FMO DATABASE

FMODB ID: VRNY1

Calculation Name: 2CIU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CIU

Chain ID: A

ChEMBL ID:

UniProt ID: P53220

Base Structure: X-ray

Registration Date: 2023-03-13

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	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1062080.007486
FMO2-HF: Nuclear repulsion	1011653.161707
FMO2-HF: Total energy	-50426.845779
FMO2-MP2: Total energy	-50574.357439

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:103:SER)

Summations of interaction energy for fragment #1(A:103:SER)

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.
-7.208	-3.488	7.651	-4.975	-6.395	0.017

Interaction energy analysis for fragmet #1(A:103:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.083 / q_NPA : 0.034

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	105	ASP	-1	-0.722	-0.848	3.875	-1.527	-0.364	-0.008	-0.472	-0.683	0.001
4	A	106	THR	0	0.039	0.016	2.424	-2.690	-0.365	0.870	-1.326	-1.869	-0.005
5	A	107	GLN	0	0.016	0.021	2.025	-5.430	-5.341	6.790	-3.147	-3.731	0.021
6	A	108	LEU	0	-0.047	-0.013	4.299	1.070	1.213	-0.001	-0.030	-0.112	0.000
7	A	109	PHE	0	0.083	0.019	7.182	0.391	0.391	0.000	0.000	0.000	0.000
8	A	110	ASN	0	0.026	0.007	5.636	0.041	0.041	0.000	0.000	0.000	0.000
9	A	111	ARG	1	0.856	0.942	8.288	0.635	0.635	0.000	0.000	0.000	0.000
10	A	112	ALA	0	0.034	0.012	10.222	0.104	0.104	0.000	0.000	0.000	0.000
11	A	113	VAL	0	0.029	0.004	11.347	0.069	0.069	0.000	0.000	0.000	0.000
12	A	114	SER	0	-0.031	-0.015	11.897	0.075	0.075	0.000	0.000	0.000	0.000
13	A	115	MET	0	-0.025	-0.017	14.370	0.009	0.009	0.000	0.000	0.000	0.000
14	A	116	VAL	0	-0.016	-0.005	16.373	0.019	0.019	0.000	0.000	0.000	0.000
15	A	117	GLU	-1	-0.846	-0.903	17.375	0.039	0.039	0.000	0.000	0.000	0.000
16	A	118	LYS	1	0.831	0.885	15.572	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	119	ASN	0	-0.004	0.009	20.224	0.012	0.012	0.000	0.000	0.000	0.000
18	A	120	LYS	1	0.931	0.948	22.539	0.004	0.004	0.000	0.000	0.000	0.000
19	A	121	ASP	-1	-0.767	-0.859	26.072	-0.026	-0.026	0.000	0.000	0.000	0.000
20	A	122	ILE	0	-0.019	-0.011	21.403	0.000	0.000	0.000	0.000	0.000	0.000
21	A	123	ARG	1	0.765	0.834	21.934	0.000	0.000	0.000	0.000	0.000	0.000
22	A	124	SER	0	0.004	0.014	25.522	0.005	0.005	0.000	0.000	0.000	0.000
23	A	125	LEU	0	-0.021	-0.007	26.685	0.001	0.001	0.000	0.000	0.000	0.000
24	A	126	LEU	0	-0.014	-0.027	22.221	0.000	0.000	0.000	0.000	0.000	0.000
25	A	127	GLN	0	-0.041	0.001	26.892	0.006	0.006	0.000	0.000	0.000	0.000
26	A	128	CYS	0	-0.059	-0.015	25.589	0.002	0.002	0.000	0.000	0.000	0.000
27	A	129	ASP	-1	-0.825	-0.896	28.147	0.015	0.015	0.000	0.000	0.000	0.000
28	A	130	ASP	-1	-0.818	-0.879	26.777	0.010	0.010	0.000	0.000	0.000	0.000
29	A	131	GLY	0	0.048	0.015	29.608	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	132	ILE	0	-0.003	-0.005	31.669	0.002	0.002	0.000	0.000	0.000	0.000
31	A	133	THR	0	0.024	0.017	32.366	0.001	0.001	0.000	0.000	0.000	0.000
32	A	134	GLY	0	-0.025	-0.004	28.654	0.005	0.005	0.000	0.000	0.000	0.000
33	A	135	LYS	1	0.897	0.958	22.332	-0.019	-0.019	0.000	0.000	0.000	0.000
34	A	136	GLU	-1	-0.776	-0.874	25.154	0.012	0.012	0.000	0.000	0.000	0.000
35	A	137	ARG	1	0.951	0.975	21.519	-0.055	-0.055	0.000	0.000	0.000	0.000
36	A	138	LEU	0	0.008	0.012	19.847	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	139	LYS	1	0.835	0.919	18.980	0.010	0.010	0.000	0.000	0.000	0.000
38	A	140	ALA	0	0.007	-0.010	15.183	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	141	TYR	0	-0.066	-0.047	14.721	0.008	0.008	0.000	0.000	0.000	0.000
40	A	142	GLY	0	0.054	0.020	14.307	-0.023	-0.023	0.000	0.000	0.000	0.000
41	A	143	GLU	-1	-0.854	-0.928	14.808	-0.043	-0.043	0.000	0.000	0.000	0.000
42	A	144	LEU	0	0.006	0.002	17.842	0.012	0.012	0.000	0.000	0.000	0.000
43	A	145	ILE	0	-0.033	-0.011	20.215	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	146	THR	0	0.047	0.005	22.926	0.003	0.003	0.000	0.000	0.000	0.000
45	A	147	ASN	0	0.003	0.011	26.254	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	148	ASP	-1	-0.850	-0.925	28.923	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	149	LYS	1	0.828	0.921	30.575	0.004	0.004	0.000	0.000	0.000	0.000
48	A	150	TRP	0	0.098	0.041	25.104	0.001	0.001	0.000	0.000	0.000	0.000
49	A	151	THR	0	0.010	0.011	24.303	0.000	0.000	0.000	0.000	0.000	0.000
50	A	152	ARG	1	0.842	0.919	21.434	0.004	0.004	0.000	0.000	0.000	0.000
51	A	153	ASN	0	-0.014	-0.003	15.821	0.003	0.003	0.000	0.000	0.000	0.000
52	A	154	ARG	1	0.895	0.945	15.398	0.038	0.038	0.000	0.000	0.000	0.000
53	A	155	PRO	0	0.032	0.007	11.581	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	156	ILE	0	0.000	0.005	8.477	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	157	VAL	0	-0.005	0.001	8.434	-0.022	-0.022	0.000	0.000	0.000	0.000
56	A	158	SER	0	-0.067	-0.062	9.576	-0.039	-0.039	0.000	0.000	0.000	0.000
57	A	159	THR	0	0.024	0.022	11.523	0.106	0.106	0.000	0.000	0.000	0.000
58	A	160	LYS	1	0.839	0.903	8.939	-0.205	-0.205	0.000	0.000	0.000	0.000
59	A	161	LYS	1	0.935	0.963	14.787	0.071	0.071	0.000	0.000	0.000	0.000
60	A	162	LEU	0	0.042	0.039	18.124	-0.017	-0.017	0.000	0.000	0.000	0.000
61	A	163	ASP	-1	-0.751	-0.858	20.097	-0.092	-0.092	0.000	0.000	0.000	0.000
62	A	164	LYS	1	0.984	0.968	22.745	0.049	0.049	0.000	0.000	0.000	0.000
63	A	165	GLU	-1	-0.809	-0.882	22.424	-0.095	-0.095	0.000	0.000	0.000	0.000
64	A	166	GLY	0	0.018	0.021	22.258	0.000	0.000	0.000	0.000	0.000	0.000
65	A	167	ARG	1	0.819	0.895	16.640	0.144	0.144	0.000	0.000	0.000	0.000
66	A	168	THR	0	0.001	-0.014	13.627	0.003	0.003	0.000	0.000	0.000	0.000
67	A	169	HIS	1	0.759	0.860	15.172	0.086	0.086	0.000	0.000	0.000	0.000
68	A	170	HIS	0	-0.022	-0.014	8.516	0.071	0.071	0.000	0.000	0.000	0.000
69	A	171	TYR	0	-0.059	-0.048	13.597	-0.025	-0.025	0.000	0.000	0.000	0.000
70	A	172	MET	0	-0.026	-0.010	8.521	0.015	0.015	0.000	0.000	0.000	0.000
71	A	173	ARG	1	0.860	0.931	13.747	0.095	0.095	0.000	0.000	0.000	0.000
72	A	174	PHE	0	-0.028	-0.013	13.843	-0.015	-0.015	0.000	0.000	0.000	0.000
73	A	175	HIS	0	0.029	0.025	15.977	0.009	0.009	0.000	0.000	0.000	0.000
74	A	176	VAL	0	0.004	-0.013	17.076	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	177	GLU	-1	-0.770	-0.845	19.522	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	178	SER	0	0.031	-0.001	22.595	0.005	0.005	0.000	0.000	0.000	0.000
77	A	179	LYS	1	0.830	0.882	25.465	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	180	LYS	1	0.878	0.948	28.543	0.004	0.004	0.000	0.000	0.000	0.000
79	A	181	LYS	1	0.763	0.890	27.312	0.017	0.017	0.000	0.000	0.000	0.000
80	A	182	ILE	0	0.028	0.015	22.932	0.000	0.000	0.000	0.000	0.000	0.000
81	A	183	ALA	0	0.015	0.007	21.756	0.000	0.000	0.000	0.000	0.000	0.000
82	A	184	LEU	0	-0.040	-0.014	20.001	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	185	VAL	0	-0.009	-0.007	16.851	0.003	0.003	0.000	0.000	0.000	0.000
84	A	186	HIS	0	0.044	0.029	17.943	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	187	LEU	0	-0.015	-0.017	12.185	0.002	0.002	0.000	0.000	0.000	0.000
86	A	188	GLU	-1	-0.789	-0.856	15.762	-0.120	-0.120	0.000	0.000	0.000	0.000
87	A	189	ALA	0	-0.006	-0.004	12.869	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	190	LYS	1	0.760	0.867	14.307	0.152	0.152	0.000	0.000	0.000	0.000
89	A	191	GLU	-1	-0.774	-0.858	12.057	-0.240	-0.240	0.000	0.000	0.000	0.000
90	A	192	SER	0	0.019	0.013	13.340	0.058	0.058	0.000	0.000	0.000	0.000
91	A	193	LYS	1	0.798	0.863	15.229	0.188	0.188	0.000	0.000	0.000	0.000
92	A	194	GLN	0	0.012	0.023	17.333	0.012	0.012	0.000	0.000	0.000	0.000
93	A	195	ASN	0	-0.045	-0.029	13.964	0.035	0.035	0.000	0.000	0.000	0.000
94	A	196	TYR	0	0.005	-0.011	5.121	-0.085	-0.085	0.000	0.000	0.000	0.000
95	A	197	GLN	0	0.004	0.004	9.210	-0.128	-0.128	0.000	0.000	0.000	0.000
96	A	198	PRO	0	-0.012	-0.006	8.844	0.081	0.081	0.000	0.000	0.000	0.000
97	A	199	ASP	-1	-0.744	-0.841	11.784	-0.206	-0.206	0.000	0.000	0.000	0.000
98	A	200	PHE	0	-0.028	-0.043	10.861	-0.010	-0.010	0.000	0.000	0.000	0.000
99	A	201	ILE	0	-0.021	-0.008	15.817	0.031	0.031	0.000	0.000	0.000	0.000
100	A	202	ASN	0	-0.017	-0.033	18.413	0.027	0.027	0.000	0.000	0.000	0.000
101	A	203	MET	0	-0.013	0.002	15.447	-0.031	-0.031	0.000	0.000	0.000	0.000
102	A	204	TYR	0	-0.050	-0.019	19.184	0.015	0.015	0.000	0.000	0.000	0.000
103	A	205	VAL	0	0.024	0.012	20.165	-0.012	-0.012	0.000	0.000	0.000	0.000
104	A	206	ASP	-1	-0.744	-0.828	22.475	-0.051	-0.051	0.000	0.000	0.000	0.000
105	A	207	VAL	0	0.023	-0.008	24.644	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	208	PRO	0	0.029	0.018	27.119	0.002	0.002	0.000	0.000	0.000	0.000
107	A	209	GLY	0	0.021	0.012	30.328	0.002	0.002	0.000	0.000	0.000	0.000
108	A	210	GLU	-1	-0.828	-0.882	29.514	-0.019	-0.019	0.000	0.000	0.000	0.000
109	A	211	LYS	1	0.923	0.960	30.788	0.030	0.030	0.000	0.000	0.000	0.000
110	A	212	ARG	1	0.801	0.874	25.773	0.058	0.058	0.000	0.000	0.000	0.000
111	A	213	TYR	0	-0.033	-0.042	23.818	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	214	TYR	0	-0.022	-0.031	23.452	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	215	LEU	0	0.002	0.006	18.420	0.006	0.006	0.000	0.000	0.000	0.000
114	A	216	ILE	0	-0.013	-0.005	17.396	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	217	LYS	1	0.933	0.958	21.485	0.046	0.046	0.000	0.000	0.000	0.000
116	A	218	PRO	0	0.013	0.011	23.405	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	219	LYS	1	0.986	0.997	24.106	0.081	0.081	0.000	0.000	0.000	0.000
118	A	220	LEU	0	-0.027	-0.005	26.055	0.007	0.007	0.000	0.000	0.000	0.000
119	A	221	HIS	0	-0.025	-0.016	27.923	0.001	0.001	0.000	0.000	0.000	0.000
120	A	222	PRO	0	0.035	0.004	30.095	0.003	0.003	0.000	0.000	0.000	0.000
121	A	223	VAL	0	0.072	0.031	33.261	0.000	0.000	0.000	0.000	0.000	0.000
122	A	224	SER	0	0.033	0.038	36.313	0.001	0.001	0.000	0.000	0.000	0.000
123	A	225	ASN	0	-0.039	-0.011	30.732	-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:103:SER)