FMO DATABASE

FMODB ID: YYRL2

Calculation Name: 4CZD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4CZD

Chain ID: A

ChEMBL ID:

UniProt ID: B8J364

Base Structure: X-ray

Registration Date: 2023-03-14

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	145
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1132799.511357
FMO2-HF: Nuclear repulsion	1076054.099166
FMO2-HF: Total energy	-56745.412191
FMO2-MP2: Total energy	-56911.704344

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:22:ASP)

Summations of interaction energy for fragment #1(A:22:ASP)

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.
-89.902	-86.524	0.071	-1.446	-2.003	0.007

Interaction energy analysis for fragmet #1(A:22:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.940 / q_NPA : -0.968

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	24	ASP	-1	-0.746	-0.841	3.886	34.163	36.108	-0.018	-0.910	-1.017	0.004
4	A	25	SER	0	-0.035	-0.045	6.970	-2.084	-2.084	0.000	0.000	0.000	0.000
5	A	26	MET	0	0.057	0.053	9.551	-1.571	-1.571	0.000	0.000	0.000	0.000
6	A	27	ASP	-1	-0.750	-0.896	7.470	31.864	31.864	0.000	0.000	0.000	0.000
7	A	28	ARG	1	0.843	0.922	3.985	-44.965	-44.797	0.000	-0.020	-0.148	0.000
8	A	29	GLN	0	0.030	0.017	8.925	-2.482	-2.482	0.000	0.000	0.000	0.000
9	A	30	LEU	0	0.026	0.016	11.742	-1.485	-1.485	0.000	0.000	0.000	0.000
10	A	31	LEU	0	-0.018	-0.037	7.613	-1.361	-1.361	0.000	0.000	0.000	0.000
11	A	32	ASP	-1	-0.944	-0.950	11.618	16.631	16.631	0.000	0.000	0.000	0.000
12	A	33	ILE	0	-0.028	-0.008	13.634	-1.360	-1.360	0.000	0.000	0.000	0.000
13	A	34	ILE	0	-0.027	-0.034	13.464	-0.845	-0.845	0.000	0.000	0.000	0.000
14	A	35	GLN	0	-0.089	-0.029	12.046	-0.888	-0.888	0.000	0.000	0.000	0.000
15	A	36	THR	0	-0.079	-0.028	15.989	-0.956	-0.956	0.000	0.000	0.000	0.000
16	A	37	GLY	0	0.015	-0.011	19.122	-0.750	-0.750	0.000	0.000	0.000	0.000
17	A	38	PHE	0	-0.030	-0.003	18.454	0.331	0.331	0.000	0.000	0.000	0.000
18	A	39	PRO	0	0.001	0.000	20.434	-0.514	-0.514	0.000	0.000	0.000	0.000
19	A	40	LEU	0	-0.010	0.001	23.672	-0.055	-0.055	0.000	0.000	0.000	0.000
20	A	41	SER	0	-0.009	-0.018	26.581	-0.359	-0.359	0.000	0.000	0.000	0.000
21	A	42	PRO	0	0.005	-0.008	27.683	0.241	0.241	0.000	0.000	0.000	0.000
22	A	43	ARG	1	0.900	0.962	27.128	-11.010	-11.010	0.000	0.000	0.000	0.000
23	A	44	PRO	0	0.026	0.029	22.738	0.209	0.209	0.000	0.000	0.000	0.000
24	A	45	TYR	0	0.046	0.000	18.066	0.188	0.188	0.000	0.000	0.000	0.000
25	A	46	ALA	0	0.031	0.029	21.562	0.423	0.423	0.000	0.000	0.000	0.000
26	A	47	GLU	-1	-0.913	-0.948	23.950	11.856	11.856	0.000	0.000	0.000	0.000
27	A	48	LEU	0	-0.033	-0.026	17.729	0.173	0.173	0.000	0.000	0.000	0.000
28	A	49	GLY	0	0.046	0.028	19.984	0.460	0.460	0.000	0.000	0.000	0.000
29	A	50	GLN	0	-0.024	-0.025	21.203	0.061	0.061	0.000	0.000	0.000	0.000
30	A	51	ARG	1	0.894	0.959	20.707	-13.781	-13.781	0.000	0.000	0.000	0.000
31	A	52	LEU	0	-0.037	-0.028	15.299	0.206	0.206	0.000	0.000	0.000	0.000
32	A	53	GLY	0	-0.006	0.021	18.545	0.528	0.528	0.000	0.000	0.000	0.000
33	A	54	LEU	0	-0.024	-0.031	15.252	0.662	0.662	0.000	0.000	0.000	0.000
34	A	55	ASP	-1	-0.830	-0.916	19.801	13.938	13.938	0.000	0.000	0.000	0.000
35	A	56	GLU	-1	-0.843	-0.953	20.222	12.846	12.846	0.000	0.000	0.000	0.000
36	A	57	GLN	0	-0.077	-0.048	20.355	-0.351	-0.351	0.000	0.000	0.000	0.000
37	A	58	GLU	-1	-0.783	-0.880	15.238	21.208	21.208	0.000	0.000	0.000	0.000
38	A	59	VAL	0	-0.001	0.009	16.104	1.361	1.361	0.000	0.000	0.000	0.000
39	A	60	LEU	0	-0.042	-0.027	16.128	0.747	0.747	0.000	0.000	0.000	0.000
40	A	61	ASP	-1	-0.883	-0.936	15.803	17.961	17.961	0.000	0.000	0.000	0.000
41	A	62	ARG	1	0.770	0.854	10.191	-25.971	-25.971	0.000	0.000	0.000	0.000
42	A	63	VAL	0	-0.023	-0.004	11.968	1.322	1.322	0.000	0.000	0.000	0.000
43	A	64	ARG	1	0.902	0.943	13.647	-15.161	-15.161	0.000	0.000	0.000	0.000
44	A	65	GLY	0	0.050	0.031	11.421	-0.057	-0.057	0.000	0.000	0.000	0.000
45	A	66	LEU	0	0.015	-0.006	7.117	1.530	1.530	0.000	0.000	0.000	0.000
46	A	67	LYS	1	0.933	0.986	10.003	-17.022	-17.022	0.000	0.000	0.000	0.000
47	A	68	ALA	0	-0.038	-0.015	12.188	-0.507	-0.507	0.000	0.000	0.000	0.000
48	A	69	ARG	1	0.871	0.929	2.920	-57.356	-56.209	0.088	-0.465	-0.770	0.003
49	A	70	LYS	1	0.908	0.951	9.009	-18.593	-18.593	0.000	0.000	0.000	0.000
50	A	71	ILE	0	0.005	0.029	4.321	-0.808	-0.690	0.001	-0.051	-0.068	0.000
51	A	72	ILE	0	-0.027	-0.001	8.514	-1.838	-1.838	0.000	0.000	0.000	0.000
52	A	73	ARG	1	0.969	0.977	11.898	-16.827	-16.827	0.000	0.000	0.000	0.000
53	A	74	ARG	1	0.869	0.915	14.508	-13.869	-13.869	0.000	0.000	0.000	0.000
54	A	75	LEU	0	0.014	0.022	16.834	0.443	0.443	0.000	0.000	0.000	0.000
55	A	76	GLY	0	0.011	-0.006	18.642	-0.463	-0.463	0.000	0.000	0.000	0.000
56	A	77	ALA	0	0.028	0.032	21.952	0.186	0.186	0.000	0.000	0.000	0.000
57	A	78	ASN	0	0.000	-0.013	20.412	0.180	0.180	0.000	0.000	0.000	0.000
58	A	79	PHE	0	0.055	0.028	24.335	-0.106	-0.106	0.000	0.000	0.000	0.000
59	A	80	GLN	0	0.006	0.011	27.469	-0.103	-0.103	0.000	0.000	0.000	0.000
60	A	81	SER	0	0.073	0.007	29.695	-0.174	-0.174	0.000	0.000	0.000	0.000
61	A	82	ALA	0	0.061	0.039	32.216	-0.191	-0.191	0.000	0.000	0.000	0.000
62	A	83	LYS	1	0.889	0.937	33.006	-8.768	-8.768	0.000	0.000	0.000	0.000
63	A	84	LEU	0	-0.036	-0.006	31.780	-0.065	-0.065	0.000	0.000	0.000	0.000
64	A	85	GLY	0	0.011	0.018	35.725	-0.123	-0.123	0.000	0.000	0.000	0.000
65	A	86	PHE	0	-0.011	0.012	35.072	-0.088	-0.088	0.000	0.000	0.000	0.000
66	A	87	VAL	0	-0.044	-0.024	36.708	0.090	0.090	0.000	0.000	0.000	0.000
67	A	88	SER	0	0.009	-0.007	33.115	0.045	0.045	0.000	0.000	0.000	0.000
68	A	89	THR	0	-0.032	-0.018	36.144	-0.153	-0.153	0.000	0.000	0.000	0.000
69	A	90	LEU	0	0.018	0.029	34.125	0.245	0.245	0.000	0.000	0.000	0.000
70	A	91	CYS	0	-0.015	-0.004	37.043	-0.264	-0.264	0.000	0.000	0.000	0.000
71	A	92	ALA	0	0.021	0.019	38.594	0.185	0.185	0.000	0.000	0.000	0.000
72	A	93	ALA	0	0.035	0.015	41.052	-0.197	-0.197	0.000	0.000	0.000	0.000
73	A	94	LYS	1	0.924	0.977	42.756	-6.093	-6.093	0.000	0.000	0.000	0.000
74	A	95	VAL	0	-0.003	-0.007	42.758	-0.146	-0.146	0.000	0.000	0.000	0.000
75	A	96	PRO	0	0.027	0.028	44.829	0.073	0.073	0.000	0.000	0.000	0.000
76	A	97	GLN	0	0.023	-0.015	42.780	0.113	0.113	0.000	0.000	0.000	0.000
77	A	98	ASP	-1	-0.932	-0.957	46.275	6.115	6.115	0.000	0.000	0.000	0.000
78	A	99	LYS	1	0.952	0.969	47.478	-5.987	-5.987	0.000	0.000	0.000	0.000
79	A	100	MET	0	-0.027	0.001	41.072	0.123	0.123	0.000	0.000	0.000	0.000
80	A	101	ASP	-1	-0.891	-0.953	41.707	7.406	7.406	0.000	0.000	0.000	0.000
81	A	102	ALA	0	-0.001	0.007	42.517	0.087	0.087	0.000	0.000	0.000	0.000
82	A	103	PHE	0	0.013	-0.009	41.118	0.077	0.077	0.000	0.000	0.000	0.000
83	A	104	VAL	0	0.007	-0.006	37.218	0.121	0.121	0.000	0.000	0.000	0.000
84	A	105	ALA	0	-0.007	0.006	38.818	0.197	0.197	0.000	0.000	0.000	0.000
85	A	106	GLU	-1	-0.899	-0.949	40.592	6.895	6.895	0.000	0.000	0.000	0.000
86	A	107	VAL	0	-0.038	-0.010	37.210	0.049	0.049	0.000	0.000	0.000	0.000
87	A	108	ASN	0	0.023	-0.009	34.815	0.160	0.160	0.000	0.000	0.000	0.000
88	A	109	ALA	0	-0.023	0.017	36.344	0.168	0.168	0.000	0.000	0.000	0.000
89	A	110	LYS	1	0.844	0.922	38.337	-7.301	-7.301	0.000	0.000	0.000	0.000
90	A	111	PRO	0	0.034	0.005	34.999	0.185	0.185	0.000	0.000	0.000	0.000
91	A	112	GLY	0	0.012	0.011	33.963	0.219	0.219	0.000	0.000	0.000	0.000
92	A	113	VAL	0	-0.035	-0.007	34.210	0.070	0.070	0.000	0.000	0.000	0.000
93	A	114	THR	0	-0.026	-0.007	29.058	0.053	0.053	0.000	0.000	0.000	0.000
94	A	115	HIS	0	-0.035	-0.020	25.591	0.088	0.088	0.000	0.000	0.000	0.000
95	A	116	ASN	0	0.058	0.011	30.692	-0.350	-0.350	0.000	0.000	0.000	0.000
96	A	117	TYR	0	-0.049	-0.024	26.252	0.361	0.361	0.000	0.000	0.000	0.000
97	A	118	LEU	0	0.053	0.042	33.140	-0.217	-0.217	0.000	0.000	0.000	0.000
98	A	119	ARG	1	0.838	0.904	29.942	-8.911	-8.911	0.000	0.000	0.000	0.000
99	A	120	GLU	-1	-0.932	-0.969	35.887	7.880	7.880	0.000	0.000	0.000	0.000
100	A	121	HIS	0	0.005	0.006	37.839	-0.029	-0.029	0.000	0.000	0.000	0.000
101	A	122	ASP	-1	-0.873	-0.930	41.003	6.628	6.628	0.000	0.000	0.000	0.000
102	A	123	TYR	0	-0.040	-0.033	41.658	-0.128	-0.128	0.000	0.000	0.000	0.000
103	A	124	ASN	0	0.073	0.045	39.423	0.152	0.152	0.000	0.000	0.000	0.000
104	A	125	ILE	0	-0.005	0.021	37.964	0.243	0.243	0.000	0.000	0.000	0.000
105	A	126	TRP	0	-0.025	-0.040	35.355	-0.083	-0.083	0.000	0.000	0.000	0.000
106	A	127	PHE	0	0.023	-0.002	34.534	0.250	0.250	0.000	0.000	0.000	0.000
107	A	128	THR	0	-0.048	-0.011	31.629	-0.088	-0.088	0.000	0.000	0.000	0.000
108	A	129	LEU	0	0.010	0.008	34.318	0.030	0.030	0.000	0.000	0.000	0.000
109	A	130	ILE	0	-0.070	-0.040	31.290	-0.071	-0.071	0.000	0.000	0.000	0.000
110	A	131	SER	0	0.003	-0.027	35.869	-0.054	-0.054	0.000	0.000	0.000	0.000
111	A	132	PRO	0	0.039	0.011	38.709	0.099	0.099	0.000	0.000	0.000	0.000
112	A	133	SER	0	0.018	0.009	40.394	-0.078	-0.078	0.000	0.000	0.000	0.000
113	A	134	ARG	1	0.878	0.914	39.077	-7.270	-7.270	0.000	0.000	0.000	0.000
114	A	135	GLU	-1	-0.870	-0.937	44.193	6.407	6.407	0.000	0.000	0.000	0.000
115	A	136	GLU	-1	-0.847	-0.909	43.574	6.833	6.833	0.000	0.000	0.000	0.000
116	A	137	THR	0	-0.009	0.002	40.088	0.039	0.039	0.000	0.000	0.000	0.000
117	A	138	GLN	0	-0.034	-0.004	42.911	0.117	0.117	0.000	0.000	0.000	0.000
118	A	139	ALA	0	0.057	0.032	46.189	-0.053	-0.053	0.000	0.000	0.000	0.000
119	A	140	ILE	0	-0.029	-0.017	40.866	-0.007	-0.007	0.000	0.000	0.000	0.000
120	A	141	LEU	0	-0.042	-0.036	41.492	0.016	0.016	0.000	0.000	0.000	0.000
121	A	142	ASP	-1	-0.826	-0.906	45.090	6.118	6.118	0.000	0.000	0.000	0.000
122	A	143	GLY	0	0.002	0.002	47.837	-0.108	-0.108	0.000	0.000	0.000	0.000
123	A	144	ILE	0	-0.019	-0.013	41.815	-0.020	-0.020	0.000	0.000	0.000	0.000
124	A	145	THR	0	-0.021	-0.009	46.334	-0.038	-0.038	0.000	0.000	0.000	0.000
125	A	146	GLN	0	-0.061	-0.020	48.985	-0.081	-0.081	0.000	0.000	0.000	0.000
126	A	147	ALA	0	-0.008	0.008	48.093	-0.097	-0.097	0.000	0.000	0.000	0.000
127	A	148	THR	0	-0.023	-0.027	45.804	-0.008	-0.008	0.000	0.000	0.000	0.000
128	A	149	GLY	0	-0.004	-0.002	49.241	-0.042	-0.042	0.000	0.000	0.000	0.000
129	A	150	VAL	0	-0.060	-0.026	46.176	-0.076	-0.076	0.000	0.000	0.000	0.000
130	A	151	PRO	0	0.013	0.008	48.159	0.060	0.060	0.000	0.000	0.000	0.000
131	A	152	ILE	0	-0.021	-0.009	42.840	0.133	0.133	0.000	0.000	0.000	0.000
132	A	153	LEU	0	-0.050	-0.016	43.482	-0.110	-0.110	0.000	0.000	0.000	0.000
133	A	154	ASN	0	0.034	0.003	42.441	0.365	0.365	0.000	0.000	0.000	0.000
134	A	155	LEU	0	-0.033	-0.028	40.044	-0.142	-0.142	0.000	0.000	0.000	0.000
135	A	156	PRO	0	0.013	0.017	39.120	0.210	0.210	0.000	0.000	0.000	0.000
136	A	157	ALA	0	0.002	0.006	36.436	-0.082	-0.082	0.000	0.000	0.000	0.000
137	A	158	THR	0	-0.020	-0.023	38.380	0.012	0.012	0.000	0.000	0.000	0.000
138	A	159	LYS	1	0.934	0.965	38.365	-6.999	-6.999	0.000	0.000	0.000	0.000
139	A	160	LEU	0	0.025	0.023	30.509	0.069	0.069	0.000	0.000	0.000	0.000
140	A	161	PHE	0	0.016	-0.001	33.281	-0.072	-0.072	0.000	0.000	0.000	0.000
141	A	162	LYS	1	0.970	0.974	25.672	-10.464	-10.464	0.000	0.000	0.000	0.000
142	A	163	ILE	0	0.021	0.013	26.190	-0.139	-0.139	0.000	0.000	0.000	0.000
143	A	164	ARG	1	0.809	0.903	19.651	-13.392	-13.392	0.000	0.000	0.000	0.000
144	A	165	VAL	0	-0.001	-0.011	21.271	-0.195	-0.195	0.000	0.000	0.000	0.000
145	A	166	ASP	-1	-0.809	-0.873	15.531	14.046	14.046	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:22:ASP)