FMO DATABASE

FMODB ID: ZVRVN

Calculation Name: 1ZO2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZO2

Chain ID: A

ChEMBL ID:

UniProt ID: Q5CQI4

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	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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1083225.159612
FMO2-HF: Nuclear repulsion	1033572.91793
FMO2-HF: Total energy	-49652.241682
FMO2-MP2: Total energy	-49797.19126

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:3:SER)

Summations of interaction energy for fragment #1(A:3: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.
-3.14	-1.173	0.003	-0.948	-1.023	0

Interaction energy analysis for fragmet #1(A:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / 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	5	ASN	0	-0.041	-0.024	3.342	-2.869	-0.902	0.003	-0.948	-1.023
4	A	6	LEU	0	0.025	0.014	5.814	0.390	0.390	0.000	0.000	0.000
5	A	7	ASN	0	0.041	0.019	9.451	0.175	0.175	0.000	0.000	0.000
6	A	8	PRO	0	0.022	-0.001	12.223	0.091	0.091	0.000	0.000	0.000
7	A	9	GLN	0	-0.026	-0.021	15.069	0.059	0.059	0.000	0.000	0.000
8	A	10	PHE	0	0.019	0.010	15.070	0.040	0.040	0.000	0.000	0.000
9	A	11	ASP	-1	-0.770	-0.856	16.969	-0.227	-0.227	0.000	0.000	0.000
10	A	12	GLN	0	0.028	0.026	20.594	0.006	0.006	0.000	0.000	0.000
11	A	13	ILE	0	-0.011	-0.007	16.661	0.025	0.025	0.000	0.000	0.000
12	A	14	GLY	0	0.033	0.006	20.030	0.018	0.018	0.000	0.000	0.000
13	A	15	LYS	1	0.857	0.904	20.941	0.244	0.244	0.000	0.000	0.000
14	A	16	GLN	0	-0.036	-0.007	23.901	0.012	0.012	0.000	0.000	0.000
15	A	17	PHE	0	-0.003	-0.007	21.880	0.016	0.016	0.000	0.000	0.000
16	A	18	VAL	0	0.020	0.000	23.799	0.019	0.019	0.000	0.000	0.000
17	A	19	GLN	0	-0.043	-0.023	25.946	0.010	0.010	0.000	0.000	0.000
18	A	20	HIS	0	0.058	0.027	26.158	0.017	0.017	0.000	0.000	0.000
19	A	21	TYR	0	0.003	0.024	25.559	0.017	0.017	0.000	0.000	0.000
20	A	22	TYR	0	0.050	-0.021	27.843	0.010	0.010	0.000	0.000	0.000
21	A	23	GLN	0	0.000	0.032	31.219	0.016	0.016	0.000	0.000	0.000
22	A	24	THR	0	0.000	-0.001	30.251	0.010	0.010	0.000	0.000	0.000
23	A	25	PHE	0	-0.022	-0.019	29.940	0.011	0.011	0.000	0.000	0.000
24	A	26	GLN	0	-0.032	-0.018	33.143	0.015	0.015	0.000	0.000	0.000
25	A	27	THR	0	-0.070	-0.036	35.617	0.005	0.005	0.000	0.000	0.000
26	A	28	ASN	0	-0.020	-0.023	34.731	0.007	0.007	0.000	0.000	0.000
27	A	29	ARG	1	0.932	0.965	33.138	0.076	0.076	0.000	0.000	0.000
28	A	30	PRO	0	0.033	0.018	32.173	-0.007	-0.007	0.000	0.000	0.000
29	A	31	ALA	0	-0.008	0.006	31.131	-0.005	-0.005	0.000	0.000	0.000
30	A	32	LEU	0	0.013	0.012	28.197	-0.013	-0.013	0.000	0.000	0.000
31	A	33	GLY	0	0.010	-0.004	26.745	-0.013	-0.013	0.000	0.000	0.000
32	A	34	GLY	0	-0.042	-0.016	26.238	-0.005	-0.005	0.000	0.000	0.000
33	A	35	LEU	0	-0.031	-0.003	23.158	-0.017	-0.017	0.000	0.000	0.000
34	A	36	TYR	0	-0.046	-0.050	21.136	-0.023	-0.023	0.000	0.000	0.000
35	A	37	GLY	0	0.078	0.033	20.005	0.002	0.002	0.000	0.000	0.000
36	A	38	PRO	0	-0.013	-0.024	19.925	0.011	0.011	0.000	0.000	0.000
37	A	39	GLN	0	-0.015	-0.015	16.160	-0.007	-0.007	0.000	0.000	0.000
38	A	40	SER	0	-0.011	0.001	18.387	-0.009	-0.009	0.000	0.000	0.000
39	A	41	MET	0	-0.062	-0.024	16.172	0.039	0.039	0.000	0.000	0.000
40	A	42	LEU	0	0.007	0.014	21.030	-0.018	-0.018	0.000	0.000	0.000
41	A	43	THR	0	-0.020	-0.017	23.200	0.019	0.019	0.000	0.000	0.000
42	A	44	TRP	0	0.041	0.003	25.607	-0.010	-0.010	0.000	0.000	0.000
43	A	45	GLU	-1	-0.803	-0.910	29.112	-0.060	-0.060	0.000	0.000	0.000
44	A	46	ASP	-1	-0.825	-0.895	28.472	-0.047	-0.047	0.000	0.000	0.000
45	A	47	THR	0	-0.053	-0.009	28.728	0.006	0.006	0.000	0.000	0.000
46	A	48	GLN	0	-0.015	-0.006	22.114	-0.007	-0.007	0.000	0.000	0.000
47	A	49	PHE	0	0.007	-0.008	25.804	0.009	0.009	0.000	0.000	0.000
48	A	50	GLN	0	-0.007	-0.009	22.825	-0.012	-0.012	0.000	0.000	0.000
49	A	51	GLY	0	0.064	0.040	22.684	0.012	0.012	0.000	0.000	0.000
50	A	52	GLN	0	-0.057	-0.046	23.602	0.012	0.012	0.000	0.000	0.000
51	A	53	ALA	0	0.033	0.018	25.222	0.005	0.005	0.000	0.000	0.000
52	A	54	ASN	0	-0.020	-0.023	27.204	0.010	0.010	0.000	0.000	0.000
53	A	55	ILE	0	-0.023	0.007	23.273	0.005	0.005	0.000	0.000	0.000
54	A	56	VAL	0	0.013	0.010	27.823	0.002	0.002	0.000	0.000	0.000
55	A	57	ASN	0	-0.026	-0.015	30.449	0.004	0.004	0.000	0.000	0.000
56	A	58	LYS	1	0.891	0.978	30.105	0.078	0.078	0.000	0.000	0.000
57	A	59	PHE	0	0.023	-0.012	27.159	0.005	0.005	0.000	0.000	0.000
58	A	60	ASN	0	-0.014	-0.011	32.717	0.002	0.002	0.000	0.000	0.000
59	A	61	SER	0	-0.032	-0.018	35.441	0.005	0.005	0.000	0.000	0.000
60	A	62	LEU	0	-0.066	-0.017	32.918	0.004	0.004	0.000	0.000	0.000
61	A	63	ASN	0	-0.063	-0.031	37.097	0.003	0.003	0.000	0.000	0.000
62	A	64	PHE	0	0.019	0.021	35.610	0.001	0.001	0.000	0.000	0.000
63	A	65	GLN	0	0.034	0.025	40.806	-0.003	-0.003	0.000	0.000	0.000
64	A	66	ARG	1	0.760	0.843	42.218	0.063	0.063	0.000	0.000	0.000
65	A	67	VAL	0	-0.018	-0.001	36.558	0.001	0.001	0.000	0.000	0.000
66	A	68	GLN	0	-0.011	0.000	38.529	0.002	0.002	0.000	0.000	0.000
67	A	69	PHE	0	0.000	-0.015	32.682	0.001	0.001	0.000	0.000	0.000
68	A	70	GLU	-1	-0.912	-0.944	36.176	-0.091	-0.091	0.000	0.000	0.000
69	A	71	ILE	0	-0.043	-0.015	29.793	0.002	0.002	0.000	0.000	0.000
70	A	72	THR	0	0.022	0.005	33.098	-0.004	-0.004	0.000	0.000	0.000
71	A	73	ARG	1	0.794	0.855	27.113	0.136	0.136	0.000	0.000	0.000
72	A	74	VAL	0	0.040	0.012	24.572	-0.004	-0.004	0.000	0.000	0.000
73	A	75	ASP	-1	-0.854	-0.878	23.239	-0.158	-0.158	0.000	0.000	0.000
74	A	76	CYS	0	-0.023	0.001	18.995	-0.004	-0.004	0.000	0.000	0.000
75	A	77	GLN	0	-0.005	-0.007	15.614	0.018	0.018	0.000	0.000	0.000
76	A	78	PRO	0	-0.008	0.015	12.015	-0.033	-0.033	0.000	0.000	0.000
77	A	79	SER	0	0.022	0.007	10.986	-0.064	-0.064	0.000	0.000	0.000
78	A	80	PRO	0	0.020	0.002	5.440	-0.034	-0.034	0.000	0.000	0.000
79	A	81	ASN	0	-0.005	-0.025	5.736	-1.566	-1.566	0.000	0.000	0.000
80	A	82	ASN	0	0.025	0.001	7.532	0.391	0.391	0.000	0.000	0.000
81	A	83	GLY	0	0.024	0.019	9.537	0.245	0.245	0.000	0.000	0.000
82	A	84	SER	0	-0.075	-0.049	12.517	-0.008	-0.008	0.000	0.000	0.000
83	A	85	ILE	0	0.008	0.017	12.686	0.024	0.024	0.000	0.000	0.000
84	A	86	VAL	0	-0.012	-0.007	16.242	0.019	0.019	0.000	0.000	0.000
85	A	87	PHE	0	-0.010	-0.003	20.085	0.017	0.017	0.000	0.000	0.000
86	A	88	VAL	0	0.024	0.008	22.894	-0.002	-0.002	0.000	0.000	0.000
87	A	89	THR	0	-0.057	-0.047	26.545	0.012	0.012	0.000	0.000	0.000
88	A	90	GLY	0	0.003	0.010	29.964	-0.005	-0.005	0.000	0.000	0.000
89	A	91	ASP	-1	-0.802	-0.872	33.528	-0.065	-0.065	0.000	0.000	0.000
90	A	92	VAL	0	0.012	0.007	35.118	-0.006	-0.006	0.000	0.000	0.000
91	A	93	ARG	1	0.781	0.892	37.165	0.064	0.064	0.000	0.000	0.000
92	A	94	ILE	0	0.038	0.015	37.039	-0.004	-0.004	0.000	0.000	0.000
93	A	95	ASP	-1	-0.780	-0.902	41.080	-0.055	-0.055	0.000	0.000	0.000
94	A	96	ASP	-1	-0.825	-0.889	44.310	-0.055	-0.055	0.000	0.000	0.000
95	A	97	GLY	0	0.033	0.034	44.915	0.003	0.003	0.000	0.000	0.000
96	A	98	GLN	0	-0.005	-0.012	43.370	-0.001	-0.001	0.000	0.000	0.000
97	A	99	PRO	0	-0.030	-0.015	41.276	-0.002	-0.002	0.000	0.000	0.000
98	A	100	LEU	0	-0.009	0.002	38.136	0.004	0.004	0.000	0.000	0.000
99	A	101	LYS	1	0.835	0.891	35.365	0.061	0.061	0.000	0.000	0.000
100	A	102	PHE	0	-0.014	0.008	29.456	0.003	0.003	0.000	0.000	0.000
101	A	103	SER	0	0.023	0.020	27.363	0.001	0.001	0.000	0.000	0.000
102	A	104	GLN	0	-0.007	-0.009	24.869	0.012	0.012	0.000	0.000	0.000
103	A	105	VAL	0	-0.014	0.000	19.571	-0.007	-0.007	0.000	0.000	0.000
104	A	106	PHE	0	0.009	0.002	19.837	0.004	0.004	0.000	0.000	0.000
105	A	107	ASN	0	-0.037	-0.025	12.245	-0.080	-0.080	0.000	0.000	0.000
106	A	108	LEU	0	0.013	0.017	16.189	0.006	0.006	0.000	0.000	0.000
107	A	109	MET	0	0.007	0.015	10.185	-0.113	-0.113	0.000	0.000	0.000
108	A	110	PRO	0	0.046	0.020	11.301	0.105	0.105	0.000	0.000	0.000
109	A	111	SER	0	-0.035	-0.025	14.066	-0.012	-0.012	0.000	0.000	0.000
110	A	112	GLY	0	0.002	0.008	14.905	0.048	0.048	0.000	0.000	0.000
111	A	113	ASN	0	-0.009	-0.012	15.868	-0.027	-0.027	0.000	0.000	0.000
112	A	114	GLY	0	-0.002	0.002	17.444	0.027	0.027	0.000	0.000	0.000
113	A	115	GLY	0	-0.003	0.017	18.476	-0.002	-0.002	0.000	0.000	0.000
114	A	116	PHE	0	-0.014	-0.021	14.067	-0.063	-0.063	0.000	0.000	0.000
115	A	117	MET	0	-0.034	0.004	16.697	0.037	0.037	0.000	0.000	0.000
116	A	118	ILE	0	0.033	0.015	17.253	-0.055	-0.055	0.000	0.000	0.000
117	A	119	PHE	0	0.006	0.018	13.904	0.024	0.024	0.000	0.000	0.000
118	A	120	ASN	0	0.004	-0.011	14.976	-0.009	-0.009	0.000	0.000	0.000
119	A	121	ASP	-1	-0.716	-0.830	18.209	-0.199	-0.199	0.000	0.000	0.000
120	A	122	LEU	0	-0.020	-0.009	19.943	0.019	0.019	0.000	0.000	0.000
121	A	123	PHE	0	0.004	0.010	23.830	-0.004	-0.004	0.000	0.000	0.000
122	A	124	ARG	1	0.850	0.897	27.069	0.068	0.068	0.000	0.000	0.000
123	A	125	LEU	0	-0.012	-0.001	30.036	-0.005	-0.005	0.000	0.000	0.000
124	A	126	ASN	0	-0.051	-0.034	30.793	0.009	0.009	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)