Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: Z69VN

Calculation Name: 1RHH-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1RHH

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2425263.425072
FMO2-HF: Nuclear repulsion 2337763.480887
FMO2-HF: Total energy -87499.944185
FMO2-MP2: Total energy -87753.59184


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(B:3:GLN)


Summations of interaction energy for fragment #1(B:3:GLN)
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.
2.6823.2497.267-1.856-5.980.001
Interaction energy analysis for fragmet #1(B:3:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / 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   
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].
3B5LEU00.0340.0032.7770.4292.8290.046-0.741-1.7050.004
4B6GLU-1-0.979-0.9703.612-4.481-3.8720.005-0.260-0.355-0.002
5B7GLN00.0350.0025.5310.9200.9200.0000.0000.0000.000
6B8SER00.0500.0418.234-0.121-0.1210.0000.0000.0000.000
7B9GLY0-0.030-0.01211.248-0.043-0.0430.0000.0000.0000.000
8B10ALA0-0.002-0.00113.0890.0860.0860.0000.0000.0000.000
9B11GLU-1-0.913-0.96215.169-0.425-0.4250.0000.0000.0000.000
10B12VAL0-0.027-0.00818.7950.0300.0300.0000.0000.0000.000
11B13LYS10.8870.95021.4000.2640.2640.0000.0000.0000.000
12B14LYS10.9810.99324.0990.2050.2050.0000.0000.0000.000
13B15PRO00.0150.01827.5020.0020.0020.0000.0000.0000.000
14B16GLY0-0.060-0.03128.9370.0010.0010.0000.0000.0000.000
15B17SER0-0.070-0.04826.085-0.003-0.0030.0000.0000.0000.000
16B18SER00.0880.02424.4310.0160.0160.0000.0000.0000.000
17B19VAL0-0.048-0.02318.211-0.023-0.0230.0000.0000.0000.000
18B20GLN00.0460.02817.450-0.004-0.0040.0000.0000.0000.000
19B21VAL0-0.024-0.00112.460-0.061-0.0610.0000.0000.0000.000
20B22SER0-0.005-0.00612.4850.0350.0350.0000.0000.0000.000
21B23CYS0-0.038-0.0057.8720.0000.0000.0000.0000.0000.000
22B24LYS10.9741.0068.4101.2441.2440.0000.0000.0000.000
23B25ALA00.0520.0337.273-0.386-0.3860.0000.0000.0000.000
24B26SER0-0.064-0.0525.691-0.298-0.2980.0000.0000.0000.000
25B27GLY0-0.0100.0027.6470.0100.0100.0000.0000.0000.000
26B28GLY0-0.040-0.0119.0800.0430.0430.0000.0000.0000.000
27B29THR00.019-0.00211.6420.0510.0510.0000.0000.0000.000
28B30PHE00.0060.00911.8510.0930.0930.0000.0000.0000.000
29B31SER0-0.0100.00513.6020.1140.1140.0000.0000.0000.000
30B32MET00.0500.01715.309-0.099-0.0990.0000.0000.0000.000
31B33TYR0-0.016-0.00510.6980.1030.1030.0000.0000.0000.000
32B34GLY0-0.011-0.00314.328-0.171-0.1710.0000.0000.0000.000
33B35PHE0-0.066-0.0439.8820.1550.1550.0000.0000.0000.000
34B35ASN00.017-0.00513.032-0.203-0.2030.0000.0000.0000.000
35B36TRP00.0060.01312.7210.0350.0350.0000.0000.0000.000
36B37VAL0-0.0010.00413.6180.0130.0130.0000.0000.0000.000
37B38ARG10.7900.86314.130-0.048-0.0480.0000.0000.0000.000
38B39GLN00.005-0.01815.2440.0290.0290.0000.0000.0000.000
39B40ALA00.0330.03617.569-0.057-0.0570.0000.0000.0000.000
40B41PRO00.015-0.01318.3950.0220.0220.0000.0000.0000.000
41B42GLY00.0050.00919.6500.0070.0070.0000.0000.0000.000
42B43HIS0-0.060-0.02520.7300.0330.0330.0000.0000.0000.000
43B44GLY00.0340.01319.7990.0080.0080.0000.0000.0000.000
44B45LEU00.0010.00514.770-0.037-0.0370.0000.0000.0000.000
45B46GLU-1-0.788-0.87618.3640.0800.0800.0000.0000.0000.000
46B47TRP0-0.001-0.00717.277-0.058-0.0580.0000.0000.0000.000
47B48MET0-0.043-0.01818.219-0.048-0.0480.0000.0000.0000.000
48B49GLY00.048-0.00118.480-0.024-0.0240.0000.0000.0000.000
49B50GLY00.0190.02217.3210.0230.0230.0000.0000.0000.000
50B51ILE0-0.037-0.01616.859-0.044-0.0440.0000.0000.0000.000
51B52ILE00.0620.03917.1050.0490.0490.0000.0000.0000.000
52B52PRO0-0.055-0.04016.193-0.040-0.0400.0000.0000.0000.000
53B53ILE00.0100.01418.878-0.035-0.0350.0000.0000.0000.000
54B54PHE00.0210.03320.706-0.019-0.0190.0000.0000.0000.000
55B55GLY0-0.0190.00522.453-0.026-0.0260.0000.0000.0000.000
56B56THR0-0.030-0.00322.918-0.019-0.0190.0000.0000.0000.000
57B57SER0-0.017-0.01621.3480.0110.0110.0000.0000.0000.000
58B58ASN00.0020.00022.148-0.001-0.0010.0000.0000.0000.000
59B59TYR00.0170.00022.0170.0020.0020.0000.0000.0000.000
60B60ALA00.0210.03023.2430.0040.0040.0000.0000.0000.000
61B61GLN00.045-0.00325.006-0.032-0.0320.0000.0000.0000.000
62B62LYS10.8660.95625.036-0.070-0.0700.0000.0000.0000.000
63B63PHE0-0.002-0.01222.366-0.020-0.0200.0000.0000.0000.000
64B64ARG10.9760.99026.147-0.072-0.0720.0000.0000.0000.000
65B65GLY0-0.047-0.01928.722-0.008-0.0080.0000.0000.0000.000
66B66ARG10.7770.87625.5780.0320.0320.0000.0000.0000.000
67B67VAL00.0000.00521.933-0.020-0.0200.0000.0000.0000.000
68B68THR00.0020.01422.3540.0210.0210.0000.0000.0000.000
69B69PHE00.0110.00217.768-0.019-0.0190.0000.0000.0000.000
70B70THR00.0010.00318.9560.0090.0090.0000.0000.0000.000
71B71ALA00.0180.00117.093-0.007-0.0070.0000.0000.0000.000
72B72ASP-1-0.788-0.85817.153-0.190-0.1900.0000.0000.0000.000
73B73GLN00.000-0.01617.136-0.050-0.0500.0000.0000.0000.000
74B74ALA0-0.0230.00017.805-0.013-0.0130.0000.0000.0000.000
75B75THR0-0.040-0.05315.523-0.051-0.0510.0000.0000.0000.000
76B76SER0-0.039-0.01012.622-0.100-0.1000.0000.0000.0000.000
77B77THR0-0.021-0.02212.165-0.124-0.1240.0000.0000.0000.000
78B78ALA0-0.0050.00212.5800.0850.0850.0000.0000.0000.000
79B79TYR00.010-0.02513.577-0.132-0.1320.0000.0000.0000.000
80B80MET00.0150.02216.0370.0840.0840.0000.0000.0000.000
81B81GLU-1-0.984-0.98717.716-0.193-0.1930.0000.0000.0000.000
82B82LEU0-0.0090.00120.6850.0340.0340.0000.0000.0000.000
83B82THR00.0560.00522.337-0.025-0.0250.0000.0000.0000.000
84B82ASN0-0.048-0.03325.8550.0170.0170.0000.0000.0000.000
85B82LEU0-0.0150.00922.4710.0120.0120.0000.0000.0000.000
86B83ARG10.9790.98426.3810.0750.0750.0000.0000.0000.000
87B84SER00.0710.01626.011-0.006-0.0060.0000.0000.0000.000
88B85ASP-1-0.941-0.96425.584-0.053-0.0530.0000.0000.0000.000
89B86ASP-1-0.728-0.81922.635-0.049-0.0490.0000.0000.0000.000
90B87THR0-0.042-0.00521.092-0.033-0.0330.0000.0000.0000.000
91B88ALA0-0.023-0.01718.0540.0300.0300.0000.0000.0000.000
92B89VAL00.0000.01312.263-0.068-0.0680.0000.0000.0000.000
93B90TYR0-0.033-0.05513.7730.1080.1080.0000.0000.0000.000
94B91TYR00.0020.0028.778-0.178-0.1780.0000.0000.0000.000
95B93ALA00.019-0.0098.3860.1500.1500.0000.0000.0000.000
96B94ARG10.8320.9097.533-3.218-3.2180.0000.0000.0000.000
97B95ASP-1-0.751-0.86311.0650.9660.9660.0000.0000.0000.000
98B96PHE0-0.009-0.02113.481-0.013-0.0130.0000.0000.0000.000
99B97GLY00.0840.02015.400-0.029-0.0290.0000.0000.0000.000
100B98PRO0-0.076-0.01817.495-0.033-0.0330.0000.0000.0000.000
101B99ASP-1-0.748-0.83820.1710.5340.5340.0000.0000.0000.000
102B100TRP0-0.037-0.02623.483-0.037-0.0370.0000.0000.0000.000
103B100GLU-1-0.919-0.95623.0470.4720.4720.0000.0000.0000.000
104B100ASP-1-0.906-0.90724.4890.3660.3660.0000.0000.0000.000
105B100GLY0-0.087-0.07422.3550.0460.0460.0000.0000.0000.000
106B100ASP-1-0.792-0.95922.3690.5660.5660.0000.0000.0000.000
107B100SER0-0.237-0.14524.872-0.049-0.0490.0000.0000.0000.000
108B100TYR0-0.032-0.02526.677-0.035-0.0350.0000.0000.0000.000
109B100ASP-1-0.912-0.93725.0300.5830.5830.0000.0000.0000.000
110B100GLY0-0.006-0.00526.608-0.008-0.0080.0000.0000.0000.000
111B100SER0-0.128-0.06222.891-0.024-0.0240.0000.0000.0000.000
112B100GLY00.1110.07122.5490.0290.0290.0000.0000.0000.000
113B100ARG10.7540.87516.974-0.606-0.6060.0000.0000.0000.000
114B100GLY0-0.034-0.01118.834-0.014-0.0140.0000.0000.0000.000
115B100PHE0-0.055-0.01614.905-0.003-0.0030.0000.0000.0000.000
116B100PHE0-0.008-0.02912.0390.0140.0140.0000.0000.0000.000
117B101ASP-1-0.807-0.8889.9292.8712.8710.0000.0000.0000.000
118B102PHE0-0.021-0.0192.1431.345-1.2547.218-0.840-3.780-0.001
119B103TRP00.0190.0066.620-0.963-0.9630.0000.0000.0000.000
120B104GLY00.0270.0233.9600.5670.665-0.001-0.012-0.0850.000
121B105GLN0-0.090-0.0594.5690.4380.497-0.001-0.003-0.0550.000
122B106GLY00.0140.0156.0170.2760.2760.0000.0000.0000.000
123B107THR0-0.011-0.0069.276-0.194-0.1940.0000.0000.0000.000
124B108LEU0-0.063-0.02411.9950.1200.1200.0000.0000.0000.000
125B109VAL00.0390.03015.232-0.035-0.0350.0000.0000.0000.000
126B110THR0-0.010-0.01018.1530.0500.0500.0000.0000.0000.000
127B111VAL0-0.0110.01021.478-0.012-0.0120.0000.0000.0000.000
128B112SER00.025-0.00124.5960.0200.0200.0000.0000.0000.000
129B113SER0-0.014-0.01327.449-0.010-0.0100.0000.0000.0000.000
130B114ALA0-0.0120.00428.9770.0000.0000.0000.0000.0000.000
131B115SER00.008-0.00527.879-0.008-0.0080.0000.0000.0000.000
132B116THR0-0.031-0.02023.488-0.009-0.0090.0000.0000.0000.000
133B117LYS10.9440.96825.3210.2610.2610.0000.0000.0000.000
134B118GLY00.0190.01323.949-0.015-0.0150.0000.0000.0000.000
135B119PRO0-0.022-0.01322.2210.0260.0260.0000.0000.0000.000
136B120SER00.0020.01725.443-0.004-0.0040.0000.0000.0000.000
137B121VAL00.002-0.00823.4970.0040.0040.0000.0000.0000.000
138B122PHE0-0.014-0.02026.8060.0080.0080.0000.0000.0000.000
139B123PRO00.0060.00528.318-0.012-0.0120.0000.0000.0000.000
140B124LEU0-0.0260.01127.2770.0190.0190.0000.0000.0000.000
141B125ALA00.005-0.01930.071-0.008-0.0080.0000.0000.0000.000
142B126PRO00.0160.02930.5060.0130.0130.0000.0000.0000.000
143B127SER00.016-0.01332.9000.0070.0070.0000.0000.0000.000
144B128SER00.0270.00436.5180.0020.0020.0000.0000.0000.000
145B129LYS10.9250.95638.2380.1230.1230.0000.0000.0000.000
146B130SER0-0.0140.01532.8900.0040.0040.0000.0000.0000.000
147B131THR0-0.021-0.00433.506-0.008-0.0080.0000.0000.0000.000
148B132SER00.0190.00234.1640.0110.0110.0000.0000.0000.000
149B133GLY00.0490.03434.718-0.003-0.0030.0000.0000.0000.000
150B134GLY00.003-0.00134.989-0.003-0.0030.0000.0000.0000.000
151B135THR0-0.045-0.01129.627-0.013-0.0130.0000.0000.0000.000
152B136ALA00.0110.01130.7580.0110.0110.0000.0000.0000.000
153B137ALA00.0080.00528.800-0.014-0.0140.0000.0000.0000.000
154B138LEU0-0.030-0.00925.7050.0100.0100.0000.0000.0000.000
155B139GLY00.0710.00225.223-0.010-0.0100.0000.0000.0000.000
156B140CYS0-0.0880.00320.246-0.032-0.0320.0000.0000.0000.000
157B141LEU00.0280.02225.055-0.001-0.0010.0000.0000.0000.000
158B142VAL0-0.037-0.02221.951-0.007-0.0070.0000.0000.0000.000
159B143LYS10.9610.96125.2020.2160.2160.0000.0000.0000.000
160B144ASP-1-0.860-0.92827.752-0.230-0.2300.0000.0000.0000.000
161B145TYR0-0.024-0.01921.355-0.006-0.0060.0000.0000.0000.000
162B146PHE00.0200.03424.4810.0180.0180.0000.0000.0000.000
163B147PRO00.0070.00820.899-0.013-0.0130.0000.0000.0000.000
164B148GLU-1-0.756-0.86518.995-0.382-0.3820.0000.0000.0000.000
165B149PRO00.001-0.01014.6230.0060.0060.0000.0000.0000.000
166B150VAL00.005-0.01417.481-0.034-0.0340.0000.0000.0000.000
167B151THR0-0.0250.00112.0860.0440.0440.0000.0000.0000.000
168B152VAL00.004-0.01515.1260.0170.0170.0000.0000.0000.000
169B153SER0-0.0020.00513.629-0.052-0.0520.0000.0000.0000.000
170B154TRP00.0070.00615.7040.0740.0740.0000.0000.0000.000
171B155ASN00.009-0.00417.246-0.041-0.0410.0000.0000.0000.000
172B156SER0-0.017-0.02214.888-0.014-0.0140.0000.0000.0000.000
173B157GLY00.0020.00712.798-0.155-0.1550.0000.0000.0000.000
174B158ALA0-0.027-0.00313.7920.0060.0060.0000.0000.0000.000
175B159LEU0-0.040-0.01216.1840.0850.0850.0000.0000.0000.000
176B160THR00.014-0.00513.2520.0000.0000.0000.0000.0000.000
177B161SER00.010-0.00116.6300.0540.0540.0000.0000.0000.000
178B162GLY00.0530.02019.530-0.005-0.0050.0000.0000.0000.000
179B163VAL0-0.062-0.02418.0550.0070.0070.0000.0000.0000.000
180B164HIS00.0210.01719.7510.0040.0040.0000.0000.0000.000
181B165THR0-0.007-0.01017.5660.0000.0000.0000.0000.0000.000
182B166PHE0-0.0190.00219.8650.0150.0150.0000.0000.0000.000
183B167PRO00.0140.01420.773-0.034-0.0340.0000.0000.0000.000
184B168ALA00.011-0.00121.6950.0110.0110.0000.0000.0000.000
185B169VAL0-0.0190.00123.5760.0240.0240.0000.0000.0000.000
186B170LEU0-0.031-0.01727.157-0.017-0.0170.0000.0000.0000.000
187B171GLN0-0.059-0.05928.7890.0200.0200.0000.0000.0000.000
188B172SER00.0560.01931.961-0.002-0.0020.0000.0000.0000.000
189B173SER0-0.017-0.01032.8940.0040.0040.0000.0000.0000.000
190B174GLY00.0230.01531.364-0.002-0.0020.0000.0000.0000.000
191B175LEU0-0.067-0.02028.443-0.016-0.0160.0000.0000.0000.000
192B176TYR00.0270.00924.5230.0110.0110.0000.0000.0000.000
193B177SER0-0.021-0.01226.292-0.011-0.0110.0000.0000.0000.000
194B178LEU00.0250.03819.8660.0140.0140.0000.0000.0000.000
195B179SER00.004-0.00623.8570.0000.0000.0000.0000.0000.000
196B180SER00.0030.00219.818-0.008-0.0080.0000.0000.0000.000
197B181VAL00.0200.00222.4490.0030.0030.0000.0000.0000.000
198B182VAL00.0390.02221.960-0.019-0.0190.0000.0000.0000.000
199B183THR0-0.0120.00024.1020.0220.0220.0000.0000.0000.000
200B184VAL00.0100.00224.681-0.012-0.0120.0000.0000.0000.000
201B185PRO00.0720.03326.8180.0190.0190.0000.0000.0000.000
202B186SER00.0590.02330.054-0.016-0.0160.0000.0000.0000.000
203B187SER0-0.026-0.01132.906-0.008-0.0080.0000.0000.0000.000
204B188SER0-0.002-0.00328.609-0.010-0.0100.0000.0000.0000.000
205B189LEU0-0.008-0.00529.984-0.015-0.0150.0000.0000.0000.000
206B190GLY0-0.0010.01231.744-0.005-0.0050.0000.0000.0000.000
207B191THR0-0.041-0.02230.990-0.003-0.0030.0000.0000.0000.000
208B192GLN0-0.027-0.01223.801-0.006-0.0060.0000.0000.0000.000
209B193THR0-0.034-0.01024.9660.0150.0150.0000.0000.0000.000
210B194TYR00.037-0.00323.493-0.035-0.0350.0000.0000.0000.000
211B195ILE00.0200.00121.1450.0290.0290.0000.0000.0000.000
212B197ASN0-0.002-0.02116.216-0.019-0.0190.0000.0000.0000.000
213B198VAL00.0410.01817.075-0.045-0.0450.0000.0000.0000.000
214B199ASN0-0.024-0.00713.666-0.089-0.0890.0000.0000.0000.000
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