FMO DATABASE

FMODB ID: 1N98Z

Calculation Name: 3COO-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3COO

Chain ID: B

ChEMBL ID:

UniProt ID: Q9HCB6

Base Structure: X-ray

Registration Date: 2023-09-23

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1383245.480181
FMO2-HF: Nuclear repulsion	1325567.634783
FMO2-HF: Total energy	-57677.845397
FMO2-MP2: Total energy	-57845.541068

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:42:GLY)

Summations of interaction energy for fragment #1(B:42:GLY)

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.
-31.038	-35.483	30.074	-14.093	-11.533	-0.06

Interaction energy analysis for fragmet #1(B:42:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.012

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	44	CYS	0	-0.016	-0.001	3.843	0.370	1.559	-0.015	-0.631	-0.543	0.001
4	B	45	SER	0	0.053	0.011	2.026	-10.817	-13.556	9.559	-3.673	-3.146	0.030
5	B	46	ARG	1	0.864	0.944	3.092	0.517	1.398	0.066	-0.370	-0.577	0.001
6	B	47	ILE	0	0.026	0.014	5.872	-0.626	-0.626	0.000	0.000	0.000	0.000
7	B	48	LEU	0	-0.005	-0.015	7.573	-0.323	-0.323	0.000	0.000	0.000	0.000
8	B	49	ARG	1	0.860	0.923	5.313	-2.177	-2.177	0.000	0.000	0.000	0.000
9	B	50	ALA	0	0.000	0.020	10.107	-0.230	-0.230	0.000	0.000	0.000	0.000
10	B	51	GLN	0	-0.049	-0.023	11.544	-0.120	-0.120	0.000	0.000	0.000	0.000
11	B	52	GLY	0	-0.004	0.009	13.246	-0.030	-0.030	0.000	0.000	0.000	0.000
12	B	53	THR	0	-0.070	-0.049	14.279	-0.094	-0.094	0.000	0.000	0.000	0.000
13	B	54	ARG	1	0.801	0.866	9.957	-0.378	-0.378	0.000	0.000	0.000	0.000
14	B	55	ARG	1	0.795	0.865	15.348	-0.326	-0.326	0.000	0.000	0.000	0.000
15	B	56	GLU	-1	-0.678	-0.820	14.194	0.449	0.449	0.000	0.000	0.000	0.000
16	B	57	GLY	0	0.007	0.017	17.374	-0.031	-0.031	0.000	0.000	0.000	0.000
17	B	58	TYR	0	0.051	0.014	19.806	0.030	0.030	0.000	0.000	0.000	0.000
18	B	59	THR	0	-0.027	-0.020	21.345	-0.013	-0.013	0.000	0.000	0.000	0.000
19	B	60	GLU	-1	-0.785	-0.864	23.643	0.233	0.233	0.000	0.000	0.000	0.000
20	B	61	PHE	0	-0.032	-0.007	21.069	-0.004	-0.004	0.000	0.000	0.000	0.000
21	B	62	SER	0	-0.024	-0.015	21.477	-0.002	-0.002	0.000	0.000	0.000	0.000
22	B	63	LEU	0	0.006	0.011	15.804	-0.010	-0.010	0.000	0.000	0.000	0.000
23	B	64	ARG	1	0.910	0.952	19.998	-0.251	-0.251	0.000	0.000	0.000	0.000
24	B	65	VAL	0	0.043	0.018	20.601	0.025	0.025	0.000	0.000	0.000	0.000
25	B	66	GLU	-1	-0.792	-0.874	23.248	0.167	0.167	0.000	0.000	0.000	0.000
26	B	67	GLY	0	-0.002	-0.014	26.982	-0.002	-0.002	0.000	0.000	0.000	0.000
27	B	68	ASP	-1	-0.940	-0.953	24.364	0.186	0.186	0.000	0.000	0.000	0.000
28	B	69	PRO	0	-0.005	0.017	23.331	-0.009	-0.009	0.000	0.000	0.000	0.000
29	B	70	ASP	-1	-0.866	-0.937	23.710	0.134	0.134	0.000	0.000	0.000	0.000
30	B	71	PHE	0	-0.047	-0.021	22.336	0.004	0.004	0.000	0.000	0.000	0.000
31	B	72	TYR	0	-0.036	-0.056	16.991	0.010	0.010	0.000	0.000	0.000	0.000
32	B	73	LYS	1	0.957	0.969	22.290	-0.125	-0.125	0.000	0.000	0.000	0.000
33	B	74	PRO	0	0.042	0.003	21.621	0.013	0.013	0.000	0.000	0.000	0.000
34	B	75	GLY	0	-0.014	0.005	21.711	-0.012	-0.012	0.000	0.000	0.000	0.000
35	B	76	THR	0	-0.056	-0.020	23.394	-0.005	-0.005	0.000	0.000	0.000	0.000
36	B	77	SER	0	-0.013	0.003	22.706	0.015	0.015	0.000	0.000	0.000	0.000
37	B	78	TYR	0	0.029	0.018	21.755	-0.020	-0.020	0.000	0.000	0.000	0.000
38	B	79	ARG	1	0.840	0.905	22.352	-0.166	-0.166	0.000	0.000	0.000	0.000
39	B	80	VAL	0	0.027	0.024	18.122	-0.008	-0.008	0.000	0.000	0.000	0.000
40	B	81	THR	0	-0.051	-0.031	21.435	-0.017	-0.017	0.000	0.000	0.000	0.000
41	B	82	LEU	0	0.025	0.023	17.995	0.015	0.015	0.000	0.000	0.000	0.000
42	B	83	SER	0	-0.029	-0.018	21.698	-0.032	-0.032	0.000	0.000	0.000	0.000
43	B	84	ALA	0	-0.017	-0.009	23.717	0.019	0.019	0.000	0.000	0.000	0.000
44	B	85	ALA	0	0.029	0.019	26.185	-0.014	-0.014	0.000	0.000	0.000	0.000
45	B	86	PRO	0	0.028	0.021	29.124	0.000	0.000	0.000	0.000	0.000	0.000
46	B	87	PRO	0	-0.001	-0.001	32.330	-0.004	-0.004	0.000	0.000	0.000	0.000
47	B	88	SER	0	-0.037	-0.021	26.844	0.003	0.003	0.000	0.000	0.000	0.000
48	B	89	TYR	0	-0.003	-0.008	27.689	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	90	PHE	0	0.013	0.000	22.299	0.005	0.005	0.000	0.000	0.000	0.000
50	B	91	ARG	1	0.870	0.907	23.832	-0.223	-0.223	0.000	0.000	0.000	0.000
51	B	92	GLY	0	0.074	0.033	20.874	-0.018	-0.018	0.000	0.000	0.000	0.000
52	B	93	PHE	0	-0.053	-0.037	17.302	-0.013	-0.013	0.000	0.000	0.000	0.000
53	B	94	THR	0	0.021	0.025	12.829	0.079	0.079	0.000	0.000	0.000	0.000
54	B	95	LEU	0	-0.025	-0.015	13.767	-0.018	-0.018	0.000	0.000	0.000	0.000
55	B	96	ILE	0	0.014	0.020	6.782	0.002	0.002	0.000	0.000	0.000	0.000
56	B	97	ALA	0	0.024	0.002	10.220	-0.124	-0.124	0.000	0.000	0.000	0.000
57	B	98	LEU	0	-0.008	0.005	5.802	0.107	0.107	0.000	0.000	0.000	0.000
58	B	99	ARG	1	0.838	0.911	8.598	-0.195	-0.195	0.000	0.000	0.000	0.000
59	B	100	GLU	-1	-0.822	-0.904	8.635	0.114	0.114	0.000	0.000	0.000	0.000
60	B	101	ASN	0	-0.063	-0.055	8.063	-0.187	-0.187	0.000	0.000	0.000	0.000
61	B	102	ARG	1	0.786	0.885	8.898	-0.177	-0.177	0.000	0.000	0.000	0.000
62	B	103	GLU	-1	-0.830	-0.899	6.788	-1.130	-1.130	0.000	0.000	0.000	0.000
63	B	104	GLY	0	0.036	0.002	4.021	-0.154	0.173	-0.001	-0.177	-0.149	0.000
64	B	105	ASP	-1	-0.877	-0.938	1.851	-20.581	-23.885	20.405	-10.508	-6.593	-0.091
65	B	106	LYS	1	0.813	0.895	3.028	2.956	1.857	0.062	1.326	-0.289	-0.001
66	B	107	GLU	-1	-0.793	-0.888	4.427	0.857	0.828	-0.001	-0.012	0.042	0.000
67	B	108	GLU	-1	-0.869	-0.933	4.106	-0.008	0.306	0.000	-0.047	-0.266	0.000
68	B	109	ASP	-1	-0.858	-0.952	5.091	1.624	1.639	-0.001	-0.001	-0.012	0.000
69	B	110	HIS	0	-0.035	0.011	7.794	-0.021	-0.021	0.000	0.000	0.000	0.000
70	B	111	ALA	0	-0.013	-0.012	10.098	-0.054	-0.054	0.000	0.000	0.000	0.000
71	B	112	GLY	0	0.046	0.030	12.078	0.030	0.030	0.000	0.000	0.000	0.000
72	B	113	THR	0	-0.058	-0.039	14.454	0.004	0.004	0.000	0.000	0.000	0.000
73	B	114	PHE	0	-0.008	0.001	12.477	-0.036	-0.036	0.000	0.000	0.000	0.000
74	B	115	GLN	0	0.009	0.001	17.268	-0.022	-0.022	0.000	0.000	0.000	0.000
75	B	116	ILE	0	0.013	0.013	19.362	0.008	0.008	0.000	0.000	0.000	0.000
76	B	117	ILE	0	-0.037	-0.008	22.360	-0.021	-0.021	0.000	0.000	0.000	0.000
77	B	118	ASP	-1	-0.813	-0.895	25.480	0.194	0.194	0.000	0.000	0.000	0.000
78	B	119	GLU	-1	-0.899	-0.951	24.941	0.206	0.206	0.000	0.000	0.000	0.000
79	B	120	GLU	-1	-0.846	-0.904	25.984	0.161	0.161	0.000	0.000	0.000	0.000
80	B	121	GLU	-1	-0.822	-0.849	25.615	0.227	0.227	0.000	0.000	0.000	0.000
81	B	122	THR	0	-0.110	-0.057	20.960	0.029	0.029	0.000	0.000	0.000	0.000
82	B	123	GLN	0	0.004	-0.009	19.107	-0.051	-0.051	0.000	0.000	0.000	0.000
83	B	124	PHE	0	0.039	0.013	15.556	0.044	0.044	0.000	0.000	0.000	0.000
84	B	125	MET	0	-0.025	0.001	12.680	0.018	0.018	0.000	0.000	0.000	0.000
85	B	126	SER	0	0.040	0.017	14.031	0.029	0.029	0.000	0.000	0.000	0.000
86	B	127	ASN	0	-0.019	-0.019	12.500	-0.025	-0.025	0.000	0.000	0.000	0.000
87	B	129	PRO	0	0.047	0.024	10.648	0.075	0.075	0.000	0.000	0.000	0.000
88	B	130	VAL	0	0.036	0.036	8.464	-0.051	-0.051	0.000	0.000	0.000	0.000
89	B	131	ALA	0	-0.026	-0.012	9.908	0.031	0.031	0.000	0.000	0.000	0.000
90	B	132	VAL	0	-0.011	-0.009	11.863	-0.144	-0.144	0.000	0.000	0.000	0.000
91	B	133	THR	0	-0.039	-0.027	14.977	0.101	0.101	0.000	0.000	0.000	0.000
92	B	134	GLU	-1	-0.824	-0.912	17.383	0.376	0.376	0.000	0.000	0.000	0.000
93	B	135	SER	0	-0.030	-0.025	21.059	0.010	0.010	0.000	0.000	0.000	0.000
94	B	136	THR	0	0.060	0.016	23.596	-0.016	-0.016	0.000	0.000	0.000	0.000
95	B	137	PRO	0	0.002	0.018	23.723	0.005	0.005	0.000	0.000	0.000	0.000
96	B	138	ARG	1	0.763	0.845	25.103	-0.213	-0.213	0.000	0.000	0.000	0.000
97	B	139	ARG	1	0.857	0.934	26.858	-0.144	-0.144	0.000	0.000	0.000	0.000
98	B	140	ARG	1	0.810	0.894	24.510	-0.275	-0.275	0.000	0.000	0.000	0.000
99	B	141	THR	0	-0.002	-0.011	27.397	0.003	0.003	0.000	0.000	0.000	0.000
100	B	142	ARG	1	0.827	0.880	25.861	-0.201	-0.201	0.000	0.000	0.000	0.000
101	B	143	ILE	0	0.005	0.029	20.165	-0.009	-0.009	0.000	0.000	0.000	0.000
102	B	144	GLN	0	-0.022	-0.033	23.133	-0.001	-0.001	0.000	0.000	0.000	0.000
103	B	145	VAL	0	0.028	0.023	18.308	0.003	0.003	0.000	0.000	0.000	0.000
104	B	146	PHE	0	0.028	0.005	21.758	-0.007	-0.007	0.000	0.000	0.000	0.000
105	B	147	TRP	0	-0.025	-0.017	14.598	0.003	0.003	0.000	0.000	0.000	0.000
106	B	148	ILE	0	-0.009	-0.003	19.110	-0.028	-0.028	0.000	0.000	0.000	0.000
107	B	149	ALA	0	0.019	0.019	18.206	0.026	0.026	0.000	0.000	0.000	0.000
108	B	150	PRO	0	0.001	0.012	15.270	-0.019	-0.019	0.000	0.000	0.000	0.000
109	B	151	PRO	0	0.013	-0.011	17.648	-0.012	-0.012	0.000	0.000	0.000	0.000
110	B	152	ALA	0	0.015	0.021	19.350	0.007	0.007	0.000	0.000	0.000	0.000
111	B	153	GLY	0	-0.030	-0.015	20.122	-0.010	-0.010	0.000	0.000	0.000	0.000
112	B	154	THR	0	-0.040	-0.025	14.276	-0.019	-0.019	0.000	0.000	0.000	0.000
113	B	155	GLY	0	0.035	0.019	14.844	-0.010	-0.010	0.000	0.000	0.000	0.000
114	B	156	CYS	0	-0.059	-0.022	14.979	0.043	0.043	0.000	0.000	0.000	0.000
115	B	157	VAL	0	0.019	0.011	12.294	0.004	0.004	0.000	0.000	0.000	0.000
116	B	158	ILE	0	-0.025	-0.014	10.495	-0.052	-0.052	0.000	0.000	0.000	0.000
117	B	159	LEU	0	0.023	0.020	11.161	0.169	0.169	0.000	0.000	0.000	0.000
118	B	160	LYS	1	0.848	0.921	6.852	-1.210	-1.210	0.000	0.000	0.000	0.000
119	B	161	ALA	0	0.028	0.010	12.059	0.095	0.095	0.000	0.000	0.000	0.000
120	B	162	SER	0	-0.054	-0.019	12.977	-0.014	-0.014	0.000	0.000	0.000	0.000
121	B	163	ILE	0	0.018	0.004	14.893	-0.048	-0.048	0.000	0.000	0.000	0.000
122	B	164	VAL	0	0.032	0.030	18.455	-0.017	-0.017	0.000	0.000	0.000	0.000
123	B	165	GLN	0	0.023	0.032	20.577	-0.039	-0.039	0.000	0.000	0.000	0.000
124	B	166	LYS	1	0.844	0.903	23.920	-0.208	-0.208	0.000	0.000	0.000	0.000
125	B	167	ARG	1	0.986	0.980	22.896	-0.189	-0.189	0.000	0.000	0.000	0.000
126	B	168	ILE	0	0.030	0.032	19.730	0.017	0.017	0.000	0.000	0.000	0.000
127	B	169	ILE	0	0.057	0.035	14.783	-0.017	-0.017	0.000	0.000	0.000	0.000
128	B	170	TYR	0	-0.005	-0.007	16.145	0.020	0.020	0.000	0.000	0.000	0.000
129	B	171	PHE	0	0.046	0.015	10.551	0.100	0.100	0.000	0.000	0.000	0.000
130	B	172	GLN	0	-0.038	-0.008	12.525	-0.112	-0.112	0.000	0.000	0.000	0.000
131	B	173	ASP	-1	-0.836	-0.903	8.351	1.009	1.009	0.000	0.000	0.000	0.000
132	B	174	GLU	-1	-0.789	-0.863	11.341	0.143	0.143	0.000	0.000	0.000	0.000
133	B	175	GLY	0	0.013	-0.003	14.903	-0.021	-0.021	0.000	0.000	0.000	0.000
134	B	176	SER	0	-0.025	-0.023	18.110	0.008	0.008	0.000	0.000	0.000	0.000
135	B	177	LEU	0	-0.071	-0.029	15.769	-0.012	-0.012	0.000	0.000	0.000	0.000
136	B	178	THR	0	-0.020	-0.025	13.291	0.132	0.132	0.000	0.000	0.000	0.000
137	B	179	LYS	1	0.813	0.908	15.394	-0.292	-0.292	0.000	0.000	0.000	0.000
138	B	180	LYS	1	0.846	0.907	14.926	-0.100	-0.100	0.000	0.000	0.000	0.000
139	B	181	LEU	0	-0.008	0.006	16.312	-0.024	-0.024	0.000	0.000	0.000	0.000
140	B	183	GLU	-1	-0.732	-0.851	19.148	0.078	0.078	0.000	0.000	0.000	0.000
141	B	184	GLN	0	-0.047	-0.024	21.836	-0.008	-0.008	0.000	0.000	0.000	0.000
142	B	185	ASP	-1	-0.957	-0.963	25.105	0.048	0.048	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:42:GLY)