FMO DATABASE

FMODB ID: NN3KQ

Calculation Name: 4CZD-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4CZD

Chain ID: B

ChEMBL ID:

UniProt ID: B8J364

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:

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	159
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1329534.792447
FMO2-HF: Nuclear repulsion	1265813.121325
FMO2-HF: Total energy	-63721.671121
FMO2-MP2: Total energy	-63904.350028

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(B:1:MET)

Summations of interaction energy for fragment #1(B:1:MET)

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.
-15.758	-4.36	7.24	-5.096	-13.543	-0.029

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : -0.001

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	B	3	HIS	0	0.011	0.004	3.099	-2.463	-0.413	0.001	-0.864	-1.188	0.001
4	B	4	GLN	0	-0.075	-0.016	3.193	-1.483	0.005	0.247	-0.482	-1.252	-0.001
5	B	5	PHE	0	-0.003	-0.004	2.938	-1.390	0.166	0.977	-0.519	-2.014	0.001
6	B	6	SER	0	0.065	0.052	5.203	-0.426	-0.426	0.000	0.000	0.000	0.000
7	B	7	PRO	0	0.030	-0.012	6.488	-0.211	-0.211	0.000	0.000	0.000	0.000
8	B	8	GLU	-1	-0.865	-0.928	7.838	-0.263	-0.263	0.000	0.000	0.000	0.000
9	B	9	GLU	-1	-0.814	-0.927	7.173	-0.054	-0.054	0.000	0.000	0.000	0.000
10	B	10	GLN	0	-0.066	-0.057	2.764	-2.241	-0.567	0.727	-0.831	-1.570	-0.007
11	B	11	ALA	0	-0.043	-0.009	5.572	-0.263	-0.263	0.000	0.000	0.000	0.000
12	B	12	VAL	0	0.057	0.028	9.094	-0.020	-0.020	0.000	0.000	0.000	0.000
13	B	13	LEU	0	-0.033	-0.026	5.370	-0.001	-0.001	0.000	0.000	0.000	0.000
14	B	14	ARG	1	0.879	0.947	6.226	0.914	0.914	0.000	0.000	0.000	0.000
15	B	15	ILE	0	-0.003	0.011	8.206	0.076	0.076	0.000	0.000	0.000	0.000
16	B	16	VAL	0	0.009	-0.008	9.437	0.041	0.041	0.000	0.000	0.000	0.000
17	B	17	GLN	0	-0.065	-0.022	6.370	-0.372	-0.372	0.000	0.000	0.000	0.000
18	B	18	ALA	0	-0.076	-0.021	9.539	0.063	0.063	0.000	0.000	0.000	0.000
19	B	19	ASN	0	-0.050	-0.048	12.931	0.075	0.075	0.000	0.000	0.000	0.000
20	B	20	LEU	0	-0.010	0.013	15.519	-0.023	-0.023	0.000	0.000	0.000	0.000
21	B	21	PRO	0	0.015	0.004	16.486	0.010	0.010	0.000	0.000	0.000	0.000
22	B	22	ASP	-1	-0.941	-0.971	19.496	-0.182	-0.182	0.000	0.000	0.000	0.000
23	B	23	SER	0	-0.042	-0.050	22.892	0.021	0.021	0.000	0.000	0.000	0.000
24	B	24	LEU	0	-0.005	-0.014	24.309	-0.005	-0.005	0.000	0.000	0.000	0.000
25	B	25	THR	0	-0.019	0.002	24.383	0.010	0.010	0.000	0.000	0.000	0.000
26	B	26	PRO	0	0.023	0.027	19.225	-0.006	-0.006	0.000	0.000	0.000	0.000
27	B	27	TYR	0	0.021	-0.024	16.639	-0.032	-0.032	0.000	0.000	0.000	0.000
28	B	28	ALA	0	0.026	0.023	18.836	-0.003	-0.003	0.000	0.000	0.000	0.000
29	B	29	ASP	-1	-0.766	-0.860	20.246	-0.189	-0.189	0.000	0.000	0.000	0.000
30	B	30	LEU	0	-0.053	-0.034	13.938	-0.022	-0.022	0.000	0.000	0.000	0.000
31	B	31	ALA	0	-0.038	-0.021	15.789	-0.017	-0.017	0.000	0.000	0.000	0.000
32	B	32	GLU	-1	-0.948	-0.970	17.168	-0.144	-0.144	0.000	0.000	0.000	0.000
33	B	33	GLN	0	-0.050	-0.021	16.034	0.009	0.009	0.000	0.000	0.000	0.000
34	B	34	ALA	0	-0.081	-0.037	12.183	-0.016	-0.016	0.000	0.000	0.000	0.000
35	B	35	GLY	0	-0.002	0.018	13.510	0.012	0.012	0.000	0.000	0.000	0.000
36	B	36	MET	0	-0.033	-0.012	11.312	0.018	0.018	0.000	0.000	0.000	0.000
37	B	37	THR	0	0.009	-0.001	16.291	0.001	0.001	0.000	0.000	0.000	0.000
38	B	38	GLU	-1	-0.843	-0.946	17.720	-0.130	-0.130	0.000	0.000	0.000	0.000
39	B	39	ALA	0	0.006	-0.005	18.994	-0.009	-0.009	0.000	0.000	0.000	0.000
40	B	40	GLN	0	0.022	0.012	15.285	-0.008	-0.008	0.000	0.000	0.000	0.000
41	B	41	VAL	0	0.032	0.035	14.327	-0.002	-0.002	0.000	0.000	0.000	0.000
42	B	42	LEU	0	-0.028	-0.012	14.941	-0.011	-0.011	0.000	0.000	0.000	0.000
43	B	43	GLU	-1	-0.853	-0.906	14.752	0.027	0.027	0.000	0.000	0.000	0.000
44	B	44	LEU	0	0.034	0.025	8.751	0.025	0.025	0.000	0.000	0.000	0.000
45	B	45	LEU	0	-0.044	-0.038	11.108	0.009	0.009	0.000	0.000	0.000	0.000
46	B	46	GLY	0	-0.018	-0.015	13.305	0.002	0.002	0.000	0.000	0.000	0.000
47	B	47	ARG	1	0.838	0.904	10.076	-0.120	-0.120	0.000	0.000	0.000	0.000
48	B	48	LEU	0	0.000	-0.003	7.318	0.039	0.039	0.000	0.000	0.000	0.000
49	B	49	LYS	1	0.932	0.975	10.861	0.109	0.109	0.000	0.000	0.000	0.000
50	B	50	ALA	0	-0.056	-0.022	13.505	0.003	0.003	0.000	0.000	0.000	0.000
51	B	51	SER	0	0.002	-0.002	10.570	0.002	0.002	0.000	0.000	0.000	0.000
52	B	52	GLY	0	0.000	0.013	12.332	0.022	0.022	0.000	0.000	0.000	0.000
53	B	53	ALA	0	-0.045	-0.015	6.888	-0.033	-0.033	0.000	0.000	0.000	0.000
54	B	54	ILE	0	-0.034	-0.002	7.737	-0.206	-0.206	0.000	0.000	0.000	0.000
55	B	55	ARG	1	0.975	0.978	10.005	0.432	0.432	0.000	0.000	0.000	0.000
56	B	56	ARG	1	0.894	0.929	12.573	0.284	0.284	0.000	0.000	0.000	0.000
57	B	57	PHE	0	0.055	0.037	12.755	-0.049	-0.049	0.000	0.000	0.000	0.000
58	B	58	GLY	0	0.026	0.003	15.180	0.044	0.044	0.000	0.000	0.000	0.000
59	B	59	ALA	0	0.022	0.025	17.332	-0.030	-0.030	0.000	0.000	0.000	0.000
60	B	60	SER	0	-0.006	0.000	16.809	0.008	0.008	0.000	0.000	0.000	0.000
61	B	61	ILE	0	0.000	-0.002	19.601	0.005	0.005	0.000	0.000	0.000	0.000
62	B	62	LYS	1	0.966	0.967	23.164	0.193	0.193	0.000	0.000	0.000	0.000
63	B	63	HIS	0	0.008	0.017	24.451	0.006	0.006	0.000	0.000	0.000	0.000
64	B	64	GLN	0	0.072	0.013	24.846	-0.001	-0.001	0.000	0.000	0.000	0.000
65	B	65	LYS	1	0.911	0.963	27.596	0.106	0.106	0.000	0.000	0.000	0.000
66	B	66	THR	0	-0.018	0.000	27.238	0.008	0.008	0.000	0.000	0.000	0.000
67	B	67	GLY	0	0.048	0.030	30.237	-0.004	-0.004	0.000	0.000	0.000	0.000
68	B	68	DTR	0	-0.039	-0.003	27.882	-0.011	-0.011	0.000	0.000	0.000	0.000
69	B	69	THR	0	-0.022	-0.032	31.855	0.002	0.002	0.000	0.000	0.000	0.000
70	B	70	HIS	0	0.022	-0.013	31.119	-0.006	-0.006	0.000	0.000	0.000	0.000
71	B	71	ASN	0	-0.025	-0.006	26.626	-0.009	-0.009	0.000	0.000	0.000	0.000
72	B	72	ALA	0	0.044	0.015	29.705	0.004	0.004	0.000	0.000	0.000	0.000
73	B	73	MET	0	-0.004	0.023	24.163	-0.004	-0.004	0.000	0.000	0.000	0.000
74	B	74	VAL	0	-0.006	-0.001	28.520	0.005	0.005	0.000	0.000	0.000	0.000
75	B	75	ALA	0	0.030	0.031	29.075	-0.002	-0.002	0.000	0.000	0.000	0.000
76	B	76	TRP	0	0.004	-0.021	30.335	0.005	0.005	0.000	0.000	0.000	0.000
77	B	77	LYS	1	0.894	0.956	31.912	0.014	0.014	0.000	0.000	0.000	0.000
78	B	78	VAL	0	-0.026	-0.011	30.501	-0.002	-0.002	0.000	0.000	0.000	0.000
79	B	79	THR	0	0.014	0.010	33.576	0.001	0.001	0.000	0.000	0.000	0.000
80	B	80	PRO	0	0.027	-0.020	32.198	-0.002	-0.002	0.000	0.000	0.000	0.000
81	B	81	ASP	-1	-0.897	-0.929	32.867	0.001	0.001	0.000	0.000	0.000	0.000
82	B	82	GLN	0	0.038	0.017	34.922	-0.002	-0.002	0.000	0.000	0.000	0.000
83	B	83	VAL	0	-0.017	0.004	28.192	-0.004	-0.004	0.000	0.000	0.000	0.000
84	B	84	ASP	-1	-0.858	-0.927	28.765	-0.005	-0.005	0.000	0.000	0.000	0.000
85	B	85	ASP	-1	-0.887	-0.930	30.473	-0.019	-0.019	0.000	0.000	0.000	0.000
86	B	86	CYS	0	-0.028	-0.020	32.678	-0.004	-0.004	0.000	0.000	0.000	0.000
87	B	87	GLY	0	0.025	0.010	28.731	-0.005	-0.005	0.000	0.000	0.000	0.000
88	B	88	ARG	1	0.966	0.973	29.242	0.014	0.014	0.000	0.000	0.000	0.000
89	B	89	LYS	1	0.815	0.893	30.223	0.016	0.016	0.000	0.000	0.000	0.000
90	B	90	ALA	0	0.026	0.013	30.545	-0.003	-0.003	0.000	0.000	0.000	0.000
91	B	91	ALA	0	-0.061	-0.040	27.329	-0.005	-0.005	0.000	0.000	0.000	0.000
92	B	92	GLU	-1	-0.949	-0.962	29.112	-0.049	-0.049	0.000	0.000	0.000	0.000
93	B	93	HIS	0	-0.089	-0.039	31.931	-0.004	-0.004	0.000	0.000	0.000	0.000
94	B	94	SER	0	0.021	0.005	30.953	-0.003	-0.003	0.000	0.000	0.000	0.000
95	B	95	HIS	0	-0.082	-0.040	30.832	-0.007	-0.007	0.000	0.000	0.000	0.000
96	B	96	ILE	0	-0.013	-0.001	27.563	-0.005	-0.005	0.000	0.000	0.000	0.000
97	B	97	SER	0	-0.004	0.008	23.905	-0.002	-0.002	0.000	0.000	0.000	0.000
98	B	98	HIS	0	-0.066	-0.029	19.274	-0.001	-0.001	0.000	0.000	0.000	0.000
99	B	99	VAL	0	0.076	0.041	23.569	0.005	0.005	0.000	0.000	0.000	0.000
100	B	100	TYR	0	-0.066	-0.016	18.248	-0.005	-0.005	0.000	0.000	0.000	0.000
101	B	101	TYR	0	0.073	0.029	23.337	0.002	0.002	0.000	0.000	0.000	0.000
102	B	102	ARG	1	0.833	0.914	18.398	0.088	0.088	0.000	0.000	0.000	0.000
103	B	103	PRO	0	0.021	0.011	23.498	-0.002	-0.002	0.000	0.000	0.000	0.000
104	B	104	SER	0	-0.044	-0.035	25.285	-0.001	-0.001	0.000	0.000	0.000	0.000
105	B	105	SER	0	-0.008	0.000	27.927	0.000	0.000	0.000	0.000	0.000	0.000
106	B	106	ALA	0	0.000	0.002	29.258	0.002	0.002	0.000	0.000	0.000	0.000
107	B	107	PRO	0	0.006	-0.010	31.030	-0.003	-0.003	0.000	0.000	0.000	0.000
108	B	108	ASP	-1	-0.956	-0.972	33.294	-0.013	-0.013	0.000	0.000	0.000	0.000
109	B	109	TRP	0	-0.030	-0.016	27.732	-0.007	-0.007	0.000	0.000	0.000	0.000
110	B	110	PRO	0	0.037	0.017	31.222	0.002	0.002	0.000	0.000	0.000	0.000
111	B	111	TYR	0	-0.043	-0.015	30.649	0.001	0.001	0.000	0.000	0.000	0.000
112	B	112	GLU	-1	-0.798	-0.899	27.804	-0.004	-0.004	0.000	0.000	0.000	0.000
113	B	113	MET	0	-0.004	0.024	27.066	-0.004	-0.004	0.000	0.000	0.000	0.000
114	B	114	TYR	0	-0.042	-0.027	24.906	-0.006	-0.006	0.000	0.000	0.000	0.000
115	B	115	THR	0	0.067	0.033	26.264	-0.001	-0.001	0.000	0.000	0.000	0.000
116	B	116	MET	0	-0.100	-0.040	24.431	-0.001	-0.001	0.000	0.000	0.000	0.000
117	B	117	ILE	0	0.037	0.020	26.976	-0.002	-0.002	0.000	0.000	0.000	0.000
118	B	118	HIS	1	0.830	0.891	25.486	0.110	0.110	0.000	0.000	0.000	0.000
119	B	119	GLY	0	0.088	0.048	30.866	0.007	0.007	0.000	0.000	0.000	0.000
120	B	120	ARG	1	0.884	0.936	33.759	0.058	0.058	0.000	0.000	0.000	0.000
121	B	121	SER	0	-0.003	-0.014	36.337	0.001	0.001	0.000	0.000	0.000	0.000
122	B	122	GLU	-1	-0.812	-0.908	37.329	-0.060	-0.060	0.000	0.000	0.000	0.000
123	B	123	ALA	0	0.034	0.006	38.496	0.001	0.001	0.000	0.000	0.000	0.000
124	B	124	GLU	-1	-0.865	-0.928	37.316	-0.064	-0.064	0.000	0.000	0.000	0.000
125	B	125	CYS	0	-0.032	-0.004	34.334	-0.001	-0.001	0.000	0.000	0.000	0.000
126	B	126	LEU	0	0.019	-0.013	36.182	0.001	0.001	0.000	0.000	0.000	0.000
127	B	127	GLY	0	0.030	0.025	38.724	0.003	0.003	0.000	0.000	0.000	0.000
128	B	128	VAL	0	0.033	0.025	33.526	0.002	0.002	0.000	0.000	0.000	0.000
129	B	129	VAL	0	-0.019	-0.010	35.078	0.001	0.001	0.000	0.000	0.000	0.000
130	B	130	GLU	-1	-0.893	-0.950	37.077	-0.030	-0.030	0.000	0.000	0.000	0.000
131	B	131	ASP	-1	-0.885	-0.934	37.679	-0.042	-0.042	0.000	0.000	0.000	0.000
132	B	132	VAL	0	-0.007	-0.006	33.927	0.002	0.002	0.000	0.000	0.000	0.000
133	B	133	LYS	1	0.914	0.973	36.882	0.032	0.032	0.000	0.000	0.000	0.000
134	B	134	ARG	1	0.917	0.974	39.834	0.035	0.035	0.000	0.000	0.000	0.000
135	B	135	THR	0	-0.100	-0.053	37.773	0.002	0.002	0.000	0.000	0.000	0.000
136	B	136	THR	0	-0.017	-0.015	34.685	0.001	0.001	0.000	0.000	0.000	0.000
137	B	137	SER	0	0.031	0.012	37.678	0.000	0.000	0.000	0.000	0.000	0.000
138	B	138	LEU	0	-0.012	0.003	32.733	0.002	0.002	0.000	0.000	0.000	0.000
139	B	139	LYS	1	0.987	0.984	37.121	0.014	0.014	0.000	0.000	0.000	0.000
140	B	140	GLU	-1	-0.923	-0.974	38.265	-0.016	-0.016	0.000	0.000	0.000	0.000
141	B	141	HIS	0	-0.032	-0.024	34.699	-0.002	-0.002	0.000	0.000	0.000	0.000
142	B	142	ALA	0	0.033	0.026	32.819	0.002	0.002	0.000	0.000	0.000	0.000
143	B	143	ILE	0	-0.013	-0.015	32.533	-0.004	-0.004	0.000	0.000	0.000	0.000
144	B	144	LEU	0	-0.022	-0.005	27.585	0.002	0.002	0.000	0.000	0.000	0.000
145	B	145	ARG	1	0.943	0.957	29.777	0.048	0.048	0.000	0.000	0.000	0.000
146	B	146	SER	0	0.014	0.005	27.807	0.003	0.003	0.000	0.000	0.000	0.000
147	B	147	LEU	0	0.003	0.017	29.816	0.001	0.001	0.000	0.000	0.000	0.000
148	B	148	LYS	1	0.956	0.947	29.063	0.100	0.100	0.000	0.000	0.000	0.000
149	B	149	GLU	-1	-0.932	-0.947	23.686	-0.183	-0.183	0.000	0.000	0.000	0.000
150	B	150	LEU	0	0.003	-0.007	23.901	-0.001	-0.001	0.000	0.000	0.000	0.000
151	B	151	LYS	1	0.969	0.982	15.670	0.300	0.300	0.000	0.000	0.000	0.000
152	B	152	LYS	1	0.951	0.989	18.967	0.218	0.218	0.000	0.000	0.000	0.000
153	B	153	THR	0	-0.048	-0.028	13.870	0.001	0.001	0.000	0.000	0.000	0.000
154	B	154	SER	0	0.003	0.014	12.701	0.018	0.018	0.000	0.000	0.000	0.000
155	B	155	MET	0	0.018	0.005	6.138	0.103	0.103	0.000	0.000	0.000	0.000
156	B	156	THR	0	-0.007	0.001	7.292	0.046	0.046	0.000	0.000	0.000	0.000
157	B	157	TYR	0	-0.009	-0.011	2.648	-0.384	0.244	0.548	-0.221	-0.955	0.000
158	B	158	PHE	0	0.020	0.022	2.754	-9.184	-5.386	4.739	-2.161	-6.376	-0.023
159	B	159	THR	0	0.055	0.027	4.008	0.995	1.199	0.001	-0.018	-0.188	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:1:MET)