FMO DATABASE

FMODB ID: 397GL

Calculation Name: 3ZRI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZRI

Chain ID: A

ChEMBL ID:

UniProt ID:

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	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	166
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1689042.872872
FMO2-HF: Nuclear repulsion	1624243.214229
FMO2-HF: Total energy	-64799.658643
FMO2-MP2: Total energy	-64992.69562

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:-7:HIS)

Summations of interaction energy for fragment #1(A:-7:HIS)

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.
-21.706	-17.5	12.015	-6.228	-9.991	0.025

Interaction energy analysis for fragmet #1(A:-7:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.077 / q_NPA : 0.040

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	-5	HIS	0	-0.091	-0.061	2.009	-13.915	-13.186	10.270	-4.907	-6.091	0.038
4	A	-4	HIS	0	-0.031	-0.016	2.279	-2.322	-0.919	1.583	-0.264	-2.722	-0.001
5	A	-3	HIS	0	0.012	0.023	2.984	-6.451	-4.513	0.163	-1.054	-1.046	-0.012
6	A	-2	HIS	0	-0.002	-0.018	5.173	0.030	0.166	-0.001	-0.003	-0.132	0.000
7	A	-1	THR	0	-0.048	-0.030	6.324	0.133	0.133	0.000	0.000	0.000	0.000
8	A	0	ASP	-1	-0.859	-0.905	9.294	0.435	0.435	0.000	0.000	0.000	0.000
9	A	1	PRO	0	-0.015	-0.020	12.598	0.029	0.029	0.000	0.000	0.000	0.000
10	A	2	ILE	0	0.012	0.008	14.554	-0.027	-0.027	0.000	0.000	0.000	0.000
11	A	3	ARG	1	0.954	0.978	16.289	-0.310	-0.310	0.000	0.000	0.000	0.000
12	A	4	ILE	0	-0.033	-0.012	20.015	0.009	0.009	0.000	0.000	0.000	0.000
13	A	5	GLU	-1	-0.886	-0.944	22.280	0.199	0.199	0.000	0.000	0.000	0.000
14	A	6	LEU	0	0.043	0.024	24.711	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	7	PRO	0	0.012	-0.008	27.464	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	8	THR	0	-0.004	-0.001	26.066	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	9	LEU	0	-0.005	0.000	26.258	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	10	ILE	0	0.001	-0.006	29.861	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	11	ALA	0	-0.055	-0.029	31.870	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	12	LYS	1	0.868	0.946	30.627	-0.114	-0.114	0.000	0.000	0.000	0.000
21	A	13	LEU	0	-0.048	0.006	33.582	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	14	ASN	0	0.047	0.027	36.411	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	15	ALA	0	0.004	0.009	39.785	0.000	0.000	0.000	0.000	0.000	0.000
24	A	16	GLN	0	0.009	0.001	42.363	0.002	0.002	0.000	0.000	0.000	0.000
25	A	17	SER	0	-0.012	-0.019	39.268	0.001	0.001	0.000	0.000	0.000	0.000
26	A	18	LYS	1	0.836	0.906	38.128	-0.077	-0.077	0.000	0.000	0.000	0.000
27	A	19	LEU	0	0.004	0.011	40.179	0.000	0.000	0.000	0.000	0.000	0.000
28	A	20	ALA	0	0.048	0.021	42.586	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	21	LEU	0	0.021	0.004	35.991	0.000	0.000	0.000	0.000	0.000	0.000
30	A	22	GLU	-1	-0.830	-0.895	39.986	0.076	0.076	0.000	0.000	0.000	0.000
31	A	23	GLN	0	-0.021	-0.012	41.646	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	24	ALA	0	0.030	0.016	40.310	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	25	ALA	0	0.012	-0.002	39.396	0.000	0.000	0.000	0.000	0.000	0.000
34	A	26	SER	0	-0.059	-0.036	40.975	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	27	LEU	0	-0.020	-0.003	43.746	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	28	CYS	0	-0.025	0.007	39.990	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	29	ILE	0	0.023	0.018	42.198	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	30	GLU	-1	-0.908	-0.919	44.697	0.052	0.052	0.000	0.000	0.000	0.000
39	A	31	ARG	1	0.770	0.867	44.811	-0.059	-0.059	0.000	0.000	0.000	0.000
40	A	32	GLN	0	-0.080	-0.035	44.850	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	33	HIS	0	0.035	0.012	40.342	0.003	0.003	0.000	0.000	0.000	0.000
42	A	34	PRO	0	0.043	0.008	36.598	0.000	0.000	0.000	0.000	0.000	0.000
43	A	35	GLU	-1	-0.930	-0.981	32.244	0.110	0.110	0.000	0.000	0.000	0.000
44	A	36	VAL	0	0.001	-0.001	35.869	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	37	THR	0	0.024	0.002	34.885	0.006	0.006	0.000	0.000	0.000	0.000
46	A	38	LEU	0	0.033	0.005	35.194	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	39	GLU	-1	-0.744	-0.862	36.898	0.085	0.085	0.000	0.000	0.000	0.000
48	A	40	HIS	0	0.043	0.036	39.500	0.000	0.000	0.000	0.000	0.000	0.000
49	A	41	TYR	0	-0.039	-0.032	37.805	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	42	LEU	0	-0.003	-0.016	39.743	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	43	ASP	-1	-0.776	-0.862	42.516	0.057	0.057	0.000	0.000	0.000	0.000
52	A	44	VAL	0	0.022	0.027	44.220	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	45	LEU	0	-0.024	-0.013	40.966	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	46	LEU	0	-0.010	0.010	45.490	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	47	ASP	-1	-0.839	-0.901	48.269	0.052	0.052	0.000	0.000	0.000	0.000
56	A	48	ASN	0	0.001	0.003	47.362	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	49	PRO	0	-0.053	-0.050	49.567	0.002	0.002	0.000	0.000	0.000	0.000
58	A	50	LEU	0	-0.026	0.003	50.194	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	51	SER	0	0.037	0.017	45.044	0.001	0.001	0.000	0.000	0.000	0.000
60	A	52	ASP	-1	-0.701	-0.816	41.756	0.072	0.072	0.000	0.000	0.000	0.000
61	A	53	VAL	0	0.006	0.005	41.762	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	54	ARG	1	0.902	0.956	44.240	-0.054	-0.054	0.000	0.000	0.000	0.000
63	A	55	LEU	0	-0.014	0.008	47.001	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	56	VAL	0	-0.001	-0.004	42.605	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	57	LEU	0	-0.009	-0.005	45.350	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	58	LYS	1	0.948	0.981	47.866	-0.048	-0.048	0.000	0.000	0.000	0.000
67	A	59	GLN	0	-0.048	-0.030	46.177	0.000	0.000	0.000	0.000	0.000	0.000
68	A	60	ALA	0	-0.034	-0.022	46.752	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	61	GLY	0	-0.021	0.007	48.863	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	62	LEU	0	-0.051	-0.020	46.676	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	63	GLU	-1	-0.867	-0.948	50.659	0.047	0.047	0.000	0.000	0.000	0.000
72	A	64	VAL	0	-0.010	-0.007	50.980	0.002	0.002	0.000	0.000	0.000	0.000
73	A	65	ASP	-1	-0.844	-0.926	51.033	0.047	0.047	0.000	0.000	0.000	0.000
74	A	66	GLN	0	-0.051	-0.013	50.495	0.001	0.001	0.000	0.000	0.000	0.000
75	A	67	VAL	0	0.033	0.004	45.699	0.001	0.001	0.000	0.000	0.000	0.000
76	A	68	LYS	1	0.787	0.884	47.399	-0.055	-0.055	0.000	0.000	0.000	0.000
77	A	69	GLN	0	-0.051	-0.037	48.892	0.000	0.000	0.000	0.000	0.000	0.000
78	A	70	ALA	0	-0.042	-0.008	46.193	0.000	0.000	0.000	0.000	0.000	0.000
79	A	71	ILE	0	0.055	0.037	43.368	0.001	0.001	0.000	0.000	0.000	0.000
80	A	72	ALA	0	0.014	0.020	45.000	0.001	0.001	0.000	0.000	0.000	0.000
81	A	73	SER	0	-0.135	-0.081	46.707	0.000	0.000	0.000	0.000	0.000	0.000
82	A	74	THR	0	-0.084	-0.061	41.597	0.001	0.001	0.000	0.000	0.000	0.000
83	A	75	TYR	0	-0.023	-0.035	41.837	0.004	0.004	0.000	0.000	0.000	0.000
84	A	76	SER	0	-0.035	-0.012	41.059	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	77	ARG	1	0.935	0.967	43.107	-0.055	-0.055	0.000	0.000	0.000	0.000
86	A	78	GLU	-1	-0.857	-0.922	44.351	0.055	0.055	0.000	0.000	0.000	0.000
87	A	79	GLN	0	-0.101	-0.062	39.270	0.001	0.001	0.000	0.000	0.000	0.000
88	A	80	VAL	0	0.014	0.000	43.023	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	81	LEU	0	-0.008	0.008	40.747	0.003	0.003	0.000	0.000	0.000	0.000
90	A	82	ASP	-1	-0.940	-0.965	38.689	0.064	0.064	0.000	0.000	0.000	0.000
91	A	83	THR	0	-0.065	-0.039	35.535	0.000	0.000	0.000	0.000	0.000	0.000
92	A	84	TYR	0	-0.005	0.001	38.189	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	85	PRO	0	0.012	0.005	37.179	0.005	0.005	0.000	0.000	0.000	0.000
94	A	86	ALA	0	0.003	0.019	32.787	0.000	0.000	0.000	0.000	0.000	0.000
95	A	87	PHE	0	-0.003	-0.019	31.939	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	88	SER	0	0.037	0.026	31.434	0.006	0.006	0.000	0.000	0.000	0.000
97	A	89	PRO	0	-0.010	-0.022	26.066	0.005	0.005	0.000	0.000	0.000	0.000
98	A	90	LEU	0	0.007	0.013	27.270	0.008	0.008	0.000	0.000	0.000	0.000
99	A	91	LEU	0	0.041	0.020	29.000	0.003	0.003	0.000	0.000	0.000	0.000
100	A	92	VAL	0	-0.021	-0.015	25.881	0.001	0.001	0.000	0.000	0.000	0.000
101	A	93	GLU	-1	-0.869	-0.905	23.897	0.180	0.180	0.000	0.000	0.000	0.000
102	A	94	LEU	0	0.008	0.019	26.240	0.004	0.004	0.000	0.000	0.000	0.000
103	A	95	LEU	0	-0.009	-0.010	29.523	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	96	GLN	0	-0.003	0.005	20.832	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	97	GLU	-1	-0.809	-0.878	25.394	0.182	0.182	0.000	0.000	0.000	0.000
106	A	98	ALA	0	0.048	0.029	27.351	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	99	TRP	0	-0.001	0.019	27.407	-0.010	-0.010	0.000	0.000	0.000	0.000
108	A	100	LEU	0	0.002	0.014	24.024	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	101	LEU	0	0.019	0.022	27.837	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	102	SER	0	-0.034	-0.048	30.891	-0.009	-0.009	0.000	0.000	0.000	0.000
111	A	103	SER	0	-0.070	-0.042	29.055	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	104	THR	0	-0.035	-0.039	27.677	0.000	0.000	0.000	0.000	0.000	0.000
113	A	105	GLU	-1	-0.833	-0.902	31.099	0.112	0.112	0.000	0.000	0.000	0.000
114	A	106	LEU	0	-0.037	-0.004	33.610	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	107	GLU	-1	-0.954	-0.960	35.098	0.073	0.073	0.000	0.000	0.000	0.000
116	A	108	GLN	0	-0.039	-0.023	35.537	-0.008	-0.008	0.000	0.000	0.000	0.000
117	A	109	ALA	0	-0.001	-0.009	34.947	0.006	0.006	0.000	0.000	0.000	0.000
118	A	110	GLU	-1	-0.874	-0.940	35.133	0.080	0.080	0.000	0.000	0.000	0.000
119	A	111	LEU	0	-0.016	-0.009	31.882	0.001	0.001	0.000	0.000	0.000	0.000
120	A	112	ARG	1	0.803	0.871	35.243	-0.078	-0.078	0.000	0.000	0.000	0.000
121	A	113	SER	0	-0.004	-0.046	37.248	0.005	0.005	0.000	0.000	0.000	0.000
122	A	114	GLY	0	0.026	0.005	38.911	0.002	0.002	0.000	0.000	0.000	0.000
123	A	115	ALA	0	-0.005	-0.003	34.683	0.001	0.001	0.000	0.000	0.000	0.000
124	A	116	ILE	0	0.003	-0.008	33.861	0.006	0.006	0.000	0.000	0.000	0.000
125	A	117	PHE	0	0.026	0.012	35.050	0.003	0.003	0.000	0.000	0.000	0.000
126	A	118	LEU	0	0.023	0.013	35.471	0.001	0.001	0.000	0.000	0.000	0.000
127	A	119	ALA	0	0.005	0.017	31.230	0.002	0.002	0.000	0.000	0.000	0.000
128	A	120	ALA	0	0.021	0.000	32.653	0.004	0.004	0.000	0.000	0.000	0.000
129	A	121	LEU	0	-0.039	-0.013	34.213	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	122	THR	0	-0.055	-0.050	31.823	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	123	ARG	1	0.786	0.888	25.151	-0.164	-0.164	0.000	0.000	0.000	0.000
132	A	124	ALA	0	0.043	0.023	31.650	0.001	0.001	0.000	0.000	0.000	0.000
133	A	125	ASP	-1	-0.890	-0.945	28.817	0.139	0.139	0.000	0.000	0.000	0.000
134	A	126	ARG	1	0.763	0.868	25.345	-0.156	-0.156	0.000	0.000	0.000	0.000
135	A	127	TYR	0	-0.039	-0.066	27.009	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	128	LEU	0	-0.006	0.011	32.721	-0.005	-0.005	0.000	0.000	0.000	0.000
137	A	129	SER	0	0.005	-0.020	36.283	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	130	PHE	0	0.015	-0.009	38.304	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	131	LYS	1	0.944	0.974	39.754	-0.060	-0.060	0.000	0.000	0.000	0.000
140	A	132	LEU	0	0.009	-0.003	40.483	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	133	ILE	0	-0.021	0.003	36.197	0.000	0.000	0.000	0.000	0.000	0.000
142	A	134	SER	0	-0.005	-0.026	40.044	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	135	LEU	0	-0.112	-0.036	43.403	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	136	PHE	0	0.048	0.003	40.533	-0.002	-0.002	0.000	0.000	0.000	0.000
145	A	137	GLU	-1	-0.870	-0.909	42.009	0.072	0.072	0.000	0.000	0.000	0.000
146	A	138	GLY	0	-0.031	-0.007	43.060	0.001	0.001	0.000	0.000	0.000	0.000
147	A	139	ILE	0	-0.009	0.008	42.225	-0.002	-0.002	0.000	0.000	0.000	0.000
148	A	140	ASN	0	-0.031	-0.016	41.525	0.004	0.004	0.000	0.000	0.000	0.000
149	A	141	ARG	1	0.864	0.914	36.536	-0.090	-0.090	0.000	0.000	0.000	0.000
150	A	142	GLU	-1	-0.855	-0.928	37.491	0.090	0.090	0.000	0.000	0.000	0.000
151	A	143	ASN	0	-0.040	-0.030	39.499	-0.002	-0.002	0.000	0.000	0.000	0.000
152	A	144	LEU	0	0.019	0.010	40.047	-0.001	-0.001	0.000	0.000	0.000	0.000
153	A	145	LYS	1	0.849	0.901	33.005	-0.113	-0.113	0.000	0.000	0.000	0.000
154	A	146	LYS	1	0.893	0.951	38.718	-0.068	-0.068	0.000	0.000	0.000	0.000
155	A	147	HIS	0	-0.002	-0.008	40.861	-0.002	-0.002	0.000	0.000	0.000	0.000
156	A	148	PHE	0	0.034	0.029	39.109	-0.003	-0.003	0.000	0.000	0.000	0.000
157	A	149	ALA	0	0.044	0.003	42.006	-0.002	-0.002	0.000	0.000	0.000	0.000
158	A	150	MET	0	-0.067	-0.028	43.806	-0.004	-0.004	0.000	0.000	0.000	0.000
159	A	151	ILE	0	-0.070	-0.024	43.891	-0.003	-0.003	0.000	0.000	0.000	0.000
160	A	152	LEU	0	-0.018	0.005	42.103	-0.001	-0.001	0.000	0.000	0.000	0.000
161	A	153	SER	0	0.000	-0.006	46.378	0.001	0.001	0.000	0.000	0.000	0.000
162	A	154	ASP	-1	-0.925	-0.947	49.063	0.047	0.047	0.000	0.000	0.000	0.000
163	A	155	SER	0	-0.045	-0.038	45.208	-0.001	-0.001	0.000	0.000	0.000	0.000
164	A	156	ALA	0	-0.016	-0.021	48.088	-0.001	-0.001	0.000	0.000	0.000	0.000
165	A	157	GLU	-1	-0.794	-0.866	41.656	0.076	0.076	0.000	0.000	0.000	0.000
166	A	158	THR	0	-0.048	-0.017	43.307	0.003	0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:-7:HIS)