FMO DATABASE

FMODB ID: 3978L

Calculation Name: 4EMZ-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EMZ

Chain ID: C

ChEMBL ID:

UniProt ID: P35585

Base Structure: X-ray

Registration Date: 2023-06-22

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	142
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1361145.391976
FMO2-HF: Nuclear repulsion	1302598.532015
FMO2-HF: Total energy	-58546.859961
FMO2-MP2: Total energy	-58719.576784

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(C:7:LYS)

Summations of interaction energy for fragment #1(C:7:LYS)

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.
30.059	34.75	2.951	-3.116	-4.526	-0.009

Interaction energy analysis for fragmet #1(C:7:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.020 / q_NPA : 0.991

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	C	9	SER	0	0.044	0.038	2.773	-2.938	-0.031	0.087	-1.385	-1.609	-0.004
4	C	10	VAL	0	0.010	0.007	2.210	1.944	2.647	2.848	-1.451	-2.099	-0.004
5	C	11	ILE	0	-0.066	-0.052	3.823	0.842	1.327	0.003	-0.092	-0.396	0.000
6	C	12	GLY	0	0.063	0.038	6.602	3.534	3.534	0.000	0.000	0.000	0.000
7	C	13	TRP	0	0.021	0.006	8.490	2.093	2.093	0.000	0.000	0.000	0.000
8	C	14	PRO	0	-0.014	-0.009	9.850	1.931	1.931	0.000	0.000	0.000	0.000
9	C	15	ALA	0	0.074	0.043	12.898	1.480	1.480	0.000	0.000	0.000	0.000
10	C	16	VAL	0	-0.013	-0.011	11.630	1.437	1.437	0.000	0.000	0.000	0.000
11	C	17	ARG	1	0.865	0.936	12.492	24.273	24.273	0.000	0.000	0.000	0.000
12	C	18	GLU	-1	-0.981	-0.993	15.503	-14.150	-14.150	0.000	0.000	0.000	0.000
13	C	19	ARG	1	0.960	0.979	16.657	16.786	16.786	0.000	0.000	0.000	0.000
14	C	20	MET	0	-0.052	0.003	15.318	0.649	0.649	0.000	0.000	0.000	0.000
15	C	21	ARG	1	0.896	0.929	18.563	16.049	16.049	0.000	0.000	0.000	0.000
16	C	22	ARG	1	0.958	0.974	21.513	12.182	12.182	0.000	0.000	0.000	0.000
17	C	23	ALA	0	0.060	0.048	23.524	0.122	0.122	0.000	0.000	0.000	0.000
18	C	55	CYS	0	-0.032	-0.030	48.407	0.010	0.010	0.000	0.000	0.000	0.000
19	C	56	ALA	0	0.007	-0.002	44.163	-0.027	-0.027	0.000	0.000	0.000	0.000
20	C	57	TRP	0	-0.008	-0.003	37.962	-0.028	-0.028	0.000	0.000	0.000	0.000
21	C	58	LEU	0	-0.011	-0.004	39.478	0.018	0.018	0.000	0.000	0.000	0.000
22	C	59	GLU	-1	-0.958	-0.968	32.950	-9.302	-9.302	0.000	0.000	0.000	0.000
23	C	60	ALA	0	-0.037	-0.022	33.330	0.213	0.213	0.000	0.000	0.000	0.000
24	C	61	GLN	0	-0.017	-0.009	33.075	-0.325	-0.325	0.000	0.000	0.000	0.000
25	C	62	GLU	-1	-0.950	-0.974	27.767	-10.402	-10.402	0.000	0.000	0.000	0.000
26	C	63	GLU	-1	-0.990	-0.991	31.672	-8.019	-8.019	0.000	0.000	0.000	0.000
27	C	64	GLU	-1	-1.000	-0.987	29.937	-9.059	-9.059	0.000	0.000	0.000	0.000
28	C	65	GLU	-1	-0.934	-0.969	27.128	-9.698	-9.698	0.000	0.000	0.000	0.000
29	C	66	VAL	0	-0.025	-0.023	28.676	-0.222	-0.222	0.000	0.000	0.000	0.000
30	C	67	GLY	0	-0.005	-0.002	28.346	-0.063	-0.063	0.000	0.000	0.000	0.000
31	C	68	PHE	0	-0.013	-0.017	24.334	-0.244	-0.244	0.000	0.000	0.000	0.000
32	C	69	PRO	0	-0.006	0.003	21.696	-0.022	-0.022	0.000	0.000	0.000	0.000
33	C	70	VAL	0	0.023	0.011	19.615	-0.460	-0.460	0.000	0.000	0.000	0.000
34	C	71	THR	0	-0.045	-0.013	14.982	0.442	0.442	0.000	0.000	0.000	0.000
35	C	72	PRO	0	0.071	0.018	18.245	-0.275	-0.275	0.000	0.000	0.000	0.000
36	C	73	GLN	0	-0.023	-0.022	17.727	-0.037	-0.037	0.000	0.000	0.000	0.000
37	C	74	VAL	0	-0.037	0.001	12.861	-0.341	-0.341	0.000	0.000	0.000	0.000
38	C	75	PRO	0	0.009	0.015	13.832	0.398	0.398	0.000	0.000	0.000	0.000
39	C	76	LEU	0	0.014	0.019	14.767	-1.109	-1.109	0.000	0.000	0.000	0.000
40	C	77	ARG	1	0.794	0.893	10.955	22.098	22.098	0.000	0.000	0.000	0.000
41	C	78	PRO	0	0.087	0.033	16.869	-0.569	-0.569	0.000	0.000	0.000	0.000
42	C	79	MET	0	-0.008	0.021	11.954	-1.231	-1.231	0.000	0.000	0.000	0.000
43	C	80	THR	0	-0.005	-0.009	13.314	0.523	0.523	0.000	0.000	0.000	0.000
44	C	81	TYR	0	0.017	0.001	13.764	-1.758	-1.758	0.000	0.000	0.000	0.000
45	C	82	LYS	1	0.853	0.893	8.166	32.725	32.725	0.000	0.000	0.000	0.000
46	C	83	ALA	0	0.021	0.021	9.255	-2.608	-2.608	0.000	0.000	0.000	0.000
47	C	84	ALA	0	0.049	0.028	9.393	-2.723	-2.723	0.000	0.000	0.000	0.000
48	C	85	VAL	0	0.065	0.053	10.084	-0.605	-0.605	0.000	0.000	0.000	0.000
49	C	86	ASP	-1	-0.848	-0.890	5.594	-40.043	-40.043	0.000	0.000	0.000	0.000
50	C	87	LEU	0	-0.015	-0.011	6.448	-5.102	-5.102	0.000	0.000	0.000	0.000
51	C	88	SER	0	-0.014	-0.035	8.028	0.246	0.246	0.000	0.000	0.000	0.000
52	C	89	HIS	0	-0.060	-0.041	7.256	2.889	2.889	0.000	0.000	0.000	0.000
53	C	90	PHE	0	-0.032	-0.015	3.404	-3.224	-2.628	0.013	-0.188	-0.422	-0.001
54	C	91	LEU	0	0.024	-0.007	5.769	2.495	2.495	0.000	0.000	0.000	0.000
55	C	92	LYS	1	0.809	0.925	9.378	22.719	22.719	0.000	0.000	0.000	0.000
56	C	93	GLU	-1	-0.875	-0.911	5.318	-46.432	-46.432	0.000	0.000	0.000	0.000
57	C	94	LYS	1	0.811	0.896	5.183	49.821	49.821	0.000	0.000	0.000	0.000
58	C	95	GLY	0	0.058	0.045	9.657	2.575	2.575	0.000	0.000	0.000	0.000
59	C	96	GLY	0	-0.013	-0.033	12.853	-0.811	-0.811	0.000	0.000	0.000	0.000
60	C	97	LEU	0	0.013	0.006	13.761	0.961	0.961	0.000	0.000	0.000	0.000
61	C	98	GLU	-1	-0.807	-0.909	15.420	-17.140	-17.140	0.000	0.000	0.000	0.000
62	C	99	GLY	0	-0.019	-0.009	17.468	0.295	0.295	0.000	0.000	0.000	0.000
63	C	100	LEU	0	-0.038	0.005	18.410	0.723	0.723	0.000	0.000	0.000	0.000
64	C	101	ILE	0	0.024	0.002	21.112	0.039	0.039	0.000	0.000	0.000	0.000
65	C	102	HIS	0	-0.052	-0.021	21.966	0.269	0.269	0.000	0.000	0.000	0.000
66	C	103	SER	0	0.017	-0.005	23.806	0.483	0.483	0.000	0.000	0.000	0.000
67	C	104	GLN	0	0.019	-0.009	23.542	-0.257	-0.257	0.000	0.000	0.000	0.000
68	C	105	ARG	1	1.019	1.013	23.526	10.633	10.633	0.000	0.000	0.000	0.000
69	C	106	ARG	1	0.866	0.943	20.799	13.094	13.094	0.000	0.000	0.000	0.000
70	C	107	GLN	0	-0.008	-0.025	19.470	-0.472	-0.472	0.000	0.000	0.000	0.000
71	C	108	ASP	-1	-0.789	-0.887	18.524	-14.275	-14.275	0.000	0.000	0.000	0.000
72	C	109	ILE	0	-0.057	-0.012	17.726	-0.557	-0.557	0.000	0.000	0.000	0.000
73	C	110	LEU	0	-0.021	-0.011	12.824	-1.226	-1.226	0.000	0.000	0.000	0.000
74	C	111	ASP	-1	-0.785	-0.878	13.950	-18.497	-18.497	0.000	0.000	0.000	0.000
75	C	112	LEU	0	0.025	0.011	14.939	-0.683	-0.683	0.000	0.000	0.000	0.000
76	C	113	TRP	0	0.009	0.019	7.250	-1.018	-1.018	0.000	0.000	0.000	0.000
77	C	114	ILE	0	-0.018	-0.009	9.360	-1.300	-1.300	0.000	0.000	0.000	0.000
78	C	115	TYR	0	-0.001	-0.001	11.336	-0.430	-0.430	0.000	0.000	0.000	0.000
79	C	116	HIS	0	0.021	0.006	12.679	-0.183	-0.183	0.000	0.000	0.000	0.000
80	C	117	THR	0	-0.094	-0.058	7.017	-1.180	-1.180	0.000	0.000	0.000	0.000
81	C	118	GLN	0	-0.046	-0.029	6.479	-1.409	-1.409	0.000	0.000	0.000	0.000
82	C	119	GLY	0	0.067	0.050	9.122	0.360	0.360	0.000	0.000	0.000	0.000
83	C	120	TYR	0	-0.065	-0.047	9.896	-0.206	-0.206	0.000	0.000	0.000	0.000
84	C	121	PHE	0	0.048	0.022	14.529	-0.060	-0.060	0.000	0.000	0.000	0.000
85	C	122	PRO	0	0.009	0.004	17.744	-0.574	-0.574	0.000	0.000	0.000	0.000
86	C	123	ASP	-1	-0.889	-0.939	18.697	-14.019	-14.019	0.000	0.000	0.000	0.000
87	C	124	TRP	0	0.017	0.000	14.146	0.140	0.140	0.000	0.000	0.000	0.000
88	C	125	GLN	0	-0.002	0.016	17.352	0.149	0.149	0.000	0.000	0.000	0.000
89	C	126	ASN	0	0.004	0.002	19.704	0.736	0.736	0.000	0.000	0.000	0.000
90	C	127	TYR	0	-0.014	-0.036	19.072	-0.536	-0.536	0.000	0.000	0.000	0.000
91	C	128	THR	0	0.004	0.012	24.861	0.335	0.335	0.000	0.000	0.000	0.000
92	C	129	PRO	0	-0.014	-0.013	28.051	-0.155	-0.155	0.000	0.000	0.000	0.000
93	C	130	GLY	0	-0.044	0.022	31.043	-0.026	-0.026	0.000	0.000	0.000	0.000
94	C	131	PRO	0	0.002	-0.031	32.675	0.154	0.154	0.000	0.000	0.000	0.000
95	C	132	GLY	0	0.033	0.011	31.895	0.104	0.104	0.000	0.000	0.000	0.000
96	C	133	VAL	0	-0.035	-0.019	25.627	-0.190	-0.190	0.000	0.000	0.000	0.000
97	C	134	ARG	1	0.779	0.887	25.488	11.019	11.019	0.000	0.000	0.000	0.000
98	C	135	TYR	0	0.054	0.001	23.766	-0.803	-0.803	0.000	0.000	0.000	0.000
99	C	136	PRO	0	0.037	0.034	19.488	0.397	0.397	0.000	0.000	0.000	0.000
100	C	137	LEU	0	0.021	0.003	21.722	0.380	0.380	0.000	0.000	0.000	0.000
101	C	138	THR	0	-0.041	-0.044	16.986	0.270	0.270	0.000	0.000	0.000	0.000
102	C	139	PHE	0	-0.024	-0.007	18.462	-0.760	-0.760	0.000	0.000	0.000	0.000
103	C	140	GLY	0	0.077	0.012	15.333	-0.458	-0.458	0.000	0.000	0.000	0.000
104	C	141	TRP	0	-0.031	-0.015	11.853	-2.391	-2.391	0.000	0.000	0.000	0.000
105	C	142	CYS	0	-0.051	-0.032	13.870	1.291	1.291	0.000	0.000	0.000	0.000
106	C	143	TYR	0	0.014	0.002	12.046	0.324	0.324	0.000	0.000	0.000	0.000
107	C	144	LYS	1	0.866	0.915	17.550	14.280	14.280	0.000	0.000	0.000	0.000
108	C	145	LEU	0	-0.001	0.000	21.319	-0.226	-0.226	0.000	0.000	0.000	0.000
109	C	146	VAL	0	-0.012	-0.004	23.888	0.541	0.541	0.000	0.000	0.000	0.000
110	C	147	PRO	0	0.027	0.001	26.160	-0.186	-0.186	0.000	0.000	0.000	0.000
111	C	148	VAL	0	-0.008	0.006	27.921	-0.058	-0.058	0.000	0.000	0.000	0.000
112	C	149	GLU	-1	-0.932	-0.973	30.410	-8.789	-8.789	0.000	0.000	0.000	0.000
113	C	150	PRO	0	-0.008	0.000	32.184	0.099	0.099	0.000	0.000	0.000	0.000
114	C	151	ASP	-1	-0.898	-0.947	30.195	-10.421	-10.421	0.000	0.000	0.000	0.000
115	C	152	LYS	1	0.846	0.942	32.532	9.732	9.732	0.000	0.000	0.000	0.000
116	C	178	ARG	1	0.998	0.991	32.972	9.456	9.456	0.000	0.000	0.000	0.000
117	C	179	GLU	-1	-0.820	-0.904	31.680	-9.926	-9.926	0.000	0.000	0.000	0.000
118	C	180	VAL	0	0.010	0.011	28.865	-0.179	-0.179	0.000	0.000	0.000	0.000
119	C	181	LEU	0	-0.009	-0.009	26.083	0.065	0.065	0.000	0.000	0.000	0.000
120	C	182	GLU	-1	-0.782	-0.857	22.849	-13.043	-13.043	0.000	0.000	0.000	0.000
121	C	183	TRP	0	-0.010	0.003	18.115	0.175	0.175	0.000	0.000	0.000	0.000
122	C	184	ARG	1	0.827	0.896	19.164	13.997	13.997	0.000	0.000	0.000	0.000
123	C	185	PHE	0	-0.007	-0.008	12.058	0.123	0.123	0.000	0.000	0.000	0.000
124	C	186	ASP	-1	-0.814	-0.908	16.938	-13.725	-13.725	0.000	0.000	0.000	0.000
125	C	187	SER	0	0.067	0.032	15.361	0.048	0.048	0.000	0.000	0.000	0.000
126	C	188	ARG	1	0.895	0.952	16.839	13.139	13.139	0.000	0.000	0.000	0.000
127	C	189	LEU	0	-0.028	-0.013	18.293	0.594	0.594	0.000	0.000	0.000	0.000
128	C	190	ALA	0	-0.017	-0.006	15.733	0.046	0.046	0.000	0.000	0.000	0.000
129	C	191	PHE	0	-0.017	-0.002	16.470	-0.055	-0.055	0.000	0.000	0.000	0.000
130	C	192	HIS	0	-0.030	-0.017	20.546	0.289	0.289	0.000	0.000	0.000	0.000
131	C	193	HIS	0	-0.010	0.012	22.861	-0.225	-0.225	0.000	0.000	0.000	0.000
132	C	194	VAL	0	0.036	0.002	23.808	0.483	0.483	0.000	0.000	0.000	0.000
133	C	195	ALA	0	0.037	0.014	24.824	0.537	0.537	0.000	0.000	0.000	0.000
134	C	196	ARG	1	0.919	0.960	26.064	11.743	11.743	0.000	0.000	0.000	0.000
135	C	197	GLU	-1	-0.865	-0.926	27.914	-10.658	-10.658	0.000	0.000	0.000	0.000
136	C	198	LEU	0	-0.042	-0.016	28.298	0.355	0.355	0.000	0.000	0.000	0.000
137	C	199	HIS	1	0.838	0.899	30.306	10.167	10.167	0.000	0.000	0.000	0.000
138	C	200	PRO	0	0.024	0.033	31.070	-0.234	-0.234	0.000	0.000	0.000	0.000
139	C	201	GLU	-1	-0.822	-0.901	32.112	-9.495	-9.495	0.000	0.000	0.000	0.000
140	C	202	TYR	0	-0.055	-0.029	28.786	-0.043	-0.043	0.000	0.000	0.000	0.000
141	C	203	PHE	0	-0.067	-0.018	24.485	-0.433	-0.433	0.000	0.000	0.000	0.000
142	C	204	LYS	1	0.981	0.998	27.528	9.868	9.868	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:7:LYS)