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: NNJ8Q

Calculation Name: 3CRM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CRM

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HUL9

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2933851.517288
FMO2-HF: Nuclear repulsion 2842004.975568
FMO2-HF: Total energy -91846.541721
FMO2-MP2: Total energy -92114.539855


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(A:3:SER)


Summations of interaction energy for fragment #1(A:3:SER)
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.
0.4662.044-0.02-0.66-0.8980.003
Interaction energy analysis for fragmet #1(A:3:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.013
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].
3A5PRO00.0400.0333.800-0.7990.779-0.020-0.660-0.8980.003
4A6PRO00.0350.0175.9710.5530.5530.0000.0000.0000.000
5A7ALA00.0240.0088.3710.0740.0740.0000.0000.0000.000
6A8ILE0-0.0120.00411.9210.0580.0580.0000.0000.0000.000
7A9PHE0-0.003-0.00115.0580.0170.0170.0000.0000.0000.000
8A10LEU00.0220.00818.1110.0190.0190.0000.0000.0000.000
9A11MET00.0190.01420.2660.0180.0180.0000.0000.0000.000
10A12GLY00.0550.01024.1010.0070.0070.0000.0000.0000.000
11A13PRO0-0.056-0.01827.552-0.002-0.0020.0000.0000.0000.000
12A14THR00.0400.00731.124-0.004-0.0040.0000.0000.0000.000
13A15ALA0-0.035-0.03633.3900.0050.0050.0000.0000.0000.000
14A16ALA0-0.0090.00730.2100.0040.0040.0000.0000.0000.000
15A17GLY00.0530.05531.1290.0010.0010.0000.0000.0000.000
16A18LYS10.8980.96226.1580.1400.1400.0000.0000.0000.000
17A19THR00.025-0.00126.225-0.013-0.0130.0000.0000.0000.000
18A20ASP-1-0.838-0.91227.438-0.118-0.1180.0000.0000.0000.000
19A21LEU0-0.012-0.00523.200-0.002-0.0020.0000.0000.0000.000
20A22ALA00.001-0.01022.703-0.013-0.0130.0000.0000.0000.000
21A23MET0-0.0130.00623.021-0.014-0.0140.0000.0000.0000.000
22A24ALA00.0330.02624.773-0.003-0.0030.0000.0000.0000.000
23A25LEU0-0.027-0.03318.503-0.004-0.0040.0000.0000.0000.000
24A26ALA0-0.039-0.02220.134-0.018-0.0180.0000.0000.0000.000
25A27ASP-1-0.834-0.87321.557-0.157-0.1570.0000.0000.0000.000
26A28ALA0-0.070-0.02220.5420.0110.0110.0000.0000.0000.000
27A29LEU0-0.033-0.02414.649-0.009-0.0090.0000.0000.0000.000
28A30PRO00.0480.04114.7630.0100.0100.0000.0000.0000.000
29A31CYS0-0.023-0.00315.734-0.079-0.0790.0000.0000.0000.000
30A32GLU-1-0.778-0.86417.417-0.302-0.3020.0000.0000.0000.000
31A33LEU0-0.0110.01318.754-0.027-0.0270.0000.0000.0000.000
32A34ILE0-0.017-0.00617.9180.0100.0100.0000.0000.0000.000
33A35SER00.0180.02121.8430.0020.0020.0000.0000.0000.000
34A36VAL0-0.014-0.01121.677-0.005-0.0050.0000.0000.0000.000
35A37ASP-1-0.851-0.96425.002-0.110-0.1100.0000.0000.0000.000
36A38SER0-0.006-0.00528.770-0.002-0.0020.0000.0000.0000.000
37A39ALA0-0.035-0.00931.1220.0060.0060.0000.0000.0000.000
38A40LEU00.0200.00730.0350.0020.0020.0000.0000.0000.000
39A41ILE0-0.0130.00829.362-0.004-0.0040.0000.0000.0000.000
40A42TYR0-0.077-0.05031.886-0.001-0.0010.0000.0000.0000.000
41A43ARG10.9340.98934.3320.1060.1060.0000.0000.0000.000
42A44GLY0-0.007-0.00637.4010.0040.0040.0000.0000.0000.000
43A45MET0-0.057-0.00938.1250.0050.0050.0000.0000.0000.000
44A46ASP-1-0.840-0.90637.402-0.099-0.0990.0000.0000.0000.000
45A47ILE0-0.012-0.01338.099-0.003-0.0030.0000.0000.0000.000
46A48GLY00.015-0.01140.1860.0000.0000.0000.0000.0000.000
47A49THR0-0.087-0.06535.4430.0000.0000.0000.0000.0000.000
48A50ALA0-0.119-0.06235.211-0.005-0.0050.0000.0000.0000.000
49A51LYS10.7630.87533.0580.1000.1000.0000.0000.0000.000
50A52PRO0-0.039-0.01930.0690.0050.0050.0000.0000.0000.000
51A53SER00.017-0.02133.308-0.001-0.0010.0000.0000.0000.000
52A54ARG11.0421.01534.2030.0820.0820.0000.0000.0000.000
53A55GLU-1-0.827-0.89634.680-0.095-0.0950.0000.0000.0000.000
54A56LEU0-0.033-0.01630.010-0.005-0.0050.0000.0000.0000.000
55A57LEU00.002-0.01729.638-0.011-0.0110.0000.0000.0000.000
56A58ALA0-0.037-0.00629.776-0.010-0.0100.0000.0000.0000.000
57A59ARG10.8800.94329.7290.1170.1170.0000.0000.0000.000
58A60TYR0-0.066-0.05825.349-0.005-0.0050.0000.0000.0000.000
59A61PRO00.0200.01825.271-0.001-0.0010.0000.0000.0000.000
60A62HIS0-0.036-0.02624.635-0.020-0.0200.0000.0000.0000.000
61A63ARG10.7770.85821.4000.2790.2790.0000.0000.0000.000
62A64LEU00.008-0.01322.928-0.002-0.0020.0000.0000.0000.000
63A65ILE00.0130.01826.6620.0070.0070.0000.0000.0000.000
64A66ASP-1-0.824-0.90129.843-0.117-0.1170.0000.0000.0000.000
65A67ILE0-0.056-0.03327.8660.0000.0000.0000.0000.0000.000
66A68ARG10.8750.93129.0260.1330.1330.0000.0000.0000.000
67A69ASP-1-0.779-0.86734.563-0.075-0.0750.0000.0000.0000.000
68A70PRO00.0210.00338.160-0.001-0.0010.0000.0000.0000.000
69A71ALA00.0260.03840.0040.0020.0020.0000.0000.0000.000
70A72GLU-1-0.883-0.91936.003-0.097-0.0970.0000.0000.0000.000
71A73SER0-0.012-0.00535.2860.0010.0010.0000.0000.0000.000
72A74TYR0-0.044-0.05626.640-0.006-0.0060.0000.0000.0000.000
73A75SER0-0.057-0.05129.9340.0010.0010.0000.0000.0000.000
74A76ALA00.010-0.01426.289-0.010-0.0100.0000.0000.0000.000
75A77ALA00.0090.00425.191-0.015-0.0150.0000.0000.0000.000
76A78GLU-1-0.734-0.84025.018-0.127-0.1270.0000.0000.0000.000
77A79PHE00.0260.02321.627-0.019-0.0190.0000.0000.0000.000
78A80ARG10.8650.92317.8650.1510.1510.0000.0000.0000.000
79A81ALA0-0.010-0.00520.427-0.036-0.0360.0000.0000.0000.000
80A82ASP-1-0.788-0.88120.966-0.220-0.2200.0000.0000.0000.000
81A83ALA0-0.014-0.01619.666-0.030-0.0300.0000.0000.0000.000
82A84LEU0-0.015-0.01415.173-0.059-0.0590.0000.0000.0000.000
83A85ALA00.0050.01716.144-0.075-0.0750.0000.0000.0000.000
84A86ALA0-0.034-0.01917.735-0.032-0.0320.0000.0000.0000.000
85A87MET0-0.003-0.00113.870-0.037-0.0370.0000.0000.0000.000
86A88ALA00.0480.05312.802-0.122-0.1220.0000.0000.0000.000
87A89LYS10.9530.97213.6400.2480.2480.0000.0000.0000.000
88A90ALA0-0.015-0.00815.1200.0160.0160.0000.0000.0000.000
89A91THR00.0510.0028.859-0.053-0.0530.0000.0000.0000.000
90A92ALA0-0.042-0.00711.167-0.046-0.0460.0000.0000.0000.000
91A93ARG10.8650.93312.7590.4060.4060.0000.0000.0000.000
92A94GLY00.0170.01311.5260.0800.0800.0000.0000.0000.000
93A95ARG10.8230.90912.6130.3820.3820.0000.0000.0000.000
94A96ILE00.010-0.01111.433-0.115-0.1150.0000.0000.0000.000
95A97PRO0-0.018-0.00512.3400.1210.1210.0000.0000.0000.000
96A98LEU00.0150.01214.948-0.018-0.0180.0000.0000.0000.000
97A99LEU00.0160.00216.6400.0380.0380.0000.0000.0000.000
98A100VAL00.0290.03519.7190.0180.0180.0000.0000.0000.000
99A101GLY00.005-0.00723.0260.0090.0090.0000.0000.0000.000
100A102GLY00.0540.01425.8030.0010.0010.0000.0000.0000.000
101A103THR0-0.0020.01627.3130.0130.0130.0000.0000.0000.000
102A104MET0-0.002-0.00925.122-0.013-0.0130.0000.0000.0000.000
103A105LEU00.0170.01324.646-0.004-0.0040.0000.0000.0000.000
104A106TYR00.0160.00624.1910.0020.0020.0000.0000.0000.000
105A107TYR00.013-0.01519.6330.0000.0000.0000.0000.0000.000
106A108LYS10.8220.90620.0180.0550.0550.0000.0000.0000.000
107A109ALA00.0070.00820.8790.0040.0040.0000.0000.0000.000
108A110LEU0-0.029-0.00817.049-0.001-0.0010.0000.0000.0000.000
109A111LEU0-0.034-0.01115.393-0.021-0.0210.0000.0000.0000.000
110A112GLU-1-0.844-0.90116.724-0.036-0.0360.0000.0000.0000.000
111A113GLY0-0.0060.01319.038-0.015-0.0150.0000.0000.0000.000
112A199LEU00.009-0.01612.1780.0070.0070.0000.0000.0000.000
113A200PRO0-0.0110.0138.5980.0770.0770.0000.0000.0000.000
114A201TYR0-0.034-0.0497.769-0.470-0.4700.0000.0000.0000.000
115A202THR0-0.0060.0055.1410.6230.6230.0000.0000.0000.000
116A203VAL0-0.024-0.0297.671-0.027-0.0270.0000.0000.0000.000
117A204ALA00.0150.03211.4420.1040.1040.0000.0000.0000.000
118A205GLN00.003-0.00513.995-0.008-0.0080.0000.0000.0000.000
119A206LEU00.001-0.00417.2800.0320.0320.0000.0000.0000.000
120A207ALA0-0.006-0.00120.504-0.004-0.0040.0000.0000.0000.000
121A208ILE0-0.0130.00024.0750.0060.0060.0000.0000.0000.000
122A209ALA0-0.015-0.03327.1700.0010.0010.0000.0000.0000.000
123A210PRO0-0.0190.00730.8610.0010.0010.0000.0000.0000.000
124A211GLU-1-0.901-0.92833.425-0.048-0.0480.0000.0000.0000.000
125A212GLN0-0.0020.00434.6940.0030.0030.0000.0000.0000.000
126A213ARG10.9390.95135.3690.0490.0490.0000.0000.0000.000
127A214GLN00.0170.00237.971-0.003-0.0030.0000.0000.0000.000
128A215VAL00.0650.03538.3850.0000.0000.0000.0000.0000.000
129A216LEU00.0170.01834.550-0.001-0.0010.0000.0000.0000.000
130A217HIS0-0.021-0.03238.177-0.003-0.0030.0000.0000.0000.000
131A218ALA00.0230.02841.2450.0000.0000.0000.0000.0000.000
132A219ARG10.9770.98837.0910.0720.0720.0000.0000.0000.000
133A220ILE0-0.025-0.01937.176-0.001-0.0010.0000.0000.0000.000
134A221ALA0-0.012-0.01040.8320.0000.0000.0000.0000.0000.000
135A222GLN00.0330.02142.720-0.002-0.0020.0000.0000.0000.000
136A223ARG10.9200.95335.5910.0800.0800.0000.0000.0000.000
137A224PHE00.0300.01342.281-0.001-0.0010.0000.0000.0000.000
138A225ARG10.9710.97143.9450.0430.0430.0000.0000.0000.000
139A226GLN00.0220.02744.0390.0000.0000.0000.0000.0000.000
140A227MET0-0.0270.00739.2460.0010.0010.0000.0000.0000.000
141A228LEU0-0.034-0.02944.5140.0000.0000.0000.0000.0000.000
142A229GLU-1-0.962-0.96948.071-0.043-0.0430.0000.0000.0000.000
143A230GLN0-0.072-0.04344.297-0.001-0.0010.0000.0000.0000.000
144A231GLY00.0530.03846.293-0.002-0.0020.0000.0000.0000.000
145A232PHE0-0.048-0.01943.392-0.001-0.0010.0000.0000.0000.000
146A233ILE00.021-0.00546.084-0.001-0.0010.0000.0000.0000.000
147A234ALA00.0850.05049.3020.0000.0000.0000.0000.0000.000
148A235GLU-1-0.755-0.83141.916-0.075-0.0750.0000.0000.0000.000
149A236VAL0-0.031-0.03645.131-0.001-0.0010.0000.0000.0000.000
150A237GLU-1-0.921-0.95647.119-0.044-0.0440.0000.0000.0000.000
151A238ALA0-0.012-0.00147.1180.0010.0010.0000.0000.0000.000
152A239LEU0-0.076-0.04543.059-0.001-0.0010.0000.0000.0000.000
153A240HIS0-0.039-0.05147.0990.0000.0000.0000.0000.0000.000
154A241ALA00.0100.01650.2640.0020.0020.0000.0000.0000.000
155A242ARG10.6970.79842.8120.0660.0660.0000.0000.0000.000
156A243SER00.0420.01649.9640.0010.0010.0000.0000.0000.000
157A244ASP-1-0.884-0.90745.719-0.058-0.0580.0000.0000.0000.000
158A245LEU0-0.035-0.00743.513-0.003-0.0030.0000.0000.0000.000
159A246HIS00.0610.02645.7950.0040.0040.0000.0000.0000.000
160A247ALA00.0350.00546.048-0.003-0.0030.0000.0000.0000.000
161A248GLY0-0.017-0.00845.358-0.001-0.0010.0000.0000.0000.000
162A249LEU00.0110.01741.823-0.001-0.0010.0000.0000.0000.000
163A250PRO0-0.040-0.03837.0810.0000.0000.0000.0000.0000.000
164A251SER00.0400.00737.9820.0000.0000.0000.0000.0000.000
165A252ILE00.0040.01739.008-0.001-0.0010.0000.0000.0000.000
166A253ARG10.8660.92838.3020.0640.0640.0000.0000.0000.000
167A254ALA0-0.0350.00537.4530.0000.0000.0000.0000.0000.000
168A255VAL0-0.040-0.04837.3480.0040.0040.0000.0000.0000.000
169A256GLY00.0190.01239.842-0.002-0.0020.0000.0000.0000.000
170A257TYR00.017-0.02239.8480.0020.0020.0000.0000.0000.000
171A258ARG10.8800.94744.0100.0470.0470.0000.0000.0000.000
172A259GLN0-0.014-0.01345.0620.0000.0000.0000.0000.0000.000
173A260VAL00.0420.01746.8090.0030.0030.0000.0000.0000.000
174A261TRP00.0450.03146.7960.0000.0000.0000.0000.0000.000
175A262ASP-1-0.830-0.91849.660-0.038-0.0380.0000.0000.0000.000
176A263TYR0-0.046-0.02551.7820.0020.0020.0000.0000.0000.000
177A264LEU00.0430.02350.7790.0010.0010.0000.0000.0000.000
178A265ASP-1-0.854-0.89953.341-0.039-0.0390.0000.0000.0000.000
179A266GLY0-0.016-0.00655.8580.0020.0020.0000.0000.0000.000
180A267LYS10.7560.87952.7690.0390.0390.0000.0000.0000.000
181A268LEU0-0.060-0.02951.8460.0000.0000.0000.0000.0000.000
182A269SER00.029-0.00556.024-0.001-0.0010.0000.0000.0000.000
183A270TYR00.0960.02352.593-0.001-0.0010.0000.0000.0000.000
184A271ALA00.0110.00753.598-0.002-0.0020.0000.0000.0000.000
185A272GLU-1-0.747-0.83453.287-0.032-0.0320.0000.0000.0000.000
186A273MET0-0.0040.02249.785-0.002-0.0020.0000.0000.0000.000
187A274THR0-0.009-0.02149.217-0.003-0.0030.0000.0000.0000.000
188A275GLU-1-0.992-0.99448.344-0.036-0.0360.0000.0000.0000.000
189A276ARG10.8970.92447.9920.0320.0320.0000.0000.0000.000
190A277GLY00.0530.04145.207-0.002-0.0020.0000.0000.0000.000
191A278ILE0-0.0230.00743.604-0.003-0.0030.0000.0000.0000.000
192A279ILE0-0.035-0.02143.237-0.002-0.0020.0000.0000.0000.000
193A280ALA00.0110.00642.350-0.001-0.0010.0000.0000.0000.000
194A281THR00.011-0.01738.500-0.004-0.0040.0000.0000.0000.000
195A282ARG10.9310.96438.4130.0410.0410.0000.0000.0000.000
196A283GLN0-0.009-0.00938.7840.0010.0010.0000.0000.0000.000
197A284LEU00.0000.01333.4680.0010.0010.0000.0000.0000.000
198A285ALA00.0600.03334.246-0.003-0.0030.0000.0000.0000.000
199A286LYS10.8770.94334.1260.0390.0390.0000.0000.0000.000
200A287ARG10.9800.99533.8910.0620.0620.0000.0000.0000.000
201A288GLN00.0210.00030.3810.0040.0040.0000.0000.0000.000
202A289PHE00.0420.00429.678-0.003-0.0030.0000.0000.0000.000
203A290THR0-0.077-0.04030.5420.0040.0040.0000.0000.0000.000
204A291TRP00.0130.00226.0200.0020.0020.0000.0000.0000.000
205A292LEU00.0210.00224.9350.0000.0000.0000.0000.0000.000
206A293ARG10.9310.97826.1410.0340.0340.0000.0000.0000.000
207A294SER0-0.041-0.01226.8800.0070.0070.0000.0000.0000.000
208A295TRP0-0.068-0.03819.3960.0140.0140.0000.0000.0000.000
209A296SER00.0250.02119.0180.0050.0050.0000.0000.0000.000
210A297HIS00.004-0.01715.726-0.026-0.0260.0000.0000.0000.000
211A298LEU00.0290.02217.842-0.032-0.0320.0000.0000.0000.000
212A299HIS0-0.0050.01119.5200.0200.0200.0000.0000.0000.000
213A300TRP00.000-0.02121.295-0.015-0.0150.0000.0000.0000.000
214A301MET0-0.052-0.01223.179-0.004-0.0040.0000.0000.0000.000
215A302ASP-1-0.725-0.88626.391-0.067-0.0670.0000.0000.0000.000
216A303SER0-0.067-0.06630.141-0.003-0.0030.0000.0000.0000.000
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