FMO DATABASE

FMODB ID: JL2M9

Calculation Name: 3CYP-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CYP

Chain ID: B

ChEMBL ID:

UniProt ID: P56427

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1208190.230587
FMO2-HF: Nuclear repulsion	1154701.45092
FMO2-HF: Total energy	-53488.779668
FMO2-MP2: Total energy	-53645.344466

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:119:GLY)

Summations of interaction energy for fragment #1(B:119: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.
-2.111	0.779	1.388	-1.882	-2.397	0

Interaction energy analysis for fragmet #1(B:119:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.015

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	121	ASP	-1	-0.837	-0.880	3.807	-6.142	-4.475	-0.009	-0.864	-0.795	0.004
4	B	122	PRO	0	-0.053	-0.037	6.037	0.629	0.629	0.000	0.000	0.000	0.000
5	B	123	PHE	0	0.038	-0.014	9.705	-0.059	-0.059	0.000	0.000	0.000	0.000
6	B	124	THR	0	0.062	0.022	11.773	0.118	0.118	0.000	0.000	0.000	0.000
7	B	125	PHE	0	-0.039	-0.041	14.238	0.042	0.042	0.000	0.000	0.000	0.000
8	B	126	GLU	-1	-0.914	-0.944	17.335	-0.581	-0.581	0.000	0.000	0.000	0.000
9	B	127	ASN	0	0.008	-0.007	19.716	0.050	0.050	0.000	0.000	0.000	0.000
10	B	128	ALA	0	0.087	0.029	22.404	-0.009	-0.009	0.000	0.000	0.000	0.000
11	B	129	THR	0	0.001	0.010	23.373	0.009	0.009	0.000	0.000	0.000	0.000
12	B	130	SER	0	-0.083	-0.028	23.384	0.013	0.013	0.000	0.000	0.000	0.000
13	B	131	ASP	-1	-0.708	-0.835	22.494	-0.337	-0.337	0.000	0.000	0.000	0.000
14	B	132	ALA	0	-0.020	-0.015	22.594	-0.013	-0.013	0.000	0.000	0.000	0.000
15	B	133	ILE	0	0.017	0.005	17.662	-0.019	-0.019	0.000	0.000	0.000	0.000
16	B	134	ASN	0	0.048	0.033	17.401	-0.007	-0.007	0.000	0.000	0.000	0.000
17	B	135	GLN	0	0.061	0.011	18.705	-0.021	-0.021	0.000	0.000	0.000	0.000
18	B	136	ASP	-1	-0.865	-0.929	14.849	-0.658	-0.658	0.000	0.000	0.000	0.000
19	B	137	MET	0	0.013	0.030	12.284	-0.177	-0.177	0.000	0.000	0.000	0.000
20	B	138	MET	0	-0.058	-0.026	14.938	-0.046	-0.046	0.000	0.000	0.000	0.000
21	B	139	LEU	0	0.017	0.013	15.211	0.009	0.009	0.000	0.000	0.000	0.000
22	B	140	TYR	0	-0.032	-0.035	5.675	0.130	0.130	0.000	0.000	0.000	0.000
23	B	141	ILE	0	-0.007	-0.024	11.515	-0.085	-0.085	0.000	0.000	0.000	0.000
24	B	142	GLU	-1	-0.831	-0.892	13.754	-0.426	-0.426	0.000	0.000	0.000	0.000
25	B	143	ARG	1	0.822	0.898	6.206	1.554	1.554	0.000	0.000	0.000	0.000
26	B	144	ILE	0	0.022	0.009	7.258	0.105	0.105	0.000	0.000	0.000	0.000
27	B	145	ALA	0	-0.002	-0.004	10.744	0.156	0.156	0.000	0.000	0.000	0.000
28	B	146	LYS	1	0.871	0.926	13.605	0.531	0.531	0.000	0.000	0.000	0.000
29	B	147	ILE	0	-0.015	0.006	7.358	0.105	0.105	0.000	0.000	0.000	0.000
30	B	148	ILE	0	0.002	-0.013	11.456	0.136	0.136	0.000	0.000	0.000	0.000
31	B	149	GLN	0	-0.102	-0.056	13.391	0.109	0.109	0.000	0.000	0.000	0.000
32	B	150	LYS	1	0.845	0.921	11.953	0.217	0.217	0.000	0.000	0.000	0.000
33	B	151	LEU	0	-0.036	0.004	10.949	0.075	0.075	0.000	0.000	0.000	0.000
34	B	152	PRO	0	-0.010	-0.007	15.054	-0.015	-0.015	0.000	0.000	0.000	0.000
35	B	153	LYS	1	0.998	0.981	18.255	0.027	0.027	0.000	0.000	0.000	0.000
36	B	154	ARG	1	0.798	0.886	20.799	-0.079	-0.079	0.000	0.000	0.000	0.000
37	B	155	VAL	0	-0.025	0.009	14.530	0.007	0.007	0.000	0.000	0.000	0.000
38	B	156	HIS	0	-0.039	-0.007	17.999	-0.015	-0.015	0.000	0.000	0.000	0.000
39	B	157	ILE	0	-0.011	-0.006	12.951	0.007	0.007	0.000	0.000	0.000	0.000
40	B	158	ASN	0	-0.042	-0.026	15.564	0.008	0.008	0.000	0.000	0.000	0.000
41	B	159	VAL	0	0.014	0.001	15.220	-0.053	-0.053	0.000	0.000	0.000	0.000
42	B	160	ARG	1	0.898	0.945	15.374	0.326	0.326	0.000	0.000	0.000	0.000
43	B	161	GLY	0	0.027	0.015	16.187	-0.082	-0.082	0.000	0.000	0.000	0.000
44	B	162	PHE	0	-0.018	-0.014	15.206	0.062	0.062	0.000	0.000	0.000	0.000
45	B	163	THR	0	-0.039	-0.055	19.504	-0.032	-0.032	0.000	0.000	0.000	0.000
46	B	164	ASP	-1	-0.737	-0.829	21.223	-0.293	-0.293	0.000	0.000	0.000	0.000
47	B	165	ASP	-1	-0.840	-0.929	22.369	-0.187	-0.187	0.000	0.000	0.000	0.000
48	B	166	THR	0	-0.048	-0.030	24.743	0.026	0.026	0.000	0.000	0.000	0.000
49	B	167	PRO	0	-0.014	0.003	27.274	0.001	0.001	0.000	0.000	0.000	0.000
50	B	168	LEU	0	-0.011	-0.007	27.494	-0.010	-0.010	0.000	0.000	0.000	0.000
51	B	169	VAL	0	0.033	0.003	31.343	0.012	0.012	0.000	0.000	0.000	0.000
52	B	170	LYS	1	0.929	0.972	31.663	0.176	0.176	0.000	0.000	0.000	0.000
53	B	171	THR	0	0.001	-0.007	28.626	-0.009	-0.009	0.000	0.000	0.000	0.000
54	B	172	ARG	1	0.825	0.900	27.467	0.262	0.262	0.000	0.000	0.000	0.000
55	B	173	PHE	0	-0.072	-0.028	27.075	0.002	0.002	0.000	0.000	0.000	0.000
56	B	174	LYS	1	0.904	0.922	31.655	0.160	0.160	0.000	0.000	0.000	0.000
57	B	175	SER	0	0.025	0.010	30.547	0.005	0.005	0.000	0.000	0.000	0.000
58	B	176	HIS	0	0.082	0.022	25.787	0.000	0.000	0.000	0.000	0.000	0.000
59	B	177	TYR	0	0.051	0.023	25.382	-0.022	-0.022	0.000	0.000	0.000	0.000
60	B	178	GLU	-1	-0.806	-0.867	26.057	-0.187	-0.187	0.000	0.000	0.000	0.000
61	B	179	LEU	0	-0.008	0.024	23.894	-0.010	-0.010	0.000	0.000	0.000	0.000
62	B	180	ALA	0	-0.001	0.001	22.003	-0.029	-0.029	0.000	0.000	0.000	0.000
63	B	181	ALA	0	0.015	-0.003	21.816	-0.030	-0.030	0.000	0.000	0.000	0.000
64	B	182	ASN	0	-0.058	-0.037	23.722	-0.005	-0.005	0.000	0.000	0.000	0.000
65	B	183	ARG	1	0.767	0.895	19.526	0.412	0.412	0.000	0.000	0.000	0.000
66	B	184	ALA	0	0.032	0.019	18.822	-0.038	-0.038	0.000	0.000	0.000	0.000
67	B	185	TYR	0	-0.021	-0.008	19.875	-0.011	-0.011	0.000	0.000	0.000	0.000
68	B	186	ARG	1	0.836	0.905	21.572	0.348	0.348	0.000	0.000	0.000	0.000
69	B	187	VAL	0	0.058	0.022	15.203	0.004	0.004	0.000	0.000	0.000	0.000
70	B	188	MET	0	0.001	0.013	18.179	-0.006	-0.006	0.000	0.000	0.000	0.000
71	B	189	LYS	1	0.943	0.973	19.608	0.282	0.282	0.000	0.000	0.000	0.000
72	B	190	VAL	0	-0.001	0.016	18.080	0.024	0.024	0.000	0.000	0.000	0.000
73	B	191	LEU	0	0.007	-0.003	13.920	0.012	0.012	0.000	0.000	0.000	0.000
74	B	192	ILE	0	-0.030	-0.009	17.985	0.031	0.031	0.000	0.000	0.000	0.000
75	B	193	GLN	0	-0.053	-0.021	21.079	0.033	0.033	0.000	0.000	0.000	0.000
76	B	194	TYR	0	-0.065	-0.043	18.050	0.024	0.024	0.000	0.000	0.000	0.000
77	B	195	GLY	0	0.033	0.026	19.127	-0.006	-0.006	0.000	0.000	0.000	0.000
78	B	196	VAL	0	-0.030	-0.002	16.169	0.027	0.027	0.000	0.000	0.000	0.000
79	B	197	ASN	0	0.006	-0.007	19.262	0.013	0.013	0.000	0.000	0.000	0.000
80	B	198	PRO	0	0.067	0.015	21.582	-0.007	-0.007	0.000	0.000	0.000	0.000
81	B	199	ASN	0	-0.019	0.003	23.575	0.002	0.002	0.000	0.000	0.000	0.000
82	B	200	GLN	0	-0.047	-0.032	18.239	0.005	0.005	0.000	0.000	0.000	0.000
83	B	201	LEU	0	-0.018	0.005	17.045	-0.022	-0.022	0.000	0.000	0.000	0.000
84	B	202	SER	0	-0.001	0.013	19.676	0.029	0.029	0.000	0.000	0.000	0.000
85	B	203	PHE	0	0.042	0.005	19.537	-0.036	-0.036	0.000	0.000	0.000	0.000
86	B	204	SER	0	-0.053	-0.019	20.085	0.042	0.042	0.000	0.000	0.000	0.000
87	B	205	SER	0	-0.022	-0.023	20.495	-0.042	-0.042	0.000	0.000	0.000	0.000
88	B	206	TYR	0	0.038	0.022	19.292	0.035	0.035	0.000	0.000	0.000	0.000
89	B	207	GLY	0	0.021	0.027	22.198	0.018	0.018	0.000	0.000	0.000	0.000
90	B	208	SER	0	-0.007	0.011	22.241	-0.025	-0.025	0.000	0.000	0.000	0.000
91	B	209	THR	0	-0.055	-0.038	23.037	0.013	0.013	0.000	0.000	0.000	0.000
92	B	210	ASN	0	-0.052	-0.038	18.722	-0.010	-0.010	0.000	0.000	0.000	0.000
93	B	211	PRO	0	0.005	0.014	18.121	-0.041	-0.041	0.000	0.000	0.000	0.000
94	B	212	ILE	0	0.005	0.011	12.014	0.025	0.025	0.000	0.000	0.000	0.000
95	B	213	ALA	0	-0.018	-0.013	15.714	0.044	0.044	0.000	0.000	0.000	0.000
96	B	214	PRO	0	0.043	0.045	18.087	-0.015	-0.015	0.000	0.000	0.000	0.000
97	B	215	ASN	0	0.000	-0.005	21.439	-0.049	-0.049	0.000	0.000	0.000	0.000
98	B	216	ASP	-1	-0.879	-0.939	22.900	-0.131	-0.131	0.000	0.000	0.000	0.000
99	B	217	SER	0	-0.031	-0.045	21.128	0.004	0.004	0.000	0.000	0.000	0.000
100	B	218	LEU	0	0.008	0.003	21.674	-0.013	-0.013	0.000	0.000	0.000	0.000
101	B	219	GLU	-1	-0.799	-0.893	17.659	-0.292	-0.292	0.000	0.000	0.000	0.000
102	B	220	ASN	0	-0.011	-0.022	17.340	-0.088	-0.088	0.000	0.000	0.000	0.000
103	B	221	ARG	1	0.891	0.944	18.224	0.184	0.184	0.000	0.000	0.000	0.000
104	B	222	MET	0	-0.040	-0.026	17.387	-0.007	-0.007	0.000	0.000	0.000	0.000
105	B	223	LYS	1	0.950	0.989	13.354	0.418	0.418	0.000	0.000	0.000	0.000
106	B	224	ASN	0	-0.010	-0.013	14.812	-0.096	-0.096	0.000	0.000	0.000	0.000
107	B	225	ASN	0	-0.021	-0.006	17.403	0.042	0.042	0.000	0.000	0.000	0.000
108	B	226	ARG	1	0.789	0.887	13.093	0.463	0.463	0.000	0.000	0.000	0.000
109	B	227	VAL	0	-0.026	-0.018	14.501	0.117	0.117	0.000	0.000	0.000	0.000
110	B	228	GLU	-1	-0.810	-0.883	11.255	-0.786	-0.786	0.000	0.000	0.000	0.000
111	B	229	ILE	0	-0.013	-0.005	9.812	0.159	0.159	0.000	0.000	0.000	0.000
112	B	230	PHE	0	0.017	0.009	10.519	0.021	0.021	0.000	0.000	0.000	0.000
113	B	231	PHE	0	0.039	0.008	8.216	0.038	0.038	0.000	0.000	0.000	0.000
114	B	232	SER	0	-0.018	0.003	13.528	0.053	0.053	0.000	0.000	0.000	0.000
115	B	233	THR	0	0.030	-0.019	14.308	-0.012	-0.012	0.000	0.000	0.000	0.000
116	B	234	ASP	-1	-0.788	-0.851	17.443	0.134	0.134	0.000	0.000	0.000	0.000
117	B	235	ALA	0	0.077	0.017	18.002	0.020	0.020	0.000	0.000	0.000	0.000
118	B	236	ASN	0	-0.026	-0.019	17.896	0.055	0.055	0.000	0.000	0.000	0.000
119	B	237	ASP	-1	-0.805	-0.913	17.226	0.133	0.133	0.000	0.000	0.000	0.000
120	B	238	LEU	0	0.005	0.018	12.818	0.009	0.009	0.000	0.000	0.000	0.000
121	B	239	SER	0	0.026	0.013	12.951	0.098	0.098	0.000	0.000	0.000	0.000
122	B	240	LYS	1	0.857	0.923	13.231	-0.082	-0.082	0.000	0.000	0.000	0.000
123	B	241	ILE	0	0.003	0.001	9.564	0.004	0.004	0.000	0.000	0.000	0.000
124	B	242	HIS	0	-0.035	-0.008	8.361	-0.113	-0.113	0.000	0.000	0.000	0.000
125	B	243	SER	0	0.018	0.005	8.411	0.305	0.305	0.000	0.000	0.000	0.000
126	B	244	ILE	0	-0.015	0.005	9.363	0.085	0.085	0.000	0.000	0.000	0.000
127	B	245	LEU	0	-0.013	-0.021	4.847	-0.183	-0.183	0.000	0.000	0.000	0.000
128	B	246	ASP	-1	-0.863	-0.925	4.656	2.927	3.032	-0.001	-0.009	-0.095	0.000
129	B	247	ASN	0	-0.031	-0.044	6.273	0.151	0.151	0.000	0.000	0.000	0.000
130	B	248	GLU	-1	-0.856	-0.907	6.340	-0.540	-0.540	0.000	0.000	0.000	0.000
131	B	249	PHE	0	-0.051	-0.030	2.629	-2.331	-1.372	1.399	-0.989	-1.369	-0.004
132	B	250	ASN	0	-0.034	0.008	4.439	0.919	1.078	-0.001	-0.020	-0.138	0.000
133	B	251	PRO	0	-0.026	0.004	6.794	-0.322	-0.322	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:119:GLY)