FMO DATABASE

FMODB ID: KGMY3

Calculation Name: 3U4V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U4V

Chain ID: A

ChEMBL ID:

UniProt ID: D2CVN6

Base Structure: X-ray

Registration Date: 2023-09-23

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	116
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1033471.869408
FMO2-HF: Nuclear repulsion	986380.201847
FMO2-HF: Total energy	-47091.667561
FMO2-MP2: Total energy	-47232.272817

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:199:ASN)

Summations of interaction energy for fragment #1(A:199:ASN)

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.
-1.68	1.471	-0.006	-1.52	-1.623	0.006

Interaction energy analysis for fragmet #1(A:199:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.008

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	A	201	ASN	0	-0.001	-0.001	3.476	-2.739	0.083	-0.004	-1.511	-1.307	0.006
4	A	202	ILE	0	-0.018	0.001	5.989	0.547	0.547	0.000	0.000	0.000	0.000
5	A	203	GLY	0	0.013	0.010	7.980	0.197	0.197	0.000	0.000	0.000	0.000
6	A	204	SER	0	-0.003	-0.025	10.337	0.202	0.202	0.000	0.000	0.000	0.000
7	A	205	LEU	0	0.060	0.005	12.669	0.069	0.069	0.000	0.000	0.000	0.000
8	A	206	SER	0	0.063	0.034	14.958	0.066	0.066	0.000	0.000	0.000	0.000
9	A	207	ASP	-1	-0.801	-0.857	13.418	-0.642	-0.642	0.000	0.000	0.000	0.000
10	A	208	GLN	0	-0.080	-0.053	10.982	0.195	0.195	0.000	0.000	0.000	0.000
11	A	209	LEU	0	0.017	-0.001	14.840	0.054	0.054	0.000	0.000	0.000	0.000
12	A	210	SER	0	-0.020	-0.019	18.015	0.018	0.018	0.000	0.000	0.000	0.000
13	A	211	LYS	1	0.849	0.961	12.765	0.338	0.338	0.000	0.000	0.000	0.000
14	A	212	GLN	0	0.049	0.022	18.612	0.034	0.034	0.000	0.000	0.000	0.000
15	A	213	THR	0	0.009	-0.005	20.886	0.020	0.020	0.000	0.000	0.000	0.000
16	A	214	LEU	0	-0.060	-0.014	21.612	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	215	LEU	0	0.029	0.015	24.032	0.030	0.030	0.000	0.000	0.000	0.000
18	A	216	ILE	0	0.025	0.001	25.865	0.008	0.008	0.000	0.000	0.000	0.000
19	A	217	SER	0	-0.039	-0.013	26.891	0.005	0.005	0.000	0.000	0.000	0.000
20	A	218	GLN	0	0.000	0.000	26.165	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	219	LEU	0	-0.060	-0.009	21.580	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	220	GLN	0	0.026	0.002	22.916	-0.019	-0.019	0.000	0.000	0.000	0.000
23	A	221	VAL	0	0.008	-0.009	21.362	0.017	0.017	0.000	0.000	0.000	0.000
24	A	222	GLY	0	0.000	0.009	18.685	-0.033	-0.033	0.000	0.000	0.000	0.000
25	A	223	LYS	1	0.883	0.966	18.520	-0.079	-0.079	0.000	0.000	0.000	0.000
26	A	224	ASN	0	0.035	0.012	14.339	0.078	0.078	0.000	0.000	0.000	0.000
27	A	225	ARG	1	0.967	0.983	10.933	-1.063	-1.063	0.000	0.000	0.000	0.000
28	A	226	PHE	0	-0.012	0.001	7.760	-0.054	-0.054	0.000	0.000	0.000	0.000
29	A	227	SER	0	-0.065	-0.047	13.199	-0.088	-0.088	0.000	0.000	0.000	0.000
30	A	228	PHE	0	-0.048	-0.026	16.398	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	229	LYS	1	0.854	0.944	16.431	0.025	0.025	0.000	0.000	0.000	0.000
32	A	230	PHE	0	0.030	0.005	18.252	-0.021	-0.021	0.000	0.000	0.000	0.000
33	A	231	GLU	-1	-0.788	-0.885	20.258	0.140	0.140	0.000	0.000	0.000	0.000
34	A	232	GLY	0	0.009	0.007	22.937	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	233	ARG	1	0.871	0.933	24.563	-0.175	-0.175	0.000	0.000	0.000	0.000
36	A	234	VAL	0	-0.010	-0.004	23.763	0.010	0.010	0.000	0.000	0.000	0.000
37	A	235	VAL	0	0.009	0.001	26.530	-0.021	-0.021	0.000	0.000	0.000	0.000
38	A	236	TYR	0	0.015	0.001	27.293	-0.009	-0.009	0.000	0.000	0.000	0.000
39	A	237	LYS	1	0.846	0.920	22.584	-0.429	-0.429	0.000	0.000	0.000	0.000
40	A	238	SER	0	-0.008	0.014	24.511	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	239	SER	0	0.063	0.043	24.998	0.010	0.010	0.000	0.000	0.000	0.000
42	A	240	THR	0	-0.010	0.000	20.805	0.026	0.026	0.000	0.000	0.000	0.000
43	A	241	PHE	0	-0.030	-0.009	22.069	-0.054	-0.054	0.000	0.000	0.000	0.000
44	A	242	GLN	0	-0.021	-0.026	19.902	0.029	0.029	0.000	0.000	0.000	0.000
45	A	243	ASN	0	0.023	0.020	18.642	-0.046	-0.046	0.000	0.000	0.000	0.000
46	A	244	GLN	0	0.061	0.011	22.373	0.017	0.017	0.000	0.000	0.000	0.000
47	A	245	GLN	0	-0.045	-0.019	18.686	0.007	0.007	0.000	0.000	0.000	0.000
48	A	246	ASP	-1	-0.851	-0.913	18.634	0.807	0.807	0.000	0.000	0.000	0.000
49	A	247	SER	0	-0.027	0.004	15.934	0.159	0.159	0.000	0.000	0.000	0.000
50	A	248	LYS	1	0.933	0.954	16.857	-0.796	-0.796	0.000	0.000	0.000	0.000
51	A	249	TYR	0	-0.006	-0.017	16.813	0.146	0.146	0.000	0.000	0.000	0.000
52	A	250	PHE	0	-0.005	0.006	17.116	-0.077	-0.077	0.000	0.000	0.000	0.000
53	A	251	PHE	0	0.029	0.000	20.177	0.061	0.061	0.000	0.000	0.000	0.000
54	A	252	ILE	0	-0.013	-0.004	21.302	-0.022	-0.022	0.000	0.000	0.000	0.000
55	A	253	THR	0	0.011	0.010	23.846	0.012	0.012	0.000	0.000	0.000	0.000
56	A	254	ALA	0	-0.031	-0.015	24.188	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	255	GLN	0	0.025	0.021	26.259	-0.015	-0.015	0.000	0.000	0.000	0.000
58	A	256	ASP	-1	-0.739	-0.883	27.109	0.166	0.166	0.000	0.000	0.000	0.000
59	A	257	ALA	0	0.001	-0.010	28.242	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	258	ASN	0	-0.030	-0.012	30.429	-0.016	-0.016	0.000	0.000	0.000	0.000
61	A	259	ASN	0	-0.063	-0.032	32.107	0.001	0.001	0.000	0.000	0.000	0.000
62	A	260	GLN	0	0.035	0.037	30.581	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	261	GLU	-1	-0.846	-0.936	29.247	0.227	0.227	0.000	0.000	0.000	0.000
64	A	262	ILE	0	-0.040	-0.012	23.768	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	263	ASN	0	0.005	0.011	25.016	0.007	0.007	0.000	0.000	0.000	0.000
66	A	264	MET	0	-0.001	-0.001	19.834	0.005	0.005	0.000	0.000	0.000	0.000
67	A	265	SER	0	-0.011	-0.008	19.244	0.027	0.027	0.000	0.000	0.000	0.000
68	A	266	PHE	0	0.011	0.012	14.794	0.082	0.082	0.000	0.000	0.000	0.000
69	A	267	TRP	0	-0.048	-0.042	13.905	-0.079	-0.079	0.000	0.000	0.000	0.000
70	A	268	GLN	0	0.008	-0.023	11.535	0.578	0.578	0.000	0.000	0.000	0.000
71	A	269	LYS	1	0.964	0.993	10.165	-1.473	-1.473	0.000	0.000	0.000	0.000
72	A	270	VAL	0	0.037	0.033	13.129	-0.029	-0.029	0.000	0.000	0.000	0.000
73	A	271	ASP	-1	-0.896	-0.949	15.829	0.963	0.963	0.000	0.000	0.000	0.000
74	A	272	GLN	0	-0.013	-0.013	11.090	0.101	0.101	0.000	0.000	0.000	0.000
75	A	273	SER	0	0.014	-0.008	13.401	-0.061	-0.061	0.000	0.000	0.000	0.000
76	A	274	TYR	0	-0.067	-0.055	15.958	-0.121	-0.121	0.000	0.000	0.000	0.000
77	A	275	GLN	0	0.040	0.004	19.385	-0.083	-0.083	0.000	0.000	0.000	0.000
78	A	276	THR	0	0.001	0.024	17.625	-0.079	-0.079	0.000	0.000	0.000	0.000
79	A	277	LEU	0	-0.016	0.030	18.561	-0.053	-0.053	0.000	0.000	0.000	0.000
80	A	278	LYS	1	0.874	0.919	22.058	-0.276	-0.276	0.000	0.000	0.000	0.000
81	A	279	VAL	0	0.034	0.009	25.832	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	280	GLY	0	-0.026	-0.009	28.579	-0.015	-0.015	0.000	0.000	0.000	0.000
83	A	281	GLN	0	-0.044	-0.023	25.882	-0.031	-0.031	0.000	0.000	0.000	0.000
84	A	282	TYR	0	0.036	0.002	25.462	0.020	0.020	0.000	0.000	0.000	0.000
85	A	283	TYR	0	-0.042	-0.040	19.944	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	284	TYR	0	-0.014	-0.026	18.472	-0.031	-0.031	0.000	0.000	0.000	0.000
87	A	285	PHE	0	-0.004	-0.004	16.199	0.058	0.058	0.000	0.000	0.000	0.000
88	A	286	ILE	0	-0.009	-0.016	12.191	-0.092	-0.092	0.000	0.000	0.000	0.000
89	A	287	GLY	0	0.098	0.040	11.253	0.177	0.177	0.000	0.000	0.000	0.000
90	A	288	GLY	0	-0.035	-0.003	12.194	0.181	0.181	0.000	0.000	0.000	0.000
91	A	289	GLU	-1	-0.838	-0.908	14.275	0.825	0.825	0.000	0.000	0.000	0.000
92	A	290	VAL	0	0.025	0.014	15.838	0.009	0.009	0.000	0.000	0.000	0.000
93	A	291	LYS	1	0.847	0.914	19.036	-0.570	-0.570	0.000	0.000	0.000	0.000
94	A	292	GLN	0	0.030	0.008	20.879	-0.029	-0.029	0.000	0.000	0.000	0.000
95	A	293	PHE	0	-0.044	-0.038	24.088	0.035	0.035	0.000	0.000	0.000	0.000
96	A	294	LYS	1	0.970	0.988	26.374	-0.295	-0.295	0.000	0.000	0.000	0.000
97	A	295	ASN	0	0.038	0.024	29.195	0.008	0.008	0.000	0.000	0.000	0.000
98	A	296	ASN	0	-0.018	-0.004	28.669	-0.029	-0.029	0.000	0.000	0.000	0.000
99	A	297	LEU	0	0.056	0.025	24.221	0.018	0.018	0.000	0.000	0.000	0.000
100	A	298	GLU	-1	-0.844	-0.883	21.097	0.589	0.589	0.000	0.000	0.000	0.000
101	A	299	LEU	0	-0.004	0.001	18.405	0.000	0.000	0.000	0.000	0.000	0.000
102	A	300	LYS	1	0.826	0.913	15.098	-1.001	-1.001	0.000	0.000	0.000	0.000
103	A	301	PHE	0	0.034	0.008	13.403	0.036	0.036	0.000	0.000	0.000	0.000
104	A	302	LYS	1	0.933	0.964	9.289	-2.331	-2.331	0.000	0.000	0.000	0.000
105	A	303	PHE	0	-0.004	-0.013	6.813	0.479	0.479	0.000	0.000	0.000	0.000
106	A	304	GLY	0	0.039	0.017	4.847	0.414	0.616	-0.001	-0.007	-0.193	0.000
107	A	305	ASP	-1	-0.901	-0.953	5.014	3.861	3.988	-0.001	-0.002	-0.123	0.000
108	A	306	TYR	0	-0.047	-0.024	7.740	-0.924	-0.924	0.000	0.000	0.000	0.000
109	A	307	GLN	0	-0.024	-0.019	9.546	0.310	0.310	0.000	0.000	0.000	0.000
110	A	308	ILE	0	-0.023	-0.010	11.694	-0.078	-0.078	0.000	0.000	0.000	0.000
111	A	309	ILE	0	0.009	0.008	15.116	-0.023	-0.023	0.000	0.000	0.000	0.000
112	A	310	PRO	0	0.041	0.019	17.549	-0.017	-0.017	0.000	0.000	0.000	0.000
113	A	311	LYS	1	0.885	0.939	21.028	-0.149	-0.149	0.000	0.000	0.000	0.000
114	A	312	GLU	-1	-0.852	-0.882	23.826	0.206	0.206	0.000	0.000	0.000	0.000
115	A	313	THR	0	-0.077	-0.054	20.577	-0.011	-0.011	0.000	0.000	0.000	0.000
116	A	314	LEU	0	-0.031	0.001	20.645	-0.026	-0.026	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:199:ASN)