.000	0.000	0.000	0.000
51	A	52	LEU	0	0.009	0.014	18.731	0.027	0.027	0.000	0.000	0.000	0.000
52	A	53	PRO	0	0.008	-0.005	21.646	0.018	0.018	0.000	0.000	0.000	0.000
53	A	54	VAL	0	0.008	0.014	15.167	0.018	0.018	0.000	0.000	0.000	0.000
54	A	55	VAL	0	-0.004	-0.014	16.420	0.034	0.034	0.000	0.000	0.000	0.000
55	A	56	VAL	0	-0.006	-0.004	18.659	0.016	0.016	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.023	-0.005	19.728	0.005	0.005	0.000	0.000	0.000	0.000
57	A	58	HIS	1	0.842	0.909	16.526	-0.198	-0.198	0.000	0.000	0.000	0.000
58	A	59	GLN	0	0.069	0.031	18.750	0.027	0.027	0.000	0.000	0.000	0.000
59	A	60	SER	0	-0.012	-0.013	21.363	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	61	ILE	0	-0.009	0.004	15.265	0.000	0.000	0.000	0.000	0.000	0.000
61	A	62	ALA	0	0.030	0.023	17.641	0.026	0.026	0.000	0.000	0.000	0.000
62	A	63	MET	0	-0.031	0.012	18.602	-0.010	-0.010	0.000	0.000	0.000	0.000
63	A	64	PRO	0	0.031	0.012	19.065	-0.015	-0.015	0.000	0.000	0.000	0.000
64	A	65	HIS	0	-0.015	-0.002	14.584	-0.036	-0.036	0.000	0.000	0.000	0.000
65	A	66	ILE	0	0.025	0.002	18.853	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	67	LEU	0	0.005	0.001	21.807	-0.016	-0.016	0.000	0.000	0.000	0.000
67	A	68	THR	0	-0.011	-0.019	19.720	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.046	-0.014	18.900	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	70	LEU	0	-0.029	-0.013	22.759	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	71	GLN	0	-0.056	-0.037	25.378	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.010	0.027	24.329	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	73	ASN	0	-0.017	-0.023	25.330	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	74	ASP	-1	-0.833	-0.901	23.073	0.104	0.104	0.000	0.000	0.000	0.000
74	A	75	ILE	0	0.048	0.011	25.830	0.003	0.003	0.000	0.000	0.000	0.000
75	A	76	MET	0	0.010	0.016	26.116	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	77	TRP	0	-0.018	-0.018	17.669	0.003	0.003	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.826	0.905	24.407	-0.114	-0.114	0.000	0.000	0.000	0.000
78	A	79	TYR	0	-0.045	-0.039	26.386	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	80	TRP	0	-0.005	0.002	25.264	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	81	VAL	0	0.022	0.005	22.339	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	82	ILE	0	-0.005	-0.010	25.245	0.001	0.001	0.000	0.000	0.000	0.000
82	A	83	LYS	1	0.869	0.941	28.831	-0.049	-0.049	0.000	0.000	0.000	0.000
83	A	84	LEU	0	-0.012	-0.005	25.822	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	85	MET	0	-0.001	0.004	20.866	0.002	0.002	0.000	0.000	0.000	0.000
85	A	86	ILE	0	0.009	0.013	26.344	0.001	0.001	0.000	0.000	0.000	0.000
86	A	87	PRO	0	-0.029	-0.007	29.169	0.001	0.001	0.000	0.000	0.000	0.000
87	A	88	TYR	0	-0.037	-0.011	27.543	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.038	0.007	24.914	0.008	0.008	0.000	0.000	0.000	0.000
89	A	90	ILE	0	0.006	0.001	27.190	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	91	TYR	0	0.013	-0.003	29.872	0.005	0.005	0.000	0.000	0.000	0.000
91	A	92	PRO	0	0.019	0.005	28.878	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	93	ASN	0	0.032	-0.013	24.762	0.008	0.008	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.915	0.947	27.703	-0.074	-0.074	0.000	0.000	0.000	0.000
94	A	95	GLN	0	0.013	0.005	30.447	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	96	LEU	0	-0.044	-0.009	26.143	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	97	VAL	0	0.021	0.005	26.563	0.002	0.002	0.000	0.000	0.000	0.000
97	A	98	LYS	1	0.809	0.915	29.273	-0.088	-0.088	0.000	0.000	0.000	0.000
98	A	99	SER	0	0.052	0.014	31.903	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.791	-0.863	27.990	0.121	0.121	0.000	0.000	0.000	0.000
100	A	101	LEU	0	0.029	0.024	31.347	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	102	GLU	-1	-0.798	-0.892	33.443	0.075	0.075	0.000	0.000	0.000	0.000
102	A	103	ARG	1	0.852	0.920	29.835	-0.116	-0.116	0.000	0.000	0.000	0.000
103	A	104	LEU	0	0.001	-0.006	29.723	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	105	SER	0	-0.053	-0.026	34.401	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	106	SER	0	-0.039	-0.030	37.618	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	107	LEU	0	-0.051	-0.011	33.708	0.000	0.000	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.899	-0.949	38.439	0.046	0.046	0.000	0.000	0.000	0.000
108	A	109	ILE	0	-0.060	-0.026	39.653	0.002	0.002	0.000	0.000	0.000	0.000
109	A	110	ILE	0	-0.009	-0.009	37.615	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	111	ASN	0	-0.047	-0.042	35.182	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	112	GLU	-1	-0.776	-0.851	38.568	0.038	0.038	0.000	0.000	0.000	0.000
112	A	113	ASP	-1	-0.844	-0.911	33.825	0.049	0.049	0.000	0.000	0.000	0.000
113	A	114	ILE	0	-0.044	-0.026	33.866	0.004	0.004	0.000	0.000	0.000	0.000
114	A	115	ARG	1	0.839	0.888	36.071	-0.036	-0.036	0.000	0.000	0.000	0.000
115	A	116	GLU	-1	-0.819	-0.888	34.860	0.041	0.041	0.000	0.000	0.000	0.000
116	A	117	ILE	0	-0.012	0.004	30.989	0.002	0.002	0.000	0.000	0.000	0.000
117	A	118	VAL	0	0.017	0.031	34.268	0.002	0.002	0.000	0.000	0.000	0.000
118	A	119	ASN	0	-0.010	-0.023	37.437	0.001	0.001	0.000	0.000	0.000	0.000
119	A	120	LEU	0	-0.002	0.011	32.130	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	121	SER	0	-0.020	-0.024	34.103	0.004	0.004	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.855	0.912	35.705	-0.053	-0.053	0.000	0.000	0.000	0.000
122	A	123	ASP	-1	-0.878	-0.931	38.254	0.045	0.045	0.000	0.000	0.000	0.000
123	A	124	TYR	0	-0.045	-0.044	31.828	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	125	LEU	0	-0.043	-0.023	36.071	0.002	0.002	0.000	0.000	0.000	0.000
125	A	126	HIS	0	-0.087	-0.048	38.177	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	127	PHE	0	-0.029	0.006	37.957	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	128	TYR	0	-0.006	0.006	35.272	0.000	0.000	0.000	0.000	0.000	0.000
128	A	129	TYR	0	-0.046	-0.027	32.332	0.003	0.003	0.000	0.000	0.000	0.000

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