FMO DATABASE

FMODB ID: N923Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1207395.303664
FMO2-HF: Nuclear repulsion	1153907.061245
FMO2-HF: Total energy	-53488.242419
FMO2-MP2: Total energy	-53644.797219

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.
-2.161	0.676	1.378	-1.891	-2.323	0.001

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 : 0.041 / q_NPA : 0.017

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	-0.875	-0.925	3.807	-6.039	-4.349	-0.009	-0.881	-0.800	0.004
4	B	122	PRO	0	-0.053	-0.042	5.997	0.674	0.674	0.000	0.000	0.000	0.000
5	B	123	PHE	0	0.009	-0.020	9.672	-0.053	-0.053	0.000	0.000	0.000	0.000
6	B	124	THR	0	0.067	0.022	11.691	0.123	0.123	0.000	0.000	0.000	0.000
7	B	125	PHE	0	-0.045	-0.040	14.196	0.040	0.040	0.000	0.000	0.000	0.000
8	B	126	GLU	-1	-0.927	-0.952	17.381	-0.564	-0.564	0.000	0.000	0.000	0.000
9	B	127	ASN	0	0.030	0.008	19.671	0.053	0.053	0.000	0.000	0.000	0.000
10	B	128	ALA	0	0.080	0.021	22.377	-0.010	-0.010	0.000	0.000	0.000	0.000
11	B	129	THR	0	-0.026	-0.007	23.339	0.012	0.012	0.000	0.000	0.000	0.000
12	B	130	SER	0	-0.066	-0.016	23.116	0.013	0.013	0.000	0.000	0.000	0.000
13	B	131	ASP	-1	-0.726	-0.862	22.443	-0.337	-0.337	0.000	0.000	0.000	0.000
14	B	132	ALA	0	-0.015	-0.013	22.594	-0.014	-0.014	0.000	0.000	0.000	0.000
15	B	133	ILE	0	0.021	0.006	17.795	-0.018	-0.018	0.000	0.000	0.000	0.000
16	B	134	ASN	0	0.039	0.027	17.563	-0.007	-0.007	0.000	0.000	0.000	0.000
17	B	135	GLN	0	0.064	0.009	18.750	-0.028	-0.028	0.000	0.000	0.000	0.000
18	B	136	ASP	-1	-0.841	-0.915	14.823	-0.690	-0.690	0.000	0.000	0.000	0.000
19	B	137	MET	0	0.005	0.018	12.292	-0.182	-0.182	0.000	0.000	0.000	0.000
20	B	138	MET	0	-0.067	-0.030	14.938	-0.045	-0.045	0.000	0.000	0.000	0.000
21	B	139	LEU	0	0.035	0.022	15.121	0.008	0.008	0.000	0.000	0.000	0.000
22	B	140	TYR	0	0.010	0.022	5.518	0.228	0.228	0.000	0.000	0.000	0.000
23	B	141	ILE	0	0.005	-0.019	11.518	-0.082	-0.082	0.000	0.000	0.000	0.000
24	B	142	GLU	-1	-0.914	-0.953	13.755	-0.437	-0.437	0.000	0.000	0.000	0.000
25	B	143	ARG	1	0.916	0.963	6.649	1.660	1.660	0.000	0.000	0.000	0.000
26	B	144	ILE	0	0.014	0.006	7.511	0.096	0.096	0.000	0.000	0.000	0.000
27	B	145	ALA	0	0.003	-0.001	10.745	0.156	0.156	0.000	0.000	0.000	0.000
28	B	146	LYS	1	0.908	0.954	13.565	0.511	0.511	0.000	0.000	0.000	0.000
29	B	147	ILE	0	0.001	0.011	7.270	0.093	0.093	0.000	0.000	0.000	0.000
30	B	148	ILE	0	0.003	-0.011	11.457	0.134	0.134	0.000	0.000	0.000	0.000
31	B	149	GLN	0	-0.096	-0.049	13.391	0.111	0.111	0.000	0.000	0.000	0.000
32	B	150	LYS	1	0.862	0.948	12.214	0.198	0.198	0.000	0.000	0.000	0.000
33	B	151	LEU	0	-0.046	-0.003	10.961	0.075	0.075	0.000	0.000	0.000	0.000
34	B	152	PRO	0	-0.009	-0.004	15.053	-0.018	-0.018	0.000	0.000	0.000	0.000
35	B	153	LYS	1	0.997	0.981	18.253	0.024	0.024	0.000	0.000	0.000	0.000
36	B	154	ARG	1	0.814	0.902	20.797	-0.076	-0.076	0.000	0.000	0.000	0.000
37	B	155	VAL	0	-0.022	0.015	14.525	0.005	0.005	0.000	0.000	0.000	0.000
38	B	156	HIS	0	-0.029	-0.012	18.002	-0.018	-0.018	0.000	0.000	0.000	0.000
39	B	157	ILE	0	-0.009	-0.003	13.069	0.008	0.008	0.000	0.000	0.000	0.000
40	B	158	ASN	0	-0.031	-0.026	15.560	0.005	0.005	0.000	0.000	0.000	0.000
41	B	159	VAL	0	0.000	-0.002	15.220	-0.053	-0.053	0.000	0.000	0.000	0.000
42	B	160	ARG	1	0.916	0.949	15.445	0.314	0.314	0.000	0.000	0.000	0.000
43	B	161	GLY	0	0.013	0.010	16.186	-0.082	-0.082	0.000	0.000	0.000	0.000
44	B	162	PHE	0	-0.015	-0.012	15.145	0.062	0.062	0.000	0.000	0.000	0.000
45	B	163	THR	0	-0.047	-0.064	19.502	-0.033	-0.033	0.000	0.000	0.000	0.000
46	B	164	ASP	-1	-0.751	-0.827	21.202	-0.287	-0.287	0.000	0.000	0.000	0.000
47	B	165	ASP	-1	-0.860	-0.942	22.352	-0.190	-0.190	0.000	0.000	0.000	0.000
48	B	166	THR	0	-0.054	-0.047	24.826	0.025	0.025	0.000	0.000	0.000	0.000
49	B	167	PRO	0	-0.029	0.001	27.253	0.001	0.001	0.000	0.000	0.000	0.000
50	B	168	LEU	0	0.000	-0.007	27.575	-0.010	-0.010	0.000	0.000	0.000	0.000
51	B	169	VAL	0	0.020	-0.002	31.315	0.012	0.012	0.000	0.000	0.000	0.000
52	B	170	LYS	1	0.929	0.970	31.950	0.175	0.175	0.000	0.000	0.000	0.000
53	B	171	THR	0	-0.001	-0.002	28.788	-0.008	-0.008	0.000	0.000	0.000	0.000
54	B	172	ARG	1	0.821	0.898	27.613	0.261	0.261	0.000	0.000	0.000	0.000
55	B	173	PHE	0	-0.068	-0.024	27.369	0.003	0.003	0.000	0.000	0.000	0.000
56	B	174	LYS	1	0.941	0.966	31.623	0.160	0.160	0.000	0.000	0.000	0.000
57	B	175	SER	0	0.032	0.016	30.448	0.005	0.005	0.000	0.000	0.000	0.000
58	B	176	HIS	0	0.086	0.021	25.644	0.000	0.000	0.000	0.000	0.000	0.000
59	B	177	TYR	0	0.034	0.020	25.318	-0.020	-0.020	0.000	0.000	0.000	0.000
60	B	178	GLU	-1	-0.840	-0.916	26.055	-0.186	-0.186	0.000	0.000	0.000	0.000
61	B	179	LEU	0	-0.006	0.027	23.883	-0.011	-0.011	0.000	0.000	0.000	0.000
62	B	180	ALA	0	-0.001	0.002	21.933	-0.029	-0.029	0.000	0.000	0.000	0.000
63	B	181	ALA	0	0.011	-0.006	21.814	-0.030	-0.030	0.000	0.000	0.000	0.000
64	B	182	ASN	0	-0.062	-0.042	23.721	-0.005	-0.005	0.000	0.000	0.000	0.000
65	B	183	ARG	1	0.769	0.901	19.588	0.410	0.410	0.000	0.000	0.000	0.000
66	B	184	ALA	0	0.037	0.020	18.821	-0.038	-0.038	0.000	0.000	0.000	0.000
67	B	185	TYR	0	-0.008	0.000	19.874	-0.011	-0.011	0.000	0.000	0.000	0.000
68	B	186	ARG	1	0.871	0.937	21.535	0.355	0.355	0.000	0.000	0.000	0.000
69	B	187	VAL	0	0.053	0.018	15.155	0.004	0.004	0.000	0.000	0.000	0.000
70	B	188	MET	0	0.007	0.015	18.179	-0.007	-0.007	0.000	0.000	0.000	0.000
71	B	189	LYS	1	0.913	0.962	19.608	0.288	0.288	0.000	0.000	0.000	0.000
72	B	190	VAL	0	0.006	0.020	18.098	0.025	0.025	0.000	0.000	0.000	0.000
73	B	191	LEU	0	0.001	-0.005	13.947	0.012	0.012	0.000	0.000	0.000	0.000
74	B	192	ILE	0	-0.023	-0.005	17.986	0.031	0.031	0.000	0.000	0.000	0.000
75	B	193	GLN	0	-0.043	-0.019	21.280	0.024	0.024	0.000	0.000	0.000	0.000
76	B	194	TYR	0	-0.033	-0.021	18.042	0.013	0.013	0.000	0.000	0.000	0.000
77	B	195	GLY	0	0.030	0.020	19.128	-0.005	-0.005	0.000	0.000	0.000	0.000
78	B	196	VAL	0	-0.021	0.003	16.172	0.026	0.026	0.000	0.000	0.000	0.000
79	B	197	ASN	0	0.006	-0.009	19.263	0.017	0.017	0.000	0.000	0.000	0.000
80	B	198	PRO	0	0.056	0.009	21.582	-0.006	-0.006	0.000	0.000	0.000	0.000
81	B	199	ASN	0	-0.014	0.003	23.574	0.000	0.000	0.000	0.000	0.000	0.000
82	B	200	GLN	0	-0.041	-0.020	18.223	-0.002	-0.002	0.000	0.000	0.000	0.000
83	B	201	LEU	0	-0.022	0.001	17.075	-0.022	-0.022	0.000	0.000	0.000	0.000
84	B	202	SER	0	0.004	0.020	19.678	0.027	0.027	0.000	0.000	0.000	0.000
85	B	203	PHE	0	0.025	-0.003	19.537	-0.036	-0.036	0.000	0.000	0.000	0.000
86	B	204	SER	0	-0.031	-0.005	20.043	0.040	0.040	0.000	0.000	0.000	0.000
87	B	205	SER	0	-0.023	-0.021	20.494	-0.042	-0.042	0.000	0.000	0.000	0.000
88	B	206	TYR	0	0.045	0.020	19.246	0.026	0.026	0.000	0.000	0.000	0.000
89	B	207	GLY	0	0.017	0.031	22.196	0.018	0.018	0.000	0.000	0.000	0.000
90	B	208	SER	0	-0.009	0.012	22.238	-0.025	-0.025	0.000	0.000	0.000	0.000
91	B	209	THR	0	-0.049	-0.042	22.927	0.012	0.012	0.000	0.000	0.000	0.000
92	B	210	ASN	0	-0.059	-0.044	18.655	-0.009	-0.009	0.000	0.000	0.000	0.000
93	B	211	PRO	0	0.009	0.015	18.118	-0.041	-0.041	0.000	0.000	0.000	0.000
94	B	212	ILE	0	0.002	0.006	12.176	0.026	0.026	0.000	0.000	0.000	0.000
95	B	213	ALA	0	-0.013	-0.013	15.719	0.046	0.046	0.000	0.000	0.000	0.000
96	B	214	PRO	0	0.047	0.045	18.094	-0.015	-0.015	0.000	0.000	0.000	0.000
97	B	215	ASN	0	0.037	0.010	21.440	-0.047	-0.047	0.000	0.000	0.000	0.000
98	B	216	ASP	-1	-0.897	-0.948	22.894	-0.127	-0.127	0.000	0.000	0.000	0.000
99	B	217	SER	0	0.009	0.001	20.709	0.002	0.002	0.000	0.000	0.000	0.000
100	B	218	LEU	0	-0.009	-0.010	21.520	-0.012	-0.012	0.000	0.000	0.000	0.000
101	B	219	GLU	-1	-0.855	-0.944	17.688	-0.297	-0.297	0.000	0.000	0.000	0.000
102	B	220	ASN	0	-0.006	-0.016	17.325	-0.095	-0.095	0.000	0.000	0.000	0.000
103	B	221	ARG	1	0.933	0.976	18.213	0.190	0.190	0.000	0.000	0.000	0.000
104	B	222	MET	0	-0.042	-0.030	17.206	-0.005	-0.005	0.000	0.000	0.000	0.000
105	B	223	LYS	1	0.952	0.992	12.711	0.454	0.454	0.000	0.000	0.000	0.000
106	B	224	ASN	0	-0.001	-0.009	14.794	-0.097	-0.097	0.000	0.000	0.000	0.000
107	B	225	ASN	0	-0.011	0.006	17.388	0.044	0.044	0.000	0.000	0.000	0.000
108	B	226	ARG	1	0.806	0.904	12.996	0.476	0.476	0.000	0.000	0.000	0.000
109	B	227	VAL	0	-0.026	-0.015	14.360	0.120	0.120	0.000	0.000	0.000	0.000
110	B	228	GLU	-1	-0.836	-0.905	11.300	-0.813	-0.813	0.000	0.000	0.000	0.000
111	B	229	ILE	0	-0.015	-0.005	9.797	0.154	0.154	0.000	0.000	0.000	0.000
112	B	230	PHE	0	0.003	0.003	10.519	0.030	0.030	0.000	0.000	0.000	0.000
113	B	231	PHE	0	0.039	0.010	8.299	0.032	0.032	0.000	0.000	0.000	0.000
114	B	232	SER	0	-0.019	0.003	13.530	0.052	0.052	0.000	0.000	0.000	0.000
115	B	233	THR	0	0.023	-0.023	14.315	-0.011	-0.011	0.000	0.000	0.000	0.000
116	B	234	ASP	-1	-0.793	-0.854	17.446	0.133	0.133	0.000	0.000	0.000	0.000
117	B	235	ALA	0	0.075	0.011	18.004	0.022	0.022	0.000	0.000	0.000	0.000
118	B	236	ASN	0	-0.008	-0.007	17.899	0.058	0.058	0.000	0.000	0.000	0.000
119	B	237	ASP	-1	-0.885	-0.966	17.071	0.139	0.139	0.000	0.000	0.000	0.000
120	B	238	LEU	0	-0.005	0.009	12.971	0.014	0.014	0.000	0.000	0.000	0.000
121	B	239	SER	0	0.018	0.010	12.954	0.105	0.105	0.000	0.000	0.000	0.000
122	B	240	LYS	1	0.935	0.967	13.228	-0.096	-0.096	0.000	0.000	0.000	0.000
123	B	241	ILE	0	0.011	0.007	9.544	0.004	0.004	0.000	0.000	0.000	0.000
124	B	242	HIS	0	0.010	0.012	8.605	0.008	0.008	0.000	0.000	0.000	0.000
125	B	243	SER	0	0.020	0.008	8.408	0.299	0.299	0.000	0.000	0.000	0.000
126	B	244	ILE	0	-0.012	0.006	9.279	0.082	0.082	0.000	0.000	0.000	0.000
127	B	245	LEU	0	-0.013	-0.022	4.782	-0.223	-0.185	-0.001	-0.004	-0.032	0.000
128	B	246	ASP	-1	-0.935	-0.956	4.655	3.083	3.189	-0.001	-0.010	-0.095	0.000
129	B	247	ASN	0	-0.012	-0.035	6.271	0.179	0.179	0.000	0.000	0.000	0.000
130	B	248	GLU	-1	-0.921	-0.959	6.183	-0.341	-0.341	0.000	0.000	0.000	0.000
131	B	249	PHE	0	-0.099	-0.061	2.594	-2.563	-1.705	1.390	-0.971	-1.277	-0.003
132	B	250	ASN	0	-0.046	-0.012	4.411	0.369	0.514	-0.001	-0.025	-0.119	0.000
133	B	251	PRO	0	-0.020	0.008	6.748	-0.307	-0.307	0.000	0.000	0.000	0.000

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